<SEC-DOCUMENT>0001493152-25-025624.txt : 20251201
<SEC-HEADER>0001493152-25-025624.hdr.sgml : 20251201
<ACCEPTANCE-DATETIME>20251201174143
ACCESSION NUMBER:		0001493152-25-025624
CONFORMED SUBMISSION TYPE:	4
PUBLIC DOCUMENT COUNT:		1
CONFORMED PERIOD OF REPORT:	20251126
FILED AS OF DATE:		20251201
DATE AS OF CHANGE:		20251201

REPORTING-OWNER:	

	OWNER DATA:	
		COMPANY CONFORMED NAME:			Opaleye Management Inc.
		CENTRAL INDEX KEY:			0001595855
		ORGANIZATION NAME:           	
		STATE OF INCORPORATION:			MA
		FISCAL YEAR END:			1231

	FILING VALUES:
		FORM TYPE:		4
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	001-34705
		FILM NUMBER:		251540966

	BUSINESS ADDRESS:	
		STREET 1:		ONE BOSTON PLACE
		STREET 2:		SUITE 2600
		CITY:			BOSTON
		STATE:			MA
		ZIP:			02108
		BUSINESS PHONE:		617-904-9195

	MAIL ADDRESS:	
		STREET 1:		ONE BOSTON PLACE
		STREET 2:		SUITE 2600
		CITY:			BOSTON
		STATE:			MA
		ZIP:			02108

ISSUER:		

	COMPANY DATA:	
		COMPANY CONFORMED NAME:			CODEXIS, INC.
		CENTRAL INDEX KEY:			0001200375
		STANDARD INDUSTRIAL CLASSIFICATION:	INDUSTRIAL ORGANIC CHEMICALS [2860]
		ORGANIZATION NAME:           	08 Industrial Applications and Services
		EIN:				710872999
		STATE OF INCORPORATION:			DE
		FISCAL YEAR END:			1231

	BUSINESS ADDRESS:	
		STREET 1:		200 PENOBSCOT DRIVE
		CITY:			REDWOOD CITY
		STATE:			CA
		ZIP:			94063
		BUSINESS PHONE:		650-421-8100

	MAIL ADDRESS:	
		STREET 1:		200 PENOBSCOT DRIVE
		CITY:			REDWOOD CITY
		STATE:			CA
		ZIP:			94063

	FORMER COMPANY:	
		FORMER CONFORMED NAME:	CODEXIS INC
		DATE OF NAME CHANGE:	20021022
</SEC-HEADER>
<DOCUMENT>
<TYPE>4
<SEQUENCE>1
<FILENAME>ownership.xml
<DESCRIPTION>4
<TEXT>
<XML>
<?xml version="1.0"?>
<ownershipDocument>

    <schemaVersion>X0508</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2025-11-26</periodOfReport>

    <notSubjectToSection16>0</notSubjectToSection16>

    <issuer>
        <issuerCik>0001200375</issuerCik>
        <issuerName>CODEXIS, INC.</issuerName>
        <issuerTradingSymbol>CDXS</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001595855</rptOwnerCik>
            <rptOwnerName>Opaleye Management Inc.</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>ONE BOSTON PLACE, 26TH FLOOR</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>BOSTON</rptOwnerCity>
            <rptOwnerState>MA</rptOwnerState>
            <rptOwnerZipCode>02108</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle></officerTitle>
            <otherText></otherText>
        </reportingOwnerRelationship>
    </reportingOwner>

    <aff10b5One>0</aff10b5One>

    <nonDerivativeTable>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock, par value $0.001 per share</value>
            </securityTitle>
            <transactionDate>
                <value>2025-11-26</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>S</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness></transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>148318</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>1.7413</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>10305000</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>By Opaleye, L.P.</value>
                    <footnoteId id="F1"/>
                    <footnoteId id="F3"/>
                    <footnoteId id="F6"/>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock, par value $0.001 per share</value>
            </securityTitle>
            <transactionDate>
                <value>2025-11-26</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>S</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness></transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>5000</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>1.7413</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>191012</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>By Managed Account</value>
                    <footnoteId id="F2"/>
                    <footnoteId id="F3"/>
                    <footnoteId id="F6"/>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock, par value $0.001 per share</value>
            </securityTitle>
            <transactionDate>
                <value>2025-11-28</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>S</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness></transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>105000</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>1.75</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>10200000</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>By Opaleye, L.P.</value>
                    <footnoteId id="F1"/>
                    <footnoteId id="F4"/>
                    <footnoteId id="F6"/>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock, par value $0.001 per share</value>
            </securityTitle>
            <transactionDate>
                <value>2025-11-28</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>S</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness></transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>2490</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>1.75</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>188522</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>By Managed Account</value>
                    <footnoteId id="F2"/>
                    <footnoteId id="F4"/>
                    <footnoteId id="F6"/>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock, par value $0.001 per share</value>
            </securityTitle>
            <transactionDate>
                <value>2025-12-01</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>S</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness></transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>245000</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>1.6675</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>9955000</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>By Opaleye, L.P.</value>
                    <footnoteId id="F1"/>
                    <footnoteId id="F5"/>
                    <footnoteId id="F6"/>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock, par value $0.001 per share</value>
            </securityTitle>
            <transactionDate>
                <value>2025-12-01</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>S</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness></transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>8533</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>1.6675</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>179989</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>By Managed Account</value>
                    <footnoteId id="F2"/>
                    <footnoteId id="F5"/>
                    <footnoteId id="F6"/>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
    </nonDerivativeTable>

    <footnotes>
        <footnote id="F1">Represents securities owned directly by Opaleye, L.P. (the &quot;Fund&quot;). As the investment manager of the Fund, Opaleye Management Inc. may be deemed to beneficially own the securities owned directly by the Fund.</footnote>
        <footnote id="F2">Securities owned by a separately managed account (the &quot;Managed Account&quot;). As the portfolio manager of the Managed Account, Opaleye may be deemed to beneficially own the securities owned directly by the Managed Account.</footnote>
        <footnote id="F3">The price reported in column 4 is a weighted average price. These shares were sold in multiple transactions at prices ranging from $1.7316 - $1.75699 inclusive. The reporting person undertakes to provide, upon request by the SEC staff, the issuer, or a security holder of the issuer, full information regarding the number of shares sold at each price.</footnote>
        <footnote id="F4">The price reported in column 4 is a weighted average price. These shares were sold in multiple transactions at prices ranging from $1.73 - $1.7715 inclusive. The reporting person undertakes to provide, upon request by the SEC staff, the issuer, or a security holder of the issuer, full information regarding the number of shares sold at each price.</footnote>
        <footnote id="F5">The price reported in column 4 is a weighted average price. These shares were sold in multiple transactions at prices ranging from $1.65 - $1.7101 inclusive. The reporting person undertakes to provide, upon request by the SEC staff, the issuer, or a security holder of the issuer, full information regarding the number of shares sold at each price.</footnote>
        <footnote id="F6">Opaleye Management Inc. disclaims beneficial ownership of the shares reported herein except to the extent of its pecuniary interest therein, and the filing of this Form 4 shall not be construed as an admission that Opaleye Management Inc. is the beneficial owner of any such shares for purposes of Section 16(a) of the Securities Exchange Act of 1934, as amended, or for any other purpose.</footnote>
    </footnotes>

    <ownerSignature>
        <signatureName>Opaleye Management Inc., By: /s/ James Silverman, President</signatureName>
        <signatureDate>2025-12-01</signatureDate>
    </ownerSignature>
</ownershipDocument>
</XML>
</TEXT>
</DOCUMENT>
</SEC-DOCUMENT>
