Document:

Amendment No. 1 to License Agreement

 EXHIBIT 10.4 
 [*] 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 NO. 1 TO LICENSE AGREEMENT 
 This Amendment No. 1 (“Amendment No. 1”) amends that certain License Agreement effective March 28, 2002 (the “Agreement”) entered by and between Maxygen, Inc. (“MUS”) and Codexis, Inc.
(“Codexis”), and shall be effective as of September 13, 2002 (the “Amendment Date”). MUS and Codexis hereby amend the License Agreement as follows: 
 1. Article 1 is amended by the addition of the following new definitions: 
 1.54 “Category” shall mean each of the identified categories listed on Exhibit G. 
 1.55
“Reserved SubField Termination Date” shall mean the period commencing on the Amendment Date and ending on the later of (i) five (5) years after the Amendment Date, or (ii) a Separation Event. 
 1.56 “Reserved SubFields” shall mean, in the period from the Amendment Date until the Reserved SubField Termination Date, the subject
matter within the SubFields. It is understood and agreed that (i) as of the Reserved SubField Termination Date, one or more of the SubFields may become part of the Codexis Field pursuant to Section 2.1.6(d), and (ii) as of the
Reserved SubField Termination Date, the 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. 
 1.57 “Scheduled Product” shall mean any chemical described on Exhibit F. 
 1.58 “SubField” shall mean each of the identified SubFields listed on Exhibit G. 
 1.59 “Supplemental Product” shall mean (a) any chemical within a Category with regard to which Category Codexis conducts a research
project meeting the criteria set forth in Section 2.1.6(a) prior to the Reserved SubField Termination Date and (b) each chemical that is within a SubField that becomes part of the Codexis Field as of the Reserved SubField Termination Date
pursuant to Section 2.1.6(d). 
 2. Section 1.10 is amended to provide in its entirety, as follows: 
 1.10 “Bulk Production” shall mean production by Codexis via enzymatic catalysis (using an Enzyme Product or a Biocatalyst) or
fermentation of: 
 (a) any Enzyme Product or Biocatalyst for sale to a Third Party (other than an Affiliate of Codexis) for manufacture of
Catalysis Products, or 
 (b) any Catalysis Product or Fermentation Product for sale to a Third Party (other than an Affiliate of Codexis)
for further processing or formulation, or 

 (c) any Catalysis Product or Fermentation Product that will be formulated by Codexis for sale to a Third
Party, which Product contains one or more Functional Compounds approved by a Regulatory Authority for human or veterinary pharmaceutical use, where such Functional Compound(s) (i) is (are) no longer covered by issued patents in the country
where such production will occur, or (ii) is (are) covered by issued patents owned or Controlled by a Third Party (other than an Affiliate of Codexis) that has contracted to have Codexis formulate such Product on behalf of such Third Party, or

 (d) any Scheduled Product for sale to a Third Party (other than an Affiliate of Codexis) for further processing or formulation, or

 (e) any Supplemental Product for sale to a Third Party (other than an Affiliate of Codexis) for further processing or formulation.

 3. Section 1.12 is amended to provide in its entirety, as follows: 
 1.12 “Codexis Field” shall mean: 
 (a) Biocatalyst Commercialization and Enzyme Commercialization, subject to the limitations set forth in Section 2.2.2 and the rights of MUS and Third Parties described in Section 2.8; 
 (b) Building Block Development; 
 (c) Bulk
Production of Products (except Supplemental Products), subject to the limitations set forth in Section 2.2.2 and the rights of MUS and Third Parties described in Section 2.8; 
 (d) Bulk Production of Supplemental Products to which Codexis has acquired rights pursuant to Sections 2.1.6(c) or (d), subject to the limitations set
forth in Section 2.2.2 and the rights of MUS and Third Parties described in Section 2.8. 
 4. Section 1.17 is amended to
provide in its entirety, as follows: 
 1.17 “Enabling Technology” shall mean all Patent Applications and Patents Controlled
by MUS that claim (i) methods of generating genetic diversity (including, without limitation, DNA Shuffling with tangible materials or in silico), or the use thereof, and/or (ii) generally applicable screening techniques,
methodologies or processes for identifying genetic variants of interest that: (a) are filed on or before the Separation Event, or (b) claim inventions conceived and reduced to practice or otherwise developed on or before the Separation
Event, which Patent Application or Patent is filed on or before the third anniversary of the Separation Event. Enabling Technology shall include MUS’ interest in Third Party Improvements, if any. A list of Patent Applications and Patents within
the Enabling Technology existing as of the Effective Date is attached as Exhibit B hereto 
  

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 5. Section 1.40 is amended to provide in its entirety, as follows: 
 1.40 “Product” shall mean any Catalysis Product, Enzyme Product, Scheduled Product, Supplemental Product, Biocatalyst or Fermentation
Product that: 
 (a) is made or developed with the use of Enabling Technology, whether by Gene Expression Manipulation and/or Metabolic
Pathway Manipulation and/or Strain Improvement or otherwise (e.g., incorporates any variant gene made with Enabling Technology, and/or any protein or peptide expressed therefrom), and/or 
 (b) is developed with the use of Product Technology, or incorporates, or is made using, or is substantially derived from, Product Technology.

 6. Section 1.41 is amended to provide in its entirety, as follows: 
 1.41 “Product Technology” shall mean the Patent Applications and Patents Controlled by MUS on or before the Separation Event that are
necessary or useful for use in the Codexis Field, that are not included in Enabling Technology or the Assigned Patents. A list of the Patent Applications and Patents within the Product Technology existing as of the Effective Date is attached as
Exhibit D hereto. 
 7. Section 2.1.1 is amended to read in its entirety as follows: 
 2.1.1 Licenses. Subject to the terms and conditions herein, including without limitation Sections 2.2, 2.4, 2.6, 2.7 and 2.8, MUS hereby grants to
Codexis, and Codexis hereby accepts, irrevocable (except as provided in Sections 9.4.1, 12.2, 12.3 and 12.4), worldwide, royalty-free (subject to Section 2.1.5(b)) licenses, as follows: 
 (a) with respect to the Enabling Technology and related Know-How: 
 (i) an exclusive license in Microbes to develop, make, have made, use, import, have imported, offer for sale, sell or otherwise commercialize or distribute Products (including those Supplemental Products that Codexis
has acquired rights to pursuant to Section 2.1.6 (c), but excluding, until the Reserved SubField Termination Date, other Supplemental Products) and corresponding Services in the Codexis Field; and 
 (ii) a non-exclusive license in Category II Plants to develop, make, have made, use, import, have imported, offer for sale, sell or otherwise
commercialize or distribute Products (including those Supplemental Products that Codexis has acquired rights to pursuant to Section 2.1.6 (c), but excluding, until the Reserved SubField Termination Date, other Supplemental Products) and
corresponding Services in the Codexis Field; and 
 (b) subject to the terms of Section 2.1.6(a), with respect to the Enabling
Technology and related Know-How, in the period from the Amendment Date until the Reserved SubField Termination Date: 
 (i) an exclusive
license in Microbes to develop, make, have made, use, import, have imported, offer for sale, sell or otherwise commercialize or distribute Supplemental Products and corresponding Services; and 
  

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 (ii) a non-exclusive license in Category II Plants to develop, make, have made, use, import, have
imported, offer for sale, sell or otherwise commercialize or distribute Supplemental Products and corresponding Services; and 
 (c) with
respect to the Enabling Technology and related Know-How, a non-exclusive license to develop, make and use Expression Hosts for Internal Research Use; and 
 (d) with respect to the Product Technology and related Know-How: 
 (i) an exclusive license in Microbes to
develop, make, have made, use, import, have imported, offer for sale, sell or otherwise commercialize or distribute Products (including those Supplemental Products that Codexis has acquired rights to pursuant to Section 2.1.6 (c), but
excluding, until the Reserved SubField Termination Date, other Supplemental Products) and corresponding Services in the Codexis Field; and 
 (ii) a non-exclusive license in Category II Plants to develop, make, have made, use, import, have imported, offer for sale, sell or otherwise commercialize or distribute Products (including those Supplemental Products that Codexis has
acquired rights to pursuant to Section 2.1.6 (c), but excluding, until the Reserved SubField Termination Date, other Supplemental Products) and corresponding Services in the Codexis Field; and 
 (e) subject to the terms of Section 2.1.6(a), with respect to the Product Technology and related Know-How, in the period from the Amendment Date
until the Reserved SubField Termination Date: 
 (i) an exclusive license in Microbes to develop, make, have made, use, import, have
imported, offer for sale, sell or otherwise commercialize or distribute Supplemental Products and corresponding Services; and 
 (ii) a
non-exclusive license in Category II Plants to develop, make, have made, use, import, have imported, offer for sale, sell or otherwise commercialize or distribute Supplemental Products and corresponding Services. 
 8 Article 2.1 is revised by the addition of new Sections 2.1.6 and 2.1.7: 
 2.1.6 Reserved SubField. With regard to the Reserved SubFields set forth on Exhibit G: 
 (a) Until
the Reserved SubField Termination Date, Codexis may practice licenses as described in Sections 2.1.1(b) and (e), on a Category-by-Category basis, if for such Category Codexis: 
 (i) enters into a written contract (including anv government grant) with a Third Party that will provide Codexis with at least [*] over a continuous
period of [*] months or less from such Third Party to (a) conduct research using the Enabling Technology in the applicable Category, or (b) develop for commercial uses Products subject to Section 1.40(a) in the applicable Category; or

  

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 (ii) expends its own funds in an amount of at least [*] over a continuous period of [*] months or less,
to (a) conduct research using Enabling Technology in the applicable Category, or (b) develop for commercial uses Products subject to Section 1.40(a) in the applicable Category; or 
 (iii) expends its own funds and funds from a Third Party collaborator, which funds total at least [*] over a continuous period of [*] months or less, to
conduct (a) research using Enabling Technology in the applicable Category, or (b) develop for commercial uses one or more Products in the applicable Category. 
 The Codexis Board of Directors (with appropriate recusals for interested party transactions) must approve the transactions and/or Codexis expenditures described in this Section 2.1.6(a). 
 (b) Commencing on the first anniversary of the Amendment Date and annually thereafter on the
anniversary of the Amendment Date until the Reserved SubField Termination Date, and at Codexis’ option, at other times, Codexis shall provide
MUS with a written report (i) identifying all Supplemental Products and Categories with regard to which Codexis has conducted research subject to Section 2.1.6(a) above, and (ii) reporting, by Category, the amount of funds expended by
Codexis to conduct research in each such Category in the preceding twelve (12) month period. 
 (c) If Codexis has conducted activities
subject to Section 2.1.6(a) as to a particular Category, Codexis shall notify MUS in writing (the “Category Notice”) providing a detailed explanation of why it believes the Section 2.1.6(a) criteria have been fulfilled with
regard to the applicable Category. Within thirty (30) days following the date of such Category Notice, senior business representatives of MUS and Codexis shall jointly prepare and sign a written summary (the “Category Summary”)
identifying the Category and corresponding Supplemental Product(s) subject to Section 1.59(a). All Supplemental Products in such agreed Category Summary shall be included in the Codexis Field (subject to the applicable SubField exclusions set
forth on Exhibit G) for all purposes of this Agreement, as of the date of the applicable agreed Category Summary. Any dispute regarding the subject matter that will be added to the Codexis Field pursuant to this Section 2.1.6(c) shall be
resolved as set forth in Article 13. 
 (d) If Codexis has conducted activities that meet the criteria set forth in Section 2.1.6(a)
above with regard to at least one-half of the Categories of any SubField, then, from and after the date of such occurrence (the “Subfield Inclusion Date”), such entire SubField (including all its Categories) shall, subject to the
applicable SubField exclusions set forth on Exhibit G, thereafter be included in the Codexis Field for all purposes of this Agreement. Within thirty (30) days following the SubField Inclusion Date, senior business representatives of MUS 

  

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and Codexis shall jointly prepare a written summary identifying (i) those Supplemental Product(s) subject to Section 1.59(a) within Categories that
have not become part of the Codexis Field, and (ii) those Categories and SubFields have become included in the Codexis Field. Any dispute regarding the subject matter that will be added to the Codexis Field shall be resolved as set forth in
Article 13. 
 (e) After the Reserved SubField Termination Date, Codexis shall retain the right to complete research regarding a particular
Supplemental Product that it commenced prior to such date pursuant to Section 2.1.6(a) if it has expended at least [*] on such research with respect to such Supplemental Product by the Reserved SubField Termination Date, and to commercialize
Supplemental Products resulting from such activities, but otherwise Codexis shall not have any other rights with regard to any Category(ies) or SubField(s) that are not within the Codexis Field after the Reserved SubField Termination Date.

 (f) Until the date that Codexis acquires license rights under this Agreement to a particular Supplemental Product pursuant to Sections
2.1.6 (c) or (d), Codexis may not grant any Third Party (i) a sublicense to the Enabling Technology for the development or manufacture of any Supplemental Product, or (ii) an option to (1) obtain a sublicense to the Enabling
Technology for use with regard to the development or manufacture of any Supplemental Product, or (2) use the Enabling Technology to develop or manufacture any Supplemental Product. It is understood and agreed that Codexis may grant such
sublicenses and options to Supplemental Products which have become included in the Codexis Field pursuant to Section 2.1.6(c) above as a result of Codexis having satisfied the conditions of 2.1.6(a). 
 (g) Until the Reserved SubField Termination Date, MUS will not (i) itself use the Enabling Technology to develop or manufacture any Supplemental
Product, or (ii) grant a Third Party a license to use the Enabling Technology to develop or manufacture any Supplemental Product. 
 (h) It is understood and agreed that as of the Reserved SubField Termination Date, the 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. 
 2.1.7 Rights to Negotiate for Rights Outside the Codexis Field. 
 (a) Codexis Proposal. If Codexis wishes to use the Enabling Technology outside the then-current scope of the Codexis Field to make a particular
commodity chemical or fine chemical, then Codexis shall have a right of negotiation to obtain from MUS a license to use the Enabling Technology to make such specific products via processes proposed by Codexis. In any such event, Codexis shall notify
MUS in writing of the particular processes and specific commodity chemical(s) or fine chemical(s). If Codexis notifies MUS that Codexis wishes to negotiate for an expanded license to the Enabling Technology as described in this
Section 2.1.7(a), Codexis and MUS shall for a period of one hundred twenty (120) days from Codexis’ notice, or such longer period as the parties may agree in writing, negotiate terms and conditions for such license rights. 

 

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 (b) MUS Notice. If MUS wishes to use or license a Third Party to use the Enabling Technology to
make a particular commodity chemical or fine chemical for industrial manufacturing applications outside the then-current scope of the Codexis Field, then until the Separation Event, MUS shall notify Codexis, and Codexis shall have a first right of
negotiation to obtain from MUS a license to use the Enabling Technology to make such specific products. In any such event, MUS shall notify Codexis in writing of the particular processes and specific commodity chemical(s) or fine chemical(s),
subject to any obligations of confidentiality owed to a Third Party. If Codexis notifies MUS in writing within thirty (30) days of notice by MUS pursuant to this Section 2.1.7(b) that Codexis wishes to negotiate for an expanded license to
the Enabling Technology for the applicable processes and products, then for a period of one hundred twenty (120) days from MUS’ notice, or such longer period as the parties may agree in writing, MUS and Codexis shall negotiate terms and
conditions for such license rights. For the avoidance of doubt, it is understood and agreed that this Section 2.1.7(b) shall apply only to proposed uses of Enabling Technology for manufacturing of commodity chemicals or fine chemicals for
industrial applications, and shall not apply to any other application outside the Codexis Field, including, without limitation, to any proposed use for discovery, research, development or manufacturing of pharmaceuticals, vaccines or Agrochemicals
and/or for any application relating to agriculture, e.g., processing of food or feed. 
 (c) Agreement on Terms. If the Parties agree
upon mutually acceptable terms and conditions pursuant to Section 2.1.7(a) or Section 2.1.7(b), the Parties shall enter into a written amendment to this Agreement modifying the license granted to Codexis as appropriate to include the
relevant rights and applicable chemicals. Neither Party shall be obligated to accept or agree to such terms or conditions, or to enter into any agreement regarding such expanded license rights. If MUS and Codexis do not agree upon mutually
acceptable terms and conditions within the applicable time period above, Codexis shall have no right or license to use the Enabling Technology outside the then-existing Codexis Field. 
 9. Section 2.2.2(b)(i) is deleted, such that Section 2.2.2(b) provides in its entirety, as follows: 
 (b) to make, have made, use, promote, market, distribute and/or sell any products (including, without limitation, any Products) intended for use in the
Detection and Research Reagent Field; or 
 10. Section 2.2.2(c) is revised by the insertion of the word “itself’ before the
word “develop”. 
 11. Revise Sections 2.2.2(f)(ii) and 2.2.2(h) by changing each occurrence of “discovery” to
“Discovery”, and revise Section 2.8.5 by changing “discover” to “conduct Discovery of”. 
 12.
Section 2.3 is amended to read in its entirety as follows: 
 2.3 Right to Sublicense. Codexis (or its successor) may grant
sublicenses to the Enabling Technology, Product Technology and related Know-How to such Third Parties as it 

  

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deems appropriate, but such sublicenses may only grant rights to practice in the Codexis Field; provided, Codexis may not (i) sublicense the rights
granted in Section 2.1.1(c) except in connection with a grant of a sublicense of the rights granted it in Section 2.1.1(a), or (ii) sublicense the rights granted it in Section 2.1.1(b) or 2.1.1(e). Codexis (or its successor) may
grant licenses to the Assigned Patents as it deems appropriate. 
 13. Section 2.7.1 is amended to provide in its entirety as follows:

 2.7.1 MUS. Notwithstanding the license grants in Section 2.1, the Parties agree that: 
 (a) MUS and its wholly-owned Affiliates shall, until the Separation Event, retain the right to conduct research with the Enabling Technology and related
Know-How in the Codexis Field and/or the Reserved SubFields for the purpose of (i) improving and expanding Enabling Technology, and/or (ii) exploring applications of the Enabling Technology for areas outside the Codexis Field and/or the
Reserved SubFields; provided, MUS and its wholly-owned Affiliates shall not use the Enabling Technology for the primary intended purpose of developing any Products or Services for use in the Codexis Field and/or the Reserved SubFields, on its own
behalf or on behalf of any Third Party. 
 (b) At all times during and after this Agreement, nothing herein shall restrict, or be construed
to restrict, MUS’ right to practice and grant licenses to practice the Enabling Technology and Product Technology and/or use related Know-How, outside the Codexis Field and/or the Reserved SubFields. 
 (c) It is understood and agreed that, at all times, MUS shall retain (i) the right (sublicensable to its Affiliates) to internally use the Enabling
Technology, Product Technology and related Know-How to conduct Discovery and development of pharmaceutical and/or Agrochemical products by any means (which may include, without limitation, the development of Building Blocks, the addition of Building
Blocks to Templates and/or analoging of Functional Compounds), and to conduct commercialization of such products; and (ii) the sublicensable right to make and/or have made, use, import, have imported, offer for sale and/or sell any such
products. 
 14. Section 2.7.2 is revised to provide in its entirety as follows: 
 2.7.2 Codexis. Except as expressly set forth in this Agreement, nothing herein shall limit the ability of Codexis to use any intellectual property,
tangible property or technology not subject to this Agreement, whether the foregoing is developed by it or acquired by it (by license, acquisition or otherwise) for any purpose, in or outside the Codexis Field. 
 15. Section 3.2 is amended to provide in its entirety, as follows: 
 3.2 License to MUS. In partial consideration for the rights granted herein. Codexis shall grant and hereby grants, and MUS hereby accepts, the following licenses: 
 (a) with respect to Patent Applications and Patents within the scope of Section 1.4(a), an exclusive, worldwide, royalty-free, irrevocable license,
with the right to grant and authorize sublicenses; and 
  

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 (b) with respect to Patent Applications and Patents within the scope of Section 1.4(b), subject to
the terms of the applicable Third Party Agreement as described in Section 3.3.1, an exclusive (to the extent permitted by the applicable Third Party Agreement), worldwide (to the extent permitted by the applicable Third Party Agreement),
royalty-free (subject to Section 3.3.2), irrevocable (to the extent permitted by the applicable Third Party Agreement) license, with the right to grant and authorize sublicenses. 
 in each case, to develop, make, have made, use, import, have imported, offer for sale, sell or otherwise commercialize or distribute Products and
Services solely outside the Codexis Field, and until the Reserved Termination Date, the Reserved SubFields. 
 16. Article 4 is amended to
read in its entirety as follows: 
 4. COVENANTS 
 4.1 Use Within the Codexis Field. Codexis covenants that it will not knowingly practice its licenses to the Enabling Technology and related Know-How, or its licenses to the Product Technology and related
Know-How, for the purpose of developing or commercializing Products or Services for use outside the Codexis Field and/or the Reserved SubField. Codexis further covenants that it will not knowingly make or permit any of its Sublicensees or
contractors to knowingly make any release into the environment of any Microbe or any Plant which has been modified with the use of Enabling Technology (e.g., outside a container or containment vessel which precludes exit of any such Microbes or
Plants from such container or vessel), without the prior written consent of MUS. 
 4.2 Use Outside the Codexis Field. MUS covenants
that it will not knowingly use its retained rights with regard to the Enabling Technology or the Product Technology, or knowingly practice its license to Codexis Improvements (if any), for the purpose of developing or commercializing Products or
Services for use in the Codexis Field and/or the Reserved SubField; provided that such covenants shall be subject to Section 2.7.1 and further provided that such covenants shall terminate with regard to any Patent Applications and/or Patents
for which Codexis’ license terminates pursuant to Sections 9.2.3(b), 12.2, 12.3 and/or 12.4 below. 
 17. Section 9.2.1 is amended
to provide in its entirety, as follows: 
 9.2.1 Patent Prosecution. 
 (a) With regard to Patent Applications and Patents within the Product Technology owned by a Third Party, such Third Party shall have the sole right and
discretion to conduct Patent Prosecution of such Patent Applications and Patents. 
  

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 (b) With regard to Patent Applications and Patents within the Product Technology owned by MUS, MUS shall
have the initial right, but not the obligation, to conduct Patent Prosecution of such Patent Applications and Patents, unless such Patent Applications and Patents claim only methods and/or compositions that have substantial, commercially valuable
applications solely within the Codexis Field and/or the Reserved SubFields, in which case Codexis shall have the right, but not the obligation, to conduct Patent Prosecution of such Patent Applications and Patents. 
 18. Section 9.2.2 is amended to provide in its entirety, as follows: 
 9.2.2 Sharing of Prosecution Costs. Codexis shall be responsible for Prosecution Costs in connection with Patent Prosecution activities described in Section 9.2.1, as follows: 
 (a) With regard to Patent Applications and Patents within the Product Technology owned by a Third Party, the Third Party and Codexis shall agree on the
amounts to be paid by Codexis to the Third Party with regard to the Patent Prosecution of such Patent Application and/or Patent. Unless otherwise agreed in writing, Codexis agrees it shall pay a pro rata share of such Prosecution Costs based on the
following formula: Codexis’ percentage share of such Prosecution Costs = 100 (1/1+X), where X equals the number of sublicenses granted by MUS with regard to the applicable Patent Application and/or Patent. 
 (b) With regard to any Patent Applications and Patents within the Product Technology that are owned by MUS, if MUS conducts the Patent Prosecution
activities described in Section 9.2.1(b), Codexis shall pay to MUS a pro rata share of such Prosecution Costs based on the number of sublicenses granted by MUS with regard to the applicable Patent Application and/or Patent. 
 (c) With regard to any Patent Applications and Patents within the Product Technology that are owned by MUS, if Codexis conducts the Patent Prosecution
activities described in Section 9.2.1(b), Codexis shall pay one hundred percent (100%) of the Prosecution Costs incurred after the Effective Date in connection with such activities. 
 (d) Any amounts for Prosecution Costs subject to this Section 9.2.2 for which Codexis is responsible will be paid by Codexis to the applicable
Third Party (or its designee) or to MUS (or its designee), as applicable, within forty-five (45) days of an invoice therefor. 
 19.
Section 9.2 is amended by the addition of new Section 9.2.5: 
 9.2.5 Opt Out. Notwithstanding Sections 9.2.1 through 9.2.4
above, if Codexis does not wish to retain rights to any Patent Application or Patent within the Product Technology, Codexis may, with sixty (60) days written notice to MUS, relinquish its license rights to such Patent Application and Patent. In
such event, Codexis shall have no further license rights under this Agreement with regard to the applicable Patent Applications and/or Patents, (i) shall not be entitled to participate in further Patent Prosecution as described in
Section 9.2.2 with respect 

  

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thereto, and/or further consultation and/or information rights as described in Section 9.2.4, with regard to such Patent Applications and/or Patents,
(ii) shall have no obligation to pay Prosecution Costs incurred after the effective date of termination with respect to the applicable Patent Application and/or Patent; (iii) shall have no further enforcement rights described in
Section 10.3 with respect to such Patent Application and/or Patent. Codexis shall remain obligated to pay its share of any Patent Prosecution expenses incurred prior to the applicable effective date of termination. 
 20. Section 10.3 is amended to provide in its entirety, as follows: 
 10.3 Product Technology. 
 10.3.1 Infringement in the Codexis Field. 
 (a) With regard to any Patent within the Product Technology that is owned by a Third Party, such Third Party shall have the first right, but not the
obligation to enforce such Patent within the Product Technology against any infringements by Third Parties in the Codexis Field and/or the Reserved SubFields and defend any declaratory judgment action. 
 (b) With regard to any Patent within the Product Technology that is owned by MUS: 
 (i) So long as Codexis retains an exclusive license to the applicable Patent within the Product Technology and such Patent has applications only in the
Codexis Field, Codexis shall have the first right, but not the obligation, to enforce Patents within the Product Technology against any infringements by Third Parties in the Codexis Field and defend any declaratory judgment action. If Codexis fails
to initiate a suit to enforce such patent in any jurisdiction against a commercially significant infringement in the Codexis within one (1) year of a request by MUS to do so, MUS may initiate suit against such infringement, at its expense. In
such event, Codexis agrees to join in such action, if required by applicable law. 
 (ii) If Codexis does not have an exclusive license to
the applicable Patent and/or if such Patent claims inventions having one or more applications outside the Codexis Field, then MUS shall have the first right, but not the obligation, to enforce such Patent against any infringements by Third Parties
in the Codexis Field and defend any declaratory judgment action with respect thereto. If MUS fails to initiate a suit to enforce such Patent in any jurisdiction against a commercially significant infringement in the MUS Field within one
(1) year of a request by Codexis to do so, Codexis may initiate suit against such infringement, at its expense. In such event, MUS agrees to join in such action, if required by applicable law. 
 (c) Notwithstanding Section 10.3.1(b) above, Codexis acknowledges that (i) certain patents within the Product Technology are and will be owned
by Third Parties and, that in some cases, such Third Parties may have retained or may retain the first right, or the sole right to enforce such patents, and (ii) prior to the Effective Date, MUS has granted to Third Parties rights to conduct or
participate in the enforcement and/or defense of certain Patent Applications and/or Patents within the Product Technology that are owned by MUS. 
  

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 10.3.2 Infringement Outside the Codexis Field. 
 (a) With regard to any Patent within the Product Technology that is owned by a Third Party, such Third Party shall have the first right, but not the
obligation, at its sole expense, to enforce such Patents against any infringements by Third Parties outside the Codexis Field and/or the Reserved SubFields and defend any declaratory judgment action relating thereto. 
 (b) With regard to any Patent within the Product Technology that is owned by MUS, MUS (or its designee) shall have the right, but not the obligation, to
pursue infringement of such Patents outside the Codexis Field and the Reserved SubFields, but shall consult with Codexis before commencing any such suit. 
 10.3.3 Recoveries. Any recovery received by a Party hereto as a result of any claim, suit or proceeding brought pursuant to this Section 10.3 shall be used first to reimburse the Party(ies), and any
involved Third Party, for all expenses (including attorneys and professional fees) incurred in connection with such claim, suit or proceeding. Any amounts recovered by a Third Party in a claim, suit or proceeding pursued solely by such Third Party
may be retained by such Third Party. With regard to any other recovery, after reimbursement as described in the preceding sentence, the remainder shall be divided as follows: (a) in any suit relating primarily to infringement in the Codexis
Field and/or the Reserved SubFields, seventy percent (70%) to the Party initiating the suit, and thirty percent (30%) to the other Party, and (b) in any suit primarily relating to infringement outside the Codexis Field and/or the
Reserved SubFields, as MUS determines or as may be agreed by the Parties in writing. 
 21. Section 10.7.3 is revised to read in its
entirety, as follows: 
 10.7.3 Codexis Responsibility. If any claim, suit or proceeding subject to this Section 10.7 is based on
allegations relating to the conduct or activities of Codexis and/or its Sublicensees, unless such claim, suit or proceeding is based solely on an allegation that the practice of the Enabling Technology infringed a patent owned by a Third Party, then
Codexis shall have the right and responsibility to conduct the defense of such action, and shall pay the costs of defense of any such action. 
 22. Revise Sections 1.31 such that the phrase “within the Codexis Field’ shall be amended to read “within the Codexis Field, and until the Reserved SubField Termination Date, the Reserved SubFields”. 
 23. Revise Sections 1.32, 1.33, 1.41, 1.53, 2.2.1 and 7.1.3 by adding the phrase “and/or the Reserved SubFields” after each occurrence of the
phrase “in the Codexis Field”. 
  

 [*] 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 

 24. Revise Sections 2.2.2(f), 2.2.3, 2.5, 2.7.2, 2.8.2, 4.1, 8.1 and 9.2.1 by adding the phrase
“and/or the Reserved SubFields” after each occurrence of the phrase “outside the Codexis Field”. 
 25. Exhibits F and G
attached to this Amendment No. 1 shall become exhibits to the Agreement. 
 26. Except as expressly provided herein, the terms of the
Agreement shall remain in full force and effect. 
 [THE REMAINDER OF THIS PAGE HAS BEEN INTENTIONALLY LEFT BLANK] 
  

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

 13 

 IN WITNESS WHEREOF, MUS and Codexis have executed this Amendment No. 1 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 
  

	1.	Products for the following petrochemical applications: 

 Crude Oil Applications 
 enhancement of recovery of down-hole crude 
 reduction of metals or sulfur in crude oil & derivatives 
 reduction of viscosity in crude oil & derivatives 
 Refinery Applications (for crude oil
derivatives) 
 aromatic/ring-compound removal 
 sulfur removal 
 viscosity modification 
 bio-thepene removal from fuels 
 conversion
of glycerine to glycerine derivatives 
  

	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 
 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 fuels and fuel additives specified below: 
 Categories 

			
	 (a)
	  	C7-C20 hydroxyalkanes and/or biomass (cellulose) conversion into ethanol
	 (b)
	  	bioester fuel oxygenates and/or additives to increase biodegradability of hydrocarbon fuels
	 (c)
	  	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)
	  	[*]

  

 [*] 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. 

			
	 (c)
	  	[*]
	 (d)
	  	[*]
	 (e)
	  	[*]

 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 [*] and/or [*] applications): 
 Categories 

			
	 (a)
	  	[*]
	 (b)
	  	[*]
	 (c)
	  	[*]
	 (d)
	  	[*]
	 (e)
	  	[*]
	 (f)
	  	[*]

 7 SubField 7: Manufacture of the [*] specified below for [*] uses (excluding any use in, on
or for [*] or any other [*] and/or [*] applications): 
 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.Amendment No. 3 to License Agreement

 EXHIBIT 10.6 
 [*] 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 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	 	=	  	        (1 - A/B) x 100
	particular “bundle”	 		  	

 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, 

  

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

 2 

 
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 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. 
 5.2 Energy Products. In consideration for the rights granted to Codexis in this 

  

 [*] 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 

 
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 [*] 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 [*]; 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 [*] 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 [*] 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. 
 5.2.3 If Codexis directly commercializes any Energy Product, Codexis will pay to MUS a royalty of [*] 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. 
  

 [*] 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 

 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. 
 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.

  

 [*] 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 

 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 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 

  

 [*] 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 

 
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 [*] 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 [*] 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 [*] 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 [*] of such Other Consideration, and not for the total [*], 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 prorated accordingly. For example, if MUS elects to reimburse the Codexis Entity for [*] of the Other Consideration corresponding to the MUS Interest (and not [*]), 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 [*] of the amount that MUS would have received if MUS 

  

 [*] 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 

 
had reimbursed the Codexis Entity for [*] 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 [*] 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 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. 
  

 [*] 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 

 (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. 

 [THE REMAINDER OF THIS PAGE HAS BEEN INTENTIONALLY LEFT BLANK] 
  

 [*] 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 

 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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