Document:

Master Security Agreement between the Company and Oxford Finance Corporation

 Exhibit 10.21 
 Master Security Agreement No. 5081102 
 MASTER SECURITY AGREEMENT 
 No. 5081102 
 Dated as of
October 25, 2005 (“Agreement”) 
 THIS AGREEMENT is between Oxford Finance Corporation (together with its
successors and assigns, if any, “Secured Party”) and Codexis, Inc. (“Debtor”). Secured Party has an office at 133 N. Fairfax Street, Alexandria, VA 22314. Debtor is a corporation organized and
existing under the laws of the state of Delaware. Debtor’s mailing address and chief place of business is 200 Penobscot Drive, Redwood City, CA 94063. 
  

	1.	CREATION OF SECURITY INTEREST. 

 Debtor grants to
Secured Party, its successors and assigns, a security interest in and against all property listed on any collateral schedule now or in the future annexed to or made a part of this Agreement (“Collateral Schedule”), and in and
against all additions, attachments, accessories and accessions to such property, all substitutions, replacements or exchanges therefor, and all insurance and/or other proceeds thereof (all such property is individually and collectively called the
“Collateral”). This security interest is given to secure the payment and performance of all debts, obligations and liabilities of any kind whatsoever of Debtor to Secured Party, now existing or arising in the future,
including but not limited to the payment and performance of certain Promissory Notes from time to time identified on any Collateral Schedule (collectively “Notes” and each a “Note”), and any renewals,
extensions and modifications of such debts, obligations and liabilities (such Notes, debts, obligations and liabilities are called the “Indebtedness”). Debtor acknowledges that, notwithstanding that the Note(s) may be paid in
full, this Security Agreement shall continue to secure the payment and performance of all other debts, obligations and liabilities of any kind whatsoever of Debtor to Secured Party, now existing or arising in the future, and that Secured Party shall
be under no obligation to release the Collateral unless and until all Indebtedness of Debtor to Secured Party has been paid and satisfied; provided, however, Secured Party, in its sole and exclusive discretion, may elect to release some of the
Collateral without prejudice to Secured Party’s security interest in the remaining Collateral. 
  

	2.	REPRESENTATIONS, WARRANTIES AND COVENANTS OF DEBTOR. 

 Debtor represents, warrants and covenants as of the data of this Agreement and as of the date of each Collateral Schedule that: 
  

	 	(a)	Due Organization. Debtor’s exact legal name is as set forth in the preamble of this Agreement and Debtor is, and will remain, duly organized, existing and in good
standing under the laws of the State set forth in the preamble of this Agreement, has its chief executive offices at the location specified in the preamble, and is, and will remain duly qualified and licensed in every jurisdiction wherever necessary
to carry on its business and operations; 

  

	 	(b)	Power and Capacity to Enter Into and Perform Obligations. Debtor has adequate power and capacity to enter into, and to perform its obligations under this Agreement, each
Collateral Schedule, each Note and any other documents evidencing, or given in connection with, any of the Indebtedness (all of the foregoing are called the “Debt Documents”); 

  

					
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	 	(c)	Due Authorization. This Agreement and the other Debt Documents have been duly authorized, executed and delivered by Debtor and constitute legal, valid and binding agreements
enforceable in accordance with their terms, except to the extent that the enforcement of remedies may be limited under applicable bankruptcy and insolvency laws; 

  

	 	(d)	Approvals and Consents. No approval, consent or withholding of objections is required from any governmental authority or instrumentality with respect to the entry into, or
performance by Debtor of any of the Debt Documents, except any already obtained; 

  

	 	(e)	No Violations or Defaults. The entry into, and performance by, Debtor of the Debt Documents will not (i) violate any of the organizational documents of Debtor or any
judgment, order, law or regulation applicable to Debtor, or (ii) result in any breach of or constitute a default under any contract to which Debtor is a party, or result in the creation of any lien, claim or encumbrance on any of Debtor’s
property (except for liens in favor of Secured Party) pursuant to any indenture, mortgage, deed of trust, bank loan, credit agreement, or other agreement or instrument to which Debtor is a party; 

  

	 	(f)	Litigation. There are no suits or proceedings pending in court or before any commission, board or other administrative agency against or affecting Debtor which could, in the
aggregate, have a material adverse effect on Debtor, its business or operations, or its ability to perform its obligations under the Debt Documents, nor does Debtor have reason to believe that any such suits or proceedings are threatened;

  

	 	(g)	Solvency. The fair salable value of Debtor’s assets (including goodwill minus disposition costs) exceeds the fair value of its liabilities; the Debtor is not left with
unreasonably small capital after the transactions in this Agreement or any Collateral Schedule and Debtor is able to pay its debts (including trade debts) as they mature; 

  

	 	(h)	Financial Statements. All financial statements relating to Debtor that have been or may hereafter be delivered by Debtor to Secured Party present fairly in all material
respects Debtor’s financial condition as of the date thereof and Debtor’s results of operations for the period then ended, and since the date of the most recent financial statement, there has been no material adverse change in
Debtor’s financial condition; 

  

	 	(i)	Use of Collateral. The Collateral is not, and will not be, used by Debtor for personal, family or household purposes; 

  

					
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	 	(j)	Collateral in Good Condition and Repair. The Collateral is, and will remain, in good condition and repair and Debtor will not be negligent in its care and use;

  

	 	(k)	Location of Collateral. All of the tangible Collateral is located at the locations set forth on each Collateral Schedule. Debtor shall give the Secured Party 30 days prior
written notice of any relocation of any Collateral; 

  

	 	(l)	Ownership of Collateral. Debtor is, and will remain, the sole and lawful owner, and in possession of, the Collateral, and has the sole right and lawful authority to grant the
security interest described in this Agreement; 

  

	 	(m)	Encumbrances. The Collateral is, and will remain, free and clear of all liens, claims and encumbrances of any kind whatsoever, except for Permitted Liens;

  

	 	(n)	Intellectual Property Rights. Debtor will (i) protect, defend and maintain the validity and enforceability of the Intellectual Property and promptly advise Secured Party
in writing of material infringements and (ii) not allow any Intellectual Property material to Debtor’s business, as determined by Debtor in its good faith and reasonable discretion, to be abandoned, forfeited or dedicated to the public
without Secured Party’s written consent; 

  

	 	(o)	Taxes. All federal, state and local tax returns required to be filed by Debtor have been filed with the appropriate governmental agencies by the date due (including any
extensions) and all taxes due and payable by Debtor have been timely paid. Debtor will pay when due all taxes, assessments and other liabilities except as contested in good faith and by appropriate proceedings and for which adequate reserves have
been established; 

  

	 	(p)	No Defaults. No event or condition exists under any material agreement, instrument or document to which Debtor is a party or may be subject, or by which Debtor or any of its
properties are bound, which constitutes a default or an event of default thereunder, or will, with the giving of notice, passage of time, or both, would constitute a default or event of default thereunder; 

  

	 	(q)	Certification of Financial Information. All reports, certificates, schedules, notices and financial information submitted by Debtor to the Secured Party pursuant to this
Agreement shall be certified as true and correct by the president or chief financial officer of Debtor; 

  

	 	(r)	Notice of Material Adverse Change. Debtor shall give the Secured Party prompt written notice of any event, occurrence or other matter which (a) has resulted or may
result in a material adverse change in its financial condition or business operations of Debtor, or (b) which would impair the ability of Debtor to perform its obligations hereunder or under any of the other financing agreements to which it is
a party, or (c) which would impair the ability of Secured Party to enforce the Indebtedness or realize upon the Collateral; 

  

					
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	 	(s)	Change in Management. Debtor shall not, without giving prior written notice to Secured Party, change the persons holding the offices of Chief Executive Officer or Chief
Financial Officer; 

  

	 	(t)	Transactions with Affiliates. Debtor shall not, without the prior written consent of Secured Party, directly or indirectly enter into or permit to exist any material
transaction with any Affiliate of Debtor except for transactions that are in the ordinary course of Debtor’s business, upon fair and reasonable terms that are no less favorable to Debtor than would be obtained in an arm’s length
transaction with a nonaffiliated Person; 

  

	 	(u)	[intentionally omitted] 

  

	 	(v)	Perfection Certificate. Debtor has previously delivered to the Secured Party a certificate signed by the Debtor and entitled “Perfection Certificate” (the
“Perfection Certificate”). The Debtor represents and warrants to the Secured Party as follows: (a) the Debtor’s exact legal name is that indicated on the Perfection Certificate and on the signature page hereof,
(b) the Debtor is an organization of the type, and is organized in the jurisdiction set forth in the Perfection Certificate, (c) the Perfection Certificate accurately sets forth the Debtor’s organizational identification number or
accurately states that the Debtor has none, (d) the Perfection Certificate accurately sets forth the Debtor’s place of business or, if more than one, its chief executive office, as well as the Debtor’s mailing address, if different,
(e) all other information set forth on the Perfection Certificate pertaining to the Debtor is accurate and complete, and (f) that there has been no change in any information provided in the Perfection Certificate since the date on which it
was executed by the Debtor; 

  

	 	(w)	Primary Account and Wire Transfer Instructions. Debtor maintains its Primary Account (the “Primary Operating Account”) and the Wire Transfer
Instructions for the Primary Operating Account are as follows: 

 Wells Fargo Bank 
 P.O. Box 150, 400 Hamilton Ave. 
 Palo Alto, CA 94301 
 ABA No.: 121000248 
 Account No.: 403-0003362 
 Account Name: Codexis, Inc. 
 Debtor hereby agrees that Loans will be advanced to the account specified above
and regularly scheduled payments will be automatically debited from the same account; 
  

	 	(x)	[intentionally omitted] 

  

	 	(y)	 Notice of Investor Abandonment. Debtor shall give the Secured Party prompt written notice if (a) it is the clear intention of Debtor’s investors to
not continue to 

  

					
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fund the Debtor in the amounts and timeframe necessary to enable Debtor to satisfy the Indebtedness as it becomes due and payable or (b) there is a
material impairment in the perfection or priority of the Secured Party’s security interest in the Collateral; and 

  

	 	(z)	Indebtedness to Maxygen. Without the prior written consent of Secured Party, which consent shall not be unreasonably withheld or delayed, Debtor shall not create, incur,
assume or permit to exist any Indebtedness to Maxygen, Inc. (“Maxygen”) in excess of One Million, Two Hundred Twenty-Five Thousand Dollars ($1,225,000) in aggregate in any fiscal year, nor shall Debtor make any payments to Maxygen in any
fiscal year in excess of the lower of: (i) the aggregate of the fair market value of services provided by Maxygen to Debtor during such fiscal year, or (ii) the aggregate of One Million, Two Hundred Twenty-Five Thousand Dollars
($1,225,000). Notwithstanding the foregoing, Debtor shall be permitted to pay the balance of previously incurred, existing and anticipated Indebtedness to Maxygen up to a total amount of One Million, Five Hundred Thousand Dollars ($1,500,000) for
the period January 1, 2005 to December 31, 2005. 

  

	3.	COLLATERAL. 

 The Debtor covenants and agrees that,
so long as any of the Debt Documents shall remain in effect, or unless the Secured Party shall otherwise consent in writing: 
  

	 	(a)	Possession of Collateral; Inspection of Collateral. Until the declaration of any default, Debtor shall remain in possession of the Collateral, except as necessary for
maintenance and repair, except as specified in Section 3(c), and except that Secured Party shall have the right to possess (i) any chattel paper or instrument that constitutes a part of the Collateral, and (ii) any other Collateral in
which Secured Party’s security interest may be perfected only by possession. Secured Party may inspect any of the Collateral during normal business hours after giving Debtor reasonable prior notice. 

  

	 	(b)	Maintenance of Collateral. Debtor shall (i) use the Collateral only in its trade or business, (ii) maintain all of the Collateral in good operating order and
repair, normal wear and tear excepted, (iii) use and maintain the Collateral only in compliance with manufacturers recommendations and all applicable laws, and (iv) keep all of the Collateral free and clear of all liens, claims and
encumbrances (except for Permitted Liens). 

  

	 	(c)	 Disposition of Collateral. Secured Party does not authorize and Debtor agrees it shall not (i) part with possession of any of the Collateral (except to
Secured Party or for maintenance and repair), (ii) locate any of the Collateral outside the continental United States, other than any Collateral necessary for the operation of Debtor’s subsidiary location in Germany in an aggregate value
not exceeding $300,000.00, with all of any such Collateral located at Debtor’s subsidiary location in Germany to be financed by Secured Party as soft costs, and with 

  

					
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ownership to all of such Collateral located at Debtor’s subsidiary location in Germany to be retained by Debtor and not passed to its subsidiary; or
(iii) sell, rent, lease, mortgage, license, grant a security interest in or otherwise transfer or encumber (except for Permitted Liens) any of the Collateral. 

  

	 	(d)	Taxes. Debtor shall pay promptly when due all taxes, license fees, assessments and public and private charges levied or assessed on any of the Collateral, on its use, or on
this Agreement or any of the other Debt Documents. At its option, Secured Party may discharge taxes, liens, security interests or other encumbrances at any time levied or placed on the Collateral and may pay for the maintenance, insurance and
preservation of the Collateral and effect compliance with the terms of this Agreement or any of the other Debt Documents. Debtor agrees to reimburse Secured Party, on demand, all costs and expenses incurred by Secured Party in connection with such
payment or performance and agrees that such reimbursement obligation shall constitute Indebtedness. 

  

	 	(e)	Books and Records. Debtor shall, at all times, keep accurate and complete records of the Collateral, and Secured Party shall have the right to inspect and make copies of all
of Debtor’s books and records relating to the Collateral during normal business hours, after giving Debtor reasonable prior notice. 

  

	 	(f)	Third Party Possession of Collateral. Debtor agrees and acknowledges that any third person who may at any time possess all or any portion of the Collateral shall be deemed to
hold, and shall hold, the Collateral as the agent of, and as pledge holder for, Secured Party. Secured Party may at any time give notice to any third person described in the preceding sentence that such third person is holding the Collateral as the
agent of, and as pledge holder for, the Secured Party. 

  

	 	(g)	Change of Address, Name or Jurisdiction. The Debtor has not at any time within the past four (4) months either changed its name or changed the state of jurisdiction in
which it is organized and existing, nor has it maintained its chief executive office or any of the Collateral at any other location, except as set forth above, and shall not do so hereafter except upon prior written notice to the Secured Party. The
Secured Party shall be entitled to rely upon the foregoing unless it receives 14 days’ advance written notice of a change in the Debtor’s name, state of jurisdiction, address of the Debtor’s chief executive offices or location of the
Collateral. 

  

	 	(h)	Fixtures. Not permit any item of the Collateral to become a fixture to real estate or an accession to other property without the prior written consent of the Secured Party,
and the Collateral is now and shall at all times remain personal property except with the Secured Party’s prior written consent. If any of the Collateral is or will be attached to real estate in such a manner as to become a fixture under
applicable state law and if such real estate is encumbered, the Debtor will obtain from the holder of each Lien or encumbrance a written consent and subordination to the security interest hereby granted, or a written disclaimer of any interest in
the Collateral, in a form acceptable to the Secured Party. 

  

					
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	 	(i)	Distributions. Debtor shall not (i) pay any dividends or make any distributions on its equity securities; (ii) purchase, redeem, retire, defease or otherwise
acquire for value any of its equity securities, other than repurchases pursuant to the terms of employee stock purchase plans, employee restricted stock agreements or similar arrangements in an aggregate amount not to exceed One Hundred Thousand
Dollars ($100,000); (iii) return any capital to any holder of its equity securities as such; (iv) make any distribution of assets, equity securities, obligations or securities to any holder of its equity securities as such; or (v) set
apart any sum for any such purpose; provided, however, Debtor may pay dividends payable solely in common stock. 

  

	 	(j)	Indebtedness Payments. Debtor shall not (i) prepay, redeem, purchase, defease or otherwise satisfy in any manner prior to the scheduled repayment thereof any Additional
Indebtedness for borrowed money or lease obligations, (ii) amend, modify or otherwise change the terms of any Additional Indebtedness for borrowed money or lease obligations so as to accelerate the scheduled repayment thereof or
(iii) repay any notes to officers, directors or shareholders except as expressly provided for in a duly executed subordination agreement in favor of, and approved by Secured Party. 

  

	 	(k)	Bridge Loans. Debtor shall not incur any indebtedness for borrowed money or lease obligations (collectively, “Bridge Loans”) from any of its officers,
directors or shareholders (collectively, “Bridge Loan Lenders”) unless each of the Bridge Loan Lenders have executed and delivered subordination agreements in favor of Secured Party, in form satisfactory to Secured Party,
which subordinate all of the Bridge Loans to the Indebtedness, and which permit repayment of the Bridge Loans from the proceeds of new equity investments and loans. 

  

	4.	INSURANCE. 

  

	 	(a)	Risk of Loss. Debtor shall at all times bear the entire risk of any loss, theft, damage to, or destruction of, any of the Collateral from any cause whatsoever.

  

	 	(b)	 Insurance Requirements. Debtor agrees to keep the Collateral insured against loss or damage by fire and extended coverage perils, theft, burglary, and for
any or all Collateral, which are vehicles, for risk of loss by collision, and if requested by Secured Party, against such other risks as Secured Party may reasonably require. The insurance coverage shall be in an amount no less than the full
replacement value of the Collateral, and deductible amounts, insurers and policies shall be acceptable to Secured Party. Debtor shall deliver to Secured Party policies or certificates of insurance evidencing such coverage. Each policy shall name
Secured Party as a loss payee, shall provide for coverage to Secured Party regardless of the breach by Debtor of any warranty or representation made therein, shall not be subject to co-insurance, and shall provide that coverage may not be canceled
or altered by the insurer without a good faith endeavor by insurer to provide thirty (30) days prior written notice to Secured Party. Debtor appoints Secured Party as its attorney-in-fact to make proof of loss, claim for insurance and 

  

					
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adjustments with insurers, and to receive payment of and execute or endorse all documents, checks or drafts in connection with insurance payments. Secured
Party shall not act as Debtor’s attorney-in-fact unless Debtor is in default. Proceeds of insurance shall be applied, at the option of Debtor if there is no default as set forth in Section 7, or at the option of Secured Party if there is a
default as set forth in Section 7, to repair or replace the Collateral or to reduce any of the Indebtedness. 

  

	5.	REPORTS. 

  

	 	(a)	Notice of Events. Debtor shall promptly notify Secured Party of (i) any change in the name of Debtor, (ii) any change in the state of its incorporation or
registration, (iii) any relocation of its chief executive offices, (iv) any of the Collateral being lost, stolen, missing, destroyed, materially damaged or worn out, (v) any lien, claim or encumbrance other than Permitted Liens
attaching to or being made against any of the Collateral, or (vi) any occurrence of any default pursuant to Section 7 herein. 

  

	 	(b)	Financial Statements, Reports and Certificates. Debtor will deliver to Secured Party within 120 days of the close of each fiscal year of Debtor, Debtor’s complete
financial statements including a balance sheet, income statement, statement of shareholders’ equity and statement of cash flows, each prepared in accordance with Generally Accepted Accounting Principles consistently applied, certified by a
recognized firm of certified public accountants satisfactory to Secured Party. Debtor will deliver to Secured Party copies of Debtor’s quarterly financial statements including a balance sheet, income statement, and statement of cash flows, each
of which present fairly in all material respects Debtor’s financial condition as of the date thereof, and which are certified by Debtor’s chief financial officer or president, within forty-five (45) days after the close of each of
Debtor’s fiscal quarter. Debtor will deliver to Secured Party copies of all Forms 10-K and 10-Q, if any, within 30 days after the dates on which they are filed with the Securities and Exchange Commission. Debtor will deliver to Secured Party
copies of Debtor’s monthly financial statements including a balance sheet and income statement, and statement of cash flows, each of which present fairly in all material respects Debtor’s financial condition as of the date thereof, and
which are certified by Debtor’s chief financial officer or president, within thirty (30) days after the close of each month. With quarterly and monthly financial statements, Debtor shall also provide to Secured Party a copy of its bank
statement(s) for all accounts reflected in such quarterly and monthly financial statements. Concurrently with delivery of the foregoing information, and from time to time promptly upon request of Secured Party, Debtor will deliver to Secured Party a
Compliance Certificate substantially consistent with the form of the document attached hereto as Schedule A. Debtor will deliver to Secured Party promptly upon request of Secured Party, in form satisfactory to Secured Party, such other and
additional information as Secured Party may reasonably request from time to time. 

  

					
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	6.	FURTHER ASSURANCES. 

  

	 	(a)	Further Assurances Regarding Security Interests. Debtor shall, upon request of Secured Party, furnish to Secured Party such further information, execute and deliver to
Secured Party such documents and instruments (including, without limitation, Uniform Commercial Code financing statements) and shall do such other acts and things as Secured Party may at any time reasonably request relating to the perfection or
protection of the security interest created by this Agreement or for the purpose of carrying out the intent of this Agreement. Without limiting the foregoing, Debtor shall cooperate and do all acts deemed necessary or advisable by Secured Party to
continue in Secured Party a perfected first security interest in the Collateral, and shall obtain and finish to Secured Party any subordinations, releases, landlord waivers, lessor waivers, mortgagee waivers, or control agreements, and similar
documents as may be from time to time requested by, and in form and substance satisfactory to, Secured Party. 

  

	 	(b)	Authorization To File Financing Statements. Debtor shall perform any and all acts requested by the Secured Party to establish, maintain and continue the Secured Party’s
security interest and liens in the Collateral, including but not limited to, executing or authenticating financing statements and such other instruments and documents when and as reasonably requested by the Secured Party. Debtor hereby authorizes
Secured Party through any of Secured Party’s employees, agents or attorneys to file any and all financing statements, including, without limitation, any original filings, continuations, transfers or amendments thereof required to perfect
Secured Party’s security interest and liens in the Collateral under the UCC without authentication or execution by Debtor. Debtor hereby irrevocably authorizes the Secured Party at any time and from time to time to file in any filing office in
any Uniform Commercial Code jurisdiction any initial financing statements) and amendments thereto that (a) indicate the Collateral (i) is subject to Secured Party’s security interest, regardless of whether any particular asset
comprised in the Collateral falls within the scope of Article 9 of the Uniform Commercial Code of the State or such jurisdiction, or (ii) as being of an equal or lesser scope or with greater detail, and (b) provide any other information
required by part 5 of Article 9 of the Uniform Commercial Code of the State or such other jurisdiction for the sufficiency or filing office acceptance of any financing statement or amendment, including (i) whether the Debtor is an organization,
the type of organization and any organization identification number issued to the Debtor, and (ii) in the case of a financing statement filed as a fixture filing, a sufficient description of real property to which the Collateral relates. The
Debtor agrees to furnish any such information to the Secured Party promptly upon the Secured Party’s request. 

  

	 	(c)	Indemnification. Debtor shall indemnify and defend the Secured Party, its successors and assigns, and their respective directors, officers and employees, from and against all
claims, actions and suits (including, without limitation, related attorneys’ fees) of any kind whatsoever arising, directly or indirectly, in connection with any of the Collateral or the Debt Documents except to the extent resulting from the
gross negligence or willful misconduct of the persons so indemnified. 

  

					
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	7.	DEFAULT AND REMEDIES. 

  

	 	(a)	Defaults. Debtor shall be in default under this Agreement and each of the other Debt Documents if any one of the following should occur: 

  

	 	(i)	Debtor breaches its obligation to pay within three (3) business days following the due date thereof any installment or other amount due or coming due under any of the Debt
Documents, other than by Secured Party’s failure to process a deduction from Debtor’s Primary Operating Account pursuant to Section 2(w); 

  

	 	(ii)	Debtor, without the prior written consent of Secured Party, attempts to or does sell, rent, lease, license, mortgage, grant a security interest in, or otherwise transfer or
encumber, or allow Liens (except for Permitted Liens) upon, any of the Collateral; 

  

	 	(iii)	Debtor breaches any of its insurance obligations under Section 4; 

  

	 	(iv)	Debtor breaches any of its obligations under Sections 2(m) or 2(y) or Sections 3(i), (j), or (k); 

  

	 	(v)	Debtor breaches any of its other non-payment obligations under any of the Debt Documents and fails to cure that breach within thirty (30) days after it has occurred;

  

	 	(vi)	Any warranty, representation or statement made by Debtor in any of the Debt Documents or otherwise in connection with any of the Indebtedness shall be false or misleading in any
material respect; 

  

	 	(vii)	Any of the Collateral is subjected to attachment, execution, levy, seizure or confiscation in any legal proceeding or otherwise, or if any legal or administrative proceeding is
commenced against Debtor or any of the Collateral, which in the good faith judgment of Secured Party subjects any of the Collateral to a material risk of attachment, execution, levy, seizure or confiscation and no bond is posted or protective order
obtained to negate such risk; 

  

	 	(viii)	Debtor breaches or is in default under any other agreement between Debtor and Secured Party; 

  

	 	(ix)	Debtor or any guarantor or other obligor for any of the Indebtedness (collectively “Guarantor”) dissolves, terminates its existence, becomes insolvent or
ceases to do business as a going concern; 

  

					
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	 	(x)	If Debtor or any Guarantor is a natural person, and Debtor or any such Guarantor dies or becomes incompetent; 

  

	 	(xi)	A receiver is appointed for all or of any part of the property of Debtor or any Guarantor, or Debtor or any Guarantor makes any assignment for the benefit of creditors;

  

	 	(xii)	Debtor or any Guarantor files a petition under any bankruptcy, insolvency or similar law, or any such petition is filed against Debtor or any Guarantor and is not dismissed within
forty-five (45) days; 

  

	 	(xiii)	Debtor’s improper filing of an amendment or termination statement relating to a filed financing statement describing the Collateral; 

  

	 	(xiv)	Debtor shall merge with or consolidate into any other entity or sell all or substantially all of its assets or in any manner terminate its existence; 

  

	 	(xv)	If Debtor is a privately held corporation, more than 50% of Debtor’s voting capital stock, or effective control of Debtor’s voting capital stock, issued and outstanding
from time to time, is not retained by the holders of such stock on the date the Agreement is executed; 

  

	 	(xvi)	If Debtor is a publicly held corporation, there shall be a change in the ownership of Debtor’s stock such that Debtor is no longer subject to the reporting requirements of the
Securities Exchange Act of 1934 or no longer has a class of equity securities registered under Section 12 of the Securities Act of 1933; 

  

	 	(xvii)	Debtor defaults under any agreement to pay Additional Indebtedness or any other financing arrangement between Debtor and a third party in an amount exceeding $100,000;

  

	 	(xviii)	Secured Party shall have determined in its sole and good faith judgment that (a) it is the clear intention of Debtor’s investors to not continue to fund the Debtor in the
amounts and timeframe necessary to enable Debtor to satisfy the Indebtedness as it becomes due and payable or (b) there is a material impairment in the perfection or priority of the Secured Party’s security interest in the Collateral; or

  

	 	(xix)	[intentionally omitted] 

  

	 	(xx)	 Without the prior written consent of Secured Party, which consent shall not be unreasonably withheld or delayed, Debtor creates, incurs, assumes or permits to exist
any Indebtedness to Maxygen, Inc. (“Maxygen”) in excess of One Million, Two Hundred Twenty-Five Thousand Dollars ($1,225,000) in aggregate in any fiscal year, or Debtor makes any payments to Maxygen in any fiscal year in excess of the
lower of: (i) the aggregate of the fair market value of services provided by Maxygen to 

  

					
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Debtor during such fiscal year, or (ii) the aggregate of One Million, Two Hundred Twenty-Five Thousand Dollars ($1,225,000). Notwithstanding the
foregoing, Debtor shall be permitted to pay the balance of previously incurred, existing and anticipated Indebtedness to Maxygen up to a total amount of One Million, Five Hundred Thousand Dollars ($1,500,000) for the period January 1, 2005 to
December 31, 2005. 

  

	 	(b)	Acceleration. If Debtor is in default, the Secured Party, at its option, may declare any or all of the Indebtedness to be immediately due and payable, without demand or
notice to Debtor or any Guarantor (provided that if there is a default as a result of a bankruptcy or insolvency all Indebtedness shall become immediately due and payable without any action by Secured Party). The accelerated obligations and
liabilities shall bear interest (both before and after any judgment) until paid in full at the Default Rate. 

  

	 	(c)	Rights and Remedies. Secured Party shall have all of the rights and remedies of a Secured Party under the Uniform Commercial Code, and under any other applicable law. Without
limiting the foregoing, if an event of default exists, Secured Party shall have the right to (i) notify any account debtor of Debtor or any obligor on any instrument which constitutes part of the Collateral to make payment to the Secured Party,
(ii) with or without legal process, enter any premises where the Collateral may be and take possession of and remove the Collateral from the premises or store it on the premises, (iii) sell the Collateral at public or private sale, in
whole or in part, and have the right to bid and purchase at said sale, or (iv) lease or otherwise dispose of all or part of the Collateral, applying proceeds from such disposition to the obligations then in default. If requested by Secured
Party, Debtor shall promptly assemble the Collateral and make it available to Secured Party at a place to be designated by Secured Party, which is reasonably convenient to both parties. Secured Party may also render any or all of the Collateral
unusable at the Debtor’s premises and may dispose of such Collateral on such premises without liability for rent or costs. Any notice that Secured Party is required to give to Debtor under the Uniform Commercial Code of the time and place of
any public sale or the time after which any private sale or other intended disposition of the Collateral is to be made shall be deemed to constitute reasonable notice if such notice is given to the last known address of Debtor at least five
(5) days prior to such action. Upon the occurrence and during the continuation of a default, Debtor hereby appoints Secured Party as Debtor’s attorney-in-fact, with full authority in Debtor’s place and stead and in Debtor’s name
or otherwise, from time to time in Secured Party’s sole and arbitrary discretion, to take any action and to execute any instrument which Secured Party may deem necessary or advisable to accomplish the purpose of this Agreement. If an event of
Default exists and is continuing, Secured Party is granted a non-exclusive royalty free license to use Debtor’s Intellectual Property in connection with Secured Party’s disposition of Collateral in the exercise of Secured Party’s
rights or remedies hereunder. 

  

					
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 Master Security Agreement No. 5081102 
  

	 	(d)	Application of Proceeds. The proceeds and/or avails of the Collateral, or any part thereof, and the proceeds and the avails of any remedy hereunder (as well as any other
amounts of any kind held by Secured Party, at the time of or received by Secured Party after the occurrence of a default hereunder) shall be paid to and applied as follows: 

  

	 	a.	First, to the payment of out-of-pocket costs and expenses, including all amounts expended to preserve the value of the Collateral, all costs of repossession, storage, and
disposition including without limitation attorneys’, appraisers’, and auctioneers’ fees, of foreclosure or suit, if any, and of such sale and the exercise of any other rights or remedies, and of all proper fees, expenses, liability
and advances, including reasonable legal expenses and attorneys’ fees, incurred or made hereunder by Secured Party, including without limitation, Secured Party’s Expenses; 

  

	 	b.	Second, to the payment to Secured Party of the amount then owing or unpaid on the Loans for scheduled payments, any accrued and unpaid interest, and all other Indebtedness
(provided, however, if such proceeds shall be insufficient to pay in full the whole amount so due, owing or unpaid upon the Loans, then to the unpaid interest thereon, then to the outstanding principal amount of the Loans, and then to
the payment of other amounts then payable to Secured Party under any of the Debt Documents or otherwise); and 

  

	 	c.	Third, to the payment of the surplus, if any, to Debtor, its successors and assigns, or to whomsoever may be lawfully entitled to receive the same. 

 

	 	(e)	Fees and Costs. Debtor agrees to pay all reasonable attorneys’ fees and other costs incurred by Secured Party in connection with the enforcement, assertion, defense or
preservation of Secured Party’s rights and remedies under this Agreement, or if prohibited by law, such lesser sum as may be permitted. Debtor further agrees that such fees and costs shall constitute Indebtedness. 

  

	 	(f)	Remedies Cumulative. Secured Party’s rights and remedies under this Agreement or otherwise arising are cumulative and may be exercised singularly or concurrently.
Neither the failure nor any delay on the part of the Secured Party to exercise any right, power or privilege under this Agreement shall operate as a waiver, nor shall any single or partial exercise of any right, power or privilege preclude any other
or further exercise of that or any other right, power or privilege. SECURED PARTY SHALL NOT BE DEEMED TO HAVE WAIVED ANY OF ITS RIGHTS UNDER THIS AGREEMENT OR UNDER ANY OTHER AGREEMENT, INSTRUMENT OR PAPER SIGNED BY DEBTOR UNLESS SUCH WAIVER IS
EXPRESSED IN WRITING AND SIGNED BY SECURED PARTY. A waiver on any one occasion shall not be construed as a bar to or waiver of any right or remedy on any future occasion. 

  

					
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 Master Security Agreement No. 5081102 
  

	 	(g)	WAIVER OF JURY TRIAL. DEBTOR AND SECURED PARTY UNCONDITIONALLY WAIVE THEIR RIGHTS TO A JURY TRIAL OF ANY CLAIM OR CAUSE OF ACTION BASED UPON OR ARISING OUT OF THIS AGREEMENT,
ANY OF THE OTHER DEBT DOCUMENTS, ANY OF THE INDEBTEDNESS SECURED HEREBY, ANY DEALINGS BETWEEN DEBTOR AND SECURED PARTY RELATING TO THE SUBJECT MATTER OF THIS TRANSACTION OR ANY RELATED TRANSACTIONS, AND/OR THE RELATIONSHIP THAT IS BEING ESTABLISHED
BETWEEN DEBTOR AND SECURED PARTY. THE SCOPE OF THIS WAIVER IS INTENDED TO BE ALL ENCOMPASSING OF ANY AND ALL DISPUTES THAT MAY BE FILED IN ANY COURT. THIS WAIVER IS IRREVOCABLE. THIS WAIVER MAY NOT BE MODIFIED EITHER ORALLY OR IN WRITING. THE WAIVER
ALSO SHALL APPLY TO ANY SUBSEQUENT AMENDMENTS, RENEWALS, SUPPLEMENTS OR MODIFICATIONS TO THIS AGREEMENT, ANY OTHER DEBT DOCUMENTS, OR TO ANY OTHER DOCUMENTS OR AGREEMENTS RELATING TO THIS TRANSACTION OR ANY RELATED TRANSACTION. THIS AGREEMENT MAY BE
FILED AS A WRITTEN CONSENT TO A TRIAL BY THE COURT. 

  

	8.	MISCELLANEOUS. 

  

	 	(a)	Assignment. This Agreement and/or any of the other Debt Documents may be assigned, in whole or in part, by Secured Party without notice to Debtor, and Debtor agrees not to
assert against any such assignee, or assignee’s assigns, any defense, set-off, recoupment claim or counterclaim which Debtor has or may at any time have against Secured Party for any reason whatsoever. Debtor agrees that if Debtor receives
written notice of an assignment from Secured Party, Debtor will pay all amounts payable under any assigned Debt Documents to such assignee or as instructed by Secured Party. Debtor also agrees to confirm in writing receipt of the notice of
assignment as may be reasonably requested by Secured Party or assignee. 

  

	 	(b)	Notices. All notices to be given in connection with this Agreement shall be in writing, shall be addressed to the parties at their respective addresses set forth in this
Agreement (unless and until a different address may be specified in a written notice to the other party), and shall be deemed given (i) on the date of receipt if delivered in hand or by facsimile transmission, (ii) on the next business day
after being sent by express mail, and (iii) on the fourth business day after being sent by regular, registered or certified mail. As used herein, the term “business day” shall mean and include any day other than Saturdays, Sundays, or
other days on which commercial banks in California or Virginia are required or authorized to be closed. 

  

	 	(c)	Correction of Errors. Secured Party may correct patent errors and fill in all blanks in this Agreement, any Collateral Schedule or in any Note consistent with the agreement
of the parties. 

  

					
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 Master Security Agreement No. 5081102 
  

	 	(d)	Time is of the Essence. Time is of the essence of this Agreement. This Agreement shall be binding, jointly and severally, upon all parties described as the “Debtor”
and their respective heirs, executors, representatives, successors and assigns, and shall inure to the benefit of Secured Party, its successors and assigns. 

  

	 	(e)	Entire Agreement. This Agreement and the Debt Documents constitute the entire agreement between the parties with respect to the subject matter of this Agreement and supersede
all prior understandings (whether written, verbal or implied) with respect to such subject matter. NEITHER THIS AGREEMENT NOR ANY OF THE DEBT DOCUMENTS SHALL BE CHANGED OR TERMINATED ORALLY OR BY COURSE OF CONDUCT, BUT ONLY BY A WRITING SIGNED BY
BOTH PARTIES. Section headings contained in this Agreement have been included for convenience only, and shall not affect the construction or interpretation of this Agreement. This Agreement is the result of negotiations between and has been reviewed
by each of Debtor and Secured Party executing this Agreement as of the date hereof and their respective counsel; accordingly, this Agreement shall be deemed to be the product of the parties hereto, and no ambiguity shall be construed in favor of or
against Debtor or Secured Party. 

  

	 	(f)	Termination of Agreement. This Agreement shall continue in full force and effect until all of the Indebtedness has been indefeasibly paid in full to Secured Party or its
assignee; provided, that Debtor’s indemnity obligations set forth in Section 6(c) shall survive until all applicable statute of limitations periods with respect to actions that may be brought against Secured Party have
run. The surrender, upon payment or otherwise, of any Note or any of the other documents evidencing any of the Indebtedness shall not affect the right of Secured Party to retain the Collateral for such other Indebtedness as may then exist or as it
may be reasonably contemplated will exist in the future. This Agreement shall automatically be reinstated if Secured Party is ever required to return or restore the payment of all or any portion of the Indebtedness (all as though such payment had
never been made). Secured Party shall, at Debtor’s sole cost and expense, execute such further documents and take such further actions as may be reasonably necessary to effect the release of its security interests contemplated by this
paragraph, including duly executing and delivering termination statements for filing in all relevant jurisdictions under the Code. 

  

	 	(g)	 CHOICE OF LAW. DEBTOR AGREES THAT SECURED PARTY AND/OR ITS SUCCESSORS AND ASSIGNS SHALL HAVE THE OPTION BY WHICH STATE LAWS THIS AGREEMENT SHALL BE GOVERNED
AND CONSTRUED: (A) THE LAWS OF THE COMMONWEALTH OF VIRGINIA; OR (B) IF COLLATERAL HAS BEEN PLEDGED TO SECURE THE LIABILITIES, THEN BY THE LAWS OF THE STATE OR STATES WHERE THE COLLATERAL IS LOCATED, AT SECURED PARTY’S OPTION. THIS
CHOICE OF STATE LAWS IS EXCLUSIVE TO THE SECURED PARTY. DEBTOR SHALL NOT HAVE ANY OPTION TO CHOOSE THE LAWS BY WHICH THIS AGREEMENT SHALL BE GOVERNED. DEBTOR 

  

					
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 Master Security Agreement No. 5081102 
  

	 	 
ACKNOWLEDGES THAT THIS AGREEMENT IS BEING SIGNED BY THE SECURED PARTY IN PARTIAL CONSIDERATION OF SECURED PARTY’S RIGHT TO ENFORCE IN THE JURISDICTION
STATED ABOVE. DEBTOR CONSENTS TO JURISDICTION IN THE COMMONWEALTH OF VIRGINIA OR THE STATE IN WHICH ANY COLLATERAL IS LOCATED AND VENUE IN ANY FEDERAL OR STATE COURT IN THE COMMONWEALTH OF VIRGINIA OR THE STATE IN WHICH COLLATERAL IS LOCATED FOR
SUCH PURPOSES AND WAIVES ANY AND ALL RIGHTS TO CONTEST SAID JURISDICTION AND VENUE AND ANY OBJECTION THAT SAID COUNTY IS NOT CONVENIENT. DEBTOR WAIVES ANY RIGHTS TO COMMENCE ANY ACTION AGAINST SECURED PARTY IN ANY JURISDICTION EXCEPT VIRGINIA, OR IF
SECURED PARTY CHOOSES TO LITIGATE IN A STATE WHERE COLLATERAL IS LOCATED THEN IN SUCH COUNTY AND STATE. 

  

	 	(h)	Power of Attorney. To facilitate direct collection, the Debtor hereby appoints the Secured Party and any officer or employee of the Secured Party, as the Secured Party may
from time to time designate, as attorney-in-fact for the Debtor to (a) endorse the name of the Debtor in favor of the Secured Party upon any and all checks, drafts, money orders, notes, acceptances or other evidences of payment or Collateral
that may come into the Secured Party’s possession; (b) do all acts and things necessary to carry out this Agreement and the transactions contemplated hereby, including signing the name of the Debtor on any instruments required by law in
connection with the transactions contemplated hereby and on financing statements as permitted by the Virginia Uniform Commercial Code. The Debtor hereby ratifies and approves all acts of such attorneys-in-fact, and neither the Secured Party nor any
other such attorney-in-fact shall be liable for any acts of commission or omission, or for any error of judgment or mistake of fact or law of any such attorney-in-fact. This power, being coupled with an interest, is irrevocable so long as the Loan
remains unsatisfied, or any Debt Document remains effective, as solely determined by the Secured Party. Secured Party agrees to exercise this power of attorney only during the existence of an event of default. 

  

	 	(i)	Loss, Depreciation or Other Damage. The Secured Party shall not be liable for or prejudiced by any loss, depreciation or other damage to Collateral unless caused by the
Secured Party’s willful and malicious act, and the Secured Party shall have no duty to take any action to preserve or collect any Collateral. 

  

	 	(j)	Demand; Protest. Debtor waives demand, protest, notice of protest, notice of default or dishonor, notice of payment and nonpayment, notice of any default, nonpayment at
maturity, release, compromise, settlement, extension, or renewal of accounts, documents, instruments, chattel paper, and guarantees at any time held by Secured Party on which Debtor may in any way be liable. 

  

					
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 Master Security Agreement No. 5081102 
  

	9.	DEFINITIONS. 

 As used herein, the following terms,
when initial capital letters are used, shall have the respective meanings set forth below. In addition, all terms defined in the Code shall have the meanings given therein unless otherwise defined herein. 
 Defined Terms. As used in this Agreement, the following terms shall have the following meanings, unless the context otherwise requires: 
 “Additional Indebtedness” means, with respect to Debtor or any of its subsidiaries, the aggregate amount of, without duplication,
(a) all obligations of such Person for borrowed money, (b) all obligations of such Person evidenced by bonds, debentures, notes or other similar instruments, (c) all obligations of such Person to pay the deferred purchase price of
property or services (excluding trade payables aged less than one hundred eighty (180) days), (d) all capital lease obligations of such Person, (e) all obligations or liabilities of others secured by a Lien on any asset of such
Person, whether or not such obligation or liability is assumed, (f) all obligations or liabilities of others guaranteed by such Person, and (g) any other obligations or liabilities which are required by GAAP to be shown as debt on the
balance sheet of such Person. A listing of Additional Indebtedness existing on the date hereof is set forth in Schedule B. Unless otherwise indicated, the term “Additional Indebtedness” shall include all Indebtedness
of Debtor and all of its subsidiaries. 
 “Affiliate” of a Person is a Person that owns or controls directly or
indirectly the Person, any Person that controls or is controlled by or is under common control with the Person, and each of that Person’s senior executive officers, directors, partners and, for any Person that is a limited liability company,
that Person’s managers and members. 
 “Code” means the Virginia Uniform Commercial Code (including revised
Article 9 thereof). 
 “Collateral” has the meaning given such capitalized term in Section 1. 

“Collateral Schedule” has the meaning given such capitalized term in Section 1. 
 “Debt Documents” has the meaning given such capitalized term in Section 2(b). 
 “Default Rate” is the lower of thirteen percent (13%) per annum or the maximum rate not prohibited by applicable law.

 “Indebtedness” has the meaning given such capitalized term in Section 1. 
 “Intellectual Property” shall mean (a) all of the Debtor’s right, title and interest, whether now owned or existing or
hereafter acquired or arising, in and to all domestic and foreign copyrights, copyright registrations and copyright applications, whether or not registered or filed with any governmental authority, together with (i) all renewals thereof,
(ii) all present and future rights of the Debtor under all present and future license agreements relating thereto, whether the Debtor is licensee or licensor thereunder, (iii) all income, 

  

					
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 Master Security Agreement No. 5081102 
  

 
royalties, damages and payments now or hereafter due and/or payable to the Debtor thereunder or with respect thereto, including, without limitation, damages
and payments for past, present or future infringements thereof, (iv) all of the Debtor’s present and future claims, causes of action and rights to sue for past, present or future infringements thereof, and (v) all rights corresponding
thereto throughout the world (collectively “Copyright Rights”); (b) all of the Debtor’s right, title and interest, whether now owned or existing or hereafter acquired or arising, in and to all United States and foreign
patents, and pending and abandoned United States and foreign patent applications, including, without limitation, the inventions and improvements described or claimed therein, together with(i) any reissues, divisions, continuations, certificates of
re-examination, extensions and continuations-in-part thereof, (ii) all present and future rights of the Debtor under all present and future license agreements relating thereto, whether the Debtor is licensee or licensor thereunder,
(iii) all income, royalties, damages and payments now or hereafter due and/or payable to the Debtor thereunder or with respect thereto, including, without limitation, damages and payments for past, present or future infringements thereof,
(iv) all of the Debtor’s present and future claims, causes of action and rights to sue for past, present or future infringements thereof, and (v) all rights corresponding thereto throughout the world (collectively “Patent
Rights”); (c) all of the Debtor’s right, title and interest, whether now owned or existing or hereafter acquired or arising, in and to all domestic and foreign trademarks, trademark registrations, trademark applications and trade
names, whether or not registered or filed with any governmental authority, together with (i) all renewals thereof, (ii) all present and future rights of the Debtor under all present and future license agreements relating thereto, whether
the Debtor is licensee or licensor thereunder, (iii) all income, royalties, damages and payments now or hereafter due and/or payable to the Debtor thereunder or with respect thereto, including, without limitation, damages and payments for past,
present or future infringements thereof, (iv) all of the Debtor’s present and future claims, causes of action and rights to sue for past, present or future infringements thereof, and (v) all rights corresponding thereto throughout the
world (collectively “Trademark Rights”); (d) all present and future licenses and license agreements of the Debtor, and all rights of the Debtor under or in connection therewith, whether the Debtor is licensee or licensor
thereunder, including, without limitation, any present or future franchise agreements under which the Debtor is franchisee or franchisor, together with (i) all renewals thereof, (ii) all income, royalties, damages and payments now or
hereafter due and/or payable to the Debtor thereunder or with respect thereto, including, without limitation, damages and payments for past, present or future infringements thereof, (iii) all claims, causes of action and rights to sue for past,
present or future infringements thereof, and (iv) all rights corresponding thereto throughout the world (collectively “License Rights”); (e) all present and future trade secrets of the Debtor; and (f) all other
present and future intellectual property of the Debtor.] 
 “Lien(s)” shall mean any voluntary or involuntary
mortgage, pledge, deed of trust, assignment, security interest, encumbrance, hypothecation, lien, or charge of any kind (including any conditional sale or other title retention agreement, any financing lease having substantially the same economic
effect as any of the foregoing, and the filing of, or agreement to give, any financing statement under the Uniform Commercial Code or comparable law of any jurisdiction). 
  

					
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 Master Security Agreement No. 5081102 
  

 “Loan” means an advance of credit by Secured Party to Debtor. 
 “Note” has the meaning given such capitalized term in Section 1. 
 “Permitted Liens” means: (i) liens in favor of Secured Party, (ii) liens for taxes not yet due or for taxes being
contested in good faith and which do not involve, in the judgment of Secured Party, any risk of the sale, forfeiture or loss of any of the Collateral, and (iii) inchoate materialmen’s, mechanic’s, repairmen’s and similar liens
arising by operation of law in the normal course of business for amounts which are not delinquent. 
 “Person” is any
individual, sole proprietorship, partnership, limited liability company, joint venture, company association, trust, unincorporated organization, association, corporation, institution, public benefit corporation, firm, joint stock company, estate,
entity or government agency. 
 “Primary Operating Account” has the meaning given such capitalized term in
Section 2(w). 
 “Secured Party’s Expenses” means all reasonable costs or expenses (including
reasonable attorneys’ fees and expenses) incurred in connection with the preparation, negotiation, documentation, administration and funding of the Debt Documents; and Secured Party’s reasonable attorneys’ fees, costs and expenses
incurred in amending. modifying, enforcing or defending the Debt Documents (including fees and expenses of appeal or review), including the exercise of any rights or remedies afforded hereunder or under applicable law, whether or not suit is
brought, whether before or after bankruptcy or insolvency, including without limitation all fees and costs incurred by Secured Party in connection with Secured Party’s enforcement of its rights in a bankruptcy or insolvency proceeding filed by
or against Debtor or its property. 
 “Subordinated Indebtedness” means Additional Indebtedness subordinated to the
Indebtedness of Debtor to Secured Party on terms and conditions acceptable to Secured Party in its sole discretion. 
 IN WITNESS
WHEREOF, Debtor and Secured Party, intending to be legally bound hereby, have duly executed this Agreement in one or more counterparts, each of which shall be deemed to be an original, as of the day and year first aforesaid. 
  

							
	SECURED PARTY:	 	DEBTOR:
		
	Oxford Finance Corporation	 	Codexis, Inc.
				
	By:	 	 /s/ Michael J. Altenburger
	 	By:	 	 /s/ Tassos Gianakakos

	Name:	 	Michael J. Altenburger	 	Name:	 	Tassos Gianakakos
	Title:	 	Chief Financial Officer	 	Title:	 	Senior Vice President

  

					
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 Master Security Agreement No. 5081102 
  

 SCHEDULE A 
 FORM OF 
 COMPLIANCE CERTIFICATE 
  

									
	Oxford	 		 	Finance	 		 	Corporation
	133	 	N.	 		 	Fairfax	 	Street
	Alexandria, VA 22314	 		 		 		 	

  

			
	Re:	  	Codexis, Inc.

 Gentlemen: 
 Reference
is made to the Master Security Agreement dated as of October 25, 2005, (as the same have been and may be amended from time to time in writing, the “Loan Agreement”, the capitalized terms used herein as defined therein), between
Oxford Finance Corporation and Codexis, Inc. (the “Company”). 
 The undersigned authorized representative of the Company
hereby certifies that in accordance with the terms and conditions of the Loan Agreement, the Company is in complete compliance for the financial reporting period ending
                             with all required financial reporting under the Loan Agreement, except as
noted below. Attached herewith are the required documents supporting the foregoing certification. The undersigned further certifies that the accompanying financial statements present fairly in all material respects the Debtor’s financial
condition as of the date thereof, that annual audited financial statements have been prepared in accordance with Generally Accepted Accounting Principles, and all such financial statements are consistent from one period to the next, except as
explained below. 
 Indicate compliance status by circling Yes/No under “Complies” 
  

					
	 REPORTING REQUIREMENT
	 	 REQUIRED
	 	 COMPLIES

	Interim Financial Statements	 	Quarterly within 45 days	 	YES / NO
			
	Monthly Financial Statements	 	Monthly within 30 days	 	
			
	Audited Financial Statements	 	FYE within 120 days	 	
			
	Date of most recent Board-approved budget/plan
                            	 		 	
	Summary submitted with Borrowing Request	 		 	YES / NO
			
	Any material change in budget/plan since prior Borrowing Request	 		 	YES / NO

  

					
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 Master Security Agreement No. 5081102 
  

 EXPLANATIONS 
  

			
	Very truly yours,
	
	CODEXIS, INC.
		
	By:	 	  

	Name:	 	
	Title:*	 	

  
  

	 *
	 Must be executed by Debtor’s Chief Financial Officer or President. 

  

					
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 Master Security Agreement No. 5081102 
  

 SCHEDULE B 
 DEBTOR ADDITIONAL INDEBTEDNESS AS OF SEPTEMBER 30, 2005 
  

			
	 Current Liabilities
	  	
	 Accrued vacation
	  	438,019
	 Other accruals
	  	1,125,685
	 Equipment loan
	  	993,343
	 Lease Incentive
	  	62,531
	 Deferred Revenue
	  	3,618,030
		  	 
	 Subtotal
	  	6,237,608
	 Long Term Liabilities
	  	
	 Equipment Loan
	  	2,705,561
	 Lease Incentive
	  	270,966
	 Deferred Revenue
	  	1,956,092
		  	 
	 Subtotal
	  	4,932,619
		  	 
	 Total Liabilities
	  	11,170,227
		  	 

  

					
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 COLLATERAL MIX RIDER 
 TO 
 MASTER SECURITY AGREEMENT NO. 5081102 
 DATED OCTOBER 25, 2005 
 BETWEEN 
 OXFORD FINANCE CORPORATION (the “SECURED PARTY”) 
 AND 
 CODEXIS, INC. (the “DEBTOR”) 
 Debtor shall cause
the composition and mix of Collateral to conform to and meet the following concentration requirements (hereinafter “Concentration Requirement”) for the class of Collateral (hereinafter “Collateral Class”) as identified and set
forth below. Debtor herein represents and warrants that it shall maintain such Collateral Class and its respective Concentration Requirement at all times from and after December 31, 2006. If on such date the Concentration Requirement is not in
compliance (a “Concentration Variance”), Debtor will do one of the following (a “Concentration Correction”): 
  

	1.	Grant to Secured Party a security interest in additional equipment satisfactory to Secured Party, not previously subject to Secured Party’s security interest (collectively, the
“Additional Equipment”), in sufficent type and amount so that the Concentration Requirement set forth below is met and the Concentration Variance is eliminated. The Additional Equipment shall be subject to all of the terms and conditions
of the Master Security Agreement, including without limitation, Debtor’s representations, warranties, and covenants, which shall be deemed remade by Debtor upon its grant of a security interest in the Additional Equipment.

  

	2.	Pay Secured Party cash in an amount equal to the Concentration Variance to hold as cash collateral until the Note is fully repaid. Debtor hereby grants Secured Party a security
interest in such cash collateral and all proceeds and products thereof. Debtor agrees that such cash collateral held by Secured Party: (a) shall not bear interest, (b) may be commingled with other funds of Secured Party, and (c) may
be applied by Secured Party to amounts owing by Debtor upon the occurrence and during the continuance of any Event of Default under the Master Security Agreement or the Note(s) thereunder. 

 The failure of Debtor to do a Concentration Correction by December 31, 2006, shall constitute a Default under the Master Security Agreement and the Note(s)
thereunder. 
  

			
	 Collateral Class
	 	 Concentration Requirement

	New Laboratory Equipment	 	Minimum of 60%
	New Computer and Furniture	 	Maximum of 10%
	Soft Costs	 	Maximum of 30% of the outstanding principal amount as initially represented by the Promissory Notes from time to time

  

					
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 Dated as of October 25, 2005 
  

							
	OXFORD FINANCE CORPORATION	 	CODEXIS, INC.
				
	By:	 	 /s/ Michael J. Altenburger
	 	By:	 	 /s/ Tassos Gianakakos

	Name:	 	Michael J. Altenburger	 	Name:	 	Tassos Gianakakos
	Title:	 	Chief Financial Officer	 	Title:	 	Senior Vice President

  

					
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 SECRETARY’S CERTIFICATE 
 Codexis, Inc. 
  

			
	To:	  	 Oxford Finance Corporation
 133 North Fairfax Street

 Alexandria, Virginia 22314

 The undersigned hereby certifies as follows: 
  

	(i)	He is the duly appointed Secretary of Codexis, Inc., a Delaware corporation (the “Corporation”). 

 (ii) Each of the officers designated below is a duly appointed officer of the Corporation, and the signature appearing opposite his name below is his genuine signature:

  

					
	 NAME
	  	 OFFICE
	 	 SIGNATURE

	Alan Shaw	  	President and Chief Executive Officer	 	/s/ Alan Shaw
	Tassos Gianakakos	  	Senior Vice President	 	/s/ Tassos Gianakakos
	  
	  	  
	 	  

 (iii) Schedule A attached hereto is a true and correct copy of the Corporation’s Fourth Amended and
Restated Certificate of Incorporation, as filed with the Delaware Secretary of State on July 22, 2004, as amended on January 19, 2005, July 26, 2005 and October 20, 2005 (the “Certificate”). The Certificate has not
in any way been amended, annulled, rescinded, repealed, revoked or supplemented, and remains in full force and effect as of the date hereof. 
 (iv)
Schedule B attached hereto is a true and correct copy of the Corporation’s bylaws as presently in effect. 
 (v) Schedule C attached
hereto is a true and correct copy of resolutions adopted by the board of directors of the Corporation on August 11, 2005 related to Oxford Finance Corporation (the “Resolutions”). Said Resolutions have not been revoked, modified,
rescinded, or amended and are in full force and effect. 
 [Signature Page Follows] 
  

					
		  	Page 25 of 26	  	Codexis Initial Here:                     
		  		  	Oxford Initial Here:                     

 SECRETARY’S CERTIFICATE 
 IN WITNESS WHEREOF, I have hereunto set my hand, this 25th day of October, 2005. 
  

	
	 /s/ Alan C. Mendelson

	Alan Mendelson
	 Secretary
 Codexis, Inc.

 ATTEST: 
 The
undersigned does hereby certify that he is President and Chief Executive Officer of the Corporation and does hereby certify that Alan Mendelson was, at the time he executed the foregoing Certificate, a duly elected, qualified and acting Secretary of
the Corporation, and he was duly authorized and empowered to do so, and the signature thereon is genuine. 
  

	
	 /s/ Alan Shaw

	Signature of Corporate Officer
	Attesting to Secretary Signature

  

					
		  	Page 26 of 26	  	Codexis Initial Here:                     
		  		  	Oxford Initial Here:Codexis Inc. 2002 Stock Plan, as amended, and Form of Stock Option Agreement

 Exhibit 10.22 
 CODEXIS, INC. 
 2002 STOCK PLAN 
 (as amended through August 28, 2007) 
 1.
Purposes of the Plan. The purposes of this Plan are to attract and retain the best available personnel for positions of substantial responsibility, to provide additional incentive to Employees, Directors and Consultants and to
promote the success of the Company’s business. Options granted under the Plan may be Incentive Stock Options or Nonstatutory Stock Options, as determined by the Administrator at the time of grant. Stock Purchase Rights may also be granted under
the Plan. 
 2. Definitions. As used herein, the following definitions shall apply: 
 (a) “Administrator” means the Board or any of its Committees as shall be administering the Plan in accordance with Section 4 hereof.

 (b) “Applicable Laws” means the requirements relating to the administration of stock option plans under U.S. state
corporate laws, U.S. federal and state securities laws, the Code, any stock exchange or quotation system on which the Common Stock is listed or quoted and the applicable laws of any other country or jurisdiction where Options or Stock Purchase
Rights are granted under the Plan. 
 (c) “Board” means the Board of Directors of the Company. 
 (d) “Change in Control” means the occurrence of any of the following events: 
 (i) Any “person” (as such term is used in Sections 13(d) and 14(d) of the Exchange Act) becomes the “beneficial owner” (as defined in
Rule 13d-3 of the Exchange Act), directly or indirectly, of securities of the Company representing fifty percent (50%) or more of the total voting power represented by the Company’s then outstanding voting securities; or 
 (ii) The consummation of the sale or disposition by the Company of all or substantially all of the Company’s assets; or 
 (iii) The consummation of a merger or consolidation of the Company with any other corporation, other than a merger or consolidation which would result
in the voting securities of the Company outstanding immediately prior thereto continuing to represent (either by remaining outstanding or by being converted into voting securities of the surviving entity or its parent) at least fifty percent
(50%) of the total voting power represented by the voting securities of the Company or such surviving entity or its parent outstanding immediately after such merger or consolidation. 
 (e) “Code” means the Internal Revenue Code of 1986, as amended. 

 (f) “Committee” means a committee of Directors or of other individuals satisfying
Applicable Laws appointed by the Board in accordance with Section 4 hereof. 
 (g) “Common Stock” means the Common
Stock of the Company. 
 (h) “Company” means Codexis, Inc., a Delaware corporation. 
 (i) “Consultant” means any person who is engaged by the Company or any Parent or Subsidiary to render consulting or advisory services to
such entity. 
 (j) “Director” means a member of the Board. 
 (k) “Disability” means total and permanent disability as defined in Section 22(e)(3) of the Code. 
 (l) “Employee” means any person, including officers and Directors, employed by the Company or any Parent or Subsidiary of the Company.
Neither service as a Director nor payment of a director’s fee by the Company shall be sufficient to constitute “employment” by the Company. 
 (m) “Exchange Act” means the Securities Exchange Act of 1934, as amended. 
 (n)
“Fair Market Value” means, as of any date, the value of Common Stock determined as follows: 
 (i) If the Common Stock is
listed on any established stock exchange or a national market system, including without limitation the Nasdaq National Market or The Nasdaq SmallCap Market of The Nasdaq Stock Market, its Fair Market Value shall be the closing sales price for such
stock (or the closing bid, if no sales were reported) as quoted on such exchange or system on the day of determination, as reported in The Wall Street Journal or such other source as the Administrator deems reliable; 
 (ii) If the Common Stock is regularly quoted by a recognized securities dealer but selling prices are not reported, its Fair Market Value shall be the
mean between the high bid and low asked prices for the Common Stock on the day of determination; or 
 (iii) In the absence of an
established market for the Common Stock, the Fair Market Value thereof shall be determined in good faith by the Administrator. 
 (o)
“Incentive Stock Option” means an Option intended to qualify as an incentive stock option within the meaning of Section 422 of the Code. 
 (p) “Nonstatutory Stock Option” means an Option not intended to qualify as an Incentive Stock Option. 
 (q) “Option” means a stock option granted pursuant to the Plan. 
  

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 (r) “Option Agreement” means a written or electronic agreement between the Company and
an Optionee evidencing the terms and conditions of an individual Option grant. The Option Agreement is subject to the terms and conditions of the Plan. 
 (s) “Optioned Stock” means the Common Stock subject to an Option or a Stock Purchase Right. 
 (t) “Optionee” means the holder of an outstanding Option or Stock Purchase Right granted under the Plan. 
 (u)
“Parent” means a “parent corporation,” whether now or hereafter existing, as defined in Section 424(e) of the Code. 
 (v) “Plan” means this 2002 Stock Plan. 
 (w) “Restricted Stock” means Shares issued pursuant to a
Stock Purchase Right or Shares of restricted stock issued pursuant to an Option. 
 (x) “Restricted Stock Purchase
Agreement” means a written agreement between the Company and the Optionee evidencing the terms and restrictions applying to Shares purchased under a Stock Purchase Right. The Restricted Stock Purchase Agreement is subject to the terms and
conditions of the Plan and the notice of grant. 
 (y) “Securities Act means the Securities Act of 1933, as amended. 

(z) “Service Provider” means an Employee, Director or Consultant. 
 (aa) “Share” means a share of the Common Stock, as adjusted in accordance with Section 13 below. 
 (bb) “Stock Purchase Right” means a right to purchase Common Stock pursuant to Section 11 below. 
 (cc) “Subsidiary” means a “subsidiary corporation,” whether now or hereafter existing, as defined in Section 424(f) of
the Code. 
 3. Stock Subject to the Plan. Subject to the provisions of Section 13 of the Plan, the maximum
aggregate number of Shares that may be subject to Options and sold under the Plan is 12,457,642 Shares. The Shares may be authorized but unissued, or reacquired Common Stock. 
 If an Option or Stock Purchase Right expires or becomes unexercisable without having been exercised in full, the unpurchased Shares that were subject
thereto shall become available for future grant or sale under the Plan (unless the Plan has terminated). However, Shares that have actually been issued under the Plan, upon exercise of either an Option or Stock Purchase Right, shall not be returned
to the Plan and shall not become available for future distribution under the Plan, except that if unvested Shares of Restricted Stock are repurchased by the Company at their original purchase price, such Shares shall become available for future
grant under the Plan. 
  

 -3- 

 4. Administration of the Plan. 
 (a) Administrator. The Plan shall be administered by the Board or a Committee appointed by the Board, which Committee shall be constituted to
comply with Applicable Laws. 
 (b) Powers of the Administrator. Subject to the provisions of the Plan and, in the case
of a Committee, the specific duties delegated by the Board to such Committee, and subject to the approval of any relevant authorities, the Administrator shall have the authority in its discretion: 
 (i) to determine the Fair Market Value; 
 (ii) to select the Service Providers to whom Options and Stock Purchase Rights may from time to time be granted hereunder; 
 (iii)
to determine the number of Shares to be covered by each such award granted hereunder; 
 (iv) to approve forms of agreement for use under
the Plan; 
 (v) to determine the terms and conditions of any Option or Stock Purchase Right granted hereunder. Such terms and conditions
include, but are not limited to, the exercise price, the time or times when Options or Stock Purchase Rights may be exercised (which may be based on performance criteria), any vesting acceleration or waiver of forfeiture restrictions, and any
restriction or limitation regarding any Option or Stock Purchase Right or the Common Stock relating thereto, based in each case on such factors as the Administrator, in its sole discretion, shall determine; 
 (vi) to prescribe, amend and rescind rules and regulations relating to the Plan, including rules and regulations relating to sub-plans established for
the purpose of satisfying applicable foreign laws; 
 (vii) to allow Optionees to satisfy withholding tax obligations by electing to have
the Company withhold from the Shares to be issued upon exercise of an Option or Stock Purchase Right that number of Shares having a Fair Market Value equal to the minimum amount required to be withheld. The Fair Market Value of the Shares to be
withheld shall be determined on the date that the amount of tax to be withheld is to be determined. All elections by Optionees to have Shares withheld for this purpose shall be made in such form and under such conditions as the Administrator may
deem necessary or advisable; and 
 (viii) to construe and interpret the terms of the Plan and Options granted pursuant to the Plan.

 (c) Effect of Administrator’s Decision. All decisions, determinations and interpretations of the Administrator
shall be final and binding on all Optionees. 
  

 -4- 

 5. Eligibility. Nonstatutory Stock Options and Stock Purchase Rights may be granted to Service
Providers. Incentive Stock Options may be granted only to Employees. 
 6. Limitations. 
 (a) Incentive Stock Option Limit. Each Option shall be designated in the Option Agreement as either an Incentive Stock Option or a Nonstatutory
Stock Option. However, notwithstanding such designation, to the extent that the aggregate Fair Market Value of the Shares with respect to which Incentive Stock Options are exercisable for the first time by the Optionee during any calendar year
(under all plans of the Company and any Parent or Subsidiary) exceeds $100,000, such Options shall be treated as Nonstatutory Stock Options. For purposes of this Section 6(a), Incentive Stock Options shall be taken into account in the order in
which they were granted. The Fair Market Value of the Shares shall be determined as of the time the Option with respect to such Shares is granted. 
 (b) At-Will Employment. Neither the Plan nor any Option or Stock Purchase Right shall confer upon any Optionee any right with respect to continuing the Optionee’s relationship as a Service Provider with the Company, nor shall it
interfere in any way with his or her right or the Company’s right to terminate such relationship at any time, with or without cause, and with or without notice. 
 7. Term of Plan. Subject to stockholder approval in accordance with Section 19, the Plan shall become effective upon its adoption by the Board. Unless sooner terminated under Section 15, it
shall continue in effect for a term of ten (10) years from the later of (i) the effective date of the Plan, or (ii) the earlier of the most recent Board or stockholder approval of an increase in the number of Shares reserved for
issuance under the Plan. 
 8. Term of Option. The term of each Option shall be stated in the Option Agreement; provided, however,
that the term shall be no more than ten (10) years from the date of grant thereof. In the case of an Incentive Stock Option granted to an Optionee who, at the time the Option is granted, owns stock representing more than ten percent
(10%) of the voting power of all classes of stock of the Company or any Parent or Subsidiary, the term of the Option shall be five (5) years from the date of grant or such shorter term as may be provided in the Option Agreement.

 9. Option Exercise Price and Consideration. 
 (a) Exercise Price. The per share exercise price for the Shares to be issued upon exercise of an Option shall be such price as is determined by the Administrator, but shall be subject to the following:

 (i) In the case of an Incentive Stock Option 
 (A) granted to an Employee who, at the time of grant of such Option, owns stock representing more than ten percent (10%) of the voting power of all classes of stock of the Company or any Parent or Subsidiary, the
exercise price shall be no less than 110% of the Fair Market Value per Share on the date of grant. 
  

 -5- 

 (B) granted to any other Employee, the per Share exercise price shall be no less than 100% of the Fair
Market Value per Share on the date of grant. 
 (ii) In the case of a Nonstatutory Stock Option 
 (A) granted to a Service Provider who, at the time of grant of such Option, owns stock representing more than ten percent (10%) of the voting power
of all classes of stock of the Company or any Parent or Subsidiary, the exercise price shall be no less than 110% of the Fair Market Value per Share on the date of grant. 
 (B) granted to any other Service Provider, the per Share exercise price shall be no less than 85% of the Fair Market Value per Share on the date of
grant. 
 (iii) Notwithstanding the foregoing, Options may be granted with a per Share exercise price other than as required above pursuant
to a merger or other corporate transaction. 
 (b) Forms of Consideration. The consideration to be paid for the Shares to be issued
upon exercise of an Option, including the method of payment, shall be determined by the Administrator (and, in the case of an Incentive Stock Option, shall be determined at the time of grant). Such consideration may consist of, without limitation,
(1) cash, (2) check, (3) promissory note, (4) other Shares, provided Shares acquired directly from the Company (x) have been owned by the Optionee for more than six months on the date of surrender, and (y) have a Fair
Market Value on the date of surrender equal to the aggregate exercise price of the Shares as to which such Option shall be exercised, (5) consideration received by the Company under a cashless exercise program implemented by the Company in
connection with the Plan, or (6) any combination of the foregoing methods of payment. In making its determination as to the type of consideration to accept, the Administrator shall consider if acceptance of such consideration may be reasonably
expected to benefit the Company. 
 10. Exercise of Option. 
 (a) Procedure for Exercise; Rights as a Stockholder. Any Option granted hereunder shall be exercisable according to the terms hereof at
such times and under such conditions as determined by the Administrator and set forth in the Option Agreement. An Option may not be exercised for a fraction of a Share. Except in the case of Options granted to officers, Directors and Consultants,
Options shall become exercisable at a rate of no less than 20% per year over five (5) years from the date the Options are granted. 
 An Option shall be deemed exercised when the Company receives (i) written or electronic notice of exercise (in accordance with the Option Agreement) from the person entitled to exercise the Option, and (ii) full payment for the
Shares with respect to which the Option is exercised. Full payment may consist of any consideration and method of payment authorized by the Administrator and permitted by the Option Agreement and the Plan. Shares issued upon exercise of an Option
shall be issued in the name of the Optionee or, if requested by the Optionee, in the name of the Optionee and his or her spouse. Until the Shares are issued (as evidenced by the appropriate entry on the books of the Company or of a duly authorized
transfer agent of the Company), no right to vote or receive dividends or any other rights as a stockholder shall exist with respect to the Shares, notwithstanding the exercise of the Option. The Company shall issue (or cause to be issued) such

  

 -6- 

 
Shares promptly after the Option is exercised. No adjustment will be made for a dividend or other right for which the record date is prior to the date the
Shares are issued, except as provided in Section 13 of the Plan. 
 Exercise of an Option in any manner shall result in a decrease in
the number of Shares thereafter available, both for purposes of the Plan and for sale under the Option, by the number of Shares as to which the Option is exercised. 
 (b) Termination of Relationship as a Service Provider. If an Optionee ceases to be a Service Provider, such Optionee may exercise his or her Option within thirty (30) days of termination, or such
longer period of time as specified in the Option Agreement, to the extent that the Option is vested on the date of termination (but in no event later than the expiration of the term of the Option as set forth in the Option Agreement). If, on the
date of termination, the Optionee is not vested as to his or her entire Option, the Shares covered by the unvested portion of the Option shall revert to the Plan. If, after termination, the Optionee does not exercise his or her Option within the
time specified by the Administrator, the Option shall terminate, and the Shares covered by such Option shall revert to the Plan. 
 (c)
Disability of Optionee. If an Optionee ceases to be a Service Provider as a result of the Optionee’s Disability, the Optionee may exercise his or her Option within six (6) months of termination, or such longer period of time as
specified in the Option Agreement, to the extent the Option is vested on the date of termination (but in no event later than the expiration of the term of such Option as set forth in the Option Agreement). If, on the date of termination, the
Optionee is not vested as to his or her entire Option, the Shares covered by the unvested portion of the Option shall revert to the Plan. If, after termination, the Optionee does not exercise his or her Option within the time specified herein, the
Option shall terminate, and the Shares covered by such Option shall revert to the Plan. 
 (d) Death of Optionee. If an
Optionee dies while a Service Provider, the Option may be exercised within six (6) months following Optionee’s death, or such longer period of time as specified in the Option Agreement, to the extent that the Option is vested on the date
of death (but in no event later than the expiration of the term of such Option as set forth in the Option Agreement) by the Optionee’s designated beneficiary, provided such beneficiary has been designated prior to Optionee’s death in a
form acceptable to the Administrator. If no such beneficiary has been designated by the Optionee, then such Option may be exercised by the personal representative of the Optionee’s estate or by the person(s) to whom the Option is transferred
pursuant to the Optionee’s will or in accordance with the laws of descent and distribution. If, at the time of death, the Optionee is not vested as to his or her entire Option, the Shares covered by the unvested portion of the Option shall
immediately revert to the Plan. If the Option is not so exercised within the time specified herein, the Option shall terminate, and the Shares covered by such Option shall revert to the Plan. 
 (e) Leaves of Absence. 
 (i) A
Service Provider shall not cease to be an Employee in the case of (A) any leave of absence approved by the Company or (B) transfers between locations of the Company or between the Company, its Parent, any Subsidiary, or any successor.

  

 -7- 

 (ii) For purposes of Incentive Stock Options, no such leave may exceed ninety (90) days, unless
reemployment upon expiration of such leave is guaranteed by statute or contract. If reemployment upon expiration of a leave of absence approved by the Company is not so guaranteed, then three (3) months following the 91st day of such leave, any
Incentive Stock Option held by the Optionee shall cease to be treated as an Incentive Stock Option and shall be treated for tax purposes as a Nonstatutory Stock Option. 
 11. Stock Purchase Rights. 
 (a) Rights to Purchase. Stock Purchase Rights may be issued either
alone, in addition to, or in tandem with other awards granted under the Plan and/or cash awards made outside of the Plan. After the Administrator determines that it will offer Stock Purchase Rights under the Plan, it shall advise the offeree in
writing or electronically of the terms, conditions and restrictions related to the offer, including the number of Shares that such person shall be entitled to purchase, the price to be paid, and the time within which such person must accept such
offer. The terms of the offer shall comply in all respects with Section 260.140.42 of Title 10 of the California Code of Regulations. The offer shall be accepted by execution of a Restricted Stock Purchase Agreement in the form determined by
the Administrator. 
 (b) Repurchase Option. Unless the Administrator determines otherwise, the Restricted Stock Purchase Agreement
shall grant the Company a repurchase option exercisable within 90 days of the voluntary or involuntary termination of the purchaser’s service with the Company for any reason (including death or disability). The purchase price for Shares
repurchased pursuant to the Restricted Stock Purchase Agreement shall be the original price paid by the purchaser and may be paid by cancellation of any indebtedness of the purchaser to the Company. The repurchase option shall lapse at such rate as
the Administrator may determine. Except with respect to Shares purchased by officers, Directors and Consultants, the repurchase option shall in no case lapse at a rate of less than 20% per year over five (5) years from the date of
purchase. 
 (c) Other Provisions. The Restricted Stock Purchase Agreement shall contain such other terms, provisions and conditions
not inconsistent with the Plan as may be determined by the Administrator in its sole discretion. 
 (d) Rights as a Stockholder. Once
the Stock Purchase Right is exercised, the purchaser shall have rights equivalent to those of a stockholder and shall be a stockholder when his or her purchase is entered upon the records of the duly authorized transfer agent of the Company. No
adjustment shall be made for a dividend or other right for which the record date is prior to the date the Stock Purchase Right is exercised, except as provided in Section 13 of the Plan. 
 12. Limited Transferability of Options and Stock Purchase Rights. Unless determined otherwise by the Administrator, Options and Stock
Purchase Rights may not be sold, pledged, assigned, hypothecated, transferred, or disposed of in any manner other than by will or the laws of descent and distribution, and may be exercised during the lifetime of the Optionee, only by the Optionee.
If the Administrator in its sole discretion makes an Option or Stock Purchase Right transferable, such Option or Stock Purchase Right may only be transferred (i) by will, (ii) by the laws of descent and distribution, or (iii) to
family members (within the meaning of Rule 701 of the Securities Act) through gifts or domestic relations orders, as permitted by Rule 701 of the Securities Act. 
  

 -8- 

 13. Adjustments; Dissolution or Liquidation; Merger or Change in Control. 
 (a) Adjustments. In the event that any dividend or other distribution (whether in the form of cash, Shares, other securities, or other property),
recapitalization, stock split, reverse stock split, reorganization, merger, consolidation, split-up, spin-off, combination, repurchase, or exchange of Shares or other securities of the Company, or other change in the corporate structure of the
Company affecting the Shares occurs, the Administrator, in order to prevent diminution or enlargement of the benefits or potential benefits intended to be made available under the Plan and in order to comply with Section 25102(o) of the
California Corporations Code, shall adjust the number and class of Shares that may be delivered under the Plan and/or the number, class, and price of Shares covered by each outstanding Option or Stock Purchase Right. 
 (b) Dissolution or Liquidation. In the event of the proposed dissolution or liquidation of the Company, the Administrator shall notify each
Optionee as soon as practicable prior to the effective date of such proposed transaction. The Administrator in its discretion may provide for an Optionee to have the right to exercise his or her Option until ten (10) days prior to such
transaction as to all of the Optioned Stock, including Shares as to which the Option would not otherwise be exercisable. In addition, the Administrator may provide that any Company repurchase option applicable to any Shares purchased upon exercise
of an Option or Stock Purchase Right shall lapse as to all such Shares, provided the proposed dissolution or liquidation takes place at the time and in the manner contemplated. To the extent it has not been previously exercised, an Option or Stock
Purchase Right will terminate immediately prior to the consummation of such proposed action. 
 (c) Merger or Change in Control. In the
event of a merger of the Company with or into another corporation, or a Change in Control, each outstanding Option and Stock Purchase Right shall be assumed or an equivalent option substituted by the successor corporation or a Parent or Subsidiary
of the successor corporation. In the event that the successor corporation in a merger or Change in Control refuses to assume or substitute for the Option or Stock Purchase Right, then the Optionee shall fully vest in and have the right to exercise
the Option or Stock Purchase Right as to all of the Optioned Stock, including Shares as to which it would not otherwise be vested or exercisable. If an Option or Stock Purchase Right becomes fully vested and exercisable in lieu of assumption or
substitution in the event of a merger or Change in Control, the Administrator shall notify the Optionee in writing or electronically that this Option or Stock Purchase Right shall be fully exercisable for a period of fifteen (15) days from the
date of such notice, and the Option or Stock Purchase Right shall terminate upon expiration of such period. For the purposes of this paragraph, the Option or Stock Purchase Right shall be considered assumed if, following the merger or Change in
Control, the option or right confers the right to purchase or receive, for each Share of Optioned Stock subject to the Option or Stock Purchase Right immediately prior to the merger or Change in Control, the consideration (whether stock, cash, or
other securities or property) received in the merger or Change in Control by holders of Common Stock for each Share held on the effective date of the transaction (and if holders were offered a choice of consideration, the type of consideration
chosen by the holders of a majority of the outstanding Shares); provided, however, that if such consideration received in the merger or Change in Control is not solely common stock of the successor corporation or its Parent, the Administrator may,
with the consent of the successor 

  

 -9- 

 
corporation, provide for the consideration to be received upon the exercise of the Option or Stock Purchase Right, for each Share of Optioned Stock subject
to the Option or Stock Purchase Right, to be solely common stock of the successor corporation or its Parent equal in fair market value to the per share consideration received by holders of common stock in the merger or Change in Control. 

14. Time of Granting Options and Stock Purchase Rights. The date of grant of an Option or Stock Purchase Right shall, for all
purposes, be the date on which the Administrator makes the determination granting such Option or Stock Purchase Right, or such later date as is determined by the Administrator. Notice of the determination shall be given to each Service Provider to
whom an Option or Stock Purchase Right is so granted within a reasonable time after the date of such grant. 
 15.
Amendment and Termination of the Plan. 
 (a) Amendment and Termination. The Board may at any time
amend, alter, suspend or terminate the Plan. 
 (b) Stockholder Approval. The Board shall obtain stockholder approval of any Plan
amendment to the extent necessary and desirable to comply with Applicable Laws. 
 (c)
Effect of Amendment or Termination. No amendment, alteration, suspension or termination of the Plan shall impair the rights of any Optionee, unless mutually agreed otherwise between the Optionee and the Administrator,
which agreement must be in writing and signed by the Optionee and the Company. Termination of the Plan shall not affect the Administrator’s ability to exercise the powers granted to it hereunder with respect to Options granted under the Plan
prior to the date of such termination. 
 16. Conditions Upon Issuance of Shares. 
 (a) Legal Compliance. Shares shall not be issued pursuant to the exercise of an Option unless the exercise of such Option and the issuance and
delivery of such Shares shall comply with Applicable Laws and shall be further subject to the approval of counsel for the Company with respect to such compliance. 
 (b) Investment Representations. As a condition to the exercise of an Option, the Administrator may require the person exercising such Option to represent and warrant at the time of any such exercise that the
Shares are being purchased only for investment and without any present intention to sell or distribute such Shares if, in the opinion of counsel for the Company, such a representation is required. 
 17. Inability to Obtain Authority. The inability of the Company to obtain authority from any regulatory body having jurisdiction, which authority
is deemed by the Company’s counsel to be necessary to the lawful issuance and sale of any Shares hereunder, shall relieve the Company of any liability in respect of the failure to issue or sell such Shares as to which such requisite authority
shall not have been obtained. 
 18. Reservation of Shares. The Company, during the term of this Plan, shall at all times
reserve and keep available such number of Shares as shall be sufficient to satisfy the requirements of the Plan. 
  

 -10- 

 19. Stockholder Approval. The Plan shall be subject to approval by the stockholders of the Company
within twelve (12) months after the date the Plan is adopted. Such stockholder approval shall be obtained in the degree and manner required under Applicable Laws. 
 20. Information to Optionees. The Company shall provide to each Optionee and to each individual who acquires Shares pursuant to the Plan, not less frequently than annually during the period such Optionee has
one or more Options or Stock Purchase Rights outstanding, and, in the case of an individual who acquires Shares pursuant to the Plan, during the period such individual owns such Shares, copies of annual financial statements. The Company shall not be
required to provide such statements to key employees whose duties in connection with the Company assure their access to equivalent information. 
 21. Rules Particular to Specific Countries. Notwithstanding anything herein to the contrary, the terms and conditions of the Plan with respect to Optionees who are tax residents of a particular country may be subject to an addendum
to the Plan in the form of an Appendix. To the extent that the terms and conditions set forth in an Appendix conflict with any provisions of the Plan, the provisions of the Appendix shall govern. The adoption of any such Appendix shall be pursuant
to Section 15 above. 
  

 -11- 

 CODEXIS, INC. 
 2002 STOCK PLAN 
 APPENDIX 
 FOR GERMANY 
  

	1.	General 

 Each of the provisions of
the Codexis, Inc. 2002 Stock Plan shall apply to this Appendix subject to the alterations below. This Appendix shall apply in relation to Options and Stock Purchase Rights granted to Service Providers residing and providing services in Germany.

  

	2.	Exercise of Discretion 

 The
Administrator’s discretion with respect to the Plan, including, but not limited to, Section 4 (b), will be exercised in a way complying with German law, in particular with the labour law principle of equal treatment (arbeitsrechtlicher
Gleichbehandlungsgrundsatz) and with the prohibition of discrimination (Diskriminierungsverbot). 
  

	3.	Disability 

 Section 2(k) shall
read as follows: “Disability” means total and permanent disability to perform work if it results in termination of employment by the Service Provider or, if valid under German law, by the Company or the Subsidiary. 
  

 -12- 

	4.	Vesting Requirement 

 The last sentence of the first
paragraph of Section 10(a) and the last sentence of Section 11(b) shall not apply. 
  

	5.	Leaves of Absence 

 Section 10(e)(i) is amended to read in its entirety as follows: “(i) A Service Provider shall not cease to be an Employee: (A) in the case of any leave of absence approved by the Company; (B) in the case of transfers
between locations of the Company or between the Company, its Parent, any Subsidiary, or any successor; or (C) if required by German law.” 
  

	6.	Ex-gratia benefit 

 The grant of an Option or a Stock Purchase Right is an ex-gratia benefit (freiwillige Leistung). It does not create a legal claim; and even repeated granting will not create such a legal claim. 
 The Option or Stock Purchase Right granted shall not form, or be considered, part of any normal or expected compensation that is or may be
subject to severance, resignation, redundancy or similar pay nor does it affect or change in any way the terms and conditions of employment. 
  

	7.	Adjustments upon Changes in Capitalization, Merger or Asset Sale 

 The Administrator’s discretion with respect to any Adjustments pursuant to Section 13 and to any Investment Representation pursuant to Section 16(b) will be exercised taking into fair consideration the
circumstances why such adjustment or representation is deemed appropriate. 
  

	8.	Taxes/Withholding 

 The following summary of
certain German income tax considerations for German Employees is based on the tax law effective at the date of this Appendix which may be changed, even with retroactive effect. The summary does not describe all tax considerations that may be
relevant to a German Employee’s decision to accept or exercise any of the rights under the Plan. It is not a substitute for tax advice. 
  

 -13- 

 Capital gains realized upon exercise of an Option or a Stock Purchase Right is deemed to be a benefit in
kind subject to income tax. Such gain is subject to the personal income tax rate (as of 2008 between 15.8 % and 47.5 % including solidarity surcharge). The capital gain realized upon exercise of an Option or a Stock Purchase Right is
determined by the difference between the fair market value of the Shares at the date the Shares are booked out (Ausbuchung) of the account of the Company or of any transfer agent of the Company and the purchase price. The fair market value is
defined on the basis of the prices quoted on the respective stock exchange or, if the Shares are not listed, according to an appropriate appraisal method available for unlisted shares of corporations. A reduced tax rate may apply if the grant of the
option qualifies as salary for several years. 
 The employer company is obligated to deduct wage tax from the gross salary of the Employee.
Additionally, the usual social security contributions, up to the relevant maximum amount, have to be paid on the difference between the exercise price and the market value at the time the Option or Stock Purchase Right is exercised. – If the
regular salary of the Employee is not sufficient for the employer company to deduct wage tax and pay such tax to the competent tax office, the company will request the Employee to make a payment to the company in order to enable it to pay the wage
tax. The employer company will inform the tax office if the Employee fails to fulfill such request. 
 If the Employee is obliged to
retransfer the Shares to the Company under the Repurchase Option, such retransfer should be considered as negative income for the Employee thereby reducing the Employee’s overall income for the respective calendar year. The amount of the
negative income is determined by the difference between the fair market value of the Shares at the date the Shares are retransferred and the purchase price. The fair market value is defined as described above. 
 Capital gains from the sale of Shares are only subject to taxation, (i) if the sale takes place within one year from the purchase as a so-called
private transaction (privates Veräußerungsgeschäft) or – after this period has lapsed – (ii) if the Optionee (or the 

  

 -14- 

 
predecessor in the case of a transfer of Shares without consideration), at any time during the five years preceding the sale, directly or indirectly held or
holds a participation of 1% or more. Capital gains deriving from a disposal of Shares as private transactions are tax exempt for Employees if the total gains from private transactions in the respective calendar year amounts to less than
€ 512 p.a. and per person. To the extent that capital gains upon sale of Shares are subject to German income tax, 50% of such capital gains are subject to the progressive income tax rate plus a solidarity surcharge of 5.5% thereon.
According to the newly enacted Corporate Tax Reform Act 2008 (Unternehmensteuerreform 2008) capital gains will generally be subject to a uniform 25% tax (plus solidarity surcharge and, if applicable, church tax) as of 2009 if the respective
Shares have been acquired after 31 December 2008 unless a shareholder holds, or held at any time during the five years preceding the sale, directly or indirectly, an interest of 1% or more in the company, in which case 60% from any such sale
will be subject to tax at personal rates (instead of currently only 50%). Generally, the bank will levy the 25% tax on the capital gain by way of withholding if the Shares are held through a domestic bank or a domestic branch of a foreign bank (a
“Bank”). However, since the purchase price of the Shares cannot be verified for withholding purposes , the Bank will be obliged to levy the 25% tax (plus solidarity surcharge and, if applicable, church tax) on 30% of the sales price of the
Shares from which parts may possibly be recovered later by the shareholder by way of filing an income tax return. Capital gains stemming from Shares acquired before 1 January 2009 will continue to be taxed pursuant to the current tax regime
(see above). 
 In principle, 50% of the gross dividends received by Employees until 31 December 2008 will be subject to income tax at
the progressive tax rate plus solidarity surcharge. Investment income received by the Employee, including dividends, after deduction of half the income-related expenses in economic connection with the dividends or the standard amount for
income-related expenses of € 51 (€ 102 for married couples filing jointly), are tax-free up to the maximum amount of tax-free savings allowances of € 750 (or € 1,500 for married couples filing jointly) until
31 December 2008. Dividends received thereafter will be subject to the 25% tax rate as described above which will be collected by way of withholding provided the Shares are held through a Bank. The current tax allowances and deductions will be
replaced from 2009 onward by a joint lump-sum deduction for capital income (i.e., interest and 

  

 -15- 

 
dividend income as well as capital gains) of €801 (€1,602 for married couples filing tax returns jointly) per annum, whereby higher expenses
directly attributable to a capital investment will not be deductible as expenses any more. 
 Please note that a taxpayer will be able to
apply for a tax assessment if his or her personal tax rate is lower than the 25% flat-rate (Günstigerprüfung) or if the taxpayer can claim a tax credit for tax imposed by foreign Tax Authorities that has not been recognized yet by
way of withholding. 
  

	9.	Insider Dealings 

 Please note that Germany has
adopted the EC-Directive on Insider Dealings. Insiders are, among others, persons who by virtue of their position as members of managing or supervisory boards of the issuing company or its subsidiaries or by their profession or work, have knowledge
of not publicly known facts which may influence the market value of the securities issued. Insiders are subject to certain restrictions in selling or purchasing such securities or otherwise making use of their insider knowledge. Anyone in breach of
those provisions will be liable to imprisonment or fine. 
  

	10.	Administrator’s decisions 

 The
decisions of the Administrator in connection with any interpretation of the Plan or in any dispute relating to an Option or a Stock Purchase Right or other matters relating to the Plan shall be final and conclusive and binding on the relevant
parties. It may only be revised by competent courts. 
  

	11.	Governing Law 

 The Plan shall be
governed by and construed in accordance with the laws of the State of Delaware but mandatory provisions of German law may be applied. 
  

 -16- 

 CODEXIS, INC. 
 2002 STOCK PLAN 
 STOCK OPTION AGREEMENT 
 Unless otherwise defined herein, the terms defined in the 2002 Stock Plan shall have the same defined meanings in this Stock Option Agreement.

  

	I.	NOTICE OF STOCK OPTION GRANT 

 Name: 

 Address: 
 The
undersigned Optionee has been granted an Option to purchase Common Stock of the Company, subject to the terms and conditions of the Plan and this Option Agreement, as follows: 
  

							
	Date of Grant	 	                                      
                                        
     	  	
			
	Vesting Commencement Date	 	                                      
                                        
     	  	
			
	Exercise Price per Share	 	$                                      
                                        
  	  	
			
	Total Number of Shares Granted	 	                                      
                                        
     	  	
			
	Total Exercise Price	 	$                                      
                                        
  	  	
				
	Type of Option:	 	—	  	Incentive Stock Option	  	
				
		 	—	  	Nonstatutory Stock Option	  	
			
	Term/Expiration Date:	 	                                      
                                        
     	  	

 Vesting Schedule: 
 This Option shall be exercisable, in whole or in part, according to the following vesting schedule: 
 25% of the Shares subject to the Option shall vest on the one (1) year anniversary of the Vesting Commencement Date, and 1/48 of the Option shall
vest each month thereafter, subject to Optionee continuing to be a Service Provider on such dates. 

 Termination Period: 
 This Option shall be exercisable for three (3) months after Optionee ceases to be a Service Provider. Upon Optionee’s death or Disability, this Option may be exercised for one (1) year after Optionee
ceases to be a Service Provider. In no event may Optionee exercise this Option after the Term/Expiration Date as provided above. 
  

	II.	AGREEMENT 

 1. Grant of Option. The
Plan Administrator of the Company hereby grants to the Optionee named in the Notice of Grant (the “Optionee”), an option (the “Option”) to purchase the number of Shares set forth in the Notice of Grant, at the exercise price per
Share set forth in the Notice of Grant (the “Exercise Price”), and subject to the terms and conditions of the Plan, which is incorporated herein by reference. Subject to Section 15(c) of the Plan, in the event of a conflict between
the terms and conditions of the Plan and this Option Agreement, the terms and conditions of the Plan shall prevail. 
 If designated in the
Notice of Grant as an Incentive Stock Option (“ISO”), this Option is intended to qualify as an Incentive Stock Option as defined in Section 422 of the Code. Nevertheless, to the extent that it exceeds the $100,000 rule of Code
Section 422(d), this Option shall be treated as a Nonstatutory Stock Option (“NSO”). 
 2. Exercise of Option.

 (a) Right to Exercise. This Option shall be exercisable during its term in accordance with the Vesting Schedule set out in the
Notice of Grant and with the applicable provisions of the Plan and this Option Agreement. 
 (b) Method of Exercise. This Option shall
be exercisable by delivery of an exercise notice in the form attached as Exhibit A (the “Exercise Notice”) which shall state the election to exercise the Option, the number of Shares with respect to which the Option is being
exercised, and such other representations and agreements as may be required by the Company. The Exercise Notice shall be accompanied by payment of the aggregate Exercise Price as to all Exercised Shares. This Option shall be deemed to be exercised
upon receipt by the Company of such fully executed Exercise Notice accompanied by the aggregate Exercise Price. 
 No Shares shall be issued
pursuant to the exercise of an Option unless such issuance and such exercise complies with Applicable Laws. Assuming such compliance, for income tax purposes the Shares shall be considered transferred to the Optionee on the date on which the Option
is exercised with respect to such Shares. 
 3. Optionee’s Representations. In the event the Shares have not been registered
under the Securities Act of 1933, as amended, at the time this Option is exercised, the Optionee shall, if required by the Company, concurrently with the exercise of all or any portion of this Option, deliver to the Company his or her Investment
Representation Statement in the form attached hereto as Exhibit B. 
  

 -2- 

 4. Lock-Up Period. Optionee hereby agrees that Optionee shall not offer, pledge, sell, contract to
sell, sell any option or contract to purchase, purchase any option or contract to sell, grant any option, right or warrant to purchase, lend, or otherwise transfer or dispose of, directly or indirectly, any Common Stock (or other securities) of the
Company or enter into any swap, hedging or other arrangement that transfers to another, in whole or in part, any of the economic consequences of ownership of any Common Stock (or other securities) of the Company held by Optionee (other than those
included in the registration) for a period specified by the representative of the underwriters of Common Stock (or other securities) of the Company not to exceed one hundred eighty (180) days following the effective date of any registration
statement of the Company filed under the Securities Act. 
 Optionee agrees to execute and deliver such other agreements as may be reasonably
requested by the Company or the underwriter which are consistent with the foregoing or which are necessary to give further effect thereto. In addition, if requested by the Company or the representative of the underwriters of Common Stock (or other
securities) of the Company, Optionee shall provide, within ten (10) days of such request, such information as may be required by the Company or such representative in connection with the completion of any public offering of the Company’s
securities pursuant to a registration statement filed under the Securities Act. The obligations described in this Section shall not apply to a registration relating solely to employee benefit plans on Form S-1 or Form S-8 or similar forms that may
be promulgated in the future, or a registration relating solely to a Commission Rule 145 transaction on Form S-4 or similar forms that may be promulgated in the future. The Company may impose stop-transfer instructions with respect to the shares of
Common Stock (or other securities) subject to the foregoing restriction until the end of said one hundred eighty (180) day period. Optionee agrees that any transferee of the Option or Shares acquired pursuant to the Option shall be bound by
this Section. 
 5. Method of Payment. Payment of the aggregate Exercise Price shall be by any of the following, or a combination
thereof, at the election of the Optionee: 
 (a) cash or check; 
 (b) consideration received by the Company under a formal cashless exercise program adopted by the Company in connection with the Plan; or 
 (c) surrender of other Shares which, (i) in the case of Shares acquired from the Company, either directly or indirectly, have been owned by the Optionee for more than six (6) months on the date of surrender,
and (ii) have a Fair Market Value on the date of surrender equal to the aggregate Exercise Price of the Exercised Shares. 
 6.
Restrictions on Exercise. This Option may not be exercised until such time as the Plan has been approved by the stockholders of the Company, or if the issuance of such Shares upon such exercise or the method of payment of consideration for
such Shares would constitute a violation of any Applicable Law. 
 7. Non-Transferability of Option. This Option may not be
transferred in any manner otherwise than by will or by the laws of descent or distribution and may be exercised during the lifetime of Optionee only by Optionee. The terms of the Plan and this Option Agreement shall be binding upon the executors,
administrators, heirs, successors and assigns of the Optionee. 
  

 -3- 

 8. Term of Option. This Option may be exercised only within the term set out in the Notice of
Grant, and may be exercised during such term only in accordance with the Plan and the terms of this Option. 
 9. Tax Obligations.

 (a) Withholding Taxes. Optionee agrees to make appropriate arrangements with the Company (or the Parent or Subsidiary employing or
retaining Optionee) for the satisfaction of all Federal, state, local and foreign income and employment tax withholding requirements applicable to the Option exercise. Optionee acknowledges and agrees that the Company may refuse to honor the
exercise and refuse to deliver Shares if such withholding amounts are not delivered at the time of exercise. 
 (b) Notice of
Disqualifying Disposition of ISO Shares. If the Option granted to Optionee herein is an ISO, and if Optionee sells or otherwise disposes of any of the Shares acquired pursuant to the ISO on or before the later of (1) the date two years
after the Date of Grant, or (2) the date one year after the date of exercise, the Optionee shall immediately notify the Company in writing of such disposition. Optionee agrees that Optionee may be subject to income tax withholding by the
Company on the compensation income recognized by the Optionee. 
 10. Entire Agreement; Governing Law. The Plan is incorporated herein
by reference. The Plan and this Option Agreement constitute the entire agreement of the parties with respect to the subject matter hereof and supersede in their entirety all prior undertakings and agreements of the Company and Optionee with respect
to the subject matter hereof, and may not be modified adversely to the Optionee’s interest except by means of a writing signed by the Company and Optionee. This agreement is governed by the internal substantive laws but not the choice of law
rules of California. 
 11. No Guarantee of Continued Service. OPTIONEE ACKNOWLEDGES AND AGREES THAT THE VESTING OF SHARES PURSUANT TO
THE VESTING SCHEDULE HEREOF IS EARNED ONLY BY CONTINUING AS A SERVICE PROVIDER AT THE WILL OF THE COMPANY (NOT THROUGH THE ACT OF BEING HIRED, BEING GRANTED THIS OPTION OR ACQUIRING SHARES HEREUNDER). OPTIONEE FURTHER ACKNOWLEDGES AND AGREES THAT
THIS AGREEMENT, THE TRANSACTIONS CONTEMPLATED HEREUNDER AND THE VESTING SCHEDULE SET FORTH HEREIN DO NOT CONSTITUTE AN EXPRESS OR IMPLIED PROMISE OF CONTINUED ENGAGEMENT AS A SERVICE PROVIDER FOR THE VESTING PERIOD, FOR ANY PERIOD, OR AT ALL, AND
SHALL NOT INTERFERE IN ANY WAY WITH OPTIONEE’S RIGHT OR THE COMPANY’S RIGHT TO TERMINATE OPTIONEE’S RELATIONSHIP AS A SERVICE PROVIDER AT ANY TIME, WITH OR WITHOUT CAUSE. 
 Optionee acknowledges receipt of a copy of the Plan and represents that he or she is familiar with the terms and provisions thereof, and hereby accepts
this Option subject to all of the terms and provisions thereof. Optionee has reviewed the Plan and this Option in their entirety, has had an 

  

 -4- 

 
opportunity to obtain the advice of counsel prior to executing this Option and fully understands all provisions of the Option. Optionee hereby agrees to
accept as binding, conclusive and final all decisions or interpretations of the Administrator upon any questions arising under the Plan or this Option. Optionee further agrees to notify the Company upon any change in the residence address indicated
below. 
  

			
	OPTIONEE	  	CODEXIS, INC.
		
	  
	  	  

	Signature	  	By
		
	  
	  	  

	Print Name	  	Title
		
	  
	  	
	  
	  	
	Residence Address	  	

  

 -5- 

 EXHIBIT A 
 2002 STOCK PLAN 
 EXERCISE NOTICE 
 CODEXIS, INC. 
 Address:                         
 Attention:                         
 1. Exercise of Option. Effective as of today,             ,         , the undersigned
(“Optionee”) hereby elects to exercise Optionee’s option to purchase              shares of the Common Stock (the “Shares”) of Codexis, Inc. (the
“Company”) under and pursuant to the 2002 Stock Plan (the “Plan”) and the Stock Option Agreement dated             ,
         (the “Option Agreement”). 
 2. Delivery of Payment. Purchaser
herewith delivers to the Company the full purchase price of the Shares, as set forth in the Option Agreement, and any and all withholding taxes due in connection with the exercise of the Option. 
 3. Representations of Optionee. Optionee acknowledges that Optionee has received, read and understood the Plan and the Option Agreement and agrees
to abide by and be bound by their terms and conditions. 
 4. Rights as Stockholder. Until the issuance of the Shares (as evidenced by
the appropriate entry on the books of the Company or of a duly authorized transfer agent of the Company), no right to vote or receive dividends or any other rights as a stockholder shall exist with respect to the Optioned Stock, notwithstanding the
exercise of the Option. The Shares shall be issued to the Optionee as soon as practicable after the Option is exercised in accordance with the Option Agreement. No adjustment shall be made for a dividend or other right for which the record date is
prior to the date of issuance except as provided in Section 13 of the Plan. 
 5. Company’s Right of First Refusal Before
any Shares held by Optionee or any transferee (either being sometimes referred to herein as the “Holder”) may be sold or otherwise transferred (including transfer by gift or operation of law), the Company or its assignee(s) shall have a
right of first refusal to purchase the Shares on the terms and conditions set forth in this Section (the “Right of First Refusal”). 
 (a) Notice of Proposed Transfer. The Holder of the Shares shall deliver to the Company a written notice (the “Notice”) stating: (i) the Holder’s bona fide intention to sell or otherwise transfer such Shares;
(ii) the name of each proposed purchaser or other transferee (“Proposed Transferee”); (iii) the number of Shares to be transferred to each Proposed Transferee; and (iv) the bona fide cash price or other consideration for
which the Holder proposes to transfer the Shares (the “Offered Price”), and the Holder shall offer the Shares at the Offered Price to the Company or its assignee(s). 

 (b) Exercise of Right of First Refusal. At any time within thirty (30) days after receipt of
the Notice, the Company and/or its assignee(s) may, by giving written notice to the Holder, elect to purchase all, but not less than all, of the Shares proposed to be transferred to any one or more of the Proposed Transferees, at the purchase price
determined in accordance with subsection (c) below. 
 (c) Purchase Price. The purchase price (“Purchase Price”) for
the Shares purchased by the Company or its assignee(s) under this Section shall be the Offered Price. If the Offered Price includes consideration other than cash, the cash equivalent value of the non-cash consideration shall be determined by the
Board of Directors of the Company in good faith. 
 (d) Payment. Payment of the Purchase Price shall be made, at the option of the
Company or its assignee(s), in cash (by check), by cancellation of all or a portion of any outstanding indebtedness of the Holder to the Company (or, in the case of repurchase by an assignee, to the assignee), or by any combination thereof within
thirty (30) days after receipt of the Notice or in the manner and at the times set forth in the Notice. 
 (e) Holder’s Right to
Transfer. If all of the Shares proposed in the Notice to be transferred to a given Proposed Transferee are not purchased by the Company and/or its assignee(s) as provided in this Section, then the Holder may sell or otherwise transfer such
Shares to that Proposed Transferee at the Offered Price or at a higher price, provided that such sale or other transfer is consummated within 60 days after the date of the Notice, that any such sale or other transfer is effected in accordance with
any applicable securities laws and that the Proposed Transferee agrees in writing that the provisions of this Section shall continue to apply to the Shares in the hands of such Proposed Transferee. If the Shares described in the Notice are not
transferred to the Proposed Transferee within such period, a new Notice shall be given to the Company, and the Company and/or its assignees shall again be offered the Right of First Refusal before any Shares held by the Holder may be sold or
otherwise transferred. 
 (f) Exception for Certain Family Transfers. Anything to the contrary contained in this Section
notwithstanding, the transfer of any or all of the Shares during the Optionee’s lifetime or on the Optionee’s death by will or intestacy to the Optionee’s immediate family or a trust for the benefit of the Optionee’s immediate
family shall be exempt from the provisions of this Section. “Immediate Family” as used herein shall mean spouse, lineal descendant or antecedent, father, mother, brother or sister. In such case, the transferee or other recipient shall
receive and hold the Shares so transferred subject to the provisions of this Section, and there shall be no further transfer of such Shares except in accordance with the terms of this Section. 
 (g) Termination of Right of First Refusal. The Right of First Refusal shall terminate as to any Shares upon the earlier of (i) the first sale
of Common Stock of the Company to the general public, or (ii) a Change in Control in which the successor corporation has equity securities that are publicly traded. 
  

 -2- 

 6. Tax Consultation. Optionee understands that Optionee may suffer adverse tax consequences as a
result of Optionee’s purchase or disposition of the Shares. Optionee represents that Optionee has consulted with any tax consultants Optionee deems advisable in connection with the purchase or disposition of the Shares and that Optionee is not
relying on the Company for any tax advice. 
 7. Restrictive Legends and Stop-Transfer Orders. 
 (a) Legends. Optionee understands and agrees that the Company shall cause the legends set forth below or legends substantially equivalent thereto,
to be placed upon any certificate(s) evidencing ownership of the Shares together with any other legends that may be required by the Company or by state or federal securities laws: 
 THE SECURITIES REPRESENTED BY THIS CERTIFICATE HAVE NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED (THE “ACT”). THEY MAY NOT
BE SOLD, OFFERED FOR SALE, PLEDGED OR HYPOTHECATED IN THE ABSENCE OF AN EFFECTIVE REGISTRATION STATEMENT UNDER THE ACT COVERING THE SECURITIES OR AN OPINION OF COUNSEL SATISFACTORY TO THE COMPANY THAT SUCH REGISTRATION IS NOT REQUIRED. 

THE SHARES REPRESENTED BY THIS CERTIFICATE ARE SUBJECT TO CERTAIN RESTRICTIONS ON TRANSFER AND A RIGHT OF FIRST REFUSAL HELD BY THE ISSUER OR ITS
ASSIGNEE(S) AS SET FORTH IN THE EXERCISE NOTICE BETWEEN THE ISSUER AND THE ORIGINAL HOLDER OF THESE SHARES, A COPY OF WHICH MAY BE OBTAINED AT THE PRINCIPAL OFFICE OF THE ISSUER. SUCH TRANSFER RESTRICTIONS AND RIGHT OF FIRST REFUSAL ARE BINDING ON
TRANSFEREES OF THESE SHARES. 
 THE SHARES REPRESENTED BY THIS CERTIFICATE ARE SUBJECT TO RESTRICTIONS ON TRANSFER FOR A PERIOD NOT TO EXCEED
180 DAYS FOLLOWING THE EFFECTIVE DATE OF THE UNDERWRITTEN PUBLIC OFFERING OF THE COMPANY’S SECURITIES AND MAY NOT BE SOLD OR OTHERWISE DISPOSED OF BY THE HOLDER WITHOUT THE CONSENT OF THE COMPANY OR THE MANAGING UNDERWRITER. 
 (b) Stop-Transfer Notices. Optionee agrees that, in order to ensure compliance with the restrictions referred to herein, the Company may issue
appropriate “stop transfer” instructions to its transfer agent, if any, and that, if the Company transfers its own securities, it may make appropriate notations to the same effect in its own records. 
 (c) Refusal to Transfer. The Company shall not be required (i) to transfer on its books any Shares that have been sold or otherwise
transferred in violation of any of the provisions of this Exercise Notice or (ii) to treat as owner of such Shares or to accord the right to vote or pay dividends to any purchaser or other transferee to whom such Shares shall have been so
transferred. 
  

 -3- 

 8. Successors and Assigns. The Company may assign any of its rights under this Exercise Notice to
single or multiple assignees, and this Exercise Notice shall inure to the benefit of the successors and assigns of the Company. Subject to the restrictions on transfer herein set forth, this Exercise Notice shall be binding upon Optionee and his or
her heirs, executors, administrators, successors and assigns. 
 9. Interpretation. Any dispute regarding the interpretation of this
Exercise Notice shall be submitted by Optionee or by the Company forthwith to the Administrator, which shall review such dispute at its next regular meeting. The resolution of such a dispute by the Administrator shall be final and binding on all
parties. 
 10. Governing Law; Severability. This Exercise Notice is governed by the internal substantive laws, but not the choice of
law rules, of California. In the event that any provision hereof becomes or is declared by a court of competent jurisdiction to be illegal, unenforceable or void, this Exercise Notice will continue in full force and effect. 
 11. Entire Agreement. The Plan and Option Agreement are incorporated herein by reference. This Exercise Notice, the Plan, the Option Agreement and
the Investment Representation Statement constitute the entire agreement of the parties with respect to the subject matter hereof and supersede in their entirety all prior undertakings and agreements of the Company and Optionee with respect to the
subject matter hereof, and may not be modified adversely to the Optionee’s interest except by means of a writing signed by the Company and Optionee. 
  

			
	 Submitted by:
	  	Accepted by:
	OPTIONEE	  	CODEXIS, INC.
		
	  
	  	  

	Signature	  	By
		
	  
	  	  

	Print Name	  	Title
		
	Address:	  	Address:
	  
	  	  

	  
	  	  

	  
	  	
		
		  	  

		  	Date Received

  

 -4- 

 EXHIBIT B 
 INVESTMENT REPRESENTATION STATEMENT 
  

			
	OPTIONEE:	  	
		
	COMPANY:	  	CODEXIS, INC.
		
	SECURITY:	  	COMMON STOCK
		
	AMOUNT:	  	
		
	DATE:	  	

 In connection with the purchase of the above-listed Securities, the undersigned Optionee
represents to the Company the following: 
 (a) Optionee is aware of the Company’s business affairs and financial condition and has
acquired sufficient information about the Company to reach an informed and knowledgeable decision to acquire the Securities. Optionee is acquiring these Securities for investment for Optionee’s own account only and not with a view to, or for
resale in connection with, any “distribution” thereof within the meaning of the Securities Act of 1933, as amended (the “Securities Act”). 
 (b) Optionee acknowledges and understands that the Securities constitute “restricted securities” under the Securities Act and have not been registered under the Securities Act in reliance upon a specific
exemption therefrom, which exemption depends upon, among other things, the bona fide nature of Optionee’s investment intent as expressed herein. In this connection, Optionee understands that, in the view of the Securities and Exchange
Commission, the statutory basis for such exemption may be unavailable if Optionee’s representation was predicated solely upon a present intention to hold these Securities for the minimum capital gains period specified under tax statutes, for a
deferred sale, for or until an increase or decrease in the market price of the Securities, or for a period of one year or any other fixed period in the future. Optionee further understands that the Securities must be held indefinitely unless they
are subsequently registered under the Securities Act or an exemption from such registration is available. Optionee further acknowledges and understands that the Company is under no obligation to register the Securities. Optionee understands that the
certificate evidencing the Securities will be imprinted with any legend required under applicable state securities laws. 
 (c) Optionee is
familiar with the provisions of Rule 701 and Rule 144, each promulgated under the Securities Act, which, in substance, permit limited public resale of “restricted securities” acquired, directly or indirectly from the issuer
thereof, in a non-public offering subject to the satisfaction of certain conditions. Rule 701 provides that if the issuer qualifies under Rule 701 at the time of the grant of the Option to the Optionee, the exercise will be exempt from
registration under the Securities Act. In the event the Company becomes subject to the reporting requirements of 

 
Section 13 or 15(d) of the Securities Exchange Act of 1934, ninety (90) days thereafter (or such longer period as any market stand-off agreement
may require) the Securities exempt under Rule 701 may be resold, subject to the satisfaction of certain of the conditions specified by Rule 144, including: (1) the resale being made through a broker in an unsolicited
“broker’s transaction” or in transactions directly with a market maker (as said term is defined under the Securities Exchange Act of 1934); and, in the case of an affiliate, (2) the availability of certain public information
about the Company, (3) the amount of Securities being sold during any three month period not exceeding the limitations specified in Rule 144(e), and (4) the timely filing of a Form 144, if applicable. 
 In the event that the Company does not qualify under Rule 701 at the time of grant of the Option, then the Securities may be resold in certain
limited circumstances subject to the provisions of Rule 144, which requires the resale to occur not less than one year after the later of the date the Securities were sold by the Company or the date the Securities were sold by an affiliate
of the Company, within the meaning of Rule 144; and, in the case of acquisition of the Securities by an affiliate, or by a non-affiliate who subsequently holds the Securities less than two years, the satisfaction of the conditions set forth in
sections (1), (2), (3) and (4) of the paragraph immediately above. 
 (d) Optionee further understands that in the event all
of the applicable requirements of Rule 701 or 144 are not satisfied, registration under the Securities Act, compliance with Regulation A, or some other registration exemption will be required; and that, notwithstanding the fact that
Rules 144 and 701 are not exclusive, the Staff of the Securities and Exchange Commission has expressed its opinion that persons proposing to sell private placement securities other than in a registered offering and otherwise than pursuant to
Rules 144 or 701 will have a substantial burden of proof in establishing that an exemption from registration is available for such offers or sales, and that such persons and their respective brokers who participate in such transactions do so at
their own risk. Optionee understands that no assurances can be given that any such other registration exemption will be available in such event. 
  

	
	Signature of Optionee:
	
	  

	
	Date:             ,         

  

 -2- 

 CODEXIS, INC. 
 2002 STOCK PLAN, AS AMENDED 
 STOCK OPTION AGREEMENT 
 Early Exercise Permitted 
 Codexis,
Inc., a Delaware corporation (the “Company”), pursuant to its 2002 Stock Plan, as amended from time to time (the “Plan”), hereby grants to the Optionee listed below (“Optionee”), an option to purchase the number of
shares of the Company’s Common Stock set forth below (the “Option”), subject to the terms and conditions of the Plan and this Stock Option Agreement (this “Option Agreement”). Unless otherwise defined herein, the terms
defined in the Plan shall have the same defined meanings in this Option Agreement. 
  

	I.	NOTICE OF STOCK OPTION GRANT 

  

					
	Optionee:	 		  	  

			
	Date of Grant:	 		  	  

			
	Vesting Commencement Date:	 		  	  

			
	Exercise Price per Share:	 		  	  

			
	Total Number of Shares Granted:	 		  	  

			
	Total Exercise Price:	 		  	  

			
	Term/Expiration Date:	 		  	  

  

			
	Type of Option:	  	Nonstatutory Stock Option
		
	Exercise Schedule:	  	 ̈  Same as Vesting Schedule    x  Early Exercise Permitted
		
	Vesting Schedule:	  	 This Option is exercisable immediately, in whole or in part, at such times as are established by the Administrator, conditioned upon Optionee
entering into a Restricted Stock Purchase Agreement with respect to any unvested Shares (as defined below). The Shares subject to this Option shall vest and/or be released from the Company’s Repurchase Option, as set forth in the Restricted
Stock Purchase Agreement attached hereto as Exhibit C-1, according to the following schedule:
  
 Twenty-five percent (25%) of the Shares subject to the Option (rounded down to the next whole number of shares) shall vest on the first anniversary of the Date of Grant and 1/48th of the Shares subject to the Option shall vest monthly thereafter so that one hundred percent (100%) of the Shares subject to the Option are vested on the fourth anniversary of the
Date of Grant.

			
	Termination Period:	  	This Option may be exercised, to the extent vested, for three (3) months after Optionee ceases to be a Service Provider, or such longer period as may be applicable upon the death or
disability of Optionee as provided herein (or, if not provided herein, then as provided in the Plan), but in no event later than the Term/Expiration Date as set forth above.

  

	II.	AGREEMENT 

 1. Grant of Option. The
Company hereby grants to Optionee an Option to purchase the number of shares of Common Stock (the “Shares”) set forth in the Notice of Grant, at the exercise price per share set forth in the Notice of Grant (the “Exercise
Price”). Notwithstanding anything to the contrary anywhere else in this Option Agreement, this grant of an Option is subject to the terms, definitions and provisions of the Plan, which is incorporated herein by reference. 
 2. Exercise of Option. This Option is exercisable as follows: 
 (a) Right to Exercise. 
 (i) This Option shall be exercisable cumulatively according to the vesting
schedule set out in the Notice of Grant. Alternatively, at the election of Optionee, this Option may be exercised in whole or in part at such times as are established by the Administrator as to Shares which have not yet vested. For purposes of this
Option Agreement, Shares subject to this Option shall vest based on Optionee’s continued status as a Service Provider. Vested Shares shall not be subject to the Company’s Repurchase Option (as set forth in the Restricted Stock Purchase
Agreement). 
 (ii) As a condition to exercising this Option for unvested Shares, Optionee shall execute the Restricted Stock Purchase
Agreement. 
 (iii) This Option may not be exercised for a fraction of a Share. 
 (iv) In the event of Optionee’s death, disability or other termination of Optionee’s status as a Service Provider, the exercisability of the
Option shall be governed by Sections 7, 8 and 9 hereof. 
 (v) In no event may this Option be exercised after the Expiration Date of
this Option as set forth in the Notice of Grant. 
 (b) Method of Exercise. This Option shall be exercisable by written notice to the
Company (in the form attached as Exhibit A) (the “Exercise Notice”). The Exercise Notice shall state the number of Shares for which the Option is being exercised, and such other representations and agreements with respect to such
Shares of Common Stock as may be required by the Company pursuant to the provisions of the Plan. The Exercise Notice shall be signed by Optionee and, together with an executed copy of the Restricted Stock Purchase Agreement, if applicable, shall be
delivered in person or by certified mail to the Secretary of the Company. The Exercise Notice and Restricted Stock Purchase Agreement shall be accompanied by payment of the Exercise Price, including payment of any applicable withholding tax.

  

 2 

 No Shares shall be issued pursuant to the exercise of an Option unless such issuance and such exercise
comply with all relevant provisions of law and the requirements of any stock exchange upon which the Shares may then be listed. Assuming such compliance, for income tax purposes the Shares shall be considered transferred to Optionee on the date on
which the Option is exercised with respect to such Shares. 
 3. Optionee’s Representations. If the Shares purchasable pursuant
to the exercise of this Option have not been registered under the Securities Act of 1933, as amended (the “Securities Act”), at the time this Option is exercised, Optionee shall, if required by the Company, concurrently with the exercise
of all or any portion of this Option, deliver to the Company his or her Investment Representation Statement in the form attached hereto as Exhibit B. 
 4. Lock-Up Period. Optionee hereby agrees that if so requested by the Company or any representative of the underwriters (the “Managing Underwriter”) in connection with any registration of the offering
of any securities of the Company under the Securities Act, Optionee shall not sell or otherwise transfer any Shares or other securities of the Company during the 180-day period (or such longer period as may be requested in writing by the
Managing Underwriter and agreed to in writing by the Company) (the “Market Standoff Period”) following the effective date of a registration statement of the Company filed under the Securities Act; provided, however, that such
restriction shall apply only to the first registration statement of the Company to become effective under the Securities Act that includes securities to be sold on behalf of the Company to the public in an underwritten public offering under the
Securities Act. The Company may impose stop-transfer instructions with respect to securities subject to the foregoing restrictions until the end of such Market Standoff Period and these restrictions shall be binding on any transferee of such Shares.
Notwithstanding the foregoing, the 180-day period may be extended for up to such number of additional days as is deemed necessary by the Company or the Managing Underwriter to continue coverage by research analysts in accordance with NASD Rule 2711
or any successor rule. 
 5. Method of Payment. Payment of the Exercise Price shall be by any of the following, or a combination
thereof, at the election of Optionee: 
 (a) cash; 
 (b) check; 
 (c) with the consent of the Administrator, a full recourse promissory note bearing interest (at
no less than such rate as is a market rate of interest and which then precludes the imputation of interest under the Code), payable upon such terms as may be prescribed by the Administrator and structured to comply with Applicable Laws; 

(d) with the consent of the Administrator, surrender of other Shares of Common Stock of the Company which (A) in the case of Shares acquired from
the Company, have been owned by Optionee for more than six (6) months on the date of surrender, and (B) have a Fair Market Value on the date of surrender equal to the Exercise Price of the Shares as to which the Option is being exercised;

  

 3 

 (e) with the consent of the Administrator, surrendered Shares issuable upon the exercise of the Option
having an aggregate Fair Market Value on the date of exercise equal to the aggregate Exercise Price of the Option or exercised portion thereof; 
 (f) with the consent of the Administrator, property of any kind which constitutes good and valuable consideration; 
 (g) following
the consummation of the initial public offering of the Company’s Common Stock pursuant to a registration statement on Form S-1 under the Securities Act, with the consent of the Administrator, delivery of a notice that Optionee has placed a
market sell order with a broker with respect to Shares then issuable upon exercise of the Option and that the broker has been directed to pay a sufficient portion of the net proceeds of the sale to the Company in satisfaction of the aggregate
Exercise Price; provided, that payment of such proceeds is then made to the Company upon settlement of such sale; or 
 (h) with the consent
of the Administrator, any combination of the foregoing methods of payment. 
 6. Restrictions on Exercise. This Option may not be
exercised until the Plan has been approved by the stockholders of the Company. If the issuance of Shares upon such exercise or if the method of payment for such Shares would constitute a violation of any applicable federal or state securities or
other law or regulation, then the Option may also not be exercised. The Company may require Optionee to make any representation and warranty to the Company as may be required by any applicable law or regulation before allowing the Option to be
exercised. 
 7. Termination of Relationship. If Optionee ceases to be a Service Provider (other than by reason of Optionee’s
death or the total and permanent disability of Optionee within the meaning of Internal Revenue Code Section 22(e)(3)), Optionee may exercise this Option during the Termination Period set out in the Notice of Grant, to the extent the Option was
vested on the date on which Optionee ceases to be a Service Provider. To the extent that the Option is not vested on the date on which Optionee ceases to be a Service Provider, or if Optionee does not exercise this Option within the time specified
herein, the Option shall terminate. 
 8. Disability of Optionee. If Optionee ceases to be a Service Provider as a result of his or
her total and permanent disability within the meaning of Internal Revenue Code Section 22(e)(3), Optionee may exercise the Option to the extent the Option was vested at the date on which Optionee ceases to be a Service Provider, but only within
twelve (12) months from such date (and in no event later than the expiration date of the term of this Option as set forth in the Notice of Grant). To the extent that the Option is not vested at the date on which Optionee ceases to be a Service
Provider, or if Optionee does not exercise such Option within the time specified herein, the Option shall terminate. 
 9. Death of
Optionee. If Optionee ceases to be a Service Provider as a result of the death of Optionee, the vested portion of the Option may be exercised at any time within twelve (12) months following the date of death (and in no event later than the
expiration date of 

  

 4 

 
the term of this Option as set forth in the Notice of Grant) by Optionee’s estate or by a person who acquires the right to exercise the Option by
bequest or inheritance. To the extent that the Option is not vested on the date of death, or if the Option is not exercised within the time specified herein, the Option shall terminate. 
 10. Non-Transferability of Option. This Option may not be transferred in any manner except by will or by the laws of descent or distribution. It
may be exercised during the lifetime of Optionee only by Optionee. The terms of this Option shall be binding upon the executors, administrators, heirs, successors and assigns of Optionee. 
 11. Term of Option. This Option may be exercised only within the term set out in the Notice of Grant. 
 12. Restrictions on Shares. Optionee hereby agrees that Shares purchased upon the exercise of the Option shall be subject to such terms and
conditions as the Administrator shall determine in its sole discretion, including, without limitation, restrictions on the transferability of Shares, the right of the Company to repurchase Shares, and a right of first refusal in favor of the Company
with respect to permitted transfers of Shares. Such terms and conditions may, in the Administrator’s sole discretion, be contained in the Exercise Notice with respect to the Option or in such other agreement as the Administrator shall determine
and which Optionee hereby agrees to enter into at the request of the Company. 
 (Signature Page Follows) 
  

 5 

 This Agreement may be executed in two or more counterparts, each of which shall be deemed an original and
all of which shall constitute one document. 
  

			
	CODEXIS, INC.
		
	 By:
	 	  

	 Name:
	 	  

	 Title:
	 	  

 OPTIONEE ACKNOWLEDGES AND AGREES THAT THE VESTING OF SHARES PURSUANT TO THE OPTION HEREOF IS
EARNED ONLY BY CONTINUING SERVICE AS A SERVICE PROVIDER (INCLUDING AS AN EMPLOYEE, DIRECTOR OR CONSULTANT) AT THE WILL OF THE COMPANY (NOT THROUGH THE ACT OF BEGINNING SERVICE, BEING GRANTED THIS OPTION OR ACQUIRING SHARES HEREUNDER). OPTIONEE
FURTHER ACKNOWLEDGES AND AGREES THAT NOTHING IN THIS AGREEMENT, NOR IN THE COMPANY’S 2002 STOCK PLAN, AS AMENDED FROM TIME TO TIME, WHICH IS INCORPORATED HEREIN BY REFERENCE, SHALL CONFER UPON OPTIONEE ANY RIGHT WITH RESPECT TO CONTINUATION OF
SERVICE AS A SERVICE PROVIDER TO THE COMPANY, NOR SHALL IT INTERFERE IN ANY WAY WITH OPTIONEE’S RIGHT OR THE COMPANY’S RIGHT TO TERMINATE SERVICE AS A SERVICE PROVIDER AT ANY TIME, WITH OR WITHOUT CAUSE AND WITH OR WITHOUT PRIOR NOTICE.

 Optionee acknowledges receipt of a copy of the Plan and represents that he or she is familiar with the terms and provisions thereof.
Optionee hereby accepts this Option subject to all of the terms and provisions hereof. Optionee has reviewed the Plan and this Option in their entirety, has had an opportunity to obtain the advice of counsel prior to executing this Option and fully
understands all provisions of the Option. Optionee hereby agrees to accept as binding, conclusive and final all decisions or interpretations of the Administrator upon any questions arising under the Plan or this Option. Optionee further agrees to
notify the Company upon any change in the residence address indicated below. 
  

			
	Dated:                     	 	  

		 	OPTIONEE
		
		 	Residence Address:

 [Signature Page to Stock Option Agreement] 

 EXHIBIT A 
 CODEXIS, INC. 
 2002 STOCK PLAN, AS AMENDED 
 EXERCISE NOTICE 
 Codexis, Inc. 
 Attention: Stock Administration 
 1. Exercise of
Option. Effective as of today,             ,         , the undersigned (“Optionee”) hereby elects to exercise
Optionee’s option to purchase              shares of the Common Stock (the “Shares”) of Codexis, Inc., a Delaware corporation (the “Company”), under and
pursuant to the Codexis, Inc. 2002 Stock Plan, as amended from time to time (the “Plan”) and the Stock Option Agreement dated
                     (the “Option Agreement”). Capitalized terms used herein without definition shall have the meanings given in the
Option Agreement. 
  

							
	Date of Grant:	 		  	  
	  	
				
	Number of Shares as to which Option is Exercised:	 		  	  
	  	
				
	Exercise Price per Share:	 		  	$                        	  	
				
	Total Exercise Price:	 		  	$                        	  	
				
	Certificate to be issued in name of:	 		  	  
	  	
				
	Cash Payment delivered herewith:	 		  	$                        	  	
				
	Other form of consideration delivered herewith:	 		  	 Form of Consideration:
 $                        
	  	

 Type of
Option:            Nonstatutory Stock Option 
 2. Representations of
Optionee. Optionee acknowledges that Optionee has received, read and understood the Plan and the Option Agreement. Optionee agrees to abide by and be bound by their terms and conditions. 
 3. Rights as Stockholder. Until the stock certificate evidencing Shares purchased pursuant to the exercise of the Option is issued (as evidenced
by the appropriate entry on the books of the Company or of a duly authorized transfer agent of the Company), no right to vote or receive dividends or any other rights as a stockholder shall exist with respect to Shares subject to the Option,
notwithstanding the exercise of the Option. The Company shall issue (or cause to be issued) such stock certificate promptly after the Option is exercised. No adjustment will be made for a dividend or other right for which the record date is prior to
the date the stock certificate is issued, except as provided in Section 13 of the Plan. 

 Optionee shall enjoy rights as a stockholder until such time as Optionee disposes of the Shares or the
Company and/or its assignee(s) exercises the Right of First Refusal (as defined below) hereunder. Upon such exercise, Optionee shall have no further rights as a holder of the Shares so purchased except the right to receive payment for the Shares so
purchased in accordance with the provisions of this Agreement, and Optionee shall forthwith cause the certificate(s) evidencing the Shares so purchased to be surrendered to the Company for transfer or cancellation. 
 4. Optionee’s Rights to Transfer Shares 
 (a) Company’s Right of First Refusal. Before any Shares held by Optionee or any permitted transferee (each, a “Holder”) may be sold, pledged, assigned, hypothecated, transferred, or otherwise disposed of (each, a
“Transfer”), the Company or its assignee(s) shall have a right of first refusal to purchase the Shares proposed to be Transferred on the terms and conditions set forth in this Section 4 (the “Right of First Refusal”).

 (i) Notice of Proposed Transfer. In the event any Holder desires to Transfer any Shares, the Holder shall deliver to the Company a
written notice (the “Notice”) stating: (w) the Holder’s bona fide intention to sell or otherwise Transfer such Shares; (x) the name of each proposed purchaser or other transferee (“Proposed Transferee”);
(y) the number of Shares to be Transferred to each Proposed Transferee; and (z) the bona fide cash price or other consideration for which the Holder proposes to Transfer the Shares (the “Offered Price”), and the Holder shall
offer such Shares at the Offered Price to the Company or its assignee(s). 
 (ii) Exercise of Right of First Refusal. Within thirty
(30) days after receipt of the Notice, the Company and/or its assignee(s) may elect in writing to purchase all, but not less than all, of the Shares proposed to be Transferred to any one or more of the Proposed Transferees. The purchase price
shall be determined in accordance with Section 4(iii) hereof. 
 (iii) Purchase Price. The purchase price (“Purchase
Price”) for the Shares repurchased under this Section 4 shall be the Offered Price. If the Offered Price includes consideration other than cash, the cash equivalent value of the non-cash consideration shall be determined by the Board in
good faith. 
 (iv) Payment. Payment of the Purchase Price shall be made, at the option of the Company or its assignee(s), in cash
(by check), by cancellation of all or a portion of any outstanding indebtedness of the Holder to the Company (or, in the case of purchase by an assignee, of the assignee to the Company), or by any combination thereof within thirty (30) days
after receipt of the Notice or in the manner and at the times mutually agreed to by the Company and the Holder. 
 (v) Holder’s
Right to Transfer. If all of the Shares proposed in the Notice to be Transferred are not purchased by the Company and/or its assignee(s) as provided in this Section 4, then the Holder may sell or otherwise Transfer such Shares to that
Proposed Transferee at the Offered Price or at a higher price, provided that such sale or other Transfer is consummated within one hundred twenty (120) days after the date of the Notice and provided further that any such sale or other Transfer
is effected in accordance with any applicable 

 
securities laws and the Proposed Transferee agrees in writing that the provisions of this Section 4 and the Restricted Stock Purchase Agreement, if
applicable, shall continue to apply to the Shares in the hands of such Proposed Transferee. If the Shares described in the Notice are not Transferred to the Proposed Transferee within such 120-day period, a new Notice shall be given to the Company,
and the Company and/or its assignees shall again be offered the Right of First Refusal as provided herein before any Shares held by the Holder may be sold or otherwise Transferred. 
 (b) Exception for Certain Family Transfers. Anything to the contrary contained in this Section 4 notwithstanding, the Transfer of any or all
of the Shares during Optionee’s lifetime or upon Optionee’s death by will or intestacy to Optionee’s Immediate Family or a trust for the benefit of Optionee’s Immediate Family shall be exempt from the Right of First Refusal. As
used herein, “Immediate Family” shall mean spouse, lineal descendant or antecedent, father, mother, brother or sister or stepchild (whether or not adopted). In such case, the transferee or other recipient shall receive and hold the Shares
so Transferred subject to the provisions of this Section 4 (including the Right of First Refusal) and the Restricted Stock Purchase Agreement, if applicable, and there shall be no further Transfer of such Shares except in accordance with the
terms of this Section 4. 
 (c) Termination of Right of First Refusal. The Right of First Refusal shall terminate as to all
Shares upon a sale of Common Stock of the Company to the general public pursuant to a registration statement filed with and declared effective by the Securities and Exchange Commission under the Securities Act of 1933, as amended (a “Public
Offering”). 
 5. Transfer Restrictions. Any transfer or sale of the Shares is subject to restrictions on transfer imposed by any
applicable state and federal securities laws. Any Transfer or attempted Transfer of any of the Shares not in accordance with the terms of this Agreement, including the Right of First Refusal provided in this Agreement, shall be void and the Company
may enforce the terms of this Agreement by stop transfer instructions or similar actions by the Company and its agents or designees. 
 6.
Tax Consultation. Optionee understands that Optionee may suffer adverse tax consequences as a result of Optionee’s purchase or disposition of the Shares. Optionee represents that Optionee has consulted with any tax consultants Optionee
deems advisable in connection with the purchase or disposition of the Shares and that Optionee is not relying on the Company for any tax advice. 
 7. Restrictive Legends and Stop-Transfer Orders. 
 (a) Legends. Optionee understands and agrees that the Company shall
cause the legends set forth below or legends substantially equivalent thereto, to be placed upon any certificate(s) evidencing ownership of the Shares together with any other legends that may be required by state or federal securities laws:

 THE SECURITIES REPRESENTED HEREBY HAVE NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED (THE “ACT”), AND MAY NOT
BE 

 
OFFERED, SOLD OR OTHERWISE TRANSFERRED, PLEDGED OR HYPOTHECATED UNLESS AND UNTIL REGISTERED UNDER THE ACT OR, IN THE OPINION OF COUNSEL IN FORM AND SUBSTANCE
SATISFACTORY TO THE ISSUER OF THESE SECURITIES, SUCH OFFER, SALE OR TRANSFER, PLEDGE OR HYPOTHECATION IS IN COMPLIANCE THEREWITH. 
 THE
SHARES REPRESENTED BY THIS CERTIFICATE ARE SUBJECT TO CERTAIN RESTRICTIONS ON TRANSFER AND RIGHT OF FIRST REFUSAL OPTIONS HELD BY THE ISSUER OR ITS ASSIGNEE(S) AS SET FORTH IN THE EXERCISE NOTICE BETWEEN THE ISSUER AND THE ORIGINAL HOLDER OF THESE
SHARES, A COPY OF WHICH MAY BE OBTAINED AT THE PRINCIPAL OFFICE OF THE ISSUER. SUCH TRANSFER RESTRICTIONS AND RIGHT OF FIRST REFUSAL ARE BINDING ON TRANSFEREES OF THESE SHARES. 
 (b) Stop-Transfer Notices. Optionee agrees that, in order to ensure compliance with the restrictions referred to herein, the Company may issue
appropriate “stop transfer” instructions to its transfer agent, if any, and that, if the Company transfers its own securities, it may make appropriate notations to the same effect in its own records. 
 (c) Refusal to Transfer. The Company shall not be required (i) to transfer on its books any Shares that have been sold or otherwise
transferred in violation of any of the provisions of this Agreement or (ii) to treat as owner of such Shares or to accord the right to vote or pay dividends to any purchaser or other transferee to whom such Shares shall have been so
transferred. 
 8. Successors and Assigns. The Company may assign any of its rights under this Agreement to single or multiple
assignees, and this Agreement shall inure to the benefit of the successors and assigns of the Company. Subject to the restrictions on transfer herein set forth, this Agreement shall be binding upon Optionee and his or her heirs, executors,
administrators, successors and assigns. 
 9. Interpretation. Any dispute regarding the interpretation of this Agreement shall be
submitted by Optionee or by the Company forthwith to the Company’s Board of Directors or committee thereof that is responsible for the administration of the Plan (the “Administrator”), which shall review such dispute at its next
regular meeting. The resolution of such a dispute by the Administrator shall be final and binding on the Company and on Optionee. 
 10.
Governing Law; Severability. The laws of the State of California shall govern the interpretation, validity, administration, enforcement and performance of the terms of this Agreement regardless of the law that might be applied under
principles of conflicts of laws. Should any provision of this Agreement be determined by a court of law to be illegal or unenforceable, the other provisions shall nevertheless remain effective and shall remain enforceable. 

 11. Notices. Any notice required or permitted hereunder shall be given in writing and shall be
deemed effectively given upon personal delivery or upon deposit in the United States mail by certified mail, with postage and fees prepaid, addressed to the other party at its address as shown below beneath its signature, or to such other address as
such party may designate in writing from time to time to the other party. 
 12. Further Instruments. Optionee hereby agrees to
execute such further instruments and to take such further action as may be reasonably necessary to carry out the purposes and intent of this Agreement, including, without limitation, the Investment Representation Statement in the form attached to
the Option Agreement as Exhibit B. 
 13. Delivery of Payment. Optionee herewith delivers to the Company the full Exercise
Price for the Shares, as well as any applicable withholding tax. 
 14. Entire Agreement. The Plan and Option Agreement are
incorporated herein by reference. This Agreement, the Plan, the Option Agreement, the Investment Representation Statement and the Restricted Stock Purchase Agreement, if applicable, constitute the entire agreement of the parties and supersede in
their entirety all prior undertakings and agreements of the Company and Optionee with respect to the subject matter hereof. 
 (Signature Page
Follows) 

					
	Accepted by:	  	Submitted by:
		
	CODEXIS, INC.	  	OPTIONEE
			
	By:	 	  
	  	  

		 		  	Optionee
	Name:	 	  
	  	
			
	Title:	 	  
	  	Address:

 [Signature Page to Exercise Notice] 

 EXHIBIT B 
 INVESTMENT REPRESENTATION STATEMENT 
  

					
	OPTIONEE	 	:	    	
			
	COMPANY	 	:	    	Codexis, Inc.
			
	SECURITY	 	:	    	Common Stock
			
	AMOUNT	 	:	    	
			
	DATE	 	:	    	

 In connection with the purchase of the above-listed shares of Common Stock (the
“Securities”) of Codexis, Inc., a Delaware corporation (the “Company”), the undersigned (“Optionee”) represents to the Company the following: 
 (a) Optionee is aware of the Company’s business affairs and financial condition and has acquired sufficient information about the Company to reach
an informed and knowledgeable decision to acquire the Securities. Optionee is acquiring these Securities for investment for Optionee’s own account only and not with a view to, or for resale in connection with, any “distribution”
thereof within the meaning of the Securities Act of 1933, as amended (the “Securities Act”). 
 (b) Optionee acknowledges and
understands that the Securities constitute “restricted securities” under the Securities Act and have not been registered under the Securities Act in reliance upon a specific exemption therefrom, which exemption depends upon, among other
things, the bona fide nature of Optionee’s investment intent as expressed herein. Optionee understands that, in the view of the Securities and Exchange Commission, the statutory basis for such exemption may be unavailable if Optionee’s
representation was predicated solely upon a present intention to hold these Securities for the minimum capital gains period specified under tax statutes, for a deferred sale, for or until an increase or decrease in the market price of the
Securities, or for a period of one year or any other fixed period in the future. Optionee further understands that the Securities must be held indefinitely unless they are subsequently registered under the Securities Act or an exemption from such
registration is available. Optionee further acknowledges and understands that the Company is under no obligation to register the Securities. Optionee understands that the certificate evidencing the Securities will be imprinted with a legend which
prohibits the transfer of the Securities unless they are registered or such registration is not required in the opinion of counsel satisfactory to the Company and any other legend required under applicable state securities laws. 
 (c) Optionee is familiar with the provisions of Rule 701 and Rule 144, each promulgated under the Securities Act, which, in substance, permit
limited public resale of “restricted securities” acquired, directly or indirectly from the issuer thereof, in a non-public offering subject to 

 
the satisfaction of certain conditions. Rule 701 provides that if the issuer qualifies under Rule 701 at the time of the grant of the Option to
Optionee, the exercise will be exempt from registration under the Securities Act. In the event the Company becomes subject to the reporting requirements of Section 13 or 15(d) of the Securities Exchange Act of 1934, as amended (the
“Exchange Act”), ninety (90) days thereafter (or such longer period as any market stand-off agreement may require) the Securities exempt under Rule 701 may be resold, subject to the satisfaction of certain of the conditions
specified by Rule 144, including: (1) the resale being made through a broker in an unsolicited “broker’s transaction” or in transactions directly with a market maker (as said term is defined under the Exchange Act);
and, in the case of an affiliate, (2) the availability of certain public information about the Company, (3) the amount of Securities being sold during any three (3) month period not exceeding the limitations specified in
Rule 144(e) and (4) the timely filing of a Form 144, if applicable. 
 In the event that the Company does not qualify under
Rule 701 at the time of grant of the Option, then the Securities may be resold in certain limited circumstances subject to the provisions of Rule 144, which requires the resale to occur not less than one year after the later of the
date the Securities were sold by the Company or the date the Securities were sold by an affiliate of the Company, within the meaning of Rule 144; and, in the case of acquisition of the Securities by an affiliate, or by a non-affiliate who
subsequently holds the Securities less than two (2) years, the satisfaction of the conditions set forth in sections (1), (2), (3) and (4) of the paragraph immediately above. 
 (d) Optionee further understands that in the event all of the applicable requirements of Rule 701 or 144 are not satisfied, registration under the
Securities Act, compliance with Regulation A, or some other registration exemption will be required; and that, notwithstanding the fact that Rules 144 and 701 are not exclusive, the Staff of the Securities and Exchange Commission has expressed its
opinion that persons proposing to sell private placement securities other than in a registered offering and otherwise than pursuant to Rules 144 or 701 will have a substantial burden of proof in establishing that an exemption from registration is
available for such offers or sales, and that such persons and their respective brokers who participate in such transactions do so at their own risk. Optionee understands that no assurances can be given that any such other registration exemption will
be available in such event. 
  

			
		 	Signature of Optionee:
		
		 	  

		 	Optionee
		
	Date:             ,         	 	

 EXHIBIT C-1 
 CODEXIS, INC. 
 2002 STOCK PLAN, AS AMENDED 
 RESTRICTED STOCK PURCHASE AGREEMENT 
 THIS RESTRICTED STOCK PURCHASE AGREEMENT (this “Agreement”) is made between
                                        
(the “Purchaser”) and Codexis, Inc. (the “Company”), as of             ,         . 
 RECITALS 
 (1) Unless otherwise
defined herein, the terms defined in the Plan shall have the same defined meanings in this Agreement. Pursuant to the exercise of the Option granted to Purchaser under the Company’s 2002 Stock Plan, as amended, and pursuant to the Stock Option
Agreement (the “Option Agreement”) dated                     , by and between the Company and Purchaser with respect to such grant,
which Option Agreement is hereby incorporated by reference, Purchaser has elected to purchase              of those shares which have not become vested under the vesting schedule set
forth in the Option Agreement (“Unvested Shares”). The Unvested Shares and the shares subject to the Option Agreement which have become vested are sometimes collectively referred to herein as the “Shares”. 
 (2) As required by the Option Agreement, as a condition to Purchaser’s election to exercise the option, Purchaser must execute this Agreement, which
sets forth the rights and obligations of the parties with respect to Shares acquired upon exercise of the Option. 
 1. Repurchase
Option. 
 (a) If Purchaser ceases to be a Service Provider for any reason, including for cause, death and disability, the Company or its
assignee shall have the right and option to purchase from Purchaser, or Purchaser’s personal representative, as the case may be, all of Purchaser’s Unvested Shares as of the date on which Purchaser ceases to be a Service Provider at the
exercise price paid by Purchaser for such Shares in connection with the exercise of the Option (the “Repurchase Option”). 
 (b)
The Company may exercise its Repurchase Option by delivering, personally or by registered mail, to Purchaser (or his or her transferee or legal representative, as the case may be), within ninety (90) days of the date on which Purchaser ceases
to be a Service Provider, a notice in writing indicating the Company’s intention to exercise the Repurchase Option and setting forth a date for closing not later than thirty (30) days from the mailing of such notice. The closing shall take
place at the Company’s office. At the closing, the holder of the certificates for the Unvested Shares being transferred shall deliver the stock certificate or certificates evidencing the Unvested Shares, and the Company shall deliver the
purchase price therefor. 

 (c) At its option, the Company may elect to make payment for the Unvested Shares to a bank selected by
the Company. The Company shall avail itself of this option by a notice in writing to Purchaser stating the name and address of the bank, date of closing, and waiving the closing at the Company’s office. 
 (d) If the Company does not elect to exercise the Repurchase Option conferred above by giving the requisite notice within ninety (90) days following
the date on which Purchaser ceases to be a Service Provider, the Repurchase Option shall terminate. 
 (e) One hundred percent (100%) of
the Unvested Shares shall initially be subject to the Repurchase Option. The Unvested Shares shall be released from the Repurchase Option in accordance with the Vesting Schedule set forth in the Notice of Grant until all Shares are released from the
Repurchase Option. Fractional Shares shall be rounded to the nearest whole share. 
 2. Transferability of the Shares; Escrow.

 (a) Purchaser hereby authorizes and directs the secretary of the Company, or such other person designated by the Company from time to time,
to transfer the Unvested Shares as to which the Repurchase Option has been exercised from Purchaser to the Company. 
 (b) To insure the
availability for delivery of Purchaser’s Unvested Shares upon repurchase by the Company pursuant to the Repurchase Option under Section 1, Purchaser hereby appoints the Secretary, or any other person designated by the Company from time to
time as escrow agent, as its attorney-in-fact to sell, assign and transfer unto the Company, such Unvested Shares, if any, repurchased by the Company pursuant to the Repurchase Option and shall, upon execution of this Agreement, deliver and deposit
with the Secretary of the Company, or such other person designated by the Company from time to time, the share certificate(s) representing the Unvested Shares, together with the stock assignment duly endorsed in blank, attached hereto as Exhibit
C-2. The Unvested Shares and stock assignment shall be held by the Secretary in escrow, pursuant to the Joint Escrow Instructions of the Company and Purchaser attached as Exhibit C-3 hereto, until the Company exercises its Repurchase
Option as provided in Section 1, until such Unvested Shares are vested, or until such time as this Agreement no longer is in effect. As a further condition to the Company’s obligations under this Agreement, the spouse of Purchaser, if any,
shall execute and deliver to the Company the Consent of Spouse attached hereto as Exhibit C-4. Upon vesting of the Unvested Shares, the escrow agent shall promptly deliver to Purchaser the certificate or certificates representing such Shares
in the escrow agent’s possession belonging to Purchaser, and the escrow agent shall be discharged of all further obligations hereunder; provided, however, that the escrow agent shall nevertheless retain such certificate or certificates as
escrow agent if so required pursuant to other restrictions imposed pursuant to this Agreement. 
 (c) The Company, or its designee, shall not
be liable for any act it may do or omit to do with respect to holding the Shares in escrow and while acting in good faith and in the exercise of its judgment. 

 (d) Transfer or sale of the Shares is subject to restrictions on transfer imposed by any applicable state
and federal securities laws. Any transferee shall hold such Shares subject to all of the provisions hereof and the Exercise Notice executed by Purchaser with respect to any Unvested Shares purchased by Purchaser and shall acknowledge the same by
signing a copy of this Agreement. Any transfer or attempted transfer of any of the Shares not in accordance with the terms of this Agreement shall be void and the Company may enforce the terms of this Agreement by stop transfer instructions or
similar actions by the Company and its agents or designees. 
 3. Ownership, Voting Rights, Duties. This Agreement shall not affect in
any way the ownership, voting rights or other rights or duties of Purchaser, except as specifically provided herein. 
 4. Adjustment for
Stock Split. All references to the number of Shares and the purchase price of the Shares in this Agreement shall be appropriately adjusted to reflect any stock split, stock dividend or other change in the Shares which may be made by the Company
after the date of this Agreement. 
 5. Notices. Notices required hereunder shall be given in person or by registered mail to the
address of Purchaser shown on the records of the Company, and to the Company at its principal executive office. 
 6. Survival of
Terms. This Agreement shall apply to and bind Purchaser and the Company and their respective permitted assignees and transferees, heirs, legatees, executors, administrators and legal successors. 
 7. Section 83(b) Election for Unvested Shares Purchased Pursuant to a Nonstatutory Stock Option. Purchaser hereby acknowledges that he or she
has been informed that, with respect to the exercise of a Nonstatutory Stock Option for Unvested Shares, that unless an election, as set forth on Exhibit C-5, is filed by Purchaser with the Internal Revenue Service and, if necessary, the
proper state taxing authorities, within thirty (30) days of the purchase of the Shares, electing pursuant to Section 83(b) of the Internal Revenue Code (and similar state tax provisions if applicable) to be taxed currently on any
difference between the purchase price of the Shares and their Fair Market Value on the date of purchase, there will be a recognition of taxable income to the Purchaser, measured by the excess, if any, of the fair market value of the Shares, at the
time the Company’s Repurchase Option lapses over the purchase price for the Shares. Purchaser represents that Purchaser has consulted any tax consultant(s) Purchaser deems advisable in connection with the purchase of the Shares or the filing of
the Election under Section 83(b) and similar tax provisions. 
 PURCHASER ACKNOWLEDGES THAT IT IS PURCHASER’S SOLE
RESPONSIBILITY AND NOT THE COMPANY’S TO FILE TIMELY THE ELECTION UNDER SECTION 83(b), EVEN IF PURCHASER REQUESTS THE COMPANY OR ITS REPRESENTATIVE TO MAKE THIS FILING ON PURCHASER’S BEHALF. 
 8. Representations. Purchaser has reviewed with his or her own tax advisors the federal, state, local and foreign tax consequences of this
investment and the transactions contemplated by 

 
this Agreement. Purchaser is relying solely on such advisors and not on any statements or representations of the Company or any of its agents. Purchaser
understands that Purchaser (and not the Company) shall be responsible for his or her own tax liability that may arise as a result of this investment or the transactions contemplated by this Agreement. 
 9. Governing Law; Severability. The laws of the State of California shall govern the interpretation, validity, administration, enforcement and
performance of the terms of this Agreement regardless of the law that might be applied under principles of conflicts of laws. Should any provision of this Agreement be determined by a court of law to be illegal or unenforceable, the other provisions
shall nevertheless remain effective and shall remain enforceable. 
 (Signature Page Follows) 

 Purchaser represents that he or she has read this Agreement and is familiar with its terms and
provisions. Purchaser hereby agrees to accept as binding, conclusive and final all decisions or interpretations of the Board upon any questions arising under this Agreement. 
 IN WITNESS WHEREOF, this Agreement is deemed made as of the date first set forth above. 
  

			
	 CODEXIS, INC.

		
	 By:
	 	  

	 Name:
	 	  

	 Title:
	 	  

	
	 PURCHASER

		
	 By:
	 	  

	 Name:
	 	  

	 Address:
	 	

 [Signature Page to Restricted Stock Purchase Agreement] 

 EXHIBIT C-2 
 ASSIGNMENT SEPARATE FROM CERTIFICATE 
 FOR VALUE RECEIVED I,
                            , hereby sell, assign and transfer unto
                                       
                                     
(            ) shares of the Common Stock of Codexis, Inc. registered in my name on the books of said corporation represented by Certificate
No.          herewith and do hereby irrevocably constitute and appoint
                     to transfer the said stock on the books of the within named corporation with full power of substitution in the
premises. 
 This Assignment Separate from Certificate may be used only in accordance with the Restricted Stock Purchase Agreement between
Codexis, Inc. and the undersigned dated             ,         . 
 Dated:             ,          
  

			
	Signature:	 	  

 INSTRUCTIONS: Please do not fill in any blanks other than the signature line. The purpose of this
assignment is to enable the Company to exercise the Repurchase Option, as set forth in the Restricted Stock Purchase Agreement, without requiring additional signatures on the part of Purchaser. 

 EXHIBIT C-3 
 JOINT ESCROW INSTRUCTIONS 
             ,          
 Secretary 
 Codexis, Inc. 
 As Escrow
Agent for both Codexis, Inc. (the “Company”) and the undersigned purchaser of stock of the Company (the “Purchaser”), you are hereby authorized and directed to hold the documents delivered to you pursuant to the terms of that
certain Restricted Stock Purchase Agreement (“Agreement”) between the Company and the undersigned, in accordance with the following instructions: 
 1. In the event the Company and/or any assignee of the Company (referred to collectively for convenience herein as the “Company”) exercises the Company’s Repurchase Option set forth in the Agreement,
the Company shall give to Purchaser and you a written notice specifying the number of shares of stock to be purchased, the purchase price, and the time for a closing hereunder at the principal office of the Company. Purchaser and the Company hereby
irrevocably authorize and direct you to close the transaction contemplated by such notice in accordance with the terms of said notice. 
 2.
At the closing, you are directed (a) to date the stock assignments necessary for the transfer in question, (b) to fill in the number of shares being transferred, and (c) to deliver the same, together with the certificate evidencing
the shares of stock to be transferred, to the Company or its assignee, against the simultaneous delivery to you of the purchase price (by cash, a check, or a combination thereof) for the number of shares of stock being purchased pursuant to the
exercise of the Company’s Repurchase Option. 
 3. Purchaser irrevocably authorizes the Company to deposit with you any certificates
evidencing shares of stock to be held by you hereunder and any additions and substitutions to said shares as defined in the Agreement. Purchaser does hereby irrevocably constitute and appoint you as Purchaser’s attorney-in-fact and agent for
the term of this escrow to execute, with respect to such securities, all documents necessary or appropriate to make such securities negotiable and to complete any transaction herein contemplated, including but not limited to the filing with any
applicable state blue sky authority of any required applications for consent to, or notice of transfer of, the securities. Subject to the provisions of this paragraph 3, Purchaser shall exercise all rights and privileges of a stockholder of the
Company while the stock is held by you. 
 4. Upon written request of Purchaser, but no more than once per calendar year, unless the
Company’s Repurchase Option has been exercised, you will deliver to Purchaser a certificate or certificates representing the number of shares of stock as are not then subject to the Company’s Repurchase Option. Within one hundred twenty
(120) days after Purchaser ceases to be a Service 

 
Provider, you will deliver to Purchaser a certificate or certificates representing the aggregate number of shares held or issued pursuant to the Agreement
and not purchased by the Company or its assignees pursuant to exercise of the Company’s Repurchase Option. 
 5. If at the time of
termination of this escrow you should have in your possession any documents, securities, or other property belonging to Purchaser, you shall deliver all of the same to Purchaser and shall be discharged of all further obligations hereunder.

 6. Your duties hereunder may be altered, amended, modified or revoked only by a writing signed by all of the parties hereto. 

7. You shall be obligated only for the performance of such duties as are specifically set forth herein and may rely and shall be protected in relying
or refraining from acting on any instrument reasonably believed by you to be genuine and to have been signed or presented by the proper party or parties. You shall not be personally liable for any act you may do or omit to do hereunder as Escrow
Agent or as attorney-in-fact for Purchaser while acting in good faith, and any act done or omitted by you pursuant to the advice of your own attorneys shall be conclusive evidence of such good faith. 
 8. You are hereby expressly authorized to disregard any and all warnings given by any of the parties hereto or by any other person or corporation,
excepting only orders or process of courts of law and are hereby expressly authorized to comply with and obey orders, judgments or decrees of any court. In case you obey or comply with any such order, judgment or decree, you shall not be liable to
any of the parties hereto or to any other person, firm or corporation by reason of such compliance, notwithstanding any such order, judgment or decree being subsequently reversed, modified, annulled, set aside, vacated or found to have been entered
without jurisdiction. 
 9. You shall not be liable in any respect on account of the identity, authorities or rights of the parties executing
or delivering or purporting to execute or deliver the Agreement or any documents or papers deposited or called for hereunder. 
 10. You
shall not be liable for the expiration of any rights under any applicable state, federal or local statute of limitations or similar statute or regulation with respect to these Joint Escrow Instructions or any documents deposited with you.

 11. You shall be entitled to employ such legal counsel and other experts as you may deem necessary properly to advise you in connection
with your obligations hereunder, may rely upon the advice of such counsel, and may pay such counsel reasonable compensation therefor. 
 12.
Your responsibilities as Escrow Agent hereunder shall terminate if you shall cease to be an officer or agent of the Company or if you shall resign by written notice to each party. In the event of any such termination, the Company shall appoint a
successor Escrow Agent. 
  

 2 

 13. If you reasonably require other or further instruments in connection with these Joint Escrow
Instructions or obligations in respect hereto, the necessary parties hereto shall join in furnishing such instruments. 
 14. It is
understood and agreed that should any dispute arise with respect to the delivery and/or ownership or right of possession of the securities held by you hereunder, you are authorized and directed to retain in your possession without liability to
anyone all or any part of said securities until such disputes shall have been settled either by mutual written agreement of the parties concerned or by a final order, decree or judgment of a court of competent jurisdiction after the time for appeal
has expired and no appeal has been perfected, but you shall be under no duty whatsoever to institute or defend any such proceedings. 
 15.
Any notice required or permitted hereunder shall be given in writing and shall be deemed effectively given upon personal delivery or upon deposit in the United States Post Office, by registered or certified mail with postage and fees prepaid,
addressed to each of the other parties thereunto entitled at such addresses as a party may designate by written notice to each of the other parties hereto. 
 16. By signing these Joint Escrow Instructions, you become a party hereto only for the purpose of said Joint Escrow Instructions; you do not become a party to the Agreement. 
 17. This instrument shall be binding upon and inure to the benefit of the parties hereto, and their respective successors and permitted assigns.

 18. These Joint Escrow Instructions shall be governed by, and construed and enforced in accordance with, the laws of the State of
California, excluding that body of law pertaining to conflicts of law. 
 (Signature Page Follows) 
  

 3 

 IN WITNESS WHEREOF, these Joint Escrow Instructions shall be effective as of the date first set forth
above. 
  

			
	CODEXIS, INC.
		
	By:	 	  

	Name:	 	  

	Title:	 	  

	
	PURCHASER:
		
	By:	 	  

	Name:	 	  

	Address:	 	
	
	ESCROW AGENT:
		
	By:	 	  

	Name:	 	  

	Title:	 	  

 EXHIBIT C-4 
 CONSENT OF SPOUSE 
 I,
                                        ,
spouse of
                                        ,
have read and approve the Restricted Stock Purchase Agreement dated             ,         , between my spouse and Codexis, Inc. In
consideration of granting the right to my spouse to purchase shares of Codexis, Inc. set forth in the Restricted Stock Purchase Agreement, I hereby appoint my spouse as my attorney-in-fact in respect to the exercise of any rights under the Agreement
and agree to be bound by the provisions of the Restricted Stock Purchase Agreement insofar as I may have any rights in said Restricted Stock Purchase Agreement or any shares issued pursuant thereto under the community property laws or similar laws
relating to marital property in effect in the state of our residence as of the date of the signing of the foregoing Restricted Stock Purchase Agreement. 
 Dated:             ,          
  

	
	  

	Signature of Spouse

 EXHIBIT C-5 
 INFORMATION CONCERNING THE FILING OF SECTION 83(b) ELECTION 
 This information is supplied to you in
connection with your recent purchase of shares of Common Stock of Codexis, Inc. (the “Company”), at a purchase price equal to the current fair market value of the stock and subject to an Agreement for purchase of shares that gives
the Company the right to repurchase the shares under the terms stated in the Agreement in the event that you terminate your continuous status as an employee, consultant or director of the Company prior to the full vesting. 
 Section 83 of the Internal Revenue Code taxes as ordinary income the difference between the amount paid for the stock and its fair market value as
of the date any restrictions on that stock lapse. In this context, “restriction” means the right of the Company to buy back the stock at less than its fair market value, in connection with the termination of your continuous status as an
employee, consultant or director of the Company, which right expires as your stock vests pursuant to the Agreement. Thus, if the shares are worth $12.50 a share at the time the first 25% of the shares becomes fully vested (no longer subject to
repurchase) and if you purchased such shares for $0.10 per share, then you would be required to report ordinary income in the amount of $12.40 for each such share in the first year that such shares are first vested (no longer subject to repurchase).
Upon the vesting of the final portion of the shares and if the fair market value of the shares at that time is $15.00 per share, then you would be required to report ordinary income in the amount of $14.90 per share for the tax year in which such
final portion of the shares is no longer subject to repurchase. 
 To avoid the assessment of ordinary income tax at the time the
restrictions end, there is an election that can be filed under Section 83(b). This is an election to include in income in the year the stock is purchased the difference between what is paid for the stock and its then fair market value. Even
though in your case the fair market value of the stock may equal the amount paid and therefore there may be no income at this time, the Internal Revenue Service nonetheless requires that the election be filed in order to avoid adverse tax
consequences in the future. 
 You must file one executed copy of the 83(b) election form with the Internal Revenue Service within 30
days of the purchase of the shares. The steps outlined below should be followed to ensure the election is filed correctly and timely: 
  

	1)	Complete 83(b) election form; 

  

	2)	Prepare cover letter to the IRS (sample letter attached); 

  

	3)	Send cover letter with originally executed 83(b) election form and one (1) additional copy via certified mail or Federal Express to the IRS, within 30 days of the date of
purchase, with a self-addressed stamped envelope and retain receipt of mailing; 

  

	4)	Retain IRS file stamped copy for your records when returned; and 

  

	5)	One copy should be returned to the Company for its records and one copy should be filed along with your federal income tax return for the tax year. 

 For your information, the address of the IRS (if you live in Northern California, except for the Central
Valley) is as follows: 
 Internal Revenue Service 
 5045 East Butler Avenue 
 Fresno, California 93888 

 SECTION 83(b) ELECTION 
 This statement is being made under Section 83(b) of the Internal Revenue Code, pursuant to Treas. Reg. Section 1.83-2. 
 The taxpayer who performed the service is: 
 Name:

 Address: 
 Taxpayer Ident. No.

 The property with respect to which the election is being made is              shares of
common stock of Codexis, Inc. 
 The property was issued on             ,
200  . 
 The taxable year in which the election is being made in the calendar year 200  . 
 The property is subject to a repurchase right pursuant to which the issuer has the right to acquire the property at the original purchase price if for any reason the
taxpayer’s service provider relationship with the issuer is terminated. The issuer’s repurchase right lapses in a series of annual and monthly installments over a
            -year period ending on             , 200  . 
 The fair market value at the time of transfer (determined without regard to any restriction other than a restriction which by its terms will never lapse) is
$             per share. 
 The amount paid for such property is
$             per share. 
 A copy of this statement was furnished to Codexis, Inc. for
whom taxpayer rendered the services underlying the transfer of property. 
 This statement is executed on
            , 200  . 
  

			
	  
	  	  

	Spouse (if any)	  	Taxpayer

 This election must be filed with the Internal Revenue Service Center with which taxpayer files his or her
Federal income tax returns and must be made within thirty (30) days after the execution date of the Stock Purchase Agreement. This filing should be made by registered or certified mail, return receipt requested. Optionee must retain two
(2) copies of the completed form for filing with his or her Federal and state tax returns for the current tax year and an additional copy for his or her records. 

 IMPORTANT: READ THIS — 
 IF YOU WISH TO MAKE A SECTION 83(B) ELECTION, THE FILING OF SUCH ELECTION IS YOUR RESPONSIBILITY. 
 THE FORM FOR MAKING THIS SECTION 83(B) ELECTION IS ATTACHED TO THIS AGREEMENT AS PART OF EXHIBIT C-5. 
 YOU MUST FILE THIS FORM WITHIN 30 DAYS OF PURCHASING THE SHARES. 
 YOU (AND NOT THE COMPANY OR ANY OF ITS AGENTS) SHALL BE SOLELY RESPONSIBLE FOR FILING SUCH FORM WITH THE IRS, EVEN IF YOU REQUEST THE COMPANY OR ITS AGENTS TO MAKE THIS FILING ON YOUR BEHALF AND EVEN IF
THE COMPANY OR ITS AGENTS HAVE PREVIOUSLY MADE THIS FILING ON YOUR BEHALF. 
 The election should be filed by mailing a signed election form
by certified mail, return receipt requested to the IRS Service Center where you file your tax returns. See www.irs.gov 

             ,
         
 Internal Revenue Service 
 5045 East Butler Avenue 
 Fresno, California 93888 
  

			
	Re:	  	83(b) Election for Purchase of Codexis, Inc. Common Stock

 Ladies and Gentlemen: 
 Enclosed is a completed form of election under Section 83(b) of the Internal Revenue Code of 1986 (the “83(b) Election”) relating to my recent purchase of
             shares of Common Stock of Codexis, Inc. 
 Please acknowledge receipt of the
83(b) Election by stamping as filed the enclosed copy and returning it to me in the self-addressed stamped envelope provided. 
  

	
	 Sincerely,

	
	  

 Enclosures

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