Document:

EX-10.5

 Exhibit 10.5 
 CODEXIS, INC. 
 DAVID O’TOOLE 

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:	  	 David O’Toole
	  	
			
	Grant Date:	  	 September 10, 2012
	  	
			
	Total Number of Shares of Restricted Stock:	  	 50,000 shares
	  	
			
	Vesting Commencement Date:	  	 September 4, 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/ David O’Toole

	Print Name:	  	Douglas T. Sheey	 		  	Print Name:	  	David O’Toole
	Title:	  	 Senior Vice President, General
 Counsel and Secretary
	 		  		  	
					
	Address:	  	[ADDRESS]	 		  	Address:	  	[ADDRESS]

 EXHIBIT A 
 TO DAVID O’TOOLE 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 

  
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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 

  
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 (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,

  
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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 

  
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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. 

  
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 (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 

  
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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 

  
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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. 

  
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 EXHIBIT B 
 TO DAVID O’TOOLE RESTRICTED STOCK GRANT NOTICE  
 CONSENT
OF SPOUSE 
 I, Marilyn O’Toole, spouse of David O’Toole, 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: September 29, 2012	 		  	 /s/ Marilyn O’Toole

		 		  	Signature of Spouse

  
 B-1EX-10.6

 Exhibit 10.6 
 SIXTH AMENDMENT TO LEASE 
 This Sixth Amendment to Lease (“Amendment”)
is entered into, and dated for reference purposes, as of September 27, 2012 (the “Execution Date”) by and between METROPOLITAN LIFE INSURANCE COMPANY, a New York corporation (“Metropolitan”), as Landlord
(“Landlord”), and CODEXIS, INC., a Delaware corporation (“Codexis”), as Tenant (“Tenant”), with reference to the following facts (“Recitals”): 

A. Landlord and Tenant are the parties to that certain written lease which is comprised of the following: that certain written Lease,
dated as of October     , 2003 [sic], by and between Landlord and Tenant (the “Original Lease”) for certain premises described therein and commonly known as 501 Chesapeake Drive which is a part of Building 3 (the
“501 Chesapeake Space”) and all the rentable area of Building 4 (consisting of 200 and 220 Penobscot Drive (collectively, the “200 & 220 Penobscot Space”, and together with the 501 Chesapeake Space are referred to
collectively as the “Original Premises”), all as more particularly described in the Original Lease; as amended by that certain First Amendment to Lease, dated as of June 1, 2004, by and between Landlord and Tenant (the “First
Amendment”); as amended by that certain Second Amendment to Lease, dated as of March 9, 2007, by and between Landlord and Tenant (the “Second Amendment”); as amended by that certain Third Amendment to Lease, dated as of
March 31, 2008, by and between Landlord and Tenant (the “Third Amendment”) for certain premises described therein and commonly known as 400 Penobscot Drive, which is the entire Building 2 (the “Building 2 Space”), all as
more particularly described in the Third Amendment; as amended by that certain Fourth Amendment to Lease, dated as of September 17, 2010, by and between Landlord and Tenant (the “Fourth Amendment”); and as amended by that certain
Fifth Amendment to Lease, dated as of March 16, 2011, by and between Landlord and Tenant (the “Fifth Amendment”) for certain premises described therein and commonly known as 101 Saginaw Drive, which is part of Building 1 (the
“101 Saginaw Space”); all as more particularly described in the Fifth Amendment. The Original Lease, as amended, is referred to for purposes of this Amendment as the “Existing Lease”. 

B. Landlord and Tenant desire to provide for extension of the Term of the 501 Chesapeake Space and other amendments of the Existing Lease
as more particularly set forth below. 
 NOW, THEREFORE, in consideration of the foregoing, and of the mutual covenants set
forth herein and of other good and valuable consideration, the receipt and adequacy of which are hereby acknowledged, the parties hereto agree as follows: 
 Section 1. Scope of Amendment; Defined Terms. Except as expressly provided in this Amendment, the Existing Lease shall remain in full force and effect. Should any inconsistency arise
between this Amendment and the Existing Lease as to the specific matters which are the subject of this Amendment, the terms and conditions of this Amendment shall control. The term “Existing Lease” defined above shall refer to the Existing
Lease as it existed before giving effect to the modifications set forth in this Amendment and the term “Lease” as used herein and in the Existing Lease shall refer to the Existing Lease as modified by this Amendment, except as expressly
provided in this Amendment. All capitalized terms used in this Amendment and not defined herein shall have the meanings set forth in the Existing Lease unless the context clearly requires otherwise. 

Section 2. Confirmation of Term. Landlord and Tenant acknowledge and agree that notwithstanding any provision of
the Existing Lease to the contrary: (a) as contemplated by the Existing Lease, the 501 Chesapeake Space Expiration Date is January 31, 2013; (b) as contemplated by the Existing Lease, the Building 2 Expiration Date is January 31,
2020; (c) as contemplated by the Existing Lease, the expiration date of the 101 Saginaw Space is January 31, 2020 (the “101 Saginaw Space Expiration Date”, inadvertently referred to as January 30, 2020 in Section 6(c)
of the Fifth Amendment); and (d) as contemplated by the Existing Lease, the Expiration Date of the Term of the Lease of the 200 & 220 Penobscot Space is January 31, 2020. 

  
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 Section 3. Extension of Term for 501 Chesapeake Space. Landlord and
Tenant agree that the Term for the 501 Chesapeake Space is hereby extended for the period of forty-eight (48) months (the “501 Chesapeake Second Extended Term”) commencing on February 1, 2013 (the “501 Chesapeake Second
Extension Commencement Date”) and expiring January 31, 2017 (hereafter, the “501 Chesapeake Expiration Date”), unless sooner terminated pursuant to the terms of the Lease. Landlord and Tenant acknowledge and agree that this
Amendment provides all rights and obligations of the parties with respect to extension of the current Term for the 501 Chesapeake Space only, whether or not in accordance with any other provisions, if any, of the Existing Lease regarding renewal or
extension of such space. 
 Section 4. Amendment of Rent for 501 Chesapeake Second Extended Term.
Notwithstanding any provision of the Existing Lease to the contrary, commencing on 501 Chesapeake Second Extension Commencement Date and continuing through the 501 Chesapeake Expiration Date, the amount of Monthly Base Rent due and payable by Tenant
for the 501 Chesapeake Space shall be as follows: 
  

					
	 Period from/to
	  	Monthly Amount	 
	 February 1, 2013 to January 31, 2014
	  	$	18,968.60	  
	 February 1, 2014 to January 31, 2015
	  	$	19,537.66	  
	 February 1, 2015 to January 31, 2016
	  	$	20,123.79	  
	 February 1, 2016 to January 31, 2017
	  	$	20,727.50	  

 Section 5. “AS IS” Condition. Tenant acknowledges and agrees that Tenant
presently occupies and has occupied the 501 Chesapeake Space, and Tenant accepts the 501 Chesapeake Space in its AS-IS condition, without any express or implied representations or warranties of any kind by Landlord, its brokers, manager or agents,
or the employees of any of them regarding the Premises. Landlord shall not have any obligation to construct or install any tenant improvements or alterations or to pay for any such construction or installation in any portion of the Premises.

 Section 6. Negotiation Right. 
 (a) Landlord and Tenant confirms that the Negotiation Right with respect to 123 Saginaw Negotiation Space (as set forth in Section 11 of the Fifth Amendment) continues to be in effect. The following
Negotiation Rights have terminated: (i) the Negotiation Right with respect to 525 Chesapeake Drive (as set forth in Section 6 of the Second Amendment); and (ii) the Negotiation Right with respect to the 600 Galveston Negotiation Space
(as set forth in Section 7 of the Third Amendment, as amended by Section 7(b)(ii) of the Fifth Amendment)). 
 (b)
Landlord hereby grants Tenant a one-time right to negotiate the lease of the 525 Chesapeake Negotiation Space (defined below) if and to the extent such space is Available (defined below) during the period beginning on the Execution Date of this
Amendment and expiring twenty-four (24) months prior to the 501 Chesapeake Expiration Date (the “Negotiation Period”), upon and subject to the terms and conditions of this Section (the “Negotiation Right”), and provided that
at the time of exercise of such right: (i) Tenant must be conducting regular, active, ongoing business in, and be in occupancy (and occupancy by a subtenant, licensee or other party permitted or suffered by Tenant shall not satisfy such
condition) of the entire 501 Chesapeake Space, and (ii) there has been no material adverse change in Tenant’s financial position from such position as of the date of execution of the Lease, as certified by Tenant’s independent
certified public accountants, and as supported by Tenant’s certified financial statements, copies of which shall be delivered to Landlord with Tenant’s written notice exercising its right hereunder. Without limiting the generality of the
foregoing, Landlord may reasonably conclude there has been a material adverse change if Tenant’s independent certified public accountants do not certify there has been no such change. 

  
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 (c) The “525 Chesapeake Negotiation Space” shall mean the space with a street
address of 525 Chesapeake Drive and Rentable Area of approximately 15,393 square feet. For purposes of this Negotiation Right, the term “Available” shall mean that the space in question is either: (1) vacant and free and clear of all
“Prior Rights” (defined below); or (2) space as to which Landlord has received a proposal, or Landlord is making a proposal, for a lease or rights of any nature applicable in the future when such space would be free and clear of all
Prior Rights. For purposes of this Negotiation Right, the term “Prior Rights” shall mean rights of other parties, including without limitation, a lease, lease option, or option or other right of extension, renewal, expansion, refusal,
negotiation or other right, either: (i) pursuant to any lease or written agreement which is entered into within eighteen (18) months after the Execution Date; or (ii) pursuant to any extensions or renewal of any of the foregoing,
whether or not set forth in such lease or written agreement, and Landlord shall be free at any time to enter such extension or renewal; or (iii) pursuant to any amendment or modification of any of the foregoing, and Landlord shall be free at
any time to enter such amendment or modification. 
 (d) Nothing herein shall be deemed to limit or prevent Landlord from
marketing, discussing or negotiating with any other party for a lease of, or rights of any nature as to, any part of the 525 Chesapeake Negotiation Space, but during the Negotiation Period before Landlord makes any written proposal to any other
party (other than a party with Prior Rights) for any 525 Chesapeake Negotiation Space which becomes Available (including giving a written response to any proposal or offer received from another party), or contemporaneously with making any such
proposal, and in any event within thirty (30) days after such space becomes vacant and free and clear of all Prior Rights, Landlord shall give Tenant written notice (“Landlord’s Notice”), which notice identifies the space
Available and Landlord’s estimate of the projected date such space will be vacant and deliverable to Tenant. Notwithstanding any of the foregoing to the contrary, Tenant acknowledges that Landlord has disclosed that as of the date of execution
of this Lease, Landlord is marketing the 525 Chesapeake Negotiation Space, and as set forth more fully in Subsection (b) above, if Landlord entered into a lease within eighteen (18) months after the Execution Date, Landlord shall remain
free at any time to enter into an extension or renewal of such lease, whether or not any such right is set forth in such lease, and to enter into any amendment or modification of such lease, all of which constitute Prior Rights with respect to the
525 Chesapeake Negotiation Space. For a period of five (5) business days after Landlord gives Landlord’s Notice (the “Election Notice Period”), Tenant shall have the right to initiate negotiations in good faith for the lease of
all (and not less than all) the space identified in Landlord’s Notice by giving Landlord written notice (“Election Notice”) of Tenant’s election to exercise its Negotiation Right to lease such space. 

(e) If Tenant timely and properly gives the Election Notice, Landlord and Tenant shall, during the five (5) business day period (the
“Second Period”) following Landlord’s receipt of the Election Notice, negotiate in good faith for the lease of the 525 Chesapeake Negotiation Space which is the subject of the Landlord Notice as set forth below. Any lease by Tenant
pursuant to this Negotiation Right: (1) shall be for all (and not less than all) the 525 Chesapeake Negotiation Space which is the subject of the Landlord Notice; (2) the subject 525 Chesapeake Negotiation Space shall, upon delivery, be
part of the Premises under this Lease, such that the term “Premises” thereafter shall include the subject 525 Chesapeake Negotiation Space; (3) starting on such delivery date, with respect to the subject 525 Chesapeake Negotiation
Space Tenant shall additionally pay Tenant’s Share of Operating Expenses, with Tenant’s Share recalculated to reflect addition of the 525 Chesapeake Negotiation Space; (4) the number of parking spaces applicable to the subject 525
Chesapeake Negotiation Space shall be calculated at the rate of 3.3 spaces per 1000 square feet of Rentable Area of the subject 525 Chesapeake Negotiation Space, and the type of, location of and charge for such spaces shall be as otherwise provided
in the Lease; and (5) such lease shall be upon and subject to all the other terms, covenants and conditions provided in the Lease, except that the following terms shall be subject to such negotiation and agreement of the parties: (aa) the
amount of the Monthly Base Rent with respect to the 525 Chesapeake Negotiation Space; (bb) the term of the lease of the 525 Chesapeake Negotiation Space; (cc) any improvements or alterations to be done, or allowance therefor, if any, specifically
agreed upon, and absent such agreement, Tenant shall accept the 525 Chesapeake Negotiation Space in its 

  
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then AS IS condition without any obligation of Landlord to repaint, remodel, improve or alter the subject 525 Chesapeake Negotiation Space for Tenant’s occupancy or to provide Tenant any
allowance therefor, but such space shall be delivered broom clean and free of all tenants or occupants (and their personal property); (dd) increase in the Security; and (ee) Landlord shall deliver the subject 525 Chesapeake Negotiation Space to
Tenant in such AS IS condition no later than thirty (30) days after Landlord regains possession of such space, but in no event shall Landlord have any liability for failure to deliver the subject 525 Chesapeake Negotiation Space to Tenant on
any projected delivery date due to the failure of any occupant to timely vacate and surrender such space or due to Force Majeure, and such failure shall not be a default under the Lease or impair its validity. The foregoing obligation of Landlord to
negotiate is non-exclusive and nothing herein shall be deemed to prevent Landlord from negotiating with any other party for the 525 Chesapeake Negotiation Space, whether or not Landlord and Tenant are negotiating for the same, but any other such
negotiation shall be subject to the aforesaid obligation to negotiate with Tenant in good faith. 
 (f) If Tenant either fails
or elects not to exercise its Negotiation Right as to the 525 Chesapeake Negotiation Space covered by Landlord’s Notice by not giving its Election Notice within the Election Notice Period, or if Tenant gives Tenant’s Election Notice but
Tenant and Landlord do not execute (1) a written letter of intent reflecting the significant business terms for the lease of the 525 Chesapeake Negotiation Space within five (5) business days after delivery of the Election Notice, and
(2) a corresponding amendment prepared by Landlord within five (5) days after Landlord gives Tenant such proposed amendment, then in any such event Tenant’s Negotiation Right shall terminate, and be null and void, as to the subject
space identified in the applicable Landlord’s Notice (but not as to any 525 Chesapeake Negotiation Space subject to this Negotiation Right which has not become Available and been included in a Landlord’s Notice), and at any time thereafter
Landlord shall be free to lease and/or otherwise grant options or rights to the subject space on any terms and conditions whatsoever free and clear of the Negotiation Right. 
 (g) During any period that Tenant does not occupy the entire Premises or that there is an uncured default by Tenant under the Lease, or any state of facts which with the passage of time or the giving of
notice, or both, would constitute such a default, the Negotiation Right shall not apply and shall be ineffective and suspended, and Landlord shall not be obligated to give a Landlord’s Notice as to any space which becomes Available during such
suspension period, and Landlord shall not be obligated to negotiate (or enter into any amendment) with respect to any 525 Chesapeake Negotiation Space which was the subject of a pending Landlord’s Notice for which an amendment has not been
fully executed, and during such suspension period Landlord shall be free to lease and/or otherwise grant options or rights to such space on any terms and conditions whatsoever free and clear of the Negotiation Right. The Negotiation Right shall
terminate upon any of the following: (1) the termination of the Lease, whether by Landlord upon the occurrence of a Tenant default or otherwise; or (2) the failure of Tenant timely to exercise, give any notices, perform or agree, within
any applicable time period specified above, with respect to any 525 Chesapeake Negotiation Space which was the subject of any Landlord’s Notice. 
 (h) The Negotiation Right is personal to Codexis and may not be used by, and shall not be transferable or assignable (voluntarily or involuntarily) to any person or entity. 

Section 7. Option to Extend. 
 (a) Landlord and Tenant confirms that the Option to Extend with respect to the 200 & 220 Penobscot Space, Building 2 Space and 101 Saginaw Space (as set forth in Section 12 of the Fifth
Amendment) continues to be in effect. Landlord and Tenant hereby agree to delete the Option to Extend with respect to the 501 Chesapeake Space as set forth in Section 26.21 of the Original Lease, as amended by Section 3 of the Fourth
Amendment. 
 (b) Landlord hereby grants Tenant two (2) consecutive options to extend the Term of the Lease with respect to
the 501 Chesapeake Space for an additional term of five (5) years per option pursuant to the 

  
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same terms and conditions of Section 12 of the Fifth Amendment. Accordingly, Section 12(b) of the Fifth Amendment is hereby amended by deleting and replacing the phrase “as to the
portion of the Premises consisting of the 200 & 220 Penobscot Space, Building 2 Space and 101 Saginaw Space (all references in this Section 12 to the “Premises” shall instead be deemed to mean such space only)” with the
following phrase: “as to the portion of the Premises consisting of the 200 & 220 Penobscot Space, Building 2 Space, 101 Saginaw Space and 501 Chesapeake Space (all references in this Section 12 to the “Premises” shall
instead be deemed to mean such space only)”. 
 Section 8. Time of Essence. Without limiting the
generality of any provision of the Lease, time shall be of the essence with respect to all of the provisions of this Amendment. 

Section 9. Brokers. Notwithstanding any other provision of the Existing Lease to the contrary, Tenant represents and
warrants to Landlord that Cornish & Carey Commercial Newmark Knight Frank is the sole broker who negotiated and brought about the consummation of this Amendment and that no discussions or negotiations were had with any other broker
concerning this Amendment. Based on the foregoing representation and warranty, Landlord has agreed to pay any commission or fee owed to such broker pursuant to Landlord’s agreement between Landlord and such broker, and Tenant is not obligated
to pay or fund any amount to such broker. Tenant hereby indemnifies and agrees to protect, defend and hold Landlord harmless from and against any claims of brokerage commissions arising out of any discussions or negotiations allegedly had by Tenant
with any other broker in connection with the Building and the Premises. The foregoing obligations of Tenant shall survive the expiration or sooner termination of the Lease. 
 Section 10. Attorneys’ Fees. Each party to this Amendment shall bear its own attorneys’ fees and costs incurred in connection with the discussions preceding, negotiations for
and documentation of this Amendment. In the event that either party brings any suit or other proceeding with respect to the subject matter or enforcement of this Amendment or the Lease, the parties acknowledge and agree that the provisions of
Section 11.03 of the Existing Lease shall apply. 
 Section 11. Effect of Headings; Recitals: Exhibits.
The titles or headings of the various parts or sections hereof are intended solely for convenience and are not intended and shall not be deemed to or in any way be used to modify, explain or place any construction upon any of the provisions of this
Amendment. Any and all Recitals set forth at the beginning of this Amendment are true and correct and constitute a part of this Amendment as if they had been set forth as covenants herein. Exhibits, schedules, plats and riders hereto which are
referred to herein are a part of this Amendment. 
 Section 12. Entire Agreement; Amendment. This Amendment
taken together with the Existing Lease, together with all exhibits, schedules, riders and addenda to each, constitutes the full and complete agreement and understanding between the parties hereto and shall supersede all prior communications,
representations, understandings or agreements, if any, whether oral or written, concerning the subject matter contained in this Amendment and the Existing Lease, as so amended, and no provision of the Lease as so amended may be modified, amended,
waived or discharged, in whole or in part, except by a written instrument executed by all of the parties hereto. 

Section 13. OFAC. Landlord advises Tenant hereby that the purpose of this Section is to provide to the Landlord
information and assurances to enable Landlord to comply with the law relating to OFAC. 
 Tenant hereby represents, warrants and covenants to
Landlord, either that (i) Tenant is regulated by the SEC, FINRA or the Federal Reserve (a “Regulated Entity”) or (ii) neither Tenant nor any person or entity that directly or indirectly (a) controls Tenant or (b) has an
ownership interest in Tenant of twenty-five percent (25%) or more, appears on the list of Specially Designated Nationals and Blocked Persons (“OFAC List”) published by the Office of Foreign Assets Control (“OFAC”) of the
U.S. Department of the Treasury. 

  
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 If, in connection with this Lease, there is one or more Guarantors of Tenant’s obligations under this
Lease, then Tenant further represents, warrants and covenants either that (i) any such Guarantor is a Regulated Entity or (ii) neither Guarantor nor any person or entity that directly or indirectly (a) controls such Guarantor or
(b) has an ownership interest in such Guarantor of twenty-five percent (25%) or more, appears on the OFAC List. 
 Tenant covenants
that during the term of this Lease to provide to Landlord information reasonably requested by Landlord including without limitation, organizational structural charts and organizational documents which Landlord may deem to be necessary (“Tenant
OFAC Information”) in order for Landlord to confirm Tenant’s continuing compliance with the provisions of this Section. Tenant represents and warrants that the Tenant OFAC Information it has provided or to be provided to Landlord or
Landlord’s Broker in connection with the execution of this Lease is true and complete. 
 Section 14.
Ratification. Tenant represents to Landlord, as of the Execution Date, that: (a) the Existing Lease is in full force and effect and has not been modified except as provided by this Amendment; (b) to Tenant’s actual knowledge,
there are no uncured defaults or unfulfilled obligations on the part of Landlord or Tenant; and (c) Tenant is currently in possession of the entire Premises as of the Execution Date, and neither the Premises, nor any part thereof, is occupied
by any subtenant or other party other than Tenant. Landlord represents to Tenant, as of the Execution Date, that: (a) the Existing Lease is in full force and effect and has not been modified except as provided by this Amendment, and (b) to
Landlord’s actual knowledge, there are no uncured monetary defaults on the part of Tenant. 
 Section 15.
Authority. Each person executing this Amendment represents and warrants that he or she is duly authorized and empowered to execute it, and does so as the act of and on behalf of the party indicated below. Each party represents and warrants to
the other that it has full authority and power to enter into and perform its obligations under this Amendment, that the person executing this Amendment is fully empowered to do so, and that no consent or authorization is necessary from any third
party. Landlord may request that Tenant provide Landlord evidence of due authorization and execution of this Amendment. 

  
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 Section 16. Applicable Law. This Amendment shall be construed in
accordance with the Laws of the State of California 
 Section 17. Counterparts. This Amendment may be
executed in duplicates or counterparts, or both, and such duplicates or counterparts together shall constitute but one original of the Amendment. Each duplicate and counterpart shall be equally admissible in evidence, and each original shall fully
bind each party who has executed it. 
 IN WITNESS WHEREOF, the parties hereto have executed this Amendment as of the date first
set forth above. 
  

							
	TENANT:	 		 	CODEXIS, INC.,
		 		 	a Delaware corporation
				
		 		 	By:	 	 /s/ John J. Nicols

		 		 	Print Name:	 	John J. Nicols
		 		 	Title:	 	President and Chief Executive Officer
			
	LANDLORD:	 		 	METROPOLITAN LIFE INSURANCE COMPANY,
		 		 	a New York corporation
				
		 		 	By:	 	 /s/ JA Denning

		 		 	Print Name:	 	JA Denning
		 		 	Title:	 	Director

  
 Page 7

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