Ligand Pharmaceuticals Incorporated : First Quarter 2024 Presentation

M A Y 7 , 2 0 2 4

FirstQuarter2024

FinancialResults

Safe Harbor Statementand Disclaimers

Thispresentationcontainsforward-lookingstatementsbyLigandanditspartnersthatinvolverisksanduncertaintiesandreflectLigand'sanditspartners'judgmentas ofthedateofthispresentation.Wordssuchas "plans,""believes,""expects,""anticipates,"and"will,"andsimilarexpressions,areintendedtoidentifyforward-lookingstatements.Theseforward-lookingstatementsinclude,withoutlimitation:Ligand'sabilityto expanditsportfoliowithlifesciencesroyaltyopportunities;thetimingofclinicalandregulatoryeventsofLigand'spartners;thetimingoftheinitiationorcompletionofpreclinicalstudiesandclinicaltrialsbyLigand anditspartners;thetimingofproductlaunchesbyLigandoritspartners;andguidanceregardingthefull-year2024financialresults.ActualeventsorresultsmaydifferfromLigand'sexpectationsduetorisksand uncertaintiesinherentinLigand'sbusiness,including,withoutlimitation:Ligandreliesoncollaborativepartnersformilestonepayments,royalties,materialsrevenue,contractpayments andotherrevenueprojections andmaynotreceiveexpectedrevenue;LigandmaynotreceiveexpectedrevenuefromCaptisolmaterialsales;Ligandanditspartnersmaynotbeabletotimelyorsuccessfullyadvanceanyproduct(s)initsinternal orpartneredpipelineorreceiveregulatoryapprovalandtheremaynotbeamarket fortheproduct(s)evenifsuccessfullydevelopedandapproved;Ligandmaynotachieveitsguidancefor2024;Ligandfaces competitioninacquiringroyaltiesandlocatingsuitableroyaltiestoacquire;Ligandmaynotbeabletocreatefuturerevenuesandcashflowsbydevelopinginnovativetherapeutics;resultsofanyclinicalstudymay notbetimely,favorableorconfirmedbylaterstudies;thetotaladdressablemarket forourpartners'productsmaybesmallerthanestimated;Ligandfacescompetitionwithrespecttoitstechnologyplatforms whichmaydemonstrategreatermarketacceptanceorsuperiority;LigandiscurrentlydependentonasinglesourcesolesupplierforCaptisolandfailuresbysuchsuppliermayresultindelaysorinabilitytomeetthe Captisoldemandsofitspartners;Ligand'spartnersmaychangetheirdevelopmentfocusandmaynotexecuteontheirsalesandmarketingplansformarketedproductsforwhichLigandhasaneconomicinterest; Ligand'sanditspartners'productsmaynotbeprovedtobesafeandefficaciousandmaynotperformas expectedanduncertaintyregardingthecommercialperformanceofsuchproducts;Ligandoritspartners maynotbeabletoprotecttheirintellectualpropertyandpatentscoveringcertainproductsandtechnologiesmaybechallengedorinvalidated;Ligand'spartnersmayterminateanyofitsagreementsor developmentorcommercializationofanyofitsproducts;Ligandanditspartnersmayexperiencedelaysinthecommencement,enrollment,completionoranalysisofclinicaltestingforitsproductcandidates,or significantissuesregardingtheadequacyofitsclinicaltrialdesignsortheexecutionofitsclinicaltrials;challenges,costsandchargesassociatedwithintegratingacquisitionswithLigand'sexistingbusinesses; Ligand/PelthosTherapeuticsmaynotbeabletosuccessfullycommercializeZELSUVMI(berdazimer) andmaynotbeabletooutlicenseorsellthisassetsuccessfully;Ligandmaynotbeabletosuccessfully implementitsstrategicgrowthplanandcontinuethedevelopmentofitsproprietaryprograms;thepotentialimpactofsix Agenuspartneredprograms,includingBMS-986442(BristolMyersSquibb),AGEN2373(GileadSciences),INCAGN2385andINCAGN2390(Incyte),MK-4830(Merck),andUGN-301(UroGenPharma);thetrialandregulatorysuccessofAgenus'upcomingPhase3trialofbotensilimabincombinationwithbalstilimab("BOT/BAL")forpatientswithmetastatic,refractorycolorectalcancerthatisnotMSI-H/dMMRandwhodonothavelivermetastases; thetimingandamountsofroyaltypayments dueundertheroyalty financingagreementwithAgenus;restrictionsunderLigand'screditagreementmaylimititsflexibilityinoperatingitsbusinessandadefaultundertheagreementcouldresultinaforeclosureofthecollateralsecuring suchobligations;changesingeneraleconomicconditions,includingasaresultofwar,conflictorepidemicdiseases;ongoingorfuturelitigationcouldexposeLigandtosignificantliabilitiesandhaveamaterial adverseeffectonthecompany;andotherrisksanduncertaintiesdescribedinitspublicfilingswiththeSecuritiesandExchangeCommission(the"SEC"),availableatwww.sec.gov.Informationregardingpartnered productsandprograms comesfrominformationpubliclyreleasedbyourpartners.Ourtrademarks,tradenamesandservicemarks referencedhereinincludeLigand,CaptisolandZELSUVMI,aNovanproduct.Each othertrademark,tradenameorservicemarkappearinginthispresentationbelongstoitsowner.

Theprocessforreconciliationbetweenthenon-GAAPadjustedfinancialnumberspresentedonslides16and 17 andcorrespondingGAAPfiguresisshownintheearningspressreleaseforthequarterendedMarch 31,2024,availableathttps://investor.ligand.com/press-releases. However,otherthanwithrespecttototalrevenues,theCompanyonlyprovidesfinancialguidanceonanadjustedbasisanddoesnotprovide reconciliationsofsuchforward-lookingadjustedmeasurestoGAAPduetotheinherentdifficultyinforecastingandquantifyingcertainamountsthatarenecessaryforsuchreconciliation.

Readersarecautionednottoplaceunduerelianceontheseforward-lookingstatements,whichreflectourgoodfaithbeliefs(orthoseoftheindicatedthirdparties)andspeakonlyasofthedatehereof.Allforward lookingstatementsarequalifiedintheirentiretybythiscautionarystatement,andLigandundertakesnoobligationtoreviseorupdatethispresentationtoreflecteventsorcircumstancesorupdatethirdparty researchnumbersafterthedatehereof.ThiscautionismadeunderthesafeharborprovisionsofSection21EoftheSecuritiesExchangeActof1934.

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Great StartTo 2024

FINANCIAL

Strong financialperformance

Strong balance sheet with $311M in cash and investments ($82M in VKTX) at 3/31/24 Announced Agenus royalty monetization & project finance investment today Reiterating 2024 revenue and earnings guidance, on continued growth trajectory

PELTHOS THERAPEUTICS

Processunderway to commercialize

Pelthos Therapeutics formed to accelerate Zelsuvmi commercialization Scott Plesha appointed Chief Executive Officer, established BOD Employing similar strategy used with Viking, Primrose and OmniAb

PORTFOLIO

Importantcatalystsin 2024

Filspari EMA Conditional Approval Merck's V116 - PDUFA date June 17, 2024 Verona's ensifentrine - PDUFA date June 26, 2024

STRATEGIC DIFFERENTIATION

Financials,advantage,team

Long-term royalty revenue CAGR >20%, adjusted EPS>25% Inefficient market with inexhaustible demand for capital

Track record of accomplishments, building a diversified portfolio

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Ligand Strategic Differentiation

STRONG FINANCIALS

High-margin /high-growth strategy

Superior P&L, low op-ex with lean operations, high profits per employee

Predictable and diversified growth

ADVANTAGEOUS STRATEGY

High Demand: Inefficient market with inexhaustible demand for capital

Superior Information: Extensive due diligence and information available under confidentiality vs. public equity investing

Flexible Structures: Customized investment structures with non-dilutable interests

Exclusivity: Create vs. compete for deals. Novel tactics / structures enable high volume of sourcing and high investment selectivity

Scalable: Only major limitations to growth are execution and access to capital

EXPERIENCED TEAM

Track record of accomplishments, building a diversified portfolio

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Looking Ahead: 5-Year Royalty Revenue Outlook

Current Portfolio of Commercial and Late-Stage Programs + New Deals Drive Growth

Primrose &

Agenus Partnered

Programs

• Royaltyrevenuegrowthcouldexceeda20%CAGR
• Recentinvestments:Tzield willcontributein2024, Soticlestat*andZelsuvmiin2025,PalvellaMLM*in 2026/2027
• AgenusinvestmentinBOT/BAL couldcontribute royaltiesasearlyas2026*
• Addinginthefirstwaveofpotentialfuturenew investments couldincreaseroyaltyrevenuegrowth toexceeda20%CAGR
• Operatingleveragegainedfromleancorporate costsstructurecoulddriveadjustedEPSCAGR exceeding25%

$250

$200

$150

$100

$50

$0 2022

Ligand Royalty Revenue Projected Trend*

(in millions)

		Palvella MLM
	22%	BOT/BAL
	CAGR	Soticlestat
	Zelsuvmi
Tzield			Filspari

Kyprolis, Evomela, Nexterone

Rylaze, Vaxneuvance, Pneumosil, Teriparatide

2023

2024

2025

2026

2027

2028

6%

CAGR

16% CAGR

Pelican Royalties Captisol Royalties Filspari Tzield Ensifentrine Pharm Team Future New Deals

Sell-side consensus sales estimates used to arrive at royalty revenue from commercial programs

5	*Assumes regulatory approval which is subject to risks as described elsewhere in our filings with the SEC

Agenus Investment Profile

Counterparty

Assets / MOAs / Phases / Marketers

Deal Type

Deal Size

Asset Value Proposition

Key Diligence Focus Areas

Agenus Bio

Agenus Asset (Royalties):

Botensilimab +/- Balstilimab "BOT/BAL" (CTLA-4 +/- PD-1, Ph 2 with potential Accelerated Approval)

Partnered Portfolio:

INCAGN-2390(TIM-3, Incyte)

INCAGN-2385(LAG-3, Incyte)

BMS-986442 (TIGIT / CD96 Bispecific, BMS)

AGEN-2373(CD-137, Gilead)

UGN-301(CTLA-4 +RTGel, UroGen)

MK-4830(ILT-4, Merck)

BOT/BAL: Project Finance

Partnered Portfolio: Royalty Monetization

$100M (Opportunity for Agenus to syndicate up to $125M; pro-rata economics )

BOT/BAL: Agenus plans to file a BLA in late-2024, offering potential near-term cash flow

BOT/BAL: Program is generating significant excitement at major conferences

Partnered Portfolio: Multiple investment opportunities in highly active I/O MOAs

Partnered Portfolio: Reputable and experienced partners

BOT/BAL: Regulatory pathway

BOT/BAL: Agenus partnership discussions and financing strategy

Partnered Programs: Probability of technical and regulatory success

Partnered Programs: Competitive dynamics in highly active indications and targets

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Agenus Investment Criteria

Time to Cash Flow

Less than 4 years from approval

• Agenus plans to submit a BLA filing in late 2024 for BOT/BAL in r/r MSS CRC NLM, which could potentially lead to royalties to Ligand beginning in 2026
• Ligand could also receive partnered program milestone payments from 2024-2026

Clinical Differentiation

Proof of concept data supports ability to address high unmet need & strong safety profile

• Clinical data indicates BOT/BAL may demonstrate substantial improvement on clinically significant endpoints including ORR, duration of response, and OS in mCRC, as well as in other tumor types

Exclusivity

7+ years of market exclusivity

• BOT/BAL and each of the partnered programs have at least 12 years of biologics exclusivity, in addition to protective IP

Structural Alignment

Counterparty with structural alignment to Ligand

• Agenus will retain significant financial and strategic interest in BOT/BAL, which Agenus is actively seeking to partner
• Each of the partnered programs are currently in the hands of companies with proven clinical and commercial capabilities

Risk-Reward

Superior risk-reward profile

• Multiple investment opportunities across 7 attractive assets and 5 strong commercial partners
• BOT/BAL has generated significant enthusiasm among KOLs and has a wide breadth of opportunity to treat solid tumors

7 r/r MSS CRC NLM: Relapsed/refractory microsatellite stable colorectal cancer with no liver metasteses

Agenus Clinical &Regulatory Outlook

BOT/BAL

• BOT is a proprietary Fc-enhancednext-generationanti-CTLA-4 antibody designed to improve magnitude of responses as compared to first- generation anti-CTLA-4 antibodies, to expand the population of patients currently benefiting from anti-CTLA-4 therapy, and to reduce adverse events that have historically led to treatment discontinuation
• BOT alone or in combination with BAL, an anti-PD-1 antibody has shown clinical responses across nine metastatic late line cancers

PARTNERED PROGRAMS

• Agenus also has milestone and royalty contracts with leading global oncology partners for 6 innovative immuno-oncologyclinical-stage products (BMS, Merck, Incyte - 2 programs, Gilead, and UroGen), offering a diversified portfolio across different targets and indications with high unmet medical needs

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ZelsuvmiOffers Highly Differentiated Profile

• High burden of untreated, highly contagious viral disease with approximately 6M pediatric patients, with >70% of children left untreated

• Zelsuvmi approved for use in patients 1 year old and older vs. competitor approval in patients 2 years old and older, highlighting Zelsuvmi's ease of treatment administration which is advantageous for both clinicians and patients
• Home administration possible in Zelsuvmi treatment versus need to visit clinician for competitor's product used only in medical office treatments

Source: Centers for Disease Control and Prevention

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Pelthos Therapeutics

Pelthos Therapeutics

• Created in April 2024 to accelerate Zelsuvmi (berdazimer gel 10.3%) commercialization
• Scott Plesha appointed Chief Executive Officer
• Ligand has a track record of successfully executing similar strategy used in Viking Therapeutics, Primrose Bio, and OmniAb

Zelsuvmi

• First and only FDA approved topical gel for molluscum contagiosum in patients ≥ 1 year old
• Rights and all assets related to Nitricil technology platform acquired from Novan, Inc. (September 2023)
• Commercialization plans underway with potential financial/strategic partners

Scott Plesha, CEO

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