Codexis Inc. Watch

from S-3 49 pages Codexis, Inc. Indenture Dated as of , 20 [ ] Trustee

from 10-K 4 pages Description of the Registrant’s Securities Registered Pursuant to Section 12 of the Securities Exchange Act of 1934

from 8-K 10 pages Warrant to Purchase Stock

from 10-K 4 pages Description of the Registrant’s Securities Registered Pursuant to Section 12 of the Securities Exchange Act of 1934

from S-3ASR 51 pages Codexis, Inc. Indenture Dated as of , 20 [ ], Trustee

from 10-K 5 pages Description of the Registrant’s Securities Registered Pursuant to Section 12 of the Securities Exchange Act of 1934

from S-3ASR 52 pages Codexis, Inc. Indenture Dated as of , 20 [ ], Trustee

from S-3 52 pages Codexis, Inc. Indenture Dated as of , 20 [ ], Trustee

from 8-K 57 pages Codexis, Inc. and Wells Fargo Bank, N.A. as Rights Agent Rights Agreement Dated as of September 3, 2012 Rights Agreement

from 10-Q 1 page Number CDXS Shares Codexis® Incorporated Under the Laws of the State of Delaware This Certificate Is Transferable See Reverse Side in South Sain T Paul, Mn. for Certain Definitions Cusip 192005 10 6 This Certifies That Is the Owner of Fully Paid and Non-Assessable Common Shares, $0.0001 Par Value, of Codexis, Inc. Transferable on the Books of the Corporation by the Holder Hereof in Person or by Attorney Upon Surrender of This Certificate Properly Endorsed. This Certificate Is Not Valid Until Countersigned Common and Registered by the Transfer Agent and Registrar. in Witness Whereof, the Said Corporation Has Caused This Certificate to Be Signed by Facsimile Signatures of Its Duly Authorized Officers. Dated: Senior Vice President, General Counsel & Secretary President & Chiefexecutive Officer Countersigned and Registered: Wells Fargo Bank, N A. . Transfer Agent and Registrar by Authorized Signature American Financial Printing Incorporat Ed – Minneapolis

from S-1/A 2 pages CDXS Incorporated Under the Laws of the State of Delaware This Certificate Is Transferable in South Saint Paul, Mn. See Reverse Side for Certain Definitions Cusip 192005 10 6 This Certifies That Is the Owner of Fully Paid and Non-Assessable Common Shares, $0.0001 Par Value, of Transferable on the Books of the Corporation by the Holder Hereof in Person or by Attorney Upon Surrender of This Certificate Properly Endorsed. This Certificate Is Not Valid Until Countersigned and Registered by the Transfer Agent and Registrar. in Witness Whereof, the Said Corporation Has Caused This Certificate to Be Signed by Facsimile Signatures of Its Duly Authorized Officers. Dated: Countersigned and Registered: Wells Fargo Bank, N.A. by Authorized Signature Transfer Agent and Registrar Senior Vice President, General Counsel & Secretary President Chief & Executive Officer

from S-1/A 18 pages Codexis, Inc. Amendment to Fifth Amended and Restated Voting Agreement

from S-1/A 23 pages Codexis, Inc. Fifth Amended and Restated Voting Agreement

from S-1 12 pages A. Registration Rights Agreement

from S-1 16 pages Void After February 9, 2016 Warrant for the Purchase of Shares of Common Stock of Codexis, Inc. Incorporated Under the Laws of the State of Delaware

from S-1 15 pages Warrant to Purchase Shares of Series D Convertible Preferred Stock

from S-1 11 pages Codexis, Inc. Stock Purchase Warrant

from S-1 9 pages Warrant to Purchase 9,100 Shares of Common Stock

from S-1 10 pages Codexis, Inc. Effective as of February 12, 2004 Void After February 12, 2011

from S-1 50 pages Codexis, Inc. Fifth Amended and Restated Investor Rights Agreement March 4, 2009