Janux Therapeutics, Inc. 10-Q

Item 1 . Financial Statements. Janux Therapeutics, Inc. Condensed Bal ance Sheets (in thousands, except share and par value data) September 30, 2024 December 31, 2023 Assets (unaudited) Current assets: Cash and cash equivalents $ 26,754 $ 19,205 Short-term investments 631,277 324,823 Prepaid expenses and other current assets 8,290 5,213 Total current assets 666,321 349,241 Restricted cash 816 816 Property and equipment, net 5,373 7,003 Operating lease right-of-use assets 19,686 20,838 Other long-term assets 2,823 2,509 Total assets $ 695,019 $ 380,407 Liabilities and Stockholders’ Equity Current liabilities: Accounts payable $ 2,462 $ 2,424 Accrued expenses 13,022 7,387 Current portion of deferred revenue — 1,705 Current portion of operating lease liabilities 1,689 1,517 Total current liabilities 17,173 13,033 Operating lease liabilities, net of current portion 21,742 23,025 Total liabilities 38,915 36,058 Commitments and contingencies (Note 3) Stockholders’ equity: Preferred stock, $ 0.001 par value; authorized shares – 10,000,000 at September 30, 2024 and December 31, 2023, respectively; no shares issued and outstanding at September 30, 2024 and December 31, 2023 — — Common stock, $ 0.001 par value; authorized shares – 200,000,000 at September 30, 2024 and December 31, 2023, respectively; issued shares – 52,338,762 and 46,262,759 at September 30, 2024 and December 31, 2023, respectively; outstanding shares – 52,337,239 and 46,252,440 at September 30, 2024 and December 31, 2023, respectively 52 46 Additional paid-in capital 865,762 512,401 Accumulated other comprehensive income 7,831 665 Accumulated deficit ( 217,541 ) ( 168,763 ) Total stockholders’ equity 656,104 344,349 Total liabilities and stockholders’ equity $ 695,019 $ 380,407 See accompanying notes. 1 Table of Contents Janux Therapeutics, Inc. Unaudited Condensed Statemen ts of Operations and Comprehensive Loss (in thousands, except share and per share data) Three Months Ended September 30, Nine Months Ended September 30, 2024 2023 2024 2023 Collaboration revenue $ 439 $ 2,517 $ 10,588 $ 5,622 Operating expenses: Research and development 18,614 11,892 47,582 42,681 General and administrative 17,667 6,438 32,831 19,783 Total operating expenses 36,281 18,330 80,413 62,464 Loss from operations ( 35,842 ) ( 15,813 ) ( 69,825 ) ( 56,842 ) Other income: Interest income 7,783 4,245 21,047 10,307 Total other income 7,783 4,245 21,047 10,307 Net loss $ ( 28,059 ) $ ( 11,568 ) $ ( 48,778 ) $ ( 46,535 ) Other comprehensive gain (loss): Unrealized gain (loss) on available-for-sale securities, net 9,447 ( 115 ) 7,166 360 Comprehensive loss $ ( 18,612 ) $ ( 11,683 ) $ ( 41,612 ) $ ( 46,175 ) Net loss per common share, basic and diluted $ ( 0.51 ) $ ( 0.25 ) $ ( 0.93 ) $ ( 1.08 ) Weighted-average shares of common stock outstanding, basic and diluted 54,628,670 45,708,649 52,717,020 43,117,403 See accompanying notes. 2 Table of Contents Janux Therapeutics, Inc. Unaudited Condensed Statements of Stockholders’ Equity For the Nine Months Ended September 30, 2024 and 2023 (in thousands, except share data) Common Stock Additional Paid-in Accumulated Other Comprehensive Accumulated Total Stockholders’ Shares Amount Capital Income Deficit Equity Balance at December 31, 2023 46,252,440 $ 46 $ 512,401 $ 665 $ ( 168,763 ) $ 344,349 Issuance of common stock and pre-funded common stock warrants, net of $ 20,913 of issuance costs 5,397,301 5 320,054 — — 320,059 Exercise of common stock options 613,132 1 6,052 — — 6,053 Issuance of common stock upon vesting of restricted stock units 2,500 — — — — — Shares issued under employee stock purchase plan 63,070 — 473 — — 473 Vesting of restricted shares 8,796 — 13 — — 13 Stock-based compensation — — 26,769 — — 26,769 Unrealized gain on available-for-sale securities, net — — — 7,166 — 7,166 Net loss — — — — ( 48,778 ) ( 48,778 ) Balance at September 30, 2024 52,337,239 $ 52 $ 865,762 $ 7,831 $ ( 217,541 ) $ 656,104 Common Stock Additional Paid-in Accumulated Other Comprehensive Accumulated Total Stockholders’ Shares Amount Capital Loss Deficit Equity Balance at December 31, 2022 41,616,260 $ 42 $ 432,703 $ ( 1,535 ) $ ( 110,470 ) $ 320,740 Issuance of common stock and pre-funded common stock warrants, net of issuance costs 4,153,717 4 56,526 — — 56,530 Exercise of pre-funded common stock warrants 80,257 — — — — — Exercise of common stock options 191,879 — 1,659 — — 1,659 Shares issued under employee stock purchase plan 57,911 — 528 — — 528 Vesting of restricted shares 51,403 — 144 — — 144 Stock-based compensation — — 15,522 — — 15,522 Unrealized gain on available-for-sale securities, net — — — 360 — 360 Net loss — — — — ( 46,535 ) ( 46,535 ) Balance at September 30, 2023 46,151,427 $ 46 $ 507,082 $ ( 1,175 ) $ ( 157,005 ) $ 348,948 See accompanying notes. 3 Table of Contents Janux Therapeutics, Inc. Unaudited Condensed Statements of Stockholders’ Equity For the Three Months Ended September 30, 2024 and 2023 (in thousands, except share data) Common Stock Additional Paid-in Accumulated Other Comprehensive Accumulated Total Stockholders’ Shares Amount Capital Income (Loss) Deficit Equity Balance at June 30, 2024 52,162,215 $ 52 $ 848,723 $ ( 1,616 ) $ ( 189,482 ) $ 657,677 Exercise of common stock options 171,764 — 1,649 — — 1,649 Issuance of common stock upon vesting of restricted stock units 2,500 — — — — — Vesting of restricted shares 760 — 3 — — 3 Stock-based compensation — — 15,387 — — 15,387 Unrealized gain on available-for-sale securities, net — — — 9,447 — 9,447 Net loss — — — — ( 28,059 ) ( 28,059 ) Balance at September 30, 2024 52,337,239 $ 52 $ 865,762 $ 7,831 $ ( 217,541 ) $ 656,104 Common Stock Additional Paid-in Accumulated Other Comprehensive Accumulated Total Stockholders’ Shares Amount Capital Loss Deficit Equity Balance at June 30, 2023 41,867,536 $ 42 $ 445,924 $ ( 1,060 ) $ ( 145,437 ) $ 299,469 Issuance of common stock and pre-funded common stock warrants, net of issuance costs 4,153,717 4 56,526 — — 56,530 Exercise of pre-funded common stock warrants 80,257 — — — — — Exercise of common stock options 43,230 — 79 — — 79 Vesting of restricted shares 6,687 — 5 — — 5 Stock-based compensation — — 4,548 — — 4,548 Unrealized loss on available-for-sale securities, net — — — ( 115 ) — ( 115 ) Net loss — — — — ( 11,568 ) ( 11,568 ) Balance at September 30, 2023 46,151,427 $ 46 $ 507,082 $ ( 1,175 ) $ ( 157,005 ) $ 348,948 See accompanying notes. 4 Table of Contents Janux Therapeutics, Inc. Unaudited Condensed Statem ents of Cash Flows (in thousands) Nine Months Ended September 30, 2024 2023 Cash flows from operating activities Net loss $ ( 48,778 ) $ ( 46,535 ) Adjustments to reconcile net loss to net cash used in operating activities: Depreciation 1,548 1,424 Stock-based compensation 26,769 15,522 Accretion of discounts on investments, net ( 7,658 ) ( 5,627 ) Changes in operating assets and liabilities: Prepaid expenses and other current assets ( 3,077 ) ( 60 ) Other long-term assets ( 314 ) ( 924 ) Accounts payable 25 ( 50 ) Accrued expenses 6,060 ( 1,104 ) Deferred revenue ( 1,705 ) ( 3,979 ) Operating lease right-of-use assets and liabilities, net 41 659 Net cash used in operating activities ( 27,089 ) ( 40,674 ) Cash flows from investing activities Purchases of property and equipment ( 317 ) ( 1,335 ) Purchases of short-term investments ( 446,545 ) ( 284,232 ) Maturities of short-term investments 154,915 233,250 Net cash used in investing activities ( 291,947 ) ( 52,317 ) Cash flows from financing activities Proceeds from exercise of common stock options and employee stock purchase plan 6,526 2,187 Proceeds from the issuance of common stock and pre-funded common stock warrants, net of issuance costs 320,059 56,530 Net cash provided by financing activities 326,585 58,717 Net increase (decrease) in cash, cash equivalents and restricted cash 7,549 ( 34,274 ) Cash, cash equivalents and restricted cash – beginning of year 20,021 52,242 Cash, cash equivalents and restricted cash – end of period $ 27,570 $ 17,968 Supplemental disclosure of noncash investing and financing activities Unpaid property and equipment $ 42 $ 430 Vesting of restricted common stock $ 13 $ 144 Unrealized gain on available-for-sale securities, net $ 7,166 $ 360 See accompanying notes. 5 Table of Contents Janux Therapeutics, Inc. Notes to Unaudited Condensed Financial Statements 1. Organization and Summ ary of Significant Accounting Policies Organization Janux Therapeutics, Inc. (the “Company”) was incorporated in the State of Delaware in June 2017 and is based in San Diego, California. The Company is a clinical-stage biopharmaceutical company developing a broad pipeline of novel immunotherapies by applying its proprietary technology to its Tumor Activated T Cell Engager (“TRACTr”) and Tumor Activated Immunomodulator (“TRACIr”) platforms to better treat patients suffering from cancer. Liquidity and Capital Resources From its inception through September 30, 2024, the Company has devoted substantially all its efforts to organizing and staffing, business planning, raising capital and developing its TRACTr and TRACIr therapeutic platforms and assets. The Company has incurred net losses and negative cash flows from operations since inception and had an accumulated deficit of $ 217.5 million as of September 30, 2024. The Company has a limited operating history, has not generated any product revenue, and the sales and income potential of its business is unproven. To date the Company has funded its operations primarily with the net proceeds from the issuance of convertible promissory notes, the issuance of convertible preferred stock, the issuance of common stock in its initial public offering (“IPO”), the issuance of common stock and pre-funded common stock warrants in underwritten offerings, the exercise of common stock options, and amounts received under a collaboration agreement. The Company expects to incur substantial operating losses for the next several years and will need to obtain additional financing in order to continue its research and development activities, initiate and complete clinical trials and launch and commercialize any product candidates for which it receives regulatory approval. The Company plans to continue to fund its losses from operations and capital funding needs through public or private equity or debt financings or other sources. If the Company is not able to secure adequate additional funding, the Company may be forced to make reductions in spending, extend payment terms with suppliers, liquidate assets where possible, or suspend or curtail planned programs. Any of these actions could materially harm the Company’s business, results of operations and future prospects. There can be no assurance that such financing will be available or will be at terms acceptable to the Company, especially in light of public health crises, financial conditions within the banking industry, including the effects of failures of financial institutions and liquidity levels, as well as changes in interest rates and the inflationary macro environment. Management believes the Company has sufficient capital to fund its operations for at least 12 months from the issuance date of these unaudited condensed financial statements. Unaudited Interim Financial Information The unaudited condensed financial statements as of September 30, 2024, and for the three and nine months ended September 30, 2024 and 2023, have been prepared in accordance with the rules and regulations of the Securities and Exchange Commission (“SEC”), and with accounting principles generally accepted in the United States (“GAAP”) applicable to interim financial statements. These unaudited condensed financial statements have been prepared on the same basis as the Company’s audited financial statements and include all adjustments, consisting of only normal recurring accruals, which in the opinion of management are necessary to present fairly the Company’s financial position as of the interim date and results of operations for the interim periods presented. Interim results are not necessarily indicative of results for a full year or future periods. The condensed balance sheet data as of December 31, 2023 was derived from the Company’s audited financial statements but does not include all disclosures required by GAAP. These unaudited condensed financial statements should be read in conjunction with the Company’s audited financial statements for the year ended December 31, 2023. Use of Estimates The preparation of the Company’s financial statements requires it to make estimates and assumptions that impact the reported amounts of assets, liabilities, revenues and expenses and the disclosure of contingent assets and liabilities in the Company’s financial statements and accompanying notes. The most significant estimates in the Company’s financial statements relate to estimates to complete the performance obligations and the estimated transaction price for collaboration revenue, accruals for research and development expenses, stock-based compensation and fair value measurements. These estimates and assumptions are based on current facts, historical experience and various other factors believed to be reasonable under the circumstances, the results of which form the basis for making judgments about the carrying values of assets and liabilities and the recording of revenues and expenses that are not readily apparent from other sources. The Company continues to use the best information available to update its accounting estimates. Actual results may differ materially and adversely from these estimates. Fair Value Measurements 6 Table of Contents Janux Therapeutics, Inc. Notes to Unaudited Condensed Financial Statements–(Continued) The accounting guidance defines fair value, establishes a consistent framework for measuring fair value and expands disclosure for each major asset and liability category measured at fair value on either a recurring or non-recurring basis. Fair value is defined as an exit price, representing the amount that would be received to sell an asset or paid to transfer a liability in an orderly transaction between market participants. As such, fair value is a market-based measurement that should be determined based on assumptions that market participants would use in pricing an asset or liability. As a basis for considering such assumptions, the accounting guidance establishes a three-tier fair value hierarchy, which prioritizes the inputs used in measuring fair value as follows: Level 1: Observable inputs such as quoted prices in active markets. Level 2: Inputs, other than the quoted prices in active markets that are observable either directly or indirectly. Level 3: Unobservable inputs in which there is little or no market data, which require the reporting entity to develop its own assumptions. The carrying amounts of the Company’s financial instruments, including cash and cash equivalents, restricted cash, accounts receivable, prepaid and other current assets, accounts payable, and accrued expenses, approximate fair value due to the short-term nature of those instruments. The fair value of assets classified within Level 1 is based on quoted prices in active markets as provided by the Company’s investment managers. The fair value of short-term investments classified within Level 2 is based on standard observable inputs, including reported trades, broker/dealer quotes, and bids and/or offers. The Company validates the quoted market prices provided by its investment managers by comparing the investment managers’ assessment of the fair values of the Company’s investment portfolio balance against the fair values of the Company’s investment portfolio balance obtained from an independent source. The Company has no financial liabilities recorded at fair value on a recurring basis. None of the Company’s non-financial assets or liabilities are recorded at fair value on a non-recurring basis. No transfers between levels have occurred during the periods presented. The following tables summarize the Company’s financial instruments measured at fair value on a recurring basis (in thousands): Fair Value Measurements at Reporting Date Using Total Quoted Prices in Active Markets for Identical Assets (Level 1) Significant Other Observable Inputs (Level 2) Significant Unobservable Inputs (Level 3) As of September 30, 2024: Assets: Cash equivalents: Money market funds $ 22,221 $ 22,221 $ — $ — Total cash equivalents 22,221 22,221 — — Short-term investments: U.S. Treasury securities 114,464 114,464 — — U.S. agency bonds 330,158 — 330,158 — Corporate debt securities 156,729 — 156,729 — Commercial paper 29,926 — 29,926 — Total short-term investments 631,277 114,464 516,813 — Restricted cash: Money market account 816 816 — — Total restricted cash 816 816 — — Total assets measured at fair value on a recurring basis $ 654,314 $ 137,501 $ 516,813 $ — 7 Table of Contents Janux Therapeutics, Inc. Notes to Unaudited Condensed Financial Statements–(Continued) Fair Value Measurements at Reporting Date Using Total Quoted Prices in Active Markets for Identical Assets (Level 1) Significant Other Observable Inputs (Level 2) Significant Unobservable Inputs (Level 3) As of December 31, 2023: Assets: Cash equivalents: Money market funds $ 14,751 $ 14,751 $ — $ — Total cash equivalents 14,751 14,751 — — Short-term investments: U.S. Treasury securities 71,300 71,300 — — U.S. agency bonds 167,103 — 167,103 — Asset-backed securities 5,055 — 5,055 — Corporate debt securities 1,999 — 1,999 — Commercial paper 79,366 — 79,366 — Total short-term investments 324,823 71,300 253,523 — Restricted cash: Money market account 816 816 — — Total restricted cash 816 816 — — Total assets measured at fair value on a recurring basis $ 340,390 $ 86,867 $ 253,523 $ — Cash and Cash Equivalents The Company considers all highly liquid investments with original maturities of three months or less when purchased to be cash equivalents. Cash and cash equivalents include cash in readily available checking accounts and money market funds. Restricted Cash Restricted cash consists of a money market account securing a standby letter of credit issued in connection with the Company’s Torrey Plaza operating lease (as defined and described in Note 3). The following table provides a reconciliation of cash and cash equivalents and restricted cash reported within the accompanying balance sheets that sum to the amounts shown in the condensed statements of cash flows (in thousands): September 30, 2024 December 31, 2023 Cash and cash equivalents $ 26,754 $ 19,205 Restricted cash 816 816 Total cash and cash equivalents and restricted cash $ 27,570 $ 20,021 Short-Term Investments Short-term investments consist of U.S. Treasury securities, U.S. agency bonds, asset-backed securities, corporate debt securities and commercial paper, all of which are highly rated by Moody’s, S&P, and Fitch. The Company has classified these investments as available-for-sale, as the sale of such investments may be required prior to maturity to implement management strategies, and therefore has classified all investment securities as current assets. Those investments with maturity dates of three months or less at the date of purchase are presented as cash equivalents in the accompanying balance sheets. Short-term investments are carried at fair value with the unrealized gains and losses included in accumulated other comprehensive income (loss) as a component of stockholders’ equity until realized. Any premium or discount arising at purchase is amortized or accreted to interest income as an adjustment to yield using the straight-line method over the life of the instrument. The Company records an allowance for credit losses when unrealized 8 Table of Contents Janux Therapeutics, Inc. Notes to Unaudited Condensed Financial Statements–(Continued) losses are due to credit-related factors. Realized gains and losses are calculated using the specific identification method and recorded as interest income. The following tables summarize short-term investments (in thousands): As of September 30, 2024 Amortized Unrealized Estimated Cost Gains Losses Fair Value U.S. Treasury securities $ 113,468 $ 996 $ — $ 114,464 U.S. agency bonds 325,893 4,278 ( 13 ) 330,158 Corporate debt securities 154,195 2,534 — 156,729 Commercial paper 29,890 44 ( 8 ) 29,926 Total $ 623,446 $ 7,852 $ ( 21 ) $ 631,277 As of December 31, 2023 Amortized Unrealized Estimated Cost Gains Losses Fair Value U.S. Treasury securities $ 71,072 $ 242 $ ( 14 ) $ 71,300 U.S. agency bonds 166,699 591 ( 187 ) 167,103 Asset-backed securities 5,078 — ( 23 ) 5,055 Corporate debt securities 1,999 — — 1,999 Commercial paper 79,310 56 — 79,366 Total $ 324,158 $ 889 $ ( 224 ) $ 324,823 The amortized cost and estimated fair value in the tables above e xclude $ 4.5 million and $ 2.2 million of accrued interest receivable as of September 30, 2024 and December 31, 2023, respectively. Accrued interest receivable is included in prepaid expenses and other current assets in the accompanying balance sheets. Contractual maturities of available-for-sale debt securities are as follows (in thousands): As of September 30, 2024 Due in 1 Year or Less Due Between 1 and 3 Years U.S. Treasury securities $ 56,590 $ 57,874 U.S. agency bonds 95,880 234,278 Corporate debt securities — 156,729 Commercial paper 29,926 — Total $ 182,396 $ 448,881 As of December 31, 2023 Due in 1 Year or Less Due Between 1 and 3 Years U.S. Treasury securities $ 34,426 $ 36,874 U.S. agency bonds 89,801 77,302 Asset-backed securities 5,055 — Corporate debt securities 1,999 — Commercial paper 79,366 — Total $ 210,647 $ 114,176 As of September 30, 2024 , 3 out of 67 of our a vailable-for-sale debt securities were in an aggregate gross unrealized loss position. The Company relies on both qualitative and quantitative factors to determine whether the unrealized loss for each available-for-sale debt security at any balance sheet date is due to a credit loss. Qualitative factors may include a credit downgrade, severity of the decline in fair value below amortized cost and other adverse conditions related specifically to the security, as well as the intent to sell 9 Table of Contents Janux Therapeutics, Inc. Notes to Unaudited Condensed Financial Statements–(Continued) the security, or whether the Company will “more likely than not” be required to sell the security before recovery of its amortized cost basis. The Company considers the decline in market value for the securities to be primarily attributable to current economic conditions and interest rate adjustments, rather than credit-related factors and does not intend to sell any securities prior to maturity. No allowance for credit losses has been recorded as of September 30, 2024 or December 31, 2023. The following tables summarize our available-for-sale debt securities in an aggregate gross unrealized loss position for which an allowance for credit losses has not been recorded, aggregated by major security type and length of time in a continuous unrealized loss position (in thousands): As of September 30, 2024 Less Than 12 Months 12 Months or Longer Total Fair Value Unrealized Losses Fair Value Unrealized Losses Fair Value Unrealized Losses U.S. agency bonds $ 5,002 $ ( 6 ) $ 9,998 $ ( 7 ) $ 15,000 $ ( 13 ) Commercial paper 10,650 ( 8 ) — — 10,650 ( 8 ) Total $ 15,652 $ ( 14 ) $ 9,998 $ ( 7 ) $ 25,650 $ ( 21 ) As of December 31, 2023 Less Than 12 Months 12 Months or Longer Total Fair Value Unrealized Losses Fair Value Unrealized Losses Fair Value Unrealized Losses U.S. Treasury securities $ 5,892 $ ( 14 ) $ — $ — $ 5,892 $ ( 14 ) U.S. agency bonds 63,583 ( 169 ) 9,970 ( 18 ) 73,553 ( 187 ) Asset-backed securities 5,055 ( 23 ) — — 5,055 ( 23 ) Total $ 74,530 $ ( 206 ) $ 9,970 $ ( 18 ) $ 84,500 $ ( 224 ) Concentrations of Credit Risk Financial instruments that potentially subject the Company to significant concentrations of credit risk consist primarily of cash, cash equivalents and short-term investments. The Company invests its cash reserves in money market funds or available-for-sale debt securities in accordance with its investment policy. The Company’s investment policy includes guidelines on acceptable investment securities, limits interest-bearing security investments to certain types of debt and money market instruments issued by the U.S. government and institutions with investment grade credit ratings and places restrictions on maturities and concentration by asset class and issuer in order to maintain appropriate diversification. In accordance with the Company’s policies, the Company monitors exposure with its counterparties. The Company also maintains deposits in federally insured financial institutions in excess of federally insured limits. The Company has not experienced any losses in such account and management believes that the Company is not exposed to significant credit risk. The Company is also subject to credit risk from its accounts receivable. The Company generally does not perform evaluations of customers’ financial condition and generally does not require collateral. As of September 30, 2024, and December 31, 2023, all of the Company’s accounts receivable, if any, relate to a single customer. For the three and nine months ended September 30, 2024 and 2023, all of the Company’s revenue related to a single customer. Leases The Company determines if a contract contains a lease at the inception of the contract and evaluates each lease agreement to determine whether the lease is an operating or finance lease. For leases where the Company is the lessee, right-of-use (“ROU”) assets represent the Company’s right to use an underlying asset for the lease term and lease liabilities represent an obligation to make lease payments arising from the lease. Liabilities from operating leases are included in current portion of operating lease liabilities, and operating lease liabilities, net of current portion on the accompanying balance sheets. The Company does not have any financing leases. Short-term leases with an initial term of 12 months or less are not recorded on the balance sheet. The Company does not have material short-term lease costs. Lease liabilities are measured at the present value of the lease payments not yet paid discounted using the discount rate for the lease established at the lease commencement date. To determine the present value, the implicit rate is used when readily determinable. 10 Table of Contents Janux Therapeutics, Inc. Notes to Unaudited Condensed Financial Statements–(Continued) For those leases where the implicit rate is not provided, the Company determines an incremental borrowing rate (“IBR”) based on the information available at the lease commencement date in determining the present value of lease payments. The IBR is the rate of interest that a lessee would have to pay to borrow on a collateralized basis over a similar term an amount equal to the lease payments in a similar economic environment. ROU assets are measured as the present value of the lease payments and also include any prepaid lease payments made and any other indirect costs incurred and exclude any lease incentives received. Lease terms may include the impact of options to extend or terminate the lease when it is reasonably certain that the Company will exercise that option. Lease expense for operating leases is recognized on a straight-line basis over the lease term. The Company’s operating leases are subject to additional variable charges, including common area maintenance, property taxes, property insurance and other variable costs. Given the variable nature of such costs, they are recognized as expense as incurred. The Company has elected the practical expedient to account for the lease and non-lease components, such as common area maintenance charges, as a single lease component for the Company's facilities leases. The Company has elected to recognize lease incentives, such as tenant improvement allowances, at the lease commencement date as a reduction to the ROU asset and lease liabilities balance until paid to it by the lessor to the extent that the lease provides a specified fixed or maximum level of reimbursement and the Company is reasonably certain to incur reimbursable costs at least equaling such amounts. Revenue Recognition The Company recognizes revenue in a manner that depicts the transfer of control of a product or a service to a customer and reflects the amount of the consideration the Company is entitled to receive in exchange for such product or service. In doing so, the Company follows a five-step approach: (i) identify the contract 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, and (v) recognize revenue when (or as) the customer obtains control of the product or service. The Company considers the terms of a contract and all relevant facts and circumstances when applying the revenue recognition standard. A customer is a party that has entered into a contract with the Company, where the purpose of the contract is to obtain a product or a service that is an output of the Company’s ordinary activities in exchange for consideration. To be considered a contract, (i) the contract must be approved (in writing, orally, or in accordance with other customary business practices), (ii) each party’s rights regarding the product or the service to be transferred can be identified, (iii) the payment terms for the product or the service to be transferred can be identified, (iv) the contract must have commercial substance (that is, the risk, timing or amount of future cash flows is expected to change as a result of the contract), and (v) it is probable that the Company will collect substantially all of the consideration to which it is entitled to receive in exchange for the transfer of the product or the service. A performance obligation is defined as a promise to transfer a product or a service to a customer. The Company identifies each promise to transfer a product or a service (or a bundle of products or services, or a series of products and services that are substantially the same and have the same pattern of transfer) that is distinct. A product or a service is distinct if both (i) the customer can benefit from the product or the service either on its own or together with other resources that are readily available to the customer and (ii) the Company’s promise to transfer the product or the service to the customer is separately identifiable from other promises in the contract. Each distinct promise to transfer a product or a service is a unit of accounting for revenue recognition. If a promise to transfer a product or a service is not separately identifiable from other promises in the contract, such promises should be combined into a single performance obligation. The transaction price is the amount of consideration the Company is entitled to receive in exchange for the transfer of control of a product or a service to a customer. To determine the transaction price, the Company considers the existence of any significant financing component, the effects of any variable elements, noncash considerations and consideration payable to the customer. If a significant financing component exists, the transaction price is adjusted for the time value of money. If an element of variability exists, the Company must estimate the consideration it expects to receive and uses that amount as the basis for recognizing revenue as the product or the service is transferred to the customer. There are two methods for determining the amount of variable consideration: (i) the expected value method, which is the sum of probability-weighted amounts in a range of possible consideration amounts, and (ii) the mostly likely amount method, which identifies the single most likely amount in a range of possible consideration amounts. With respect to variable consideration relating to development and regulatory milestone payments, if it is probable that a significant revenue reversal would not occur, the associated payment value is included in the transaction price. For development and regulatory milestones that are uncertain in nature and highly dependent on factors outside of our control, the aggregate consideration is determined to be fully constrained and is not included in the transaction price until the underlying events occur or the associated approvals are received. At the end of each reporting period, the Company re-evaluates the probability of achievement of each milestone and any related constraint, and if necessary, adjust our estimate of the overall transaction price. Any such adjustments are recorded on a cumulative catch-up basis, which would affect the reported amount of revenues in the period of adjustment. 11 Table of Contents Janux Therapeutics, Inc. Notes to Unaudited Condensed Financial Statements–(Continued) For arrangements that include sales-based royalties, including milestone payments based on a 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). If a contract has multiple performance obligations, the Company allocates the transaction price to each distinct performance obligation in an amount that reflects the consideration the Company is entitled to receive in exchange for satisfying each distinct performance obligation. For each distinct performance obligation, revenue is recognized when (or as) the Company transfers control of the product or the service applicable to such performance obligation. In those instances where the Company first receives consideration in advance of satisfying its performance obligation, the Company classifies such consideration as deferred revenue until (or as) the Company satisfies such performance obligation. In those instances where the Company first satisfies its performance obligation prior to its receipt of consideration, the consideration is recorded as accounts receivable. The Company expenses incremental costs of obtaining and fulfilling a contract as and when incurred if the expected amortization period of the asset that would be recognized is one year or less, or if the amount of the asset is immaterial. Otherwise, such costs are capitalized as contract assets if they are incremental to the contract and amortized to expense proportionate to revenue recognition of the underlying contract. Research and Development Expenses All research and development costs are expensed in the period incurred. Payments for these activities are based on the terms of the individual agreements, which may differ from the pattern of costs incurred, and payments made in advance of performance are reflected in the accompanying balance sheets as prepaid expenses. The Company records accruals for estimated costs incurred for ongoing research and development activities. When evaluating the adequacy of the accrued expenses, the Company analyzes progress of the services, including the phase or completion of events, invoices received and contracted costs. Significant judgments and estimates may be made in determining the prepaid or accrued balances at the end of any reporting period. Actual results could differ from the Company’s estimates. Stock-Based Compensation Stock-based compensation expense represents the grant date fair value of equity awards, consisting of stock options, restricted stock units and employee stock purchase plan rights, recognized on a straight-line basis over the requisite service period for stock options and restricted stock units, and over the respective offering period for employee stock purchase plan rights. The Company estimates the fair value of stock options and employee stock purchase plan rights using the Black-Scholes option pricing model. The fair value of restricted stock units is based on the closing price of the Company’s common stock as reported on The Nasdaq Global Market on the date of grant. The Company recognizes forfeitures for all awards as they occur. Comprehensive Loss Comprehensive loss is defined as a change in equity during a period from transactions and other events and circumstances from non-owner sources. The only component of other comprehensive gain (loss) is unrealized gain (loss) on available-for-sale securities. Comprehensive losses have been reflected in the condensed statements of operations and comprehensive loss and as a separate component in the condensed statements of stockholders’ equity. Net Loss Per Share Basic net loss per share is computed by dividing the net loss by the weighted-average number of shares of common stock outstanding for the period, including pre-funded common stock warrants that were issued in underwritten offerings (Note 4), without consideration for potentially dilutive securities. The pre-funded common stock warrants are included in the calculation of basic and diluted net loss per share as the exercise price of $ 0.001 per share is non-substantive and the shares are issuable for little or no consideration. The Company has excluded weighted-average unvested shares of 1,895 shares, 20,274 shares, 4,618 shares and 32,132 shares from the weighted-average number of shares of common stock outstanding for the three months ended September 30, 2024 and 2023 and nine months ended September 30, 2024 and 2023, respectively. Diluted net loss per share is computed by dividing the net loss by the weighted-average number of shares of common stock and dilutive common stock equivalents outstanding for the period determined using the treasury-stock and if-converted methods. For all periods presented, there is no difference in the number of shares used to calculate basic and diluted shares outstanding as inclusion of the potentially dilutive securities would be anti-dilutive. 12 Table of Contents Janux Therapeutics, Inc. Notes to Unaudited Condensed Financial Statements–(Continued) Potentially dilutive securities not included in the calculation of diluted net loss per share, because to do so would be anti-dilutive, are as follows (in common stock equivalent shares): September 30, 2024 2023 Common stock options outstanding 9,590,050 8,495,581 Restricted stock units outstanding 80,562 — Unvested common stock 1,523 17,003 Employee stock purchase plan shares 28,560 23,172 Total potentially dilutive shares 9,700,695 8,535,756 Recent Accounting Pronouncements In August 2020, the Financial Accounting Standards Board (“FASB”) issued Accounting Standards Update ("ASU") No. 2020-06, Debt - Debt with Conversion and Other Options (Subtopic 470-20) and Derivatives and Hedging - Contracts in Entity’s Own Equity (Subtopic 815-40) - Accounting for Convertible Instruments and Contracts in an Entity’s Own Equity, which simplifies the accounting for certain financial instruments with characteristics of liabilities and equity, including convertible instruments and contracts on an entity’s own equity. The Company adopted ASU No. 2020-06 on January 1, 2024 and the adoption of the standard had no material impact on its financial statements and related disclosures. Accounting Pronouncements Pending Adoption In November 2023, the FASB issued ASU 2023-07, Segment Reporting (Topic 280) - Improvements to Reportable Segment Disclosures. The new standard requires a company to disclose incremental segment information on an annual and interim basis, including significant segment expenses and measures of profit or loss that are regularly provided to the chief operating decision maker. The standard is effective for the Company beginning in fiscal year 2024 and interim periods within fiscal year 2025, with early adoption permitted. The Company does not expect to early adopt the new standard. The Company is currently evaluating the impact of ASU 2023-07 on its financial statements and related disclosures and will adopt the new standard using a retrospective approach. In December 2023, the FASB also issued ASU 2023-09, Income Taxes (Topic 740) - Improvements to Income Tax Disclosures. The new standard requires a company to expand its existing income tax disclosures, specifically related to the rate reconciliation and income taxes paid. The standard is effective for the Company for annual periods beginning after December 15, 2024 , with early adoption permitted. The Company does not expect to early adopt the new standard. The new standard is expected to be applied prospectively, but retrospective application is permitted. The Company is currently evaluating the impact of ASU 2023-09 on its financial statements and related disclosures. 2. Balance Sheet Details Prepaid expenses and other current assets consist of the following (in thousands): September 30, 2024 December 31, 2023 Interest receivable $ 4,454 $ 2,161 Prepaid research and development 2,678 2,318 Other prepaid expenses 1,158 734 Prepaid expenses and other current assets $ 8,290 $ 5,213 13 Table of Contents Janux Therapeutics, Inc. Notes to Unaudited Condensed Financial Statements–(Continued) Property and equipment, net consist of the following (in thousands): September 30, 2024 December 31, 2023 Laboratory equipment $ 8,366 $ 8,454 Furniture and fixtures 792 792 Computer equipment and software 658 628 Assets not placed in service — 43 Total property and equipment 9,816 9,917 Less: accumulated depreciation ( 4,443 ) ( 2,914 ) Property and equipment, net $ 5,373 $ 7,003 Accrued expenses consist of the following (in thousands): September 30, 2024 December 31, 2023 Accrued research and development $ 8,349 $ 3,535 Accrued compensation 3,895 3,303 Other accrued expenses 778 549 Accrued expenses $ 13,022 $ 7,387 3. Commitments and Contingencies License Agreement with WuXi Biologics (Hong Kong) Limited In April 2021, the Company entered into a cell line license agreement (“Cell Line License Agreement”) with WuXi Biologics (Hong Kong) Limited (“WuXi Biologics”), pursuant to which the Company received a non-exclusive, worldwide, sublicensable license under certain of WuXi Biologics’ patent rights, know-how and biological materials (“WuXi Biologics Licensed Technology”), to use the WuXi Biologics Licensed Technology to make, use, sell, offer for sale and import certain therapeutic products produced through the use of the cell line licensed by WuXi Biologics under the Cell Line License Agreement (“WuXi Biologics Licensed Product”). In consideration for the license, the Company paid WuXi Biologics a non-refundable, one-time license fee of $ 0.2 million upon WuXi Biologics’ achievement of a certain technical milestone. This one-time license fee was recognized as research and development expense when incurred since the WuXi Biologics Licensed Technology had no alternative future use. If the Company does not engage WuXi Biologics or its affiliates to manufacture the WuXi Biologics Licensed Products for its commercial supplies, the Company is required to make royalty payments to WuXi Biologics in an amount equal to a low single-digit percentage of specified portions of net sales of WuXi Biologics Licensed Products manufactured by a third-party manufacturer. The Company has the right (but not the obligation) to buy out its remaining royalty obligations with respect to each WuXi Biologics Licensed Product by paying WuXi Biologics a one-time payment in an amount ranging from low single digit million dollars to a maximum of $ 15.0 million depending on the development and commercialization stage of the WuXi Biologics Licensed Product (the “Buyout Option”), and upon such payment, the Company's license with respect to such WuXi Biologics Licensed Product will become fully paid-up, irrevocable, and perpetual. The royalty obligations will remain in effect during the term of the Cell Line License Agreement so long as the Company has not exercised the Buyout Option. The Cell Line License Agreement will continue indefinitely unless terminated (i) by the Company upon three months’ prior written notice and the Company’s payment of all amounts due to WuXi Biologics through the effective date of termination, (ii) by either party for the other party’s material breach that remains uncured for 30 days after written notice, and (iii) by WuXi Biologics if the Company fails to make a payment and such failure continues for 30 days after receiving notice of such failure. Operating Leases In October 2021, the Company entered into a lease agreement (the “Torrey Plaza Lease”) to lease office and laboratory space in San Diego, California. The Company determined this facilities lease was an operating lease at the inception of the lease contract. According to accounting standards, the Torrey Plaza Lease commenced on April 1, 2022 and has a term of 130 months from the commencement date. The Torrey Plaza Lease provides an option to extend the term of the lease for a period of 5 years beyond the 14 Table of Contents Janux Therapeutics, Inc. Notes to Unaudited Condensed Financial Statements–(Continued) initial term, which the Company is not reasonably certain to exercise and therefore was not considered in determining the ROU assets and lease liabilities balance. As required under the terms of the Torrey Plaza Lease, in October 2021 the Company entered into a standby letter of credit, which is secured by a money market account in the amount of $ 0.8 million. The letter of credit is subject to draw down by the landlord upon certain events of breach or default by the Company. The letter of credit amount is subject to a 50 % reduction subject to certain conditions on or following the date that is 54 months following the contractual lease commencement date. Future minimum noncancelable operating lease payments as of September 30, 2024 are as follows (in thousands): 2024 (remaining) $ 866 2025 3,505 2026 3,611 2027 3,719 2028 3,830 Thereafter 16,872 Total minimum lease payments 32,403 Less: Imputed interest ( 8,972 ) Total operating lease liabilities 23,431 Less: Current portion of operating lease liabilities ( 1,689 ) Operating lease liabilities, net of current portion $ 21,742 The Torrey Plaza lease has a remaining lease term of 8.3 years and a discount rate of 8 % as of September 30, 2024. Operating lease expense included in the measurement of lease liabilities for the three and nine months ended September 30, 2024 was $ 0.9 million and $ 2.6 million, respectively. Cash paid for amounts included in the measurement of lease liabilities for the three and nine months ended September 30, 2024 wa s $ 0.9 million and $ 2.5 million, re spectively. Operating lease expense included in the measurement of lease liabilities for the three and nine months ended September 30, 2023 was $ 0.9 million and $ 2.6 million, respectively. Cash paid for amounts included in the measurement of lease liabilities for the three and nine months ended September 30, 2023 was $ 0.8 million and $ 1.9 million, respectively. Contingencies From time to time, the Company may be subject to claims or lawsuits arising in the ordinary course of business. The Company accrues a liability for such matters when it is probable that future expenditures will be made and such expenditures can be reasonably estimated. As of September 30, 2024, the Company is not currently party to any material le gal proceedings. 4. Stockholders’ Equity Shelf Registration Statement In May 2023, the Company entered into an ATM Equity Offering SM Sales Agreement (“Sale Agreement”) with BofA Securities, Inc. (“BofA”) to sell shares of common stock, from time to time, through an “at the market offering” program having an aggregate offering price of up to $ 150.0 million through which BofA would act as sales agent. In February 2024, the Company delivered written notice to BofA that it was suspending and terminating the prospectus related to the shares of its common stock issuable pursuant to the terms of the Sale Agreement. In May 2024 , the Company filed a shelf registration statement on Form S-3 which included a new prospectus which covers the offering, issuance and sale of up to a maximum aggregate offering price of $ 150.0 million of the Company’s common under the Sale Agreement . There was no activity from the Sale Agreement during the three and nine months ended September 30, 2024. As of September 30, 2024 , $ 150.0 million of common stock remained available for sale under the Sale Agreement. In July 2023, the Company closed an underwritten offering of 4,153,717 shares of its common stock and pre-funded warrants to purchase 583,483 shares of common stock at an exercise price of $ 0.001 per share. The shares of common stock were sold at a price of $ 12.46 per share and the pre-funded common stock warrants were sold at a price of $ 12.459 per pre-funded common stock warrant, resulting in gross proceeds of $ 59.0 million. Fees related to the offering included underwriting discounts, commissions, and offering expenses in the aggregate amount of $ 2.5 million, resulting in net proceeds of $ 56.5 million. The pre-funded common stock warrants will not expire until exercised in full and are exercisable in cash or by means of a cashless exercise. 15 Table of Contents Janux Therapeutics, Inc. Notes to Unaudited Condensed Financial Statements–(Continued) In March 2024, the Company closed an underwritten offering of 5,397,301 shares of its common stock and pre-funded warrants to purchase 1,935,483 shares of common stock at an exercise price of $ 0.001 per share . The shares of common stock were sold at a price of $ 46.50 per share and the pre-funded common stock warrants were sold at a price of $ 46.499 per pre-funded common stock warrant, resulting in gross proceeds of $ 341.0 million. Fees related to the offering included underwriting discounts, commissions, and offering expenses in the aggregate amount of $ 20.9 million, resulting in net proceeds of $ 320.1 million. The pre-funded common stock warrants will not expire until exercised in full and are exercisable in cash or by means of a cashless exercise. The Company has assessed the pre-funded common stock warrants for appropriate equity or liability classification. The pre-funded common stock warrants are equity classified because they (i) are freestanding financial instruments that are legally detachable and separately exercisable from the equity instruments, (ii) are immediately exercisable, (iii) do not embody an obligation for the Company to repurchase its shares, (iv) permit the holders to receive a fixed number of shares of common stock upon exercise, (v) are indexed to the Company’s common stock and (vi) meet the equity classification criteria. In addition, such pre-funded common stock warrants do not provide any guarantee of value or return and do not provide the warrant holders with the option to settle any unexercised warrants for cash outside of the Company’s control. The pre-funded common stock warrants also include a separate provision whereby the exercisability of the warrants may be limited if, upon exercise, the warrant holder or any of its affiliates would beneficially own more than a certain percentage of the Company’s outstanding common stock. The Company valued the pre-funded common stock warrants at issuance, concluding that their sale price approximated their fair value. Accordingly, the pre-funded common stock warrants are accounted for as a component of additional paid-in capital at the time of issuance. 2017 Equity Incentive Plan In August 2017, the Company adopted the Janux Therapeutics, Inc. 2017 Equity Incentive Plan (the “2017 Plan”), which provided for the grant of incentive stock options, nonstatutory stock options, restricted stock awards and other stock awards to its employees, members of its board of directors and consultants. The maximum term of options granted under the 2017 Plan is ten years and, in general, the options issued under the 2017 Plan vest over a four-year period from the vesting commencement date. The 2017 Plan allows for the early exercise of stock options, which may be subject to repurchase by the Company at the original exercise price. Upon the effectiveness of the 2021 Plan defined and described below, no further grants will be made under the 2017 Plan. Any outstanding awards granted under the 2017 Plan will remain subject to the terms of the 2017 Plan and applicable award agreements. 2021 Equity Incentive Plan In June 2021, the Company adopted the 2021 Equity Incentive Plan (the “2021 Plan,” and together with the 2017 Plan the “Plans”). Under the 2021 Plan, the Company may grant stock options, stock appreciation rights, restricted stock, restricted stock units, performance stock awards, performance cash awards and other forms of stock awards to employees, directors and consultants. The maximum term of options granted under the 2021 Plan is ten years and, in general, the options issued under the 2021 Plan vest over a four-year period from the vesting commencement date. The 2021 Plan does not permit early exercises. Any future cancellations under the 2017 Plan will become available for future issuance under the 2021 Plan. In addition, the number of shares of common stock available for issuance under the 2021 Plan automatically increases on January 1 of each calendar year through January 1, 2031, in an amount equal to 5 % of the total number of shares of the Company’s common stock on the last day of the calendar month before the date of each automatic increase, or a lesser number of shares determined by the Company’s board of directors. As of September 30, 2024 , there were 11,231,951 shar es authorized for issuance under the 2021 Plan, inclusive of shares added from 2017 Plan cancellations. 16 Table of Contents Janux Therapeutics, Inc. Notes to Unaudited Condensed Financial Statements–(Continued) Stock Options A summary of the Company’s stock option activity under its Plans is as follows (in thousands, except share, per share data and years): Number of Options Weighted- Average Exercise Price Weighted- Average Remaining Contractual Term (in years) Aggregate Intrinsic Value Outstanding at December 31, 2023 7,989,192 $ 12.08 7.8 $ 16,733 Granted 2,325,838 $ 14.56 Exercised ( 613,132 ) $ 9.87 Forfeited or cancelled ( 111,848 ) $ 15.36 Outstanding at September 30, 2024 9,590,050 $ 12.78 7.6 $ 313,486 Vested and expected to vest at September 30, 2024 9,511,862 $ 12.79 7.6 $ 310,843 Exercisable at September 30, 2024 5,720,842 $ 11.23 6.8 $ 195,641 The weighted-average grant date fair value per share of option grants for the nine months ended September 30, 2024 and 2023 was $ 10.86 and $ 10.09 , respectively. The total intrinsic value of stock options exercised for the nine months ended September 30, 2024 and 2023 was $ 22.1 million and $ 1.9 million, respectively. As of September 30, 2024 , total unrecognized stock-based compensation cost associated with option grants was $ 39.1 million, which is expected to be recognized over a remaining weighted-average period of approximately 2.3 years. The assumptions used in the Black-Scholes option pricing model to determine the fair value of stock option grants under the Plans were as follows: Nine Months Ended September 30, 2024 2023 Risk-free interest rate 3.7 % – 4.6 % 3.5 % – 4.2 % Expected volatility 83 % – 106 % 83 % – 87 % Expected term (in years) 5.3 – 6.1 5.3 – 6.1 Expected dividend yield — — Risk-free interest rate . The risk-free interest rate is based on the U.S. Treasury yield in effect at the time of grant for zero coupon U.S. Treasury notes with maturities similar to the expected term of the awards. Expected volatility. For options granted in the initial years following the Company’s IPO, given the Company’s limited historical stock price volatility data, the expected volatility assumption is based on volatilities of a peer group of similar companies whose share prices are publicly available, including the Company’s historical volatility, weighted by years of available trading data within the expected term. The peer group was developed based on companies in the biotechnology industry. As sufficient historical data is now available for the Company’s stock price, the Company is currently applying and will continue to apply the volatility of its own stock price in determining volatility. Expected term . The expected term represents the period of time that options are expected to be outstanding. Because the Company does not have sufficient historical exercise behavior to provide a reasonable basis upon which to estimate the expected term, it determines the expected life assumption using the simplified method, for employees and nonemployee directors, which is an average of the contractual term of the option and its vesting period. The expected term for nonemployee options is generally the contractual term. Expected dividend yield . The Company bases the expected dividend yield assumption on the fact that it has never paid cash dividends and has no present intention to pay cash dividends and, therefore, used an expected dividend yield of zero. 17 Table of Contents Janux Therapeutics, Inc. Notes to Unaudited Condensed Financial Statements–(Continued) Restricted Stock Units A summary of the Company’s restricted stock unit (“RSU”) activity under the 2021 Plan is as follows: Number of Restricted Stock Units Weighted- Average Grant Date Fair Value per Share Outstanding at December 31, 2023 — $ — Granted 83,062 $ 43.70 Vested ( 2,500 ) $ 39.80 Forfeited or cancelled — $ — Outstanding at September 30, 2024 80,562 $ 43.82 RSU awards are share awards that, upon vesting, will deliver to the holder shares of the Company’s common stock. The grant-date fair value is recognized as compensation expense over the vesting period. As of September 30, 2024, total unrecognized stock-based compensation cost associated wit h RSUs was $ 3.3 million, which is expected to be recognized over a remaining weighted-average period of approximately 3.1 years. 2021 Employee Stock Purchase Plan In June 2021, the Company adopted the 2021 Employee Stock Purchase Plan (the “ESPP”), which became effective on June 10, 2021. The ESPP permits eligible employees who elect to participate in an offering under the ESPP to have up to 15 % of their eligible earnings withheld, subject to certain limitations, to purchase shares of common stock pursuant to the ESPP. The price of common stock purchased under the ESPP is equal to 85 % of the lower of the fair market value of the common stock at the commencement date of each offering period or the relevant date of purchase. In addition, the number of shares of common stock available for issuance under the ESPP automatically increases on January 1 of each calendar year through January 1, 2031, in an amount equal to the lesser of (i) 1 % of the total number of shares of the Company’s common stock on the last day of the calendar month before the date of each automatic increase and (ii) 932,000 shares; provided that before the date of any such increase, the Company’s board of directors may determine that such increase will be less than the amount set forth in clauses (i ) and (ii). For the three and nine months ended September 30, 2024 , stock-based compensation expense related to the ESPP was $ 0.1 million and $ 0.6 million, respectively. Stock-based compensation expense related to the ESPP for the three and nine months ended September 30, 2023 was $ 0.2 million and $ 0.7 million, respectively. As of September 30, 2024 , total unrecognized stock-based compensation expense related to the ESPP was $ 0.5 million, which is expected to be recognized over a remaining weighted-average period of approximately 1.2 years. Stock-Based Compensation Expense Stock-based compensation expense has been reported in the condensed statements of operations and comprehensive loss as follows (in thousands): Three Months Ended September 30, Nine Months Ended September 30, 2024 2023 2024 2023 Research and development $ 2,374 $ 1,572 $ 6,882 $ 6,379 General and administrative 13,013 2,976 19,887 9,143 Total $ 15,387 $ 4,548 $ 26,769 $ 15,522 Modification of equity awards In July 2024, and in connection with the resignation of a former director, the board of directors approved the following modifications to the terms of the former director’s outstanding equity awards: (a) acceleration of the vesting of all unvested stock options and awards in full, effective as of the former director's resignation date; and (b) extension of the post-termination exercise period for outstanding options until the earlier of the third anniversary of such resignation date or the original expiration date of such options, subject to the Company’s ability to take any actions permitted under the 2021 Plan. The incremental stock-based compensation expense resulting from these modifications recognized during the three and nine months ended September 30, 2024 was $ 0.7 million. 18 Table of Contents Janux Therapeutics, Inc. Notes to Unaudited Condensed Financial Statements–(Continued) In August 2024, and in connection with the resignation of a former executive officer, the compensation committee of the board of directors approved the following modifications to the terms of the former officer’s outstanding equity awards as defined within a transition and consulting agreement with the former officer (the “Transition Agreement”): (a) acceleration of the vesting of unvested stock options such that the number of options that would have vested through June 30, 2026, are vested and exercisable, with such acceleration deemed effective as of December 31, 2024, subject to service conditions described within the Transition Agreement; and (b) extension of the post-termination exercise period for outstanding options until the earlier of December 31, 2027 or the original expiration date of such options, subject to the Company’s ability to take any actions permitted under the Plans, as applicable. The incremental stock-based compensation expense resulting from these modifications recognized during the three and nine months ended September 30, 2024 was $ 8.7 million. Unvested Stock Liabilities A summary of the Company’s unvested shares and unvested stock liabilities is as follows (in thousands, except share data): Number of Unvested Shares Weighted-Average Grant Date Fair Value Unvested Stock Liabilities Balance at December 31, 2023 10,319 $ 1.57 $ 20 Vested shares ( 8,796 ) $ 1.23 ( 13 ) Balance at September 30, 2024 1,523 $ 3.53 $ 7 Common Stock Reserved for Future Issuance Common stock reserved for future issuance consists of the following: September 30, 2024 December 31, 2023 Common stock options outstanding 9,590,050 7,989,192 RSUs outstanding 80,562 — Shares available for issuance under the Plans 5,215,026 5,198,941 Shares available for issuance under the ESPP 1,542,307 1,142,750 Pre-funded common stock warrants outstanding 2,438,709 503,226 Total 18,866,654 14,834,109 5. Research Collaboration and Exclusive License Agreement In December 2020, the Company entered into a research collaboration and exclusive license agreement (the “Merck Agreement”), pursuant to which the Company granted Merck Sharp & Dohme Corp. (“Merck”) an exclusive, worldwide, royalty-bearing, sublicensable license to certain of its patent rights and know-how for up to two collaboration targets (“First Collaboration Target” and “Second Collaboration Target”, together the “Collaboration Targets”) related to next generation T cell engager immunotherapies for the treatment of cancer. In each case, once the Collaboration Targets are designated by Merck, they have the right to research, develop, make, have made, use, import, offer to sell, and sell compounds and any licensed products related thereto. Merck selected the First Collaboration Target upon execution of the Merck Agreement and selected the Second Collaboration Target in May 2022. Following the research term, Merck has the sole right to research, develop, manufacture, and commercialize the licensed compounds and products directed against the Collaboration Targets. Consideration in the Merck Agreement consists of (i) an $ 8.0 million non-refundable and non-creditable upfront fee, (ii) $ 8.0 million paid upon the selection of the Second Collaboration Target, (iii) research program funding (iv) development and regulatory milestones, (v) commercial milestones, and (vi) royalty payments. Under the Merck Agreement, the Company is eligible to receive up to an aggregate of $ 142.5 million per Collaboration Target in milestone payments ($ 285.0 million collectively for both Collaboration Targets), contingent on the achievement of certain regulatory and development milestones. Merck is also required to make milestone payments to the Company upon the successful completion of certain commercial milestones, in an aggregate amount not to exceed $ 350.0 million for each licensed product under either of the Collaboration Targets. The Merck Agreement provides that Merck is obligated to pay to the Company tiered royalty payments on a product-by-product and country-by-country basis, ranging from low single-digit to low teens percentage royalty rates on specified portions of annual net sales for licensed products under either of the Collaboration Targets that are commercialized. Such royalties are subject to reduction, on a product-by-product and country-by-country basis, for licensed products not covered by patent claims, or that require Merck to obtain a 19 Table of Contents Janux Therapeutics, Inc. Notes to Unaudited Condensed Financial Statements–(Continued) license to obtain a license to third-party intellectual property in order to commercialize the licensed products, or that are subject to compulsory licensing. The Merck Agreement will terminate at the end of the calendar year in which the expiration of all royalty obligations occurs for all licensed products under the agreement. Merck has the unilateral right to terminate the Merck Agreement in its entirety or on a Collaboration Target by Collaboration Target basis at any time and for any reason upon prior written notice to the Company. Both parties have the right to terminate the agreement for an uncured material breach, certain illegal or unethical activities, and insolvency of the other party. Upon expiration of the agreement but not early termination thereof, and provided all payments due under the agreement have been made, Merck’s exclusive licenses under the agreement will become fully paid-up and perpetual. In June 2024, a developmental milestone of $ 7.5 million related to the First Collaboration Target was achieved, at which time the Company recognized the associated revenue. All other future potential milestone payments are considered constrained as of September 30, 2024 as they are uncertain in nature and highly dependent on factors outside of the Company’s control until the underlying events occur or the associated approvals are received. The Company recognized $ 0.4 million, $ 2.5 million, $ 10.6 m illion, and $ 5.6 million of revenue under the Merck Agreement for the three months ended September 30, 2024 and 2023 and nine months ended September 30, 2024 and 2023, respectively. The Company's performance obligations related to the Collaboration Targets were completed as of September 30, 2024 . 20 Table of Contents