-----BEGIN PRIVACY-ENHANCED MESSAGE-----
Proc-Type: 2001,MIC-CLEAR
Originator-Name: webmaster@www.sec.gov
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MIC-Info: RSA-MD5,RSA,
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 Ge+IZ8QlSdH1ULjqYtxu8A==

<SEC-DOCUMENT>0001104659-06-068608.txt : 20061025
<SEC-HEADER>0001104659-06-068608.hdr.sgml : 20061025
<ACCEPTANCE-DATETIME>20061025191123
ACCESSION NUMBER:		0001104659-06-068608
CONFORMED SUBMISSION TYPE:	3
PUBLIC DOCUMENT COUNT:		1
CONFORMED PERIOD OF REPORT:	20061023
FILED AS OF DATE:		20061025
DATE AS OF CHANGE:		20061025

REPORTING-OWNER:	

	OWNER DATA:	
		COMPANY CONFORMED NAME:			KNOTT DAVID M
		CENTRAL INDEX KEY:			0000808722

	FILING VALUES:
		FORM TYPE:		3
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	001-33093
		FILM NUMBER:		061163966

	MAIL ADDRESS:	
		STREET 1:		485 UNDERHILL BLVD
		STREET 2:		STE 205
		CITY:			SYOSSET
		STATE:			NY
		ZIP:			11791-3419

ISSUER:		

	COMPANY DATA:	
		COMPANY CONFORMED NAME:			LIGAND PHARMACEUTICALS INC
		CENTRAL INDEX KEY:			0000886163
		STANDARD INDUSTRIAL CLASSIFICATION:	PHARMACEUTICAL PREPARATIONS [2834]
		IRS NUMBER:				770160744
		STATE OF INCORPORATION:			DE
		FISCAL YEAR END:			1231

	BUSINESS ADDRESS:	
		STREET 1:		10275 SCIENCE CENTER DRIVE
		CITY:			SAN DIEGO
		STATE:			CA
		ZIP:			92121-1117
		BUSINESS PHONE:		8585507500

	MAIL ADDRESS:	
		STREET 1:		10275 SCIENCE CENTER DRIVE
		CITY:			SAN DIEGO
		STATE:			CA
		ZIP:			92121-1117
</SEC-HEADER>
<DOCUMENT>
<TYPE>3
<SEQUENCE>1
<FILENAME>a3.xml
<DESCRIPTION>3
<TEXT>
<XML>
<?xml version="1.0"?>
<ownershipDocument>

    <schemaVersion>X0202</schemaVersion>

    <documentType>3</documentType>

    <periodOfReport>2006-10-23</periodOfReport>

    <noSecuritiesOwned>0</noSecuritiesOwned>

    <issuer>
        <issuerCik>0000886163</issuerCik>
        <issuerName>LIGAND PHARMACEUTICALS INC</issuerName>
        <issuerTradingSymbol>LGND</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0000808722</rptOwnerCik>
            <rptOwnerName>KNOTT DAVID M</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>485 UNDERHILL BLVD.</rptOwnerStreet1>
            <rptOwnerStreet2>SUITE 205</rptOwnerStreet2>
            <rptOwnerCity>SYOSSET</rptOwnerCity>
            <rptOwnerState>NY</rptOwnerState>
            <rptOwnerZipCode>11791</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeHolding>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>2271000</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>By Knott Parners, L.P.</value>
                    <footnoteId id="F1"/>
                    <footnoteId id="F4"/>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeHolding>
        <nonDerivativeHolding>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>1256700</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>By Shoshone Partners, L.P.</value>
                    <footnoteId id="F1"/>
                    <footnoteId id="F4"/>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeHolding>
        <nonDerivativeHolding>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>18400</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>By Mulsanne Partners, L.P.</value>
                    <footnoteId id="F1"/>
                    <footnoteId id="F4"/>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeHolding>
        <nonDerivativeHolding>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>3788400</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>By Matterhorn Offshore Fund Limited</value>
                    <footnoteId id="F2"/>
                    <footnoteId id="F4"/>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeHolding>
        <nonDerivativeHolding>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>32400</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>By Ostra Capital Partners VII, L.P.</value>
                    <footnoteId id="F2"/>
                    <footnoteId id="F4"/>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeHolding>
        <nonDerivativeHolding>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>448700</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>By Managed Accounts</value>
                    <footnoteId id="F3"/>
                    <footnoteId id="F4"/>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeHolding>
    </nonDerivativeTable>

    <derivativeTable>
        <derivativeHolding>
            <securityTitle>
                <value>6% Convertible Subordinated Notes due 2007</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>6.1732</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <value>2002-11-26</value>
            </exerciseDate>
            <expirationDate>
                <value>2007-11-16</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>148383</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>By Knott Partners, L.P.</value>
                    <footnoteId id="F1"/>
                    <footnoteId id="F4"/>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>6% Convertible Subordinated Notes due 2007</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>6.1732</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <value>2002-11-26</value>
            </exerciseDate>
            <expirationDate>
                <value>2007-11-16</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>70141</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>By Shoshone Partners, L.P.</value>
                    <footnoteId id="F1"/>
                    <footnoteId id="F4"/>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>6% Convertible Subordinated Notes due 2007</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>6.1732</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <value>2002-11-26</value>
            </exerciseDate>
            <expirationDate>
                <value>2007-11-16</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>140931</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>By Matterhorn Offshore Fund Limited</value>
                    <footnoteId id="F2"/>
                    <footnoteId id="F4"/>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>6% Convertible Subordinated Notes due 2007</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>6.1732</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <value>2002-11-26</value>
            </exerciseDate>
            <expirationDate>
                <value>2007-11-16</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>259184</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>By Ostra Capital Partners, L.P.</value>
                    <footnoteId id="F2"/>
                    <footnoteId id="F4"/>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>6% Convertible Subordinated Notes due 2007</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>6.1732</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <value>2002-11-26</value>
            </exerciseDate>
            <expirationDate>
                <value>2007-11-16</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>29318</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>By Managed Accounts</value>
                    <footnoteId id="F3"/>
                    <footnoteId id="F4"/>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeHolding>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">The Reporting Person is the managing member of Knott Partners Management, LLC, which is (i) the sole general partner of Shoshone Partners, L.P. and Mulsanne Partners, L.P. and (ii) the managing general partner of Knott Partners, L.P.  The Reporting Person is also a general partner of Knott Partners, L.P.</footnote>
        <footnote id="F2">The Reporting Person is the sole shareholder, director and president of Dorset Management Corporation, which (i) provides investment management services to Matterhorn Offshore Fund Limited and (ii) is the employer of Richard Murawczyk, the managing member of the general partner of Ostra Capital Partners, L.P. and Ostra Capital Partners VII, L.P., with which Dorset Management Corporation has a trading relationship.</footnote>
        <footnote id="F3">The entry represents securities of the issuer held by managed accounts for which Dorset  Management Corporation provides investment management services (the &quot;Managed Accounts&quot;).</footnote>
        <footnote id="F4">As a result of the Reporting Person's interests in Knott Partners Management, LLC and in Dorset Management Corporation, the Reporting Person has investment discretion and control of the securities represented in this entry. The Reporting Person may be deemed to beneficially own an indirect pecuniary interest in the securities represented in this entry as a result of a performance related fee. Except with respect to Knott Partners, L.P. and Shoshone Partners, L.P., in which the Reporting Person owns a beneficial interest, the Reporting Person disclaims beneficial ownership therein except to the extent ultimately realized.  Each of the Knott Partners, L.P., Shoshone Partners, L.P., Mulsanne Partners, L.P., Matterhorn Offshore Fund Limited, Ostra Capital Partners, L.P., Ostra Capital Partners VII, L.P. and the Managed Accounts disclaims beneficial ownership of securities reported as owned by any other party.</footnote>
    </footnotes>

    <ownerSignature>
        <signatureName>/s/ David M. Knott</signatureName>
        <signatureDate>2006-10-24</signatureDate>
    </ownerSignature>
</ownershipDocument>
</XML>
</TEXT>
</DOCUMENT>
</SEC-DOCUMENT>
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