aTYR PHARMA INC 10-K

Item 9A. Controls and Procedures. Evaluation of Disclosure Controls and Procedures We maintain disclosure controls and procedures, as defined in Rules 13a-15(e) and 15d-15(e) under the Exchange Act that are designed to ensure that information required to be disclosed in our periodic and current reports that we file with the SEC is recorded, processed, summarized and reported within the time periods specified in the SEC’s rules and forms, and that such information is accumulated and communicated to our management, including our Principal Executive Officer and Principal Financial Officer, as appropriate, to allow timely decisions regarding required disclosure. In designing and evaluating the disclosure controls and procedures, management recognizes that any controls and procedures, no matter how well designed and operated, can provide only reasonable and not absolute assurance of achieving the desired control objectives. In reaching a reasonable level of assurance, management necessarily is required to apply its judgment in evaluating the cost-benefit relationship of possible controls and procedures. In addition, the design of any system of controls also is based in part upon certain assumptions about the likelihood of future events, and there can be no assurance that any design will succeed in achieving its stated goals under all potential future conditions; over time, control may become inadequate because of changes in conditions, or the degree of compliance with policies or procedures may deteriorate. Because of the inherent limitations in a cost-effective control system, misstatements due to error or fraud may occur and not be detected. We carried out an evaluation, under the supervision and with the participation of our management, including our Principal Executive Officer and Principal Financial Officer, of the effectiveness of the design and operation of our disclosure controls and procedures, as defined in Rules 13a-15(e) and 15d-15(e) under the Exchange Act. Based on this evaluation, our Principal Executive Officer and Principal Financial Officer concluded that our disclosure controls and procedures were effective at the reasonable assurance level as of December 31, 2020. Management’s Report on Internal Control Over Financial Reporting Our management is responsible for establishing and maintaining adequate internal control over financial reporting as such term is defined in Rules 13a-15(f) and 15-d-15(f) of the Exchange Act. Internal control over financial reporting is a process designed under the supervision and with the participation of our management, including our Principal Executive Officer and Principal Financial Officer, to provide reasonable assurance regarding the reliability of financial reporting and the preparation of financial statements for external purposes in accordance with accounting principles generally accepted in the United States of America. As of December 31, 2020, our management assessed the effectiveness of our internal control over financial reporting using the criteria set forth by the Committee of Sponsoring Organizations of the Treadway Commission in Internal Control – 2013 Integrated Framework (2013 Framework). Based on this assessment, our management concluded that our internal control over financial reporting was effective as of December 31, 2020. This Annual Report does not include an attestation report of our registered public accounting firm under Section 404(b) of the Sarbanes-Oxley Act (15 U.S.C. 7262(b)). Changes in Internal Control Over Financial Reporting During the quarter ended December 31, 2020, there have been no changes in our internal control over financial reporting, as such term is defined in Rules 13a-15(f) and 15d-15(f) promulgated under the Exchange Act, that have materially affected, or are reasonably likely to materially affect, our internal control over financial reporting. Item 9B. Other Information. On March 23, 2021, we entered into a Capital on Demand TM Sales Agreement (the Sales Agreement) with JonesTrading Institutional Services LLC (JonesTrading) pursuant to which we may sell from time to time, at our option, up to an aggregate of $25.0 million of shares of our common stock through JonesTrading, as sales agent or principal. Sales of our common stock made pursuant to the Sales Agreement, if any, will be made on the Nasdaq Capital Market under our Registration Statement on Form S-3 (File No. 333-250095), in sales deemed to be “at the market offerings” as defined in Rule 415 promulgated under the Securities Act of 1933, as amended. Under the terms of the Sales Agreement, JonesTrading may not engage in any proprietary trading for JonesTrading’s own 84 account. JonesTrading will use its commercially reasonable efforts to sell the shares of our common stock from time to time, based upon our instructions (including any price, time or size limits or other customary parameters or conditions we may impose). We are not obligated to make any sales of our common stock under the Sales Agreement, and we cannot provide any assurances that we will issue any shares pursuant to the Sales Agreement. The offering of our common stock pursuant to the Sales Agreement will terminate upon the earlier of (i) the sale of all of the shares of our common stock subject to the Sales Agreement or (ii) the termination of the Sales Agreement as permitted therein. The Sales Agreement may be terminated by us or JonesTrading at any time upon notice to the other party. We are obligated to pay JonesTrading an aggregate sales agent commission equal to up to 3% of the gross proceeds of the sale price for our common stock sold under the Sales Agreement. We have also provided JonesTrading with customary indemnification rights and expense reimbursements for up to $45,000 of expenses and quarterly disbursements of counsel to JonesTrading of up to $2,500 per calendar quarter. PART III Item 10. Directors, Executive Officers and Corporate Governance. Except as set forth below, the information required by this item will be contained in our Definitive Proxy Statement to be filed with the SEC in connection with our 2021 Annual Meeting of Stockholders within 120 days after the end of the fiscal year ended December 31, 2020, and is incorporated herein by reference. We have adopted a written code of ethics for directors, officers (including our principal executive officer, principal financial officer and principal accounting officer or persons performing similar functions) and employees, known as the Code of Business Conduct and Ethics. The Code of Business Conduct and Ethics is available on our website at http://www.atyrpharma.com under the Corporate Governance section of our Investors page. If we make any substantive amendments to, or grant any waivers from, the Code of Business Conduct and Ethics for any officer or director, we will disclose the nature of such amendment or waiver on our website or in a Current Report on Form 8-K. Item 11. Executive Compensation. The information required by this item will be contained in our Definitive Proxy Statement and is incorporated herein by reference. Item 12. Security Ownership of Certain Beneficial Owners and Management and Related Stockholder Matters. The information required by this item will be contained in our Definitive Proxy Statement and is incorporated herein by reference. Item 13. Certain Relationships and Related Transactions, and Director Independence. The information required by this item will be contained in our Definitive Proxy Statement and is incorporated herein by reference. Item 14. Principal Accountant Fees and Services. The information required by this item will be contained in our Definitive Proxy Statement and is incorporated herein by reference. 85 PART IV Item 15. Exhibits and Financial Statement Schedules. (a) The following documents are filed as part of this Annual Report. 1. Index list to Financial Statements : Page Report of Independent Registered Public Accounting Firm 64 Consolidated Balance Sheets 65 Consolidated Statements of Operations 66 Consolidated Statements of Comprehensive Loss 67 Consolidated Statements of Stockholders’ Equity 68 Consolidated Statements of Cash Flows 69 Notes to Consolidated Financial Statements 70 2. Financial Statement Schedules . Schedules have been omitted as all required information has been disclosed in the financial statements and related footnotes. 3. Exhibits . The Exhibits listed in the Exhibit Index are filed as a part of this Annual Report. 86 EXHIBIT INDEX Incorporated by Reference Exhibit Number Exhibit Title Form File No. Exhibit Filing Date 3.1 Restated Certificate of Incorporation of the Registrant S-1/A 333-203272 3.2 May 1, 2015 3.2 Certificate of Amendment to Restated Certificate of Incorporation of the Registrant 8-K 001-37378 3.1 June 28, 2019 3.3 Certificate of Amendment to Restated Certificate of Incorporation of the Registrant 10-Q 001-37378 3.3 May 12, 2020 3.4 Amended and Restated Bylaws of the Registrant S-1/A 333-203272 3.4 April 27, 2015 3.5 Certificate of Designation of Preferences, Rights and Limitations of Class X Convertible Preferred Stock 8-K 001-37378 3.1 August 31, 2017 4.1 Specimen Common Stock Certificate S-1/A 333-203272 4.1 April 27, 2015 4.2 Warrant to Purchase Stock issued to Comerica Bank on March 18, 2011 S-1 333-203272 4.3 April 6, 2015 4.3 Warrant to Purchase Stock issued to Silicon Valley Bank on July 24, 2013 S-1 333-203272 4.4 April 6, 2015 4.4 Warrant to Purchase Stock issued to Silicon Valley Bank on November 18, 2016 10-K 001-37378 4.5 March 16, 2017 4.5 Warrant to Purchase Stock issued to Solar Capital Ltd on November 18, 2016 10-K 001-37378 4.6 March 16, 2017 4.6 Warrant to Purchase Stock issued to Silicon Valley Bank on June 30, 2017 10-Q 001-37378 4.7 August 14, 2017 4.7 Warrant to Purchase Stock issued to Solar Capital Ltd on June 30, 2017 10-Q 001-37378 4.8 August 14, 2017 4.8 Warrant to Purchase Stock issued to Silicon Valley Bank on December 22, 2017 10-K 001-37378 4.8 March 20, 2018 4.9 Warrant to Purchase Stock issued to Solar Capital Ltd on December 22, 2017 10-K 001-37378 4.9 March 20, 2018 4.10 Registration Rights Agreement, by and between the Registrant and Aspire Capital Fund, LLC, dated September 11, 2020 8-K 001-37378 4.1 September 14, 2020 4.11 Description of Common Stock of the Registrant 10-K 001-37378 4.10 March 26, 2020 5.1 Opinion of Cooley LLP — — — Filed herewith 10.1* 2014 Stock Plan and forms of agreements thereunde r S-1/A 333-203272 10.1 April 27, 2015 10.2* 2015 Stock Option and Incentive Plan, as amended 8-K 001-37378 10.1 May 8, 2020 10.3* Forms of agreement under 2015 Stock Option and Incentive Plan S-1/A 333-203272 10.2 April 27, 2015 10.4 Lease by and between the Registrant and BMR-John Hopkins Court LLC, dated December 22, 2011 S-1 333-203272 10.9 April 6, 2015 10.5 First Amendment to Lease between the Registrant and BMR-3545-3575 JOHN HOPKINS LP (as successor-in-interest to BMR-John Hopkins Court LLC), dated January 4, 2017 10-K 001-37378 10.8 March 16, 2017 10.6 Form of Indemnification Agreement entered into between the Registrant and its directors S-1/A 333-203272 10.12 April 27, 2015 10.7 Form of Indemnification Agreement entered into between the Registrant and its officers S-1/A 333-203272 10.13 April 27, 2015 87 Incorporated by Reference Exhibit Number Exhibit Title Form File No. Exhibit Filing Date 10.8* 2015 Employee Stock Purchase Plan S-1/A 333-203272 10.14 April 27, 2015 10.9* Senior Executive Cash Incentive Bonus Plan 8-K 001-37378 10.1 January 29, 2016 10.10* Executive Severance and Change in Control Policy 10-K 001-37378 10.16 March 30, 2016 10.11* Registrant’s Non-Qualified Stock Option Agreement for Non-Plan Inducement Grant 10-Q 001-37378 10.1 November 14, 2016 10.12 Second Amendment to Lease between the Registrant and BMR-3545-3575 John Hopkins LP (as successor-in-interest to BMR-John Hopkins Court, LLC), dated April 27, 2017 10-Q 001-37378 10.1 May 11, 2017 10.13* Employment Agreement, dated November 1, 2017, by and between the Company and Sanjay S. Shukla, M.D., M.S. 10-Q 001-37378 10.4 November 14, 2017 10.14# Employment Offer Letter by and between the Registrant and Jill M. Broadfoot, dated July 16, 2018 8-K 001-37378 10.1 August 1, 2018 10.15 Third Amendment to Lease between Registrant and BMR-3545-3575 John Hopkins LP (as successor-in interest to BMR-John Hopkins Court, LLC), dated July 30, 2018 10-Q 001-37378 10.1 November 11, 2018 10.16* Employment Offer Letter by and between Registrant and Ms. Nancy Krueger, Esq., dated October 7, 2014 10-Q 001-37378 10.2 May 14, 2019 10.17 † Collaboration and License Agreement by and between Registrant and Kyorin Pharmaceutical Co., Ltd., dated January 6, 2020 S-1/A 333-235951 10.21 February 3, 2020 10.18 Common Stock Purchase Agreement, by and between the Registrant and Aspire Capital Fund, LLC, dated September 11, 2020 8-K 001-37378 99.1 September 14, 2020 10.19* First Amendment to Employment Agreement dated February 5, 2021, by and between the Company and Sanjay S. Shukla, M.D., M.S. — — — Filed herewith 10.20 Common Stock Capital on Demand TM Sales Agreement, between the Registrant and JonesTrading Institutional Services LLC — — — Filed herewith 14.1 Code of Business Conduct and Ethics, as amended — — — Filed herewith 21.1 Subsidiaries of the Registrant S-1 333-203272 21.1 April 6, 2015 23.1 Consent of Independent Registered Public Accounting Firm — — — Filed herewith 23.2 Opinion of Cooley LLP (included in Exhibit 5.1) — — — Filed herewith 24.1 Power of Attorney (included on signature page to this Annual Report) — — — Filed herewith 31.1# Certification of Principal Executive Officer required by Rule 13a-14(a) or Rule 15d-14(a) of the Securities Exchange Act of 1934, as adopted pursuant to Section 302 of the Sarbanes-Oxley Act of 2002 — — — Filed herewith 31.2# Certification of Principal Financial Officer required by Rule 13a-14(a) or Rule 15d-14(a) of the Securities Exchange Act of 1934, as adopted pursuant to Section 302 of the Sarbanes-Oxley Act of 2002 — — — Filed herewith 32.1# Certification of Principal Executive Officer pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002 — — — Filed herewith 32.2# Certification of Principal Financial Officer pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002 — — — Filed herewith 88 Incorporated by Reference Exhibit Number Exhibit Title Form File No. Exhibit Filing Date 101.INS XBRL Instance Document — — — Filed herewith 101.SCH XBRL Taxonomy Extension Schema Document — — — Filed herewith 101.CAL XBRL Taxonomy Extension Calculation Linkbase Document — — — Filed herewith 101.DEF XBRL Taxonomy Extension Definition Linkbase Document — — — Filed herewith 101.LAB XBRL Taxonomy Extension Label Linkbase Document — — — Filed herewith 101.PRE XBRL Taxonomy Extension Presentation Linkbase Document — — — Filed herewith * Indicates a management contract or compensatory plan, contract or arrangement. † Certain portions have been omitted because the Registrant has determined that the information is not material and would likely cause competitive harm to the Registrant if publicly disclosed. # The information in Exhibits 32.1 and 32.2 shall not be deemed “filed” for purposes of Section 18 of the Exchange Act, or otherwise subject to the liabilities of that section, nor shall it be deemed incorporated by reference in any filing under the Securities Act or the Exchange Act (including this Quarterly Report on Form 10-Q), unless the Registrant specifically incorporates the foregoing information into those documents by reference. Item 16. Form 10-K Summary. None. 89 SIGNATURES Pursuant to the requirements of Section 13 or 15(d) of the Securities Exchange Act of 1934, the registrant has duly caused this report to be signed on its behalf by the undersigned, thereunto duly authorized. aTyr Pharma, Inc. Date: March 23, 2021 By /s/ Sanjay S. Shukla Sanjay S. Shukla, M.D., M.S. President, Chief Executive Officer and Director (Principal Executive Officer) POWER OF ATTORNEY KNOW ALL PERSONS BY THESE PRESENTS, that each person whose signature appears below constitutes and appoints Sanjay S. Shukla, M.D., M.S. and Jill M. Broadfoot, jointly and severally, and each of them, his or her true and lawful attorneys-in-fact, each with full power of substitution, for him or her in any and all capacities, to sign any amendments to this Annual Report on Form 10-K and to file the same, with exhibits thereto and other documents in connection therewith, with the Securities and Exchange Commission, hereby ratifying and confirming all that each of said attorneys-in-fact or their substitute or substitutes may do or cause to be done by virtue hereof. Pursuant to the requirements of the Securities Exchange Act of 1934, this report has been signed below by the following persons on behalf of the registrant and in the capacities and on the dates indicated. Signature Title Date /s/ Sanjay S. Shukla President, Chief Executive Officer and Director March 23, 2021 Sanjay S. Shukla, M.D., M.S. (Principal Executive Officer) /s/ Jill M. Broadfoot Chief Financial Officer March 23, 2021 Jill M. Broadfoot (Principal Financial and Accounting Officer) /s/ John K. Clarke Chairman of the Board March 23, 2021 John K. Clarke /s/ Timothy P. Coughlin Director March 23, 2021 Timothy P. Coughlin /s/ Jane A. Gross Director March 23, 2021 Jane A. Gross, Ph.D. /s/ Jeffrey S. Hatfield Director March 23, 2021 Jeffrey S. Hatfield /s/ Svetlana Lucas Director March 23, 2021 Svetlana Lucas, Ph.D. /s/ Paul Schimmel Director March 23, 2021 Paul Schimmel, Ph.D. 90