Deutsche Bank 40th Annual Health Care Conference

Boston, MA May 6, 2015 NASDAQ: LGND

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The following presentation contains forward-looking statements regarding Ligand’s prospects, plans and strategies, drug development programs and collaborations. Forward-looking statements include financial projections, expectations regarding research and development programs, and other statements including words such as “will,“ “should,” “could,” “plan,” etc. Actual events or results may differ from Ligand’s expectations. For example, drug development program benefits may not be realized and there can be no assurance that Ligand will achieve its guidance in 2015 or thereafter or that third party research summarized herein is correct or complete. The forward-looking statements made in the presentation are subject to several risk factors, including, statements regarding intent, belief, or current expectations of Ligand, its internal and partnered programs, including Promacta™, Kyprolis®, and Duavee™, Ligand’s reliance on collaborative partners for milestone and royalty payments, royalty and other revenue projections based on third party research, regulatory hurdles facing Ligand's and partners’ product candidates, uncertainty regarding Ligand's and partners’ product development costs, the possibility that Ligand's and partners’ drug candidates might not be proved to be safe and efficacious and commercial performance of Ligand's and/or its partners’ products, risks related to Ligand’s internal controls, its compliance with regulations, accounting principles and public disclosure, and other risks and uncertainties described in its public filings with the Securities and Exchange Commission, available at www.sec.gov. Additional risks may apply to forward-looking statements made in this presentation. Readers are cautioned not to place undue reliance on these forward-looking statements, which reflect our good faith beliefs (or those of the indicated third parties) and speak only as of the date hereof. All forward-looking statements are qualified in their entirety by this cautionary statement, and Ligand undertakes no obligation to revise or update this presentation to reflect events or circumstances or update third party research numbers after the date hereof. This caution is made under the safe harbor provisions of Section 21E of the Securities Exchange Act of 1934. Our trademarks, trade names and service marks referenced herein include Ligand and Captisol. Each other trademark, trade name or service mark appearing in this presentation belongs to its owner. The process for reconciliation between non-GAAP financial numbers presented on slide 15, and the corresponding GAAP figures is explained in the footnotes on those slides and a full reconciliation can be found in our earnings press release dated, February 9, 2015.

Safe Harbor Statement

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Ligand: 2015 and Beyond

• Ligand is a high-growth company with economic rights to some of the world’s most important medicines

• Largest portfolio ever and projected to continue to drive the business significantly

• Cutting-edge innovations with Captisol and LTP technology are making major drugs possible

• Well positioned for strong revenue and profitability growth

Ligand Fast Facts

4

Portfolio Size

Blockbusters

Catalysts

Outlook

Over 100 fully-funded programs

Currently 2: Promacta® and Kyprolis®

6 major programs highlighted

Over 20 revenue-generating products expected by 2020

Financials Revenue

Profits

Cash Flow

> 30% annualized growth projected

> 45% annualized growth projected

High due to low costs and low taxes

5

Recent Events are Transforming Ligand

Date Program Event

November ’14 Promacta EU submission - Severe Aplastic Anemia

December ’14 Duavive EU approval

December ’14 Promacta sNDA submission - Pediatric ITP

December ’14 CE-Melphalan NDA submission

January ‘15 Delafloxacin Phase 3 study - Positive interim results

January ’15 Sparsentan Orphan drug designation - Focal Segmental Glomerulosclerosis

January ’15 SAGE-547 Phase 1/2 study - Positive data update

January ’15 Kyprolis US and EU submissions - Relapsed Multiple Myeloma

February ’15 Lasofoxifene Sermonix licensing agreement

February ’15 Promacta EU submission - Pediatric ITP

March ’15 Kyprolis Phase 3 ENDEAVOR study - Positive results

March ’15 Promacta Promacta acquisition closed (GSK to Novartis)

March ’15 Kyprolis Priority FDA review – Relapsed Multiple Myeloma

April ‘15 SAGE-547 Phase 1/2 completion – Positive results

April ’15 SAGE-547 Phase 3 trial initiated

April ’15 IRAK-4 Positive preclinical data presented

0

2

4

6

8

2008 2014

6

Fully

-Fu

nd

ed P

rogr

ams

(“Sh

ots

-on

-Go

al”)

Ligand’s Portfolio Continues to Grow

100 +

0

20

40

60

80

100

2008 2014

9

Ligand’s Achievement: Portfolio Expansion

Partners’ Achievement: Products Generating Revenue for LGND

Excellent record as drug researcher, innovator and licensor

Our partners are doing their job getting new products to the market

1

7

Co

mm

erc

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s G

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g R

even

ue

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Liga

nd

Technology and Novel R&D Drive Deal Making

Potential Launch

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Our Platform Technologies

Our Novel R&D

LTP Technology™

Glucagon Receptor Antagonist Program for Diabetes Phase 1

Positive Phase 1a data showing robust effects after single dose Phase 1b study expected to complete in coming weeks

Change in fasting glucose(24 hr post dose)

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Solving solubility and stability challenges

Designed to selectively deliver broad range of pharmaceutical agents to the liver

Oral GCSF Preclinical Leveraging our technology and heritage in small molecule discovery

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20 Products by 2020 Significant Expansion of Revenue Generating Assets Projected

• Over 20 commercial programs projected to be generating revenue for Ligand by the end of this decade

• Programs expected to come from existing portfolio; no new deals required to drive that expansion

2008 2014 2020Projected

1

7

> 20

Ligand’s Revenue Generating Assets

Biotech44%

Big Pharma34%

Generic12%

Spec Pharma10%

9

65 Different Partners

Select Big Pharma

Select Biotech Select Spec Pharma

Select Generic

Diverse Portfolio Among Drug Companies

• We estimate our partners will spend over $1.1 billion in 2015 on R&D to advance our programs

• More partnered programs and late-stage trials are pushing spending up over 30% higher than 2014

Fully-funded Partnerships Driving Growth

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– 13 Phase 3 trials – 14 preclinical programs

– 38 Phase 2 trials – Manufacturing scale-up

– 58 Phase 1 trials – Regulatory filing fees

– 2 Phase 4 trials

• Continued strong financial performance

• Business model provides tremendous earnings leverage

— Growing total revenues

— Flat cash operating costs

— Significant estate of tax assets

• Accelerating revenue and earnings growth going forward

Financial Overview

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Accelerating Projected Revenue Growth

$0

$30

$60

$90

$120

$150

2011 2012 2013 2014 2015 2016 2017

• Growth due to:

– New products launched

– Growth in existing brands

– Higher royalties

12

$ m

illio

ns

$0

$20

$40

$60

$80

$100

$120

$140

$160

2013 2014 2015 2016 2017

License and other

Material Sales

Royalties

Projected Revenue

$49.0

$64.5

$81-$83

$ m

illio

ns

13

>$146

>$107

14

Ligand’s Cash-Generating Power Becoming Increasingly Clear

$0

$30

$60

$90

$120

$150

2011 2012 2013 2014 2015 2016 2017

Revenue Cash Expenses

Actual Outlook

• Strong revenue growth

• Operating expense levels projected to remain similar the next few years

• Significant increase in cash-flow projected

$ M

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Accelerating Projected Non-GAAP EPS Growth

$0.00

$0.50

$1.00

$1.50

$2.00

$2.50

$3.00

$3.50

$4.00

$4.50

2011 2012 2013 2014 2015 2016 2017

• Growth due to:

– Higher revenues

– High gross margins

– Low and flat expenses

– Lean share count

15 Note: Non-GAAP EPS excludes changes in contingent liabilities, mark-to-market adjustment for amounts owed to licensors, non-cash SBC expense and non-cash debt related costs

Promacta®

• Oral medicine that boosts platelets. Ligand owed royalties

• Long patent protection, Orange Book patent expiration in 2027

• Blockbuster commercial potential (>$1 billion) due to growing and large list of potential therapeutic indications

ITP HCV ORT Idiopathic

Thrombocytopenia

Thrombocytopenia Induced by Hepatitis C

Oncology Related

Thrombocytopenia

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Promacta®: Blockbuster Commercial Potential

Aplastic Anemia

95 Countries

Recently filed in the EU Recent Pediatric ITP filings

53 Countries

Global filing and launch investment

Major clinical investment ongoing: MDS, AML, CLL, CIT,

others

AA Currently Approved Indications

Ongoing Development New Markets

3 Countries

Myelodysplastic Syndromes

(MDS)

Acute Myeloid Leukemia

(AML)

Chronic Lymphocytic Leukemia

(CLL)

Cancers of the Blood

Severe cytopenia, patients need frequent transfusions

Fast-progressing cancer of the blood

Slow-progressing cancer

Excess bleeding results in major complications or death for nearly

25% of patients1

Clinically, Promacta shown to increase platelets

and pre-clinically, inhibits leukemia growth

Clinical data in CLL indicates 80% response rate

in CLL-associated ITP, 55% overall response rate

Global Phase 3 studies

in progress

Abnormal red blood cells and platelets can quickly crowd out

normal cells

Focused in white blood cells

~19,000 new diagnoses

in US each year2

~14,500

new diagnoses in US each year2

~16,000 new diagnoses

in US each year2

1Expert Opinion: Thrombocytopenia & Myelodysplastic Syndrome medscape.org/viewarticle/565023 2 National Cancer Institute, SEER Cancer Review, 2012

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Promacta®: Oncology-Related Thrombocytopenia

$ m

illio

ns

GSK reported quarterly sales. Figures converted from GBP to USD 1Growth calculations 2014 vs. 2013

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2011

Promacta®: Regional Quarterly Revenue

$0.0

$20.0

$40.0

$60.0

$80.0

$100.0

Q1 Q2 Q3 Q4 Q1 Q2 Q3 Q4 Q1 Q2 Q3 Q4 Q1 Q2 Q3 Q4

ROW

EU

US

2012 2013 2014

ROW 26%

EU 8%

US 39%

TOTAL 25%

Expected strong growth of LGND royalties

— New territories being added — New indications being pursued — Higher royalties on higher sales

Strong year-over-year growth in all geographies1

70

85

GSK Novartis

1,300

8,000

GSK Novartis

$2.0

$11.7

GSK Novartis

GSK and Novartis: Business Unit Profiles1

Novartis has a superior oncology business, ~6 times larger than GSK’s; Promacta® transitioned to Novartis on March 1st

Oncology Employees Countries with Presence 2014 Oncology Revenue ($B)

1 GSK and Novartis company disclosures relating to revenue and business unit structures; GSK.com, Novartis.com

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Promacta® Projections: NOVN Analysts Annual Revenue Projections

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$0

$100

$200

$300

$400

$500

$600

$700

$800

$900

2016 2017 2018 2019 2020

$ M

illio

ns High

Low

Average

4 NOVN covering analyst reports as of 4/27/15

Kyprolis®

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• Leading 3rd-line treatment for multiple myeloma (MM) in the US

— Viewed as best-in-class proteosome inhibitor

— 25% year-over-year growth in 2014

Kyprolis®

• Royalty rates of 1.5% to 3.0%

ASPIRE Phase 3 Data

Dr. Keith Stewart The Mayo Clinic

“We are observing an unprecedented duration of remission, without additional toxicity, in relapsed and heavily pretreated patients.”

• Amgen has submitted US and EU applications for relapsed MM

— Granted priority FDA review; July 26, 2015 PDUFA date — Also granted EU Accelerated Assessment

• Major investment by Amgen focused on further expansion of the label

— Front-Line MM: Phase 3 (CLARION) — Small-cell Lung Cancer: Phase 2

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• Recent data and events have continued to demonstrate the significant potential of Kyprolis

Kyprolis®

• APSIRE Phase 3 trial demonstrated an unprecedented PFS (26.3 months) in relapsed MM

• ENDEAVOR Phase 3 trial demonstrated a DOUBLING of median PFS over Velcade® (18.7 vs. 9.4 months) in relapsed MM

• Significant unmet needs remain in MM, and the market is expected to double to over $13 billion by 2020

Reference AMGN March 2, 2015 corporate presentation

$0.0

$0.5

$1.0

$1.5

$2.0

$2.5

$3.0

2016 2017 2018 2019 2020

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Kyprolis® Projections: AMGN Analysts Annual Revenue Projections

$ B

illio

ns High

Low

Average

16 AMGN covering analyst reports as of 4/27/15

The Big Six

• Certain portfolio assets stand above others, having the potential to add significantly to Ligand’s top and bottom line

• They do so as a result of a mixture of factors, including:

— Market size or therapy area addressed

— Upcoming potential milestone events

— Royalty rate or specifics of deal economics

• Major news catalysts expected over the next 6 to 24 months

• More potential programs could move into the Big Six

The Big Six: Major Pipeline Assets

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Partner

Program (Therapy Area)

Stage

Royalty Rate

Potential Launch

Potential 2015 Events

CE- Melphalan (Oncology)

NDA

20% 2015 Approval

Delafloxacin IV (Infection)

Phase 3 Undisclosed 2016 Phase 3 data

SAGE-547 (Neurology)

Phase 2 Undisclosed 2017 Pivotal Initiation

Sparsentan (FSGS - Kidney Disease)

Phase 2 9% 2017 Enrollment Completion

MK-8931 (Alzheimer’s Disease)

Phase 3 Undisclosed 2018 Updates

IRAK-4 (Oncology)

Preclinical 6.0-9.5% 2019 Clinical Start

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The Big Six: Major Pipeline Assets

Viking Therapeutics

VKTX: Company Overview

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• San Diego-based biotech, developing novel, first-in-class or best-in-class drugs for metabolic disorders

— Clinical-stage programs with preliminary efficacy signals in humans

• VK5211: Entering Phase 2 development for hip fracture

— Non-steroidal selective androgen receptor modulator (SARM)

— Promising efficacy in both bone and muscle

— Phase 2 data expected 2Q16

• TR-β agonists: X-linked adrenoleukodystrophy (X-ALD)

— VK0214, VK2809: Novel, selective thyroid receptor-β agonists

— Strong scientific rationale for application in X-ALD, rare neurodegenerative disorder

— Preclinical work on-going

— Potential human POC data 1H16

— Additional opportunities in lipid disorders such as NASH and cholesterolemia

• Three additional programs targeting diabetes, anemia, lipid disorders

VKTX: Investment Overview

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• Initial single-program partnership with Ligand in 2012

• Partnership expanded to five programs in 2014

• Viking IPO priced last week

— Equity milestone payment to Ligand initially valued at ~$27M, subject to adjustment on issuance of IPO over-allotment shares

— Ligand invested additional $9M in offering

• Benefits to Ligand

— Potential to receive significant future royalties through 5 additional Shots-on-Goal

— Equity stake in promising growth biotech

Ligand’s Novel R&D:

Glucagon Receptor Antagonist

• Novel, highly potent, oral GCGR antagonist for treatment of type 2 diabetes completed Phase 1a trial in mid-2014, and Phase 1b trial initiated late last year

— One of Ligand’s most promising un-partnered assets

— Potential best-in-class properties

• Diabetes market is expected to double to $60 billion by 20201

— Combo therapy highly prevalent and necessary to optimize management of disease

— Creates significant opportunity for novel treatment mechanisms

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Novel R&D: Glucagon Receptor Antagonist LGD-6972 for Diabetes

1 Brinson Patrick report 12/3/12; SunTrust report 6/25/13

Existing Class

Product Profile GCGR Advantage

DPP-IV Inhibitors

Modest reduction of plasma glucose Higher glucose

reduction

GLP-1 Agonists

Only available as injectables Oral

SGLT-2 Inhibitors

Contraindicated for renally impaired patients Spares kidney

• Product profile and recent clinical data suggest significant market advantages for a safe, highly potent, oral GCGR antagonist as compared to existing classes of new mechanisms

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Novel R&D: Glucagon Receptor Antagonist Advantages of Potent GCGR Antagonist

Novel R&D: Glucagon Receptor Antagonist Positive Phase 1a Clinical Data for LGD-6972

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Change in fasting glucose(24 hr post dose)

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40 m

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480 mg

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• Positive clinical data presented in 2014

• Excellent safety profile

• Dose-dependent decreases in fasting plasma glucose in normals

• Robust decreases in glucose in type 2 diabetics after just a single dose

• Recent scientific ripening of the field, glucagon receptor antagonism widely seen as one of the most promising novel approaches to treatment of diabetes

• Multi-dose trial currently in progress, data expected in coming weeks

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Potential Upcoming Events

Target Date Program Event

Q2’15 Duavive EU product launch

Q2’15 LGD-6972 Phase 1b results

7/26/15 Kyprolis Multiple Myeloma sNDA PDUFA date

2H’15 Promacta Pediatric ITP NDA and MAA approvals

2H’15 Kyprolis Relapsed multiple myeloma NDA and MAA approvals

2H’15 NS-2 Phase 2 trial initiation

2H’15 Delafloxacin NDA Submission

Q4’15 Promacta Severe Aplastic Anemia MAA approval

Q4’15 CE-Melphalan NDA approval

Q4’15 Carbella NDA approval

Q4’15 Topiramate Phase 2 trial initiation

Q4’15 IRAK-4 Phase 1 trial initiation

Deutsche Bank 40th Annual Health Care Conference

Boston, MA May 6, 2015 NASDAQ: LGND