Side Letter dated September 24, 2007



 EXHIBIT 10.9 
 [*] 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. 
  

			
	

	  	 Maxygen, Inc.
 200 Penobscot Drive

Redwood City, CA 94063
 650.298.5300 main
 650.364.2715 fax
 www.maxygen.com


 September 24, 2007 
 Codexis, Inc. 
 Attn: Doug Sheehy 
 200 Penobscot Drive 
 Redwood City, CA 94063 
  

	 	Re:	License Agreement effective as of March 28, 2002, by and between 

 Maxygen, Inc. and Codexis, Inc., as amended (the “Agreement”) 
 Dear Doug: 
 This letter confirms that, as of the date hereof, SubField 8 of Exhibit G to the Agreement is hereby deleted in its entirety and replaced with the following:

 “SubField 8: Manufacture of fuels, fuel additives and lubricants (and intermediates of the foregoing) as specified below:

  

	 	a.	Manufacture of fuel and/or fuel additives and/or lubricants, where Biomass (as defined below) is the starting material for the applicable fuel and/or fuel additive and/or lubricant,
including without limitation the manufacture of compounds (e.g., fermentable sugars) which are intermediates in the process of producing fuel or fuel additives and/or lubricants, where Biomass is the starting material for the applicable fuel and/or
fuel additive and/or lubricant and such intermediates are used solely in the production of fuel or fuel additives and/or lubricants, but specifically excluding the fuels and/or fuel additives and/or lubricants in Category (b) below.


  

	 	b.	Conversion of Biomass-derived oils into fuel and/or fuel additives and/or lubricants, including without limitation the manufacture of compounds which are intermediates in the
process of converting Biomass-derived oils into fuel and/or fuel additives and/or lubricants, where such intermediates are used solely in the production of fuel or fuel additives and/or lubricants. 

 For purposes of clarification, as used in this SubField 8 (and with regard to any Supplemental Products that may result due to activation of any Category
of SubField 8), “fuel additives” are substances which are intended to be added to fuel to modify the characteristics of such fuel, including, for example, biodegradability, combustibility, viscosity and/or emissions profile, and
“lubricants” are [*]. 







 “Biomass” shall mean 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).  
 Notwithstanding the above, for purposes of this SubField 8, no right or license is granted to Codexis to
use any Enabling Technology to alter or modify any gene(s) of any Plant to (a) [*], or (b) [*]; provided, however, Codexis may produce in Category II Plants chemicals that are Supplemental Products resulting from the activation of any
Category of this SubField 8.” 
 The parties acknowledge and agree that all of Subfield 8, as amended by this letter, is subject to that certain letter
dated September 11, 2007, and that all fuels, fuel additives and/or lubricants within amended Subfield 8 shall be Supplemental Products. 
 Capitalized
terms used but not otherwise defined herein shall have the meanings set forth in the Agreement. 
 Please indicate Codexis’ agreement to the foregoing
by countersigning below. 
  

	
	Yours sincerely,
	
	/s/ Michael S. Rabson
	Michael S. Rabson


  

			
	UNDERSTOOD AND AGREED
	BY CODEXIS, INC.
		
	By:	 	 /s/ Douglas T. Sheehy

	Name:	 	Douglas T. Sheehy
	Title:	 	VP & General Counsel
	Date:	 	September 24, 2007

  

 [*] 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.