Document:

Amendment to the Amended and Restated Collaborative Research Agreement

 EXHIBIT 10.3B 
 [*] Certain information in this document has been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted
portions. 
 AMENDMENT TO THE AMENDED AND RESTATED COLLABORATIVE 
 RESEARCH AGREEMENT 
 THIS AMENDMENT TO THE AMENDED AND RESTATED COLLABORATIVE RESEARCH
AGREEMENT, together with exhibits and schedules attached hereto, (the “Amendment”) is entered into and effective as of March 4, 2009 (the “Amendment Date”) by and between
Equilon Enterprises LLC dba Shell Oil Products US, a Delaware limited liability company, having a place of business at 910 Louisiana Street, Houston, Texas 77002, (“Shell”) and Codexis, Inc., a Delaware corporation,
having a place of business at 200 Penobscot Drive, Redwood City, California 94063 (“Codexis”). Shell and Codexis may each be referred to herein individually as a “Party” or, collectively, as the
“Parties.” 
 WHEREAS, Shell and Codexis entered into (a) a certain Amended and
Restated Collaborative Research Agreement, effective as of November 1, 2006, (the “Research Agreement”) pursuant to which the Parties have collaborated to develop certain new biocatalytic processes for use in the conversion of
biomass to fuels and/or fuel additives and/or lubricants, and (b) a certain Amended and Restated License Agreement, effective as of November 1, 2006 (the “License Agreement”); and 
 WHEREAS, the Parties desire to amend certain of the terms of the Research Agreement to revise the scope
of, and to increase the resources devoted to, the collaboration between the Parties, all on the terms and conditions set forth below. 
 NOW, THEREFORE, in consideration of the promises and undertakings set forth herein, the Parties hereby agree as follows: 
  

	1.	ARTICLE 1, DEFINITIONS, shall be amended as follows: 

  

	 	(a)	Section 1.12 is hereby deleted and replaced in its entirety by the following: 

 1.12 “FTE” means the efforts of one or more employees of Codexis (hereinafter a “Codexis
FTE”) or Codexis Laboratories Hungary Kft, an Affiliate of Codexis, (“CLH”) (hereinafter a “CLH FTE”) equivalent to the efforts of one full time employee (i.e., an employee that works at least one thousand
seven hundred sixty (1760) hours per year). 
  

	 	(b)	Section 1.24 is hereby deleted and replaced in its entirety by the following: 

 1.24 “Shell Technology” means (a) any Technology that is or was (i) developed by employees of or
consultants to Shell or an Affiliate of Shell, alone or jointly with Third Parties, prior to or during the Term outside the scope of activities described in any Research Plan; or (ii) acquired during the Term by purchase, license, assignment or
other means from Third Parties by Shell or an Affiliate of Shell, in each of case (b)(i) or (b)(ii), introduced by Shell into the activities to be conducted under any Research Plan; and (b) any Fuel Innovation. 

	 	(c)	Section 1.31 is hereby deleted and replaced in its entirety by the following: 

 1.31 “Year Four Goal(s)” shall have the meaning set forth in Section 2.8(d). 

 

	 	(d)	Section 1.33 is hereby deleted and replaced in its entirety by the following: 

 1.33 “Year Six Goal(s)” shall have the meaning set forth in Section 2.8(f). 

 

	 	(e)	ARTICLE 1, DEFINITIONS, is hereby amended to include the following: 

 “FTE Month” means the efforts of one (1) FTE for one (1) calendar month. 
 “Fuel Innovation” means any technology and/or materials relating specifically to (a) a
novel compound suitable for use as a liquid fuel, or as a fuel additive to a liquid fuel, or a Lubricant, and/or (b) the use of any compound as a liquid fuel, including without limitation any liquid fuel blend, or as a fuel additive to a liquid
fuel, or a Lubricant, that, in (a) and/or (b), is or was developed under the Program by employees of or consultants to Codexis or an Affiliate of Codexis, alone or jointly with employees of or consultants to Shell or an Affiliate of Shell,
during the Term, where (i) “liquid” means [*], and (ii) “fuel additive” means [*]. For purposes of clarification, Fuel Innovation shall exclude any and all materials, technology, technical information, know-how,
expertise and trade secrets relating to the biological manufacture of any compound that is, or the use of which is, Fuel Innovation. 
 “Series F Stock Purchase Agreement” shall have the meaning set forth in Section 3.5(d). 
 “Year Three Goal(s)” shall have the meaning set forth in Section 2.8(c). 
 “Year Five Goal(s)” shall have the meaning set forth in Section 2.8(e). 
  

	2.	ARTICLE 2, PROGRAM ACTIVITIES, shall be amended as follows: 

  

	 	(a)	Section 2.2(a)(vi) is hereby deleted and replaced in its entirety by the following: 

 (vi) review the Year Six Goal(s) proposed by the Parties pursuant to Section 2.8(f), and to make recommendations
to the Oversight Committee with respect to such proposed Year Six Goal(s) on or before May 1, 2011; 
  

	 	(b)	Section 2.2(a) is hereby amended to include the following: 

 (xi) review the Year Three Goal(s) proposed by the Parties pursuant to Section 2.8(c), and to make
recommendations to the Oversight Committee with respect to such proposed Year Three Goal(s) on or before March 1, 2009. 
  

 [*] Certain information in this document has been omitted and filed separately with the Securities and
Exchange Commission. Confidential treatment has been requested with respect to the omitted portions. 
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 (xii) review the Year Four Goal(s) proposed by the Parties pursuant
to Section 2.8(d), and to make recommendations to the Oversight Committee with respect to such proposed Year Four Goal(s) on or before July 1, 2009. 
 (xiii) review the Year Five Goal(s) proposed by the Parties pursuant to Section 2.8(e), and to make
recommendations to the Oversight Committee with respect to such proposed Year Five Goal(s) on or before May 1, 2010. 
  

	 	(c)	Section 2.2(f)(i) is hereby deleted and replaced in its entirety by the following: 

 (i) Decision Making Process of the Research Committee. All decisions of the Research Committee shall be made by
unanimous vote or written consent, as indicated by both co-chairpersons of the Research Committee signing the final written minutes thereof. Codexis representatives collectively shall have one (1) vote and Shell representatives collectively
shall have one (1) vote; provided, however, that in the case of a deadlock where unanimity has not been reached, the final decision with respect to matters concerning technical aspects within the scope of an approved Research Plan
shall be made by Codexis; provided further, that the scope and goal(s) of such Research Plan, including (A) the annual Milestone(s) for such Research Plan, the Year Three Goal(s), the Year Four Goal(s), the Year Five Goal(s) and
the Year Six Goal(s), and (B) whether such Milestone(s), Year Three Goal(s), Year Four Goal(s), Year Five Goal(s) and Year Six Goal(s) have been achieved, shall never be considered “technical aspects.” If a disagreement among members
of the Research Committee with respect to matters other than “technical aspects” remains unresolved for more than thirty (30) business days after the Research Committee first addresses such matter (or such longer period as the Parties
may mutually agree upon), such disagreement shall be submitted to the Oversight Committee for resolution. Notwithstanding anything to the contrary, the Research Committee shall have no authority to alter, modify or amend any of the rights and
obligations of the Parties set forth under this Amended and Restated Research Agreement. 
  

	 	(d)	Sections 2.3(a)(iii) and 2.3(a)(iv) are hereby deleted and replaced in their entirety by the following: 

 (iii) review and approve recommendations from the Research Committee with respect to the Milestones for the
activities to be carried out for each Research Plan, the Year Three Goal(s), the Year Four Goal(s), the Year Five Goal(s) and the Year Six Goal(s), and to approve such Milestones; 
 (iv) determine whether Milestones for the activities to be carried out under each Research Plan, the Year Three
Goal(s), the Year Four Goal(s), the Year Five Goal(s) and the Year Six Goal(s) have been achieved; 
  

	 	(e)	Section 2.3(f)(i) is hereby deleted and replaced in its entirety by the following: 

 (i) Decision Making Process of the Oversight Committee. All decisions of the Oversight Committee shall be made by
unanimous vote or written

  

 [*] Certain information in this document has been omitted and filed separately with the Securities and
Exchange Commission. Confidential treatment has been requested with respect to the omitted portions. 
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consent, as indicated by the co-chairpersons of the Oversight Committee signing the written minutes thereof, with Codexis representatives collectively having one (1) vote and Shell
representatives collectively having one (1) vote; provided, however, that in the case of a deadlock where unanimity has not been reached, the final decisions shall be made by Shell except with respect to (A) the approval or
modification of the annual Milestone(s) for each Research Plan, the Year Three Goal(s), the Year Four Goal(s), the Year Five Goal(s) or the Year Six Goal(s), (B) the approval or amendment of any Research Plan, (C) the determination as to
whether Milestones for the activities to be carried out under each Research Plan, the Year Three Goal(s), the Year Four Goal(s), the Year Five Goal(s) or the Year Six Goal(s) have been achieved, (D) the acquisition of Third Party rights
pursuant to Section 7.1, (E) the determination to have any party that is a Third Party as of the Execution Date participate in the activities to be conducted under the Program, (F) the introduction of Third Party Information into the
Program, or (G) any decision that has a reasonable likelihood of having a material adverse impact on Codexis’ business as conducted at the time of such decision or as contemplated to be conducted at the time of such decision.
Notwithstanding anything to the contrary, except with respect to the approval of the Research Plans, the annual milestones for the activities carried out under each Research Plan, the Year Three Goal(s), the Year Four Goal(s), the Year Five Goal(s)
and the Year Six Goal(s), and any amendments to any of the foregoing, the Oversight Committee shall have no authority to alter, modify or amend any of the rights and obligations of the Parties set forth under this Amended and Restated Research
Agreement. If the Oversight Committee is unable to resolve any dispute, controversy, or claim with respect to items (A) – (G) above in this Section 2.3(f)(i) within thirty (30) days after it first addresses such matter (or
such longer period as the Parties may mutually agree upon), then the dispute shall be referred to Executives of each Party. For purposes of clarification, all matters related to “technical aspects” of an approved Research Plan shall be
resolved in accordance with Section 2.2(f)(i). 
  

	 	(f)	Section 2.6(b)(iii) is hereby deleted and replaced in its entirety by the following: 

 (iii) Subject to Section 2.6(c), after the first anniversary of the Effective Date, during the Term, Codexis
shall assign, on or before the dates set forth in the table in this Section 2.6(b)(iii), below, no less than the corresponding number of FTEs set forth in the table in this Section 2.6(b)(iii), below, to perform Codexis’ obligations
under the Program, and to complete the tasks assigned to Codexis in the Research Plans. 
  

 [*] Certain information in this document has been omitted and filed separately with the Securities and
Exchange Commission. Confidential treatment has been requested with respect to the omitted portions. 
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	 Total Number of FTEs
	 	 Date

	 [*]
	 	November 1, 2007
	 [*]
	 	April 1, 2008
	 [*]
	 	August 1, 2008
	 [*]
	 	September 1. 2008
	 [*]
	 	October 1, 2008
	 [*]
	 	January 1, 2009
	 [*]
	 	February 1, 2009
	 [*]
	 	March 1, 2009

 The Parties agree that as of April 1, 2009, the allocation of FTEs between
Codexis FTEs and CLH FTEs shall be approximately [*] Codexis FTEs and [*] CLH FTEs; provided, however, that Codexis shall have the right to make adjustments to such allocation as reasonably required to achieve the Milestones for the
activities to be carried out under each Research Plan, the Year Three Goal(s), the Year Four Goal(s), the Year Five Goal(s) and/or the Year Six Goal(s), as applicable; provided, further, that Codexis, at each meeting of the Oversight
Committee, shall inform the Oversight Committee of the then-current allocation of FTEs between Codexis FTEs and CLH FTEs and provide information to support such allocation, and in the event that any concern regarding such allocation is raised by the
Oversight Committee, Codexis will re-allocate FTEs between Codexis FTEs and CLH FTEs in accordance with the recommendation of the Oversight Committee as soon as practicable. 
  

	 	(g)	Section 2.6(b)(iv) is hereby deleted and replaced in its entirety by the following: 

 (iv) Prior to May 1, 2010, Codexis, upon the written request of Shell, shall increase the number of FTEs to
perform Codexis’ obligations under the Program by up to [*] to a total number of FTEs of up to [*]. In the event that Shell delivers such a written request to Codexis, the Parties will agree upon the timing and rate of such FTE increase as well
as the allocation of such additional FTEs between Codexis FTEs and CLH FTEs. On or after May 1, 2010, Shell, by written notice, may request that Codexis increase the number of FTEs to perform Codexis’ obligations under the Program by up to
[*] to a total number of FTEs of up to [*], and Codexis and Shell, in good faith, will discuss the benefits of implementing an increase in the number of such FTEs, but Codexis will have no obligation to agree to implement any increase in the number
of such FTEs. In the event that Shell and Codexis agree that an increase in the number of FTEs should be implemented, the Parties, prior to the implementation of such FTE increase, will discuss and agree on the timing and rate of such FTE increase
as well as the allocation of such additional FTEs between Codexis FTEs and CLH FTEs. 
  

 [*] Certain information in this document has been omitted and filed separately with the Securities and
Exchange Commission. Confidential treatment has been requested with respect to the omitted portions. 
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	 	(h)	Section 2.6(b) is hereby amended to include the following: 

 (v) Notwithstanding anything to the contrary, in the event that Shell, in accordance with Section 2.6(c),
exercises its right to reduce the total number of FTEs assigned by Codexis to perform Codexis’ obligations under the Program, Codexis shall have the right to determine the allocation of Codexis FTEs and CLH FTEs comprising such reduction;
provided, however, that Codexis shall consult with the Oversight Committee prior to making such determination. 
  

	 	(i)	Section 2.6(c) is hereby deleted and replaced in its entirety by the following: 

  

	 	(c)	Reduction in FTEs. 

 (i) During the period beginning on May 1, 2009 and ending on [*], Shell shall have the right to reduce the total number of FTEs assigned by Codexis to perform Codexis’ obligations under
the Program by up to [*] FTEs upon [*] advance notice. 
 (ii) After the fourth (4th) anniversary of
the Effective Date, Shell shall have the right to reduce the total number of FTEs assigned by Codexis to perform Codexis’ obligations under the Program upon advance notice; provided, however, that the number of FTEs that may be
reduced will not be greater than as set forth in, and implemented after written notice thereof in accordance with, the table in this Section 2.6(c)(ii), below; provided, further, however, that no reductions may be noticed
during the applicable standstill period set forth in this Section 2.6(c)(ii), below, immediately after a FTE reduction already noticed (each such period during which no subsequent notice may be given, a “Standstill Period”).

  

					
	 Number of FTEs that
 May Be Reduced
	 	 Standstill Period
	 	 Advance Notice Required

	 [*]
	 	[*]	 	[*]
	 [*]
	 	[*]	 	[*]
	 [*]
	 	[*]	 	[*]
	 [*]
	 	[*]	 	[*]

 By way of example, if Shell elects to reduce the number of FTEs by [*] FTEs or less,
no additional reductions may be made by Shell during the [*] day Standstill Period beginning on the date of advance written notice of such reduction election. Similarly, if

  

 [*] Certain information in this document has been omitted and filed separately with the Securities and
Exchange Commission. Confidential treatment has been requested with respect to the omitted portions. 
 6 

 
Shell elects to reduce the number of FTEs by more than [*] FTEs but less than or equal to [*] FTEs, no additional reductions may be made by Shell during the [*] day Standstill Period beginning on
the date of advance written notice of such reduction election. 
  

	 	(j)	Section 2.8 is hereby deleted and replaced in its entirety by the following: 

 2.8 Milestones. 
 (a) Year One Final Milestone. Shell acknowledges that, as of the Execution Date, Codexis has achieved the Year One Final Milestone. 
 (b) Annual Milestones. Prior to beginning work, Codexis shall provide a proposal to Shell for annual milestones for
each work stream. The Parties shall submit such proposed milestones to the Research Committee for consideration and recommendation to the Oversight Committee for approval. 
 (c) Year Three Goal(s). Unless otherwise agreed by the Parties in writing, prior to February 14, 2009, Codexis
shall provide a proposal to Shell for Program progress goal(s) to be achieved as of the third (3rd) anniversary of the Effective Date (the “Year Three Goal(s)”). The Parties shall submit such proposed Year Three Goal(s) to the
Research Committee for consideration and recommendation to the Oversight Committee for approval. For purposes of clarification, it is the intent of the Parties that the Year Three Goal(s) will be more technically challenging to achieve than the
annual Milestones established in accordance with Section 2.8(b). 
 (d) Year Four Goal(s). Unless
otherwise agreed by the Parties in writing, prior to May 1, 2009, Codexis shall provide a proposal to Shell for Program progress goal(s) to be achieved as of the fourth (4th) anniversary of the Effective Date (the “Year Four
Goal(s)”). The Parties shall submit such proposed Year Four Goal(s) to the Research Committee for consideration and recommendation to the Oversight Committee for approval. For purposes of clarification, it is the intent of the Parties that
the Year Four Goal(s) will be more technically challenging to achieve than the annual Milestones established in accordance with Section 2.8(b). 
 (e) Year Five Goal(s). Unless otherwise agreed by the Parties in writing, prior to March 1, 2010, Codexis shall provide a proposal to Shell for Program progress goal(s) to be achieved as of
the fifth (5th) anniversary of the Effective Date (the “Year Five Goal(s)”). The Parties shall submit such proposed Year Five Goal(s) to the Research Committee for consideration and recommendation to the Oversight Committee for
approval. For purposes of clarification, it is the intent of the Parties that the Year Five Goal(s) will be more technically challenging to achieve than the annual Milestones established in accordance with Section 2.8(b). 
 (f) Year Six Goal(s). Unless otherwise agreed by the Parties in writing, prior to March 1, 2011, Codexis shall
provide a proposal to Shell for Program progress goal(s) to be achieved as of the sixth (6th) anniversary of the Effective Date (the “Year Six Goal(s)”). The Parties shall submit such proposed Year Six Goal(s) to the

  

 [*] Certain information in this document has been omitted and filed separately with the Securities and
Exchange Commission. Confidential treatment has been requested with respect to the omitted portions. 
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Research Committee for consideration and recommendation to the Oversight Committee for approval. For purposes of clarification, it is the intent of the Parties that the Year Six Goal(s) will be
more technically challenging to achieve than the annual Milestones established in accordance with Section 2.8(b). 
  

	 	(e)	Milestone Verification. 

 (i) In the event that Codexis reasonably believes that it has achieved a particular annual Milestone, the Year Three Goal(s), the Year Four Goal(s), the Year Five Goal(s) or the Year Six Goal(s),
Codexis shall deliver written notice thereof to Shell (each such notice, a “Milestone Notice”). Within ten (10) business days after delivery of a particular Milestone Notice, Codexis shall provide to Shell sufficient quantities
of any relevant Biocatalyst to permit Shell to verify that the annual Milestone, the Year Three Goal(s), the Year Four Goal(s), the Year Five Goal(s) or the Year Six Goal(s), as the case may be, in such Milestone Notice has been achieved.

 (ii) In the event that Shell cannot verify Codexis’ assertion that Codexis has achieved the
annual Milestone, the Year Three Goal(s), the Year Four Goal(s), the Year Five Goal(s) or the Year Six Goal(s), as the case may be, identified in a particular Milestone Notice, Shell shall provide written notice thereof to Codexis (each such notice,
a “Nonreplication Notice”). The annual Milestone, the Year Three Goal(s), the Year Four Goal(s), the Year Five Goal(s) or the Year Six Goal(s), as the case may be, identified in each Milestone Notice shall be deemed to have been
achieved unless Shell provides a Nonreplication Notice within ninety (90) days after Shell’s receipt of such Milestone Notice; provided that, upon written notice provided prior to the expiration of such ninety (90) day period,
Shell may seek an extension of such ninety (90) day period of up to forty-five (45) days to provide such Nonreplication Notice, not to be unreasonably withheld by Codexis. Upon Codexis’ receipt of a Nonreplication Notice, the Parties
will determine a mutually agreeable time to perform the applicable tests necessary to replicate the identified annual asserted Milestone, the Year Three Goal(s), the Year Four Goal(s), the Year Five Goal(s) or the Year Six Goal(s), as the case may
be, that is the subject of such Nonreplication Notice, such tests to be performed, at Shell’s sole option and expense (A) by Shell at a Shell facility, with Codexis observing; (B) by Codexis at a Codexis facility, with Shell
observing; or (C) by a mutually agreeable Third Party at such Third Party’s facilities, with both Codexis and Shell observing. The outcome of such test shall be determinative of whether the annual Milestone, the Year Three Goal(s), the
Year Four Goal(s), the Year Five Goal(s) or the Year Six Goal(s), as the case may be, has been achieved. In the event that Shell elects to have such test performed by a mutually agreeable Third Party, Codexis shall first execute a sponsored research
agreement with such Third Party substantially in the form attached hereto as Exhibit 2.8(e)(ii). 
  

 [*] Certain information in this document has been omitted and filed separately with the Securities and
Exchange Commission. Confidential treatment has been requested with respect to the omitted portions. 
 8 

	 	(k)	ARTICLE 2, PROGRAM ACTIVITIES, is hereby amended to include the following: 

 2.9 Fuel Innovation. For each invention within the Fuel Innovation, Shell, for a period beginning on the date of
filing of the first non-provisional patent application claiming such invention (the date of each such filing, the “Filing Date”) and continuing until the three (3) year anniversary of the Filing Date (for each such invention, the
“Exclusivity Period”), shall work exclusively with Codexis to identify biological methods of synthesis of the compound(s) that are claimed, or whose use as a liquid fuel, including without limitation any liquid fuel blend, or as a fuel
additive to a liquid fuel, or a Lubricant, is claimed in such patent filing using biological materials, technology, technical information, know-how, expertise and trade secrets. For purposes of clarification, the term “exclusively,” as
used in the previous sentence with respect to Shell, shall permit Shell to conduct activities internally within Shell and with any party that is an Affiliate of Shell as of the Amendment Date (other than [*]), and that Shell shall not enter into any
agreement with any Third Party, or with [*], in each case, to develop biological methods of synthesis of any molecule within the Fuel Innovation, without the prior written consent of Codexis. Notwithstanding anything to the contrary, in the event
that Shell or a Shell Affiliate (other than [*]) acquires one hundred percent (100%) of the voting shares of [*], then the restrictions in this Section 2.9 with respect to the development of biological methods of synthesis of any molecule
within the Fuel Innovation will not apply to [*]. In the event that Shell has not funded at least [*] FTE Months for the identification of biological methods of synthesis of the compound(s) disclosed in such patent filings using biological
materials, technology, technical information, know-how, expertise and trade secrets during the applicable Exclusivity Period, such applicable Exclusivity Period shall be extended automatically for an additional two (2) year period and will
expire on the five (5) year anniversary of the applicable Filing Date, and not on the three (3) year anniversary of the applicable Filing Date. Upon expiration of the applicable Exclusivity Period, either on the three (3) year
anniversary of the applicable Filing Date, or on the five (5) year anniversary of the applicable Filing Date, Shell may continue to work with Codexis, but also may work on its own, with any Shell Affiliate or with any Third Party, to identify
biological methods of synthesis of the compound(s) claimed in the applicable patent filings using biological materials, technology, technical information, know-how, expertise and trade secrets. Any and all patent applications and patents covering
patentable inventions arising from the activities of Codexis and Shell under this Section 2.9 shall be deemed to be Program Patent Rights and any and all technology and materials arising from the activities of Codexis and Shell under this
Section 2.9 shall be deemed to be Program Licensed Technology, as set forth in the Amended and Restated License Agreement. 
 2.10 [*]. Promptly after the Amendment Date, the Parties shall meet and discuss in good faith the advantages and desirability of [*] in connection with the research and commercialization activities
regarding [*] contemplated under the terms of this Agreement, including without limitation [*]. 
  

 [*] Certain information in this document has been omitted and filed separately with the Securities and
Exchange Commission. Confidential treatment has been requested with respect to the omitted portions. 
 9 

	3.	ARTICLE 3, FEES AND PAYMENTS, shall be amended as follows: 

  

	 	(a)	Section 3.3(b) is hereby deleted and replaced in its entirety by the following: 

 (b) Second Contract Year. During the second (2nd) Contract Year of the Term, Shell shall pay to Codexis a
research funding fee based on a FTE rate equal to [*] per year for each of the FTEs assigned by Codexis to perform Codexis’ obligations under the Program during the second (2nd) Contract Year of the Term. Such FTE rate includes any and all
associated overhead expenses, normal laboratory supplies and consumables expenses, and typical operational research expenses for the conduct of the Program. For the avoidance of doubt, except as expressly set forth in this Agreement or as set forth
under the terms of the Series F Stock Purchase Agreement, no additional funds will be provided by Shell for the conduct of the Program, including, for example, funds for facilities, infrastructure, software, capital expenditures, equipment or any
other type of expenditure. 
  

	 	(b)	Section 3.3 is hereby amended to include the following: 

 (c) After the Second Contract Year. After the second (2nd) Contract Year of the Term, beginning on the second
(2nd) anniversary of the Effective Date, Shell shall pay to Codexis a research funding fee based on (i) a Codexis FTE rate equal to [*] per year for each of the Codexis FTEs assigned by Codexis to perform Codexis’ obligations under
the Program and (ii) a CLH FTE rate equal to [*] per year for each of the CLH FTEs assigned by Codexis to perform Codexis’ obligations under the Program; in each case during the third (3rd) Contract Year of the Term. The Codexis FTE
rate and the CLH FTE rate each shall be increased annually at the beginning of each subsequent Contract Year of the Term by an amount equal to the annual change in the index set forth on Schedule E (the “FTE Index”) for each Codexis
FTE and each CLH FTE. The increase in FTE rate, if any, with respect to each of the Codexis FTE rate and the CLH FTE rate, will be based on the change in the FTE Index during the most recent twelve (12) month period for which final, corrected
data are available; provided, however, in the event that such change is a negative number, the relevant FTE rate shall remain unchanged for the subsequent Contract Year. Notwithstanding the previous sentence, in the event that the
index set forth on Schedule F (the “CLH FTE Index”) for a twelve (12) month period for which final, corrected data are available is greater than twice the FTE Index for such twelve (12) month period, the increase in FTE
rate for CLH FTEs, but not for Codexis FTEs, will be based on the change in the CLH FTE Index. The Codexis FTE rate and the CLH FTE rate, each as set forth in this Section 3.3(c), include any and all associated overhead expenses, normal
laboratory supplies and consumables expenses, and typical operational research expenses for the conduct of the Program. For the avoidance of doubt, except as expressly set forth in this Agreement or as set forth under the terms of the Series F Stock
Purchase Agreement, no additional funds will be provided by Shell for the conduct of the Program, including, for example, funds for facilities, infrastructure, software, capital expenditures, equipment or any other type of expenditure. FTE payments
in each Contract Year shall be made in six (6) equal installments (each an “FTE Installment”), each in advance of work actually performed

  

 [*] Certain information in this document has been omitted and filed separately with the Securities and
Exchange Commission. Confidential treatment has been requested with respect to the omitted portions. 
 10 

 
based on the planned utilization of FTEs for the following two (2) months; provided, however, that, in the event either Party elects to reduce the number of FTEs working on the
Program pursuant to Section 2.6(c), a corresponding reduction will be made to the amount of the next FTE Installment. 
  

	 	(c)	Sections 3.4(b), (c), (d) and (e) are hereby deleted and replaced in their entirety by the following: 

 (b) For each Contract Year during the Initial Term beginning with the third (3rd) Contract Year, Shell shall pay
to Codexis a non-refundable, non-creditable Milestone payment equal to [*] (for a total of [*]) upon achievement of the Milestones for each of the then-current Research Plans established in accordance with Section 2.8(b), such amount to be
distributed among all such then-current Research Plans in accordance with the recommendation of the Oversight Committee. For purposes of clarification, for purposes of this Section 3.4(b), “achievement of the applicable Milestone”
means that Codexis delivers to Shell a Milestone Notice for such Milestone within the relevant time period, even if the verification of such Milestone Notice occurs after the expiration of such time period; provided, however, that
payment for any Milestone due pursuant to this Section 3.4(b) will be due and payable in accordance with Section 3.6 only after the achievement of such Milestone has been verified in accordance with Section 2.8(e). 
 (c) Upon the achievement of the Year Three Goal(s), Shell shall pay to Codexis a one-time, non-refundable,
non-creditable Milestone payment equal to [*], such amount to be distributed among all such then-current Research Plans in accordance with the recommendation of the Oversight Committee; provided, however, that payment for the Year
Three Goal(s) due pursuant to this Section 3.4(c) will be due and payable in accordance with Section 3.6 only after the achievement of such Year Three Goal(s) has been verified in accordance with Section 2.8(e). 
 (d) Upon the achievement of the Year Four Goal(s), Shell shall pay to Codexis a one-time, non-refundable,
non-creditable Milestone payment equal to [*], such amount to be distributed among all such then-current Research Plans in accordance with the recommendation of the Oversight Committee; provided, however, that payment for the Year Four
Goal(s) due pursuant to this Section 3.4(d) will be due and payable in accordance with Section 3.6 only after the achievement of such Year Four Goal(s) has been verified in accordance with Section 2.8(e). 
 (e) Upon the achievement of the Year Five Goal(s), Shell shall pay to Codexis a one-time, non-refundable,
non-creditable Milestone payment equal to [*], such amount to be distributed among all such then-current Research Plans in accordance with the recommendation of the Oversight Committee; provided, however, that payment for the Year Five
Goal(s) due pursuant to this Section 3.4(e) will be due and payable in accordance with Section 3.6 only after the achievement of such Year Five Goal(s) has been verified in accordance with Section 2.8(e). 
  

 [*] Certain information in this document has been omitted and filed separately with the Securities and
Exchange Commission. Confidential treatment has been requested with respect to the omitted portions. 
 11 

	 	(d)	Section 3.4 is hereby amended to include the following: 

 (f) Upon the achievement of the Year Six Goal(s), Shell shall pay to Codexis a one-time, non-refundable,
non-creditable Milestone payment equal to [*], such amount to be distributed among all such then-current Research Plans in accordance with the recommendation of the Oversight Committee; provided, however, that payment for the Year Six
Goal(s) due pursuant to this Section 3.4(f) will be due and payable in accordance with Section 3.6 only after the achievement of such Year Six Goal(s) has been verified in accordance with Section 2.8(e). 
 (g) For each Contract Year, if any, of (i) the Initial Term beyond the sixth (6th) Contract Year in the
event that the Parties agree to extend the Initial Term beyond the six (6) year anniversary of the Effective Date in accordance with Section 11.1, and (ii) each Renewal Term, Shell shall pay to Codexis a non-refundable, non-creditable
Milestone payment equal to [*] upon achievement of the Milestones for each of the then-current Research Plans established in accordance with Section 2.8(b), such amount to be distributed among all then-current Research Plans in accordance with
the recommendation of the Oversight Committee. For purposes of clarification, for purposes of this Section 3.4(g), “achievement of the applicable Milestone” means that Codexis delivers to Shell a Milestone Notice for such Milestone
within the relevant time period, even if the verification of such Milestone Notice occurs after the expiration of such time period; provided, however, that payment for any such Milestone due pursuant to this Section 3.4(g) will be
due and payable in accordance with Section 3.6 only after the achievement of such Milestone has been verified in accordance with Section 2.8(e). 
 (h) Shell shall pay to Codexis a one-time, non-refundable, non-creditable milestone payment equal to [*] within thirty (30) days after the receipt by Shell of an invoice from Codexis, such
invoice to be issued by Codexis to Shell after receipt by Codexis of notification, in writing, from Shell of the First Sale (as defined in the License Agreement) of the first Licensed Product (as defined in the License Agreement) pursuant to
Section 3.1(d) of the License Agreement. 
  

	 	(e)	Section 3.5 is hereby amended to include the following: 

 (d) Series F Stock Purchase Agreement. On or before the Amendment Date, Shell shall purchase Thirty Million United
States Dollars ($30,000,000) of Series F Preferred Stock of Codexis, pursuant to the terms and conditions of a stock purchase agreement substantially in the form attached hereto as Schedule G, appended to and made part of this Amended and
Restated Research Agreement, (the “Series F Stock Purchase Agreement”) at Eight United States Dollars and Fifty Cents ($8.50) per share. 
  

 [*] Certain information in this document has been omitted and filed separately with the Securities and
Exchange Commission. Confidential treatment has been requested with respect to the omitted portions. 
 12 

	4.	ARTICLE 4, INTELLECTUAL PROPERTY RIGHTS, shall be amended as follows: 

  

	 	(a)	Section 4.1(c) is hereby deleted and replaced in its entirety by the following: 

 (c) Program Technology. Shell hereby sells, assigns, delivers, conveys, transfers and sets over to Codexis the entire
right, title and interest in and to any invention disclosed in any Program Technology and any patent application and/or patent arising therefrom. Subject to the rights expressly granted to Shell under the terms and conditions of this Amended and
Restated Research Agreement and the Amended and Restated License Agreement, Codexis owns or otherwise controls and shall own or otherwise control all right, title and interest in, to and under any and all Program Technology. 
  

	 	(b)	Section 4.3 (Limitation) is hereby re-numbered and, hereafter, shall be referred to as Section 4.4. 

  

	 	(c)	ARTICLE 4, INTELLECTUAL PROPERTY RIGHTS, is hereby amended to include the following 

  

	 	4.3	[*]. 

 (a) Assignment. Subject to the terms of this Amended and Restated Research Agreement and of the Amended and Restated License Agreement, Codexis hereby sells, assigns, delivers, conveys, transfers and sets over to Shell the entire
right, title and interest in and to any invention disclosed in any [*], including, but not limited to, the patent family designated by Codexis as Codexis internal reference number [*], and any patent application and/or patent arising therefrom (the
“[*]”). 
 (b) Costs and Expenses. After the date of the assignment set forth in
Section 4.3(a), Shell shall control and shall bear all costs of (i) filing, prosecuting, responding to opposition and maintaining patent applications and patents in the [*], including without limitation the [*], and (ii) filing,
prosecuting, and responding to oppositions, nullity actions, re-examinations, revocation actions and similar proceedings against the grant of letters patent owned by Third Parties that may limit the ability to exploit the [*]. The Parties
acknowledge and agree that Codexis, as of the date of the assignment set forth in Section 4.3(a), has incurred costs and expenses relating to the prosecution of the [*] in an amount approximately equal to Eighty Three Thousand Six Hundred
Eighty Five United States Dollars ($83,645) and that, in partial consideration for the assignment by Codexis set forth in Section 4.3(a), Shell will reimburse Codexis Forty One Thousand Eight Hundred Forty Two United States Dollars ($41,842),
such reimbursement to be made within thirty (30) days after receipt by Shell of an invoice from Codexis, such invoice to include copies of the invoices received by Codexis constituting the costs and expenses relating to the prosecution of the
[*].
  

	5.	ARTICLE 10, INDEMNIFICATION, shall be amended as follows: 

  

	 	(a)	Section 10.4 (Notification of Claim; Conditions to Indemnification Obligations) is hereby re-numbered and, hereafter, shall be referred to as
Section 10.5. 

  

 [*] Certain information in this document has been omitted and filed separately with the Securities and
Exchange Commission. Confidential treatment has been requested with respect to the omitted portions. 
 13 

	 	(b)	ARTICLE 10, INDEMNIFICATION, is hereby amended to include the following: 

 10.4 Fuel Innovation Indemnification. Shell shall fully indemnify, defend and hold the Codexis Indemnitees harmless
from and against any and all Losses arising out of any Third Party claims or suits arising from use by Shell or any Affiliate of Shell, or any Third Party acting on behalf or for the benefit of Shell or any Affiliate of Shell, of Fuel Innovation;
provided that nothing in this Section 10.4 shall limit Codexis’ indemnification obligations under Section 10.2(a) with respect to any Losses arising out of any Third Party claims or suits arising from materials, technology,
technical information, know-how, expertise and trade secrets relating to the biological manufacture of any compound that is, or the use of which is, Fuel Innovation. 
  

	6.	ARTICLE 11, TERM AND TERMINATION, shall be amended as follows: 

  

	 	(a)	Section 11.2 is hereby deleted and replaced in its entirety by the following: 

  

	 	11.2	Termination for Convenience. 

 (a) At any time after the fourth (4th) anniversary of the Effective Date, Shell, in its sole discretion, may terminate this Amended and Restated Research Agreement, such termination to be
effective after nine (9) months written notice to Codexis. Notwithstanding the previous sentence, in the event that, pursuant to Section 2.6(b)(iv), the number of FTEs was increased to greater than [*], Shell, at any time after the fourth
(4th) anniversary of the Effective Date, in its sole discretion, may terminate this Amended and Restated Research Agreement, such termination to be effective after twelve (12) months written notice to Codexis. 
 (b) If at any time after the fourth (4th) anniversary of the Effective Date, Shell determines, in accordance
with Section 2.6(c), to decrease the number of FTEs assigned by Codexis to perform Codexis’ obligations under the Program to less than [*], Codexis shall have the right, but not the obligation, to terminate this Amended and Restated
Research Agreement upon ninety (90) days written notice to Shell; provided, however that in the event that (i) each such FTE reduction by Shell occurs after successful achievement of the applicable Milestone for each Research
Plan and (ii) Shell (or a Shell Affiliate or sublicensee) is actively developing the Program Technology for commercial application, then Codexis shall have no right to terminate this Amended and Restated Research Agreement pursuant to this
Section 11.2(b). 
  

	 	(b)	Section 11.4(b) is hereby deleted and replaced in its entirety by the following: 

 (b) The following Articles and Sections of this Amended and Restated Agreement shall survive its termination or
expiration: Articles 4, 5, 10 and 12, and Sections 2.4(a)(iii), 2.9, 6.1, 8.3, 9.4, 9.5 and 11.4. 
  

	7.	ARTICLE 12 – GENERAL PROVISIONS shall be amended to include the following: 

 12.15 Forecasts; Updates. After the Amendment Date, at the first meeting of the Research Committee in each calendar
year, and at the first meeting of the Oversight Committee in each calendar year, Codexis shall provide a forecast of the anticipated

  

 [*] Certain information in this document has been omitted and filed separately with the Securities and
Exchange Commission. Confidential treatment has been requested with respect to the omitted portions. 
 14 

 
expenditures by Codexis, if any, relating to acquisition of capital equipment or to improvement of facilities, in either case, for support of the Program during such calendar year. In addition,
after the Amendment Date, at each meeting of the Research Committee, after the first such meeting, in each calendar year, Codexis shall provide an update regarding deviations, if any, from the forecast of the anticipated expenditures for such
calendar year relating to acquisition of capital equipment or to improvement of facilities, in either case, for support of the Program, together with an explanation for such deviations. 
 12.16 Reports. After the Amendment Date, at each meeting of the Research Committee and the Oversight Committee,
Codexis shall present a summary report of the number of FTEs assigned by Codexis to perform Codexis’ obligations under the Program, including the allocation of such FTEs between Codexis FTEs and CLH FTEs. After the Amendment Date, within
forty-five (45) days after the end of each calendar quarter, Codexis shall provide Shell a summary report of actual expenditures by Codexis, if any, relating to acquisition of capital equipment or to improvement of facilities, in either case,
for support of the Program during the just ended calendar quarter. 
 12.17 Books and Records; Audit
Rights. Codexis shall keep complete, true and accurate books of account and records for the purpose of verifying the reports presented by Codexis pursuant to Section 12.16. Said books and records will be kept for a period of at least three
(3) years following the end of the calendar year to which they pertain and shall be available, after not less than fifteen (15) business days prior written notice, for inspection, such inspection to occur not more frequently than once in
any calendar year during the Term, by Shell using Shell personnel or by an independent public accountant, certified in the U.S. and affiliated with an internationally recognized accounting firm selected by Shell and reasonably acceptable to Codexis,
solely in order to, and only to the extent necessary to, verify the accuracy of the reports presented by Codexis pursuant to Section 12.16 that (a) Codexis assigned the number of FTEs set forth in Section 2.6(b), subject to
Section 2.6(c), to perform Codexis’ obligations under the Program, and (b) the expenditure by Codexis, if any, for the acquisition of any capital equipment and any facilities improvements indentified in such reports as being used in
support of the Program. All materials made available for inspection by Codexis shall be Confidential Information in accordance with Article 6 and, in the event that Shell uses an independent public accountant to conduct such inspection, such public
accountant will be obliged by Shell to treat all such materials as Confidential Information in accordance with Article 6. Shell share bear the full cost of the performance of any audit performed pursuant to this Section 12.17. 
 12.17 HSE. Codexis will take actions as are necessary to ensure that: 
 (a) it has a health, safety and environment policy that is in accordance with applicable law for the operations of
Codexis’ facilities that are involved in the Program (the “HSE Policy”); 
  

 [*] Certain information in this document has been omitted and filed separately with the Securities and
Exchange Commission. Confidential treatment has been requested with respect to the omitted portions. 
 15 

 (b) it routinely advises Shell of any accidents arising directly out
of or in connection with activities conducted under the Program which cause casualties or injuries or any negative effect on the environment which would be classified as a recordable OSHA event; and 
 (c) Shell, using Shell personnel, will have the right to audit Codexis’ facilities for compliance with the HSE
Policy, provided that the findings of such audit will be provided to both Codexis and Shell and will be deemed to be Confidential Information of Codexis, that at least ten (10) business days prior written notice of any such audit will be given
to Codexis, and that such audits will not occur more frequently that annually. 
  

	8.	OTHER PROVISIONS. 

 All
provisions of the Research Agreement not expressly modified by this Amendment shall remain in full force and effect. 
 [Signature Page Follows] 
  

 [*] Certain information in this document has been omitted and filed separately with the Securities and
Exchange Commission. Confidential treatment has been requested with respect to the omitted portions. 
 16 

 IN WITNESS WHEREOF, the
Parties have caused this Amendment to be executed by their respective duly authorized officers as of the Amendment Date, each copy of which will for all purposes be deemed to be an original. 
  

									
	 EQUILON ENTERPRISES LLC
 DBA SHELL OIL PRODUCTS US
	 		 	CODEXIS, INC.
					
	By:	 	 /s/    Richard M. Oblath
	 		 	By:	 	 /s/    Alan Shaw

	Name:	 	Richard M. Oblath	 		 	Name:	 	Alan Shaw
	Title:	 	Attorney in Fact	 		 	Title:	 	President & CEO

 [Signature Page to the Amendment to the 
 Amended and Restated Collaborative Research Agreement] 
  

 [*] Certain information in this document has been omitted and filed separately with the Securities and
Exchange Commission. Confidential treatment has been requested with respect to the omitted portions. 

 Schedule E 
 FTE Index 
 “FTE Index” means
[*]. In the event that such index becomes unavailable, the Parties will agree on an index to be used in substitution of such unavailable index within sixty (60) days after the date that such index is no longer available. 
  

 [*] Certain information in this document has been omitted and filed separately with the Securities and
Exchange Commission. Confidential treatment has been requested with respect to the omitted portions. 

 Schedule F 
 CLH FTE Index 
 “CLH FTE
Index” means [*]. In the event that such index becomes unavailable, the Parties will agree on an index to be used in substitution of such unavailable index within sixty (60) days after the date that such index is no longer available.

  

 [*] Certain information in this document has been omitted and filed separately with the Securities and
Exchange Commission. Confidential treatment has been requested with respect to the omitted portions. 

 Schedule G 
 Form of Series F Stock Purchase Agreement 
  

 [*] Certain information in this document has been omitted and filed separately with the Securities and
Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.Amended and Restated License Agreement

 EXHIBIT 10.4A 
 [*] Certain information in this document has been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted
portions. 
 AMENDED AND RESTATED LICENSE AGREEMENT 
 THIS AMENDED AND RESTATED LICENSE
AGREEMENT, together with exhibits attached hereto, (the “Amended and Restated License Agreement”) is entered into as of the Execution Date and effective as of November 1, 2006 (the
“Effective Date”), by and between Equilon Enterprises LLC dba Shell Oil Products US, a Delaware limited liability company, having a place of business at 910 Louisiana Street, Houston, Texas 77002 (“Shell”),
and Codexis, Inc., a Delaware corporation, having a place of business at 200 Penobscot Drive, Redwood City, California 94063 (“Codexis”). Shell and Codexis may each be referred to herein individually as a
“Party” or, collectively, as the “Parties.” 
 RECITALS 
 WHEREAS, Shell and Codexis entered into a certain License Agreement effective as of November 1,
2006, pursuant to which Codexis granted to Shell certain license rights under Codexis Patent Rights, Codexis Licensed Technology, Program Patent Rights and Program Technology (in each case, as defined below) so that Shell can manufacture, use, sell,
offer for sale and import Licensed Products, including without limitation through the grant of sublicense rights for such purposes under such Codexis Patent Rights, Codexis Licensed Technology, Program Patent Rights and Program Technology.

 WHEREAS, the Parties desire to amend and restate such License Agreement, all on the
terms and conditions set forth below. 
 NOW, THEREFORE, in consideration of
the promises and undertakings set forth herein, the Parties agree as follows: 
 ARTICLE 1 
 DEFINITIONS 
 Capitalized terms not otherwise defined herein will have the meaning set forth below. 
 1.1 “Acquired
Technology” has the meaning set forth in the Amended and Restated Research Agreement. 
 1.2
“Affiliate” means, 
 (a) with respect to Codexis, any business entity controlling, controlled by, or under
common control with Codexis. For the purpose of this Section 1.2(a) only, “control” means (i) the possession, directly or indirectly, of the power to direct the management or policies of a business entity, whether through the
ownership of voting securities, by contract or otherwise, or (ii) the ownership, directly or indirectly, of at least fifty percent (50%) of the voting securities or other ownership interest of a business entity; provided that, if
local law requires a minimum

 
percentage of local ownership, control will be established by direct or indirect beneficial ownership of one hundred percent (100%) of the maximum ownership percentage that may, under such
local law, be owned by foreign interests; and 
 (b) with respect to Shell, Royal Dutch Shell plc and any company (other
than Shell) which is from time to time directly or indirectly affiliated with Royal Dutch Shell plc. For the purpose of this Section 1.2(b) only, a particular company is (i) directly affiliated with another company or companies if that
latter company beneficially owns or those latter companies together beneficially own fifty per cent or more of the voting rights attached to the ownership interest of the particular company; and (ii) is indirectly affiliated with company or
companies if a series of companies can be specified, beginning with that latter company or companies and ending with the first mentioned company, so related that each company of the series (except the latter company or companies) is directly
affiliated with one or more of the companies earlier in the series. 
 1.3 “Amended and Restated Research
Agreement” means the Amended and Restated Collaborative Research Agreement entered into by Shell and Codexis on the Execution Date and effective as of the Effective Date. 
 1.4 “Biocatalyst” means an enzyme or a Microbe that can enzymatically catalyze a particular chemical reaction, and which
enzyme or Microbe arose out of the Program. 
 1.5 “Biomass” means organic, non-fossil, plant-derived matter
available on a renewable basis, including, for example, crops and/or trees grown or harvested for use for fuel and/or fuel additive production, agricultural food and feed crops, aquatic plants and, in each case, organic wastes derived from the
foregoing, including municipal wastes (e.g., newspapers). 
 1.6 “Codexis Licensed Technology” means any
Technology and Materials Controlled by Codexis as of the earlier of the expiration or termination of the Program that is necessary or useful for the practice of the Program Technology; provided that the Codexis Licensed Technology shall
expressly exclude the Shuffling Technology. 
 1.7 “Codexis Patent Rights” means all Patents Controlled by
Codexis covering Codexis Licensed Technology. 
 1.8 “Confidential Information” means any and all non-public
and proprietary Information that is specifically designated as such and that is disclosed by either Party to the other in written or other similar form in connection with this Amended and Restated License Agreement and that, if orally or visually
disclosed, shall be summarized in writing in detail and specifically designated as proprietary and such summary delivered to the receiving Party within thirty (30) days after such disclosure. 
 1.9 “Contract Year” means a year beginning on the Effective Date, or an anniversary of the Effective Date during the Term,
and ending one (1) year after such respective date. 
 1.10 “Control” means, with respect to an item,
Information, Patent or an intellectual property right, possession of the ability, whether arising by ownership or license or otherwise, to grant a license or sublicense as provided for herein under such item, Information, Patent or right without
violating the terms of any written agreement with any Third Party. 
  

 [*] Certain information in this document has been omitted and filed separately with the Securities and
Exchange Commission. Confidential treatment has been requested with respect to the omitted portions. 
 2 

 1.11 “Execution Date” means November 1, 2007. 
 1.12 “First Sale” means the first transfer by Shell or a Shell Affiliate or a sublicensee of a Licensed Product to
(a) Shell or a Shell Affiliate (where Shell or such Shell Affiliate is the end-user of such Licensed Product) or (b) a Third Party, in exchange for cash, or cash equivalent to which value can be assigned after production of the [*]
(i) [*] of Licensed Product in the [*] Field of Use, (ii) [*] of Licensed Product in the [*] Field of Use, and (iii) [*] of Licensed Product in the [*] Field of Use. 
 1.13 “Fuel Field of Use” means the conversion of fermentable sugars derived from Biomass into liquid fuel and/or liquid
fuel additives. For purposes of this Section 1.13 only, (a) “liquid” means [*], and (b) “fuel additive” means [*]. 
 1.14 “Index” means [*]. In the event that such index becomes unavailable, the Parties will agree on an index to be used in substitution of such unavailable index within sixty
(60) days after the date that such index is no longer available. 
 1.15 “Information” means data,
results, evaluations, inventories, Microbes, show-how, know-how, computer chip and programs, processes, machines, biological chemicals, intermediates, trade secrets, techniques, methods, developments, materials, methods of analysis, compositions of
matter, copyrights or other information. 
 1.16 “Intermediate Field of Use” means the conversion of Biomass
into fermentable sugars, such sugars to be converted into (a) liquid fuel and/or liquid fuel additives and/or (b) Lubricants. For purposes of this Section 1.16 only, (i) “liquid” means [*], and (ii) “fuel
additive” means [*]. For purposes of clarification, the Intermediate Field of Use shall not include the Fuel Field of Use or the Lubricant Field of Use. 
 1.17 “Licensed Field of Use” means the Fuel Field of Use, the Intermediate Field of Use and the Lubricant Field of Use. 
 1.18 “Licensed Product” means any product, the manufacture, use, offer for sale, sale or importation of which, (a) is
covered by one or more claims within the Program Patent Rights or the Codexis Patent Rights which has not expired and has not been held invalid or unenforceable by a court of competent jurisdiction from which no appeal can be taken, or
(b) utilizes the Program Technology or the Codexis Licensed Technology. 
 1.19 “Lubricant” means [*].

 1.20 “Lubricant Field of Use” means the conversion of fermentable sugars derived from Biomass into a
Lubricant. 
  

 [*] Certain information in this document has been omitted and filed separately with the Securities and
Exchange Commission. Confidential treatment has been requested with respect to the omitted portions. 
 3 

 1.21 “Microbes” means whole (live or dead) prokaryotic organisms and/or
yeasts and/or fungi or extracts thereof. Microbes shall not include land plants, including nonseed plants (Bryophytes, Tracheophytes) such as liverworts, mosses, ferns, and seed plants, such as gymnosperms and angiosperms (monocot and dicots);
and/or non-land plants, including Prasinophytes, Chlorophyceae, Trebouxiouphyceae, Ulvophyceae, Chlorokybales, Streptophyta, Klebsormidiales, Zygnematales, Charales, Coleochaetales and Embryophytes. 
 1.22 “Monthly Index Average” means the sum of the monthly values for the Index in the relevant period divided by the number
of months in such period. 
 1.23 “Patents” means all patent applications and patents, whether domestic or
foreign, covering patentable inventions within the Codexis Licensed Technology or the Program Technology, as applicable, all continuations, continuations in part and divisions of such patent applications and of patent applications from which such
patents issued, all patents issuing from any of such patent applications, and all renewals, reissues, re-examinations and extensions of any of such patents. 
 1.24 “Program” has the meaning set forth in the Amended and Restated Research Agreement. 
 1.25 “Program Licensed Technology” means any Technology and Materials developed under the Amended and Restated Research Agreement related to the Program; provided, however,
that Program Licensed Technology expressly excludes Shuffling Technology. 
 1.26 “Program Patent Rights” means
the Patents covering Program Technology set forth on Exhibit 1.26 attached hereto, as updated by the Parties from time to time in accordance with Section 4.1. 
 1.27 “Royalty Adjustment Date” means the date of First Sale of the first Licensed Product in the Licensed Field of Use or each anniversary of such date, as the context requires.

 1.28 “Shuffling” means the characterization, development and optimization of genes and proteins for
commercial uses through the recombination and/or rearrangement and/or mutation of genetic material for the creation of genetic diversity. 
 1.29 “Shuffling Technology” means any and all techniques, methodologies, processes, materials and/or instrumentation Controlled by Codexis, including without limitation any and all patent
rights, know-how, confidential information and materials relating thereto, that, in each case, relates to Shuffling, and generally applicable screening techniques, methodologies, or processes of using the resulting genetic material to identify
potential usefulness. 
 1.30 “Technology and Materials” means and includes all materials, technology,
technical information, intellectual property, know-how, expertise and trade secrets related to the Licensed Field of Use. 
 1.31 “Third Party” means any party other than Codexis, Shell or Affiliates of either Party. 
  

 [*] Certain information in this document has been omitted and filed separately with the Securities and
Exchange Commission. Confidential treatment has been requested with respect to the omitted portions. 
 4 

 ARTICLE 2 
 LICENSE GRANT 
 2.1 Grants to Shell. Subject to
the terms and conditions of this Amended and Restated License Agreement: 
 (a) Codexis hereby grants to Shell, under all
of Codexis’ rights and interest in Program Patent Rights and Program Licensed Technology, an exclusive, worldwide, royalty-free license to manufacture and have manufactured (such have manufactured right subject to Section 2.4) Biocatalysts
developed under the Program solely for the purpose of using such Biocatalysts in the manufacture of a Licensed Product in the Licensed Field of Use, such use in accordance with the license granted by Codexis to Shell under Section 2.1(b) and
such license to include the right to grant sublicenses provided that any such grant of a sublicense is made together with a grant of a sublicense under the rights granted to Shell pursuant to Section 2.1(b); and 
 (b) Codexis hereby grants to Shell, under all of Codexis’ rights and interest in Program Patent Rights and Program Licensed
Technology, an exclusive, worldwide, royalty-bearing license, including the right to grant sublicenses, to manufacture, have manufactured, use, sell, offer for sale and import any Licensed Product in the Licensed Field of Use; and 
 (c) Codexis hereby grants to Shell, under all of Codexis’ rights and interest in Codexis Patent Rights and Codexis Licensed
Technology, a non-exclusive, worldwide, royalty-free (subject to Acquired Technology Third Party Payments in Section 3.2) license to: 
 (i) manufacture and have manufactured (such have manufactured right subject to Section 2.4) Biocatalysts developed under the Program solely for the purpose of using such Biocatalysts in the
manufacture of a Licensed Product in the Licensed Field of Use, such use in accordance with the license granted by Codexis to Shell under Section 2.1(b) and such license to include the right to grant sublicenses provided that any such
grant of a sublicense is made together with a grant of a sublicense under the rights granted to Shell pursuant to Section 2.1(b); and 
 (ii) manufacture, have manufactured, use, sell, offer for sale and import any Licensed Product in the Licensed Field of Use, such license to include the right to grant sublicenses provided
that any such grant of a sublicense is made together with a grant of a sublicense under the rights granted to Shell pursuant to Section 2.1(b). 
 For purposes of clarification, Shell and Codexis acknowledge and agree that use of a Biocatalyst to manufacture a Licensed Product may generate by-products and other materials other than Licensed Products, and that the disposition of such
by-products and other materials, whether by sale, use or disposal, is the exclusive responsibility and solely within the control and discretion of Shell, without any obligation to Codexis. 
 2.2 Reservation. Notwithstanding anything to the contrary, Codexis retains the right to use Program Patent Rights and Program
Technology for internal research purposes in the Licensed Field of Use in accordance with the terms and conditions of the Amended and Restated Research Agreement. 
  

 [*] Certain information in this document has been omitted and filed separately with the Securities and
Exchange Commission. Confidential treatment has been requested with respect to the omitted portions. 
 5 

 2.3 Limitation. 
 (a) Except as expressly provided in this Amended and Restated License Agreement and the Amended and Restated Research Agreement, no
right, title, or interest is granted by Codexis to Shell. 
 (b) Notwithstanding anything to the contrary, the licenses
granted by Codexis to Shell under Section 2.1 do not include, and Shell shall not acquire by virtue of such license grants, any right in, to or under the Shuffling Technology. 
 2.4 Right of First Negotiation – Biocatalyst Manufacturing. In the event Shell, either itself or through an Affiliate of Shell,
seeks to out-source the manufacture of any particular Biocatalyst developed under the Program, Shell shall provide written notice to Codexis and Codexis shall have a right of first negotiation for the manufacture of such particular Biocatalyst,
under the terms and conditions of a separate Biocatalyst supply agreement which will be negotiated. The date of Codexis’ receipt of such written notice will be the start of a one hundred twenty (120) day period during which, upon
Codexis’ election, the terms and conditions of such supply agreement will be negotiated. If mutually acceptable terms and conditions have not been agreed prior to the end of such one hundred twenty (120) day period, Shell, either itself or
through an Affiliate of Shell, will be free to negotiate with Third Parties for the manufacture of such particular Biocatalyst, but may not enter into any agreement for such manufacture under terms and conditions that are less favorable to Shell (or
its Affiliate) than the terms and conditions last offered to Codexis. For purposes of clarification, in the event that Shell grants a sublicense right under the Program Patent Rights or the Codexis Patent Rights to a Third Party pursuant to
Section 2.1, Shell shall use best efforts to include similar rights of negotiation in favor of Codexis in any such sublicense. 
 ARTICLE 3 
 PAYMENTS, REPORTS AND RECORDS 
 3.1 Consideration. 
 (a) In consideration of the rights and license granted herein, Shell shall pay to Codexis [*] cents per gallon of Licensed Product, where such Licensed Product is sold or transferred in exchange for cash or cash equivalent or other
consideration to which value can be assigned for use in the Intermediate Field of Use, by either Shell or a Shell Affiliate or a sublicensee to (1) Shell or a Shell Affiliate (where Shell or such Shell Affiliate is the end-user of such Licensed
Product) or (2) a Third Party, in each case after the First Sale (in all cases, the “Intermediate Royalty”); provided that the Intermediate Royalty shall be adjusted on each Royalty Adjustment Date according to changes
in the Index as set forth below: 
 (i) The initial adjustment shall be made on the date of First Sale of the first
Licensed Product in the Licensed Field of Use by multiplying the initial Intermediate

  

 [*] Certain information in this document has been omitted and filed separately with the Securities and
Exchange Commission. Confidential treatment has been requested with respect to the omitted portions. 
 6 

 
Royalty by (A/B), where A = the Monthly Index Average during the most recent twelve (12) month period for which final, corrected data are available preceding the date of First Sale of such
first Licensed Product in the Licensed Field of Use, and B = the Monthly Index Average between November 1, 2007 and the most recent date for which final, corrected data are available prior to the date of First Sale of such Licensed Product.

 (ii) After the year following the date of First Sale of the first Licensed Product in the Licensed Field of Use, the
Intermediate Royalty shall be adjusted annually on each Royalty Adjustment Date by multiplying the then-current Intermediate Royalty by (X/Y), where X = the Monthly Index Average during the most recent twelve (12) month period preceding such
Royalty Adjustment Date for which final, corrected data are available, and Y = the Monthly Index Average for the twelve (12) month period beginning sixteen (16) months prior to such Royalty Adjustment Date and ending twenty-seven
(27) months prior to such Royalty Adjustment Date. 
 The adjustments to the Intermediate Royalty shall be rounded to the nearest [*]. The
Intermediate Royalty obtained after each adjustment shall be the Intermediate Royalty due from the applicable Royalty Adjustment Date until the subsequent Royalty Adjustment Date. 
 By way of example, if the Monthly Index Average during the twelve (12) month period preceding the date of First Sale of the first Licensed Product in the Licensed Field of Use for which final,
corrected data are available equals two hundred twenty (220) and the Monthly Index Average between November 1, 2007 and the most recent date for which final, corrected data are available prior to the date of First Sale of such Licensed
Product equals two hundred (200), then the Intermediate Royalty shall be adjusted by an amount equal to 220/200, or 1.1, such that the Intermediate Royalty for the subsequent twelve (12) month period shall equal [*] cents per gallon of Licensed
Product in the Intermediate Field of Use times 1.1, or [*] cents per gallon of Licensed Product in the Intermediate Field of Use. 
 By way of
further example, if the Monthly Index Average during the most recent twelve (12) month period preceding the subsequent Royalty Adjustment Date for which final, corrected data are available equals two hundred nine (209), and the Monthly Index
Average for the twelve (12) month period beginning sixteen (16) months prior to such Royalty Adjustment Date and ending twenty-seven (27) months prior to such Royalty Adjustment Date equals two hundred twenty (220), then on such
Royalty Adjustment Date the Intermediate Royalty shall be adjusted by an amount equal to 209/220, or 0.95, such that, if the Intermediate Royalty on such Royalty Adjustment Date is equal to [*] cents per gallon, the Intermediate Royalty for the
subsequent twelve (12) month period shall equal [*] cents per gallon of Licensed Product in the Intermediate Field of Use times 0.95, or [*] cents per gallon of Licensed Product in the Intermediate Field of Use. 
 (b) Subject to the last sentence of this paragraph, in consideration of the rights and license granted herein, Shell shall pay to
Codexis [*] cents per gallon of Licensed Product, where such Licensed Product is sold or transferred in exchange for cash or cash equivalent or other consideration to which value can be assigned for use in the Fuel Field of Use, by either Shell or a
Shell Affiliate or a sublicensee to (1) Shell or a Shell Affiliate (where Shell or such

  

 [*] Certain information in this document has been omitted and filed separately with the Securities and
Exchange Commission. Confidential treatment has been requested with respect to the omitted portions. 
 7 

 
Shell Affiliate is the end-user of such Licensed Product) or (2) a Third Party, in each case after the First Sale (in all cases, the “Fuel Royalty”). Notwithstanding the
foregoing, Shell and Codexis acknowledge and agree that as of Execution Date, there is insufficient data available to definitively determine the appropriate royalty rate for the manufacture, use, offer for sale, sale or importation of Licensed
Product(s) in the Fuel Field of Use. The Parties thus agree to engage in negotiations regarding such royalty on or before [*]; provided, however, that, if the Parties are unable to agree upon such royalty rate after such negotiations,
the royalty rate shall equal [*] cents per gallon of such Licensed Product; provided, further, that the Fuel Royalty shall be adjusted on each Royalty Adjustment Date according to changes in the Index as set forth below. 
 (i) The initial adjustment shall be made on the date of First Sale of the first Licensed Product in the Licensed Field of Use by
multiplying the initial Fuel Royalty by (A/B), where A = the Monthly Index Average during the most recent twelve (12) month period for which final, corrected data are available preceding the date of First Sale of such first Licensed Product in
the Licensed Field of Use, and B = the Monthly Index Average between November 1, 2007 and the most recent date for which final data are available prior to the date of First Sale of such Licensed Product. 
 (ii) After the year following the date of First Sale of the first Licensed Product in the Licensed Field of Use, the Fuel Royalty
shall be adjusted annually on each Royalty Adjustment Date by multiplying the then-current Fuel Royalty by (X/Y), where X = the Monthly Index Average during the most recent twelve (12) month period preceding such Royalty Adjustment
Date for which final, corrected data are available, and Y = the Monthly Index Average for the twelve (12) month period beginning sixteen (16) months prior to such Royalty Adjustment Date and ending twenty-seven (27) months prior to
such Royalty Adjustment Date. 
 The adjustments to the Fuel Royalty shall be rounded to the nearest [*]. The Fuel Royalty obtained after each
adjustment shall be the Fuel Royalty due from the applicable Royalty Adjustment Date until the subsequent Royalty Adjustment Date. 
 By way of
example, if the Monthly Index Average during the twelve (12) month period preceding the date of First Sale of the first Licensed Product in the Licensed Field of Use for which final, corrected data are available equals two hundred twenty
(220) and the Monthly Index Average between November 1, 2007 and the most recent date for which final, corrected data are available prior to the date of First Sale of such Licensed Product equals two hundred (200), then the Fuel Royalty
shall be adjusted by an amount equal to 220/200, or 1.1, such that the Fuel Royalty for the subsequent twelve (12) month period shall equal [*] cents per gallon of Licensed Product in the Fuel Field of Use times 1.1, or [*] cents per gallon of
Licensed Product in the Fuel Field of Use. 
 By way of further example, if the Monthly Index Average during the most recent twelve
(12) month period preceding the subsequent Royalty Adjustment Date for which final, corrected data are available equals two hundred nine (209), and the Monthly Index Average for the twelve (12) month period beginning sixteen
(16) months prior to such Royalty Adjustment Date and ending twenty-seven (27) months prior to such Royalty Adjustment Date equals two hundred twenty (220), then on such Royalty Adjustment Date the Fuel Royalty shall be adjusted by an
amount

  

 [*] Certain information in this document has been omitted and filed separately with the Securities and
Exchange Commission. Confidential treatment has been requested with respect to the omitted portions. 
 8 

 
equal to 209/220, or 0.95, such that, if the Fuel Royalty on such Royalty Adjustment Date is equal to [*] cents per gallon, the Fuel Royalty for the subsequent twelve (12) month period shall
equal [*] cents per gallon of Licensed Product in the Fuel Field of Use times 0.95, or [*] cents per gallon of Licensed Product in the Fuel Field of Use. 
 (c) Shell and Codexis acknowledge and agree that Codexis will initiate work to develop Program Patent Rights and Program Licensed Technology with respect to Licensed Product(s) in the Lubricant
Field of Use only after an appropriate royalty rate for such Licensed Products has been agreed upon by the Parties and, as of Execution Date, there is insufficient data available to definitively determine the appropriate royalty rate for the
manufacture, use, offer for sale, sale or importation of Licensed Product(s) in the Lubricant Field of Use. The Parties thus agree to engage in negotiations regarding such royalty prior to initiating development of a Licensed Product within the
Lubricant Field of Use. Notwithstanding, Codexis agrees to grant a right for the Lubricant Field of Use in similar scope to Section 2.1 at an agreed upon price per gallon or percentage of gross revenues. 
 (d) Shell shall notify Codexis promptly, in writing, of the date of the First Sale for each Licensed Product and, in the case where
such First Sale is made by a sublicensee of Shell or a Shell Affiliate, the identity of such sublicensee. 
 (e)
Beginning with the date of the First Sale of any Licensed Product, Shell, within ninety (90) days after the end of each calendar quarter after such date, shall provide to Codexis a statement of royalties due to Codexis pursuant to Sections
3.1(a), 3.1(b) and/or 3.1(c) and, together with such statement, the payments due to Codexis pursuant to such Sections 3.1(a), 3.1(b) and/or 3.1(c). All such reports will be held as Confidential Information in accordance with Article 5. 

3.2 Third Party Payments. If Codexis is required to pay a royalty or any other payment to any Third Party, other than Maxygen,
Inc. or its successor, for the use of the Codexis Patent Rights and the Codexis Licensed Technology as a result of the use of any Acquired Technology, Shell shall reimburse Codexis for such royalty or other payment provided Shell has agreed in
writing to obtain such Acquired Technology. For purposes of clarification, if Codexis uses such Acquired Technology for purposes outside the Licensed Field of Use, the Parties shall first agree on the proportion of such payments to be reimbursed by
Shell for the use of such Acquired Technology in the Licensed Field of Use in accordance with Section 7.2 of the Amended and Restated Research Agreement. 
 3.3 Mode of Payment. All payments made pursuant to this Amended and Restated License Agreement shall be made by direct wire transfer of United States Dollars in immediately available funds in the
requisite amount to such bank account as Codexis may from time to time designate by written notice to Shell. To the extent permitted under applicable law, the Parties shall use diligent efforts to utilize any exemption available to minimize any
taxes, fees or other charges imposed on payments to Codexis under the terms of this Amended and Restated License Agreement. 
  

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Exchange Commission. Confidential treatment has been requested with respect to the omitted portions. 
 9 

 3.4 Late Payment Interest. Any payment due and payable to Codexis under the terms and
conditions of this Amended and Restated License Agreement made by Shell after the date such payment is due to be paid shall bear interest as of the day after the date such payment was due to be paid and shall continue to accrue such interest until
payment of the amount due is made. The interest rate to be applied to any payment not paid when due shall be equal to the lesser of either (a) two percent (2%) above the prime rate as reported by Citibank, New York, New York on the date
such payment was due to be paid, or (b) the maximum rate permitted by applicable law on such date, and shall apply until the date that payment is issued by Shell to Codexis. 
 3.5 Records. 
 (a) Shell will keep, and will require its Affiliates and sublicensees to keep, complete, true and accurate books of account and records for the purpose of showing the derivation of all Royalties payable to Codexis under this Amended
and Restated License Agreement. Said books and records will be kept for at least three (3) years following the end of the calendar year to which they pertain and shall be available, after not less than fifteen (15) business days prior
written notice, for inspection by an independent public accountant, certified in the U.S. and affiliated with an internationally recognized accounting firm selected by Codexis and reasonably acceptable to Shell, for the purpose of verifying
statements provided to Codexis pursuant to Section 3.1(e) regarding royalties due to Codexis. Such independent public accountant will be obliged by Codexis to treat all materials made available for inspection by Shell as Confidential
Information in accordance with Article 5. 
 (b) In the event that the independent public accountant described in
Section 3.5(a) alleges that an underpayment or an overpayment has been made, and the Parties agree on the amount of such underpayment or such overpayment, Shell, in the event of an underpayment, will pay to Codexis the full amount of such
underpayment within ten (10) days after such agreement between the Parties or, in the event of an overpayment, may credit the amount of such overpayment against any future payment due to Codexis under this Amended and Restated License
Agreement. Codexis shall bear the full cost of the performance of any audit performed under Section 3.5(a), unless such audit discloses a variance to the detriment of Codexis of more than ten percent (10%) (determined on an aggregate basis
for all payments covered by the audit), and the Parties agree that such variance is correct, in which case, Shell shall bear the full cost of the performance of such audit. 
 (c) Notwithstanding the provisions of Section 10.7, in the event that the independent public accountant described in
Section 3.5(a) alleges that an underpayment or an overpayment has been made, and the Parties do not agree on the amount of such underpayment or such overpayment, the Parties, within thirty (30) days, shall mutually select a U.S.-based
internationally recognized public accounting firm which shall review the amount in dispute (including supporting documentation) and resolve such dispute within thirty (30) days after selection of such firm. Such U.S.-based internationally
recognized public accounting firm will be obliged to Codexis to treat all materials made available for inspection as Confidential Information of Codexis or Shell in accordance with Article 5. In the event that such U.S.-based internationally
recognized public accounting firm determines that an underpayment or an overpayment has been

  

 [*] Certain information in this document has been omitted and filed separately with the Securities and
Exchange Commission. Confidential treatment has been requested with respect to the omitted portions. 
 10 

 
made, Shell, in the event of an underpayment, will pay to Codexis the full amount of such underpayment within ten (10) days after such agreement between the Parties or, in the event of an
overpayment, may credit the amount of such overpayment against any future payment due to Codexis under this Agreement. Each Party shall pay fifty percent (50%) of the expenses for such public accounting firm; provided, however,
that if the audit performed by such accounting firm discloses a variance to the detriment of Codexis of more than ten percent (10%) (determined on an aggregate basis for all payments covered by the audit), Shell shall reimburse Codexis for
Codexis’ portion of the expenses for such audit with fifteen (15) days after Codexis’ written request for such reimbursement and, in addition, the cost of the initial audit by Codexis pursuant to Section 3.5(a). The
recommendation of such U.S.-based internationally recognized public accounting firm pursuant to this Section 3.5(c) shall be final and binding upon the Parties. 
 3.6 Payment Term. Unless otherwise terminated as provided herein, Shell’s payment obligations to Codexis pursuant to Section 3.1 of this Amended and Restated License Agreement shall
continue: 
 (a) In the Intermediate Field of Use until the later of (i) twenty (20) years after the First Sale
of a Licensed Product in the Intermediate Field of Use or (ii) the expiration of the last to expire patent included in the Codexis Patent Rights and Program Patent Rights; 
 (b) In the Fuel Field of Use until the later of (i) twenty (20) years after the First Sale of a Licensed Product in the
Fuel Field of Use or (ii) the expiration of the last to expire patent included in the Codexis Patent Rights and Program Patent Rights; and 
 (c) In the Lubricant Field of Use until the later of (i) twenty (20) years after the First Sale of a Licensed Product in the Lubricant Field of Use or (ii) the expiration of the last
to expire patent included in the Codexis Patent Rights and Program Patent Rights; 
 provided, however, in the event of the
expiration of this Amended and Restated License Agreement as a result of expiration of the last to expire patent included in the Codexis Patent Rights and Program Patent Rights, or in the event of termination by Shell pursuant to Section 9.2,
all licenses granted by Codexis to Shell pursuant to Section 2.1 shall remain in place in perpetuity. 
 ARTICLE 4 

 PATENT MATTERS 
 4.1 Provisions Concerning Filing, Prosecution and Maintenance of Patent Rights. The filing, prosecution and maintenance of Program Patent Rights during the term of this Amended and Restated License
Agreement will be governed by Article 5 of the Amended and Restated Research Agreement. From time to time during the term of this Amended and Restated License Agreement, but at least once per each Contract Year, the Parties will update the list of
patent applications and patents within the Program Patent Rights set forth on Exhibit 1.26 based on the filing, issuance or lapse of the relevant patent applications and patents. 
  

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Exchange Commission. Confidential treatment has been requested with respect to the omitted portions. 
 11 

 4.2 Notice. Each Party shall promptly provide written notice to the other Party of
any (a) alleged infringement by a Third Party of any Patents licensed to Shell hereunder, or (b) claim of infringement by a Third Party that the activities of a Party infringe patent rights of such Third Party. Together with such notice,
the notifying Party shall provide the other Party with all available evidence of such alleged infringement which is not under confidentiality obligations with respect to a Third Party. 
 4.3 Enforcement by Codexis. During the term of this Amended and Restated License Agreement, Codexis shall have the right, but not the
obligation, to institute legal action against a Third Party for infringement of any Patents licensed to Shell hereunder. Codexis shall bear the entire cost of such legal action, and shall be entitled to retain the entire amount of any recovery.

 4.4 Enforcement by Shell. In the event that Codexis elects not to initiate legal action for infringement of any
Patents exclusively licensed to Shell hereunder, Shell, after not less than twenty (20) business days prior written notice to Codexis, may initiate legal action for patent infringement and, to the extent necessary to initiate and maintain such
legal action, join Codexis as a party plaintiff; provided that credible evidence of continuing infringement exists. Shell shall have the right to compromise, litigate, settle or otherwise dispose of any such legal action; provided,
however, Shell shall keep Codexis informed of the status of any such legal action in a timely manner, and shall obtain Codexis’ prior written consent to such part of any settlement which contemplates payment or other action by Codexis or
has a material adverse effect on Codexis’ business or the Program Patent Rights or the Codexis Patent Rights. In any such legal action, Codexis shall have the right, but not the obligation, at Codexis’ expense, to be represented by counsel
of Codexis’ choosing. 
 4.5 Defense. [*] shall, at [*] expense, initiate legal action in defense of any claim of
infringement by a Third Party of patents owned or otherwise controlled by such Third Party by the practice of the Program Licensed Technology or the Codexis Licensed Technology in the Licensed Field of Use. [*] shall have the right to compromise,
litigate, settle or otherwise dispose of any such legal action; provided, however, [*] shall keep [*] informed of the status of any such legal action in a timely manner, and shall not settle any such legal action under terms which
would contemplate payment or other similar action by [*] or would have a material adverse effect on [*] business with respect to the Program Patent Rights or the Codexis Patent Rights in the Field of Use without [*] prior written consent. In any
such legal action, [*] shall have the right, but not the obligation, at [*] expense (such expense not to be reimbursed by [*]), to be represented by counsel of [*] choosing. 
 4.6 Cooperation. In any suit or legal action to enforce and/or defend the Program Patent Rights or the Codexis Patent Rights, the
Party not in control of such suit or legal action, at the reasonable request of the controlling Party, shall cooperate in all respects and, to the extent reasonably possible, have its employees testify when requested and make available relevant
documents and information, including, for example, records, papers, samples, specimens, and the like. 
  

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Exchange Commission. Confidential treatment has been requested with respect to the omitted portions. 
 12 

 ARTICLE 5 
 CONFIDENTIALITY 
 5.1 Confidentiality
Obligations. The Parties agree that, during the term of this Amended and Restated License Agreement and for five (5) years thereafter, all Confidential Information disclosed by one Party to the other Party hereunder shall be received and
maintained by the receiving Party in strict confidence, shall not be used for any purpose other than the purposes expressly permitted by this Amended and Restated License Agreement, and shall not be disclosed to any Third Party except to the extent
necessary to grant a sublicense to the rights granted to Shell hereunder; provided that such disclosure is made under obligations of confidentiality and non-use no less restrictive than the obligations placed upon Shell herein. The Parties
acknowledge and agree that the structure and composition of each particular Biocatalyst developed under the Program shall be deemed Confidential Information of Codexis, subject to the confidentiality and non-use obligations set forth in this Article
5. The obligations of confidentiality and non-use set forth in the first sentence of this Section 5.1 will not apply to any information to the extent that it can be established by the receiving Party that such information: 
 (a) was already known to the receiving Party or its Affiliates at the time of disclosure without restriction as to confidentiality or
use, as evidenced by competent evidence; 
 (b) was generally available to the public or was otherwise part of the public
domain at the time of its disclosure to the receiving Party or its Affiliates; 
 (c) became generally available to the
public or otherwise becomes part of the public domain after its disclosure and other than through any fault of the receiving Party or its Affiliates in breach of this Amended and Restated License Agreement; 
 (d) was subsequently lawfully disclosed to the receiving Party or its Affiliates by a Third Party without restriction as to
confidentiality or use and other than in contravention of a confidentiality obligation of such Third Party to the disclosing Party or its Affiliates; or 
 (e) is independently developed by employees or agents of the receiving Party or its Affiliates without reliance upon or access to Confidential Information of the disclosing Party or its Affiliates,
as evidenced by competent evidence. 
 Each Party represents and warrants that it has or will obtain written agreements from each person who has
a need to know the other Party’s Confidential Information, which agreements will obligate such person to obligations of confidentiality and non-use no less restrictive than the obligations set forth herein, and to assign to such Party all
inventions made by such person during the course of performing any tasks associated with the other Party’s Confidential Information. Further, each Party represents and warrants that those of its employees which have a need to know the other
Party’s Confidential Information are bound by obligations of confidentiality and non-use to the employer Party. Either Party may disclose Confidential Information of the other Party to such Party’s Affiliates or to sublicensees or, in the
case of Shell, Third Parties for purposes of having any Biocatalyst manufactured in accordance with Section 2.4; provided that any such Affiliate, sublicensee or Third Party agrees prior to such disclosure to be bound by obligations of
confidentiality and non-use no less restrictive than those assumed by such disclosing Party herein. 
  

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Exchange Commission. Confidential treatment has been requested with respect to the omitted portions. 
 13 

 Notwithstanding this Article 5 the receiving Party may disclose any Confidential Information of the
disclosing Party that the receiving Party is required to disclose under applicable laws or regulations or an order by a court or other regulatory body having competent jurisdiction; provided, however, that except where impracticable,
the receiving Party shall give the disclosing Party reasonable advance notice of such disclosure requirement (which shall include a copy of any applicable subpoena or order) and shall afford the disclosing Party a reasonable opportunity to oppose,
limit or secure confidential treatment for such required disclosure. In the event of any such required disclosure, the receiving Party shall disclose only that portion of the Confidential Information of the disclosing Party that the receiving Party
is legally required to disclose and, in the event a protective order is obtained by the disclosing Party, nothing in this Article 5 shall be construed to authorize the receiving Party to use or disclose any disclosing Party Confidential Information
to parties other than such court or regulatory body or beyond the scope of the protective order. Codexis and its Affiliates may disclose this Amended and Restated License Agreement if required to be disclosed by applicable State or federal tax or
securities laws to the extent, and only to the extent, such laws require such disclosure and Codexis provides Shell a reasonable opportunity to review and comment on the general text of such disclosure. 
 ARTICLE 6 
 OTHER AGREEMENTS 
 6.1 Other Agreements. Concurrently with the execution of this Amended and Restated
License Agreement, Codexis and Shell shall enter into the Amended and Restated Research Agreement and the Series E Stock Purchase Agreement (as defined in the Amended and Restated Research Agreement).  
 6.2 Entire Agreement. This Amended and Restated License Agreement, the Amended and Restated Research Agreement, the Series D Stock
Purchase Agreement (as defined in the Amended and Restated Research Agreement), and the Series E Stock Purchase Agreement are the sole agreements with respect to the subject matter hereof and supersede all other prior and contemporaneous agreements
and understandings between the Parties with respect to same, including without limitation that certain Non-Binding Term Sheet by and between Codexis and Shell dated as of August 23, 2006, that certain Collaborative Research Agreement by and
between Codexis and Shell effective as of November 1, 2006, as amended, and that certain License Agreement by and between Codexis and Shell effective as of November 1, 2006.  
  

 [*] Certain information in this document has been omitted and filed separately with the Securities and
Exchange Commission. Confidential treatment has been requested with respect to the omitted portions. 
 14 

 ARTICLE 7 
 REPRESENTATIONS AND WARRANTIES 
 7.1
Representations by Codexis. Codexis represents and warrants that, as of the Execution Date: (a) it is duly organized and validly existing under the laws of the jurisdiction of its incorporation and has full corporate power and authority to
enter into this Amended and Restated License Agreement; (b) it is in good standing with all relevant governmental authorities; (c) it has taken all corporate actions necessary to authorize the execution and delivery of this Amended and
Restated License Agreement and the performance of its obligations under this Amended and Restated License Agreement; (d) the performance of its obligations under this Amended and Restated License Agreement do not conflict with, or constitute a
default under its charter documents, any contractual obligation of Codexis or any court order; (e) it has the right to make the license grants set forth in this Amended and Restated License Agreement; and (f) there are no preexisting
agreements, commitments or other arrangements with any Third Party, including the United States government or any agency thereof, which will inhibit or restrict Codexis from carrying out the terms of this Amended and Restated License Agreement.
Codexis further represents and warrants that it shall not, during the term of this Amended and Restated License Agreement, without the prior written consent of Shell (i) provide any Third Party, including the United States government or agency
thereof, any claim to rights relating to the Codexis Licensed Technology (to the extent such Codexis Licensed Technology is licensed to Shell hereunder) or the Program Technology, or (ii) enter into any agreements, commitments or other
arrangement with any Third Party, including the United States government or agency thereof, in each case that would (1) prohibit Codexis from fulfilling its obligations hereunder or (2) be inconsistent with the rights granted by Codexis to
Shell under Section 2.1 and its obligations under Articles 4 and 5. 
 7.2 Representations by Shell. Shell
represents and warrants that, as of the Execution Date: (a) it is duly organized and validly existing under the laws of the jurisdiction of its formation and has full corporate power and authority to enter into this Amended and Restated License
Agreement; (b) it is in good standing with all relevant governmental authorities; (c) it has taken all corporate actions necessary to authorize the execution and delivery of this Amended and Restated License Agreement and the performance
of its obligations under this Amended and Restated License Agreement; and (d) the performance of its obligations under this Amended and Restated License Agreement do not conflict with, or constitute a default under its charter documents, any
contractual obligation of Shell or any court order. 
 7.3 Covenants of Shell. Shell covenants that it will not, without
the prior written consent of Codexis, (a) reverse engineer, deconstruct or in any way determine, or attempt to reverse engineer, deconstruct or in any way determine, the structure or composition of any Biocatalyst licensed to Shell hereunder;
provided, however, that Shell may determine the structure and composition of a particular Biocatalyst developed under the Program for the purpose of manufacturing or having manufactured such a particular Biocatalyst solely for the
purpose of manufacturing or having manufactured a Licensed Product in the Licensed Field of Use in accordance with the rights granted by Codexis to Shell pursuant to Section 2.1; or (b) modify or otherwise create any derivative of any such
Biocatalyst; or (c) do indirectly, either

  

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 15 

 
through a Third Party or a Shell Affiliate, any of the activities contained in (a) or (b) above that Shell itself agrees not to do. Notwithstanding the foregoing, in the event that
Shell desires to modify or otherwise create any derivative of any particular Biocatalyst developed under the Program and licensed by Codexis hereunder and Codexis notifies Shell in writing within one hundred twenty (120) days after receipt by
Codexis of a written request by Shell to modify or otherwise create any derivative of any such Biocatalyst that it is unwilling or unable to perform such modification or otherwise create such derivative under commercially reasonable terms, then
Shell shall be relieved of its obligations under this Section 7.3 with respect to such particular Biocatalyst. 
 7.4
Disclaimer of Warranties. EXCEPT AS SPECIFICALLY SET FORTH IN THIS ARTICLE 7, NEITHER PARTY MAKES ANY REPRESENTATION OR WARRANTY, EXPRESS OR IMPLIED, INCLUDING ANY IMPLIED WARRANTY OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE OR USE,
NON-INFRINGEMENT, AND ANY OTHER STATUTORY WARRANTY. 
 ARTICLE 8 
 INDEMNIFICATION 
 8.1 Indemnification by
Codexis. Codexis shall fully indemnify, defend and hold Shell and its Affiliates, and their respective agents, employees, consultants, officers and directors (the “Shell Indemnitees”) harmless from and against any and all
liability, damage, loss, cost or expense (including reasonable attorneys’ fees) arising out of Third Party claims or suits (collectively “Losses”) arising from: (a) breach by Codexis of any of its representations and
warranties under this Amended and Restated License Agreement; (b) failure to perform its obligations under this Amended and Restated License Agreement; (c) infringement of patent rights owned or otherwise controlled by such Third Party by
the practice of the Program Patent Rights or the Program Licensed Technology pursuant to the terms of this Amended and Restated License Agreement; provided that Codexis’ indemnification obligations pursuant to this Section 8.1(c)
shall not extend to any intellectual property provided to Codexis or any Affiliate of Codexis by or on behalf of Shell or any Affiliate of Shell, or to improvements made by Codexis or any Affiliate of Codexis to such intellectual property;
provided, further, that for purposes of this Section 8.1(c) only, “Losses” shall not include attorneys’ fees; provided, further, that Codexis’ indemnification obligations pursuant to this
Section 8.1(c) shall not extend to any patent rights owned or otherwise controlled by a Third Party identified in a written notice by Codexis to Shell that would be infringed by the practice of the Program Patent Rights or the Program Licensed
Technology, such notice to be provided to Shell within ninety (90) days after Codexis becomes aware of such patent rights and prior to the later of (1) the expiration or termination of the Amended and Restated Research Agreement and
(2) the entry by Shell or a Shell Affiliate into a non-alterable commitment with respect to the use of the allegedly infringing Program Patent Rights or Program Licensed Technology; provided, further, that Codexis’
indemnification obligations pursuant to this Section 8.1(c) shall be limited for any particular Loss to five million dollars ($5,000,000) where, for purposes of clarity, such five million dollars ($5,000,000) shall not include attorneys’
fees; and provided, further, that the aggregate indemnification obligations of Codexis pursuant to this Section 8.1(c) shall be capped for all

  

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Exchange Commission. Confidential treatment has been requested with respect to the omitted portions. 
 16 

 
Losses at fifteen million dollars ($15,000,000) where, for purposes of clarity, such fifteen million dollars ($15,000,000) shall not include attorneys’ fees; or (d) the negligence or
willful misconduct of Codexis or its Affiliates, and its or their directors, officers, agents, employees, sublicensees or consultants; except in any such case for Losses to the extent, and only to the extent, reasonably attributable to a breach by
Shell of its representations and warranties set forth in this Amended and Restated License Agreement or the Shell Indemnitees having committed an act or acts of gross negligence, recklessness or willful misconduct. 
 8.2 Indemnification by Shell. Shell shall fully indemnify, defend and hold Codexis and its Affiliates, and their respective agents,
employees, consultants, officers and directors (the “Codexis Indemnitees”) harmless from and against any and all Losses arising from: (a) breach by Shell of any of its representations and warranties under this Amended and
Restated License Agreement; (b) failure to perform its obligations under this Amended and Restated License Agreement; (c) the use under this Amended and Restated License Agreement by Shell or a Shell Affiliate of any Biocatalyst except to
the extent such Losses relate to the infringement of any intellectual property right of a Third Party; (d) the use under this Amended and Restated License Agreement by a Third Party sublicensee of any Biocatalyst except to the extent such
Losses relate to the infringement of any intellectual property right of a Third Party; provided, however, that Shell’s indemnification obligations pursuant to this Section 8.2(d) shall be limited for any particular Loss
incurred as a result of activities conducted (i) in the Intermediate Field of Use to five million dollars ($5,000,000) and (ii) in the Fuel Field of Use to fifteen million dollars ($15,000,000); and provided, further, that
the aggregate indemnification obligations of Shell pursuant to this Section 8.2(d) shall be capped for all Losses incurred as a result of activities conducted (i) in the Intermediate Field of Use at twenty-five million dollars
($25,000,000) and (ii) in the Fuel Field of Use at seventy-five million dollars ($75,000,000); or (e) infringement of patent rights owned or otherwise controlled by such Third Party by the practice of intellectual property provided to
Codexis or any Affiliate of Codexis by or on behalf of Shell or any Affiliate of Shell, or to improvements made by Codexis or any Affiliate of Codexis to such intellectual property; or (f) the negligence or willful misconduct of Shell or its
Affiliates, and its or their directors, officers, agents, employees, sublicensees, or consultants; except in any such case for Losses to the extent, and only to the extent, reasonably attributable to a breach by Codexis of its representations and
warranties set forth in this Amended and Restated License Agreement or the Codexis Indemnitees having committed an act or acts of gross negligence, recklessness or willful misconduct. Shell shall use commercially reasonable efforts to require Third
Party sublicensees to indemnify Shell and Codexis against Losses due to such Third Party sublicensee’s use of any Biocatalyst sublicensed to such Third Party sublicensee pursuant to this Amended and Restated License Agreement. 
 8.3 Environmental. Notwithstanding any other indemnification obligation in this Amended and Restated License Agreement, and in
addition to any rights the Parties may have under relevant federal, state, or local statutory and common laws, each Party shall fully indemnify, defend and hold the other Party and its Affiliates harmless from and against any and all Losses incurred
as a result of Environmental Matters; provided, however, that this indemnification shall not apply to the extent any such Losses result from the acts or omissions of personnel of the indemnified

  

 [*] Certain information in this document has been omitted and filed separately with the Securities and
Exchange Commission. Confidential treatment has been requested with respect to the omitted portions. 
 17 

 
Party or its Affiliates which occur at any site of the indemnified Party or the site of any supplier of the indemnified Party. For purposes of this Section 8.3, “Environment
Matters” shall mean: 
 (a) the operation by the indemnifying Party, its Affiliates, sublicensees, or
subcontractors of any site or facility in a manner that is not in compliance with and in violation of any Environmental Law; 
 (b) any release of Hazardous Materials into the environment by the indemnifying Party, its Affiliates, sublicensees, or its subcontractors; or any Hazardous Materials that have been Disposed of at a site of the indemnifying Party or
any site of any supplier (other than Codexis as supplier) of the indemnifying Party or other site or facility operated by the indemnifying Party, its Affiliates or its subcontractors, as the term Disposed is defined in applicable Environmental Laws;

 (c) any failure to obtain or maintain all permits and provide all notices required by Environmental Laws for the
lawful operation of any site of the indemnifying Party or any site of any supplier of the indemnifying Party or other facilities or sites operated by the indemnifying Party, its Affiliates, sublicensees, or its subcontractors; and 
 (d) any other actual or alleged act or omission relating to the handling or disposal of Hazardous Materials at any site of the
indemnifying Party or any site of any supplier of the indemnifying Party or the handling or disposal of Hazardous Materials by the indemnifying Party, its Affiliates, sublicensees, or its subcontractors at any other facility or site. 
 For purposes of this Section 8.3, “Environmental Law” shall mean any treaty, law, ordinance, regulation or order of any jurisdiction,
relating to environmental matters, including, but not limited to, matters governing air pollution; water pollution; the use, handling, reporting, release, storage, transport, or disposal of Hazardous Materials as defined herein above; exposure to or
discharge of Hazardous Materials; occupational safety and health; and public health. 
 For purposes of this Section 8.3,
“Hazardous Materials” includes, but is not limited to, air contaminant, water pollutant, hazardous material, hazardous waste, hazardous substance, toxic and hazardous substance, medical waste, infectious waste, “chemicals know
to the State of California to cause cancer or reproductive toxicity”, asbestos and PCB’s, as such substances are defined under any applicable federal, state or local statute, regulation, rule or ordinance 
 8.4 Notification of Claim; Conditions to Indemnification Obligations. 
 (a) Except with respect to Shell’s right to receive indemnification under Section 8.1(c), as a condition to a Party’s
right to receive indemnification under this Article 8, that Party shall: (a) promptly notify (“Claim Notice”) the other Party as soon as it becomes aware of a claim or suit for which indemnification may be sought pursuant
hereto (provided that the failure to give a Claim Notice promptly shall not prejudice the rights of an indemnified Party except to the extent that the failure to give such prompt notice materially adversely affects the ability of the
indemnifying Party to defend the claim or suit); (b) cooperate with the indemnifying Party in the defense of such claim or suit, at the expense of the indemnifying Party; and (c) if the indemnifying Party confirms in writing to the
indemnified Party its intention to defend such claim

  

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Exchange Commission. Confidential treatment has been requested with respect to the omitted portions. 
 18 

 
or suit within fifteen (15) business days of receipt of the Claim Notice, permit the indemnifying Party to control the defense of such claim or suit, including without limitation the right
to select defense counsel; provided that if the indemnifying Party fails to (i) provide such confirmation in writing within the fifteen (15) business day period; or (ii) diligently and reasonably defend such suit or claim at
any time, its right to defend the claim or suit shall terminate immediately in the case of (i) and otherwise upon twenty (20) days’ written notice to the indemnifying Party and the indemnified Party may assume the defense of such
claim or suit at the sole expense of the indemnifying Party and may settle or compromise such claim or suit without the consent of the indemnifying Party. In no event, however, may the indemnifying Party compromise or settle any claim or suit in a
manner which admits fault or negligence on the part of any indemnified Party or that otherwise materially affects such indemnified Party’s rights under this Amended and Restated License Agreement or requires any payment by an indemnified Party
without the prior written consent of such indemnified Party. Except as expressly provided above, the indemnifying Party will have no liability under this Article 8 with respect to claims or suits settled or compromised without its prior written
consent. The indemnified Party shall have the right, but not the duty, at its sole cost and expense, to participate in the defense of any claim or suit hereunder with attorneys of its own selection without relieving the indemnifying Party of any of
its obligations hereunder. 
 (b) As a condition to Shell’s right to receive indemnification under
Section 8.1(c), Shell shall (i) promptly provide Codexis with a Claim Notice as soon as it becomes aware of a claim or suit for which indemnification may be sought pursuant to Section 8.1(c) (provided that the failure to give a
Claim Notice promptly shall not prejudice the rights of Shell except to the extent that the failure to give such prompt notice materially adversely affects the ability of Codexis to defend the claim or suit); (ii) cooperate with Codexis in the
defense of any suit, action or proceeding alleging the infringement of the intellectual property rights of a Third Party by reason of the use of Program Patent Rights or Codexis Patent Rights in the manufacture, use or sale of a Licensed Product;
and (iii) give to Codexis all authority (including the right to exclusive control of the defense of any such suit, action or proceeding and the exclusive right after consultation with Shell, to compromise, litigate, settle or otherwise dispose
of any such suit, action or proceeding), at Codexis’ expense, including by providing information and assistance necessary to defend or settle any such suit, action or proceeding; provided, however, Codexis shall keep Shell
informed of the status of any such suit, action or proceeding in a timely manner, and must obtain Shell’s prior written consent to such part of any settlement which contemplates payment or other action by Shell or has a material adverse effect
on Shell’s business or the use of Program Patent Rights or the Codexis Patent Rights. Codexis shall give Shell prompt written notice of the commencement of any such suit, action or proceeding or claim of infringement and will furnish Shell a
copy of each communication relating to the alleged infringement. If it becomes necessary for defense of the suit, action or proceeding for Codexis to join Shell in any such suit, action or proceeding, Codexis may join Shell as a co-defendant if
necessary or desirable, and thereafter Shell may participate in the prosecution of such suit, action or proceeding, at Shell’s expense, and shall execute all documents and take all other actions, including giving testimony, which may reasonably
be required in connection with such suit, action or proceeding. 
  

 [*] Certain information in this document has been omitted and filed separately with the Securities and
Exchange Commission. Confidential treatment has been requested with respect to the omitted portions. 
 19 

 ARTICLE 9 
 TERM AND TERMINATION 
 9.1 Term. The term of
this Amended and Restated License Agreement will commence on the Effective Date and, unless earlier terminated in accordance with Section 9.2 or 9.3 below, shall continue in effect until the expiration of Shell’s payments obligation to
Codexis in accordance with Section 3.6. 
 9.2 Termination Upon Material Breach. Material failure by a Party to
comply with any of its obligations contained herein shall entitle the Party not in default to give to the Party in default written notice (a “Default Notice”) specifying the nature of the default, requiring such defaulting Party to
make good or otherwise cure such default, and stating the non-defaulting Party’s intention to terminate this Amended and Restated License Agreement if such default is not cured. If such default is not cured within sixty (60) days after the
date the Default Notice was sent, then the Party not in default shall be entitled, without prejudice to any other rights conferred on it by this Amended and Restated License Agreement, and in addition to any other remedies available to it by law or
in equity, to terminate this Amended and Restated License Agreement by written notice of termination to the defaulting Party; provided, however, that if the Party receiving such Default Notice (the “Disputing Party”)
has a reasonable basis for disputing that it is in default and such Party provides written notice thereof to the other Party before the expiration of such sixty (60) day cure period, then the Disputing Party shall have the right, prior to the
expiration of such sixty (60) day period, to submit such dispute for resolution in accordance with the provisions of Section 10.7; provided further that in the event that as a result of such resolution, the Party receiving
such Default Notice is found to be in default and such default is not cured within forty-five (45) days after the date of such resolution, then the Party not in default shall be entitled, without prejudice to any other rights conferred on it by
this Amended and Restated License Agreement, and in addition to any other remedies available to it by law or in equity, to terminate this Amended and Restated License Agreement by written notice of termination to the defaulting Party. 

 9.3 Termination by Shell. Shell shall have the right to terminate this Amended and Restated License Agreement at
any time upon six (6) months prior written notice to Codexis.  
 9.4 Consequences of Expiration or Termination.

 (a) The following Articles and Sections of this Amended and Restated License Agreement shall survive its
termination or expiration: Articles 5, 8 and 10, and Sections 2.3, 3.5, 6.2, 7.3, 7.4 and 9.4. In addition, upon the expiration of this Amended and Restated License Agreement or in the event of termination by Shell pursuant to Section 9.2,
Section 2.1 shall survive such expiration or termination, as the case may be. 
 (b) Termination of this Amended and
Restated License Agreement for any reason shall be without prejudice to (i) the rights and obligations of the Parties set forth in any Articles or Sections which provide by their terms performance by either Party subsequent to termination;
(ii) Codexis’ rights to receive all payments accrued under Article 3 prior to the effective date of such termination, or (iii) any other remedies which either Party may otherwise have. 
  

 [*] Certain information in this document has been omitted and filed separately with the Securities and
Exchange Commission. Confidential treatment has been requested with respect to the omitted portions. 
 20 

 ARTICLE 10 
 GENERAL PROVISIONS 
 10.1 Relationship of the
Parties. The Parties shall perform their obligations under this Amended and Restated License Agreement as independent contractors and nothing contained in this Amended and Restated License Agreement shall be construed to make either Codexis or
Shell partners, joint venturers, principals, representatives or employees of the other. Neither Party shall have any right, power or authority, express or implied, to bind the other. Shell and Codexis agree that this Amended and Restated License
Agreement shall not constitute a partnership for tax purposes. In the event, however, that this Amended and Restated License Agreement were so construed, then Shell and Codexis agree to be excluded from the provisions of Subchapter K of the United
States Internal Revenue Code of 1986, as amended. 
 10.2 Assignments. Neither Party may transfer or assign its rights
and obligations under this Amended and Restated License Agreement without the prior written consent of the other Party; provided that either Party may transfer or assign its rights and obligations under this Amended and Restated License
Agreement to a successor to all or substantially all of its business or assets relating to this Amended and Restated License Agreement whether by sale, acquisition, merger, operation of law or otherwise. Notwithstanding anything to the contrary, any
transferee, assignee or successor of a Party shall agree in writing to be bound by the terms of this Amended and Restated License Agreement prior to the effective date of transfer or assignment of this Amended and Restated License Agreement and,
thereafter, this Amended and Restated License Agreement shall be binding upon such transferee, assignee or successor. Any attempted transfer or assignment of this Amended and Restated License Agreement not in accordance with this Section 10.2
will be null and void. 
 10.3 Further Actions. Each Party agrees to execute, acknowledge and deliver such further
instruments and to do all such other acts as may be necessary or appropriate in order to carry out the express provisions of this Amended and Restated License Agreement. 
 10.4 Force Majeure. Except for the payment of money, neither Party shall be liable to the other for failure or delay in the performance of any of its obligations under this Amended and Restated
License Agreement for the time and to the extent such failure or delay is caused by earthquake, riot, civil commotion, war, terrorist acts, strike, flood, or governmental acts or restriction that is beyond the control of the respective Party. The
Party affected by such force majeure will provide the other Party with full particulars thereof as soon as it becomes aware of the same (including its best estimate of the likely extent and duration of the interference with its activities), and will
use commercially reasonable efforts to overcome the difficulties created thereby and to resume performance of its obligations as soon as practicable. 
  

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Exchange Commission. Confidential treatment has been requested with respect to the omitted portions. 
 21 

 10.5 Captions. The captions to this Amended and Restated License Agreement are for
convenience only, and are to be of no force or effect in construing or interpreting any of the provisions of this Amended and Restated License Agreement. 
 10.6 Governing Law. This Amended and Restated License Agreement will be governed by and interpreted in accordance with the laws of the State of New York, applicable to contracts entered into and to
be performed wholly within the State of New York, excluding conflict of laws principles. 
 10.7 Dispute Resolution;
Jurisdiction and Venue. Any controversy or claim (“Dispute”), whether based on contract, tort, statute or other legal or equitable theory (including but not limited to any claim of fraud, misrepresentation or fraudulent
inducement or any question of validity or effect of this Amended and Restated License Agreement including this clause) arising out of or related to this Amended and Restated License Agreement (including but not limited to any amendments,
annexations, and extensions) or the breach thereof shall be settled by consultation between the Parties initiated by written notice of the Dispute to the other Party. In the event such consultation does not settle the Dispute within thirty
(30) days after written notice of such Dispute, then the Dispute shall be settled by binding arbitration in accordance with the then current commercial arbitration rules of the American Arbitration Association and this provision. The
arbitration shall be governed by the United States Arbitration Act, 9 U.S.C. §§ 1-16 (the “Act”) to the exclusion of any provision of state law inconsistent therewith or which would produce a different result. Judgment
upon the award rendered by the arbitrator may be entered by any court having jurisdiction. The arbitration shall be held in Chicago, Illinois. The Parties shall agree on a single neutral arbitrator with relevant industry experience to conduct the
arbitration. If the Parties do not agree on a single neutral arbitrator within ten (10) days after receipt of an arbitration notice, each Party shall select one (1) arbitrator and the two (2) Party-selected arbitrators shall
select a third arbitrator with relevant industry experience to constitute a panel of three (3) arbitrators to conduct the arbitration in accordance with the Act. In the event that only one of the Parties selects an arbitrator, then such
arbitrator shall be entitled to act as the sole arbitrator to resolve the Dispute or any and all unresolved issues subject to the arbitration. Each and all arbitrator(s) of the arbitration panel conducting the arbitration must and shall agree
to render an opinion within twenty (20) days after the final hearing before the panel. The arbitrator(s) shall determine the claim of the Parties and render a final award in accordance with the substantive law of the State of New York,
excluding the conflicts provisions of such law. The arbitrator shall set forth the reasons for the award in writing. The terms hereof shall not limit any obligations of a Party to defend, indemnify or hold harmless another Party against court
proceedings or other claims, losses damages or expenses. All proceedings and decisions of the arbitrator(s) shall be deemed Confidential Information of each of the Parties, and shall be subject to Article 5 hereof. Notwithstanding anything herein to
the contrary, a party may seek a temporary restraining order or a preliminary injunction from any court of competent jurisdiction in order to prevent immediate and irreparable injury, loss, or damage on a provisional basis, pending the decision of
the arbitrator(s) on the ultimate merits of any Dispute. 
 10.8 Notices and Deliveries. Any notice, request, delivery,
approval or consent required or permitted to be given under this Amended and Restated License Agreement will be in writing and will be deemed to have been sufficiently given on the date of receipt if delivered

  

 [*] Certain information in this document has been omitted and filed separately with the Securities and
Exchange Commission. Confidential treatment has been requested with respect to the omitted portions. 
 22 

 
in person, transmitted by telecopier (receipt verified) or by express courier service (signature required) or five (5) days after it was sent by registered letter, return receipt requested
(or its equivalent), provided that no postal strike or other disruption is then in effect or comes into effect within two (2) days after such mailing, to the Party to which it is directed at its address or facsimile number shown below or
such other address or facsimile number as such Party will have last given by notice to the other Party. 
 If to Codexis,
addressed to: 
 Codexis, Inc. 
 200 Penobscot Drive 
 Redwood City, CA 94063 
 Attention: Chief Executive Officer 
 Telephone: 650-980-5600 
 Fax: 650-298-5449 
 with a copy to: 
 Codexis, Inc. 
 200 Penobscot Drive 
 Redwood City, CA 94063 
 Attention: General Counsel 
 Telephone: 650-421-8160 
 Fax: 650-421-8108 
 If to Shell, addressed to: 
 Shell Oil Products (US) 
 910 Louisiana Street 
 Houston, TX 77002 
 Attention: Fuel Development Program Manager (Americas) 
 Telephone: 713-241-1461 
 Fax: 713-241-9800 
 with a copy to: 
 Shell Oil Company 
 Associate General Counsel, Intellectual Property Services 
 910 Louisiana 
 Houston, TX 77002 
 Fax: 713-241-6617 
 10.9 No Consequential Damages. EXCEPT PURSUANT TO ARTICLE 8, IN NO EVENT WILL A PARTY OR ANY OF ITS RESPECTIVE AFFILIATES BE LIABLE TO THE OTHER PARTY OR ANY OF ITS AFFILIATES FOR SPECIAL,
INDIRECT, CONSEQUENTIAL OR PUNITIVE DAMAGES, WHETHER IN CONTRACT, WARRANTY,

  

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Exchange Commission. Confidential treatment has been requested with respect to the omitted portions. 
 23 

 
TORT, NEGLIGENCE, STRICT LIABILITY OR OTHERWISE, INCLUDING BUT NOT LIMITED TO, LOSS OF PROFITS OR REVENUE, OR CLAIMS OF CUSTOMERS OF ANY OF THEM OR OTHER THIRD PARTIES FOR SUCH DAMAGES.

 10.10 Waiver. A waiver by a Party of any of the terms and conditions of this Amended and Restated License Agreement in
any instance will not be deemed or construed to be a waiver of such term or condition for the future, or of any subsequent breach hereof. All rights, remedies, undertakings, obligations and agreements contained in this Amended and Restated License
Agreement will be cumulative and none of them will be in limitation of any other remedy, right, undertaking, obligation or agreement of either Party. 
 10.11 Severability. When possible, each provision of this Amended and Restated License Agreement will be interpreted in such manner as to be effective and valid under applicable law, but if any
provision of this Amended and Restated License Agreement is held to be prohibited by or invalid under applicable law, such provision will be ineffective but only to the extent of such prohibition or invalidity, without invalidating the remainder of
such provision or of this Amended and Restated License Agreement. The Parties will make an effort to replace the invalid or unenforceable provision with a valid one which in its economic effect is most consistent with the invalid or unenforceable
provision. 
 10.12 Counterparts. This Amended and Restated License Agreement may be executed simultaneously in
counterparts, any one of which need not contain the signature of more than one Party but both such counterparts taken together will constitute one and the same agreement. 
 10.13 Compliance with Laws. Each Party shall comply with all applicable statutes, laws, regulations, enactments, directives and ordinances and all injunctions, decisions, directives, judgments and
orders of any governmental authority in effect at any time in connection with the performance of its obligations under this Amended and Restated License Agreement. 
 10.14 Amendment. No amendment of any provision of this Amended and Restated License Agreement shall be binding on a Party to this Amended and Restated License Agreement unless consented to in
writing and signed by such Party. Signatures and writings in an electronic form do not constitute or create a writing signed by a Party. 
 [Signature page follows] 
  

 [*] Certain information in this document has been omitted and filed separately with the Securities and
Exchange Commission. Confidential treatment has been requested with respect to the omitted portions. 
 24 

 IN WITNESS WHEREOF, the
Parties have caused this Amended and Restated License Agreement to be executed by their respective duly authorized officers as of the Execution Date, each copy of which will for all purposes be deemed to be an original. 
  

			
	CODEXIS, INC.
		
	By:	 	 /s/    Alan Shaw

	Name:	 	Alan Shaw
	Title:	 	President
	
	 EQUILON ENTERPRISES LLC
  
 DBA SHELL OIL PRODUCTS US

		
	By:	 	 /s/    David A. Sexton

	Name:	 	David A. Sexton
	Title:	 	President

 [Signature Page to Amended and Restated License Agreement] 
 [*] Certain information in this document has been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has
been requested with respect to the omitted portions. 

 EXHIBIT 1.26 
 Program Patent Rights 
 Intentionally left blank as of the Execution Date. 
 [*] Certain information in this document has been omitted and filed separately
with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

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