Protagonist Therapeutics, Inc 10-Q

ITEM 1. FINANCIAL STATEMENTS PROTAGONIST THERAPEUTICS, INC. Condensed Consolidated Balance Sheets (Unaudited) (In thousands, except share and per share data) ​ ​ ​ ​ ​ ​ ​ ​ ​ June 30, ​ December 31, ​ 2021 2020 Assets ​ ​ ​ ​ ​ ​ Current assets: ​ ​ ​ ​ ​ ​ Cash and cash equivalents ​ $ 192,412 ​ $ 117,358 Marketable securities ​ ​ 161,868 ​ ​ 188,451 Restricted cash - current ​ ​ — ​ ​ 10 Receivable from collaboration partner and contract asset - related party ​ ​ 7,077 ​ ​ 2,426 Research and development tax incentive receivable ​ ​ 2,778 ​ ​ 1,084 Prepaid expenses and other current assets ​ ​ 7,683 ​ ​ 6,277 Total current assets ​ ​ 371,818 ​ ​ 315,606 Marketable securities - noncurrent ​ ​ 26,122 ​ ​ 2,000 Property and equipment, net ​ ​ 1,718 ​ ​ 1,462 Restricted cash - noncurrent ​ ​ 225 ​ ​ 450 Operating lease right-of-use asset ​ ​ 4,349 ​ ​ 4,950 Total assets ​ $ 404,232 ​ $ 324,468 Liabilities and Stockholders’ Equity ​ ​ ​ ​ ​ ​ Current liabilities: ​ ​ ​ ​ ​ Accounts payable ​ $ 7,905 ​ $ 3,075 Payable to collaboration partner - related party ​ ​ 11,396 ​ ​ 2,732 Accrued expenses and other payables ​ ​ 20,096 ​ ​ 18,498 Deferred revenue - related party ​ ​ 2,009 ​ ​ 14,477 Operating lease liability - current ​ ​ 1,567 ​ ​ 1,459 Total current liabilities ​ ​ 42,973 ​ ​ 40,241 Operating lease liability - noncurrent ​ ​ 3,691 ​ ​ 4,500 Other liabilities ​ ​ 121 ​ ​ 121 Total liabilities ​ ​ 46,785 ​ ​ 44,862 Commitments and contingencies ​ ​ ​ ​ ​ ​ Stockholders’ equity: ​ ​ ​ ​ ​ ​ Preferred stock, $ 0.00001 par value, 10,000,000 shares authorized; no shares issued and outstanding ​ ​ — ​ ​ — Common stock, $ 0.00001 par value, 90,000,000 shares authorized; 47,525,560 and 43,745,465 shares issued and outstanding as of June 30, 2021 and December 31, 2020, respectively ​ ​ — ​ ​ — Additional paid-in capital ​ ​ 696,157 ​ ​ 563,389 Accumulated other comprehensive (loss) gain ​ ​ ( 59 ) ​ ​ 28 Accumulated deficit ​ ​ ( 338,651 ) ​ ​ ( 283,811 ) Total stockholders’ equity ​ ​ 357,447 ​ ​ 279,606 Total liabilities and stockholders’ equity ​ $ 404,232 ​ $ 324,468 ​ The accompanying notes are an integral part of these unaudited condensed consolidated financial statements. ​ 1 Table of Contents PROTAGONIST THERAPEUTICS, INC. Condensed Consolidated Statements of Operations (Unaudited) (In thousands, except share and per share data) ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three Months Ended ​ Six Months Ended ​ ​ June 30, ​ June 30, ​ 2021 2020 2021 2020 License and collaboration revenue - related party ​ $ 2,265 ​ $ 6,217 ​ $ 8,454 ​ $ 9,864 Operating expenses: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Research and development ​ ​ 26,432 ​ ​ 20,257 ​ ​ 50,677 ​ ​ 39,025 General and administrative ​ 6,715 ​ 4,177 ​ 12,680 ​ 8,753 Total operating expenses ​ 33,147 ​ 24,434 ​ 63,357 ​ 47,778 Loss from operations ​ ( 30,882 ) ​ ( 18,217 ) ​ ( 54,903 ) ​ ( 37,914 ) Interest income ​ 97 ​ 207 ​ 199 ​ ​ 733 Interest expense ​ ​ — ​ ​ ( 209 ) ​ ​ — ​ ​ ( 452 ) Loss on early repayment of debt ​ ​ — ​ ​ ( 585 ) ​ ​ — ​ ​ ( 585 ) Other (expense) income, net ​ ​ ( 57 ) ​ ​ 512 ​ ​ ( 136 ) ​ ​ 22 Loss before income tax expense ​ ​ ( 30,842 ) ​ ​ ( 18,292 ) ​ ​ ( 54,840 ) ​ ​ ( 38,196 ) Income tax expense ​ ​ — ​ ​ ( 1,129 ) ​ ​ — ​ ​ ( 1,305 ) Net loss ​ $ ( 30,842 ) ​ $ ( 19,421 ) ​ $ ( 54,840 ) ​ $ ( 39,501 ) Net loss per share, basic and diluted ​ $ ( 0.69 ) ​ $ ( 0.59 ) ​ $ ( 1.23 ) ​ $ ( 1.31 ) Weighted-average shares used to compute net loss per share, basic and diluted ​ 44,864,637 32,799,691 ​ 44,546,172 30,251,805 ​ The accompanying notes are an integral part of these unaudited condensed consolidated financial statements. ​ 2 Table of Contents PROTAGONIST THERAPEUTICS, INC. Condensed Consolidated Statements of Comprehensive Loss (Unaudited) (In thousands) ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three Months Ended ​ Six Months Ended ​ ​ June 30, ​ June 30, ​ 2021 2020 2021 2020 Net loss ​ $ ( 30,842 ) ​ $ ( 19,421 ) ​ $ ( 54,840 ) ​ $ ( 39,501 ) Other comprehensive loss: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ (Loss) gain on translation of foreign operations ​ ( 34 ) ​ ( 324 ) ​ ( 67 ) ​ 14 Unrealized gain (loss) on marketable securities ​ 8 ​ 9 ​ ( 20 ) ​ ( 1 ) Comprehensive loss ​ $ ( 30,868 ) ​ $ ( 19,736 ) ​ $ ( 54,927 ) ​ $ ( 39,488 ) ​ The accompanying notes are an integral part of these unaudited condensed consolidated financial statements. ​ 3 Table of Contents PROTAGONIST THERAPEUTICS, INC. Condensed Consolidated Statements of Stockholders’ Equity (Unaudited) (In thousands, except share data) ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Accumulated ​ ​ ​ ​ ​ ​ ​ ​ Additional ​ Other ​ ​ ​ Total ​ ​ Common ​ Paid-In ​ Comprehensive ​ Accumulated ​ Stockholders' ​ ​ Stock ​ Capital ​ (Loss) Gain ​ Deficit ​ Equity Three months ended June 30, 2021 Shares Amount ​ ​ ​ ​ ​ ​ ​ Balance at March 31, 2021 43,939,246 $ — ​ $ 567,176 $ ( 33 ) ​ $ ( 307,809 ) $ 259,334 Issuance of common stock pursuant to public offering, net of issuance costs ​ 3,503,311 ​ ​ — ​ ​ 123,798 ​ ​ — ​ ​ — ​ ​ 123,798 Issuance of common stock under equity incentive and employee stock purchase plans 83,003 — ​ 1,247 — ​ — 1,247 Stock-based compensation expense — — ​ 3,936 — ​ — 3,936 Other comprehensive loss — — ​ — ( 26 ) ​ — ( 26 ) Net loss — — ​ — — ​ ( 30,842 ) ( 30,842 ) Balance at June 30, 2021 47,525,560 $ — ​ $ 696,157 $ ( 59 ) ​ $ ( 338,651 ) $ 357,447 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Accumulated ​ ​ ​ ​ ​ ​ ​ ​ Additional ​ Other ​ ​ ​ Total ​ ​ Common ​ Paid-In ​ Comprehensive ​ Accumulated ​ Stockholders' ​ ​ Stock ​ Capital ​ (Loss) Gain ​ Deficit ​ Equity Three months ended June 30, 2020 Shares Amount ​ ​ ​ ​ ​ ​ ​ Balance at March 31, 2020 ​ 27,434,705 ​ $ — ​ $ 300,300 ​ $ 107 ​ $ ( 237,741 ) ​ $ 62,666 Issuance of common stock pursuant to public offering, net of issuance costs ​ 8,050,000 ​ ​ — ​ ​ 105,331 ​ ​ — ​ ​ — ​ ​ 105,331 Issuance of common stock pursuant to at-the-market offering, net of issuance costs ​ 1,232,793 ​ ​ — ​ ​ 16,643 ​ ​ — ​ ​ — ​ ​ 16,643 Issuance of common stock under equity incentive and employee stock purchase plans ​ 84,641 — ​ 585 — ​ — 585 Stock-based compensation expense — — ​ 1,996 — ​ — 1,996 Other comprehensive loss — — ​ — ( 315 ) ​ — ( 315 ) Net loss — — ​ — — ​ ( 19,421 ) ( 19,421 ) Balance at June 30, 2020 36,802,139 $ — ​ $ 424,855 $ ( 208 ) ​ $ ( 257,162 ) $ 167,485 ​ The accompanying notes are an integral part of these unaudited condensed consolidated financial statements. ​ 4 Table of Contents PROTAGONIST THERAPEUTICS, INC. Condensed Consolidated Statements of Stockholders’ Equity (Unaudited) (In thousands, except share data) ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Accumulated ​ ​ ​ ​ ​ ​ ​ ​ Additional ​ Other ​ ​ ​ Total ​ ​ Common ​ Paid-In ​ Comprehensive ​ Accumulated ​ Stockholders' ​ ​ Stock ​ Capital ​ (Loss) Gain ​ Deficit ​ Equity Six months ended June 30, 2021 Shares Amount ​ ​ ​ ​ ​ ​ ​ Balance at December 31, 2020 43,745,465 $ — ​ $ 563,389 $ 28 ​ $ ( 283,811 ) $ 279,606 Issuance of common stock pursuant to public offering, net of issuance costs ​ 3,503,311 ​ ​ — ​ ​ 123,798 ​ ​ — ​ ​ — ​ ​ 123,798 Issuance of common stock under equity incentive and employee stock purchase plans 283,844 — ​ 2,563 — ​ — 2,563 Shares withheld for net settlement of tax withholding upon vesting of restricted stock units ​ ( 7,060 ) ​ ​ — ​ ​ ( 189 ) ​ ​ — ​ ​ — ​ ​ ( 189 ) Stock-based compensation expense — — ​ 6,596 — ​ — 6,596 Other comprehensive loss — — ​ — ( 87 ) ​ — ( 87 ) Net loss — — ​ — — ​ ( 54,840 ) ( 54,840 ) Balance at June 30, 2021 47,525,560 $ — ​ $ 696,157 $ ( 59 ) ​ $ ( 338,651 ) $ 357,447 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Accumulated ​ ​ ​ ​ ​ ​ ​ ​ Additional ​ Other ​ ​ ​ Total ​ ​ Common ​ Paid-In ​ Comprehensive ​ Accumulated ​ Stockholders' ​ ​ Stock ​ Capital ​ (Loss) Gain ​ Deficit ​ Equity Six months ended June 30, 2020 Shares Amount ​ ​ ​ ​ ​ ​ ​ Balance at December 31, 2019 ​ 27,217,649 ​ $ — ​ $ 297,846 ​ $ ( 221 ) ​ $ ( 217,661 ) ​ $ 79,964 Issuance of common stock pursuant to public offering, net of issuance costs ​ 8,050,000 ​ ​ — ​ ​ 105,331 ​ ​ — ​ ​ — ​ ​ 105,331 Issuance of common stock pursuant to at-the-market offering, net of issuance costs ​ 1,232,793 ​ ​ — ​ ​ 16,643 ​ ​ — ​ ​ — ​ ​ 16,643 Issuance of common stock under equity incentive and employee stock purchase plans 301,697 — ​ 991 — ​ — 991 Stock-based compensation expense — — ​ 4,044 — ​ — 4,044 Other comprehensive gain — — ​ — 13 ​ — 13 Net loss — — ​ — — ​ ( 39,501 ) ( 39,501 ) Balance at June 30, 2020 36,802,139 $ — ​ $ 424,855 $ ( 208 ) ​ $ ( 257,162 ) $ 167,485 ​ The accompanying notes are an integral part of these unaudited condensed consolidated financial statements. ​ ​ 5 Table of Contents PROTAGONIST THERAPEUTICS, INC. Condensed Consolidated Statements of Cash Flows (Unaudited) (In thousands) ​ ​ ​ ​ ​ ​ ​ ​ ​ Six Months Ended ​ ​ June 30, ​ 2021 2020 Cash Flows from Operating Activities ​ ​ ​ Net loss ​ $ ( 54,840 ) ​ $ ( 39,501 ) Adjustments to reconcile net loss to net cash used in operating activities: ​ ​ ​ ​ ​ ​ Stock-based compensation ​ ​ 6,596 ​ ​ 4,044 Operating lease right-of-use asset amortization ​ ​ 887 ​ ​ 887 Depreciation and amortization ​ ​ 365 ​ ​ 419 Net amortization of premium (accretion of discount) on marketable securities ​ ​ 821 ​ ​ ( 243 ) Loss on early repayment of debt ​ ​ — ​ ​ 585 Amortization of debt issuance costs and accretion of debt discount ​ ​ — ​ ​ 22 Change in deferred tax asset ​ ​ — ​ ​ 1,412 Changes in operating assets and liabilities: ​ ​ ​ ​ ​ ​ Research and development tax incentive receivable ​ ​ ( 1,682 ) ​ ​ ( 278 ) Receivable from collaboration partner - related party ​ ​ ( 4,651 ) ​ ​ 3,758 Prepaid expenses and other assets ​ ​ ( 1,421 ) ​ ​ ( 248 ) Accounts payable ​ ​ 4,874 ​ ​ 73 Payable to collaboration partner - related party ​ ​ 8,664 ​ ​ ( 259 ) Accrued expenses and other payables ​ ​ 1,386 ​ ​ 382 Deferred revenue - related party ​ ​ ( 12,468 ) ​ ​ ( 7,517 ) Operating lease liability ​ ​ ( 987 ) ​ ​ ( 958 ) Other liabilities ​ ​ — ​ ​ 92 Net cash used in operating activities ​ ​ ( 52,456 ) ​ ​ ( 37,330 ) Cash Flows from Investing Activities ​ ​ ​ ​ ​ ​ Purchase of marketable securities ​ ​ ( 163,460 ) ​ ​ ( 66,753 ) Proceeds from maturities of marketable securities ​ ​ 165,080 ​ ​ 104,583 Purchases of property and equipment ​ ​ ( 640 ) ​ ​ ( 271 ) Net cash provided by investing activities ​ ​ 980 ​ ​ 37,559 Cash Flows from Financing Activities ​ ​ ​ ​ ​ ​ Proceeds from public offering of common stock, net of issuance costs ​ ​ 123,995 ​ ​ 105,689 Proceeds from issuance of common stock upon exercise of stock options and purchases under employee stock purchase plan ​ ​ 2,563 ​ ​ 991 Tax withholding payments related to net settlement of restricted stock units ​ ​ ( 189 ) ​ ​ — Proceeds from at-the-market offering, net of issuance costs ​ ​ — ​ ​ 16,834 Issuance costs related to long-term debt ​ ​ — ​ ​ ( 14 ) Early repayment of long-term debt ​ ​ — ​ ​ ( 10,524 ) Net cash provided by financing activities ​ ​ 126,369 ​ ​ 112,976 Effect of exchange rate changes on cash, cash equivalents and restricted cash ​ ​ ( 74 ) ​ ​ 31 Net increase in cash, cash equivalents and restricted cash ​ ​ 74,819 ​ ​ 113,236 Cash, cash equivalents and restricted cash, beginning of period ​ 117,818 ​ 33,466 Cash, cash equivalents and restricted cash, end of period ​ $ 192,637 ​ $ 146,702 Supplemental Disclosure of Non-Cash Financing and Investing Information: ​ ​ ​ ​ ​ ​ Purchases of property and equipment in accounts payable and accrued liabilities ​ $ 63 ​ $ 21 Issuance costs related to common stock offering included in accrued liabilities and other payables ​ $ 197 ​ $ 233 Issuance costs related to common stock offering included in prepaid expenses and other assets at the end of the previous year ​ $ — ​ $ 125 Issuance costs related to at-the-market offering of common stock included in prepaid expenses and other assets at the end of the previous year ​ $ — ​ $ 191 ​ ​ ​ ​ ​ ​ ​ ​ The accompanying notes are an integral part of these unaudited condensed consolidated financial statements. ​ ​ 6 Table of Contents PROTAGONIST THERAPEUTICS, INC. Notes to Unaudited Condensed Consolidated Financial Statements Note 1. Organization and Description of Business Protagonist Therapeutics, Inc. (the “Company”) is headquartered in Newark, California. The Company is a clinical-stage biopharmaceutical company that utilizes a proprietary technology platform to discover and develop novel peptide-based drugs to address significant unmet medical needs and transform existing treatment paradigms for patients. Protagonist Pty Limited (“Protagonist Australia”) is a wholly-owned subsidiary of the Company and is located in Brisbane, Queensland, Australia. The Company manages its operations as a single operating segment. Liquidity As of June 30, 2021, the Company had cash, cash equivalents and marketable securities of $ 380.4 million. The Company has incurred net losses from operations since inception and has an accumulated deficit of $ 338.7 million as of June 30, 2021. The Company’s ultimate success depends on the outcome of its research and development and collaboration activities. The Company expects to incur additional losses in the future and anticipates the need to raise additional capital to continue to execute its long-range business plan. Since the Company’s initial public offering in August 2016, it has financed its operations primarily through offerings of common stock and payments received under license and collaboration agreements. Risks and Uncertainties The Company is subject to risks and uncertainties as a result of the ongoing COVID-19 pandemic. The Company is continuing to closely monitor the impact of the COVID-19 pandemic on its business and has taken and continues to take proactive efforts to protect the health and safety of its patients, clinical research staff and employees, and to maintain business continuity. The extent of the impact of the COVID-19 pandemic on the Company's activities remains uncertain and difficult to predict, as the response to the pandemic is ongoing and information continues to evolve. Capital markets and economies worldwide have been negatively impacted by the COVID-19 pandemic, which has contributed to the current global economic recession. Such economic disruption could have a material adverse effect on the Company’s business. Policymakers around the globe have responded with fiscal policy actions to support the healthcare industry and economy as a whole. The magnitude and overall effectiveness of these actions remains uncertain. The severity of the impact of the COVID-19 pandemic on the Company's activities will depend on a number of factors, including, but not limited to, the duration and severity of the pandemic, including the severity of any additional periods of increases or spikes in the number of cases in the areas the Company and its suppliers operate and areas where the Company’s clinical trial sites are located; the development and spread of COVID-19 variants, the timing, extent, effectiveness and durability of COVID-19 vaccine programs or other treatments; and new or continuing travel and other restrictions and public health measures, such as social distancing, business closures or disruptions. Accordingly, the extent and severity of the impact on the Company's existing and planned clinical trials, manufacturing, collaboration activities and operations, is uncertain and cannot be fully predicted. The Company has experienced delays in its existing and planned clinical trials due to the worldwide impacts of the pandemic. The Company's future results of operations and liquidity could be adversely impacted by further delays in existing and planned clinical trials, continued difficulty in recruiting patients for these clinical trials, delays in manufacturing and collaboration activities, supply chain disruptions, the ongoing impact on its operating activities and employees, and the ongoing impact of any initiatives or programs that the Company may undertake to address financial and operational challenges. As of the date of issuance of these condensed consolidated financial statements, the extent to which the COVID-19 pandemic may materially impact the Company's future financial condition, liquidity or results of operations remains uncertain. 7 Table of Contents Note 2. Summary of Significant Accounting Policies Basis of Presentation The accompanying unaudited condensed consolidated financial statements have been prepared in accordance with generally accepted accounting principles in the United States (“GAAP”) and applicable rules and regulations of the SEC regarding interim financial reporting. As permitted under those rules, certain footnotes or other financial information that are normally required by GAAP have been condensed or omitted, and accordingly the condensed consolidated balance sheet as of December 31, 2020 has been derived from the Company’s audited consolidated financial statements at that date but does not include all of the information required by GAAP for complete consolidated financial statements. These unaudited interim condensed consolidated financial statements have been prepared on the same basis as the Company’s annual consolidated financial statements and, in the opinion of management, reflect all adjustments (consisting of normal recurring adjustments) that are necessary for a fair presentation of the Company’s consolidated financial statements. The results of operations for the three and six months ended June 30, 2021 are not necessarily indicative of the results to be expected for the year ending December 31, 2021 or for any other interim period or for any other future year. The accompanying condensed consolidated financial statements and related financial information should be read in conjunction with the audited consolidated financial statements and the related notes thereto for the year ended December 31, 2020 included in the Company’s Annual Report on Form 10-K, filed with the SEC on March 10, 2021. Principles of Consolidation The accompanying unaudited interim condensed consolidated financial statements include the accounts of the Company and its wholly owned subsidiary. All intercompany transactions and balances have been eliminated upon consolidation. Use of Estimates The preparation of the condensed consolidated financial statements in conformity with GAAP requires management to make estimates, assumptions and judgments that affect the reported amounts of assets and liabilities and disclosure of contingent assets and liabilities as of the date of the condensed consolidated financial statements and the reported amounts of revenues and expenses during the reporting period. On an ongoing basis, management evaluates its estimates, including those related to revenue recognition, accruals for research and development activities, stock-based compensation, income taxes, marketable securities and leases. Estimates related to revenue recognition include actual costs incurred versus total estimated costs of the Company’s deliverables to determine percentage of completion in addition to the application and estimates of potential revenue constraints in the determination of the transaction price under its license and collaboration agreements. Management bases these estimates on historical and anticipated results, trends, and various other assumptions that the Company believes are reasonable under the circumstances, including assumptions as to forecasted amounts and future events. Due to the ongoing COVID-19 pandemic, there has been uncertainty and disruption in the global economy and financial markets. The Company has taken into consideration any known COVID-19 impacts in its accounting estimates to date and is not aware of any additional specific events or circumstances that would require any additional updates to its estimates or judgments or a revision of the carrying value of its assets or liabilities as of the date of issuance of this Quarterly Report on Form 10-Q. These estimates may change as new events occur and additional information is obtained. Actual results could differ materially from these estimates under different assumptions or conditions. Concentrations of Credit Risk Financial instruments that potentially subject the Company to a concentration of credit risk consist of cash, cash equivalents and marketable securities. Substantially all of the Company’s cash is held by two financial institutions 8 Table of Contents that management believes are of high credit quality. Such deposits may, at times, exceed federally insured limits. The primary focus of the Company’s investment strategy is to preserve capital and to meet liquidity requirements. The Company’s cash equivalents and marketable securities are managed by external managers within the guidelines of the Company’s investment policy. The Company’s investment policy addresses the level of credit exposure by limiting concentration in any one corporate issuer and establishing a minimum allowable credit rating. To manage its credit risk exposure, the Company maintains its U.S portfolio of cash equivalents and marketable securities in fixed income securities denominated and payable in U.S. dollars. Permissible investments of fixed income securities include obligations of the U.S. government and its agencies, money market instruments including commercial paper and negotiable certificates of deposit, highly rated corporate debt obligations and money market funds, and highly rated supranational and sovereign government securities. Cash Equivalents Cash equivalents that are readily convertible to cash are stated at cost, which approximates fair value. The Company considers all highly liquid investments purchased with an original maturity of three months or less to be cash equivalents. Restricted Cash Restricted cash consists of cash balances held as security in connection with a letter of credit related to the Company’s facility lease entered into in March 2017. The letter of credit balance decreased from $ 0.5 million at December 31, 2020 to $ 0.2 million at June 30, 2021 pursuant to the terms of the facility lease. Cash as Reported in Condensed Consolidated Statements of Cash Flows Cash as reported in the condensed consolidated statements of cash flows includes the aggregate amounts of cash and cash equivalents and the restricted cash as presented on the condensed consolidated balance sheets. Cash as reported in the condensed consolidated statements of cash flows consists of (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ June 30, ​ 2021 2020 Cash and cash equivalents ​ $ 192,412 ​ $ 146,242 Restricted cash - current ​ — ​ 10 Restricted cash - noncurrent ​ 225 ​ 450 Total cash reported on condensed consolidated statements of cash flows ​ $ 192,637 ​ $ 146,702 ​ Marketable Securities All marketable securities have been classified as “available-for-sale” and are carried at estimated fair value as determined based upon quoted market prices or pricing models for similar securities. Management determines the appropriate classification of its marketable securities at the time of purchase and reevaluates such designation as of each balance sheet date. Short-term marketable securities have maturities greater than three months but no longer than 365 days as of the balance sheet date. Long-term marketable securities have maturities of 365 days or longer as of the balance sheet date. Unrealized gains and losses are excluded from earnings and are reported as a component of comprehensive gain or loss. Realized gains and losses and declines in fair value judged to be other than temporary, if any, on available-for-sale securities are included in interest income. The cost of securities sold is based on the specific-identification method. Interest on marketable securities is included in interest income. Revenue Recognition ​ Under Accounting Standards Codification Topic 606, Revenue from Contracts with Customers (“ASC 606”), the Company recognizes revenue when its customer obtains control of promised goods or services, in an amount that reflects the consideration which the Company expects to receive in exchange for those goods or services. To determine 9 Table of Contents revenue recognition for arrangements that the Company determines are within the scope of ASC 606, the Company performs the following five steps: (i) identify the contract(s) with a customer; (ii) identify the performance obligations in the contract; (iii) determine the transaction price; (iv) allocate the transaction price to the performance obligations in the contract; and (v) recognize revenue when (or as) the Company satisfies a performance obligation. The Company applies the five-step model to contracts when it is probable that the Company will collect the consideration it is entitled to in exchange for the goods or services it transfers to the customer. At contract inception, the Company assesses the goods or services promised within each contract, determines those that are performance obligations, and assesses whether each promised good or service is distinct. The Company then recognizes as revenue the amount of the transaction price that is allocated to the respective performance obligations when (or as) the performance obligations are satisfied. The Company constrains its estimate of the transaction price up to the amount (the “variable consideration constraint”) that a significant reversal of recognized revenue is not probable. Licenses of intellectual property: If a license to the Company’s intellectual property is determined to be distinct from the other performance obligations identified in an arrangement, the Company recognizes revenue from non-refundable, upfront fees allocated to the license when the license is transferred to the customer and the customer is able to use and benefit from the license. For licenses that are bundled with other promises, the Company utilizes judgment to assess the nature of the combined performance obligation to determine whether the combined performance obligation is satisfied over time or at a point in time and, if over time, the appropriate method of measuring proportional performance for purposes of recognizing revenue from non-refundable, upfront fees. The Company evaluates the measure of proportional performance each reporting period and, if necessary, adjusts the measure of performance and related revenue recognition. Milestone payments: At the inception of each arrangement or amendment that includes development, regulatory or commercial milestone payments, the Company evaluates whether the milestones are considered probable of being reached and estimates the amount to be included in the transaction price. ASC 606 suggests two alternatives to use when estimating the amount of variable consideration: the expected value method and the most likely amount method. Under the expected value method, an entity considers the sum of probability-weighted amounts in a range of possible consideration amounts. Under the most likely amount method, an entity considers the single most likely amount in a range of possible consideration amounts. Whichever method is used, it should be consistently applied throughout the life of the contract; however, it is not necessary for the Company to use the same approach for all contracts. The Company expects to use the most likely amount method for development and regulatory milestone payments. If it is probable that a significant revenue reversal would not occur, the associated milestone value is included in the transaction price. Milestone payments that are not within the control of the Company or the licensee, such as regulatory approvals, are not considered probable of being achieved until those approvals are received. If there is more than one performance obligation, the transaction price is then allocated to each performance obligation on a relative stand-alone selling price basis. The Company recognizes revenue as or when the performance obligations under the contract are satisfied. At the end of each subsequent reporting period, the Company re-evaluates the probability or achievement of each such milestone and any related constraint, and if necessary, adjusts its estimates of the overall transaction price. Any such adjustments are recorded on a cumulative catch-up basis, which would affect revenues and earnings in the period of adjustment. Royalties: For arrangements that include sales-based royalties, including milestone payments based on the level of sales, and the license is deemed to be the predominant item to which the royalties relate, the Company recognizes revenue at the later of (i) when the related sales occur, or (ii) when the performance obligation to which some or all of the royalty has been allocated has been satisfied (or partially satisfied). Upfront payments and fees are recorded as deferred revenue upon receipt or when due and may require deferral of revenue recognition to a future period until the Company performs its obligations under these arrangements. Amounts payable to the Company are recorded as accounts receivable when the Company’s right to consideration is unconditional. Amounts payable to the Company and not yet billed to the collaboration partner are recorded as contract assets. The Company does not assess whether a contract has a significant financing component if the expectation at contract inception is such that the period between payment by the customer and the transfer of the promised goods or services to the customer will be one year or less. 10 Table of Contents Contractual cost sharing payments made to a customer or collaboration partner are accounted for as a reduction to the transaction price if such payments are not related to distinct goods or services received from the customer or collaboration partner. Contracts may be amended to account for changes in contract specifications and requirements. Contract modifications exist when the amendment either creates new, or changes existing, enforceable rights and obligations. When contract modifications create new performance obligations and the increase in consideration approximates the standalone selling price for goods and services related to such new performance obligations as adjusted for specific facts and circumstances of the contract, the modification is considered to be a separate contract. If a contract modification is not accounted for as a separate contract, the Company accounts for the promised goods or services not yet transferred at the date of the contract modification (the remaining promised goods or services) prospectively, as if it were a termination of the existing contract and the creation of a new contract, if the remaining goods or services are distinct from the goods or services transferred on or before the date of the contract modification. The Company accounts for a contract modification as if it were a part of the existing contract if the remaining goods or services are not distinct and, therefore, form part of a single performance obligation that is partially satisfied at the date of the contract modification. In such case the effect that the contract modification has on the transaction price, and on the entity’s measure of progress toward complete satisfaction of the performance obligation, is recognized as an adjustment to revenue (either as an increase in or a reduction of revenue) at the date of the contract modification (the adjustment to revenue is made on a cumulative catch-up basis). The period between when the Company transfers control of promised goods or services and when the Company receives payment is expected to be one year or less, and that expectation is consistent with the Company’s historical experience. Upfront payment contract liabilities resulting from the Company’s license and collaboration agreements do not represent a financing component as the payment is not financing the transfer of goods and services, and the technology underlying the licenses granted reflects research and development expenses already incurred by the Company. As such, the Company does not adjust its revenues for the effects of a significant financing component . Research and Development Costs Research and development costs are expensed as incurred unless there is an alternate future use in other research and development projects or otherwise. Research and development costs include salaries and benefits, stock-based compensation expense, laboratory supplies and facility-related overhead, outside contracted services including clinical trial costs, manufacturing and process development costs for both clinical and pre-clinical materials, research costs, development milestone payments under license and collaboration agreements, and other consulting services. The Company accrues for estimated costs of research and development activities conducted by third-party service providers, which include the conduct of pre-clinical studies and clinical trials, and contract manufacturing activities. The Company records the estimated costs of research and development activities based upon the estimated services provided but not yet invoiced and includes these costs in accrued expenses and other payables in the condensed consolidated balance sheets and within research and development expense in the condensed consolidated statements of operations. The Company accrues for these costs based on factors such as estimates of the work completed and in accordance with agreements established with its third-party service providers. As actual costs become known, the Company adjusts its accrued liabilities. The Company has not experienced any material differences between accrued liabilities and actual costs incurred. However, the status and timing of actual services performed, number of patients enrolled, the rate of patient enrollment and number of locations of sites activated may vary from the Company’s estimates, resulting in adjustments to expense in future periods. Changes in these estimates that result in material changes to the Company’s accruals could materially affect the Company’s results of operations. The Company has received orphan drug designation from the U.S. Food and Drug Administration (“FDA”) for its clinical asset rusfertide (generic name for PTG-300) for the treatment of polycythemia vera and beta-thalassemia and may qualify for a related 25 % U.S. Federal income tax credit on qualifying clinical study expenditures. 11 Table of Contents Research and Development Tax Incentive The Company is eligible under the AusIndustry research and development tax incentive program to obtain either a refundable cash tax incentive or a taxable credit in the form of a non-cash tax incentive from the Australian Taxation Office (“ATO”). The refundable cash tax incentive is available to the Company on the basis of specific criteria with which the Company must comply. Specifically, the Company must have annual turnover of less than AUD 20.0 million and cannot be controlled by income tax exempt entities. The refundable cash tax incentive is recognized as a reduction to research and development expense when the right to receive has been attained and funds are considered to be collectible. The Company may alternatively be eligible for a taxable credit in the form of a non-cash tax incentive in years when the annual turnover exceeds the limit. The Company evaluates its eligibility under tax incentive programs as of each balance sheet date and makes accrual and related adjustments based on the most current and relevant data available. Stock-based Compensation Expense In February 2021, the Company granted performance share units (“PSUs) to certain executives of the Company. Stock-based compensation expense associated with PSUs is based on the fair value of the Company’s common stock on the grant date, which equals the closing price of the Company’s common stock on the grant date. The Company recognizes compensation expense over the vesting periods of the awards that are ultimately expected to vest when the achievement of the related performance obligation becomes probable. Net Loss per Share ​ Basic net loss per share is calculated by dividing the Company’s net loss by the weighted average number of shares of common stock and Exchange Warrants outstanding during the period, without consideration of potentially dilutive securities. In accordance with Accounting Standards Codification Topic 260, Earnings Per Share , the Exchange Warrants are included in the computation of basic net loss per share because the exercise price is negligible, and they are fully vested and exercisable after the original issuance date. Diluted net loss per share is the same as basic net loss per share for all periods presented since the effect of potentially dilutive securities is anti-dilutive given the net loss of the Company in each period. See Note 11. Stockholder’s Equity for additional information regarding the Exchange Warrants. Recently Adopted Accounting Pronouncements In December 2019, the FASB issued Accounting Standards Update (“ASU”) No. 2019-12, Income Taxes (Topic 740): Simplifying the Accounting for Income Taxes, which removes certain exceptions and amends certain requirements in the existing income tax guidance to ease accounting requirements. This guidance is effective for fiscal years, and interim periods within those fiscal years, beginning after December 15, 2020 and must be applied on a retrospective basis. The Company adopted this guidance effective January 1, 2021 and there was no impact on its consolidated financial statements and disclosures. Recently Issued Accounting Pronouncements Not Yet Adopted as of June 30, 2021 In June 2016, the FASB issued ASU No. 2016-13, Financial Instruments - Credit Losses (Topic 326) , which is intended to provide financial statement users with more useful information about expected credit losses on financial assets held by a reporting entity at each reporting date. The new standard replaces the existing incurred loss impairment methodology with a methodology that requires consideration of a broader range of reasonable and supportable forward-looking information to estimate all expected credit losses. This guidance was originally effective for fiscal years and interim periods within those years beginning after December 15, 2019, with early adoption permitted for fiscal years and interim periods within those years beginning after December 15, 2018. In November 2019, the FASB issued ASU No. 2019-10, Financial Instruments – Credit Losses (Topic 326), Derivatives and Hedging (Topic 815), and Leases (Topic 842): Effective Dates , which amended the mandatory effective date of ASU No. 2016-13 for smaller reporting companies. Based on the Company’s status as a smaller reporting company as of November 15, 2019, ASU 2016-13 is 12 Table of Contents effective for the Company for fiscal years and interim periods beginning after December 15, 2022. The Company is currently evaluating the impact of this new guidance on its consolidated financial statements and disclosures. Note 3. License and Collaboration Agreement Agreement Terms On May 26, 2017, the Company and Janssen Biotech, Inc., (“Janssen”), one of the Janssen Pharmaceutical Companies of Johnson & Johnson, entered into an exclusive license and collaboration agreement (the “Janssen License and Collaboration Agreement”) for the development, manufacture and potential commercialization of PTG-200 worldwide for the treatment of Crohn’s disease (“CD”) and ulcerative colitis (“UC”). Janssen is a related party to the Company as Johnson & Johnson Innovation - JJDC, Inc., a significant stockholder of the Company, and Janssen are both subsidiaries of Johnson & Johnson. PTG-200 is the Company’s orally delivered gut-restricted Interleukin 23 receptor (“IL-23R”) antagonist drug candidate currently in development. The Janssen License and Collaboration Agreement became effective on July 13, 2017. Upon the effectiveness of the agreement, the Company received a non-refundable, upfront cash payment of $ 50.0 million from Janssen. Under the Janssen License and Collaboration Agreement, the Company granted to Janssen an exclusive worldwide license to develop, manufacture and commercialize PTG-200 and related IL-23R antagonist compounds for all indications, including CD and UC. The Company was responsible, at its own expense, for the conduct of the Phase 1 clinical trial for PTG-200, and Janssen is responsible for the conduct of the Phase 2 clinical trial for PTG-200 in CD, including filing the U.S. Investigational New Drug application (“IND”). Development costs for the Phase 2 clinical trial are shared between the parties on an 80 / 20 basis, with Janssen assuming the larger share. Janssen submitted an IND for PTG-200 in CD during the second quarter of 2019, which took effect in July 2019. Janssen and the Company initiated a Phase 2 clinical study for PTG-200 in CD in the fourth quarter of 2019. The Company entered into an amendment (the “First Amendment”) to the Janssen License and Collaboration Agreement effective May 7, 2019. The First Amendment builds upon the Company’s ongoing development collaboration with Janssen for PTG-200 and, upon the effectiveness of the First Amendment, the Company became eligible to receive a $ 25.0 million payment from Janssen, which was received during the second quarter of 2019. The First Amendment expanded the scope of the Janssen License and Collaboration Agreement by supporting research efforts towards identifying and developing second-generation IL-23R antagonists (“second-generation compounds”). Two second-generation compounds, PN-232 and PN-235, have been nominated and are currently in Phase 1 clinical studies. As part of the services added in the First Amendment, Janssen will pay certain costs and milestones related to advancing pre-clinical candidates from the second-generation research program through Phase 1 studies, including funding of a certain number of full-time equivalent employees (“FTEs”) at the Company for an agreed-upon period of time. The Company will pay 100 % of the costs for the Phase 1 studies for the first second-generation compound, and 50 % of the costs of the Phase 1 studies for the second and third second-generation compounds; thereafter Janssen will pay 100 % of any further Phase 1 development costs. Development costs for the Phase 2 clinical trials for second-generation compounds are shared between the parties on an 80 / 20 basis, with Janssen assuming the larger share. The Company’s Phase 1 and Phase 2 development costs are also limited by overall spending caps. In December 2019, the Company became eligible to receive a $ 5.0 million payment trigged by the successful nomination of a second-generation development compound, which was received during the first quarter of 2020. The Company will be eligible to receive a $ 7.5 million milestone payment at the completion of a Phase 1 study for the first second-generation compound. Payments to the Company for research and development services are generally billed and collected as services are performed or assets are delivered, including research activities and Phase 1 and Phase 2 development activities. Janssen bills the Company for its 20 % share of the Phase 2 development costs as expenses are incurred by Janssen. Milestone payments are received after the related milestones are achieved. 13 Table of Contents Pursuant to the First Amendment, the Company will be eligible to receive clinical development, regulatory and sales milestones, if and as achieved, and/or payments relating to Janssen’s elections to maintain or expand its license rights. The next possible milestone or opt-in election events based on a Phase 2 clinical trial in CD are as follows: ● Janssen can elect to advance PTG-200 into Phase 2b following receipt of the top line results of the CD Phase 2a clinical trial for PTG-200 by paying a $ 50.0 million maintenance fee (the “Amended First Opt-in Election”); or ● Janssen would make a $ 50.0 million milestone payment following dosing of the third patient in the first Phase 2b clinical trial for CD for a second-generation product. Janssen can also then elect to receive exclusive, worldwide commercial rights for both PTG-200 and second-generation products following the Phase 2b completion date for PTG-200 or a second-generation product by paying a $ 50.0 million payment (the “Amended Second Opt-in Election”). The Company will also be eligible for certain additional milestone payments including a potential payment of either $ 100.0 million upon a Phase 3 CD clinical trial meeting a primary clinical endpoint with respect to PTG-200 or $ 115.0 million upon a Phase 3 CD clinical trial meeting a primary clinical endpoint with respect to a second-generation compound. Pursuant to the First Amendment, the Company will be eligible to receive tiered royalties on net product sales at percentages ranging from mid-single digits to ten percent. Under the terms of the First Amendment, the Company is eligible to receive up to $ 1.0 billion in research, development, regulatory and sales milestones. The Janssen License and Collaboration Agreement remains in effect until the royalty obligations cease following patent and regulatory expiry, unless terminated earlier. Upon a termination of the Janssen License and Collaboration Agreement, all rights revert back to the Company, and in certain circumstances, if such termination occurs during ongoing clinical trials, Janssen would, if requested, provide certain financial and operational support to the Company for the completion of such trials. Revenue Recognition The amended Janssen License and Collaboration Agreement is accounted for as containing a single performance obligation for the development license; second-generation compound research services; Phase 1 development services for PTG-200 and potential second-generation compounds; the Company’s services associated with Phase 2 development for PTG-200 until Phase 2a; the Company’s services associated with Phase 2 development for a second-generation product until the dosing of the third patient in Phase 2b in CD or UC, or Phase 2 in an additional indication; and all other such services that the Company may perform at the request of Janssen to support the development of PTG-200, second-generation research services, or the development of second-generation compounds. The Amended First Opt-in Election and the Amended Second Opt-in Election options are not considered to be material rights. The contract duration is defined as the period in which parties to the contract have present enforceable rights and obligations. For revenue recognition purposes, the duration of the Janssen License and Collaboration Agreement, as amended, began on the effective date of July 13, 2017 and ends upon the later of end of Phase 2a for PTG-200 or upon dosing of the third patient in Phase 2b for a second-generation compound. The Company uses the most likely amount method to estimate variable consideration included in the transaction price. Variable consideration after the First Amendment consists of future milestone payments and cost sharing payments from Janssen for agreed upon services offset by development costs reimbursement payable to Janssen. Cost sharing payments from Janssen relate to the agreed upon services for development activities that the Company performs within the duration of the contract are included in the transaction price at the Company’s share of the estimated budgeted costs for these activities, including primarily internal full-time equivalent effort and third party contract costs. Cost sharing payments to Janssen relate to agreed-upon services for Phase 2 activities that Janssen performs within the duration of the contract are not a distinct service that Janssen transfers to the Company. Therefore, the consideration payable to Janssen is accounted for as a reduction in the transaction price. 14 Table of Contents The transaction price of the initial performance obligation under the Janssen License and Collaboration Agreement was $ 95.8 million as of June 30, 2021, a decrease of $ 0.5 million from the transaction price of $ 96.3 million as of March 31, 2021, following an update to the estimate for remaining services to be performed under the performance obligation. In order to determine the transaction price, the Company evaluated all payments to be received during the duration of the contract, net of development costs reimbursement expected to be payable to Janssen. The transaction price as of June 30, 2021 includes the $ 50.0 million upfront payment, the $ 25.0 million payment received upon the effectiveness of the First Amendment, the $ 5.0 million payment triggered by the successful nomination of a second-generation compound, $ 17.9 million of reimbursement from Janssen for services performed for PTG-200 Phase 2 and for second-generation compound research costs and other services, and estimated variable consideration consisting of a $ 7.5 million milestone payment subject to the completion of a Phase 1 study for a second-generation compound, offset by $ 9.6 million of net cost reimbursement to Janssen for services performed. The Company evaluated whether the variable component of the transaction price should be constrained to ensure that a significant reversal of revenue recognized on a cumulative basis as of June 30, 2021 is not probable. The Company concluded that the variable consideration constraint is appropriately reflected in the estimated transaction price as of June 30, 2021. The additional potential development, regulatory and sales milestone payments after the completion of Phase 2a activities in CD and UC that the Company would be eligible to receive are currently outside the contract term as defined for revenue recognition purposes and as such have been excluded from the transaction price. Janssen has also opted in for certain additional services to be performed by the Company that are outside the initial performance obligation, revenue is recognized as these services are performed. The Company re-evaluates the transaction price, including variable consideration, at the end of each reporting period and as uncertain events are resolved or other changes in circumstances occur. The Company and Janssen make quarterly cost sharing payments to one another in amounts necessary to ensure that each party bears its contractual share of the overall shared costs incurred. The Company utilizes a cost-based input method to measure proportional performance and to calculate the corresponding amount of revenue to recognize. In applying the cost-based input methods of revenue recognition, the Company uses actual costs incurred relative to expected costs to fulfill the combined performance obligation. These costs consist primarily of internal FTE effort and third-party contract costs. Revenue will be recognized based on actual costs incurred as a percentage of total estimated costs as the Company completes its performance obligations. A cost-based input method of revenue recognition requires management to make estimates of costs to complete the Company’s performance obligations. The Company believes this is the best measure of progress because other measures do not reflect how the Company transfers its performance obligation to Janssen. In making such estimates, significant judgment is required to evaluate assumptions related to cost estimates. The cumulative effect of revisions to estimated costs to complete the Company’s performance obligations will be recorded in the period in which changes are identified and amounts can be reasonably estimated. A significant change in these assumptions and estimates could have a material impact on the timing and amount of revenue recognized in future periods. For the three and six months ended June 30, 2021, the Company recognized license and collaboration revenue of $ 2.1 million and $ 7.7 million, respectively, which was primarily related to the transaction price for the Janssen License and Collaboration Agreement recognized based on proportional performance. In addition, the Company recorded $ 0.2 million and $ 0.8 million in revenue for the three and six months ended June 30, 2021, respectively, related to additional services provided by the Company under the Janssen Collaboration Agreement. For the three and six months ended June 30, 2020, the Company recognized license and collaboration revenue of $ 5.7 million and $ 9.4 million, respectively, which was primarily related to the transaction price for the Janssen License and Collaboration Agreement recognized based on proportional performance. In addition, the Company recorded $ 0.5 million in revenue for the three and six months ended June 30, 2020 related to additional services provided by the Company under the Janssen Collaboration Agreement. 15 Table of Contents The following tables present changes in the Company’s contract assets and liabilities during the periods presented (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Balance at ​ ​ ​ ​ ​ Balance at ​ ​ Beginning of ​ ​ ​ ​ ​ End of Six Months Ended June 30, 2021 Period ​ Additions Deductions Period Contract assets: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Receivable from collaboration partner - related party ​ $ 2,426 ​ $ 4,651 ​ $ — ​ $ 7,077 Contract liabilities: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Deferred revenue - related party ​ $ 14,477 ​ $ 3,924 ​ $ ( 16,392 ) ​ $ 2,009 Payable to collaboration partner - related party ​ $ 2,732 ​ $ 8,664 ​ $ — ​ $ 11,396 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Balance at ​ ​ ​ ​ ​ ​ ​ Balance at ​ ​ Beginning of ​ ​ ​ ​ ​ End of Six Months Ended June 30, 2020 Period ​ Additions Deductions Period Contract assets: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Receivable from collaboration partner - related party ​ $ 5,955 ​ $ 4,202 ​ $ ( 7,160 ) ​ $ 2,997 Contract asset - related party ​ $ 800 ​ $ 342 ​ $ ( 1,142 ) ​ $ — Contract liabilities: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Deferred revenue - related party ​ $ 41,530 ​ $ 2,977 ​ $ ( 10,493 ) ​ $ 34,014 Payable to collaboration partner - related party ​ $ 1,262 ​ $ 1,040 ​ $ ( 1,299 ) ​ $ 1,003 ​ During the three and six months ended June 30, 2021, the Company recognized revenue of $ 0.4 million and $ 1.5 million, respectively, from amounts included in the deferred revenue contract liability balance at the beginning of each period. During the three and six months ended June 30, 2020, the Company recognized revenue of $ 2.1 million and $ 3.3 million, respectively, for each period from amounts included in the deferred revenue contract liability balance at the beginning of each period. None of the costs to obtain or fulfill the contract were capitalized. Note 4. Fair Value Measurements Financial assets and liabilities are recorded at fair value. The accounting guidance for fair value provides a framework for measuring fair value, clarifies the definition of fair value and expands disclosures regarding fair value measurements. Fair value is defined as the price that would be received to sell an asset or paid to transfer a liability (an exit price) in an orderly transaction between market participants at the reporting date. The accounting guidance establishes a three-tiered hierarchy, which prioritizes the inputs used in the valuation methodologies in measuring fair value as follows: Level 1 —Inputs are unadjusted quoted prices in active markets for identical assets or liabilities at the measurement date. Level 2— Inputs (other than quoted market prices included in Level 1) are either directly or indirectly observable for the asset or liability through correlation with market data at the measurement date and for the duration of the instrument’s anticipated life. Level 3 —Inputs reflect management’s best estimate of what market participants would use in pricing the asset or liability at the measurement date. Consideration is given to the risk inherent in the valuation technique and the risk inherent in the inputs to the model. In determining fair value, the Company utilizes quoted market prices, broker or dealer quotations, or valuation techniques that maximize the use of observable inputs and minimize the use of unobservable inputs to the extent possible and considers counterparty credit risk in its assessment of fair value. 16 Table of Contents The following table presents the fair value of the Company’s financial assets determined using the inputs defined above (in thousands). ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ June 30, 2021 ​ Level 1 Level 2 Level 3 Total Assets: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Money market funds ​ $ 123,006 ​ $ — ​ $ — $ 123,006 Commercial paper ​ — ​ 141,440 ​ — 141,440 Corporate debt securities ​ ​ — ​ ​ 70,410 ​ ​ — ​ ​ 70,410 U.S. Treasury and agency securities ​ ​ — ​ ​ 32,090 ​ ​ — ​ ​ 32,090 Supranational and sovereign government securities ​ — ​ 6,044 — 6,044 Total financial assets ​ $ 123,006 ​ $ 249,984 $ — $ 372,990 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, 2020 ​ Level 1 Level 2 Level 3 Total Assets: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Money market funds ​ $ 27,481 ​ $ — ​ $ — $ 27,481 Commercial paper ​ — ​ 65,863 ​ — 65,863 Corporate debt securities ​ — ​ 27,590 — 27,590 U.S. Treasury and agency securities ​ — ​ 183,210 — 183,210 Total financial assets ​ $ 27,481 ​ $ 276,663 $ — $ 304,144 ​ The Company’s commercial paper, U.S. Treasury and agency securities, corporate debt securities, U.S. Treasury and agency securities, including U.S. Treasury bills, and supranational and sovereign government securities are classified as Level 2 as they were valued based upon quoted market prices for similar instruments in active markets, quoted prices for identical or similar instruments in markets that are not active and model-based valuation techniques for which all significant inputs are observable in the market or can be corroborated by observable market data for substantially the full term of the assets. Note 5. Cash Equivalents and Marketable Securities ​ Cash equivalents and marketable securities consisted of the following (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ June 30, 2021 ​ ​ Amortized ​ Gross Unrealized ​ ​ Cost Gains Losses Fair Value Money market funds ​ $ 123,006 ​ $ — ​ $ — ​ $ 123,006 Commercial paper ​ 141,443 ​ ​ 1 ​ ​ ( 4 ) ​ 141,440 Corporate debt securities ​ ​ 70,418 ​ ​ 5 ​ ​ ( 13 ) ​ ​ 70,410 U.S. Treasury and agency securities ​ ​ 32,096 ​ ​ 2 ​ ​ ( 8 ) ​ ​ 32,090 Supranational and sovereign government securities ​ 6,045 ​ ​ — ​ ​ ( 1 ) ​ 6,044 Total cash equivalents and marketable securities ​ $ 373,008 ​ $ 8 $ ( 26 ) ​ $ 372,990 Classified as: ​ ​ ​ ​ ​ ​ ​ ​ ​ Cash equivalents ​ ​ ​ ​ ​ ​ ​ $ 185,000 Marketable securities - current ​ ​ ​ ​ ​ ​ ​ 161,868 Marketable securities - noncurrent ​ ​ ​ ​ ​ ​ ​ 26,122 Total cash equivalents and marketable securities ​ ​ ​ ​ ​ ​ ​ $ 372,990 ​ 17 Table of Contents ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, 2020 ​ ​ Amortized ​ Gross Unrealized ​ ​ Cost Gains Losses Fair Value Money market funds ​ $ 27,481 ​ $ — $ — ​ $ 27,481 Commercial paper ​ 65,866 ​ — ( 3 ) ​ 65,863 Corporate debt securities ​ 27,592 ​ 2 ( 4 ) ​ 27,590 U.S. Treasury and agency securities ​ 183,203 ​ 10 ( 3 ) ​ 183,210 Total cash equivalents and marketable securities ​ $ 304,142 ​ $ 12 $ ( 10 ) ​ $ 304,144 Classified as: ​ ​ ​ ​ ​ ​ ​ ​ ​ Cash equivalents ​ ​ ​ ​ ​ ​ ​ $ 113,693 Marketable securities - current ​ ​ ​ ​ ​ ​ ​ 188,451 Marketable securities - noncurrent ​ ​ ​ ​ ​ ​ ​ 2,000 Total cash equivalents and marketable securities ​ ​ ​ ​ ​ ​ ​ $ 304,144 ​ Marketable securities – current of $ 161.9 million and $ 188.5 million held at June 30, 2021 and December 31, 2020, respectively, had contractual maturities of less than one year . Marketable securities – noncurrent of $ 26.1 million and $ 2.0 million held at June 30, 2021 and December 31, 2020 had contractual maturities of at least one year but less than two years . The Company does not intend to sell its securities that are in an unrealized loss position, and it is unlikely that the Company will be required to sell its securities before recovery of their amortized cost basis, which may be at maturity. There were no realized gains or realized losses on marketable securities for the periods presented. Factors considered in determining whether a loss is temporary include the length of time and extent to which the fair value has been less than the amortized cost basis and whether the Company intends to sell the security or whether it is more likely than not that the Company would be required to sell the security before recovery of the amortized cost basis. ​ ​ Note 6. Accrued Expenses and Other Payables Accrued expenses and other payables consisted of the following (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ June 30, ​ December 31, ​ 2021 ​ 2020 Accrued clinical and research related expenses ​ $ 14,976 ​ $ 11,335 Accrued employee related expenses ​ 3,780 ​ 6,413 Accrued professional service fees ​ ​ 829 ​ ​ 668 Other ​ 511 ​ 82 Total accrued expenses and other payables ​ $ 20,096 ​ $ 18,498 ​ ​ Note 7. Research Collaboration and License Agreement The Company and Zealand Pharma A/S (“Zealand”) entered into a collaboration agreement in June 2012. In October 2013, Zealand abandoned the collaboration, and the collaboration agreement was terminated in 2014. The agreement provides for certain post-termination payment obligations to Zealand with respect to compounds related to the collaboration that meet specified conditions set forth in the collaboration agreement and which the Company elects to further develop following Zealand’s abandonment of the collaboration. The Company has the right, but not the obligation, to further develop and commercialize such compounds. The agreement provides for payments to Zealand for the achievement of certain development, regulatory and sales milestone events that occur prior to a partnering arrangement related to such compounds between the Company and a third party. The Company previously determined that rusfertide is a compound for which the post-termination payments described above are required under the collaboration agreement and has made three development milestone payments for an aggregate amount of $ 1.0 million under the agreement. However, upon reevaluation, the Company concluded in 2019 that rusfertide is not a compound requiring post-termination payments under the agreement, and initiated the arbitration proceeding described in Note 10 Commitments and Contingencies – Legal Proceedings below. 18 Table of Contents Milestone payments to collaboration partners are recorded as research and development expenses in the period that the expense is incurred. No research and development expense was recorded under the agreement for the three and six months ended June 30, 2021 and 2020. If the Company is required to continue to make payments with respect to rusfertide under the collaboration agreement, the next two milestones that would be due under such agreement include: $ 1.0 million to $ 3.0 million for initiation of placebo-controlled Phase 2b clinical trial; and $ 1.5 million to $ 4.5 million for initiation of a Phase 3 clinical trial. The milestone amounts vary depending on the number of patients in the applicable clinical trial, and the Company expects the milestones would be the lowest amount within the specified range. See Note 10. Commitments and Contingencies – Legal Proceedings for additional information on arbitration proceedings related to this research and collaboration agreement. Note 8. Government Programs Research and Development Tax Incentive During the three and six months ended June 30, 2021, the Company recognized AUD 1.3 million ($ 1.0 million) and AUD 2.3 million ($ 1.7 million), respectively, as a reduction of research and development expenses in connection with the research and development cash tax incentive from the ATO. During the three and six months ended June 30, 2020, the Company recognized AUD 0.2 million ($ 0.1 million) and AUD 0.4 million ($ 0.3 million), respectively, as a reduction of research and development expenses in connection with the research and development cash tax incentive from the ATO. As of June 30, 2021 and December 31, 2020, the research and development cash tax incentive receivable was AUD 3.7 million ($ 2.8 million) and AUD 1.4 million ($ 1.1 million), respectively. Small Business Innovation Research (“SBIR”) Grants The Company has received SBIR grants from the National Institutes of Health (“NIH”) in support of research aimed at its product candidates. The Company recognizes a reduction to research and development expenses when expenses related to the grants have been incurred and the grant funds become contractually due from NIH. The Company recorded $ 0.1 million as a reduction of research and development expenses for the three and six months ended June 30, 2021. The Company recorded $ 0.1 million and $ 0.3 million as a reduction of research and development expenses for the three and six months ended June 30, 2020, respectively. The Company records a receivable to reflect the eligible costs incurred under the grants that are contractually due to the Company. This receivable is included in prepaid expenses and other current assets on the condensed consolidated balance sheets. There was no such receivable as of June 30, 2021 or December 31, 2020. Note 9. Term Loan Facility On October 30, 2019, the Company entered into a Credit and Security Agreement, dated as of October 30, 2019 (the “Closing Date”) by and among the Company, MidCap Financial Trust, as a lender, Silicon Valley Bank, as a lender, the other lenders party thereto from time to time and MidCap Financial Trust, as administrative agent and collateral agent (“Agent”) (such agreement, the “Term Loan Credit Agreement”), which provides for a $ 50.0 million term loan facility. The Term Loan Credit Agreement provides for (i) on the Closing Date, $ 10.0 million aggregate principal amount of term loans, (ii) at the Company’s option, until December 31, 2020, an additional $ 20.0 million term loan facility subject to the satisfaction of certain conditions, including clinical milestone achievement, and (iii) at the Company’s option, until September 30, 2021, an additional $ 20.0 million term loan facility subject to the satisfaction of certain conditions, including clinical milestone achievement, (collectively, the “Term Loans”). The Company intends to use any proceeds from drawdowns on the Term Loans for general corporate purposes. The Term Loans are subject to an origination fee of 0.25 % for each funded tranche under the Term Loan Credit Agreement and bear interest at an annual rate based on prime rate plus 2.91 %, subject to a prime rate floor of 4.94 %. The Company will make interest-only payments on the Term Loans outstanding during the initial 24 months , followed by 24 months of principal and interest payments. At the Company’s option, the Company may prepay the 19 Table of Contents outstanding principal balance of the Term Loans in whole or in part, subject to a prepayment premium of 3.0 % of any amount prepaid if the prepayment occurs through and including the first anniversary of the Closing Date, 2.0 % of the amount prepaid if the prepayment occurs after the first anniversary of the closing date through and including the second anniversary of the closing date, and 1.0 % of any amount prepaid after the second anniversary of the closing date and prior to October 1, 2023. An additional fee of 2.85 % of the amount of Term Loans advanced by the Lenders will be due upon prepayment or repayment of the Term Loans. The Term Loan Credit Agreement requires the Company to maintain cash and cash equivalents of at least 35 % of the outstanding Term Loans at all times and is secured by a perfected security interest in all of the Company's assets except for intellectual property and certain other customary excluded property pursuant to the terms of the Term Loan Credit Agreement. The Term Loan Credit Agreement contains other covenants that limit the Company’s ability and the ability of its subsidiaries to perform certain actions, including obligations to not pay dividends and to maintain unrestricted cash balance above certain threshold, non-occurrence of material adverse change, non-occurrence of change of control and other customary affirmative and negative covenants. The violation of any provision of covenants will result in default for the Company. The Term Loan Credit Agreement includes a clause which allows lenders to accelerate repayment upon the occurrence of certain events of default. In June 2020, the Company prepaid the outstanding $ 10.0 million balance on the term loan as well as $ 0.6 million for related prepayment and exit fees. Accordingly, the company accelerated amortization of $ 0.1 million related to capitalized and unamortized debt issuance costs, which is included as part of the $ 0.6 million loss on early repayment of debt. The Company had no outstanding balance as of June 30, 2021 or December 31, 2020 related to the Term Loan Credit Agreement. As of June 30, 2021, the Company was in compliance with the debt covenants, no event of default occurred and the probability of occurrence of event of default was considered remote. ​ ​ Note 10. Commitments and Contingencies Legal Proceedings The Company is a party to the legal action described below. The Company recognizes accruals for such actions to the extent that it concludes that a loss is both probable and reasonably estimable. The Company accrues for the best estimate of a loss within a range; however, if no estimate in the range is better than any other, it accrues the minimum amount in the range. If the Company determines that a loss is reasonably possible and the loss or range of loss can be estimated, it discloses the possible loss. On January 23, 2020, the Company initiated arbitration proceedings with the International Court of Arbitration of the International Chamber of Commerce against Zealand related to a collaboration agreement the Company and Zealand entered into in 2012 and terminated in 2014. The agreement provides for certain post-termination payment obligations to Zealand with respect to compounds related to the collaboration that the Company elects to further develop and meet specified conditions. In the Company’s arbitration claim, it is seeking a declaration that the Company has no past, present or future milestone or royalty payment obligations under the agreement with respect to rusfertide because it is not a compound relating to the collaboration for which post-termination payments to Zealand apply. The Company is also seeking repayment of $ 1.0 million in milestone payments it has made, as well as its costs, fees, and expenses of the proceeding. Zealand disputes the Company’s claims and has filed counterclaims for payment of a development milestone Zealand claims is due, as well as payment of their arbitration costs, fees and expenses . The arbitration is pending. If Zealand prevails in the arbitration, the Company could be required to reimburse Zealand’s arbitration costs, fees and expenses, and make contractual payments to Zealand described in its prior periodic reports filed with the SEC. If we successfully develop and commercialize rusfertide without a partner, those payments could include up to an additional aggregate of $ 28.0 million for achievement of certain development and regulatory milestones, and up to $ 100.0 million for achievement of sales milestones. In addition, Zealand could be eligible to receive a low single digit royalty on worldwide net sales of the product. ​ Although the Company cannot predict with certainty the ultimate outcome of these arbitration proceedings, it has concluded that the probability of any related loss is remote and therefore no related accruals were recognized as of June 30, 2021. 20 Table of Contents Note 11. Stockholders’ Equity In August 2018, the Company entered into a Securities Purchase Agreement with certain accredited investors (each, an “Investor” and, collectively, the “Investors”), pursuant to which the Company sold an aggregate of 2,750,000 shares of its common stock at a price of $ 8.00 per share, for aggregate net proceeds of $ 21.7 million, after deducting offering expenses payable by the Company. In a concurrent private placement, the Company issued the Investors warrants to purchase an aggregate of 2,750,000 shares of its common stock (each, a “Warrant” and, collectively, the “Warrants”). Each Warrant is exercisable from August 8, 2018 through August 8, 2023 . Warrants to purchase 1,375,000 shares of the Company’s common stock have an exercise price of $ 10.00 per share and Warrants to purchase 1,375,000 shares of the Company’s common stock have an exercise price of $ 15.00 per share. The exercise price and number of shares of common stock issuable upon the exercise of the Warrants (the “Warrant Shares”) are subject to adjustment in the event of any stock dividends and splits, reverse stock split, recapitalization, reorganization or similar transaction, as described in the Warrants. Under certain circumstances, the Warrants may be exercisable on a “cashless” basis. In connection with the issuance and sale of the common stock and Warrants, the Company granted the Investors certain registration rights with respect to the Warrants and the Warrant Shares. The common stock and warrants are classified as equity in accordance with Accounting Standards Codification Topic 480 , Distinguishing Liabilities from Equity (“ASC 480”) , and the net proceeds from the transaction were recorded as a credit to additional paid-in capital. As of June 30, 2021, none of the Warrants have been exercised. In December 2018, the Company entered into an exchange agreement (the “Exchange Agreement”) with an Investor and its affiliates (the “Exchanging Stockholders”), pursuant to which the Company exchanged an aggregate of 1,000,000 shares of the Company’s common stock, par value $ 0.00001 per share, owned by the Exchanging Stockholders for pre-funded warrants (the “Exchange Warrants”) to purchase an aggregate of 1,000,000 shares of common stock (subject to adjustment in the event of any stock dividends and splits, reverse stock split, recapitalization, reorganization or similar transaction, as described in the Exchange Warrants), with an exercise price of $ 0.00001 per share. The Exchange Warrants will expire ten years from the date of issuance. The Exchange Warrants are exercisable at any time prior to expiration except that the Exchange Warrants cannot be exercised by the Exchanging Stockholders if, after giving effect thereto, the Exchanging Stockholders would beneficially own more than 9.99 % of the Company’s common stock, subject to certain exceptions. In accordance with Accounting Standards Codification Topic 505, Equity , the Company recorded the retirement of the common stock exchanged as a reduction of common stock shares outstanding and a corresponding debit to additional paid-in-capital at the fair value of the Exchange Warrants on the issuance date. The Exchange Warrants are classified as equity in accordance with ASC 480 , and fair value of the Exchange Warrants was recorded as a credit to additional paid-in capital and is not subject to remeasurement. The Company determined that the fair value of the Exchange Warrants is substantially similar to the fair value of the retired shares on the issuance date due to the negligible exercise price for the Exchange Warrants. As of June 30, 2021, 400,000 of the Exchange Warrants remain unexercised. In October 2019, the Company filed a registration statement on Form S-3 (File No. 333-234414) that was declared effective as of November 22, 2019 and permits the offering, issuance, and sale by the Company of up to a maximum aggregate offering price of $ 250.0 million of its common stock, preferred stock, debt securities and warrants (the “2019 Form S-3”). Up to a maximum of $ 75.0 million of the maximum aggregate offering price of $ 250.0 million may be issued and sold pursuant to an ATM financing facility under a sales agreement entered into by the Company on November 27, 2019 (the “2019 Sales Agreement”). In May 2020, the Company completed an underwritten public offering of 7,000,000 shares of common stock at a public offering price of $ 14.00 per share, and issued an additional 1,050,000 shares of its common stock at a price of $ 14.00 per share following the underwriters’ exercise of their option to purchase additional shares. Net proceeds, after deducting underwriting commissions and offering costs paid by the Company, were $ 105.3 million. As of June 30, 2021, a total of $ 94.2 million of common stock remained available for sale under the 2019 Form S-3, $ 31.9 million of which remained available for sale under the ATM financing facility. In December 2020, the Company filed an automatic registration statement on Form S-3ASR and an accompanying prospectus (Registration Statement No. 333-251254), pursuant to which it completed an underwritten public offering of 4,761,904 shares of the Company’s common stock at a public offering price of $ 21.00 per share and issued an additional 714,285 shares of common stock at a price of $ 21.00 per share following the underwriters’ exercise of their option to purchase additional shares. Net proceeds, after deducting underwriting commissions and offering 21 Table of Contents costs paid by the Company, were $ 107.6 million. In June 2021, pursuant to Registration Statement No. 33-251254, the Company completed an underwritten public offering of 3,046,358 shares of its common stock at a public offering price of $ 37.75 per share and issued an additional 456,953 shares of common stock at a price of $ 37.75 per share following the underwriters’ exercise of their option to purchase additional shares. Net proceeds, after deducting underwriting commissions and offering costs paid by the Company, were $ 123.8 million. The Form S-3ASR expires in December 2023. ​ Note 12. Equity Plans Equity Incentive Plan In July 2016, the Company’s board of directors and stockholders approved the Company’s 2016 Equity Incentive Plan (the “2016 Plan”) to replace the 2007 Stock Option Plan. The 2016 Plan is administered by the board of directors or a committee appointed by the board of directors, which determines the types of awards to be granted, including the number of shares subject to the awards, the exercise price and the vesting schedule. Awards granted under the 2016 Plan expire no later than ten years from the date of grant. As of June 30, 2021, 636,010 shares were available for issuance under the 2016 Plan. Inducement Plan In May 2018, the Company’s board of directors approved the 2018 Inducement Plan, as subsequently amended. The 2018 Inducement Plan is a non-stockholder approved stock plan, under which the Company awards options and restricted stock unit awards to persons that were not previously employees or directors of the Company, or following a bona fide period of non-employment, as an inducement material to such persons entering into employment with the Company, within the meaning of Rule 5635(c)(4) of the Nasdaq Listing Rules. The 2018 Inducement Plan is administered by the board of directors or the Compensation Committee of the board, which determines the types of awards to be granted, including the number of shares subject to the awards, the exercise price and the vesting schedule. Awards granted under the 2018 Inducement Plan expire no later than ten years from the date of grant. As of June 30, 2021, 375,625 shares were available for issuance under the Amended and Restated 2018 Inducement Plan. Stock Options Stock option activity under the Company’s equity incentive and inducement plans is set forth below: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Weighted- ​ Weighted- ​ ​ ​ ​ ​ ​ Average ​ Average ​ ​ ​ ​ ​ ​ Exercise ​ Remaining ​ Aggregate ​ ​ Options ​ Price Per ​ Contractual ​ Intrinsic ​ Outstanding Share Life (years) Value (1) ​ ​ ​ ​ ​ ​ ​ ​ ​ (in millions) Balances at December 31, 2020 4,648,120 $ 11.87 7.61 $ 40.0 Options granted 1,597,040 ​ ​ 26.97 ​ ​ Options exercised ( 177,152 ) ​ ​ 11.54 ​ ​ ​ Options forfeited ​ ( 106,672 ) ​ ​ 16.66 ​ ​ ​ ​ ​ Balances at June 30, 2021 5,961,336 $ 15.84 7.77 ​ $ 173.1 Options exercisable – June 30, 2021 ​ 2,980,187 $ 12.39 6.46 ​ $ 96.8 Options vested and expected to vest – June 30, 2021 ​ 5,961,336 ​ $ 15.84 7.77 ​ $ 173.1 (1) The aggregate intrinsic values were calculated as the difference between the exercise price of the options and the closing price of the Company’s common stock on June 30, 2021. The calculation excludes options with an exercise price higher than the closing price of the Company’s common stock on June 30, 2021. The estimated weighted-average grant-date fair value of common stock underlying options granted to employees during the six months ended June 30, 2021 was $ 19.79 per share. 22 Table of Contents Stock Options Valuation Assumptions The fair value of employee stock option awards was estimated at the date of grant using a Black-Scholes option-pricing model with the following assumptions: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three Months Ended ​ Six Months Ended ​ ​ June 30, ​ June 30, ​ ​ 2021 ​ 2020 ​ 2021 ​ 2020 Expected term (in years) 5.27 - 6.08 5.50 - 6.08 ​ 5.27 - 6.08 5.27 - 6.08 Expected volatility 88.0 % - 88.8 % ​ 74.3 % - 74.5 % ​ 88.0 % - 90.2 % ​ 72.1 % - 74.5 % Risk-free interest rate 0.85 % - 1.11 % ​ 0.39 % - 0.42 % ​ 0.11 % - 1.11 % ​ 0.39 % - 1.44 % Dividend yield — — ​ — — ​ In determining the fair value of the options granted, the Company uses the Black-Scholes option-pricing model and assumptions discussed below. Each of these inputs is subjective and generally requires judgment to determine. Expected Term —The Company’s expected term represents the period that the Company’s options granted are expected to be outstanding and is determined using the simplified method (based on the mid-point between the vesting date and the end of the contractual term). The Company has limited historical information to develop reasonable expectations about future exercise patterns and post-vesting employment termination behavior for its stock option grants. Expected Volatility —For the year ended December 31, 2020, the Company’s expected volatility was estimated based upon a mix of 75 % of the average volatility for comparable publicly traded biopharmaceutical companies over a period equal to the expected term of the stock option grants and 25 % of the volatility of the Company’s stock price since its initial public offering in August 2016. Beginning January 1, 2021, the Company’s expected volatility is estimated based upon a mix of 50 % of the average volatility for comparable publicly traded biopharmaceutical companies over a period equal to the expected term of the stock option grants and 50 % of the volatility of the Company’s stock price since its initial public offering in August 2016. Risk-Free Interest Rate —The risk-free interest rate is based on the U.S. Treasury zero coupon issues in effect at the time of grant for periods corresponding with the expected term of option. Expected Dividend —The Company has never paid dividends on its common stock and has no plans to pay dividends on its common stock. Therefore, the Company used an expected dividend yield of zero. Restricted Stock Units Restricted stock unit activity under the Company’s equity incentive plans is set forth below: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Weighted ​ ​ ​ ​ Average ​ ​ Number of ​ Grant Date ​ Shares Fair Value Unvested at December 31, 2020 ​ 244,545 ​ $ 9.31 Granted 287,250 ​ 23.57 Vested ( 78,165 ) ​ 10.13 Forfeited ​ ( 30,126 ) ​ ​ 18.28 Unvested at June 30, 2021 ​ 423,504 ​ $ 19.31 ​ Performance Stock Units During the first quarter of 2021, the Company granted 110,500 PSUs to certain executives of the Company pursuant to the terms of the 2016 Plan, all of which were outstanding at June 30, 2021. The grant date fair value of the 23 Table of Contents PSUs was $ 23.57 per share. The terms of the PSUs provide for 100 % of shares to be earned based on the of achievement of certain pre-determined performance objectives, subject to the participant’s continued employment. The PSUs will expire five years from the grant date if the performance objectives are not achieved. The PSUs will vest, if at all, upon certification by the Compensation Committee of the Company’s Board of Directors of the actual achievement of the performance objectives, subject to specified change of control exceptions. Stock-based compensation expense associated with PSUs is based on the fair value of the Company’s common stock on the grant date, which equals the closing price of the Company’s common stock on the grant date. The Company recognizes compensation expense over the vesting period of the awards that are ultimately expected to vest when the achievement of the related performance objective becomes probable. The total fair value of the PSUs granted in February 2021 was $ 2.6 million. As of June 30, 2021, the achievement of the related performance objective was deemed not probable and, accordingly, no stock-based compensation for the PSUs has been recognized as expense as of June 30, 2021. Employee Stock Purchase Plan ​ The 2016 Employee Stock Purchase Plan (“2016 ESPP”) allows eligible employees to purchase shares of the Company’s common stock at a discount through payroll deductions of up to 15 % of their eligible compensation. At the end of each offering period, eligible employees are able to purchase shares at 85 % of the lower of the fair market value of the Company’s common stock at the beginning of the offering period or at the end of each applicable purchase period. During the six months ended June 30, 2021, a total of 28,527 shares of common stock were issued under the 2016 ESPP, and 1,029,120 shares remain available for issuance as of June 30, 2021. Stock-Based Compensation ​ Total stock-based compensation expense was as follows (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three Months Ended ​ Six Months Ended ​ ​ June 30, ​ June 30, ​ 2021 2020 2021 2020 Research and development ​ $ 2,155 ​ $ 1,026 ​ $ 3,630 ​ $ 2,092 General and administrative ​ 1,781 ​ 970 ​ 2,966 ​ 1,952 Total stock-based compensation expense ​ $ 3,936 ​ $ 1,996 ​ $ 6,596 ​ $ 4,044 ​ As of June 30, 2021, total unrecognized stock-based compensation expense was approximately $ 46.4 million, which the Company expects to recognize over a weighted-average period of approximately 3.0 years. Note 13. 401(k) Plan The Company has a retirement and savings plan under Section of 401(k) of Internal Revenue Code (“401(k) Plan”) covering all U.S. employees. The 401(k) Plan allows employees to make pre- and post-tax contributions up to the maximum allowable amount set by the Internal Revenue Service. The Company may make contributions to this plan at its discretion. For the three and six months ended June 30, 2021, the Company plans to match 50 % of each employee’s contribution up to a maximum of $ 3,500 , and recognized expense of approximately zero and $ 0.2 million, respectively, relating to these contributions. No contributions were made to the plan by the Company for the three and six months ended June 30, 2020. Note 14. Income Taxes No income tax expense was recorded by the Company during the three and six months ended June 30, 2021. The Company recorded income tax expense of $ 1.1 million and $ 1.3 million for the three and six months ended June 30, 2020, respectively, representing an effective income tax rate of 6.2 % and 3.4 %, respectively. During the second quarter of 2020, the Company’s Australia subsidiary sold beneficial rights to discovery intellectual property to its U.S. entity, and the U.S. entity reimbursed the Australia subsidiary for certain direct development costs. Upon completion of the sale, the Company analyzed tax planning strategies and future income and concluded that a valuation allowance is necessary for its Australia subsidiary. Income tax expense for the three and six months ended June 30, 2020 reflects this 24 Table of Contents sale of intellectual property rights, cost reimbursements and related adjustments to the deferred tax asset, establishing a valuation allowance and certain uncertain tax position liabilities. The Company’s effective income tax rate differed from the Company’s federal statutory rate of 21 %, primarily because its U.S. loss cannot be benefited due to the full valuation allowance position and reduced by foreign taxes. Note 15. Net Loss per Share As the Company had net losses for the three and six months ended June 30, 2021 and 2020, all potential dilutive common shares were determined to be anti-dilutive. The following table sets forth the computation of basic and diluted net loss per share (in thousands, except share and per share data): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three Months Ended ​ Six Months Ended ​ ​ June 30, ​ June 30, ​ 2021 2020 2021 2020 Numerator: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Net loss ​ $ ( 30,842 ) ​ $ ( 19,421 ) ​ $ ( 54,840 ) ​ $ ( 39,501 ) Denominator: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Weighted-average shares used to compute net loss per common share, basic and diluted ​ 44,864,637 ​ 32,799,691 ​ 44,546,172 30,251,805 Net loss per share, basic and diluted ​ $ ( 0.69 ) ​ $ ( 0.59 ) ​ $ ( 1.23 ) ​ $ ( 1.31 ) ​ The following outstanding shares of potentially dilutive securities have been excluded from diluted net loss per share computations for the periods presented because their inclusion would be anti-dilutive: ​ ​ ​ ​ ​ ​ ​ ​ Six Months Ended ​ ​ June 30, ​ 2021 2020 Options to purchase common stock ​ 5,961,336 4,537,986 Common stock warrants ​ 2,750,000 ​ 2,750,000 Restricted stock units ​ 423,504 ​ 262,608 Performance stock units ​ 110,500 ​ — ESPP shares ​ 15,617 ​ 38,218 Total 9,260,957 7,588,812 ​ ​ Note 16. Restructuring On May 7, 2020, the Company approved a limited reduction in force plan affecting approximately 12 % of the Company’s employee base and informed the affected employees. The reduction-in-force plan was completed by the end of the second quarter of 2020. Total cash expenditures for the reduction in force plan were $ 0.3 million, substantially all of which were related to employee severance and benefits costs. Note 17. Subsequent Events Restated Janssen License and Collaboration Agreement On July 27, 2021, the Company entered into an amended and restated License and Collaboration Agreement (the “Restated Agreement”) with Janssen. The Restated Agreement amends and restates the License and Collaboration Agreement, dated May 27, 2017, by and between the Company and Janssen (as amended by Amendment No. 1 thereto, effective May 7, 2019, the “Original Agreement”). The Restated Agreement relates to the development, manufacture and commercialization of oral IL-23 receptor antagonist drug candidates. The candidates currently in development pursuant to the Restated Agreement include PTG-200, PN-232 and PN-235. PTG-200 is an oral, IL-23 receptor antagonist in Phase 2a development for the treatment of CD. PN-235 and PN-232 are second-generation oral IL-23 receptor antagonist candidates currently in 25 Table of Contents Phase 1 studies. Janssen is primarily responsible for the conduct of the PTG-200 trial and the Company is primarily responsible for the conduct of the PN-232 and PN-235 Phase 1 studies. Pursuant to the Restated Agreement, the parties have: (a) amended development milestones to reflect Janssen’s expected development of collaboration compounds for multiple indications in the IL-23 pathway; (b) limited the Company’s further development and related expense obligations under the Restated Agreement to the ongoing PTG-200 Phase 2a study, and the ongoing Phase 1 studies in PN-232 and PN-235 described in the preceding paragraph; Janssen is responsible for all other future development and related expenses under the Restated Agreement; and (c) concluded the parties’ two-year research collaboration, while enabling Janssen to continue conducting additional research through July 2024 on compounds developed pursuant to the Original Agreement. The Company’s continuing development expense obligations under the Restated Agreement are as follows: (a) the Company will continue to fund 20 % of the costs related to the ongoing Phase 2a study evaluating PTG-200 for the treatment of CD (subject to a $ 20.0 million cap on costs related to Phase 2a and 2b costs for PTG 200); (b) the Company is responsible for 50 % of agreed-upon costs related to the ongoing Phase 1 study evaluating PN-235 incurred under the Original Agreement through January 4, 2021; (c) the Company is responsible for 100 % of agreed-upon costs related to the ongoing Phase 1 study evaluating PN-232. Certain of the Company’s previous development expense obligations under the Original Agreement have been limited or eliminated as follows: (a) the Company’s previous $ 25.0 million obligation for 20 % of costs related to Phase 2 studies for Second Generation Products has been eliminated; (b) the Company’s previous $ 5.0 million obligation for 50 % of the costs of a potential third Phase 1 study evaluating a Second Generation Product has been eliminated; and (c) the Company has no obligation to fund any portion of any Phase 2b or other study evaluating PTG-200 beyond the ongoing Phase 2a study. One milestone for Second Generation Phase 2 development was reduced from $ 50.0 million to $ 25.0 million in the Restated Agreement; otherwise, t he various milestone payment amounts in the Restated Agreement remain substantially the same as in the Original Agreement. To reflect parallel development of multiple indications in the IL-23 pathway, milestone payments under the Restated Agreement generally now correspond to the achievement of specified milestones in: (a) any initial indication (rather than CD, as in the Original Agreement); (b) any second indication (rather than UC, as in the Original Agreement); and (c) any third indication. With respect to Second Generation Products, milestone payments for second and third indications may be triggered by any Second Generation Product (i.e., not necessarily the Second Generation Product that triggered the initial payment for any indication, or the payment for a second indication). In addition, the opt-in payments contemplated by the Original Agreement related to the scope of Janssen’s license rights have been converted into development milestones in the Restated Agreement. The mid-single digit to ten percent tiered royalty rates payable pursuant to the Original Agreement remain the same in the Restated Agreement. The sales milestone payments in the Original Agreement also remain the same in the Restated Agreement. Following completion of the ongoing Phase 2a study for PTG-200 and the ongoing Phase 1 studies for PN-232 and PN-235, the Company has no further collaborative development obligations under the Restated Agreement. Any further research and development will be conducted by Janssen. Janssen retains exclusive, worldwide rights to develop and commercialize PTG-200 and any second-generation compounds derived from the research collaboration conducted under the Original Agreement, or Janssen’s further research under the Restated Agreement. 26 Table of Contents Lease Amendment On July 2, 2021, the Company entered into an amendment (the “Second Lease Amendment”) to its facility lease agreement dated as of March 6, 2017, as amended, to lease approximately 15,000 square feet of additional office space in Newark, California. The Company expects to commence operations in the additional space in the third quarter of 2021. Under the Second Lease Amendment, the Company expects to pay additional base rent of approximately $ 1.5 million over the lease term, which expires in May 2024. The Company will be responsible for its proportional share of operating expenses and tax obligations. No additional security deposit is required. ​ ​ 27 Table of Contents