Document:

EX-10.1

 Exhibit 10.1 

EXECUTION VERSION 

CODEXIS, INC. 

SECURITIES PURCHASE AGREEMENT 

This Securities Purchase Agreement (“Agreement”) is made as of June 20, 2019 (the “Effective Date”), by
and among Codexis, Inc., a Delaware corporation (the “Company”), and each entity, severally and not jointly, listed as a Purchaser on the Schedule of Purchasers attached as Exhibit A hereto (the “Schedule of
Purchasers”). Such entities are hereinafter collectively referred to herein as “Purchasers” and each individually as a “Purchaser.” 

AGREEMENT 
 In
consideration of the mutual covenants contained in this Agreement, and for other good and valuable consideration, the receipt of which is hereby acknowledged, the Company and each Purchaser (severally and not jointly) hereby agree as follows: 

SECTION 1.    AUTHORIZATION OF SALE OF THE SHARES. 

The Company has authorized the sale and issuance of 3,048,780 shares of its Common Stock, par value $0.0001 per share (the “Common
Stock”), on the terms and subject to the conditions set forth in this Agreement. The shares of Common Stock sold hereunder at the Closing (as defined below) shall be referred to as the “Shares.” 

SECTION 2.    AGREEMENT TO SELL AND PURCHASE THE SHARES. 

2.1    Sale of Shares. At the Closing (as defined in Section 3), the Company will sell to each
Purchaser, and each Purchaser will purchase from the Company, the number of Shares set forth opposite such Purchaser’s name on the Schedule of Purchasers at a purchase price of $16.40 per Share. The aggregate purchase price for the Shares
purchased by each Purchaser is set forth opposite such Purchaser’s name on the Schedule of Purchasers. 

2.2    Separate Agreement. Each Purchaser shall severally, and not jointly, be liable for only the purchase
of the Shares that appear on the Schedule of Purchasers that relate to such Purchaser. The Company’s agreement with each of the Purchasers is a separate agreement, and the sale of Shares to each of the Purchasers is a separate sale. The
obligations of each Purchaser hereunder are expressly not conditioned on the purchase by any or all of the other Purchasers of the Shares such other Purchasers have agreed to purchase. 

SECTION 3.    CLOSING AND DELIVERY. 

3.1    Closing. The closing of the purchase and sale of the Shares (which Shares are set forth in the
Schedule of Purchasers) pursuant to this Agreement (the “Closing”) shall be held on June 20, 2019 at the offices of Latham & Watkins LLP, 140 Scott Drive, Menlo Park, California 94025, or on such other date and place
as may be agreed to by the Company and the Purchasers (the “Closing Date”). At or prior to the Closing, each Purchaser shall execute any related agreements or other documents required to be executed hereunder, dated on or before the
Closing Date. 

 3.2    Issuance of the Shares at the Closing. At the
Closing, the Company shall issue or deliver to each Purchaser evidence of a book entry position evidencing the Shares purchased by such Purchaser hereunder, registered in the name of such Purchaser, or in such nominee name(s) as designated by such
Purchaser, representing the number of Shares to be purchased by such Purchaser at such Closing as set forth in the Schedule of Purchasers against payment of the purchase price for such Shares. The name(s) in which the Shares are to be issued to each
Purchaser are set forth in the Purchaser Questionnaire and the Selling Stockholder Notice and Questionnaire in the form attached hereto as Appendices I and II (the “Purchaser Questionnaire” and the “Selling Stockholder
Questionnaire,” respectively), as completed by each Purchaser, which shall be provided to the Company no later than the Closing Date. 

3.3    Delivery of the Registration Rights Agreement. At or before the Closing, the Company and each
Purchaser shall execute and deliver the Registration Rights Agreement in the form attached hereto as Appendix III (the “Registration Rights Agreement”), with respect to the registration of the Shares under the Securities Act of
1933, as amended (the “Securities Act”). 
 SECTION 4.    REPRESENTATIONS, WARRANTIES AND COVENANTS OF THE COMPANY.

 The Company hereby represents and warrants as of the date hereof to, and covenants with, the Purchasers as follows: 

4.1    Incorporation and Good Standing of the Company. The Company has been duly incorporated and is existing
and in good standing under the laws of the State of Delaware, with full corporate power and authority to own or lease, as the case may be, and to operate its properties and conduct its business as described in the SEC Documents; and the Company is
duly qualified to do business as a foreign corporation in good standing in all other jurisdictions in which its ownership or lease of property or the conduct of its business requires such qualification, except where the failure to be so qualified or
in good standing in such other jurisdictions would not, individually or in the aggregate, reasonably be expected to result in a material adverse effect on the condition (financial or otherwise), results of operations, business or properties of the
Company and its Subsidiaries (as defined below) taken as a whole (“Material Adverse Effect”). 

4.2    Subsidiaries. Other than the subsidiaries set forth on Exhibit B attached hereto
(collectively, the “Active Subsidiaries”) and Codexis Laboratories India Pty. Ltd. (the “Indian Subsidiary” and together with the Active Subsidiaries, the “Subsidiaries”), the Company does not own
or control, directly or indirectly, any interest in any other corporation, partnership, trust, joint venture, limited liability company, association or other business entity. Each Active Subsidiary of the Company (i) has been duly organized and
is validly existing in good standing under the laws of the jurisdiction of its incorporation or organization, has corporate or similar power and authority to own, lease and operate its properties and to conduct its business as presently conducted,
and (ii) is duly qualified to transact business and is in good standing in each jurisdiction in which such qualification is required, whether by reason of the ownership or leasing of property or the conduct of business, except in the case of
clause (ii) above, to the extent that the failure to be so qualified or be in good standing would not reasonably be expected to result in a Material Adverse Effect. All of the issued and outstanding capital stock of each Active Subsidiary of
the Company has been duly authorized and validly issued, is fully paid and nonassessable and is owned by the Company, 

  
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directly or through Subsidiaries, free and clear of any security interest, mortgage, pledge, lien, encumbrance, claim or equity. The Indian Subsidiary is in the process of being liquidated, which
liquidation is not reasonably expected to have a Material Adverse Effect. 
 4.3    Corporate Power;
Authorization. The Company has all requisite corporate power, and has taken all requisite corporate action, to execute and deliver this Agreement, and the Registration Rights Agreement (as defined below and collectively, the
“Transaction Documents”), sell and issue the Shares and carry out and perform all of its obligations under the Transaction Documents. Each Transaction Document constitutes the legal, valid and binding obligation of the Company,
enforceable in accordance with its terms, except (i) as limited by applicable bankruptcy, insolvency, reorganization, moratorium or similar laws relating to or affecting the enforcement of creditors’ rights generally, (ii) as limited
by equitable principles generally, including any specific performance and (iii) with respect to the Registration Rights Agreement, as rights to indemnity or contribution may be limited by state or federal laws or public policy underlying such
laws. 
 4.4    Issuance and Delivery of the Shares. The Shares have been duly authorized and, when issued
and paid for in compliance with the provisions of this Agreement, will be validly issued, fully paid and nonassessable, and will be free and clear of any security interests, liens or other encumbrances created by or on behalf of the Company (other
than restrictions on transfer under applicable securities laws). Assuming the accuracy of the representations made by each Purchaser in Section 5, the offer and issuance by the Company of the Shares is exempt from registration under the
Securities Act. 
 4.5    SEC Documents; Financial Statements. The Company has filed all reports,
schedules, forms, statements and other documents required to be filed by it with the Securities and Exchange Commission (the “Commission”) under Sections 13, 14(a) and 15(d) of the Securities Exchange Act of 1934, as amended (the
“Exchange Act”), in the three years preceding the Effective Time on a timely basis, except for such reports of which the failure to file (or timely file) has not adversely affected the Company’s eligibility to use Form S-3 for registration under the Securities Act. As of their respective filing dates (or, if amended prior to the date of this Agreement, when amended), all documents filed by the Company with the Commission (the
“SEC Documents”) in the three years preceding the date hereof complied in all material respects with the requirements of the Exchange Act and the rules and regulations of the Commission promulgated thereunder. None of the SEC
Documents as of their respective dates contained any untrue statement of material fact or omitted to state a material fact required to be stated therein or necessary to make the statements made therein, in light of the circumstances under which they
were made, not misleading. The financial statements of the Company, together with the related notes and any supporting schedules thereto, included in the SEC Documents (the “Financial Statements”) present fairly, in all material
respects, the consolidated financial condition, results of operations and cash flows of the Company and each of its Subsidiaries as of and at the dates indicated and the results of their operations and cash flows for the periods specified as of the
dates and for the periods indicated. The Financial Statements and any supporting schedules have been prepared in conformity with generally accepted accounting principles as applied in the United States (“GAAP”) applied on a
consistent basis throughout the periods involved, except as may be expressly stated in the related notes thereto. BDO USA, LLP, who have expressed their opinion with respect to the audited financial statements and schedules included in the SEC
Documents, is an independent registered public accounting firm as required by the Securities Act and the Exchange Act. 

  
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 4.6    Capitalization. The authorized capital stock of the
Company consists of 100,000,000 shares of Common Stock and 5,000,000 shares of preferred stock, par value $0.0001 per share (the “Preferred Stock”), of which 100,000 shares have been designated Series A Junior Participating
Preferred Stock. There are no other shares of any other class or series of capital stock of the Company issued or outstanding. The Company has not issued any capital stock since the date of its most recently filed SEC Document other than to reflect
stock option and warrant exercises and vesting of restricted stock units and performance stock units. As of March 31, 2019, there were (i) 54,540,929 shares of Common Stock issued and outstanding and no shares of the Preferred Stock issued and
outstanding; (ii) options to purchase up to 6,533,771 shares of Common Stock outstanding; and (iii) up to 299,547 shares of Common Stock issuable upon vesting of outstanding unvested restricted stock units and performance stock units.
There are no bonds, debentures, notes or other indebtedness having general voting rights (or convertible into securities having such rights) (“Voting Debt”) of the Company issued and outstanding and no shares of Common Stock or
Preferred Stock, or any Voting Debt, have been issued since March 31, 2019 (other than shares of Common Stock issued pursuant to awards granted pursuant to the Company’s stock option, incentive award or stock purchase plans, including
without limitation the Company’s 2002 Stock Plan, as amended, 2010 Equity Incentive Award Plan and 2019 Incentive Award Plan (collectively, the “Equity Plans”)). Except as stated above, there are no existing options, warrants,
calls, subscriptions or other rights, agreements, arrangements or commitments relating to the issued or unissued capital stock of the Company, obligating the Company to issue, transfer, sell, redeem, purchase, repurchase or otherwise acquire or
cause to be issued, transferred, sold, redeemed, purchased, repurchased or otherwise acquired any capital stock or Voting Debt of, or other equity interest in, the Company or securities or rights convertible into or exchangeable for such shares or
equity interests or obligations of the Company to grant, extend or enter into any such option, warrant, call, subscription or other right, agreement, arrangement or commitment. The issuance of Common Stock or other securities pursuant to any
provision of this Agreement will not give rise to any preemptive rights or rights of first refusal on behalf of any individual or corporation, partnership, trust, incorporated or unincorporated association, joint venture, limited liability company,
joint stock company, government (or an agency or subdivision thereof) or other entity of any kind (each, a “Person”) or result in the triggering of any anti-dilution rights. There are no agreements or arrangements under which the
Company or any of its Subsidiaries is obligated to register the sale of any of their securities under the Securities Act. 

4.7    Litigation. Except as described in the SEC Documents, there are no pending actions, suits or
proceedings (including, to the Company’s knowledge, any inquiries or investigations by any court or governmental agency or body, domestic or foreign) against or affecting the Company, any of its Subsidiaries or any of their respective
properties that, (i) if determined adversely to the Company or any of its Subsidiaries, would individually or in the aggregate have a Material Adverse Effect, or (ii) would materially and adversely affect the ability of the Company to
perform its obligations under the Transaction Documents and no such actions, suits or proceedings (including, to the Company’s knowledge, any inquiries or investigations by any court or governmental agency or body, domestic or foreign) are, to
the Company’s knowledge, threatened. 
 4.8    Governmental Consents. No consent, approval, order or
authorization of, or registration, qualification, designation, declaration or filing with, any federal, state, or local governmental authority on the part of the Company is required in connection with the

  
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consummation of the transactions contemplated by the Transaction Documents except for (a) the filing of a Form D with the Commission under the Securities Act and compliance with the
securities and blue sky laws in the states and other jurisdictions in which shares of Common Stock are offered and/or sold, which compliance will be effected in accordance with such laws, and (b) the filing of one or more registration
statements and all amendments thereto with the Commission as contemplated by the Registration Rights Agreement. 

4.9    No Default or Consents. Neither the execution, delivery or performance of the Transaction Documents
by the Company nor the consummation of any of the transactions contemplated thereby (including, without limitation, the issuance and sale by the Company of the Shares) conflict with, result in a breach or violation of, or imposition of any lien,
charge or encumbrance upon any property or assets of the Company or each of its Subsidiaries pursuant to, (i) the certificate of incorporation, charter, articles of association or bylaws (or similar organizational document) of the Company or
each of its Subsidiaries, (ii) to the knowledge of the Company and its Subsidiaries, any statute, rule, regulation or order of any governmental agency or body or any court, domestic or foreign, having jurisdiction over the Company or any of its
Subsidiaries or any of their properties, or (iii) any agreement or instrument to which the Company or any of its Subsidiaries is a party or by which the Company or any of its Subsidiaries is bound or to which any of the properties of the
Company or any of its Subsidiaries is subject, except in the case of clause (iii), where such breaches, violations, defaults, liens, charges or encumbrances would not, individually or in the aggregate, reasonably be expected to have a Material
Adverse Effect or result in a material adverse effect on the consummation of the transactions contemplated by this Agreement. 

4.10    No Material Adverse Change. Since March 31, 2019, (i) there have been no events, occurrences or
developments that have had or would reasonably be expected to have, either individually or in the aggregate, a Material Adverse Effect, (ii) the Company has not incurred any material liabilities (contingent or otherwise) other than
(A) trade payables and accrued expenses incurred in the ordinary course of business consistent with past practice and (B) liabilities not required to be reflected in the Company’s financial statements pursuant to GAAP or disclosed in
filings made with the Commission, (iii) the Company has not altered materially its method of accounting or the manner in which it keeps its accounting books and records, (iv) the Company has not declared or made any dividend or
distribution of cash or other property to its stockholders or purchased, redeemed or made any agreements to purchase or redeem any shares of its capital stock (other than in connection with repurchases of unvested stock issued to employees of the
Company), and (v) the Company has not issued any equity securities to any officer, director or affiliate, except Common Stock issued pursuant to existing Equity Plans or executive and director compensation arrangements disclosed in the SEC
Documents. 
 4.11    No General Solicitation. Neither the Company nor any Person acting on its behalf has
engaged in any form of general solicitation or general advertising (within the meaning of Regulation D promulgated under the Securities Act) in connection with the offer or sale of the Shares. 

4.12    No Integrated Offering. Neither of the Company or any Person acting on its behalf has, directly or
indirectly, made any offers or sales of any security or solicited any offers to buy any security of the Company or any of its Subsidiaries, under circumstances that would adversely 

  
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affect reliance by the Company on Section 4(a)(2) of the Securities Act or require registration of any of the Shares under the Securities Act or cause this offering of the Shares to be
integrated with prior offerings by the Company or any Person acting on its behalf for purposes of the Securities Act. 

4.13    Intellectual Property. The Company owns, possesses, licenses or has other rights to use, on
reasonable terms, all patents, patent applications, trade and service marks, trade and service mark registrations, trade names, copyrights, licenses, inventions, trade secrets, technology, know-how and other
intellectual property (collectively, the “Intellectual Property”) necessary for the conduct of the Company’s business as now conducted or as proposed in the SEC Documents to be conducted (the “Company Intellectual
Property”). To the knowledge of the Company, there are no rights of third parties to any Company Intellectual Property, other than as licensed by the Company. To the knowledge of the Company, there is no infringement by third parties of any
Company Intellectual Property. There is no pending or, to the Company’s knowledge, threatened action, suit, proceeding or claim by others challenging the Company’s rights in or to any Company Intellectual Property. There is no pending or,
to the Company’s knowledge, threatened action, suit, proceeding or claim by others challenging the validity or scope of any Company Intellectual Property. There is no pending or, to the Company’s knowledge, threatened action, suit,
proceeding or claim by others that the Company infringes or otherwise violates any patent, trademark, copyright, trade secret or other proprietary rights of others. The Company is not aware of any facts required to be disclosed to the U.S. Patent
and Trademark Office (“USPTO”) which have not been disclosed to the USPTO and which would preclude the grant of a patent in connection with any patent application of the Company Intellectual Property or could form the basis of a
finding of invalidity with respect to any issued patents of the Company Intellectual Property. 

4.14    Disclosure. The Company understands and confirms that the Purchasers will rely on the
Representations in this Section 4 in effecting transactions in securities of the Company. To the knowledge of the executive officers of the Company, all due diligence materials regarding the Company, its business and the transactions
contemplated hereby, furnished by or on behalf of the Company to the Purchasers upon their request are, when taken together with the SEC Documents, true and correct in all material respects and do not contain any untrue statement of a material fact
or omit to state any material fact necessary in order to make the statements made therein, in light of the circumstances under which they were made, not misleading. 

4.15    Contracts. Each franchise, contract or other document of a character required as of the date hereof
to be described in the SEC Documents or to be filed as an exhibit to the SEC Documents under the Securities Act and the rules and regulations promulgated thereunder is so described or filed. No Purchaser is receiving rights or benefits in connection
with the issuance contemplated hereby which are more favorable than those received by any other Purchaser hereunder. 

4.16    Properties and Assets. The Company and its Subsidiaries own or lease all such properties as are
necessary to the conduct of their respective operations as presently conducted. 
 4.17    Possession of Licenses and
Permits; Compliance with Law. The Company and its Subsidiaries (i) possess, and are in material compliance with the terms of, all adequate certificates, authorizations, franchises, licenses and permits (“Licenses”)
from, and have made all 

  
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declarations, filings, listings, registrations, reports and submissions with, the appropriate federal, state, local or foreign governmental or regulatory authorities, in each case that are
necessary or material to the conduct of the business now conducted or proposed in the SEC Documents to be conducted by them, (ii) during the three years prior to the Effective Date, have not received any notice of proceedings relating to the
revocation or modification of any Licenses, and (iii) are not in violation of, or in default under, any such License. To the Company’s knowledge, neither the Company nor any of its Subsidiaries is, nor has been in the three years prior to
the Effective Date, in violation of any laws, ordinances, governmental rules or regulations to which it is subject, except for such violations as would not reasonably be expected to have, individually or in the aggregate, a Material Adverse Effect.

 4.18    Taxes. The Company and each of its Subsidiaries have filed all federal, state, local and
foreign tax returns required to be filed through the date of this Agreement or have requested extensions thereof (except where the failure to file would not, individually or in the aggregate, have a Material Adverse Effect) and have paid all taxes
required to be paid thereon (except for cases in which the failure to file or pay would not have a Material Adverse Effect, or, except as currently being contested in good faith and for which reserves required by GAAP have been created in the
financial statements of the Company), and no tax deficiency has been determined adversely to the Company or any of its Subsidiaries which has had (nor does the Company nor any of its Subsidiaries have any notice or knowledge of any tax deficiency
which could reasonably be expected to be determined adversely to the Company or its Subsidiaries and which could reasonably be expected to) have a Material Adverse Effect. 

4.19    Investment Company. The Company is not and, after giving effect to the offering and sale of the
Shares, will not be an “investment company” as defined in the Investment Company Act of 1940, as amended. 

4.20    Insurance. The Company and its Subsidiaries are insured by insurers with appropriately rated claims
paying abilities against such losses and risks and in such amounts as are prudent and customary for similarly sized companies in the businesses in which they are engaged; all policies of insurance and fidelity or surety bonds insuring the Company or
any of its Subsidiaries or their respective businesses, assets, employees, officers and directors are in full force and effect, except as would not, individually or in the aggregate, have a Material Adverse Effect; the Company and its Subsidiaries
are in compliance with the terms of such policies and instruments in all material respects; and there are no claims by the Company or any of its Subsidiaries under any such policy or instrument as to which any insurance company is denying liability
or defending under a reservation of rights clause; neither the Company nor any such Subsidiary has been refused any insurance coverage sought or applied for; neither the Company nor any such Subsidiary has any reason to believe that it will not be
able to renew its existing insurance coverage as and when such coverage expires or to obtain similar coverage from similar insurers as may be necessary to continue its business at a cost that would not have a Material Adverse Effect; and the Company
has obtained directors’ and officers’ insurance in such amounts as is customary for issuers of similar size and development stage. 

  
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 4.21    Price of Common Stock. Neither the Company nor its
Subsidiaries has taken, directly or indirectly, any action designed to cause or result in, or that has constituted or that might reasonably be expected to constitute, the stabilization or manipulation of the price of any securities of the Company to
facilitate the sale or resale of the Shares. 
 4.22    Internal Control over Financial Reporting; Sarbanes-Oxley
Matters. The Company, its Subsidiaries and the Company’s Board of Directors (the “Board”) are in compliance with Sarbanes-Oxley and all applicable rules thereof and all applicable rules of the Nasdaq Stock Market
Exchange (the “Exchange Rules”). The Company maintains a system of “internal controls over financial reporting” (as defined in Rule 13a-15(f) of the Exchange Act), including, but not
limited to, disclosure controls and procedures and internal controls over accounting matters (collectively, “Internal Controls”) sufficient to provide reasonable assurances that (i) transactions are executed in accordance with
management’s general or specific authorizations, (ii) transactions are recorded as necessary to permit preparation of financial statements in conformity with GAAP and to maintain accountability for assets, (iii) access to assets is
permitted only in accordance with management’s general or specific authorization and (iv) the recorded accountability for assets is compared with the existing assets at reasonable intervals and appropriate action is taken with respect to
any differences. The Internal Controls are overseen by the Audit Committee (the “Audit Committee”) of the Board in accordance with Exchange Rules. The Company has not publicly disclosed or reported to the Audit Committee or the
Board, and within the next 135 days the Company does not reasonably expect to publicly disclose or report to the Audit Committee or the Board, material weakness, adverse change in Internal
Controls or fraud involving management or other employees who have a significant role in Internal Controls (each, an “Internal Control Event”), or any violation of, or failure to comply with, the Sarbanes-Oxley Act of 2002, the
Securities Act, the Exchange Act, the rules and regulations of the Commission, the auditing principles, rules, standards and practices applicable to auditors of “issuers” (as defined in Sarbanes-Oxley) promulgated or approved by the Public
Company Accounting Oversight Board and the Exchange Rules, which, if determined adversely, would have a Material Adverse Effect. 

4.23    Foreign Corrupt Practices. The Company is not nor, to the knowledge of the Company, is any director,
officer, agent, or employee of the Company aware of or has taken any action, directly or indirectly, that would result in a violation by such persons of the Foreign Corrupt Practices Act of 1977, as amended, and the rules and regulations thereunder
(the “FCPA”), including, without limitation, making use of the mails or any means or instrumentality of interstate commerce corruptly in furtherance of an offer, payment, promise to pay or authorization of the payment of any money,
or other property, gift, promise to give, or authorization of the giving of anything of value to any “foreign official” (as such term is defined in the FCPA) or any foreign political party or official thereof or any candidate for foreign
political office, in contravention of the FCPA. 
 4.24    Labor. No labor dispute with the employees of
the Company or any of its Subsidiaries exists or, to the knowledge of the Company, is imminent that could reasonably be expected to have a Material Adverse Effect. 

4.25    Money Laundering Laws. The operations of the Company and its Subsidiaries are and have been
conducted at all times in compliance with all applicable financial recordkeeping and reporting requirements, including those of the Bank Secrecy Act, as amended by Title III of the Uniting and Strengthening America by Providing Appropriate Tools
Required to Intercept and Obstruct Terrorism Act of 2001 (USA PATRIOT Act), and the applicable anti-money laundering 

  
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statutes of jurisdictions where the Company and its Subsidiaries conduct business, the rules and regulations thereunder and any related or similar rules, regulations or guidelines, issued,
administered or enforced by any governmental agency (collectively, the “Anti-Money Laundering Laws”), and no action, suit or proceeding by or before any court or governmental agency, authority or body or any arbitrator involving the
Company or any of its Subsidiaries with respect to the Anti-Money Laundering Laws is pending or, to the best knowledge of the Company, threatened. 

4.26    OFAC. (a) Neither the Company nor any of its Subsidiaries, nor any director or officer thereof,
nor, to the Company’s knowledge, any employee, agent, affiliate or representative of the Company or any of its Subsidiaries, is a Person that is, or is owned or controlled by a Person that is: 

(i) the subject of any sanctions administered or enforced by the U.S. Department of Treasury’s Office of Foreign Assets Control, the
United Nations Security Council, the European Union, Her Majesty’s Treasury, or other relevant sanctions authority (collectively, “Sanctions”), nor 

(ii) located, organized or resident in a country or territory that is the subject of Sanctions (including, without limitation, Burma/Myanmar,
Cuba, Iran, Libya, North Korea, Sudan and Syria). 
 (b)    The Company will not, directly or indirectly, use the
proceeds of the offering, or lend, contribute or otherwise make available such proceeds to any Subsidiary, joint venture partner or other Person: 

(i) to fund or facilitate any activities or business of or with any Person or in any country or territory that, at the time of such funding
or facilitation, is the subject of Sanctions; or 
 (ii) in any other manner that will result in a violation of Sanctions by any Person
(including any Person participating in the offering, whether as underwriter, advisor, investor or otherwise). 
 (c)
    For the past five years, the Company and its Subsidiaries have not knowingly engaged in, are not now knowingly engaged in, and will not engage in, any dealings or transactions with any Person, or in any country or territory,
that at the time of the dealing or transaction is or was the subject of Sanctions. 
 4.26.     Shell
Company. The Company is not now and has not been, at any time during the past three (3) years, a shell company as defined by Rule 405 of the Securities Act and has never been an issuer subject to Rule 144(i) under the Securities Act.

  
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 SECTION 5.    REPRESENTATIONS, WARRANTIES AND COVENANTS OF THE PURCHASERS. 

5.1    Each Purchaser, severally and not jointly, represents and warrants to and covenants with the Company that: 

(a)    Such Purchaser (if an entity) is a validly existing corporation, limited partnership or limited liability company
and has all requisite corporate, partnership or limited liability company power and authority to enter into and consummate the transactions contemplated by the Transaction Documents and to carry out its obligations hereunder and thereunder, and to
invest in the Shares pursuant to this Agreement. 
 (b)    Such Purchaser acknowledges that it can bear the economic
risk and complete loss of its investment in the Shares and has such knowledge and experience in financial or business matters that it is capable of evaluating the merits and risks of the investment contemplated hereby. Such Purchaser has had an
opportunity to receive, review and understand all information related to the Company requested by it and to ask questions of and receive answers from the Company regarding the Company, its business and the terms and conditions of the offering of the
Shares, and has conducted and completed its own independent due diligence. Such Purchaser acknowledges that the Company has made available the SEC Documents. Based on the information such Purchaser has deemed appropriate, and without reliance upon
any placement agent, it has independently made its own analysis and decision to enter into the Transaction Documents. Such Purchaser is relying exclusively on its own sources of information, investment analysis and due diligence (including
professional advice it deems appropriate) with respect to the execution, delivery and performance of the Transaction Documents, the Shares and the business, condition (financial and otherwise), management, operations, properties and prospects of the
Company, including but not limited to all business, legal, regulatory, accounting, credit and tax matters. 
 (c)    The
Shares to be received by such Purchaser hereunder will be acquired for such Purchaser’s own account, not as nominee or agent, and not with a view to the resale or distribution of any part thereof in violation of the Securities Act, and such
Purchaser has no present intention of selling, granting any participation in, or otherwise distributing the same in violation of the Securities Act without prejudice, however, to such Purchaser’s right at all times to sell or otherwise dispose
of all or any part of such Shares in compliance with applicable federal and state securities laws. Such Purchaser is not a broker-dealer registered with the Commission under the Exchange Act or an entity engaged in a business that would require it
to be so registered. Such Purchaser understands that the Shares are characterized as “restricted securities” under the U.S. federal securities laws inasmuch as they are being acquired from the Company in a transaction not involving a
public offering and that under such laws and applicable regulations such securities may be resold without registration under the Securities Act only in certain limited circumstances. Purchaser will not, directly or indirectly, offer, sell, pledge,
transfer or otherwise dispose of (or solicit any offers to buy, purchase or otherwise acquire or take a pledge of) any of the securities purchased hereunder except in compliance with the Securities Act, applicable blue sky laws, and the rules and
regulations promulgated thereunder. 
 (d)    Such Purchaser is an “accredited investor” within the meaning of
Rule 501(a) under the Securities Act. Such Purchaser has determined based on its own independent review and such professional advice as it deems appropriate that its purchase of the Shares and participation in the transactions contemplated by the
Transaction Documents have been duly authorized and approved by all necessary action by or on behalf of the Purchaser, and do not and will not violate or constitute a default under such Purchaser’s certificate of incorporation, articles of
association, charter, bylaws or other constituent document or under any law, rule, regulation, agreement or other obligation by which such Purchaser is bound. 

  
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 (e)    The execution, delivery and performance by such Purchaser of the
Transaction Documents to which such Purchaser is a party have been duly authorized and each has been duly executed and when delivered will constitute the valid and legally binding obligation of such Purchaser, enforceable against such Purchaser in
accordance with their respective terms, subject to bankruptcy, insolvency, fraudulent transfer, reorganization, moratorium and similar laws of general applicability, relating to or affecting creditors’ rights generally. 

(f)    Such Purchaser is not a broker or dealer registered pursuant to Section 15 of the Exchange Act (a
“registered broker-dealer”) and is not affiliated with a registered broker dealer. Purchaser is not party to any agreement for distribution of any of the Shares. 

(g)    Such Purchaser shall have completed or caused to be completed and delivered to the Company at no later than the
Closing Date, the Purchaser Questionnaire and the Selling Stockholder Questionnaire for use in preparation of the registration statement meeting the requirements set forth in the Registration Rights Agreement and covering the resale by the
Purchasers of the Registrable Securities (as defined in the Registration Rights Agreement) (the “Registration Statement”), and the answers to the Purchaser Questionnaire and the Selling Stockholder Questionnaire are true and correct
in all material respects as of the date of this Agreement and will be true and correct in all material respects as of the Closing and the effective date of the Registration Statement; provided, that the Purchasers shall be entitled to update
such information by providing notice thereof to the Company before the effective date of such Registration Statement. 

(h)    Such Purchaser understands that no United States federal or state agency, or similar agency of any other country,
has reviewed, approved, passed upon, or made any recommendation or endorsement of the Company or the purchase of the Shares. 

(i)    Such Purchaser has no present intent to effect a “change of control” of the Company as such term is
understood under the rules promulgated pursuant to Section 13(d) of the Exchange Act. 
 (j)    Such Purchaser has
not taken any of the actions set forth in, and is not subject to, the disqualification provisions of Rule 506(d)(1) of the Securities Act. 

(k)    Such Purchaser did not learn of the investment in the Shares as a result of any general solicitation or general
advertising. 
 (l)    Such Purchaser’s residence (if an individual) or offices in which its investment decision
with respect to the Shares was made (if an entity) are located at the address immediately below such Purchaser’s name on its signature page hereto. 

(m)     Such Purchaser (including any person controlling, controlled by, or under common control with such Purchaser, as
the term “control” is defined pursuant to the Hart-Scott-Rodino Antitrust Improvements Act of 1976, as amended, and its implementing regulations (the “HSR Act”)) in connection with the consummation of the transactions
contemplated by this Agreement will not be required to and will not complete a filing with the U.S. government pursuant to the HSR Act. 

  
 11 

 5.2    Other than consummating the transactions contemplated hereunder,
such Purchaser has not, nor has any person acting on behalf of or pursuant to any understanding with such Purchaser, directly or indirectly executed any purchases or sales, including all “short sales” as defined in Rule 200 of Regulation
SHO under the Exchange Act (but shall not be deemed to include the location and/or reservation of borrowable shares of Common Stock) (“Short Sales”), of the securities of the Company during the period commencing as of the time that
such Purchaser was first contacted by the Company or any other person regarding the transactions contemplated hereby and ending immediately prior to the Effective Date. Notwithstanding the foregoing, in the case of a Purchaser that is a
multi-managed investment vehicle whereby separate portfolio managers manage separate portions of such Purchaser’s assets and the portfolio managers have no direct knowledge of the investment decisions made by the portfolio managers managing
other portions of such Purchaser’s assets, the representation set forth above shall only apply with respect to the portion of assets managed by the portfolio manager that made the investment decision to purchase the Shares covered by this
Agreement. Other than to other persons party to this Agreement, such Purchaser has maintained the confidentiality of all disclosures made to it in connection with this transaction (including the existence and terms of this transaction).
Notwithstanding the foregoing, for avoidance of doubt, nothing contained herein shall constitute a representation or warranty, or preclude any actions, with respect to the identification of the availability of, or securing of, available shares to
borrow in order to effect Short Sales or similar transactions in the future. 
 5.3    Purchaser understands that
nothing in this Agreement or any other materials presented to Purchaser in connection with the purchase and sale of the Shares constitutes legal, tax or investment advice. Purchaser has consulted such legal, tax and investment advisors as it, in its
sole discretion, has deemed necessary or appropriate in connection with its purchase of the Shares. 

5.4    Legends. 

(a)    Purchaser understands that, until such time as the Shares have been registered for resale pursuant to the
Registration Statement or the Shares may be sold pursuant to Rule 144 under the Securities Act (“Rule 144”) without any restriction as to the number of securities as of a particular date that can then be immediately sold, the book
entry notations evidencing the Shares may bear one or more legends in substantially the following form and substance: 
 “THESE
SECURITIES HAVE NOT BEEN REGISTERED UNDER THE U.S. SECURITIES ACT OF 1933, AS AMENDED (THE “SECURITIES ACT”), OR ANY OTHER APPLICABLE SECURITIES LAWS AND HAVE BEEN ISSUED IN RELIANCE UPON AN EXEMPTION FROM THE REGISTRATION REQUIREMENTS OF
THE SECURITIES ACT AND SUCH OTHER SECURITIES LAWS. NEITHER THIS SECURITY NOR ANY INTEREST OR PARTICIPATION HEREIN MAY BE REOFFERED, SOLD, ASSIGNED, TRANSFERRED, PLEDGED, ENCUMBERED, HYPOTHECATED OR OTHERWISE DISPOSED OF, EXCEPT PURSUANT TO AN
EFFECTIVE REGISTRATION STATEMENT UNDER THE SECURITIES ACT OR PURSUANT TO A TRANSACTION WHICH IS EXEMPT FROM, OR NOT 

  
 12 

 
SUBJECT TO, SUCH REGISTRATION, IN EACH CASE IN ACCORDANCE WITH ALL APPLICABLE SECURITIES LAWS, AND IN THE CASE OF A TRANSACTION EXEMPT FROM, OR NOT SUBJECT TO, SUCH REGISTRATION, UNLESS THE
COMPANY HAS RECEIVED AN OPINION OF COUNSEL REASONABLY SATISFACTORY TO IT THAT SUCH TRANSACTION DOES NOT REQUIRE REGISTRATION UNDER THE SECURITIES ACT AND SUCH OTHER APPLICABLE LAWS.” 

In addition, book entry notations representing the Shares may contain: 

(i)    Any legend required by the laws of the State of California, including any legend required by the California
Department of Corporations. 
 (ii)    Any legend required by the blue sky laws of any other state to the extent such
laws are applicable to the sale of such Shares hereunder. 
 (b)    The restrictive legend set forth in section 5.4(a)
above shall be removed and the Company shall, no later than three business days following the written request of a holder of Shares together with such representations and covenants of such holder and/or such holder’s executing broker as the
Company may reasonably require in connection therewith and, if such Shares are certificated, the delivery to the Company’s transfer agent of a certificate representing Shares, issue or cause to be issued a certificate or book entry position
without such restrictive legend or any other restrictive legend to the holder of the applicable shares upon which it is stamped or issue to such holder by electronic delivery with the applicable balance account at DTC or in physical certificated
shares, as requested by such holder, if: (i) such Shares are then registered for resale pursuant to a registration statement that is effective under the Securities Act (provided that the Purchaser agrees to only sell such Shares during
such time that such registration statement is effective and such Purchaser has not been notified by the Company that such registration statement has been withdrawn or suspended, and only as permitted by such registration statement); (ii) such Shares
are sold or transferred in accordance with Rule 144 (provided that such restrictive legend shall only be removed pursuant to this clause (ii) from such portion of the Shares as are sold or transferred in accordance with Rule 144); or
(iii) such Shares are eligible for sale without the requirement for the Company to be in compliance with the current public information required under Rule 144 as to such securities and without volume or manner-of-sale restrictions. Subject to receipt of such representations, and covenants as are contemplated hereby, following the earlier of (i) the effective date of the Registration Statement or
(ii) Rule 144 becoming available for the resale of the Shares, without the requirement for the Company to be in compliance with the current public information required under Rule 144 as to the Shares and without volume or manner-of-sale restrictions, the Company shall issue to the Company’s transfer agent the instructions with respect to legend removal consistent with this section and
shall cause to be delivered any legal opinion required by the transfer agent with respect thereto. Any fees (with respect to the transfer agent, the Company’s counsel or otherwise) associated with the issuance of such opinion or the removal of
such legend shall be borne by the Company. 
 5.5    Restricted Shares. Purchaser understands that the
Shares are characterized as “restricted securities” under the federal securities laws inasmuch as they are being acquired from the Company in a transaction not involving a public offering and that under such laws and

  
 13 

 
applicable regulations such Shares may be resold without registration under the Securities Act only in certain limited circumstances. In this connection, such Purchaser represents that it is
familiar with Rule 144, as presently in effect, and understands the resale limitations imposed thereby and by the Securities Act. 

5.6    Exculpation Among Purchasers. Purchaser acknowledges that it is not relying upon any other Purchaser,
or any officer, director, employee, agent, partner, member or affiliate of any such other Purchaser, in making its investment or decision to invest in the Company. Purchaser agrees that neither any Purchaser nor the respective controlling Persons,
officers, directors, partners, agents, or employees of any Purchaser shall be liable to any other Purchaser for any action heretofore taken or omitted to be taken by any of them in connection with the purchase of the Shares. 

SECTION 6.    CONDITIONS TO COMPANY’S OBLIGATIONS AT THE CLOSING. 

The Company’s obligation to complete the sale and issuance of the Shares and deliver Shares to each Purchaser, individually, as set forth
in the Schedule of Purchasers at the Closing shall be subject to the following conditions to the extent not waived by the Company: 

6.1    Receipt of Payment. The Company shall have received payment, by wire transfer of immediately
available funds, in the full amount of the purchase price for the number of Shares being purchased by such Purchaser at the Closing as set forth in the Schedule of Purchasers. 

6.2    Representations and Warranties. The representations and warranties made by the Purchasers in
Section 5 hereof shall be true and correct in all material respects when made, and shall be true and correct in all material respects on the Closing Date with the same force and effect as if they had been made on and as of said date. The
Purchaser shall have performed in all material respects all obligations and covenants herein required to be performed by them on or prior to the Closing Date. 

6.3    Receipt of Executed Documents. Such Purchaser shall have executed and delivered to the Company the
Registration Rights Agreement, the Purchaser Questionnaire and the Selling Stockholder Questionnaire. 
 SECTION 7.    CONDITIONS TO
PURCHASERS’ OBLIGATIONS AT THE CLOSING. 
 Each Purchaser’s obligation to accept delivery of the Shares and to pay for the
Shares shall be subject to the following conditions to the extent not waived by such Purchaser: 

7.1    Representations and Warranties. The representations and warranties made by the Company in
Section 4 hereof shall be true and correct in all material respects as of, and as if made on, the date of this Agreement and as of the Closing Date, except to the extent any such representation or warranty expressly speaks as of an earlier
date, in which case such representation or warranty shall be true and correct as of such earlier date. 

7.2    Performance. The Company shall have performed in all material respects all obligations and covenants
herein required to be performed by it on or prior to the Closing Date.  

  
 14 

 7.3    Receipt of Executed Registration Rights Agreement.
The Company shall have executed and delivered to the Purchasers the Registration Rights Agreement. 
 7.4    Legal
Opinion. The Purchasers shall have received an opinion of Latham & Watkins LLP, special counsel to the Company, dated as of the Closing Date, in form and substance reasonably acceptable to the Purchasers. 

7.5    Certificate. Each Purchaser shall have received a certificate signed by the Chief Executive Officer
or the Chief Financial Officer to the effect that the representations and warranties of the Company in Section 4 hereof are true and correct in all material respects as of, and as if made on, the date of this Agreement and as of the Closing
Date and that the Company has satisfied all of the conditions set forth in this Section 7. 
 7.6    Good
Standing. The Company is validly existing as a corporation in good standing under the laws of Delaware. 

7.7    Judgments. No judgment, writ, order, injunction, award or decree of or by any court, or judge,
justice or magistrate, including any bankruptcy court or judge, or any order of or by any governmental authority, shall have been issued, and no action or proceeding shall have been instituted by any governmental authority, enjoining or preventing
the consummation of the transactions contemplated hereby. 
 7.8    Stop Orders. No stop order or
suspension of trading shall have been imposed by the Nasdaq Global Select Market, the Commission or any other governmental regulatory body with respect to public trading in the Common Stock. 

SECTION 8.    TERMINATION OF OBLIGATIONS TO EFFECT CLOSING; EFFECTS. 

8.1    The obligations of the Company, on the one hand, and the Purchasers, on the other hand, to effect the Closing shall
terminate as follows: 
 (a)    upon the mutual written consent of the Company and Purchasers that agreed to purchase a
majority of the Shares to be issued and sold pursuant to this Agreement; 
 (b)    by the Company if any of the
conditions set forth in Section 6 shall have become incapable of fulfillment, and shall not have been waived by the Company; 

(c)    by a Purchaser (with respect to itself only) if any of the conditions set forth in Section 7 shall have become
incapable of fulfillment, and shall not have been waived by the Purchaser; or 
 (d)    by either Company or Purchaser
if the Closing has not occurred by June 30, 2019; 
 provided, however, that, except in the case of clauses (b) and (c) above,
the party seeking to terminate its obligation to effect the Closing shall not then be in breach of any of its representations, warranties, covenants or agreements contained in this Agreement or the other Transaction Documents if such breach has
resulted in the circumstances giving rise to such party’s seeking to terminate its obligation to effect the Closing. 

  
 15 

 8.2    Nothing in this Section 8 shall be deemed to release any
party from any liability for any breach by such party of the terms and provisions of this Agreement or the other Transaction Documents or to impair the right of any party to compel specific performance by any other party of its obligations under
this Agreement or the other Transaction Documents. 
 SECTION 9.    BROKER’S FEES. 

The Company and each Purchaser (severally and not jointly) hereby represent that there are no other brokers or finders entitled to
compensation, commissions, placement agent’s fees or similar payments in connection with the sale of the Shares, and shall indemnify each other for any such fees for which they are responsible. 

SECTION 10.    ADDITIONAL AGREEMENTS OF THE PARTIES. 

10.1    Nasdaq Listing. The Company will use reasonable best efforts to continue the listing and trading of
its Common Stock on the Nasdaq Global Select Market or the Nasdaq Global Market (or a substantially equivalent “national securities exchange” as defined under the Exchange Act) and, in accordance, therewith, will use reasonable best
efforts to comply in all respects with the Company’s reporting, filing and other obligations under the bylaws or rules of such market or exchange, as applicable; provided, however, that the Company’s obligations pursuant to this
Section 10.1 shall terminate and be of no further force and effect on the date on which the Company’s obligations under the Registration Rights Agreement to register or maintain the effectiveness of any registration statement covering the
Registrable Securities (as such term is defined in the Registration Rights Agreement) shall terminate, but only to the extent that the Company is not then in breach in any material respect of its obligations under the Registration Rights Agreement.

 10.2    Access to Information. From the date hereof until the Closing, the Company will make reasonably
available to the Purchasers’ representatives, consultants and their respective counsels for inspection, such information and documents as the Purchasers reasonably request, and will make available at reasonable times and to a reasonable extent
officers and employees of the Company to discuss the business and affairs of the Company. 
 10.3    Form D; Blue Sky
Filings. The Company agrees to timely file a Form D with respect to the Shares and to provide a copy thereof, promptly upon request of any Purchaser. The Company shall take such action as the Company shall reasonably determine is
necessary in order to obtain an exemption for, or to qualify the Shares for, sale to the Purchaser at the Closing under applicable securities or “Blue Sky” laws of the states of the United States, and shall provide evidence of such actions
promptly upon request of any Purchaser. 
 10.4    Integration. The Company shall not, and shall use its
commercially reasonable efforts to ensure that no affiliate of the Company shall, sell, offer for sale or solicit offers to buy or otherwise negotiate in respect of any security (as defined in Section 2 of the Securities Act) that will be
integrated with the offer or sale of the Shares in a manner that would require the registration under the Securities Act of the sale of the Shares to the Purchasers, or that will be integrated with 

  
 16 

 
the offer or sale of the Shares for purposes of the rules and regulations of any trading market such that it would require stockholder approval prior to the closing of such other transaction
unless stockholder approval is obtained before the closing of such subsequent transaction. 
 10.5    Short Sales and
Confidentiality After the Date Hereof. Each Purchaser covenants that neither it nor any affiliates acting on its behalf or pursuant to any understanding with it will execute any Short Sales during the period from the date hereof until the
earlier of such time as (i) after the transactions contemplated by this Agreement are first publicly announced or (ii) this Agreement is terminated in full. Each Purchaser covenants that until such time as the transactions contemplated by
this Agreement are publicly disclosed by the Company under the 8-K (defined below) contemplated to be filed pursuant to Section 10.6 hereof, such Purchaser will maintain the confidentiality of all
disclosures made to it in connection with this transaction (including the existence and terms of this transaction). Each Purchaser understands and acknowledges that the Commission currently takes the position that coverage of short sales of shares
of the Common Stock “against the box” prior to effectiveness of a resale registration statement with securities included in such registration statement would be a violation of Section 5 of the Securities Act, as set forth in
Item 239.10 of the Securities Act Rules Compliance and Disclosure Interpretations compiled by the Office of Chief Counsel, Division of Corporation Finance. 

10.6    Securities Laws Disclosure; Publicity. By 5:00 P.M., New York City time, on the trading day
immediately following the Effective Date, the Company shall issue a press release disclosing the material terms of the transactions contemplated hereby. On or before 9:00 A.M., New York City time, on the third trading day immediately following
the execution of this Agreement, the Company will file a Current Report on Form 8-K (the “8-K”) with the Commission describing the material terms
of the Transaction Documents (and including as exhibits to such Current Report on Form 8-K the agreements required to be filed in connection therewith). Notwithstanding the foregoing, the Company shall
not publicly disclose the name of any Purchaser, or include the name of any Purchaser in any public filing with the Commission or any regulatory agency or Nasdaq, without the prior written consent of such Purchaser, which consent shall not be
unreasonably withheld, conditioned or delayed, except: (a) as required by federal securities law in connection with (i) any registration statement contemplated by the Registration Rights Agreement and (ii) the filing of final
Transaction Documents with the Commission; (b) the filing of a Form D with the Commission under the Securities Act and (c) to the extent such disclosure is required by law or Nasdaq regulations, in which case the Company shall provide the
Purchasers with prior notice of such disclosure permitted under this clause (c). As of the time of the filing of the 8-K, no Purchaser shall be in possession of any material,
non-public information received from the Company, any subsidiary of the Company or any of their respective officers, directors, employees or agents, pursuant to the transactions contemplated by this Agreement
that is not disclosed in the 8-K, press release or other disclosure by the Company that complies with the requirements of Regulation FD. 

SECTION 11.    INDEMNIFICATION. 

11.1    Indemnification by the Company. The Company agrees to indemnify and hold harmless each of the
Purchasers and each Person, if any, who controls any Purchaser within the meaning of the Securities Act (each, an “Indemnified Party”), against any losses, claims, damages, liabilities or expenses, joint or several, to which such
Indemnified Party may become subject under 

  
 17 

 
the Securities Act, the Exchange Act, or any other federal or state statutory law or regulation, or at common law (including in settlement of any litigation, if such settlement is effected with
the written consent of the Company), insofar as such losses, claims, damages, liabilities or expenses (or actions in respect thereof as contemplated below) arise out of or are based in whole or in part on the inaccuracy in the representations and
warranties of the Company contained in this Agreement or the failure of the Company to perform its obligations hereunder, and will reimburse each Indemnified Party for legal and other expenses reasonably incurred as such expenses are reasonably
incurred by such Indemnified Party in connection with investigating, defending, settling, compromising or paying such loss, claim, damage, liability, expense or action; provided, however, that the Company will not be liable in any such
case to the extent that any such loss, claim, damage, liability or expense arises out of or is based upon (i) the failure of such Indemnified Party to comply with the covenants and agreements contained in Section 5 and 10.6 above
respecting sale of the Shares, or (ii) the inaccuracy of any representations made by such Indemnified Party herein. 

11.2    Indemnification by Purchasers. Each Purchaser shall severally, and not jointly, indemnify and hold
harmless the other Purchasers and the Company, each of its directors, and each Person, if any, who controls the Company within the meaning of the Securities Act, against any losses, claims, damages, liabilities or expenses to which the Company, each
of its directors or each of its controlling Persons may become subject, under the Securities Act, the Exchange Act, or any other federal or state statutory law or regulation, or at common law or otherwise (including in settlement of any litigation,
if such settlement is effected with the written consent of such Purchaser) insofar as such losses, claims, damages, liabilities or expenses (or actions in respect thereof as contemplated below) arise out of or are based upon (i) any failure by
such Purchaser to comply with the covenants and agreements contained in Sections 5 and 10.6 above respecting the sale of the Shares unless such failure by such Purchaser is directly caused by the Company’s failure to provide written notice of a
withdrawal or suspension of the Registration Statement to such Purchaser or (ii) the inaccuracy of any representation made by such Purchaser herein, in each case to the extent, and will reimburse the Company, each of its directors, and each of
its controlling Persons for any legal and other expense reasonably incurred, as such expenses are reasonably incurred by the Company, each of its directors, and each of its controlling Persons in connection with investigating, defending, settling,
compromising or paying any such loss, claim, damage, liability, expense or action. No Purchaser shall be liable for the indemnification obligations of any other Purchaser. 

SECTION 12.    NOTICES. 

All notices, requests, consents and other communications hereunder shall be in writing, shall be sent by confirmed electronic mail, or mailed
by first-class registered or certified airmail, or nationally recognized overnight express courier, postage prepaid, and shall be deemed given when so sent in the case of electronic mail transmission, or when so received in the case of mail or
courier, and addressed as follows: 
 if to the Company, to: 

Codexis, Inc. 
 ##### 

E-Mail: ##### 

  
 18 

 with a copy (which shall not constitute notice) to: 

Latham & Watkins LLP 

##### 
 E-Mail: ##### 
 or to such other person at such other place as the Company shall designate to the
Purchasers in writing; and if to the Purchasers, at the address as set forth at the end of this Agreement, or at such other address or addresses as may have been furnished to the Company in writing. 

SECTION 13.    MISCELLANEOUS. 

13.1    Waivers and Amendments. Neither this Agreement nor any provision hereof may be changed, waived,
discharged, terminated, modified or amended except upon the written consent of the Company and holders of at least a majority of the Shares. 

13.2    Headings. The headings of the various sections of this Agreement have been inserted for convenience
of reference only and shall not be deemed to be part of this Agreement. 
 13.3    Severability. In case
any provision contained in this Agreement should be invalid, illegal or unenforceable in any respect, the validity, legality and enforceability of the remaining provisions contained herein shall not in any way be affected or impaired thereby. 

13.4    Replacement of Shares. If the Shares are certificated and any certificate or instrument evidencing
any Shares is mutilated, lost, stolen or destroyed, the Company shall issue or cause to be issued in exchange and substitution for and upon cancellation thereof, or in lieu of and substitution therefor, a new certificate or instrument, but only upon
receipt of evidence reasonably satisfactory to the Company and the Company’s transfer agent of such loss, theft or destruction and the execution by the holder thereof of a customary lost certificate affidavit of that fact and an agreement to
indemnify and hold harmless the Company and the Company’s transfer agent for any losses in connection therewith or, if required by the transfer agent, a bond in such form and amount as is required by the transfer agent. The applicants for a new
certificate or instrument under such circumstances shall also pay any reasonable third-party costs associated with the issuance of such replacement Shares. If a replacement certificate or instrument evidencing any Shares is requested due to a
mutilation thereof, the Company may require delivery of such mutilated certificate or instrument as a condition precedent to any issuance of a replacement. 

13.5    Independent Nature of Purchasers’ Obligations and Rights. The obligations of each Purchaser
under this Agreement are several and not joint with the obligations of any other Purchaser, and no Purchaser shall be responsible in any way for the performance of the obligations of any other Purchaser under this Agreement. Nothing contained herein
and no action taken by any Purchaser pursuant hereto, shall be deemed to constitute the Purchasers as a partnership, an association, a joint venture or any other kind of entity, or create a presumption that the Purchasers are in any way acting in
concert or as a group, or are deemed affiliates (as such term is defined under the Exchange Act) with respect to such obligations or the transactions contemplated by this Agreement. Each Purchaser shall be entitled to independently protect and
enforce its rights, including without limitation the rights arising out of this Agreement, and it shall not be necessary for any other Purchaser to be joined as an additional party in any proceeding for such purpose. 

  
 19 

 13.6    Governing Law; Venue. All questions concerning the
construction, validity, enforcement and interpretation of the Transaction Documents shall be governed by and construed and enforced in accordance with the internal laws of the State of California, without regard to the principles of conflicts of law
thereof. With respect to any disputes arising out of or related to this Agreement, the parties consent to the exclusive jurisdiction of, and venue in, the state courts in San Mateo County in the State of California (or in the event of exclusive
federal jurisdiction, the courts of the Northern District of California). Each party hereby irrevocably waives personal service of process and consents to process being served in any such suit, action or proceeding by mailing a copy thereof via
registered or certified mail or overnight delivery (with evidence of delivery) to such party at the address in effect for notices to it under this Agreement and agrees that such service shall constitute good and sufficient service of process and
notice thereof. Nothing contained herein shall be deemed to limit in any way any right to serve process in any other manner permitted by law. EACH PARTY HERETO HEREBY IRREVOCABLY WAIVES, TO THE FULLEST EXTENT PERMITTED BY APPLICABLE LAW, ANY AND
ALL RIGHT TO TRIAL BY JURY IN ANY LEGAL PROCEEDING ARISING OUT OF OR RELATING TO THIS AGREEMENT OR THE TRANSACTIONS CONTEMPLATED HEREBY. 

13.7    Counterparts. This Agreement may be executed in two or more counterparts, each of which shall
constitute an original, but all of which, when taken together, shall constitute but one instrument, and shall become effective when one or more counterparts have been signed by each party hereto and delivered to the other parties. In the event that
any signature is delivered by facsimile transmission or by e-mail delivery of a “.pdf” format data file, such signature shall create a valid and binding obligation of the party executing (or on whose
behalf such signature is executed) the same with the same force and effect as if such facsimile of “.pdf” signature were the original thereof. 

13.8    Successors and Assigns. Except as otherwise expressly provided herein, the provisions hereof shall
inure to the benefit of, and be binding upon, the successors, assigns, heirs, executors and administrators of the parties hereto. 

13.9    Entire Agreement. This Agreement and other documents delivered pursuant hereto, including the
exhibits, constitute the full and entire understanding and agreement between the parties with regard to the subjects hereof and thereof. 

13.10    Payment of Fees and Expenses. Each of the Company and the Purchasers shall bear its own expenses
and legal fees incurred on its behalf with respect to this Agreement and the transactions contemplated hereby; provided that the Company shall reimburse the Purchasers for up to $25,000 of their reasonable documented
out-of-pocket legal expenses incurred in connection with the transactions contemplated by this Agreement and the Registration Rights Agreement promptly following receipt
of an invoice therefor. If any action at law or in equity is necessary to enforce or interpret the terms of this Agreement, the prevailing party shall be entitled to reasonable attorney’s fees, costs and necessary disbursements in addition to
any other relief to which such party may be entitled. 

  
 20 

 13.11    Survival. The representations, warranties,
covenants and agreements made in this Agreement shall survive any investigation made by the Company or the Purchasers and the Closing. 

13.12    Waiver of Potential Conflicts of Interest. Each of the Purchasers and the Company acknowledges that
Latham & Watkins LLP (“Latham”) may have represented and may currently represent certain of the Purchasers. In the course of such representation, Latham may have come into possession of confidential information relating to
such Purchasers. Each of the Purchasers and the Company acknowledges that Latham is representing only the Company in this transaction. By executing this Agreement, each of the Purchasers and the Company hereby waives any actual or potential conflict
of interest which has or may arise as a result of Latham’s representation of such persons and entities, and represents that it has had the opportunity to consult with independent counsel concerning the giving of this waiver. 

[Signature pages follow] 

  
 21 

 IN WITNESS WHEREOF, the parties hereto have caused this Agreement to be executed by
their duly authorized representatives as of the day and year first above written. 
  

			
	CODEXIS, INC.
		
	By:	 	/s/ John Nicols
	Name:	 	John Nicols
	Title:	 	President and Chief Executive Officer

  
 SIGNATURE PAGES TO 

SECURITIES PURCHASE AGREEMENT 

 IN WITNESS WHEREOF, the parties hereto have caused this Agreement to be executed by
their duly authorized representatives as of the day and year first above written. 
  

			
	PURCHASERS:
	
	CASDIN PARTNERS MASTER FUND, L.P.
	By:	 	Casdin Partners GP, LLC, its General Partner
	By:	 	 /s/ Eli Casdin

	Name:	 	Eli Casdin
	Title:	 	Managing Member
	
	Address:
	#####
	Email: #####

  
 SIGNATURE PAGES TO 

SECURITIES PURCHASE AGREEMENT 

 EXHIBIT A 

SCHEDULE OF PURCHASERS 
  

									
	 Name and Address
	  	Number of
Shares	 	  	Aggregate
Purchase Price of
Shares	 
	 Casdin Partners Master Fund, L.P. #####
	  	 	3,048,780	 	  	$	49,999,992.00	 

 EXHIBIT B 

ACTIVE SUBSIDIARIES 
 Codexis Mayflower
Holdings LLC 
 Codexis Brazil Holdings A LLC 
 Codexis Brazil
Holdings B LLC 
 Codexis Laboratories Netherlands B.V. 

Codexis Laboratories Hungary LLC 
 Wasabi Acquisition LLC 

 APPENDIX I 

PURCHASER QUESTIONNAIRE 

 APPENDIX II 

SELLING STOCKHOLDER QUESTIONNAIRE 

 APPENDIX III 

FORM OF REGISTRATION RIGHTS AGREEMENTEX-10.2

 Exhibit 10.2 

EXECUTION VERSION 

REGISTRATION RIGHTS AGREEMENT 

This Registration Rights Agreement (this “Agreement”) is made and entered into as of June 20, 2019, by and among
Codexis, Inc., a Delaware corporation (the “Company”), and the investors signatory hereto (each a “Purchaser” and collectively, the “Purchasers”). 

This Agreement is made pursuant to the Securities Purchase Agreement, dated as of June 20, 2019, among the Company and the Purchasers
(the “Purchase Agreement”). 
 NOW, THEREFORE, IN CONSIDERATION of the mutual covenants contained in this Agreement, and
for other good and valuable consideration the receipt and adequacy of which are hereby acknowledged, the Company and the Purchasers agree as follows: 

1.      Definitions. Capitalized terms used and not otherwise defined herein that are defined in the
Purchase Agreement have the meanings given such terms in the Purchase Agreement. As used in this Agreement, the following terms have the respective meanings set forth in this Section 1: 

“Affiliate” means, with respect to any Person, any other Person that, directly or indirectly through one or more
intermediaries, Controls, is controlled by or is under common control with such Person, as such terms are used in and construed under Rule 405 under the Securities Act. 

“Advice” shall have the meaning set forth in Section 7(c). 

“Automatic Shelf Registration Statement” means an “automatic shelf registration statement” as such term is defined
in Rule 405. 
 “Control” (including the terms “controlling”, “controlled by” or “under common
control with”) means the possession, direct or indirect, of the power to direct or cause the direction of the management and policies of a Person, whether through the ownership of voting securities, by contract or otherwise. 

“Commission” means the United States Securities and Exchange Commission, or any successor entity or entities, including, if
applicable, the staff of the Commission. 
 “Common Stock” means the common stock, par value $0.0001 per share, of the
Company. 
 “Effectiveness Date” means: (a) with respect to the Initial Registration Statement required to be filed
hereunder, the 180th day following the Closing Date, provided however if the Company is not a Well Known Seasoned Issuer as of the filing date of such Initial Registration Statement, then the 210th day following the Closing Date, (b) with respect to any additional Registration Statements which may be required pursuant to Section 2, the
60th day following the date on which the Company first knows, or reasonably should have known, that such additional Registration Statement is required under such Section (or if the Company is not
a Well Known Seasoned Issuer as such filing date, the 90th day following such date in the event such additional Registration Statement is reviewed by the Commission). If the Effectiveness Date
falls on a Saturday, Sunday or other date that the Commission is closed for business, the Effectiveness Date shall be extended to the next day on which the Commission is open for business. 

 “Effectiveness Period” shall have the meaning set forth in
Section 2(a). 
 “Exchange Act” means the Securities Exchange Act of 1934, as amended. 

“Filing Date” means: (a) with respect to the Initial Registration Statement, the 180th calendar day following the Closing Date, and (b) with respect to any additional Registration Statements that may be required pursuant to Section 2 hereof, the 60th day following the date on which the Company first knows, or reasonably should have known, that such additional Registration Statement is required under such Section. 

“Form S-3” means such form under the Securities Act as in effect on the date hereof
or any successor registration form under the Securities Act subsequently adopted by the Commission. 
 “Holder” or
“Holders” means the holder or holders, as the case may be, from time to time of Registrable Securities. 

“Indemnified Party” shall have the meaning set forth in Section 6(c). 

“Indemnifying Party” shall have the meaning set forth in Section 6(c). 

“Initial Registration Statement” shall mean the initial Registration Statement required to be filed to cover the resale by
the Holders of the Registrable Securities pursuant to Section 2(a). 
 “Losses” shall have the meaning set forth in
Section 6(a). 
 “Person” means an individual or corporation, partnership, trust, incorporated or unincorporated
association, joint venture, limited liability company, joint stock company, government (or an agency or subdivision thereof) or other entity of any kind. 

“Proceeding” means an action, claim, suit, investigation or proceeding (including, without limitation, an investigation or
partial proceeding, such as a deposition), whether commenced or threatened. 
 “Prospectus” means the prospectus included
in a Registration Statement (including, without limitation, a prospectus that includes any information previously omitted from a prospectus filed as part of an effective registration statement in reliance upon Rule 430A or Rule 430B promulgated by
the Commission pursuant to the Securities Act), as amended or supplemented by any prospectus supplement, with respect to the terms of the offering of any portion of the Registrable Securities covered by a Registration Statement, and all other
amendments and supplements to the Prospectus, including post-effective amendments, and all material incorporated by reference or deemed to be incorporated by reference in such Prospectus. 

“Reduction Securities” shall have the meaning set forth in Section 2(b). 

  
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 “Registrable Securities” means (i) the Shares issued pursuant to the
Purchase Agreement and (ii) any other shares of Common Stock issued as (or issuable upon conversion or exercise of any warrant, right or other security which is issued as) a dividend or other distribution with respect to, in exchange for or in
replacement of the Shares; provided, however, that any such Registrable Securities shall cease to be Registrable Securities (and the Company shall not be required to maintain the effectiveness of any, or file another, Registration
Statement hereunder with respect thereto) for so long as (a) a Registration Statement with respect to the sale of such Registrable Securities is declared effective by the Commission (or otherwise becomes automatically effective, if the Company
is a Well-Known Seasoned Issuer and files an Automatic Shelf Registration Statement pursuant to this Agreement) under the Securities Act and such Registrable Securities have been disposed of by the Holder in accordance with such effective
Registration Statement, (b) such Registrable Securities have been previously sold or transferred in accordance with Rule 144, or (c) such securities become eligible for resale without volume or manner-of-sale restrictions and without current public information pursuant to Rule 144 as set forth in a written opinion letter to such effect, addressed, delivered and acceptable to the Company’s
transfer agent and the affected Holders (assuming that such securities and any securities issuable upon exercise, conversion or exchange of which, or as a dividend upon which, such securities were issued or are issuable, were at no time held by any
Affiliate of the Company), as reasonably determined by the Company, upon the advice of counsel to the Company. 
 “Registration
Statement” means each of the following: (i) an initial registration statement which is required to register the resale of the Registrable Securities, and (ii) such additional registration statement, if any, contemplated by
Section 2, and including, in each case, the Prospectus, amendments and supplements to each such registration statement or Prospectus, including pre- and post-effective amendments, all exhibits thereto,
and all material incorporated by reference or deemed to be incorporated by reference in such registration statement. 
 “Rule
144” means Rule 144 promulgated by the Commission pursuant to the Securities Act, as such Rule may be amended from time to time, or any similar rule or regulation hereafter adopted by the Commission having substantially the same effect as
such Rule. 
 “Rule 405” means Rule 405 promulgated by the Commission pursuant to the Securities Act, as such Rule may be
amended from time to time, or any similar rule or regulation hereafter adopted by the Commission having substantially the same effect as such Rule. 

“Rule 415” means Rule 415 promulgated by the Commission pursuant to the Securities Act, as such Rule may be amended from time
to time, or any similar rule or regulation hereafter adopted by the Commission having substantially the same effect as such Rule. 

“Rule 424” means Rule 424 promulgated by the Commission pursuant to the Securities Act, as such Rule may be amended from time
to time, or any similar rule or regulation hereafter adopted by the Commission having substantially the same effect as such Rule. 

“Securities Act” means the Securities Act of 1933, as amended. 

“Shares” means the shares of Common Stock issued pursuant to the Purchase Agreement. 

  
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 “Trading Day” means any day on which the Common Stock is traded on the
Nasdaq Global Select Market, or, if the Nasdaq Global Select Market is not the principal trading market for the Common Stock, then on the principal securities exchange or securities market on which the Common Stock is then traded. 

“Well-Known Seasoned Issuer” means as “well-known seasoned issuer” as defined in Rule 405. 

2.    Registration. 

(a)    If the Company is eligible for the use of Form S-3, on or prior to each
Filing Date, the Company shall prepare and file with the Commission a Registration Statement covering the resale of all of the Registrable Securities that are not then registered on an existing and effective Registration Statement for an offering to
be made on a continuous basis pursuant to Rule 415. The Registration Statement shall contain the “Plan of Distribution” in substantially the form attached hereto as Annex A (which may be modified to respond to comments, if any,
provided by the Commission, or otherwise reasonably modified by the Company, upon advice of counsel, with the prior written consent of the Majority Holders (as defined below), not to be unreasonably withheld). If the Company is a Well-Known Seasoned
Issuer, then the Company shall file the Registration Statement in the form of an Automatic Shelf Registration Statement. If the Company is not a Well-Known Seasoned Issuer, the Company shall use its commercially reasonable best efforts to cause each
Registration Statement filed under this Agreement to be declared effective under the Securities Act promptly but, in any event, no later than the Effectiveness Date for such Registration Statement, and shall, subject to Section 7(c) hereof, use
its commercially reasonable best efforts to keep such Registration Statement continuously effective under the Securities Act, including by filing any necessary post-effective amendments and/or replacement shelf registration statements and prospectus
supplements, until the earlier of (i) such time as all Registrable Securities covered by such Registration Statement have been sold by the Holder or (ii) the date that all shares of Common Stock covered by such Registration Statement cease
to be Registrable Securities hereunder (the “Effectiveness Period”). Notwithstanding the foregoing, the Company shall be entitled to suspend the effectiveness of the Registration Statement at any time prior to the expiration of the
Effectiveness Period for up to an aggregate of 30 consecutive Trading Days or an aggregate of 60 Trading Days (which need not be consecutive) in any given 360-day period. It is agreed and understood that the
Company shall, from time to time, be obligated to file one or more additional Registration Statements to cover any Registrable Securities which are not registered for resale pursuant to a pre-existing
Registration Statement. 
 (b)    Notwithstanding anything contained herein to the contrary, in the event that,
following the filing of the Registration Statement pursuant to Section 2(a) above, the Commission limits the amount of Registrable Securities that may be included and sold by Holders in any Registration Statement, including the Initial
Registration Statement, pursuant to Rule 415 or any other basis, the Company may reduce the number of Registrable Securities included in such Registration Statement on behalf of the Holders in whole or in part (in case of an exclusion as to a
portion of such Registrable Securities, such portion shall be allocated pro rata among such Holders in proportion to the respective numbers of Registrable Securities represented by Shares requested to be registered by each such Holder over the total
amount of Registrable Securities represented by Shares) (such Registrable Securities, the “Reduction Securities”); provided that, 

  
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notwithstanding anything to the contrary set forth herein, any reduction in respect of the Reduction Securities shall be first applied to shares of Common Stock which were issued other than
pursuant to the Purchase Agreement. In such event the Company shall give the Holders prompt notice of the number of such Reduction Securities excluded and the Company will not be liable for any damages under this Agreement in connection with the
exclusion of such Reduction Securities. The Company shall use its commercially reasonable best efforts at the first opportunity that is permitted by the Commission to register for resale the Reduction Securities. Such new Registration Statement
shall be on Form S-3 (except if the Company is not then eligible to register for resale the Reduction Securities on Form S-3, in which case such registration shall
be on another appropriate form for such purpose) and shall contain (except if otherwise required pursuant to written comments received from the Commission upon a review of such Registration Statement) the “Plan of Distribution” in
substantially the form attached hereto as Annex A (which may be modified to respond to comments, if any, provided by the Commission, or otherwise reasonably modified by the Company, upon advice of counsel, with the prior written consent of
the Majority Holders, not to be unreasonably withheld). The Company shall use its commercially reasonable best efforts to cause such new Registration Statement to be declared effective (or become automatically effective, if the Company is a
Well-Known Seasoned Issued and files an Automatic Shelf Registration Statement pursuant to this Agreement) under the Securities Act as soon as possible but, in any event, no later than the Effectiveness Date, and shall, subject to Section 7(c)
hereof, use its commercially reasonable best efforts to keep such new Registration Statement continuously effective under the Securities Act during the entire Effectiveness Period. Notwithstanding the foregoing, the Company shall be entitled to
suspend the effectiveness of such Registration Statement at any time prior to the expiration of the Effectiveness Period for an aggregate of no more than 30 consecutive Trading Days or an aggregate of 50 Trading Days (which need not be consecutive)
in any given 360-day period. 
 3.    Registration Procedures. In
connection with the Company’s registration obligations hereunder, the Company shall: 
 (a)    Not less than three
Trading Days prior to the filing of a Registration Statement or any related Prospectus or any amendment or supplement thereto, furnish to the Holders copies of all such documents proposed to be filed (other than those incorporated by reference).
Notwithstanding the foregoing, the Company shall not be required to furnish to the Holders any prospectus supplement being prepared and filed solely to name new or additional selling stockholders unless such Holders are named in such prospectus
supplement. In addition, in the event that any Registration Statement is on Form S-1 (or other form which does not permit incorporation by reference), the Company shall not be required to furnish to the
Holders any prospectus supplement containing information included in a report or proxy statement filed under the Exchange Act that would be incorporated by reference in such Registration Statement if such Registration Statement were on Form S-3 (or other form which permits incorporation by reference). The Company shall duly consider any comments made by Holders and received by the Company not later than two Trading Days prior to the filing of the
Registration Statement,but shall not be required to accept any such comments to which it reasonably objects; provided, however, that notwithstanding the foregoing, the Company shall accept and include in the Registration Statement and any related
Prospectus all reasonable comments made by Holders in good faith and received by the Company not later than two Trading Days prior to the filing of the Registration Statement to the extent that such comments relate directly to information describing
the Holders in their 

  
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capacity as selling stockholders; provided further, however, that nothing contained herein shall require the Company to include in any Registration Statement or related Prospectus any untrue
statement of a material fact or to omit to state any material fact required to be stated therein or necessary to make the statements therein, in light of the circumstances under which they were made, not misleading. 

(b)    Subject to Section 7(c): (i) prepare and file with the Commission such amendments, including post-effective
amendments, to each Registration Statement and the Prospectus used in connection therewith as may be necessary to keep such Registration Statement continuously effective as to the applicable Registrable Securities for its Effectiveness Period and
prepare and file with the Commission such additional Registration Statements in order to register for resale under the Securities Act all of the Registrable Securities; (ii) cause the related Prospectus to be amended or supplemented by any
required Prospectus supplement, and as so supplemented or amended to be filed pursuant to Rule 424; (iii) respond as promptly as reasonably possible to any comments received from the Commission with respect to each Registration Statement or any
amendment thereto and, as promptly as reasonably possible provide the Holders true and complete copies of all correspondence from and to the Commission relating to such Registration Statement that pertains to the Holders as selling stockholders but
not any comments that would result in the disclosure to the Holders of material and non-public information concerning the Company; and (iv) comply in all material respects with the provisions of the
Securities Act and the Exchange Act with respect to the Registration Statements and the disposition of all Registrable Securities covered by each Registration Statement. 

(c)    Notify the Holders as promptly as reasonably possible (and, in the case of (i)(A) below, not less than three
Trading Days prior to such filing) and (if requested by any such Person) confirm such notice in writing no later than one Trading Day following the day: (i)(A) when a Prospectus or any prospectus supplement (but only to the extent notice is required
under Section 3(a) above) or post-effective amendment to a Registration Statement is proposed to be filed; (B) when the Commission notifies the Company whether there will be a “review” of such Registration Statement and whenever
the Commission comments in writing on such Registration Statement (in which case the Company shall provide true and complete copies thereof and all written responses thereto to each of the Holders that pertain to the Holders as a selling stockholder
or to the Plan of Distribution, but not information which the Company believes would constitute material and non-public information); and (C) with respect to each Registration Statement or any
post-effective amendment, when the same has been declared effective or becomes automatically effective, as the case may be; (ii) of any request by the Commission or any other Federal or state governmental authority for amendments or supplements
to a Registration Statement or Prospectus or for additional information that pertains to the Holders as selling stockholders or the Plan of Distribution; (iii) of the issuance by the Commission of any stop order suspending the effectiveness of
a Registration Statement covering any or all of the Registrable Securities or the initiation of any Proceedings for that purpose; (iv) of the receipt by the Company of any notification with respect to the suspension of the qualification or
exemption from qualification of any of the Registrable Securities for sale in any jurisdiction, or the initiation or threatening of any Proceeding for such purpose; (v) of the occurrence of any event or passage of time that makes the financial
statements included or incorporated by reference in a Registration Statement ineligible for inclusion or incorporation by reference therein or any statement made in such Registration Statement or Prospectus or any document incorporated or deemed to
be incorporated therein by reference untrue 

  
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in any material respect or that requires any revisions to such Registration Statement, Prospectus or other documents so that, in the case of such Registration Statement or the Prospectus, as the
case may be, it will not contain any untrue statement of a material fact or omit to state any material fact required to be stated therein or necessary to make the statements therein, in light of the circumstances under which they were made, not
misleading; and (vi) of the occurrence or existence of any pending corporate development with respect to the Company that the Company believes may be material and that, in the determination of the Company, makes it not in the best interest of
the Company to allow continued availability of a Registration Statement or Prospectus; provided, that unless such information is publicly available other than a result of a breach of this Agreement by the Holder, any and all of such
information shall remain confidential to each Holder until such information otherwise becomes public, unless disclosure by a Holder is required by law; provided, further, that notwithstanding each Holder’s agreement to keep such
information confidential, each such Holder makes no acknowledgement that any such information is material, non-public information. 

(d)    Use its reasonable best efforts to avoid the issuance of, or, if issued, obtain the withdrawal of (i) any
order suspending the effectiveness of a Registration Statement, or (ii) any suspension of the qualification (or exemption from qualification) of any of the Registrable Securities for sale in any jurisdiction, at the earliest practicable moment.

 (e)    If requested by a Holder, furnish to each Holder, without charge, at least one conformed copy of each
Registration Statement and each amendment thereto and all exhibits to the extent reasonably requested by such Person (including those previously furnished or incorporated by reference) promptly after the filing of such documents with the Commission;
provided, that the Company shall have no obligation to provide any document pursuant to this clause that is available on the EDGAR system. 

(f)    If requested by a Holder, promptly deliver to each Holder, without charge, as many copies of each Prospectus or
Prospectuses (including each form of prospectus) and each amendment or supplement thereto as such Persons may reasonably request. Subject to Section 7(c) hereof, the Company hereby consents to the use of such Prospectus and each amendment or
supplement thereto by each of the selling Holders in connection with the offering and sale of the Registrable Securities covered by such Prospectus and any amendment or supplement thereto. 

(g)    Prior to any public offering of Registrable Securities, use its commercially reasonable efforts to register or
qualify or cooperate with the selling Holders in connection with the registration or qualification (or exemption from such registration or qualification) of such Registrable Securities for offer and sale under the securities or Blue Sky laws of
those jurisdictions within the United States as any Holder reasonably requests in writing to keep each such registration or qualification (or exemption therefrom) effective during the Effectiveness Period and to do any and all other acts or things
necessary or advisable to enable the disposition in such jurisdictions of the Registrable Securities covered by the Registration Statements; provided, that the Company shall not be required to qualify generally to do business in any
jurisdiction where it is not then so qualified or would subject the Company to any material tax in any such jurisdiction where it is not then so subject. 

  
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 (h)    Cooperate with the Holders to facilitate the timely preparation
and delivery of certificates or book-entry statements representing Registrable Securities to be delivered to a transferee pursuant to the Registration Statements, which certificates or book-entry statements shall be free, to the extent permitted by
the Purchase Agreement, of all restrictive legends, and to enable such Registrable Securities to be in such denominations and registered in such names as any such Holders may request. 

(i)    Upon the occurrence of any event contemplated by Section 3(c)(v), as promptly as reasonably possible, prepare
a supplement or amendment, including a post-effective amendment, to the affected Registration Statements or a supplement to the related Prospectus or any document incorporated or deemed to be incorporated therein by reference, and file any other
required document so that, as thereafter delivered, no Registration Statement nor any Prospectus will contain an untrue statement of a material fact or omit to state a material fact required to be stated therein or necessary to make the statements
therein, in light of the circumstances under which they were made, not misleading. 
 (j)    The Company may require
each selling Holder to furnish to the Company the number of shares of Common Stock beneficially owned by such Holder and any Affiliate thereof, the natural persons thereof that have voting and dispositive control over the shares and any other
information with respect to such Holder as the Commission requests. 
 4.    Holder’s Obligations. Each
Holder agrees, by acquisition of the Registrable Securities, that no Holder shall be entitled to sell any of such Registrable Securities pursuant to a Registration Statement or to receive a Prospectus relating thereto, unless such Holder has
furnished the Company with all material information required to be set forth in the Purchaser Questionnaire and Selling Stockholder Questionnaire pursuant to the Purchase Agreement. Any sale of any Registrable Securities by any Holder shall
constitute a representation and warranty by such Holder that the information regarding such Holder is as set forth in the Prospectus delivered by such Holder in connection with such disposition, and that such Prospectus does not as of the date of
such Prospectus contain any untrue statement of a material fact regarding such Holder or omit to state any material fact regarding such Holder necessary to make the statements in such Prospectus, in the light of the circumstances under which they
were made, not misleading, solely to the extent such facts are based upon information regarding such Holder furnished in writing to the Company by such Holder for use in such Prospectus. 

5.    Registration Expenses. All fees and expenses incident to the Company’s performance of or compliance with
its obligations under this Agreement (excluding any underwriting discounts and selling commissions) shall be borne by the Company whether or not any Registrable Securities are sold pursuant to a Registration Statement. The fees and expenses referred
to in the foregoing sentence shall include, without limitation, (i) all registration and filing fees (including, without limitation, fees and expenses (A) with respect to filings required to be made with the Principal Market on which the
Common Stock is then listed for trading, and (B) in compliance with applicable state securities or Blue Sky laws), (ii) printing expenses (including, without limitation, expenses of printing certificates for Registrable Securities and of
printing prospectuses if the printing of prospectuses is reasonably requested by the holders of a majority of the Registrable Securities included in the Registration Statement), (iii) messenger, telephone and delivery expenses, (iv) reasonable
fees and disbursements of counsel for the Company, (v) 

  
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Securities Act liability insurance, if the Company so desires such insurance, and (vi) reasonable fees and expenses of all other Persons retained by the Company in connection with the
consummation of the transactions contemplated by this Agreement. In addition, the Company shall be responsible for all of its internal expenses incurred in connection with the consummation of the transactions contemplated by this Agreement
(including, without limitation, all salaries and expenses of its officers and employees performing legal or accounting duties), the expense of any annual audit and the fees and expenses incurred in connection with the listing of the Registrable
Securities on any securities exchange as required hereunder. In no event shall the Company be responsible for any broker or similar commissions of any Holder or, except to the extent provided for in the Transaction Documents, any legal fees or other
costs of the Holders. 
 6.    Indemnification. 

(a)    Indemnification by the Company. The Company shall, notwithstanding any termination of this Agreement,
indemnify and hold harmless each Holder, the officers, directors, agents, partners, members, stockholders and employees of each Holder, each Person who controls any such Holder (within the meaning of Section 15 of the Securities Act or
Section 20 of the Exchange Act) and the officers, directors, agents, partners, members, stockholders and employees of each such controlling Person, to the fullest extent permitted by applicable law, from and against any and all losses, claims,
damages, liabilities, costs (including, without limitation, reasonable costs of preparation and reasonable attorneys’ fees) and expenses (collectively, “Losses”), as incurred, arising out of or relating to any untrue or alleged
untrue statement of a material fact contained in any Registration Statement, any Prospectus or any form of prospectus or in any amendment or supplement thereto (it being understood that the Holder has approved Annex A hereto for this
purpose), or arising out of or relating to any omission or alleged omission of a material fact required to be stated therein or necessary to make the statements therein (in the case of any Prospectus or form of prospectus or supplement thereto, in
light of the circumstances under which they were made) not misleading, except to the extent, but only to the extent, that (1) such untrue statements, alleged untrue statements, omissions or alleged omissions are based solely upon information
regarding such Holder furnished in writing to the Company by such Holder expressly for use therein, or to the extent that such information relates to such Holder or such Holder’s proposed method of distribution of Registrable Securities and was
reviewed and expressly approved in writing by such Holder expressly for use in the Registration Statement, such Prospectus or such form of Prospectus or in any amendment or supplement thereto (it being understood that the Holder has approved
Annex A hereto for this purpose) or (2) in the case of an occurrence of an event of the type specified in Section 3(c)(ii)-(v), the use by such Holder of an outdated or defective Prospectus after the Company has validly notified
such Holder in writing (in accordance with Section 7(h) below) that the Prospectus is outdated or defective and prior to the receipt by such Holder of an Advice (as defined below) or an amended or supplemented Prospectus, but only if and to the
extent that following the receipt of the Advice or the amended or supplemented Prospectus the misstatement or omission giving rise to such Loss would have been corrected. The Company shall notify the Holders promptly of the institution, threat or
assertion of any Proceeding of which the Company is aware in connection with the transactions contemplated by this Agreement. 

  
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 (b)    Indemnification by Holders. Each Holder shall,
notwithstanding any termination of this Agreement, severally and not jointly, indemnify and hold harmless the Company, its directors, officers, agents and employees, each Person who controls the Company (within the meaning of Section 15 of the
Securities Act and Section 20 of the Exchange Act), and the directors, officers, agents, partners, members, stockholders or employees of such controlling Persons, to the fullest extent permitted by applicable law, from and against all Losses,
as incurred, arising solely out of or based solely upon: (x) for so long as the Company is not a “Seasoned Issuer” and the prospectus delivery requirements of the Securities Act apply to sales by such Holder, such Holder’s
failure to comply with the prospectus delivery requirements of the Securities Act or (y) any untrue statement of a material fact contained in any Registration Statement, any Prospectus, or any form of prospectus, or in any amendment or
supplement thereto, or arising solely out of or based solely upon any omission of a material fact required to be stated therein or necessary to make the statements therein (in the case of any Prospectus, or any form of prospectus or supplement
thereto, in light of the circumstances under which they were made) not misleading to the extent, but only to the extent that, (1) such untrue statements or omissions are based solely upon information regarding such Holder furnished in writing
to the Company by such Holder expressly for use therein, or to the extent that such information relates to such Holder or such Holder’s proposed method of distribution of Registrable Securities and was reviewed and expressly approved in writing
by such Holder expressly for use in the Registration Statement, such Prospectus or such form of Prospectus or in any amendment or supplement thereto (it being understood that the Holder has approved Annex A hereto for this purpose) or (2) in
the case of an occurrence of an event of the type specified in Section 3(c)(ii)-(v), the use by such Holder of an outdated or defective Prospectus after the Company has validly notified such Holder in writing (in accordance with
Section 7(h) below) that the Prospectus is outdated or defective and prior to the receipt by such Holder of an Advice or an amended or supplemented Prospectus, but only if and to the extent that following the receipt of the Advice or the
amended or supplemented Prospectus the misstatement or omission giving rise to such Loss would have been corrected. In no event shall the liability of any selling Holder hereunder be greater in amount than the dollar amount of the net proceeds
received by such Holder upon the sale of the Registrable Securities giving rise to such indemnification obligation. 

(c)    Conduct of Indemnification Proceedings. If any Proceeding shall be brought or asserted against any Person
entitled to indemnity hereunder (an “Indemnified Party”), such Indemnified Party shall promptly notify the Person from whom indemnity is sought (the “Indemnifying Party”) in writing, and the Indemnifying Party shall
assume the defense thereof, including the employment of counsel reasonably satisfactory to the Indemnified Party and the payment of all fees and expenses incurred in connection with defense thereof; provided, that the failure of any
Indemnified Party to give such notice shall not relieve the Indemnifying Party of its obligations or liabilities pursuant to this Agreement, except (and only) to the extent that it shall be finally determined by a court of competent jurisdiction
(which determination is not subject to appeal or further review) that such failure shall have proximately and materially adversely prejudiced the Indemnifying Party. 

An Indemnified Party shall have the right to employ separate counsel in any such Proceeding and to participate in the defense thereof, but the
fees and expenses of such counsel shall be at the expense of such Indemnified Party or Parties unless: (1) the Indemnifying Party has agreed in writing to pay such fees and expenses; (2) the Indemnifying Party shall have failed promptly to
assume the defense of such Proceeding and to employ counsel reasonably satisfactory to such Indemnified Party in any such Proceeding; or (3) the named parties to any such Proceeding 

  
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(including any impleaded parties) include both such Indemnified Party and the Indemnifying Party, and such Indemnified Party shall have been advised by counsel that a conflict of interest is
likely to exist if the same counsel were to represent such Indemnified Party and the Indemnifying Party (in which case, if such Indemnified Party notifies the Indemnifying Party in writing that it elects to employ separate counsel at the expense of
the Indemnifying Party, the Indemnifying Party shall not have the right to assume the defense thereof and such counsel shall be at the expense of the Indemnifying Party); provided, that the Indemnifying Party shall not be liable for the fees
and expenses of more than one separate firm of attorneys at any time for all Indemnified Parties pursuant to this Section 6(c). The Indemnifying Party shall not be liable for any settlement of any such Proceeding effected without its written
consent, which consent shall not be unreasonably withheld. No Indemnifying Party shall, without the prior written consent of the Indemnified Party, effect any settlement of any pending Proceeding in respect of which any Indemnified Party is a party,
unless such settlement includes an unconditional release of such Indemnified Party from all liability on claims that are the subject matter of such Proceeding. Each Indemnified Party shall furnish such information regarding itself or the claim in
question as an Indemnifying Party may reasonably request in writing and as shall be reasonably required in connection with defense of such claim and litigation resulting therefrom. 

All fees and expenses of the Indemnified Party (including reasonable fees and expenses to the extent incurred in connection with investigating
or preparing to defend such Proceeding in a manner not inconsistent with this Section) shall be paid to the Indemnified Party, as incurred, within ten Trading Days of written notice thereof to the Indemnifying Party (regardless of whether it is
ultimately determined that an Indemnified Party is not entitled to indemnification hereunder; provided, that the Indemnifying Party may require such Indemnified Party to undertake to reimburse all such fees and expenses to the extent it is
finally judicially determined that such Indemnified Party is not entitled to indemnification hereunder). 

(d)    Contribution. If a claim for indemnification under Section 6(a) or 6(b) is unavailable to an
Indemnified Party (by reason of public policy or otherwise), then each Indemnifying Party, in lieu of indemnifying such Indemnified Party, shall contribute to the amount paid or payable by such Indemnified Party as a result of such Losses, in such
proportion as is appropriate to reflect the relative fault of the Indemnifying Party and Indemnified Party in connection with the actions, statements or omissions that resulted in such Losses as well as any other relevant equitable considerations.
The relative fault of such Indemnifying Party and Indemnified Party shall be determined by reference to, among other things, whether any action in question, including any untrue or alleged untrue statement of a material fact or omission or alleged
omission of a material fact, has been taken or made by, or relates to information supplied by, such Indemnifying Party or Indemnified Party, and the parties’ relative intent, knowledge, access to information and opportunity to correct or
prevent such action, statement or omission. The amount paid or payable by a party as a result of any Losses shall be deemed to include, subject to the limitations set forth in Section 6(c), any reasonable attorneys’ or other reasonable
fees or expenses incurred by such party in connection with any Proceeding to the extent such party would have been indemnified for such fees or expenses if the indemnification provided for in this Section was available to such party in accordance
with its terms. 

  
 11 

 The parties hereto agree that it would not be just and equitable if contribution pursuant to
this Section 6(d) were determined by pro rata allocation or by any other method of allocation that does not take into account the equitable considerations referred to in the immediately preceding paragraph. Notwithstanding the provisions of
this Section 6(d), no Holder shall be required to contribute, in the aggregate, any amount in excess of the amount by which the proceeds actually received by such Holder from the sale of the Registrable Securities subject to the Proceeding
exceeds the amount of any damages that such Holder has otherwise been required to pay by reason of such untrue or alleged untrue statement or omission or alleged omission. No person guilty of fraudulent misrepresentation (within the meaning of
Section 11(f) of the Securities Act) shall be entitled to contribution from any person who was not guilty of such fraudulent misrepresentation. 

The indemnity and contribution agreements contained in this Section 6 are in addition to any liability that the Indemnifying Parties may
have to the Indemnified Parties and are not in diminution or limitation of the indemnification provisions under the Purchase Agreement. 

7.    Miscellaneous. 

(a)    Remedies. In the event of a breach by the Company or by a Holder, of any of their obligations under this
Agreement, each Holder or the Company, as the case may be, in addition to being entitled to exercise all rights granted by law and under this Agreement, including recovery of damages, will be entitled to specific performance of its rights under this
Agreement. The Company and each Holder agree that monetary damages would not provide adequate compensation for any losses incurred by reason of a breach by it of any of the provisions of this Agreement and hereby further agree that, in the event of
any action for specific performance in respect of such breach, it shall waive the defense that a remedy at law would be adequate. 

(b)    Compliance. Each Holder covenants and agrees that it will comply with the prospectus delivery requirements
of the Securities Act as applicable to it in connection with sales of Registrable Securities pursuant to the Registration Statement. 

(c)    Discontinued Disposition. Each Holder agrees by its acquisition of such Registrable Securities that, upon
receipt of a notice from the Company of the occurrence of any event of the kind described in Section 3(c), such Holder will forthwith discontinue disposition of such Registrable Securities under the Registration Statement until such
Holder’s receipt of the copies of the supplemented Prospectus and/or amended Registration Statement or until it is advised in writing (the “Advice”) by the Company that the use of the applicable Prospectus may be resumed, and,
in either case, has received copies of any additional or supplemental filings that are incorporated or deemed to be incorporated by reference in such Prospectus or Registration Statement. The Company may provide appropriate stop orders to enforce
the provisions of this paragraph. For the avoidance of doubt, nothing in this Section 7(c) shall prohibit the Holder from selling Registrable Securities in accordance with any available exemption from registration under the Securities Act in
the event of its receipt of a notice of the occurrence of an event described in 3(c), subject to compliance with all applicable securities laws (including without limitation Rule 10b-5 promulgated under the
Exchange Act). 
 (d)    Furnishing of Information. Each Holder shall furnish in writing to the Company such
information regarding itself, the Registrable Securities held by it and the intended method of disposition of the Registrable Securities held by it, as shall be reasonably requested by the Company to effect the registration of such Registrable
Securities and shall execute such documents in connection with such registration as the Company may reasonably request. 

  
 12 

 (e)    Piggy-Back Registrations. If at any time during the
Effectiveness Period, except as contemplated by Section 2(b) hereof, there is not an effective Registration Statement covering all of the Registrable Securities and the Company shall determine to prepare and file with the Commission a
registration statement relating to an offering for its own account or the account of others under the Securities Act of any of its equity securities, other than on Form S-4 or Form S-8 (each as promulgated under the Securities Act) or their then equivalents relating to equity securities to be issued solely in connection with any acquisition of any entity or business or equity securities
issuable in connection with stock option or other employee benefit plans, then the Company shall send to each Holder a written notice of such determination and, if within 15 days after the date of such notice, any such Holder shall so request in
writing, the Company shall include in such registration statement all or any part of such Registrable Securities such Holder requests to be registered; provided, however, that the Company shall not be required to register any
Registrable Securities pursuant to this Section 7(e) that are eligible for resale pursuant to Rule 144 promulgated under the Securities Act without volume limitation or that are the subject of a then effective Registration Statement;
provided, further, however, if there is not an effective Registration Statement covering all of the Registrable Securities during the Effectiveness Period, the Company may file a registration statement with the Commission to
register equity securities of the Company to be sold on a primary basis, provided that the Company does not sell any such shares until there is an effective Registration Statement covering all of the Registrable Securities. The Company shall have
the right to terminate or withdraw any registration initiated by it under this Section 7(e) prior to the effectiveness of such registration whether or not any Holder has elected to include securities in such registration. 

(f)    Amendments and Waivers. No provision of this Agreement may be waived or amended except in a written
instrument signed by the Company and the Holder or Holders (as applicable) of no less than a majority of the then outstanding Registrable Securities (the “Major Holders”). The Company shall provide prior notice to all Holders of any
proposed waiver or amendment. No waiver of any default with respect to any provision, condition or requirement of this Agreement shall be deemed to be a continuing waiver in the future or a waiver of any subsequent default or a waiver of any other
provision, condition or requirement hereof, nor shall any delay or omission of either party to exercise any right hereunder in any manner impair the exercise of any such right. 

(g)    Termination of Registration Rights. For the avoidance of doubt, it is expressly agreed and understood that
(i) in the event that there are no Registrable Securities outstanding as of a Filing Date, then the Company shall have no obligation to file, cause to be declared effective (or becomes automatically effective, if the Company is a Well-Known
Seasoned Issuer and files an Automatic Shelf Registration Statement pursuant to this Agreement) or to keep effective any Registration Statement hereunder (including any Registration Statement previously filed pursuant to this Agreement) and
(ii) all registration rights granted to the Holders hereunder (including the rights set forth in Sections 7(c) and 7(f)), shall terminate in their entirety effective on the first date on which there shall cease to be any Registrable Securities
outstanding. If not previously terminated pursuant to the foregoing sentence, it is expressly agreed and understood that all registration rights granted to the Holder pursuant to this Agreement shall terminate as to

  
 13 

 
the Holder on the earlier of (a) such time following the date that is five (5) years following the date of this Agreement that the Holders own in the aggregate less than 25% of the
number of Registrable Securities that the Holders owned in the aggregate as of the date hereof (as adjusted for stock splits, combinations, dividends, recapitalizations and the like) and (b) the date that is ten (10) years following the
date of this Agreement. 
 (h)    Notices. All notices, requests, consents and other communications hereunder
shall be in writing, shall be sent by confirmed electronic mail, or mailed by first-class registered or certified airmail, or nationally recognized overnight express courier, postage prepaid, and shall be deemed given when so sent in the case of
electronic mail transmission, or when so received in the case of mail or courier, and addressed as follows: 
 if to the Company, to: 

Codexis, Inc. 
 ##### 

Email: ##### 
 with a copy (which
shall not constitute notice) to: 
 Latham & Watkins LLP 

##### 
 Email: ##### 

 

			
	If to a Purchaser:	  	To the address set forth under such Purchaser’s name on the signature pages hereto
		
	 If to any other
 Person who is then the
registered
 Holder:
	  	To the address of such Holder as it appears in the stock transfer books of the Company

 or such other address as may be designated in writing hereafter, in the same manner, by such Person. 

(i)    Successors and Assigns. This Agreement shall inure to the benefit of and be binding upon the successors and
permitted assigns of each of the parties and shall inure to the benefit of each Holder. The rights of the Holder hereunder, including the right to have the Company register Registrable Securities pursuant to this Agreement, may be assigned by the
Holder (i) at any time, to an Affiliate of the Holder or (ii) subject to transfer restrictions set forth in the Purchase Agreement, to any third party in connection with a transfer of Registrable Securities; but only if such transferee
executes a Joinder in the form attached as Exhibit A hereto. Nothing herein shall be deemed to permit any assignment, transfer or other disposition of Registrable Securities in violation of the terms of applicable law and any applicable
agreement. If any transferee of any Holder shall acquire Registrable Securities, in any manner, whether by operation of law or otherwise, such Registrable Securities shall be held subject to and benefit from

  
 14 

 
all of the terms of this Agreement, and by taking and holding such Registrable Securities, such person shall be conclusively deemed to have agreed to be bound by and to perform all of the terms
and provisions of this Agreement and such person shall be entitled to receive the benefits hereof. 

(j)    Execution and Counterparts. This Agreement may be executed in any number of counterparts, each of which when
so executed shall be deemed to be an original and, all of which taken together shall constitute one and the same Agreement and shall become effective when counterparts have been signed by each party and delivered to the other party, it being
understood that both parties need not sign the same counterpart. In the event that any signature is delivered by facsimile transmission or by e-mail delivery of a “.pdf” format data file, such
signature shall create a valid binding obligation of the party executing (or on whose behalf such signature is executed) the same with the same force and effect as if such facsimile or “.pdf” signature were the original thereof. 

(k)    Governing Law; Venue. All questions concerning the construction, validity, enforcement and
interpretation of this Agreement shall be governed by and construed and enforced in accordance with the internal laws of the State of California, without regard to the principles of conflicts of law thereof. With respect to any disputes arising out
of or related to this Agreement, the parties consent to the exclusive jurisdiction of, and venue in, the state courts in San Mateo County in the State of California (or in the event of exclusive federal jurisdiction, the courts of the Northern
District of California). Each party hereby irrevocably waives personal service of process and consents to process being served in any such suit, action or proceeding by mailing a copy thereof via registered or certified mail or overnight delivery
(with evidence of delivery) to such party at the address in effect for notices to it under this Agreement and agrees that such service shall constitute good and sufficient service of process and notice thereof. Nothing contained herein shall be
deemed to limit in any way any right to serve process in any other manner permitted by law. EACH PARTY HERETO HEREBY IRREVOCABLY WAIVES, TO THE FULLEST EXTENT PERMITTED BY APPLICABLE LAW, ANY AND ALL RIGHT TO TRIAL BY JURY IN ANY LEGAL PROCEEDING
ARISING OUT OF OR RELATING TO THIS AGREEMENT OR THE TRANSACTIONS CONTEMPLATED HEREBY. 
 (l)    Cumulative
Remedies. The remedies provided herein are cumulative and not exclusive of any remedies provided by law. 

(m)    Severability. If any term, provision, covenant or restriction of this Agreement is held by a court of
competent jurisdiction to be invalid, illegal, void or unenforceable, the remainder of the terms, provisions, covenants and restrictions set forth herein shall remain in full force and effect and shall in no way be affected, impaired or invalidated,
and the parties hereto shall use their reasonable best efforts to find and employ an alternative means to achieve the same or substantially the same result as that contemplated by such term, provision, covenant or restriction. It is hereby
stipulated and declared to be the intention of the parties that they would have executed the remaining terms, provisions, covenants and restrictions without including any of such that may be hereafter declared invalid, illegal, void or
unenforceable. 
 (n)    Use of Terms. The parties agree and acknowledge that when, in this Agreement, the
Company is required to use its reasonable best efforts to perform any covenant under this Agreement, such requirement shall not obligate the Company, in the reasonable judgment of the disinterested members of its Board of Directors, to perform any
act that will have a material adverse effect on the Company. 

  
 15 

 (o)    Headings. The headings in this Agreement are for
convenience of reference only and shall not limit or otherwise affect the meaning hereof. 
 (p)    Independent
Nature of Purchasers’ Obligations and Rights. The obligations of each Purchaser hereunder is several and not joint with the obligations of any other Purchaser hereunder, and no Purchaser shall be responsible in any way for the performance
of the obligations of any other Purchaser hereunder. The decision of each Purchaser to purchase Securities pursuant to the Transaction Documents has been made independently of any other Purchaser. Nothing contained herein or in any other agreement
or document delivered at any closing, and no action taken by any Purchaser pursuant hereto or thereto, shall be deemed to constitute the Purchasers as a partnership, an association, a joint venture or any other kind of entity, or create a
presumption that the Purchasers are in any way acting in concert with respect to such obligations or the transactions contemplated by this Agreement. Each Purchaser acknowledges that no other Purchaser has acted as agent for such Purchaser in
connection with making its investment hereunder and that no Purchaser will be acting as agent of such Purchaser in connection with monitoring its investment in the Securities or enforcing its rights under the Transaction Documents. Each Purchaser
shall be entitled to protect and enforce its rights, including without limitation the rights arising out of this Agreement, and it shall not be necessary for any other Purchaser to be joined as an additional party in any proceeding for such purpose.

 [Signature pages follow] 

  
 16 

 EXECUTION VERSION 

 

 IN WITNESS WHEREOF, the parties have executed this Registration Rights Agreement as of the
date first written above. 
  

			
	CODEXIS, INC.
		
	By:	 	/s/ John Nicols
	Name:	 	John Nicols
	Title:	 	President and Chief Executive Officer

  
 SIGNATURE PAGE TO
CODEXIS, INC. REGISTRATION RIGHTS AGREEMENT 

 IN WITNESS WHEREOF, the parties have executed this Registration Rights Agreement as of the
date first written above. 
  

			
	PURCHASERS:
	
	CASDIN PARTNERS MASTER FUND, L.P.
	By:	 	Casdin Partners GP, LLC, its General Partner
	By:	 	 /s/ Eli Casdin

	Name:	 	Eli Casdin
	Title:	 	Managing Member
		
	Address:	 	
	#####	 	
	Email:	 	#####

  
 SIGNATURE PAGE TO
CODEXIS, INC. REGISTRATION RIGHTS AGREEMENT 

 ANNEX A 

PLAN OF DISTRIBUTION 
 We
are registering the shares of common stock issued to the selling stockholder[s] to permit the resale of these shares of common stock by the holder of the shares of common stock from time to time after the date of this prospectus. We will not receive
any of the proceeds from the sale by the selling stockholder[s] of the shares of common stock. We will bear all fees and expenses incident to our obligation to register the shares of common stock. 

The selling stockholder[s] and any of its transferees, donees, pledgees or other successors in interest may, from time to time, sell all or a
portion of the shares of common stock beneficially owned by the selling stockholder[s] and offered hereby from time to time directly or through one or more underwriters, broker-dealers or agents. If the shares of common stock are sold through
underwriters or broker-dealers, the selling stockholder[s] will be responsible for underwriting discounts or commissions or agent’s commissions. The shares of common stock may be sold on any national securities exchange or quotation service on
which the securities may be listed or quoted at the time of sale, in the over-the-counter market or in transactions otherwise than on these exchanges or systems or in
the over-the-counter market and in one or more transactions at fixed prices, at prevailing market prices at the time of the sale, at varying prices determined at the
time of sale, or at negotiated prices. These sales may be effected in transactions, which may involve crosses or block transactions. The selling stockholder[s] may use any one or more of the following methods when selling shares: 

 

	 	•	 	 ordinary brokerage transactions and transactions in which the broker-dealer solicits purchasers;

  

	 	•	 	 block trades in which the broker-dealer will attempt to sell the shares as agent but may position and resell a
portion of the block as principal to facilitate the transaction; 

  

	 	•	 	 purchases by a broker-dealer as principal and resale by the broker-dealer for its account; 

 

	 	•	 	 an exchange distribution in accordance with the rules of the applicable exchange; 

 

	 	•	 	 privately negotiated transactions; 

 

	 	•	 	 settlement of short sales entered into after the effective date of the registration statement of which this
prospectus is a part; 

  

	 	•	 	 in transactions through broker-dealers that agree with the selling stockholder[s] to sell a specified number of
such shares at a stipulated price per share; 

  

	 	•	 	 through the writing or settlement of options or other hedging transactions, whether such options are listed on an
options exchange or otherwise; 

  

	 	•	 	 through one or more underwritten offerings on a firm commitment or best efforts basis; 

  
 Annex A, Page 1 

	 	•	 	 a combination of any such methods of sale; and 

 

	 	•	 	 any other method permitted pursuant to applicable law. 

The selling stockholder[s] also may resell all or a portion of the shares in open market transactions in reliance upon Rule 144 under the
Securities Act, as permitted by that rule, or Section 4(a)(1) under the Securities Act, if available, rather than under this prospectus, provided that the selling stockholder[s] meet[s] the criteria and conforms to the requirements of those
provisions. 
 Broker-dealers engaged by the selling stockholder[s] may arrange for other broker-dealers to participate in sales. If the
selling stockholder[s] effect[s] such transactions by selling shares of common stock to or through underwriters, broker-dealers or agents, such underwriters, broker-dealers or agents may receive commissions in the form of discounts, concessions or
commissions from the selling stockholder[s] or commissions from purchasers of the shares of common stock for whom they may act as agent or to whom they may sell as principal. Such commissions will be in amounts to be negotiated, but, except as set
forth in a supplement to this prospectus, in the case of an agency transaction will not be in excess of a customary brokerage commission in compliance with FINRA Rule 2121 (and any successor); and in the case of a principal transaction a markup
or markdown in compliance with FINRA 2121. 
 In connection with sales of the shares of common stock or otherwise, the selling
stockholder[s] may enter into hedging transactions with broker-dealers or other financial institutions, which may in turn engage in short sales of the shares of common stock in the course of hedging in positions they assume. The selling
stockholder[s] may also sell shares of common stock short and if such short sale shall take place after the date that the registration statement of which this prospectus is a part is declared effective by the Commission, the selling stockholder[s]
may deliver shares of common stock covered by this prospectus to close out short positions and to return borrowed shares in connection with such short sales. The selling stockholder[s] may also loan or pledge shares of common stock to broker-dealers
that in turn may sell such shares, to the extent permitted by applicable law. The selling stockholder[s] may also enter into option or other transactions with broker-dealers or other financial institutions or the creation of one or more derivative
securities which require the delivery to such broker-dealer or other financial institution of shares offered by this prospectus, which shares such broker-dealer or other financial institution may resell pursuant to this prospectus (as supplemented
or amended to reflect such transaction). 
 The selling stockholder[s] may, from time to time, pledge or grant a security interest in some
or all of the shares of common stock owned by the selling stockholder[s] and, if the selling stockholder[s] default[s] in the performance of its secured obligations, the pledgees or secured parties may offer and sell the shares of common stock from
time to time pursuant to this prospectus or any amendment to this prospectus under Rule 424(b)(3) or other applicable provision of the Securities Act, as amended, amending, if necessary, the list of selling stockholder[s] to include the
pledgee, transferee or other successors in interest as a selling stockholder[s] under this prospectus. The selling stockholder[s] also may transfer and donate the shares of common stock in other circumstances in which case the transferees, donees,
pledgees or other successors in interest will be the selling beneficial owners for purposes of this prospectus. 

  
 Annex A, Page 2 

 The selling stockholder[s] and any broker-dealer or agents participating in the distribution
of the shares of common stock may be deemed to be “underwriters” within the meaning of Section 2(11) of the Securities Act in connection with such sales. In such event, any commissions paid, or any discounts or concessions allowed to,
any such broker-dealer or agent and any profit on the resale of the shares purchased by them may be deemed to be underwriting commissions or discounts under the Securities Act. If the selling stockholder[s] [is][are] deemed to be an
“underwriter” within the meaning of Section 2(11) of the Securities Act, it will be subject to the applicable prospectus delivery requirements of the Securities Act and may be subject to certain statutory liabilities of, including but
not limited to, Sections 11, 12 and 17 of the Securities Act and Rule 10b-5 under the Securities Exchange Act of 1934, as amended, or the Exchange Act. 

[The][Each] selling stockholder has informed us that it is not a registered broker-dealer and does not have any written or oral agreement or
understanding, directly or indirectly, with any person to distribute the common stock. Upon our being notified in writing by the selling stockholder[s] that any material arrangement has been entered into with a broker-dealer for the sale of common
stock through a block trade, special offering, exchange distribution or secondary distribution or a purchase by a broker-dealer, a supplement to this prospectus will be filed, if required, pursuant to Rule 424(b) under the Securities Act,
disclosing: 
  

	 	•	 	 the name of the selling stockholder[s] and of the participating broker-dealer(s), 

 

	 	•	 	 the number of shares involved, 

 

	 	•	 	 the price at which such the shares of common stock were sold, 

 

	 	•	 	 the commissions paid or discounts or concessions allowed to such broker-dealer(s), where applicable,

  

	 	•	 	 that such broker-dealer(s) did not conduct any investigation to verify the information set out or incorporated by
reference in this prospectus, and 

  

	 	•	 	 other facts material to the transaction. 

In no event shall any broker-dealer receive fees, commissions and markups, which, in the aggregate, would exceed eight percent (8%). 

Under the securities laws of some states, the shares of common stock may be sold in such states only through registered or licensed brokers or
dealers. In addition, in some states the shares of common stock may not be sold unless such shares have been registered or qualified for sale in such state or an exemption from registration or qualification is available and is complied with. 

There can be no assurance that the selling stockholder[s] will sell any or all of the shares of common stock registered pursuant to the
registration statement, of which this prospectus forms a part. 
 The selling stockholder[s] and any other person participating in such
distribution will be subject to applicable provisions of the Exchange Act, as amended, and the rules and regulations thereunder, including, without limitation, Regulation M of the Exchange Act, which may limit the

  
 Annex A, Page 3 

 
timing of purchases and sales of any of the shares of common stock by the selling stockholder[s] and any other participating person. Regulation M may also restrict the ability of any person
engaged in the distribution of the shares of common stock to engage in market-making activities with respect to the shares of common stock. All of the foregoing may affect the marketability of the shares of common stock and the ability of any person
or entity to engage in market-making activities with respect to the shares of common stock. 
 We will pay all expenses of the registration
of the shares of common stock pursuant to the registration rights agreement, including, without limitation, Securities and Exchange Commission filing fees and expenses of compliance with state securities or “blue sky” laws;
provided, however, that the selling stockholder[s] will pay all underwriting discounts and selling commissions, if any. We will indemnify the selling stockholder[s] against certain liabilities, including some liabilities under the
Securities Act, in accordance with the registration rights agreement, or the selling stockholder[s] will be entitled to contribution. We may be indemnified by the selling stockholder[s] against civil liabilities, including liabilities under the
Securities Act, that may arise from any written information furnished to us by the selling stockholder[s] specifically for use in this prospectus, in accordance with the registration rights agreement, or we may be entitled to contribution. 

To the extent required, this prospectus may be amended and/or supplemented from time to time to describe a specific plan of distribution. 

  
 Annex A, Page 4 

 EXHIBIT A 

FORM OF JOINDER 
 THIS JOINDER is made on
this      day of             , 20     
 BETWEEN 

(1) (the “New Party”); 
 AND 

(2) [NAME OF THEN-CURRENT HOLDER] (the “Current Party”); 

AND 
 (3) CODEXIS, INC. (the “Company”). 

WHEREAS, a Registration Rights Agreement was entered into on June 20, 2019 by and among, inter alia, the Current Party and the Company (the
“Registration Rights Agreement”), a copy of which the New Party hereby confirms that it has been supplied with and acknowledges the terms therein. 

NOW IT IS AGREED as follows: 

1.    In this Joinder, unless the context otherwise requires, words and expressions respectively defined or construed in
the Registration Rights Agreement shall have the same meanings when used or referred to herein. 
 2.    The New Party
hereby accedes to and ratifies the Registration Rights Agreement and covenants and agrees with the Current Party and the Company to be bound by the terms of the Registration Rights Agreement as a “Purchaser” and to duly and punctually
perform and discharge all liabilities and obligations whatsoever from time to time to be performed or discharged by it under or by virtue of the Registration Rights Agreement in all respects as if named as a party therein. 

3.    The Company covenants and agrees that the New Party shall be entitled to all the benefits of the terms and
conditions of the Registration Rights Agreement to the intent and effect that the New Party shall be deemed, with effect from the date on which the New Party executes this Joinder, to be a party to the Registration Rights Agreement as a
“Purchaser.” 
 4.    This Joinder shall hereafter be read and construed in conjunction and as one document
with the Registration Rights Agreement and references in the Registration Rights Agreement to “the Agreement” or “this Agreement,” and references in all other instruments and documents executed thereunder or pursuant thereto to
the Registration Rights Agreement, shall for all purposes refer to the Registration Rights Agreement incorporating and as supplemented by this Joinder. 

  
 Exhibit A, Page 1 

 5.    THIS JOINDER SHALL BE GOVERNED BY AND CONSTRUED IN ACCORDANCE WITH
THE LAWS OF THE STATE OF CALIFORNIA, WITHOUT REGARD TO THE PRINCIPLES OF CONFLICTS OF LAW THEREOF. 
 6.    Any action
or proceeding against any party hereto relating in any way to this Joinder or the transactions contemplated hereby may be brought and enforced in the state courts in San Mateo County in the State of California (or in the event of exclusive federal
jurisdiction, the courts of the Northern District of California), and each party, on behalf of itself and its respective successors and assigns, irrevocably consents to the jurisdiction of each such court in respect of any such action or proceeding.
Each party, on behalf of itself and its respective successors and assigns, irrevocably consents to the service of process in any such action or proceeding by the mailing of copies thereof by registered or certified mail, postage prepaid, return
receipt requested, to such person or entity at the address for such person or entity set forth in Section 7(h) of the Registration Rights Agreement or such other address such person or entity shall notify the other in writing. The foregoing
shall not limit the right of any person or entity to serve process in any other manner permitted by law or to bring any action or proceeding, or to obtain execution of any judgment, in any other jurisdiction. 

7.    Each party, on behalf of itself and its respective successors and assigns, hereby irrevocably waives any objection
that it may now or hereafter have to the laying of venue of any action or proceeding arising under or relating to this Joinder or the transactions contemplated hereby in any court located in San Mateo County in the State of California (or in the
event of exclusive federal jurisdiction, the courts of the Northern District of California). Each party, on behalf of itself and its respective successors and assigns, hereby irrevocably waives any claim that a court located in the State of
California is not a convenient forum for any such action or proceeding. 
 8.    Each party, on behalf of itself and its
respective successors and assigns, hereby irrevocably waives, to the fullest extent permitted by applicable United States federal and state law, all immunity from jurisdiction, service of process, attachment (both before and after judgment) and
execution to which he might otherwise be entitled in any action or proceeding relating in any way to this Joinder or the transactions contemplated hereby in the courts of the State of California, of the United States or of any other country or
jurisdiction, and hereby waives any right he might otherwise have to raise or claim or cause to be pleaded any such immunity at or in respect of any such action or proceeding. 

9.    The address of the undersigned for purposes of all notices under the Registration Rights Agreement is set forth
below. 
  

			
	[NEW PARTY]
		
	By:	 	  

	Name:	 	  

	Title:	 	  

	Address:	 	  

  
 Exhibit A, Page 2

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