Document:

Amendment No. 2 to the Maxygen License

 Exhibit 10.2C 
 AMENDMENT NO. 2 TO LICENSE AGREEMENT 
 This Amendment
No. 2 (“Amendment No. 2”) amends that certain License Agreement effective March 28, 2002, entered into by and between Maxygen, Inc. (“MUS”) and Codexis, Inc. (“Codexis”), as amended by Amendment
No. 1 to License Agreement effective September 13, 2002 (as amended, the “Agreement”), and shall be effective as of October 1, 2002. MUS and Codexis hereby amend the Agreement as follows: 
 1. Section 1.44 of the Agreement shall be amended to provide in its entirety, as follows: 
 1.44 “Separation Event” shall mean the earlier of (i) four (4) years after the Amendment Date, and
(ii) the date upon which a Change of Control of Codexis occurs. 
 2. Article 1 is amended by the addition of the following new definition:

 1.59 “Change of Control of Codexis” means (i) a dissolution or liquidation of Codexis;
(ii) a sale of all or substantially all the assets of Codexis, (iii) any consolidation or merger of Codexis with or into any other corporation or other entity or person, or any other corporate reorganization, in which the stockholders of
Codexis immediately prior to such consolidation, merger or reorganization, own less than fifty percent (50%) of the Company’s voting power immediately after such consolidation, merger or reorganization, excluding any consolidation, merger
or reorganization effected exclusively to change the domicile of Codexis, or (iv) acquisition by any person, entity or group within the meaning of Section 13(d) or 14(d) of the Exchange Act, or any comparable successor provisions (other
than MUS, CMEA Ventures Life Sciences 2000, L.P., Chevron Technology Ventures, LLC, Pequot Private Equity Fund III, L.P. and their respective Affiliates (collectively, the “Current Stockholders”, or any group including any Current
Stockholder that does not include, within the reasonable discretion of Maxygen, a competitor of Codexis) of the beneficial ownership (within the meaning of Rule 13d-3 promulgated under the Exchange Act, or comparable successor rule) of securities of
the Company such that after the acquisition the person, entity or group owns securities of Codexis representing at least fifty percent (50%) of the combined voting power entitled to vote in the election of directors. 
 3. Subsections 2.1.1(b)(i) and (ii) and 2.1.1(e)(i) and (ii) are amended to add the words “in the Codexis Field” as the last words of
each such clause. 
 4. As soon as practicable after the date hereof, an Amended and Restated License Agreement will be prepared reflecting the
amendments to the Agreement contained in this Amendment No. 2 and the September 13, 2002 amendment to the Agreement, without the need for any additional approval by the Board of Directors of Codexis or any member thereof. 

 IN WITNESS WHEREOF, MUS and Codexis have executed this Amendment No. 2 to License
Agreement as of the first above written. 
  

									
	MAXYGEN, INC.	 		 	CODEXIS, INC.
					
	By:	 	 /s/ Russell J. Howard
	 		 	By:	 	 /s/ Alan Shaw

	Name:	 	 Russell J. Howard
	 		 	Name:	 	 Alan Shaw

	Title:	 	 Chief Executive Officer
	 		 	Title:	 	 President

  

 2Amendment No. 3 to the Maxygen License

 [*] 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 10.2D 

 AMENDMENT NO. 3 TO LICENSE AGREEMENT 
 This Amendment No. 3 (“Amendment No. 3”) amends that certain License Agreement effective March 28, 2002 entered by and between Maxygen, Inc. (“MUS”) and Codexis, Inc.
(“Codexis”), as previously amended by Amendment No. 1 to License Agreement effective September 13, 2002, and Amendment No. 2 to License Agreement effective October 1, 2002, (as amended, the “Agreement”), and
shall be effective as of August __, 2006 (the “Third Amendment Date”). MUS and Codexis hereby amend the Agreement as follows: 
  

	1.	Article 1 is amended by the addition of the following new definitions: 

 1.60 “Consumer Price Index” or “CPI” means the Consumer Price Index, All Urban Consumers,
as published by the U.S. Bureau of Labor Statistics 
 1.61 “Energy Product” means any
(i) Supplemental Product subject to any Modified SubField, and (ii) Scheduled Product subject to 1 of Exhibit F of the Agreement. 
 1.62 “FTE” means the efforts of one or more employees of Codexis equivalent to the efforts of one Codexis full time employee (i.e., an employee that works at least one thousand seven
hundred sixty (1760) hours per year.
 1.63 “Net Sales” shall mean means the consideration
received by Codexis or its Affiliates for the sale or use of Energy Products in arm’s length sales to an independent Third Party, after deduction of the following items, provided and to the extent such items are actually incurred and documented
and do not exceed reasonable and customary amounts in the market in which such sale occurred: (i) ordinary and customary trade discounts actually allowed; (ii) credits, rebates and returns; (iii) freight, insurance and duties paid for
and separately identified on the invoice or other documentation maintained in the ordinary course of business, and (iv) taxes, duties and other compulsory payments to governmental authorities actually paid and separately identified on the
invoice or other documentation maintained in the ordinary course of business. All sales or use of Energy Products between Codexis and any of its Affiliates shall be disregarded for purposes of computing Net Sales. A “sale” shall include
any transfer or other disposition for consideration, and Net Sales shall include all consideration received by Codexis or its Affiliates in respect of any sale or use of Energy Products, whether such consideration is in cash, payment in kind,
exchange or another form. 
 In the case of discounts on “bundles” of products and/or services which include Energy
Products, Codexis may with notice to MUS calculate the Net Sales by discounting the bona fide list price of an Energy Product by no more than the average percentage discount of all products and services of Codexis and/or its Affiliates in a
particular “bundle”, calculated as follows: 

					
	 Average percentage
 discount on
a
 particular “bundle”
	  	=	 	(1 – A/B) x 100

 where A equals the total discounted price of a particular “bundle” of
products and services, and B equals the sum of the undiscounted bona fide list prices of each unit of every product and service in such “bundle”. Codexis shall provide MUS documentation, reasonably acceptable to MUS, establishing such
average discount with respect to each “bundle”. If Codexis cannot so establish the average discount of a bundle, the Net Sales shall be based on the undiscounted list price of the Energy Product in the bundle. If an Energy Product in a
bundle is not sold separately and no bona fide list price exists for such Energy Product, the Parties shall negotiate in good faith an imputed list price for such Energy Product, and Net Sales with respect thereto shall be based on such imputed list
price. 
  

	2.	The following definitions in Article 1 shall be amended to read as follows: 

 1.55 “Reserved SubField Termination Date” shall mean (a) for SubFields 1, 2, 4, 5, 6 and 7, the period
commencing on the Amendment Date and ending on the later of (i) five (5) years after Amendment Date, or (ii) a Separation Event, and (b) for SubFields 3, 8, 9 and 10 (the “Modified SubFields”), the period commencing on
the Amendment Date and ending six (6) years after the Amendment Date; provided, however, that in the event Codexis has satisfied the criteria set forth in Section 2.1.6(a) as to a particular SubField within the Modified SubFields such that
such entire SubField becomes included in the Codexis Field, as provided in Section 2.1.6(d), on or before six (6) years after the Amendment Date, then the Reserved SubField Termination Date shall be extended by one additional year; and
further provided that upon the satisfaction of the criteria set forth in Section 2.1.6(d) for each additional SubField within the Modified SubFields, if any, the Reserved SubField Termination Date for the remaining Modified SubFields shall be
extended for an additional one (1) year period, up to a maximum of three (3) such additional one (1) year extensions. 
 1.56 “Reserved SubFields” shall mean, in the period from the Amendment Date until the applicable Reserved SubField Termination Date, the subject matter within the applicable SubField(s).
It is understood and agreed that as of the applicable Reserved SubField Termination Date, (a) one or more Categories within the Reserved SubFields may become part of the Codexis Field pursuant to Section 2.1.6(c), (b), one or more of the
Reserved SubFields may become part of the Codexis Field pursuant to Section 2.1.6(d), and (c) any Category and any Reserved SubField that is not within the scope of the Codexis Field pursuant to subsection (a) or (b) above as of
the applicable Reserved SubField Termination Date, shall be terminated, and shall no longer be within the Reserved SubFields. 
 1.57 “Scheduled Product” shall mean any Product described on Exhibit F. 
 1.59 “Supplemental Product” shall mean any Biocatlyst or Enzyme Product, and/or chemical made with the use of a Biocatlyst or Enzyme Product, in each case, that is (a) within a
Category, where Codexis conducts with regard to such Category 
  
 [*] 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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a research project meeting the criteria set forth in Section 2.1.6(a) prior to the applicable Reserved SubField Termination Date, and (b) within a Reserved SubField that becomes part of
the Codexis Field at any time prior to the applicable Reserved SubField Termination Date pursuant to Section 2.1.6(d).” 
  

	3.	Section 2.1.1 is amended as follows: 

  

	 	a.	In the first clause, revise the phrase “. . . worldwide, royalty-free (subject to Section 2.1.5(b) licenses, . . .” to read: “. . . worldwide,
royalty-free (subject to Section 2.1.5(b) and the terms of Article 5) licenses, . . .” 

  

	 	b.	Revise Sections 2.1.1(a)(i), 2.1.1(a)(ii), 2.1.1(d)(i) and 2.1.1(d)(ii) by adding the phrase “and/or Section 2.1.6(d)” after each occurrence of the
phrase “pursuant to Section 2.1.6(c)”. 

  

	 	c.	Revise Section 2.1.1 by changing each occurrence of “the Reserved SubField Termination Date” to “the applicable Reserved SubField Termination
Date”. 

  

	4.	Section 2.1.6 is amended as follows: 

 Revise Section 2.1.6 by changing each occurrence of “the Reserved SubField Termination Date” to “the applicable Reserved SubField Termination Date”. 
  

	5.	Section 2.1.6(h) is amended in its entirely as follows: 

 “Except with respect to (i) any Category for which Codexis has satisfied the criteria set forth in Section 2.1.6(c), and (ii) any Reserved SubField for which Codexis has satisfied the
criteria set forth in Section 2.1.6(d), it is understood and agreed that as of the applicable Reserved SubField Termination Date, the applicable Reserved SubFields (including each Category and SubField) shall be terminated and shall have no
content or force or effect for the remainder of the term of the Agreement, and, as of the applicable Reserved SubField Termination Date, MUS (and/or its designee) shall have, as between the Parties, the exclusive rights in and to and shall be free,
at its sole discretion, to work in, such Reserved SubField(s) without restriction or obligation to Codexis.” 
  

	6.	Article 5 shall be revised to read in its entirety as follows: 

 5.1 Codexis Stock. In partial consideration for the rights granted hereunder, Codexis shall issue to MUS one million
(1,000,000) shares of Common Stock and six million (6,000,000) shares of Series A Preferred Stock of Codexis pursuant to the Stock Issuance and Asset Contribution Agreement by and between MUS and Codexis of even date hereof. 
  
 [*] 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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 5.2 Energy Products. In consideration for the rights granted to
Codexis in this Amendment No. 3, for all Energy Products and/or any grant of rights with regard to the use of any Enabling Technology for the development and commercialization of any Energy Product, Codexis will pay MUS: 
 5.2.1 Twenty percent (20%) of all consideration received by Codexis from any Sublicensee or Third Party for: 

a. option and/or license fees for rights to use any Enabling Technology to develop and/or make any Energy Product; and

 b. development payments (e.g., milestone payments) in respect of any Energy Product, and/or any product made
with the use of any Energy Product; and 
 c. royalties and/or other payments for the commercialization of any
Energy Product, and/or any product made with the use of any such Energy Product; and 
 d. the purchase of any
equity securities of Codexis; provided, that the consideration received by Codexis from such Sublicensee or Third Party in connection with such purchase shall be deemed to be the amount obtained by multiplying (A) the aggregate number of shares
of any equity securities of Codexis purchased by such Sublicensee or Third Party by (B) the amount, if any, by which the price per share of such equity securities exceeds the Original Issue Price (as defined in Codexis’ Fifth Amended and
Restated Certificate of Incorporation, as amended from time to time) per share of the Series D Preferred Stock (as may be adjusted from time to time); provided that at the time of such purchase such Sublicensee or Third Party has a contractual
relationship with Codexis (or proposes to have a contractual relationship with Codexis in connection with such purchase and the contractual relationship thereafter becomes effective), and the primary business purpose of the relationship is the
development and/or commercialization of (i) any Energy Product, or (ii) any product made with the use of any Energy Product; and
 5.2.2 Notwithstanding anything to the contrary in Section 5.2.1 above, Codexis shall not be required to pay to MUS any share of research and/or development funding received (and not subject to any
further performance criteria) by Codexis from a Third Party for the support of Codexis personnel (i.e., payments on an FTE basis to support Codexis employees for activities conducted by Codexis); provided that (i) such payments are actually
used by Codexis for FTE funding, and (ii) the applicable rate per FTE does not exceed the Base FTE Rate. The Base FTE Rate for 2006 shall be three hundred fifty thousand dollars ($350,000) per FTE per year, and shall be revised annually at the
beginning of each subsequent calendar year to reflect annual changes in the Consumer Price Index, using September 2006 as the baseline comparison. Codexis shall pay to MUS twenty percent (20%) of any research funding received from a Third Party
for the development of any Energy Product, and/or any product made with the use of any Energy Product, in each case only to the extent such funding does not satisfy the criteria listed in subsections (i) and (ii) above. 
  
 [*] 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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 5.2.3 If Codexis directly commercializes any Energy Product, Codexis will pay to MUS a
royalty of two percent (2%) of (a) Net Sales of such Energy Products sold by Codexis or its Affiliates, and/or (b) amounts received by Codexis or its Affiliates from any Sublicensee or other Third Party for the use of Energy Products,
to the extent Codexis or its Affiliates utilize such Product(s) to provide services to such Sublicensee or Third Party, as the case may be. 
 5.3 Quarterly Reports. Commencing in the first calendar quarter in which Codexis receives any payment subject to Section 5.2, Codexis shall make quarterly written reports to MUS within sixty
(60) days after the end of each calendar quarter, stating in each such report the consideration subject to Section 5.2 received by it during such calendar quarter. Such reports shall provide separately for Codexis and each of its
Affiliates and Sublicensees, in each case, on a country-by-country and Energy Product-by-Energy Product basis: 
  

	 	(i)	the type (e.g., license fee, milestone payment) and amount of consideration received; 

  

	 	(ii)	for payments based on Energy Products, the quantity and description of each such Energy Product sold or used; and 

  

	 	(iii)	the calculation of amounts due to MUS, accompanied by sufficient information to enable MUS to verify the accuracy of the calculations made by Codexis, and a detailed
explanation of the methodology used to determine the applicable payment. 

 5.4 Payment.
Concurrently with providing to MUS each quarterly report described in Section 5.3, Codexis shall pay MUS all amounts due under Section 5.2 for the calendar quarter corresponding to such report. 
 5.5 Audit. Codexis and its Affiliates shall keep complete, true and accurate books of account and records for the
purpose of determining the amounts payable under Section 5.2 of this Agreement. Such books and records shall be kept at the principal place of business of such party, as the case may be, for at least four (4) years following the end of the
calendar quarter to which they pertain. Such records will be open for inspection during such four (4) year period by a public accounting firm selected by MUS reasonably acceptable to Codexis, solely for the purpose of verifying the reports and
payments hereunder. Such inspections may be made no more than once each calendar year, at reasonable times and on reasonable notice. Inspections conducted under this Section 5.5 shall be at the expense of MUS, unless a variation or error
producing an increase exceeding ten percent (10%) of the amount stated for any period covered by the inspection is established in the course of any such inspection, whereupon all reasonable costs relating to the inspection and any unpaid
amounts that are discovered will be paid promptly by Codexis together with interest thereon as set forth in Section 5.6 below. 
  
 [*] 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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 5.6 Payment Method; Late Payments. All payments due to MUS under this
Agreement shall be paid in U.S. dollars by bank wire transfer in immediately available funds to a bank account designated by MUS. Any payment or portion thereof that is not paid on the date such payments are due under this Agreement shall bear
interest at the lesser of (i) the prime rate as reported by the Chase Manhattan Bank, New York, New York (or its successor) on the date such payment is due, plus an additional two percent (2%), or (ii) the maximum rate permitted by law, in
each case calculated on the number of days such payment is delinquent. This Section 5.6 shall in no way limit any other remedies available for late payment. 
 5.7 Currency Conversion. All payments due to MUS under this Agreement shall first be determined in local currency
and then, if necessary, converted to its equivalent in United States currency. The buying rates of exchange for converting the currencies involved into the currency of the United States quoted by the Wall Street Journal (or its successor in
interest) on the last business day of the quarterly period in which the payments were received by Codexis shall be used to determine any such conversion. 
 5.8 Restrictions on Payment. The obligation of Codexis to pay amounts to MUS under this Agreement with respect to sales of Energy Products in a particular country shall be waived and excused to the
extent that statutes, laws, codes or government regulations in a particular country prevent such payments; provided, however, in such event, if legally permissible, Codexis shall pay the amounts owed to MUS by depositing such amounts in a bank
account in such country that has been designated by MUS and promptly report such payment to MUS in writing. 
 5.9 Taxes. Any tax that Codexis is required to withhold and pay on behalf of MUS with respect to amounts payable to MUS under this Agreement shall be deducted from and offset against said payments prior to remittance to MUS;
provided, however, that in regard to any tax so deducted, Codexis shall give or cause to be given to MUS such assistance as may reasonably be necessary to enable MUS to claim exemption therefrom or credit therefor, and in each case shall furnish MUS
with proper evidence of the taxes paid on its behalf. 
 5.10 Energy Affiliate. 
 (a) If (i) Codexis or any of its Affiliates or subsidiaries (each, a “Codexis Entity”) proposes to
form, establish or acquire, directly or indirectly, any Affiliate or subsidiary that engages in a line of business related to the use of any Energy Products, and/or any Enabling Technology in or for any energy application (the “Energy
Rights”), or any Affiliate or subsidiary of Codexis proposes, at any time, to engage, directly or indirectly, in such line of business (in each case, an “Energy Affiliate”); (ii) a Codexis Entity proposes to acquire or
obtain, directly or indirectly, by merger, consolidation, acquisition of equity interests or otherwise, any assets, rights or other interests of whatever kind and nature in any business or Third Party (e.g. any individual, corporation, partnership,
limited liability company, joint venture or other business 
  
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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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organization or division thereof) that engages in a line of business related to the use of any of the Energy Rights (or at any time in the future proposes to engage in such line of business); or
(iii) a Codexis Entity proposes to acquire or obtain, directly or indirectly, by merger, consolidation, acquisition of equity interests or otherwise, or becomes entitled to, any assets, rights or other interests of whatever kind and nature in
any business or Third Party, in whole or partial consideration for the sale, assignment, license, contribution, pledge or other transfer by a Codexis Entity of any assets, interests or rights relating to any of the Energy Rights, then Codexis shall
give written notice to MUS at least thirty (30) days prior to the effectiveness or consummation of such event or transaction. The notice shall describe in reasonable detail the proposed event or transaction including, without limitation, the
nature of such event or transaction, the consideration to be paid and the amount constituting the applicable MUS Interest (as defined in Section 5.10(b) below). 
 (b) In consideration for the rights granted to Codexis in this Amendment No. 3, Codexis shall take, or cause to be
taken, all actions, and do, or cause to be done, all things necessary, proper and advisable under applicable laws, so as to assign, transfer and deliver the MUS Interest to MUS immediately upon the effectiveness or consummation of any event or
transaction described in Section 5.10(a) above or cause the MUS Interest to be so assigned, transferred and delivered, without cost to MUS. For purposes of this Section 5.10, the term “MUS Interest” shall mean all legal
and beneficial title to the equity interests, assets, rights or other interests of whatever kind and nature (other than consideration received by Codexis subject to Codexis’ payment obligations to MUS pursuant to Section 5.2.1 above) of
the Energy Affiliate or Third Party in an amount equal to twenty percent (20%) of each asset, interest or right held, acquired or obtained by the Codexis Entity(ies) in connection with any event, transaction or series of transactions described
in Section 5.10(a) above. 
 (c) If, in connection with the transaction or series of transactions described
in Section 5.10(a), a Codexis Entity has provided consideration other than assets, interests or rights relating to the use of any of the Energy Rights (the “Other Consideration”), then, as a condition of the transfer to MUS of
the portion of the MUS Interest held, acquired or obtained by the Codexis Entity specifically for such Other Consideration, MUS shall reimburse the Codexis Entity for up to twenty percent (20%) of the cash value of the Other Consideration (as
of the date of transfer of the Other Consideration by the Codexis Entity). The election to reimburse the Codexis Entity and the amount of such reimbursement (up to the aforementioned 20% limit) shall be determined by MUS in its sole discretion. Upon
reimbursement, the Codexis Entity shall transfer to MUS the applicable portion of the MUS Interest attributable to the amount reimbursed by MUS for the Other Consideration. If MUS elects to reimburse the Codexis Entity for a portion of the Other
Consideration corresponding to the MUS Interest equal to less than twenty percent (20%) of such Other Consideration, and not for the total twenty percent (20%), MUS’ right to receive additional equity interests, assets, rights or other
interests of whatever kind and nature of the applicable Energy Affiliate or Third Party pursuant to Section 5.10(b) that are directly attributable to the equity 
  
 [*] 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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interests, assets, rights or other interests held, acquired or obtained for such Other Consideration will be prorated accordingly. For example, if MUS elects to reimburse the Codexis Entity for
ten percent (10%) of the Other Consideration corresponding to the MUS Interest (and not twenty percent (20%)), MUS’ right to receive additional equity interests, assets, rights or other interests of whatever kind and nature of the
applicable Energy Affiliate or Third Party pursuant to Section 5.10(b) that are directly attributable to the equity interests, assets, rights or other interests held, acquired or obtained for such Other Consideration will be equal to one-half
of the amount that MUS would have received if MUS had reimbursed the Codexis Entity for twenty percent (20%) of the Other Consideration corresponding to the MUS Interest. If MUS elects not to pay any amount to the Codexis Entity for the
reimbursement of the Other Consideration, MUS’ right to receive additional equity interests, assets, rights or other interests of whatever kind and nature of the applicable Energy Affiliate or Third Party pursuant to Section 5.10(b) that
are directly attributable to the equity interests, assets, rights or other interests held, acquired or obtained for such Other Consideration shall terminate. Except as otherwise provided in this Section 5.10(c) with respect to an election by
MUS to reimburse the applicable Codexis Entity for Other Consideration, MUS shall, in all cases, be entitled to receive, and shall not be required to reimburse any Codexis Entity, Energy Affiliate or Third Party or otherwise pay any amounts to any
Codexis Entity, Energy Affiliate or Third Party for, the MUS Interest and any additional equity interests, assets, rights or other interests of the applicable Energy Affiliate or Third Party that are attributable to or received in consideration for
any of the Energy Rights (and not attributable to or received in consideration for Other Consideration). 
 (d)
If any Codexis Entity proposes to subsequently sell, assign, or otherwise transfer any assets, rights or interests acquired or obtained in connection with an event, transaction or series of transactions described in Section 5.10(a) above, then
Codexis shall give written notice to MUS at least thirty (30) days prior to the effectiveness or consummation of such transaction, which notice shall describe the proposed transaction in reasonable detail, including, without limitation, the
nature of such transaction and the consideration to be received. MUS shall have the right, exercisable upon written notice to Codexis within fifteen (15) days after receipt of such notice, to participate in such transaction and to sell, assign
or otherwise transfer up to a pro rata portion of the MUS Interest on the same terms and conditions as described in the notice; provided, however, that in no event shall MUS be required to sell, assign or transfer any portion of the MUS Interest to
any party, except as required by applicable law; provided, further, that MUS’ pro rata portion of the MUS Interest shall be deemed to be twenty percent (20%) of each asset, right or interest proposed to be sold, assigned or transferred by
the applicable Codexis Entity(ies). 
 (e) Notwithstanding the foregoing, if for any reason all or any portion of
the MUS Interest is not transferable to MUS in accordance with Section 5.10(b) above, or if the sale, assignment or other transfer by MUS of all or any portion of the MUS Interest in accordance with Section 5.10(d) above is not permitted,
then the applicable 
  
 [*] 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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Codexis Entity(ies) shall not consummate or effectuate, directly or indirectly, such event or transaction without the prior written consent of MUS in its sole discretion. 
 (f) In the event that (i) sufficient information does not exist to determine the value, amount or allocation of any
assets, rights or interests for purposes of calculating the applicable MUS Interest, the applicable Other Consideration or any other amount in accordance with this Section 5.10, or (ii) Codexis and MUS cannot otherwise agree as to such
value, amount or allocation, such value, amount or allocation shall be determined through an appraisal to be performed by an independent Third Party reasonably acceptable to both Parties, and the expenses incurred in obtaining such appraisal shall
be shared equally by Codexis and MUS. 
 (g) In furtherance of the foregoing, Codexis acknowledges that, in
consideration for the rights granted to Codexis in this Amendment No. 3, this Section 5.10 is intended to provide MUS with the applicable portion of any value or potential value attributable to or derived from any business related to
energy applications engaged in by any Codexis Entity or otherwise attributable to or derived from any of the Energy Rights and agrees that it shall not authorize, commit or agree to take, and shall not permit any Affiliate, nor any subsidiary, to
authorize, commit or agree to take, any action that would be inconsistent with this Section 5.10 or impair any portion of the MUS Interest. 
 5.11 MUS not an Affiliate. Notwithstanding anything to the contrary, for purposes of this Article 5, MUS shall not be considered, or deemed to be, an Affiliate of Codexis. 
  

	7.	Article 12 of the Agreement is amended by the addition of new Section 12.7: 

 12.7 Termination for Cause. In the event that Codexis materially breaches any of its obligations pursuant to Article 5 of the
Agreement, and such breach has continued for sixty (60) days after receipt of written notice thereof from MUS, MUS may terminate any and all rights received by Codexis under the terms of this Amendment No. 3. 
  

	8.	Exhibit F shall be revised such that Exhibit F shall read in its entirety as attached to this Amendment No. 3. 

  

	9.	Exhibit G shall be revised such that Exhibit G shall read in its entirety as attached to this Amendment No. 3. 

  

	10.	Except as expressly provided herein, the terms of the Agreement shall remain in full force and effect. 

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 [*] 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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 IN WITNESS WHEREOF, MUS and Codexis have executed this Amendment No. 3 to License
Agreement as of the first above written. 
  

									
	MAXYGEN, INC.	 		 	CODEXIS, INC.
					
	By: 	 	/s/ Russell J. Howard	 		 	By: 	 	/s/ Alan Shaw
					
	Name: 	 	Russell J. Howard	 		 	Name: 	 	Alan Shaw
					
	Title: 	 	Chief Executive Officer	 		 	Title: 	 	President

 EXHIBIT F 
 SCHEDULED PRODUCTS 
 (REVISED AUGUST __, 2006) 
  

	1.	Products for the extraction, modification, purification and/or transformation of oil and/or petroleum (including oil shale) with regard to the following applications:

 Crude Oil and Oil Shale Applications 
 enhancement of recovery of down-hole crude oil 
 metal removal 
 sulfur removal 
 viscosity and/or molecular weight modification 
 Refinery Applications (for crude oil and oil shale derivatives) 
 aromatic/ring-compound removal or addition 
 thiophene removal 
 conversion of glycerine to glycerine derivatives 
 creation of cyclo-paraffins for purposes of improving octane number 
 enhanced
energy and combustion properties 
 improved emissions profile 
 metal removal 
 sulfur removal 
 viscosity and/or molecular weight modification 
  

	2.	Products for the following textile/paper manufacturing applications: 

 manufacture of dyes/pigments 
 manufacture of sizing agents 
 enhanced fiber bio-degradation 
 enhanced pulping 
  

	3.	Products for the following environmental clean-up applications: 

 soil/water bioremediation (e.g., hydrocarbons/chlorocarbon contamination) 
 sulfur/CO2 sequestration 
 radioisotope contamination 
 nuclear waste processing 
 treatment (i.e., degradation) of effluent waste products from wood product/paper processing 
 treatment (i.e.,
degradation) of effluent waste products from grain/oil seed processing 
  
 [*] 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 G 
 RESERVED SUBFIELDS 
 (REVISED AUGUST __, 2006) 
  

	1.	SubField 1: Manufacture of the [*] monomers specified below, for use to make polymers (excluding polymers for use for [*] and/or [*] applications):

 Categories 

	 	a.	[*] 

	 	b.	carboxylic acids, as follows: amino carboxylic acids, hydroxy carboxylic acids, olefinic carboxylates and hydroxy acids 

	 	c.	[*] 

	 	d.	[*] 

	 	e.	[*] 

  

	2.	SubField 2: Manufacture of the [*] agents specified below (excluding agents for use for [*] and/or [*] applications): 

 Categories 

	 	a.	[*] 

	 	b.	[*] 

	 	c.	[*] 

	 	d.	[*] 

  

	3.	SubField 3: Manufacture of the [*] (and intermediates thereof) specified below: 

 Categories 

	 	a.	production of [*] for use as a [*] 

  

	4.	SubField 4: [*], as specified below: 

 Categories 

	 	a.	[*] 

	 	b.	[*] 

	 	c.	[*] 

  

	5.	SubField 5: Manufacture of the following [*], to the extent not covered by SubField 1: 

 Categories 

	 	a.	[*] 

	 	b.	[*] 

	 	c.	[*] 

	 	d.	[*] 

	 	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. 

	6.	SubField 6: Manufacture of polymers made from the monomers specified below, for use as [*] (excluding any use in, on or for [*] or any other [*] applications):

 Categories 

	 	a.	[*] 

	 	b.	[*] 

	 	c.	[*] 

	 	d.	[*] 

	 	e.	[*] 

	 	f.	[*] 

  

	7.	SubField 7: Manufacture of the [*] specified below for [*] (excluding any use in, on or for [*] or any other [*] and/or [*] applications):

 Categories 

	 	a.	[*] 

	 	b.	[*] 

	 	c.	[*] 

	 	d.	[*] 

	 	e.	[*] 

  

	8.	SubField 8: Manufacture of fuels and fuel additives (and intermediates thereof) as specified below: 

  

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

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

 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. 
 “Biomass” shall mean [*]. 
 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 
  
 [*] 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. 

 
(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.

  

	9.	SubField 9: Manufacture of Products for the [*] for the following specific applications: 

  

	 	a.	[*] 

	 	b.	[*] 

	 	c.	[*] 

	 	d.	[*] 

	 	e.	[*] 

	 	f.	[*] 

  

	10.	SubField 10: Manufacture of Products for the [*], for the following specific applications: 

  

	 	a.	[*] 

	 	b.	[*] 

	 	c.	[*] 

	 	d.	[*] 

	 	e.	[*] 

	 	f.	[*] 

  
 [*] 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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