Document:

EX-10.3

 CODEXIS, INC. 
 JOHN NICOLS 
 STOCK OPTION GRANT NOTICE AND 

STOCK OPTION AGREEMENT 
 Codexis, Inc., a Delaware corporation, (the “Company”) hereby grants to the holder listed below (“Participant”), an option to purchase the number of shares of the
Company’s common stock (“Stock”), set forth below (the “Option”). This Option is subject to all of the terms and conditions set forth herein and the Stock Option Agreement attached hereto as Exhibit A
(the “Stock Option Agreement”), which is incorporated herein by reference. Unless otherwise defined herein, the terms are defined in Article 1 of the Stock Option Agreement. 

 

			
	Participant:	  	John J. Nicols
		
	Grant Date:	  	June 13, 2012
		
	Exercise Price per Share:	  	$3.46
		
	Total Exercise Price:	  	 1,384,000

		
	Total Number of Shares Subject to the Option:	  	400,000 shares
		
	Expiration Date:	  	June 13, 2022
		
	Vesting Schedule:	  	The shares subject to this Option shall vest and become exercisable as to 25% of the total number of shares subject to the Option on June 13, 2013, and 1/48th of the total number of shares subject to the Option shall vest and
become exercisable monthly thereafter, such that the Option would be fully vested and exercisable on June 13, 2016, subject to Participant’s continued service with the Company through each such vesting date.
		
	Type of Option:	  	This Option is a Non-Qualified Stock Option

 By executing this Grant Notice below, Participant agrees to be bound by the terms and conditions of the
Stock Option Agreement and this Grant Notice. Participant has reviewed the Stock Option Agreement and this Grant Notice in their entirety, has had an opportunity to obtain the advice of counsel prior to executing this Grant Notice and fully
understands all provisions of this Grant Notice and the Stock Option Agreement. Participant hereby agrees to accept as binding, conclusive and final all decisions or interpretations of the Administrator upon any questions arising under this Grant
Notice or the Stock Option Agreement. 
  

							
	CODEXIS, INC.:	  	PARTICIPANT:
				
	By:	  	 /s/ Douglas T. Sheehy
	  	By:	 	 /s/ John J. Nicols

	Print Name:	  	 Douglas T. Sheehy
	  	Print Name:	 	 John J. Nicols

	Title:	  	 SVP, General Council & Secretary
	  		 	
	Address:	  	 200 Penobscot Drive
	  	Address:	 	  

		  	 Redwood City, CA 94063
	  		 	  

 EXHIBIT A 
 TO JOHN NICOLS STOCK OPTION GRANT NOTICE 
 STOCK OPTION AGREEMENT

 Pursuant to the Stock Option Grant Notice (the “Grant Notice”) to which this Stock Option Agreement
(this “Agreement”) is attached, Codexis, Inc., a Delaware corporation (the “Company”), has granted to Participant an Option to purchase the number of shares of Stock indicated in the Grant Notice. 

ARTICLE 1. 

DEFINED TERMS 
 Wherever the following terms are used in this Agreement, they shall have the meanings specified below. 
 1.1 “Administrator” shall mean the Committee. 
 1.2
“Board” shall mean the Board of Directors of the Company. 
 1.3 “Change in Control” shall
mean and includes each of the following: 
 (a) A transaction or series of transactions (other than an offering of Stock to the
general public through a registration statement filed with the Securities and Exchange Commission) whereby any “person” or related “group” of “persons” (as such terms are used in Sections 13(d) and 14(d)(2) of the
Exchange Act) (other than the Company, any of its parents or subsidiaries, an employee benefit plan maintained by the Company or any of its subsidiaries or a “person” that, prior to such transaction, directly or indirectly controls, is
controlled by, or is under common control with, the Company) directly or indirectly acquires beneficial ownership (within the meaning of Rule 13d-3 under the Exchange Act) of securities of the Company possessing more than 50% of the total combined
voting power of the Company’s securities outstanding immediately after such acquisition; or 
 (b) During any period of two
consecutive years, individuals who, at the beginning of such period, constitute the Board together with any new director(s) (other than a director designated by a person who shall have entered into an agreement with the Company to effect a
transaction described in Section 1.2(a) or Section 1.2(c)) whose election by the Board or nomination for election by the Company’s stockholders was approved by a vote of at least two-thirds of the directors then still in office who
either were directors at the beginning of the two-year period or whose election or nomination for election was previously so approved, cease for any reason to constitute a majority thereof; or 

(c) The consummation by the Company (whether directly involving the Company or indirectly involving the Company through one or more
intermediaries) of (x) a merger, consolidation, reorganization, or business combination or (y) a sale or other disposition of all or substantially all of the Company’s assets in any single transaction or series of related transactions
or (z) the acquisition of assets or stock of another entity, in each case other than a transaction: 
 (i) Which results
in the Company’s voting securities outstanding immediately before the transaction continuing to represent (either by remaining outstanding or by being converted into voting securities of the Company or the person that, as a result of the
transaction, controls, directly or indirectly, the Company or owns, directly or indirectly, all or substantially all of the 

  
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Company’s assets or otherwise succeeds to the business of the Company (the Company or such person, the “Successor Entity”)) directly or indirectly, at least a majority of
the combined voting power of the Successor Entity’s outstanding voting securities immediately after the transaction, and 

(ii) After which no person or group beneficially owns voting securities representing 50% or more of the combined voting power of the
Successor Entity; provided, however, that no person or group shall be treated for purposes of this Section 1.2(c)(ii) as beneficially owning 50% or more of combined voting power of the Successor Entity solely as a result of the voting
power held in the Company prior to the consummation of the transaction; or 
 (d) The Company’s stockholders approve a
liquidation or dissolution of the Company. 
 The Administrator shall have full and final authority, which shall be exercised in its discretion,
to determine conclusively whether a Change in Control of the Company has occurred pursuant to the above definition, and the date of the occurrence of such Change in Control and any incidental matters relating thereto. 

1.4 “Code” shall mean the Internal Revenue Code of 1986, as amended from time to time. 

1.5 “Committee” shall mean the Compensation Committee of the Board. 

1.6 “Consultant” shall mean any consultant or adviser engaged to provide services to the Company or any Subsidiary that
qualifies as a consultant under the applicable rules of the Securities and Exchange Commission for registration of shares on a Form S-8 Registration Statement. 
 1.7 “Employee” shall mean any officer or other employee (as determined in accordance with Section 3401(c) of the Code and the Treasury Regulations thereunder) of the Company or of
any Subsidiary. 
 1.8 “Equity Restructuring” shall mean a nonreciprocal transaction between the Company and
its stockholders, such as a stock dividend, stock split, spin-off, rights offering or recapitalization through a large, nonrecurring cash dividend, that affects the number or kind of shares of Stock (or other securities of the Company) or the share
price of Stock (or other securities) and causes a change in the per share value of the Stock underlying the Option. 
 1.9
“Exchange Act” shall mean the Securities Exchange Act of 1934, as amended from time to time. 
 1.10
“Fair Market Value” shall mean, as of any given date, the value of a share of Stock determined as follows: 

(a) If the Stock is listed on any established stock exchange (such as the New York Stock Exchange, the NASDAQ Global Market and the
NASDAQ Global Select Market) or national market system, its Fair Market Value shall be the closing sales price for a share of Stock as quoted on such exchange or system for such date or, if there is no closing sales price for a share of Stock on the
date in question, the closing sales price for a share of Stock on the last preceding date for which such quotation exists, as reported in The Wall Street Journal or such other source as the Administrator deems reliable; 

(b) If the Stock is not listed on an established stock exchange or national market system, but the Stock is regularly quoted by a
recognized securities dealer, its Fair Market Value shall be 

  
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the mean of the high bid and low asked prices for such date or, if there are no high bid and low asked prices for a share of Stock on such date, the high bid and low asked prices for a share of
Stock on the last preceding date for which such information exists, as reported in The Wall Street Journal or such other source as the Administrator deems reliable; or 
 (c) If the Stock is neither listed on an established stock exchange or a national market system nor regularly quoted by a recognized securities dealer, its Fair Market Value shall be established by the
Administrator in good faith. 
 1.11 “Non-Employee Director” shall mean a Director of the Company who is not an
Employee. 
 1.12 “Non-Qualified Stock Option” shall mean a stock option not described in Sections 422(b) or
423(b) of the Code. 
 1.13 “Subsidiary” means any entity (other than the Company), whether domestic or
foreign, in an unbroken chain of entities beginning with the Company if each of the entities other than the last entity in the unbroken chain beneficially owns, at the time of the determination, securities or interests representing more than 50% of
the total combined voting power of all classes of securities or interests in one of the other entities in such chain. 
 1.14
“Termination of Service” shall mean the time when the employee-employer relationship between Participant and the Company or any Subsidiary is terminated for any reason, including, without limitation, a termination by resignation,
discharge, death, disability or retirement; but excluding terminations where Participant simultaneously commences or remains in employment or service with the Company or any Subsidiary. The Administrator, in its sole discretion, shall determine the
effect of all matters and questions relating to a Termination of Service, including, without limitation, the question of whether a Termination of Service resulted from a discharge for cause and all questions of whether particular leaves of absence
constitute a Termination of Service. 
 ARTICLE 2. 

GRANT OF OPTION 
 2.1 Grant of Option. In consideration of Participant’s agreement to commence and continue in the employ of the Company or a Subsidiary and for other good and valuable consideration, effective
as of the Grant Date set forth in the Grant Notice (the “Grant Date”), the Company grants to Participant the Option to purchase any part or all of an aggregate of the number of shares of Stock set forth in the Grant Notice, upon the
terms and conditions set forth in this Agreement, subject to adjustments as provided in Section 5.1 hereof. This Option shall be a Non-Qualified Stock Option. 
 2.2 Exercise Price. The exercise price of the shares of Stock subject to the Option shall be as set forth in the Grant Notice, without commission or other charge; provided, however,
that the price per share of the shares of Stock subject to the Option shall not be less than 100% of the Fair Market Value of a share of Stock on the Grant Date. 
 2.3 Consideration to the Company. In consideration of the grant of the Option by the Company, Participant agrees to render faithful and efficient services to the Company or any Subsidiary. Nothing
in this Agreement shall confer upon Participant any right to continue in the employ of the Company or any Subsidiary or shall interfere with or restrict in any way the rights of the Company and its Subsidiaries, which rights are hereby expressly
reserved, to discharge or terminate the services of Participant at any time for any reason whatsoever, with or without cause, except to the extent expressly provided otherwise in a written agreement between the Company or a Subsidiary and
Participant. 

  
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 ARTICLE 3. 
 PERIOD OF EXERCISABILITY 
 3.1 Commencement of Exercisability.

 (a) Subject to Sections 3.2, 3.3, 5.10 and 5.15 hereof, the Option shall become vested and exercisable in such amounts and at
such times as are set forth in the Grant Notice. 
 (b) No portion of the Option which has not become vested and exercisable at
the date of Participant’s Termination of Service shall thereafter become vested and exercisable, except as may be otherwise provided by the Administrator or as set forth in a written agreement between the Company and Participant. 

(c) Notwithstanding Sections 3.1(a) hereof and the Grant Notice, but subject to Section 3.1(b) hereof, pursuant to Section 5.1
hereof, the Option shall become fully vested and exercisable with respect to all shares of Stock covered thereby in the event of a Change in Control, in connection with which the successor corporation does not assume the Option or substitute an
equivalent right for the Option. Should the successor corporation assume the Option or substitute an equivalent right, then no such acceleration shall apply. 
 3.2 Duration of Exercisability. The installments provided for in the vesting schedule set forth in the Grant Notice are cumulative. Each such installment which becomes vested and exercisable
pursuant to the vesting schedule set forth in the Grant Notice shall remain vested and exercisable until it becomes unexercisable under Section 3.3 hereof. The vesting of the Option may be accelerated by the Administrator at such times and in
such amounts as it shall determine in its sole discretion, as otherwise provided for in this Agreement or as set forth in a written agreement between the Company and Participant. 

3.3 Expiration of Option. The Option may not be exercised to any extent by anyone after the first to occur of the following
events: 
 (a) The Expiration Date set forth in the Grant Notice, which shall in no event be more than ten (10) years from
the Grant Date; 
 (b) The expiration of three (3) months from the date of Participant’s Termination of Service,
unless such termination occurs by reason of Participant’s death or disability or the exercise period is extended by the Administrator until a date not later than the Expiration Date of the Option; or 

(c) The expiration of one (1) year from the date of Participant’s Termination of Service by reason of Participant’s death
or disability, unless the exercise period is extended by the Administrator until a date not later than the Expiration Date of the Option. 
 (d) Unvested Options shall terminate immediately upon Participant’s Termination of Services. 

  
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 3.4 Tax Indemnity. 

(a) The Participant agrees to indemnify and keep indemnified the Company, any Subsidiary and his/her employing company, if different,
from and against any liability for or obligation to pay any Tax Liability (a “Tax Liability” being any liability for income tax, withholding tax and any other employment related taxes or social security contributions in any
jurisdiction) that is attributable to (1) the grant or exercise of, or any benefit derived by the Participant from, the Option, (2) the acquisition by the Participant of the Stock on exercise of the Option, or (3) the disposal of any
Stock. 
 (b) The Option cannot be exercised until the Participant has made such arrangements as the Company may require for the
satisfaction of any Tax Liability that may arise in connection with the exercise of the Option and/or the acquisition of the Stock by the Participant. The Company shall not be required to issue, allot or transfer Stock until the Employee has
satisfied this obligation. 
 ARTICLE 4. 
 EXERCISE OF OPTION 
 4.1 Person Eligible to Exercise. During the
lifetime of Participant, only Participant may exercise the Option or any portion thereof. After the death of Participant, any exercisable portion of the Option may, prior to the time when the Option becomes unexercisable under Section 3.3
hereof, be exercised by Participant’s personal representative or by any person empowered to do so under the deceased Participant’s will or under the then applicable laws of descent and distribution. 

4.2 Partial Exercise. Any exercisable portion of the Option or the entire Option, if then wholly exercisable, may be exercised in
whole or in part at any time prior to the time when the Option or portion thereof becomes unexercisable under Section 3.3 hereof. 
 4.3 Manner of Exercise. The Option, or any exercisable portion thereof, may be exercised prior to its expiration to the extent such Option is vested, solely by delivery to the Secretary of the
Company (or any third party administrator or other person or entity designated by the Company), during regular business hours, of all of the following prior to the time when the Option or such portion thereof becomes unexercisable under
Section 3.3 hereof: 
 (a) An exercise notice in a form specified by the Administrator, stating that the Option or portion
thereof is thereby exercised, such notice complying with all applicable rules established by the Administrator. Such notice of exercise shall be executed and delivered by the person exercising such Options; 

(b) The receipt by the Company of full payment for the shares of Stock with respect to which the Option or portion thereof is exercised,
including payment of any applicable withholding tax, which shall be made by deduction from other compensation payable to Participant or in such other form of consideration permitted under Section 4.4 hereof that is acceptable to the Company;

 (c) Any other written representations as may be required in the Administrator’s reasonable discretion to evidence
compliance with the Securities Act of 1933, as amended (the “Securities Act”) or any other applicable law, rule or regulation; and 
 (d) In the event the Option or portion thereof shall be exercised pursuant to Section 4.1 hereof by any person or persons other than Participant, appropriate proof (satisfactory to the Company in its
sole discretion) of the right of such person or persons to exercise the Option. 

  
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 Notwithstanding any of the foregoing, the Company shall have the right to specify all conditions of the
manner of exercise, which conditions may vary by country and which may be subject to change from time to time. 
 4.4 Method
of Payment. Payment of the exercise price shall be by any of the following, or a combination thereof, at the election of Participant: 
 (a) Cash or check; 
 (b) With the consent of the Administrator, surrender of
shares of Stock (including, without limitation, shares of Stock otherwise issuable upon exercise of the Option) held for such period of time as may be required by the Administrator in order to avoid adverse accounting consequences and having a Fair
Market Value on the date of delivery equal to the aggregate exercise price of the Option or exercised portion thereof; or 
 (c)
Other property acceptable to the Administrator (including, without limitation, through the delivery of a notice that Participant has placed a market sell order with a broker with respect to shares of Stock 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 Option exercise price; provided that payment of such proceeds is then made to the Company at such time as
may be required by the Company, but in any event not later than the settlement of such sale). 
 4.5 Tax Withholding.
Participant shall pay to the Company by one of the permitted payment methods under Section 4.4, promptly upon exercise of an Option or, if later, the date that the amount of such obligations becomes determinable, all applicable federal, state,
local and foreign withholding taxes that the Administrator, in its discretion, determines to result upon exercise of an Option or from a transfer or other disposition of shares of Stock acquired upon exercise of an Option or otherwise related to an
Option or shares of Stock acquired in connection with an Option. The Administrator may in its sole discretion and in satisfaction of the foregoing requirement withhold, or allow Participant to elect to have the Company withhold shares of Stock
otherwise issuable under the Option (or allow the surrender of shares of Stock). Unless determined otherwise by the Administrator, the number of shares of Stock which may be so withheld or surrendered shall be limited to the number of shares which
have a Fair Market Value on the date of withholding or repurchase no greater than the aggregate amount of such liabilities based on the minimum statutory withholding rates for federal, state, local and foreign income tax and payroll tax purposes
that are applicable to such supplemental taxable income. The Administrator shall determine the fair market value of the Stock, consistent with applicable provisions of the Code, for tax withholding obligations due in connection with a
broker-assisted cashless Option exercise involving the sale of shares to pay the Option exercise price or any tax withholding obligation. 
 4.6 Conditions to Issuance of Stock. The shares of Stock deliverable upon the exercise of the Option, or any portion thereof, may be either previously authorized but unissued shares of Stock or
issued shares of Stock which have then been reacquired by the Company. Such shares of Stock shall be fully paid and nonassessable. The Company shall not be required to issue or deliver any shares of Stock purchased upon the exercise of the Option or
portion thereof prior to fulfillment of all of the following conditions: 
 (a) The admission of such shares of Stock to listing
on all stock exchanges on which such Stock is then listed; 

  
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 (b) The completion of any registration or other qualification of such shares of Stock under
any state or federal law or under rulings or regulations of the Securities and Exchange Commission or of any other governmental regulatory body, which the Administrator shall, in its absolute discretion, deem necessary or advisable; 

(c) The obtaining of any approval or other clearance from any state or federal governmental agency which the Administrator shall, in its
absolute discretion, determine to be necessary or advisable; 
 (d) The receipt by the Company of a properly completed and
executed notice of exercise, as specified in Section 4.3(a) above, and full payment for such shares of Stock, including payment of any applicable withholding tax, which may be in one or more of the forms of consideration permitted under
Section 4.4 hereof; and 
 (e) The lapse of such reasonable period of time following the exercise of the Option as the
Administrator may from time to time establish for reasons of administrative convenience. 
 4.7 Rights as Stockholder.
The holder of the Option shall not be, nor have any of the rights or privileges of, a stockholder of the Company, including, without limitation, voting rights and rights to dividends, in respect of any shares of Stock purchasable upon the exercise
of any part of the Option unless and until such shares of Stock shall have been issued by the Company and held of record by such holder (as evidenced by the appropriate entry on the books of the Company or of a duly authorized transfer agent of the
Company). No adjustment will be made for a dividend or other right for which the record date is prior to the date the shares of Stock are issued, except as provided in Section 5.1 hereof. 

ARTICLE 5. 

OTHER PROVISIONS 
 5.1 Changes in Stock or Assets of the Company, Acquisition or Liquidation of the Company and Other Corporate Events. 
 (a) In the event of any stock dividend, stock split, combination or exchange of shares, merger, consolidation or other distribution (other than normal cash dividends) of Company assets to stockholders, or
any other change affecting the shares of the Company’s stock or the share price of the Company’s stock other than an Equity Restructuring, the Administrator may make equitable adjustments, if any, to reflect such change with respect to
(i) the number and kind of shares of Stock (or other securities or property) subject to the Option; (ii) the terms and conditions of the Option; and (iii) the exercise price per share for the Option. 

(b) In the event of any transaction or event described in Section 5.1(a) or any unusual or nonrecurring transactions or events
affecting the Company, any affiliate of the Company, or the financial statements of the Company or any affiliate, or of changes in applicable laws, regulations or accounting principles, the Administrator, in its sole discretion, and on such terms
and conditions as it deems appropriate, either by the terms of the Option or by action taken prior to the occurrence of such transaction or event and either automatically or upon Participant’s request, is hereby authorized to take any one or
more of the following actions whenever the Administrator determines that such action is appropriate in order to prevent dilution or enlargement of the benefits or potential benefits intended to be made available under the Agreement. 

  
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 (i) To provide for either (A) termination of the Option in exchange for an amount of
cash, if any, equal to the amount that would have been attained upon the exercise of the Option or realization of Participant’s rights (and, for the avoidance of doubt, if as of the date of the occurrence of the transaction or event described
in this Section 5.1 the Administrator determines in good faith that no amount would have been attained upon the exercise of the Option or realization of Participant’s rights, then the Option may be terminated by the Company without
payment) or (B) the replacement of the Option with other rights or property selected by the Administrator in its sole discretion having an aggregate value not exceeding the amount that could have been attained upon the exercise of the Option or
realization of Participant’s rights had the Option been currently exercisable or payable or fully vested; 
 (ii) To
provide that the Option be assumed by the successor or survivor corporation, or a parent or subsidiary thereof, or shall be substituted for by similar options, rights or awards covering the stock of the successor or survivor corporation, or a parent
or subsidiary thereof, with appropriate adjustments as to the number and kind of shares and prices; 
 (iii) To make
adjustments in the number and type of shares of the Company’s stock (or other securities or property) subject to the Option and/or in the terms and conditions of (including the exercise price), and the criteria included in, the Option;

 (iv) To provide that the Option shall be exercisable or payable or fully vested with respect to all shares covered thereby,
notwithstanding anything to the contrary in the Agreement; and 
 (v) To provide that the Option cannot vest, be exercised or
become payable after such event. 
 (c) In connection with the occurrence of any Equity Restructuring, and notwithstanding
anything to the contrary in Sections 5.1(a) and 5.1(b), the number and type of securities subject to the Option and/or the exercise price hereof, if applicable, shall be equitably adjusted. The adjustments provided under this Section 5.1(c)
shall be nondiscretionary and shall be final and binding on Participant and the Company. 
 (d) Notwithstanding any other
provision herein, but subject to Section 5.1(e), in the event of a Change in Control, the Option shall be assumed or an equivalent award substituted by the successor corporation or a parent or subsidiary of the successor corporation.

 (e) In the event that the successor corporation in a Change in Control refuses to assume or substitute for the Option upon a
Change in Control, the Option shall become fully vested and, if applicable, exercisable and all forfeiture restrictions on the Option shall lapse, in each case, as of immediately prior to the consummation of such Change in Control. If the Option is
exercisable in lieu of assumption or substitution in the event of a Change in Control, the Administrator shall notify Participant that the Option shall be fully exercisable for a period of fifteen (15) days from the date of such notice,
contingent upon the occurrence of the Change in Control, and the Option shall terminate upon the expiration of such period. 

(f) No such adjustment or action shall be authorized to the extent such adjustment or action would result in short-swing profits
liability under Section 16 of the Exchange Act or violate the exemptive conditions of Rule 16b-3 of the Exchange Act unless the Administrator determines that the Option is not to comply with such exemptive conditions. 

(g) The existence of the Grant Notice, Agreement and the Option shall not affect or restrict in any way the right or power of the Company
or the stockholders of the Company to make or 

  
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authorize any adjustment, recapitalization, reorganization or other change in the Company’s capital structure or its business, any merger or consolidation of the Company, any issue of stock
or of options, warrants or rights to purchase stock or of bonds, debentures, preferred or prior preference stocks whose rights are superior to or affect the Stock or the rights thereof or which are convertible into or exchangeable for Stock, or the
dissolution or liquidation of the company, or any sale or transfer of all or any part of its assets or business, or any other corporate act or proceeding, whether of a similar character or otherwise. 

(h) No action shall be taken under this Section 5.1 which shall cause the Option to fail to comply with Section 409A of the
Code or the Treasury Regulations thereunder, to the extent applicable to the Option. 
 (i) In the event of any pending stock
dividend, stock split, combination or exchange of shares, merger, consolidation or other distribution (other than normal cash dividends) of Company assets to stockholders, or any other change affecting the shares of Stock or the share price of the
Stock including any Equity Restructuring, for reasons of administrative convenience, the Company in its sole discretion may refuse to permit the exercise of the Option during a period of up to thirty (30) days prior to the consummation of any
such transaction. 
 5.2 Administration. The Administrator shall have the power to interpret this Agreement and to adopt
such rules for the administration, interpretation and application of this Agreement as are consistent therewith and to interpret, amend or revoke any such rules. All actions taken and all interpretations and determinations made by the Administrator
in good faith shall be final and binding upon Participant, the Company and all other interested persons. No member of the Administrator shall be personally liable for any action, determination or interpretation made in good faith with respect to
this Agreement or the Option. 
 5.3 Whole Shares. The Option may only be exercised for whole shares of Stock.

 5.4 Option Not Transferable. Subject to Section 4.1 hereof, the Option may not be sold, pledged, assigned or
transferred in any manner other than by will or the laws of descent and distribution, unless and until the shares of Stock underlying the Option have been issued, and all restrictions applicable to such shares of Stock have lapsed. Neither the
Option nor any interest or right therein shall be liable for the debts, contracts or engagements of Participant or his or her successors in interest or shall be subject to disposition by transfer, alienation, anticipation, pledge, encumbrance,
assignment or any other means whether such disposition be voluntary or involuntary or by operation of law by judgment, levy, attachment, garnishment or any other legal or equitable proceedings (including bankruptcy), and any attempted disposition
thereof shall be null and void and of no effect, except to the extent that such disposition is permitted by the preceding sentence. 
 5.5 Binding Agreement. Subject to the limitation on the transferability of the Option contained herein, this Agreement will be binding upon and inure to the benefit of the heirs, legatees, legal
representatives, successors and assigns of the parties hereto. 
 5.6 Notices. Any notice to be given under the terms of
this Agreement to the Company shall be addressed to the Company in care of the Secretary of the Company at the Company’s principal office, and any notice to be given to Participant shall be addressed to Participant at Participant’s last
address reflected on the Company’s records. By a notice given pursuant to this Section 5.6, either party may hereafter designate a different address for notices to be given to that party. Any notice which is required to be given to
Participant shall, if Participant is then deceased, be given to the person entitled to exercise his or her Option pursuant to Section 4.1 hereof by written notice under this Section 5.6.

  
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 Any notice shall be deemed duly given when sent via email or when sent by certified mail (return receipt
requested) and deposited (with postage prepaid) in a post office or branch post office regularly maintained by the United States Postal Service. 
 5.7 Titles. Titles are provided herein for convenience only and are not to serve as a basis for interpretation or construction of this Agreement. 

5.8 Governing Law. The laws of the State of Delaware 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. 

5.9 Conformity to Securities Laws. Participant acknowledges that this Agreement is intended to conform to the extent necessary
with all provisions of the Securities Act and the Exchange Act and any and all regulations and rules promulgated by the Securities and Exchange Commission thereunder, and state securities laws and regulations. Notwithstanding anything herein to the
contrary, the Option is granted and may be exercised, only in such a manner as to conform to such laws, rules and regulations. To the extent permitted by applicable law, this Agreement shall be deemed amended to the extent necessary to conform to
such laws, rules and regulations. 
 5.10 Amendments, Suspension and Termination. This Agreement may be wholly or
partially amended or otherwise modified, suspended or terminated at any time or from time to time by the Administrator; provided that, except as may otherwise be provided herein, no amendment, modification, suspension or termination of this
Agreement shall adversely affect the Option in any material way without the prior written consent of Participant. 
 5.11
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 in Section 5.4 hereof, this Agreement shall be binding upon Participant and his or her heirs, executors, administrators, successors and assigns. 
 5.12 Limitations Applicable to Section 16 Persons. Notwithstanding any other provision of this Agreement, if Participant is subject to Section 16 of the Exchange Act, the Option and this
Agreement shall be subject to any additional limitations set forth in any applicable exemptive rule under Section 16 of the Exchange Act (including any amendment to Rule 16b-3 of the Exchange Act) that are requirements for the application of
such exemptive rule. To the extent permitted by applicable law, this Agreement shall be deemed amended to the extent necessary to conform to such applicable exemptive rule. 
 5.13 Not a Contract of Employment. Nothing in this Agreement or in the Grant Notice shall confer upon the Participant any right to continue to serve as an employee or other service provider of the
Company or any of its Subsidiaries. 
 5.14 Entire Agreement. The Grant Notice and this Agreement (including all Exhibits
thereto) constitute the entire agreement of the parties and supersede in their entirety all prior undertakings and agreements of the Company and Participant with respect to the subject matter hereof. 

5.15 Section 409A. This Option is not intended to constitute “nonqualified deferred compensation” within the
meaning of Section 409A of the Code (together with any Department of Treasury regulations and other interpretive guidance issued thereunder, including without limitation any such regulations or other guidance that may be issued after the date
hereof, “Section 409A”). However, 

  
 A-10

 
notwithstanding any other provision of the Grant Notice or this Agreement (or any Exhibits hereto), if at any time the Administrator determines that the Option (or any portion thereof) may be
subject to Section 409A, the Administrator shall have the right in its sole discretion (without any obligation to do so or to indemnify Participant or any other person for failure to do so) to adopt such amendments to the Grant Notice or this
Agreement (or any Exhibits hereto), or adopt other policies and procedures (including amendments, policies and procedures with retroactive effect), or take any other actions, as the Administrator determines are necessary or appropriate either for
the Option to be exempt from the application of Section 409A or to comply with the requirements of Section 409A. 

5.16 Limitation on Participant’s Rights. The Option confers no rights or interests other than as herein provided. This
Agreement creates only a contractual obligation on the part of the Company as to amounts payable and shall not be construed as creating a trust. Neither this Agreement nor any underlying program, in and of itself, has any assets. Participant shall
have only the rights of a general unsecured creditor of the Company with respect to amounts credited and benefits payable, if any, with respect to the Option, and rights no greater than the right to receive the Stock as a general unsecured creditor
with respect to options, as and when exercised pursuant to the terms hereof. 
 5.17 Signature in Counterparts. This
Agreement, if provided for acceptance on a paper copy, may be signed in counterparts, each of which shall be an original, with the same effect as if the signatures thereto and hereto were upon the same instrument. 

  
 A-11EX-10.4

 CODEXIS, INC. 
 JOHN NICOLS 
 RESTRICTED STOCK GRANT NOTICE AND 

RESTRICTED STOCK AGREEMENT 
 Codexis, Inc., a Delaware corporation, (the “Company”), hereby grants to the individual listed below (“Participant”), the number of shares (the
“Shares”) of the Company’s common stock (“Stock”) set forth below. These Shares are subject to all of the terms and conditions as set forth herein and in the Restricted Stock Agreement attached
hereto as Exhibit A (the “Restricted Stock Agreement”) (including without limitation the Restrictions on the Shares set forth in the Restricted Stock Agreement), which is incorporated herein by reference. Unless
otherwise defined herein, the terms are defined in Article 1 of the Restricted Stock Agreement. 
  

					
	Participant’s Name:	  	 John J. Nicols
	 	
			
	Grant Date:	  	 June 13, 2012
	 	
			
	Total Number of Shares of Restricted Stock:	  	 750,000 shares
	 	
			
	Vesting Commencement Date:	  	 June 13, 2012
	 	
		
	Vesting Schedule:	  	The Shares subject to this Award shall vest and be released from the Restrictions (as defined in the Restricted Stock Agreement) as to 25% of the total number of
Shares on each anniversary of the Vesting Commencement Date so that 100% of the Shares shall be released from such Restrictions on the fourth (4th) anniversary of the Vesting Commencement Date, subject to Participant continuing to provide services
to the Company through each such vesting date.
		
	Termination:	  	Subject to Section 2.2 of the Restricted Stock Agreement, if Participant ceases to be an Employee, Consultant or Director prior to the applicable vesting date, all
Shares of Restricted Stock that have not become vested on or prior to the date of such Termination of Service (after taking into consideration any vesting that may occur in connection with such Termination of Service, if any) will thereupon be
automatically forfeited by Participant without payment of any consideration therefor.

 By executing this Grant Notice below, Participant agrees to be bound by the terms and conditions of the
Restricted Stock Agreement and this Grant Notice. Participant has reviewed the Restricted Stock Agreement and this Grant Notice in their entirety, has had an opportunity to obtain the advice of counsel prior to executing this Grant Notice and fully
understands all provisions of this Grant Notice and the Restricted Stock Agreement. Participant hereby agrees to accept as binding, conclusive and final all decisions or interpretations of the Committee upon any questions arising under this Grant
Notice or the Restricted Stock Agreement. In addition, Participant agrees that the Company, in its sole discretion, may satisfy any withholding obligations in accordance with Section 2.2(d) of the Restricted Stock Agreement by
(i) withholding Shares otherwise releasable to Participant upon vesting of the Shares, (ii) instructing a broker on Participant’s behalf to sell shares of Stock otherwise releasable to Participant upon vesting of the Shares and submit
the proceeds of such sale to the Company or (iii) using any other method permitted by Section 2.2(d) of the Restricted Stock Agreement. If Participant is married, his or her spouse has signed the Consent of Spouse attached to this Grant
Notice as Exhibit B. 
  

							
	CODEXIS, INC.:	  	PARTICIPANT:
				
	By:	  	 /s/ Douglas T. Sheehy
	  	By:	 	 /s/ John J. Nicols

	Print Name:	  	 Douglas T. Sheehy
	  	Print Name:	 	 John J. Nicols

	Title:	  	 SVP, General Council & Secretary
	  		 	
	Address:	  	 200 Penobscot Drive
	  	Address:	 	  

		  	 Redwood City, CA 94063
	  		 	  

 EXHIBIT A 
 TO JOHN NICOLS RESTRICTED STOCK GRANT NOTICE 
 RESTRICTED STOCK AGREEMENT

 Pursuant to the Restricted Stock Grant Notice (the “Grant Notice”) to which this Restricted Stock
Agreement (the “Agreement”) is attached, Codexis, Inc., a Delaware corporation, (the “Company”), effective as of the Grant Date set forth in the Grant Notice, has granted to Participant an award (the
“Award”) consisting of the number of shares of restricted stock set forth in the Grant Notice (the “Shares”), subject to the restrictions and risk of forfeiture set forth herein. 

ARTICLE I. 

DEFINED TERMS 
 Wherever the following terms are used in this Agreement, they shall have the meanings specified below. 
 1.1 “Administrator” shall mean the Committee. 
 1.2
“Board” shall mean the Board of Directors of the Company. 
 1.3 “Change in
Control” shall mean and includes each of the following: 
 (a) A transaction or series of transactions (other than
an offering of Stock to the general public through a registration statement filed with the Securities and Exchange Commission) whereby any “person” or related “group” of “persons” (as such terms are used in Sections
13(d) and 14(d)(2) of the Exchange Act) (other than the Company, any of its parents or subsidiaries, an employee benefit plan maintained by the Company or any of its subsidiaries or a “person” that, prior to such transaction, directly or
indirectly controls, is controlled by, or is under common control with, the Company) directly or indirectly acquires beneficial ownership (within the meaning of Rule 13d-3 under the Exchange Act) of securities of the Company possessing more than 50%
of the total combined voting power of the Company’s securities outstanding immediately after such acquisition; or 
 (b)
During any period of two consecutive years, individuals who, at the beginning of such period, constitute the Board together with any new director(s) (other than a director designated by a person who shall have entered into an agreement with the
Company to effect a transaction described in Section 1.2(a) or Section 1.2(c)) whose election by the Board or nomination for election by the Company’s stockholders was approved by a vote of at least two-thirds of the directors then
still in office who either were directors at the beginning of the two-year period or whose election or nomination for election was previously so approved, cease for any reason to constitute a majority thereof; or 

(c) The consummation by the Company (whether directly involving the Company or indirectly involving the Company through one or more
intermediaries) of (x) a merger, consolidation, reorganization, or business combination or (y) a sale or other disposition of all or substantially all of the Company’s assets in any single transaction or series of related transactions
or (z) the acquisition of assets or stock of another entity, in each case other than a transaction: 
 (i) Which results
in the Company’s voting securities outstanding immediately before the transaction continuing to represent (either by remaining outstanding or by being 

  
 A-1

 
converted into voting securities of the Company or the person that, as a result of the transaction, controls, directly or indirectly, the Company or owns, directly or indirectly, all or
substantially all of the Company’s assets or otherwise succeeds to the business of the Company (the Company or such person, the “Successor Entity”)) directly or indirectly, at least a majority of the combined voting
power of the Successor Entity’s outstanding voting securities immediately after the transaction, and 
 (ii) After which
no person or group beneficially owns voting securities representing 50% or more of the combined voting power of the Successor Entity; provided, however, that no person or group shall be treated for purposes of this Section 1.2(c)(ii) as
beneficially owning 50% or more of combined voting power of the Successor Entity solely as a result of the voting power held in the Company prior to the consummation of the transaction; or 

(d) The Company’s stockholders approve a liquidation or dissolution of the Company. 

The Administrator shall have full and final authority, which shall be exercised in its discretion, to determine conclusively whether a Change in Control
of the Company has occurred pursuant to the above definition, and the date of the occurrence of such Change in Control and any incidental matters relating thereto. 
 1.4 “Code” shall mean the Internal Revenue Code of 1986, as amended from time to time. 
 1.5 “Committee” shall mean the Compensation Committee of the Board. 
 1.6 “Consultant” shall mean any consultant or adviser engaged to provide services to the Company or any Subsidiary that qualifies as a consultant under the applicable rules of the
Securities and Exchange Commission for registration of shares on a Form S-8 Registration Statement. 
 1.7
“Employee” shall mean any officer or other employee (as determined in accordance with Section 3401(c) of the Code and the Treasury Regulations thereunder) of the Company or of any Subsidiary. 

1.8 “Exchange Act” shall mean the Securities Exchange Act of 1934, as amended from time to time. 

1.9 “Fair Market Value” shall mean, as of any given date, the value of a share of Stock determined as follows:

 (a) If the Stock is listed on any established stock exchange (such as the New York Stock Exchange, the NASDAQ Global Market
and the NASDAQ Global Select Market) or national market system, its Fair Market Value shall be the closing sales price for a share of Stock as quoted on such exchange or system for such date or, if there is no closing sales price for a share of
Stock on the date in question, the closing sales price for a share of Stock on the last preceding date for which such quotation exists, as reported in The Wall Street Journal or such other source as the Administrator deems reliable;

 (b) If the Stock is not listed on an established stock exchange or national market system, but the Stock is regularly quoted
by a recognized securities dealer, its Fair Market Value shall be the mean of the high bid and low asked prices for such date or, if there are no high bid and low asked prices for a share of Stock on such date, the high bid and low asked prices for
a share of Stock on the last preceding date for which such information exists, as reported in The Wall Street Journal or such other source as the Administrator deems reliable; or 

  
 A-2

 (c) If the Stock is neither listed on an established stock exchange or a national market
system nor regularly quoted by a recognized securities dealer, its Fair Market Value shall be established by the Administrator in good faith. 
 1.10 “Non-Employee Director” shall mean a Director of the Company who is not an Employee. 
 1.11 “Subsidiary” means any entity (other than the Company), whether domestic or foreign, in an unbroken chain of entities beginning with the Company if each of the entities other
than the last entity in the unbroken chain beneficially owns, at the time of the determination, securities or interests representing more than 50% of the total combined voting power of all classes of securities or interests in one of the other
entities in such chain. 
 1.12 “Termination of Service” shall mean the time when the employee-employer
relationship between Participant and the Company or any Subsidiary is terminated for any reason, including, without limitation, a termination by resignation, discharge, death, disability or retirement; but excluding terminations where Participant
simultaneously commences or remains in employment or service with the Company or any Subsidiary. The Administrator, in its sole discretion, shall determine the effect of all matters and questions relating to a Termination of Service, including,
without limitation, the question of whether a Termination of Service resulted from a discharge for cause and all questions of whether particular leaves of absence constitute a Termination of Service. 

ARTICLE II. 
 GRANT OF RESTRICTED STOCK 
 2.1 Grant of Restricted Stock.

 (a) Award. In consideration of Participant’s agreement to commence employment and continue in the employ of or
service to the Company and for other good and valuable consideration which the Committee has determined exceeds the aggregate par value of the Shares, effective as of the Grant Date, the Company has issued to Participant the Shares. Participant is
an Employee, Director or Consultant of the Company or a Subsidiary of the Company. 
 (b) Book Entry Form. At the sole
discretion of the Company, the Shares will be evidenced by documenting the Shares in either (i) uncertificated form, with the Shares recorded in the name of Participant in the books and records of the Company’s transfer agent with
appropriate notations regarding the restrictions on transfer and risk of forfeiture imposed pursuant to this Agreement; or (ii) certificate form pursuant to the terms of Sections 2.1(c) and (d) hereof. 

(c) Legend. Certificates representing Shares issued pursuant to this Agreement shall, until all Restrictions (as defined below)
imposed pursuant to this Agreement lapse or shall have been removed and the Shares shall thereby have become vested or the Shares represented thereby have been forfeited hereunder, bear the following legend (or such other legend as shall be
determined by the Committee): 
 “THE SECURITIES REPRESENTED BY THIS CERTIFICATE ARE SUBJECT TO CERTAIN VESTING REQUIREMENTS
AND MAY BE SUBJECT TO FORFEITURE UNDER THE TERMS OF A RESTRICTED STOCK AGREEMENT BY AND BETWEEN CODEXIS, INC. AND THE REGISTERED OWNER OF SUCH SHARES, AND SUCH SHARES MAY NOT BE, DIRECTLY OR INDIRECTLY, OFFERED,

  
 A-3

 
TRANSFERRED, SOLD, ASSIGNED, PLEDGED, HYPOTHECATED OR OTHERWISE DISPOSED OF UNDER ANY CIRCUMSTANCES, EXCEPT PURSUANT TO THE PROVISIONS OF SUCH AGREEMENT.” 

(d) Escrow. The Secretary of the Company or such other escrow holder as the Committee may appoint may retain physical custody of
any certificates representing the Shares until all of the Restrictions imposed pursuant to this Agreement lapse or shall have been removed. 
 (e) Delivery of Certificates Upon Vesting. As soon as administratively practicable, and, in any event, within sixty (60) days, following the vesting of any Shares subject to the Award pursuant
to Section 2.2(b) hereof, the Company shall, as applicable, either remove the notations on any Shares subject to the Award issued in book entry form which have vested or deliver to Participant a certificate or certificates evidencing the number
of Shares subject to the Award which have vested. Participant (or the beneficiary or personal representative of Participant in the event of Participant’s death or incapacity, as the case may be) shall deliver to the Company any representations
or other documents or assurances required by the Company. The Shares with respect to which such notations have been so removed or certificates so delivered shall no longer be subject to the Restrictions hereunder. Notwithstanding the foregoing, in
the event Shares cannot be issued pursuant to Section 2.2(e)(i), (ii) and (iii) hereof, then the Shares shall be issued pursuant to the preceding sentences as soon as administratively practicable after the Committee determines that
Shares can be issued in accordance with Sections 2.2(e)(i), (ii) and (iii) hereof. 
 2.2 Restrictions.

 (a) Forfeiture. Upon Participant’s Termination of Service for any or no reason, any Shares subject to the Award
that have not vested in accordance with this Agreement (after giving effect to any accelerated vesting pursuant to Sections 2.2.(b) or 2.2(c) hereof or any other written agreement or plan between Participant and the Company) will thereupon be
automatically forfeited, terminated and cancelled as of the applicable termination date without payment of any consideration by the Company, and Participant, or Participant’s beneficiary or personal representative, as the case may be, shall
have no further rights hereunder. Subject to Sections 2.2(b) and 2.2(c) hereof or this Section 2.2(a), no portion of the Award which has not become vested as of the date on which Participant incurs a Termination of Service shall thereafter
become vested. For purposes of this Agreement, “Restrictions” shall mean the restrictions on sale or other transfer set forth in Section 3.5 hereof and the exposure to forfeiture set forth in this Section 2.2(a).

 (b) Vesting and Lapse of Restrictions. Subject to Sections 2.2(a) and 2.2(c) hereof, the Shares subject to the Award
shall vest and Restrictions shall lapse in accordance with the vesting schedule set forth on the Grant Notice, contingent upon Participant’s continued employment or services through such dates. The vesting of the Shares subject to the Award may
be accelerated by the Administrator at such times and in such amounts as it shall determine in its sole discretion, as otherwise provided for in this Agreement or as set forth in a written agreement between the Company and Participant. 

(c) Acceleration of Vesting. Notwithstanding Sections 2.2(a) and 2.2(b) hereof, if a Change in Control occurs and the Award is not
assumed or substituted by a successor corporation in accordance with Section 3.1 hereof, then immediately prior to the consummation of such Change in Control, all forfeiture restrictions on the Award shall lapse in accordance with
Section 3.1 hereof. 
 (d) Tax Withholding. Notwithstanding any other provision of this Agreement (including without
limitation Section 2.1(b) hereof), no new certificate shall be delivered to Participant or 

  
 A-4

 
his or her legal representative and no notation on the books and records shall be removed unless and until Participant or his or her legal representative shall have paid to the Company the full
amount of all federal and state withholding or other taxes applicable to the taxable income of Participant resulting from the grant of Shares or the lapse or removal of the Restrictions. Such payment shall be made in such form of consideration
acceptable to the Company which may, in the sole discretion of the Company, include: 
 (i) Cash or check; 

(ii) Surrender of shares of Stock (including, without limitation, shares of Stock subject to the Award that would otherwise be vesting)
held for such period of time as may be required by the Committee in order to avoid adverse accounting consequences and having a Fair Market Value on the date of delivery equal to the aggregate payment required; or 

(iii) Other property acceptable to the Company in its sole discretion (including, without limitation, through the delivery of a notice
that Participant has placed a market sell order with a broker with respect to shares of Stock for which the Restrictions are then subject to lapse, 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 its withholding obligations; provided that payment of such proceeds is then made to the Company upon settlement of such sale). 
 The Company shall not be obligated to deliver any new certificate representing Shares to Participant or Participant’s legal representative or enter such Share in book entry form unless and until
Participant or Participant’s legal representative shall have paid or otherwise satisfied in full the amount of all federal, state and local taxes applicable to the taxable income of Participant resulting from the grant of the Award or the
issuance of Shares hereunder. 
 2.3 Conditions to Delivery of Stock. Subject to Section 2.1 hereof, the Shares
issued under this Award, or any portion thereof, may be either previously authorized but unissued shares of Stock, treasury shares of Stock or issued shares of Stock which have been reacquired by the Company on the open market. Such Shares shall be
fully paid and nonassessable. 
 2.4 Rights as Stockholder. The holder of the Award shall not be, nor have any of the
rights or privileges of, a stockholder of the Company, including, without limitation, any dividend rights and voting rights, in respect of any Shares unless and until such Shares shall have been actually issued by the Company and held of record by
such holder (as evidenced by the appropriate entry on the books of the Company or of a duly authorized transfer agent of the Company). 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 3.1 hereof. 
 ARTICLE III. 

OTHER PROVISIONS 
 3.1 Change in Control. 
 (a) In the event that the successor corporation in
a Change in Control refuses to assume or substitute for the Award upon a Change in Control, the Award shall become fully vested and all Restrictions on the Award shall lapse, in each case, as of immediately prior to the consummation of such Change
in Control. 

  
 A-5

 (b) The existence of the Grant Notice, Agreement and the Award shall not affect or restrict
in any way the right or power of the Company or the stockholders of the Company to make or authorize any adjustment, recapitalization, reorganization or other change in the Company’s capital structure or its business, any merger or
consolidation of the Company, any issue of stock or of options, warrants or rights to purchase stock or of bonds, debentures, preferred or prior preference stocks whose rights are superior to or affect the Stock or the rights thereof or which are
convertible into or exchangeable for Stock, or the dissolution or liquidation of the company, or any sale or transfer of all or any part of its assets or business, or any other corporate act or proceeding, whether of a similar character or
otherwise. 
 3.2 Administration. The Committee shall have the power to interpret this Agreement and to adopt such rules
for the administration, interpretation and application of this Agreement as are consistent therewith and to interpret, amend or revoke any such rules. All actions taken and all interpretations and determinations made by the Committee in good faith
shall be final and binding upon Participant, the Company and all other interested persons. No member of the Committee or the Board shall be personally liable for any action, determination or interpretation made in good faith with respect to this
Agreement or the Award. 
 3.3 Tax Consultation. Participant understands that Participant may suffer adverse tax
consequences in connection with the Shares issued pursuant to this Award (and the shares issuable with respect thereto). Participant represents that Participant has consulted with any tax consultants Participant deems advisable in connection with
the Award and the issuance of Shares with respect thereto and that Participant is not relying on the Company for any tax advice. 
 3.4 Tax-Related Items. Participant agrees to indemnify and keep indemnified the Company, any Subsidiary and his/her employing company, if different, from and against any liability for or obligation
to pay any liability for income tax, withholding tax and any other employment related taxes, employee’s national insurance contributions or employer’s national insurance contributions or equivalent social security contributions in any
jurisdiction (collectively, “Tax-Related Items”) that is attributable to (a) the grant, or any benefit derived by Participant from, the Award, (b) the issuance to Participant of the Shares or (c) the disposal
of the Shares. 
 3.5 Restricted Stock Not Transferable. During the lifetime of Participant, until the Restrictions
lapse, this Award and the rights and privileges conferred hereby will not be transferred, assigned, pledged or hypothecated in any way (whether by operation of law or otherwise) and will not be subject to sale under execution, attachment or similar
process. Upon any attempt to transfer, assign, pledge, hypothecate or otherwise dispose of the Award, or any right or privilege conferred hereby, or upon any attempted sale under any execution, attachment or similar process, the Award and the rights
and privileges conferred hereby immediately will become null and void. Notwithstanding anything herein to the contrary, this Section 3.5 shall not prevent transfers by will or applicable laws of descent and distribution. 

3.4 Binding Agreement. Subject to the limitation on the transferability of this Award contained herein, this Agreement will be
binding upon and inure to the benefit of the heirs, legatees, legal representatives, successors and assigns of the parties hereto. 
 3.5 Notices. Any notice to be given under the terms of this Agreement to the Company shall be addressed to the Company in care of the Secretary of the Company at the Company’s principal
office, and any notice to be given to Participant shall be addressed to Participant at Participant’s last address reflected on the Company’s records. By a notice given pursuant to this Section 3.7, either party may hereafter designate
a different address for notices to be given to that party. Any notice shall be deemed 

  
 A-6

 
duly given when sent via email or when sent by certified mail (return receipt requested) and deposited (with postage prepaid) in a post office or branch post office regularly maintained by the
United States Postal Service. 
 3.6 Titles. Titles provided herein are for convenience only and are not to serve as a
basis for interpretation or construction of this Agreement. 
 3.7 Governing Law; Severability. The laws of the State of
Delaware 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. 

3.8 Conformity to Securities Laws. Participant acknowledges that this Agreement is intended to conform to the extent necessary
with all provisions of the Securities Act and the Exchange Act and any and all regulations and rules promulgated by the Securities and Exchange Commission thereunder, and state securities laws and regulations. Notwithstanding anything herein to the
contrary, the Award is granted, only in such a manner as to conform to such laws, rules and regulations. To the extent permitted by applicable law, this Agreement shall be deemed amended to the extent necessary to conform to such laws, rules and
regulations. 
 3.9 Amendments, Suspension and Termination. This Agreement may be wholly or partially amended or
otherwise modified, suspended or terminated at any time or from time to time by the Committee or the Board, provided, that, except as may otherwise be provided herein, no amendment, modification, suspension or termination of this Agreement
shall adversely effect the Award in any material way without the prior written consent of Participant. 
 3.10 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 Participant and his or her heirs, executors, Committees, successors and assigns. 
 3.11 Limitations Applicable to Section 16 Persons. Notwithstanding any other provision of this Agreement, if Participant is subject to Section 16 of the Exchange Act, the Award, the
Shares and this Agreement shall be subject to any additional limitations set forth in any applicable exemptive rule under Section 16 of the Exchange Act (including any amendment to Rule 16b-3 of the Exchange Act) that are requirements for the
application of such exemptive rule. To the extent permitted by applicable law, this Agreement shall be deemed amended to the extent necessary to conform to such applicable exemptive rule. 

3.12 Tax Withholding and Section 83(b) Election. Participant understands that Section 83(a) of the Internal Revenue Code
taxes as ordinary income the difference between the amount, if any, paid for the Shares and the Fair Market Value of such Shares at the time the Restrictions on such Shares lapse. Participant understands that, notwithstanding the preceding sentence,
Participant may elect to be taxed at the time of the Grant Date, rather that at the time the Restrictions lapse, by filing an election under Section 83(b) of the Code (an “83(b) Election”) with the Internal Revenue
Service within thirty (30) days of the Grant Date. In the event Participant files an 83(b) Election, Participant shall provide the Company a copy thereof prior to the expiration of such thirty (30) day period. Participant understands that
in the event an 83(b) Election is filed with the Internal Revenue Service within such time period, Participant will recognize ordinary income in an amount equal to the difference between the amount, if any, paid for the Shares and the Fair Market
Value of such Shares as of the Grant Date. Participant further understands that an additional copy of such 83(b) Election form should be filed with his or her federal income tax return for the calendar year in which the date of this Agreement falls.
Participant acknowledges that the 

  
 A-7

 
foregoing is only a summary of the effect of United States federal income taxation with respect to the Award hereunder, and does not purport to be complete. PARTICIPANT FURTHER ACKNOWLEDGES THAT
THE COMPANY IS NOT RESPONSIBLE FOR FILING PARTICIPANT’S 83(b) ELECTION, AND THE COMPANY HAS DIRECTED PARTICIPANT TO SEEK INDEPENDENT ADVICE REGARDING THE APPLICABLE PROVISIONS OF THE INTERNAL REVENUE CODE, THE INCOME TAX LAWS OF ANY
MUNICIPALITY, STATE OR FOREIGN COUNTRY IN WHICH PARTICIPANT MAY RESIDE, AND THE TAX CONSEQUENCES OF PARTICIPANT’S DEATH. 
 PARTICIPANT
HEREBY ASSUMES ALL RESPONSIBILITY FOR FILING PARTICIPANT’S 83(b) ELECTION AND PAYING ANY TAXES RESULTING FROM SUCH ELECTION OR FROM FAILURE TO FILE THE ELECTION AND PAYING TAXES RESULTING FROM THE LAPSE OF THE RESTRICTIONS ON THE UNVESTED
SHARES. 
 PARTICIPANT UNDERSTANDS THAT PARTICIPANT MAY SUFFER ADVERSE TAX CONSEQUENCES AS A RESULT OF PARTICIPANT’S PURCHASE OR
DISPOSITION OF THE SHARES AND PARTICIPANT REPRESENTS THAT PARTICIPANT IS NOT RELYING ON THE COMPANY FOR ANY TAX ADVICE. 
 3.14
Not a Contract of Employment. Nothing in this Agreement or in the Grant Notice shall confer upon Participant any right to continue to serve as an employee or other service provider of the Company or any of its Subsidiaries. 

3.15 Entire Agreement. The Grant Notice and this Agreement constitute the entire agreement of the parties and supersede in their
entirety all prior undertakings and agreements of the Company and Participant with respect to the subject matter hereof. 
 3.16
Limitation on Participant’s Rights. This Award confers no rights or interests other than as herein provided. This Agreement creates only a contractual obligation on the part of the Company as to amounts payable and shall not be construed
as creating a trust. Neither this Agreement nor any underlying program, in and of itself, has any assets. Participant shall have only the rights of a general unsecured creditor of the Company with respect to amounts credited and benefits payable, if
any, with respect to the Shares issuable hereunder. 

  
 A-8

 EXHIBIT B 
 TO JOHN NICOLS RESTRICTED STOCK GRANT NOTICE 
 CONSENT OF SPOUSE

 I,
                            , spouse of John J. Nicols, have read and approve the foregoing Agreement. In
consideration of issuing to my spouse the shares of the common stock of Codexis, Inc. set forth in the 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 Agreement insofar as I may have any rights in said Agreement or any shares of the common stock of Codexis, Inc. 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 Agreement. 
  

			
	Dated:             ,         	 	  

		 	Signature of Spouse

  
 B-1

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