<?xml version="1.0"?>
<ownershipDocument>

    <schemaVersion>X0206</schemaVersion>

    <documentType>3</documentType>

    <periodOfReport>2015-06-16</periodOfReport>

    <noSecuritiesOwned>0</noSecuritiesOwned>

    <issuer>
        <issuerCik>0001626199</issuerCik>
        <issuerName>Nivalis Therapeutics, Inc.</issuerName>
        <issuerTradingSymbol>NVLS</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001645257</rptOwnerCik>
            <rptOwnerName>Hawkes Bay Master Investors (Cayman) L.P.</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O WELLINGTON MANAGEMENT COMPANY LLP</rptOwnerStreet1>
            <rptOwnerStreet2>280 CONGRESS STREET</rptOwnerStreet2>
            <rptOwnerCity>BOSTON</rptOwnerCity>
            <rptOwnerState>MA</rptOwnerState>
            <rptOwnerZipCode>02210</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <derivativeTable>
        <derivativeHolding>
            <securityTitle>
                <value>Series 2 convertible preferred stock</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <footnoteId id="F1"/>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F1"/>
            </exerciseDate>
            <expirationDate>
                <footnoteId id="F1"/>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>283390</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">Each share of Series 2 convertible preferred stock is convertible into shares of common stock on a 2.889-for-1 basis at the option of the reporting person or upon the occurrence of certain events.  All outstanding shares of Series 2 convertible preferred stock are expected to convert into shares of common stock immediately prior to the amendment and restatement by Nivalis Therapeutics, Inc. of its certificate of incorporation, provided the amendment and restatement occurs prior to, and on the same day as, the closing of its  initial public offering at an initial public offering price of no less than $8.667 per share.</footnote>
    </footnotes>

    <ownerSignature>
        <signatureName>Hawkes Bay Master Investors (Cayman) LP By: Wellington Hedge Management LLC, as General Partner, /s/Valerie Tipping, Title: Authorized Person</signatureName>
        <signatureDate>2015-06-16</signatureDate>
    </ownerSignature>
</ownershipDocument>
