CODEXIS, INC. 10-Q

ITEM 5. OTHER INFORMATION Rule 10b5-1 Trading Arrangements During the three months ended September 30, 2024, none of the directors or executive officers of the Company adopted or terminated a Rule 10b5-1 trading arrangement or a “non-Rule 10b5-1 trading arrangement” (each as defined in Item 408 of Regulation S-K). 62 ITEM 6. EXHIBITS 3.1 Amended and Restated Certificate of Incorporation of Codexis, Inc. filed with the Secretary of the State of the State of Delaware on April 27, 2010 and effective as of April 27, 2010 (incorporated by reference to Exhibit 3.1 to the Company's Quarterly Report on Form 10-Q for the quarter ended March 31, 2010, filed on May 28, 2010). 3.2 Certificate of Designations of Series A Junior Participating Preferred Stock of Codexis, Inc., filed with the Secretary of State of the State of Delaware on September 4, 2012 (incorporated by reference to Exhibit 3.1 to the Company's Current Report on Form 8-K, filed on September 4, 2012). 3.3 Certificate of Amendment to the Amended and Restated Certificate of Incorporation of Codexis, Inc., filed with the Secretary of the State of the State of Delaware on June 14, 2023 (incorporated by reference to Exhibit 3.1 to the Company’s Current Report on Form 8-K, filed on June 16, 2023). 3.4 Amended and Restated Bylaws of Codexis, Inc. effective as of February 8, 2024 (incorporated by reference to Exhibit 3.1 to the Company’s Current Report on Form 8-K filed on February 9, 2024). 4.1 Reference is made to Exhibits 3.1 through 3.4. 4.2 Form of the Company’s Common Stock Certificate (incorporated by reference to Exhibit 4.1 to the Company’s Quarterly Report on Form 10-Q for the quarter ended June 30, 2012, filed on August 9, 2012). 4.3 Description of Codexis' Securities Registered Pursuant to Section 12 of the Securities Exchange Act of 1934. ( incorporated by reference to Exhibit 4.4 to the Company’s Annual Report on Form 10-K, filed on February 28, 2024). 10.1 + Codexis, Inc. 20 24 Inducement Plan (incorporated by reference to Exhibit 4.1 to the Company's Registration Statement on Form S-8 (File No. 333- 281429 ) filed with the SEC on August 9 , 20 24 ). 10.2 + A mendment to the Codexis, Inc. 2023 Employee Stock Purchase Plan . 10.3 + Offer Letter by and between the Company and Georgia Erb ez , dated as of September 30 , 202 4 . 10.4 + Change in Control Severance Agreement by and between the Company and Georgia Erbez, dated as of September 30 , 202 4 . 10.5 + Offer Letter by and between the Company and Alison Moore , dated as of September 30 , 202 4 . 10.6 + Change in Control Severance Agreement by and between the Company and Alison Moore , dated as of September 30 , 202 4 . 31.1 Certification of Principal Executive Officer Required Under Rule 13a-14(a) and 15d-14(a) of the Securities Exchange Act of 1934, as amended. 31.2 Certification of Principal Financial Officer Required Under Rule 13a-14(a) and 15d-14(a) of the Securities Exchange Act of 1934, as amended. 32.1 Certification of Principal Executive Officer and Principal Financial Officer Required Under Rule 13a-14(b) of the Securities Exchange Act of 1934, as amended, and 18 U.S.C. §1350. 101 The following materials from the Company's Quarterly Report on Form 10-Q for the quarter ended September 30, 2024, formatted in Inline Extensible Business Reporting Language (“iXBRL”) includes: (i) Unaudited Condensed Consolidated Balance Sheets at September 30, 2024 and December 31, 2023 (ii) Unaudited Condensed Consolidated Statements of Operations for the Three and Nine Months Ended September 30, 2024 and 2023, (iii) Unaudited Condensed Consolidated Statements of Comprehensive Loss for the Three and Nine Months Ended September 30, 2024 and 2023, (iv) Unaudited Condensed Consolidated Statements of Stockholders' Equity for the Three and Nine Months Ended September 30, 2024 and 2023, (v) Unaudited Condensed Consolidated Statements of Cash Flows for the Nine Months Ended September 30, 2024 and 2023 and (v) Notes to Unaudited Condensed Consolidated Financial Statements. 101.SCH Inline XBRL Taxonomy Extension Schema Document 101.CAL Inline XBRL Taxonomy Extension Calculation Linkbase Document 101.DEF Inline XBRL Taxonomy Extension Definition Linkbase Document 101.LAB Inline XBRL Taxonomy Extension Label Linkbase Document 101.PRE Inline XBRL Taxonomy Extension Presentation Linkbase Document 63 104 The cover page from the Company’s Quarterly Report on Form 10-Q for the quarter ended September 30, 2024, formatted in Inline XBRL and contained in Exhibit 101. + Indicates a management contract or compensatory plan or arrangement. 64 SIGNATURES Pursuant to the requirements 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. Codexis, Inc. Date: October 31, 2024 By: /s/ Stephen Dilly Stephen Dilly Chairman, President and Chief Executive Officer (principal executive officer) Date: October 31, 2024 By: /s/ Georgia Erbez Georgia Erbez Chief Financial Officer (principal financial and accounting officer) 65