Exhibit 10.1

EXCLUSIVE NEGOTIATION AGREEMENT

THIS EXCLUSIVE NEGOTIATION AGREEMENT, together with exhibits and schedules
attached hereto, (the “Agreement”) is entered into and effective as of July 10,
2012 (the “Effective Date”) by and between Equilon Enterprises LLC dba Shell Oil
Products US, a Delaware limited liability company, having a place of business at
910 Louisiana Street, Houston, Texas 77002 (“Shell”), and Codexis, Inc., a
Delaware corporation, having a place of business at 200 Penobscot Drive, Redwood
City, California 94063 (“Codexis”). Shell and Codexis may each be referred to
herein individually as a “Party” or, collectively, as the “Parties.”

WHEREAS, Shell and Codexis entered into a certain Amended and Restated
Collaborative Research Agreement, effective as of November 1, 2006, as amended
(the “Research Agreement”), pursuant to which the Parties have collaborated to
develop certain new biocatalytic processes for use in the conversion of biomass
to fuels and/or fuel additives and/or lubricants; and

WHEREAS, the Parties desire to reduce the number of days of advance notice
required under Section 2.6(c) of the Research Agreement for Shell to reduce the
total number of FTEs assigned by Codexis to perform Codexis’ obligations under
the Program and, in exchange for such reduction, the Parties agree to negotiate
the terms and conditions of an agreement under which Shell would grant to
Codexis certain intellectual property rights.

NOW, THEREFORE, in consideration of the promises and undertakings set forth
herein, the Parties hereby agree as follows:

 

1. DEFINED TERMS. All terms defined in the Research Agreement shall have the
same meaning in this Agreement, unless otherwise expressly defined in this
Agreement.

 

2. ADVANCE NOTICE REQUIREMENT. Codexis and Shell each agree that the advance
notice requirement set forth in Section 2.6(c) of the Research Agreement for the
reduction of any number between 13 and < 48 of the total number of FTEs assigned
by Codexis to perform Codexis’ obligations under the Program will be changed and
reduced from 90 days to 1 day; provided that Shell may not exercise its right
under this Section 2 to deliver notice of its intention to reduce the number of
such FTEs by any number between 13 and < 48 until August 31, 2012.

 

3. EXCLUSIVE NEGOTIATION. In exchange for the reduction in the advance notice
requirement set forth in Section 2.6(c) of the Research Agreement, as set forth
in Section 2 above, Shell, on behalf of itself and its wholly owned direct and
indirect subsidiaries, agrees to negotiate with Codexis exclusively, and in good
faith, until September 1, 2012 the terms and conditions of an agreement under
which Shell would grant to Codexis certain rights and licenses in the Field of
Use to develop, make, use and sell Biocatalysts to Third Parties on a worldwide
basis, except Brazil.

[Signature Page Follows]

 

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

 

EQUILON ENTERPRISES LLC     CODEXIS, INC. DBA SHELL OIL PRODUCTS US       By:  

/s/Phillip Baxley

    By:  

/s/John J. Nicols

Name:   Phillip Baxley     Name:   John J. Nicols Title:   Attorney in Fact    
Title:   President and Chief Executive Officer

Exclusive Negotiation Agreement