Exhibit 10.21

Master Security Agreement No. 5081102

MASTER SECURITY AGREEMENT

No. 5081102

Dated as of October 25, 2005 (“Agreement”)

THIS AGREEMENT is between Oxford Finance Corporation (together with its successors and assigns, if any, “Secured Party”) and Codexis, Inc. (“Debtor”). Secured Party has an office at 133 N. Fairfax Street, Alexandria, VA 22314. Debtor is a corporation organized and existing under the laws of the state of Delaware. Debtor’s mailing address and chief place of business is 200 Penobscot Drive, Redwood City, CA 94063.

Debtor grants to Secured Party, its successors and assigns, a security interest in and against all property listed on any collateral schedule now or in the future annexed to or made a part of this Agreement (“Collateral Schedule”), and in and against all additions, attachments, accessories and accessions to such property, all substitutions, replacements or exchanges therefor, and all insurance and/or other proceeds thereof (all such property is individually and collectively called the “Collateral”). This security interest is given to secure the payment and performance of all debts, obligations and liabilities of any kind whatsoever of Debtor to Secured Party, now existing or arising in the future, including but not limited to the payment and performance of certain Promissory Notes from time to time identified on any Collateral Schedule (collectively “Notes” and each a “Note”), and any renewals, extensions and modifications of such debts, obligations and liabilities (such Notes, debts, obligations and liabilities are called the “Indebtedness”). Debtor acknowledges that, notwithstanding that the Note(s) may be paid in full, this Security Agreement shall continue to secure the payment and performance of all other debts, obligations and liabilities of any kind whatsoever of Debtor to Secured Party, now existing or arising in the future, and that Secured Party shall be under no obligation to release the Collateral unless and until all Indebtedness of Debtor to Secured Party has been paid and satisfied; provided, however, Secured Party, in its sole and exclusive discretion, may elect to release some of the Collateral without prejudice to Secured Party’s security interest in the remaining Collateral.

Debtor represents, warrants and covenants as of the data of this Agreement and as of the date of each Collateral Schedule that:

Master Security Agreement No. 5081102

Master Security Agreement No. 5081102

Master Security Agreement No. 5081102

Wells Fargo Bank

P.O. Box 150, 400 Hamilton Ave.

Palo Alto, CA 94301

ABA No.: 121000248

Account No.: 403-0003362

Account Name: Codexis, Inc.

Debtor hereby agrees that Loans will be advanced to the account specified above and regularly scheduled payments will be automatically debited from the same account;

Master Security Agreement No. 5081102

The Debtor covenants and agrees that, so long as any of the Debt Documents shall remain in effect, or unless the Secured Party shall otherwise consent in writing:

Master Security Agreement No. 5081102

Master Security Agreement No. 5081102

Master Security Agreement No. 5081102

Master Security Agreement No. 5081102

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Master Security Agreement No. 5081102

Master Security Agreement No. 5081102

Master Security Agreement No. 5081102

Master Security Agreement No. 5081102

Master Security Agreement No. 5081102

Master Security Agreement No. 5081102

Master Security Agreement No. 5081102

As used herein, the following terms, when initial capital letters are used, shall have the respective meanings set forth below. In addition, all terms defined in the Code shall have the meanings given therein unless otherwise defined herein.

Defined Terms. As used in this Agreement, the following terms shall have the following meanings, unless the context otherwise requires:

“Additional Indebtedness” means, with respect to Debtor or any of its subsidiaries, the aggregate amount of, without duplication, (a) all obligations of such Person for borrowed money, (b) all obligations of such Person evidenced by bonds, debentures, notes or other similar instruments, (c) all obligations of such Person to pay the deferred purchase price of property or services (excluding trade payables aged less than one hundred eighty (180) days), (d) all capital lease obligations of such Person, (e) all obligations or liabilities of others secured by a Lien on any asset of such Person, whether or not such obligation or liability is assumed, (f) all obligations or liabilities of others guaranteed by such Person, and (g) any other obligations or liabilities which are required by GAAP to be shown as debt on the balance sheet of such Person. A listing of Additional Indebtedness existing on the date hereof is set forth in Schedule B. Unless otherwise indicated, the term “Additional Indebtedness” shall include all Indebtedness of Debtor and all of its subsidiaries.

“Affiliate” of a Person is a Person that owns or controls directly or indirectly the Person, any Person that controls or is controlled by or is under common control with the Person, and each of that Person’s senior executive officers, directors, partners and, for any Person that is a limited liability company, that Person’s managers and members.

“Code” means the Virginia Uniform Commercial Code (including revised Article 9 thereof).

“Collateral” has the meaning given such capitalized term in Section 1.

“Collateral Schedule” has the meaning given such capitalized term in Section 1.

“Debt Documents” has the meaning given such capitalized term in Section 2(b).

“Default Rate” is the lower of thirteen percent (13%) per annum or the maximum rate not prohibited by applicable law.

“Indebtedness” has the meaning given such capitalized term in Section 1.

“Intellectual Property” shall mean (a) all of the Debtor’s right, title and interest, whether now owned or existing or hereafter acquired or arising, in and to all domestic and foreign copyrights, copyright registrations and copyright applications, whether or not registered or filed with any governmental authority, together with (i) all renewals thereof, (ii) all present and future rights of the Debtor under all present and future license agreements relating thereto, whether the Debtor is licensee or licensor thereunder, (iii) all income,

Master Security Agreement No. 5081102

royalties, damages and payments now or hereafter due and/or payable to the Debtor thereunder or with respect thereto, including, without limitation, damages and payments for past, present or future infringements thereof, (iv) all of the Debtor’s present and future claims, causes of action and rights to sue for past, present or future infringements thereof, and (v) all rights corresponding thereto throughout the world (collectively “Copyright Rights”); (b) all of the Debtor’s right, title and interest, whether now owned or existing or hereafter acquired or arising, in and to all United States and foreign patents, and pending and abandoned United States and foreign patent applications, including, without limitation, the inventions and improvements described or claimed therein, together with(i) any reissues, divisions, continuations, certificates of re-examination, extensions and continuations-in-part thereof, (ii) all present and future rights of the Debtor under all present and future license agreements relating thereto, whether the Debtor is licensee or licensor thereunder, (iii) all income, royalties, damages and payments now or hereafter due and/or payable to the Debtor thereunder or with respect thereto, including, without limitation, damages and payments for past, present or future infringements thereof, (iv) all of the Debtor’s present and future claims, causes of action and rights to sue for past, present or future infringements thereof, and (v) all rights corresponding thereto throughout the world (collectively “Patent Rights”); (c) all of the Debtor’s right, title and interest, whether now owned or existing or hereafter acquired or arising, in and to all domestic and foreign trademarks, trademark registrations, trademark applications and trade names, whether or not registered or filed with any governmental authority, together with (i) all renewals thereof, (ii) all present and future rights of the Debtor under all present and future license agreements relating thereto, whether the Debtor is licensee or licensor thereunder, (iii) all income, royalties, damages and payments now or hereafter due and/or payable to the Debtor thereunder or with respect thereto, including, without limitation, damages and payments for past, present or future infringements thereof, (iv) all of the Debtor’s present and future claims, causes of action and rights to sue for past, present or future infringements thereof, and (v) all rights corresponding thereto throughout the world (collectively “Trademark Rights”); (d) all present and future licenses and license agreements of the Debtor, and all rights of the Debtor under or in connection therewith, whether the Debtor is licensee or licensor thereunder, including, without limitation, any present or future franchise agreements under which the Debtor is franchisee or franchisor, together with (i) all renewals thereof, (ii) all income, royalties, damages and payments now or hereafter due and/or payable to the Debtor thereunder or with respect thereto, including, without limitation, damages and payments for past, present or future infringements thereof, (iii) all claims, causes of action and rights to sue for past, present or future infringements thereof, and (iv) all rights corresponding thereto throughout the world (collectively “License Rights”); (e) all present and future trade secrets of the Debtor; and (f) all other present and future intellectual property of the Debtor.]

“Lien(s)” shall mean any voluntary or involuntary mortgage, pledge, deed of trust, assignment, security interest, encumbrance, hypothecation, lien, or charge of any kind (including any conditional sale or other title retention agreement, any financing lease having substantially the same economic effect as any of the foregoing, and the filing of, or agreement to give, any financing statement under the Uniform Commercial Code or comparable law of any jurisdiction).

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“Loan” means an advance of credit by Secured Party to Debtor.

“Note” has the meaning given such capitalized term in Section 1.

“Permitted Liens” means: (i) liens in favor of Secured Party, (ii) liens for taxes not yet due or for taxes being contested in good faith and which do not involve, in the judgment of Secured Party, any risk of the sale, forfeiture or loss of any of the Collateral, and (iii) inchoate materialmen’s, mechanic’s, repairmen’s and similar liens arising by operation of law in the normal course of business for amounts which are not delinquent.

“Person” is any individual, sole proprietorship, partnership, limited liability company, joint venture, company association, trust, unincorporated organization, association, corporation, institution, public benefit corporation, firm, joint stock company, estate, entity or government agency.

“Primary Operating Account” has the meaning given such capitalized term in Section 2(w).

“Secured Party’s Expenses” means all reasonable costs or expenses (including reasonable attorneys’ fees and expenses) incurred in connection with the preparation, negotiation, documentation, administration and funding of the Debt Documents; and Secured Party’s reasonable attorneys’ fees, costs and expenses incurred in amending. modifying, enforcing or defending the Debt Documents (including fees and expenses of appeal or review), including the exercise of any rights or remedies afforded hereunder or under applicable law, whether or not suit is brought, whether before or after bankruptcy or insolvency, including without limitation all fees and costs incurred by Secured Party in connection with Secured Party’s enforcement of its rights in a bankruptcy or insolvency proceeding filed by or against Debtor or its property.

“Subordinated Indebtedness” means Additional Indebtedness subordinated to the Indebtedness of Debtor to Secured Party on terms and conditions acceptable to Secured Party in its sole discretion.

IN WITNESS WHEREOF, Debtor and Secured Party, intending to be legally bound hereby, have duly executed this Agreement in one or more counterparts, each of which shall be deemed to be an original, as of the day and year first aforesaid.

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SCHEDULE A

FORM OF

COMPLIANCE CERTIFICATE

Gentlemen:

Reference is made to the Master Security Agreement dated as of October 25, 2005, (as the same have been and may be amended from time to time in writing, the “Loan Agreement”, the capitalized terms used herein as defined therein), between Oxford Finance Corporation and Codexis, Inc. (the “Company”).

The undersigned authorized representative of the Company hereby certifies that in accordance with the terms and conditions of the Loan Agreement, the Company is in complete compliance for the financial reporting period ending                              with all required financial reporting under the Loan Agreement, except as noted below. Attached herewith are the required documents supporting the foregoing certification. The undersigned further certifies that the accompanying financial statements present fairly in all material respects the Debtor’s financial condition as of the date thereof, that annual audited financial statements have been prepared in accordance with Generally Accepted Accounting Principles, and all such financial statements are consistent from one period to the next, except as explained below.

Indicate compliance status by circling Yes/No under “Complies”

Master Security Agreement No. 5081102

EXPLANATIONS

Master Security Agreement No. 5081102

SCHEDULE B

DEBTOR ADDITIONAL INDEBTEDNESS AS OF SEPTEMBER 30, 2005

COLLATERAL MIX RIDER

TO

MASTER SECURITY AGREEMENT NO. 5081102

DATED OCTOBER 25, 2005

BETWEEN

OXFORD FINANCE CORPORATION (the “SECURED PARTY”)

AND

CODEXIS, INC. (the “DEBTOR”)

Debtor shall cause the composition and mix of Collateral to conform to and meet the following concentration requirements (hereinafter “Concentration Requirement”) for the class of Collateral (hereinafter “Collateral Class”) as identified and set forth below. Debtor herein represents and warrants that it shall maintain such Collateral Class and its respective Concentration Requirement at all times from and after December 31, 2006. If on such date the Concentration Requirement is not in compliance (a “Concentration Variance”), Debtor will do one of the following (a “Concentration Correction”):

The failure of Debtor to do a Concentration Correction by December 31, 2006, shall constitute a Default under the Master Security Agreement and the Note(s) thereunder.

Dated as of October 25, 2005

SECRETARY’S CERTIFICATE

Codexis, Inc.

The undersigned hereby certifies as follows:

(ii) Each of the officers designated below is a duly appointed officer of the Corporation, and the signature appearing opposite his name below is his genuine signature:

(iii) Schedule A attached hereto is a true and correct copy of the Corporation’s Fourth Amended and Restated Certificate of Incorporation, as filed with the Delaware Secretary of State on July 22, 2004, as amended on January 19, 2005, July 26, 2005 and October 20, 2005 (the “Certificate”). The Certificate has not in any way been amended, annulled, rescinded, repealed, revoked or supplemented, and remains in full force and effect as of the date hereof.

(iv) Schedule B attached hereto is a true and correct copy of the Corporation’s bylaws as presently in effect.

(v) Schedule C attached hereto is a true and correct copy of resolutions adopted by the board of directors of the Corporation on August 11, 2005 related to Oxford Finance Corporation (the “Resolutions”). Said Resolutions have not been revoked, modified, rescinded, or amended and are in full force and effect.

[Signature Page Follows]

SECRETARY’S CERTIFICATE

IN WITNESS WHEREOF, I have hereunto set my hand, this 25th day of October, 2005.

ATTEST:

The undersigned does hereby certify that he is President and Chief Executive Officer of the Corporation and does hereby certify that Alan Mendelson was, at the time he executed the foregoing Certificate, a duly elected, qualified and acting Secretary of the Corporation, and he was duly authorized and empowered to do so, and the signature thereon is genuine.