Ligand Pharmaceuticals 8K/A Regulation FD Disclosure | LGND 24 Jun 11

Investor and Analyst Day

June 23, 2011

Nasdaq: LGND

Exhibit 99.1

Investor and Analyst Day

John Higgins

President and Chief Executive Officer

Safe Harbor Statement

•

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, expense reductions and drug development programs may not be realized. In

addition there can be no assurance that Ligand will achieve its guidance in 2011.

•

The forward-looking statements made in the presentation are subject to several risk

factors, including, but not limited to, Ligand’s reliance on collaborative partners for

milestone and royalty payments, regulatory hurdles facing Ligand's, CyDex's and partner's

product candidates, uncertainty regarding Ligand's, CyDex's and partner's product

development costs, the possibility that Ligand's, CyDex's and partner's drug candidates

might not be proved to be safe and efficacious and commercial performance of Ligand's

and/or its partner's products. Additional risks may apply to forward-looking statements

made in this presentation.

•

The risk factors facing Ligand are explained in greater detail in Ligand’s filings with the

SEC, including the most recently filed annual reports on Form 10-K and quarterly reports

on Form 10-Q, as well as other public filings.

•

While forward-looking statements reflect our good faith beliefs (or those of the indicated

third parties), they are not guarantees of future performance. We disclaim any obligation to

update or revise any forward-looking statements, whether as a result of new information,

future events or otherwise.

Investor and Analyst Day Agenda

Welcome and Company Overview

John Higgins

Captisol

Technology

Matt Foehr

Melphalan Program

Rick White

Promacta Highlights

Rob McKay

Thrombocytopenia in Hep C

Nezam H. Afdhal, M.D.

Chief of Hepatology, Director of Liver Center,

Beth Israel Deaconess Medical Center

Financial Highlights

John Sharp

Small Group Workshops

•

Captisol –

Powerful Enabling Technology

•

“Shots on Goal”

Portfolio

Questions and Answers / Reception

Small-Group Workshops

Captisol

–

Powerful Enabling Technology

Matt

Foehr

–

Executive

Vice

President,

Chief

Operating

Officer

JD Pipkin –

Senior Director, New Product Development

Vince Antle –

Senior Director, Technical Operations and Quality Assurance

“Shots-on-Goal”

Portfolio

Rob McKay –

Senior Director, Business Development and Investor Relations

Syed Kazmi –

VP, Business Development and Strategic Planning

Rick White –

VP, Business Development and Marketing

Room

Ligand’s Business Model

Ligand's focus is to build a large portfolio of high

quality pharmaceutical assets that can drive

substantial cash flow and profitability. We operate

the

business with an emphasis on focused drug

development

and

partnerships,

with

disciplined

and

highly selective cost structure.

Revenue Outlook

Robust Pipeline

Captisol

–

Enabling Technology

High Quality Partners

The Foundation of the Ligand Opportunity

Ligand is Doing Great

•

Significant expansion (doubling of portfolio to over 60 programs) in

past 6 months as a result of Cydex acquisition

•

A number of positive news events by partners in 2011

•

Important new additions to senior management and Board of Directors

•

Most revenue generating assets ever on lowest cost structure

•

Positive clinical data announced in the past three months

•

Promacta

is a “now”

story

•

Directors have personally purchased over $1.2 million of Ligand stock

(131,125 shares) over the past 6 months. Directors now own 10% of

Ligand.

•

Over past year, daily trading volume has increased by ~30%

Ligand’s Potential Downside

Individual project set-backs

Slower growth

Partners drop programs

Risk

Reward

The Investment Proposition: Risk vs. Reward

Ligand’s Potential Upside

Potential blockbuster product approved/

in-development

Near-term profitability

Well funded/financially disciplined

royalty

partnerships

than

any

peer

Attractive fully-owned

pipeline

Substantial calendar of news flow

Large NOLs

We believe the upside reward is substantially greater than the downside risk

Ligand’s Potential Upside

List presented last summer (2010)

Updated Outlook

Potential blockbuster product approved/

in development

Data

for

Promacta

expected

over

months

Near-term profitability

Projected to turn profitable by year-end 2011

Well funded/financially disciplined

Lowest cost structure in company’s history

More royalty partnerships than any peer co

Large portfolio of assets, doubled in over last 12 months

Attractive fully-owned pipeline

SARM, diabetes, JAK 3, and melphalan programs

Substantial calendar of news flow

Continued news flow

Large NOLs

Continue to be ready to use following profitability

Potential Significant Revenue Expansion Over Next Several Years

*Plus license fees

Illustrative Growth

2015

2012

"Shots on Goal" Vision

Turning into Reality

Promacta

Avinza

Conbriza

Promacta

Nexterone

Avinza

Carfilzomib

Conbriza

Aprela

Nexterone

CXCR2

Carfilzomib

Clopidogrel

>$30 million revenue*

Melphalan

Carbamazepine

Merck Captisol

Program

>$200 million revenue*

Worldwide Quarterly Promacta

Revenue Growth

$0.0

$2.0

$4.0

$6.0

$8.0

$10.0

$12.0

$14.0

$16.0

$18.0

$20.0

4Q08

1Q09

2Q09

3Q09

4Q09

1Q10

2Q10

3Q10

4Q10

1Q11

New markets and

new indications

should help

accelerate

revenue growth

Ligand and GSK reports

Ligand expects to

receive royalties

for another

14 years

Over 50 Partnered Programs

17%

30%

39%

•

Over half of the partnered portfolio is Phase II or later

•

Portfolio is highly diversified across many partners, stages of development and

therapeutic areas

•

Merck,

GSK

and

Pfizer

are

our

partners

with

the

most

programs

Marketed /

Approved

Phase III / NDA

Phase II

Phase I

PreClin

Ligand Portfolio: Partnered Programs

19%

12%

26%

35%

•

Programs are highly diversified across more than 10 therapeutic areas

•

The therapeutic areas most represented in the portfolio are oncology,

inflammation, neurology and metabolic disease

Ligand Portfolio: Total Portfolio Snapshot

Total Portfolio (Over 60 programs)

Marketed /

Approved

Phase III / NDA

Phase II

Phase I

PreClin

Ligand's Internal Pipeline Focus

Timing*

Projected Event

3Q11

Carfilzomib NDA filing

Platform Captisol Partnership

4Q11

Promacta Phase III HepC Results

Aprela NDA filing

SARM program update

1Q12

Initiate pivotal Melphalan study

Top Line IL-9 Phase II Results

Clopidogrel 505(b)(2) study initiation

2Q12

Merck CXCR2/COPD Study Completion

Carfilzomib NDA Approval

Promacta sNDA filing for HepC

*Ligand internal estimates

Ligand Portfolio:

Potential Upcoming News Flow

•

High return late-stage

internal development

programs

•

New opportunities

New

Shots

•

High quality

relationships

•

Significant

expansion of “shots

on goal”

Deals

•

Powerful

enabling

technology

meeting key

needs

Captisol

CyDex Acquisition:

What has it brought to Ligand?

Captisol

The Need

Patented, chemically-modified cyclodextrin

Increase drug solubility, reduce site reactions

Versatile across molecule families and sizes

Safe, inactive, inert

Over 100 clinical studies

Type V Drug Master File

Captisol

Enabling New Drugs

•

Strong manufacturing technology and IP estate

•

Hovione Partnership

50 metric ton capacity for Captisol

, ability to double

Exclusive relationship with built-in site redundancy

•

Intellectual Property

8 patent families covering technology, 12 patent families for products

Formulation and process-based patent portfolio providing protection

through 2029

Trade secrets, Drug Master File

Continuing internal innovation

Captisol

Enabling New Drugs

Captisol

The Value

Approved or

pending

products

Broader

platform

relationships

with partners

who can

leverage

Captisol

more ways

Internal

Captisol-

enabled

development

programs

with potential

for high

returns

Captisol

The Value

•

Reformulation can bring meaningful innovation to

established medicines

•

Late-stage internal development can create significant

value in exchange for relatively modest investment

•

505(b)(2) pathway leverages existing data

Lower development costs

Shorter timelines

Smaller infrastructure requirements

Captisol-enabled

Internal Development Programs

•

High dose conditioning treatment prior to

hematopoietic progenitor (stem) cell transplantation

for multiple myeloma

•

Orphan Drug Status

Market exclusivity, PDUFA fee waiver

•

Phase II dosing now completed

Interim results presented at ASCO

•

Pivotal trial projected to begin early 2012

Captisol-enabled

PG-Free Melphalan

Continuing need for new

and innovative therapies

Multiple Myeloma

Second most common

hematologic cancer

50,000 patients

in the U.S., 20,000

diagnosed annually

Area of growing

industry interest

Transplant remains

a centerpiece in

managing disease

progression

Multiple

Myeloma:

Disease

Treatment

and

Progression

Deep Freeze

Thawing and infusion of

patient stem cells

Autologous

Stem

Cells

Autologous

Stem

Cells

Autologous

Stem

Cells

High Dose

Chemotherapy

Cryopreservation of

patient stem cells

Mobilization and

leukapheresis of

patient stem cells

Multiple Myeloma:

Stem Cell Transplantation

Captisol-enabled

Melphalan for

Injection

Ligand

Internal Development Asset

One vial system

Propylene glycol-free

24-hr infusion window

Treatment Flexibility

Alkeran

Launched in 1993

GlaxoSmithKline

Two vial system

Propylene glycol diluent

60-min infusion window

Per label limitations

Melphalan Product Comparison

Captisol-enabled

Melphalan for

Injection

Ligand

Internal Development Asset

One vial system

Propylene glycol-free

24-hr infusion window

Treatment Flexibility

Product Advantages:

•

Improved stability and use time in an all

aqueous formulation

•

Longer administration durations, slower

infusion rates

•

Elimination of two-vial system

Physicians expected to:

•

Safely achieve higher dose intensity

•

Easily deliver concomitant meds in high-

dose regimens

•

Modulate dose to patient tolerability

•

Higher dosage

potential for improved

response rates

Melphalan Product Comparison

•

IMS Reports Sales of $85MM for Rolling 12 Month Period

•

Majority of the Current Usage as a High Dose Conditioning Agent Prior to

Autologous Stem Cell Transplant in Multiple Myeloma Patients (currently off

label)

•

Potential Label, and Orphan Designation, for Captisol-enabled

Propylene

Glycol-Free Melphalan Addresses this Market

•

Unmet Medical Need with the Current Standard of Care:

Stability following reconstitution (60 minutes)

Limits on Absolute Daily Dosing

Limits on Duration of Infusion

Potential Adverse Reactions Due to Co-Solvent (propylene glycol)

Melphalan Market

A Marketing and Sales effort could be relatively lean and efficient

•

Melphalan therapy is well understood and entrenched, with few

influential bone-marrow-transplant hospitals

“Ultra-niche”

call universe

•

Benefits of Captisol-enabled

Melphalan formulation are easily

positioned

•

Effective promotion with lean sales organization achievable

•

Orphan Indication has favorable payer landscape (public and private)

Compass/Defined Health survey, 2009

Captisol-enabled

Melphalan: Opportunity

Captisol-enabled

Melphalan: Projected Timeline

The Shots on Goal Model

8 Assets Currently

Generating Commercial

Revenue

Over 50

Partnered Programs

Over 60

Total Programs

Over 25

Different Partners

Over 10

Therapeutic Areas

Minimizing Risk Through Portfolio Size and Diversification

10 Potential New

Approvals in

the Next 4 Years

The Value Pyramid For Ligand Assets

The Top of the Value Pyramid for Ligand is Promacta

Avinza

Carfilzomib

Aprela Nexterone

CXCR2 Viviant

Over 50 Additional Programs

from Preclinical to PIII

•

There are numerous programs in

the Ligand portfolio today which

add significant value to the

business

•

But, Ligand’s royalty interest in the

Promacta franchise at GSK is the

most valuable single asset Ligand

owns

Promacta Background

•

What is Promacta

Promacta is a once-daily oral medicine that activates the thrombopoietin

(TPO) receptor

Activation of the TPO receptor causes platelets to increase, relieving

conditions of low platelets known as thrombocytopenia

•

History

Ligand and GSK jointly discovered Promacta as part of a thrombopoietin

(TPO) receptor agonist research collaboration started in 1995

GSK later licensed from Ligand the follow-on TPO receptor agonist LGD-4665

in 2008

Approved for ITP

Marketed by GSK

PIII HepC Data Release in 3Q/4Q11

Promacta Follow-On : GSK-5921

5-10%, blended 9% on $1B in Sales

An Approved Drug in All Major Markets

Promacta

: The Foundation of the Ligand Growth Story

Aspects Of The Promacta Franchise Make It An Ideal

Foundation For Ligand’s Financial Growth Story

Significant Royalty Interest

Major Upcoming Catalyst Events

Long Patent Protection

Major Potential for Label Expansion

Marketed by a Premier Pharma Company

Life-Cycle Management Opportunity

ITP

HepC

Oncology

Others

Patented until July 2025

Promacta Program Recent Developments (1 of 2)

•

New ITP Launches Around the World

EU, Japan, South America

•

Increased ITP Sales

World-wide ITP sales in 1Q2011 increased 109% over 1Q2010

The Promacta ITP Franchise Has Continued To

Generate Positive News In The Past Year

Promacta Program Recent Developments (2 of 2)

•

Full ITP Approval Granted by FDA

GSK completed post-approval commitment of generating long-term safety

data

Label now includes efficacy and safety data from RAISE, 6-month ITP study

Since 2008, GSK has been working with FDA. Studies submitted:

•

6-month efficacy and safety data

•

2-year safety data in chronic ITP

•

Updates from chronic liver disease (ELEVATE) trial

The Promacta ITP Franchise Has Continued To

Generate Positive News In The Past Year

Idiopathic Thrombocytopenia Purpura (ITP)

Phase I

Phase II

Phase III

Approved

Hepatitis C-Related Thrombocytopenia

Oncology-Related

Thrombocytopenia

Clinical Studies

2 P-III Studies

GSK Is Investing Significantly In The

Growth Of The Promacta Franchise

11 PI and PII Studies

Approved

(Label Expansion

Studies Ongoing)

GSK Investment in Promacta Franchise Expansion

Patients

needed

to potentially

reach

$1B

in sales

Thrombocytopenia Is Comprised Of Multiple Sub-Markets of

Thrombocytopenia-Inducing Diseases, Similar to Anemia and Neutropenia

Wall Street Research on GSK published Nov. 21, 2005

Thrombocytopenia: A Multibillion Dollar Platelet Potential

Significant Revenue Growth Potential for Ligand

Territory Expansion

Indication Expansion

•

HepC

•

Oncology

•

Others

Long IP Protection

2025

Expansion of the Promacta Franchise

Translates Into Significant Revenue Growth for Ligand

Promacta Royalty

Illustrative Ligand Revenue

Annual Sales

Royalty

<$100M

4.70%

$100M-$200M

6.60%

$200M-$400M

7.5%

$400M-$1.5B

9.40%

>1.5B

9.30%

Annual

Sales

Blended

Royalty

Ligand

Revenue

$500M

7.1%

$36M

$1B

8.3%

$83M

$1.5B

8.6%

$130M

The Role for Eltrombopag (Promacta) in the

Treatment of HepC-Related Thrombocytopenia

N. Afdhal M.D

Beth Israel Deaconess Liver Center

Harvard Medical School

Agenda

Eltrombopag and thrombocytopenia

Current status of HCV therapy

The ENABLE 1 and ENABLE 2 P-III Studies

ELEVATE Study –

conclusions on Eltrombopag safety

The Unmet Medical Need for Thrombocytopenia

Thrombocytopenia is a major factor in patients being unable to

achieve a desired clinical outcome in dozens of diseases

Currently estimated to be nearly two million patients annually in the

US who need to be treated for thrombocytopenia

Current non-drug techniques used to increase platelets (i.e. platelet

transfusion, splenectomy) are costly, risky, and inconvenient.

The need for a more convenient and effective method for combating

thrombocytopenia is clear

Liver Disease–Associated Thrombocytopenia

Platelet counts may be as low as

20,000–40,000/

Prevalence of thrombocytopenia

increases with severity of liver disease

Degree of thrombocytopenia correlated

with severity of liver disease

Thrombocytopenia predictive of

reduced 5-year survival

Thrombocytopenia may develop or

worsen with interferon-based therapy

4% in recent DAA trials

Degree of Liver

Damage

Thrombocytopenia

Prevalence

Normal liver

2.3%

Fatty liver

5.1%

Chronic hepatitis

20.3%

Advanced liver

disease

31.8%

Eltrombopag

Thrombopoietin receptor agonist

Oral, once-daily tablet

Induces megakaryocyte

proliferation and differentiation

Increases platelet counts in

patients with HCV¹

1. McHutchison J, et al.N Engl J Med.

2007;357:2227–2236.

Current Status of HCV therapy

and the Role for Eltrombopag

Thrombocytopenia, HepC, and Eltrombopag

Nearly 10% of HepC

patients in the US suffer from treatment-limiting

thrombocytopenia

These patients have significantly worse outcomes due to their

underlying liver disease and inability to complete antiviral therapies

Eltrombopag

PII data demonstrates that this drug may be useful for

these patients to overcome thrombocytopenia limitations and

complete antiviral therapy

Key

question

arising

around

the

eltrombopag

HepC

opportunity

How will new HepC

therapies impact the need for eltrombopag?

there

long-term

safety

concern

for

eltrombopag

because of

the ELEVATE study results?

HCV Pipeline* by MOA and Stage of Development

3/2/2010 –

selected

compounds only.

*Publicly available information via press release, corporate

presentations, and assumptions based on patent filings.

Target “Regimen”

Outcomes

Today’s Regimen

2015+

Target

IFN + Ribavirin

(R)

G1-Naive

•

SVR = 40%

•

Duration = 48 weeks

G2-3 Naïve

•

SVR = 75%

•

Duration = 24 weeks

G1-Experienced

•

No meaningful option

•

Frequent dosing and

poor tolerability

New Triple / Quad

Combo Regimens

•

Highest possible SVR

•

No / low resistance

•

Better tolerability

•

Shorter durations

•

Simplified delivery

IFN + R + DAA

IFN + DAA + DAA

IFN + R + DAA + DAA

DAA + DAA (+ DAA)

IFN = Interferon

R = Ribavirin

DAA = Novel Direct Acting Antiviral agents

Regimen 4. High risk / low probability / far away / no PoC

SVR Rates in Telaprevir-Treated Patients Compared with

Peginterferon/Ribavirin

Alone

Jacobson IM et al. Hepatology.

2010;52(Suppl 1):Abstract 211.

Telaprevier

12 weeks +

Peg/Riba

48 weeks

Telaprevier

8 weeks +

Peg/Riba

48 weeks

Peg/Riba

48 weeks

The Impact of New HepC

Therapies on the Use

of Eltrombopag

in HepC

Underlying thrombocytopenia is still an issue for many HepC

patients

The new protease inhibitors do not change that fact

•

New protease inhibitor therapies slightly increase the rate of

thrombocytopenia

Due to increased SVR seen with new cocktails, the need for

eltrombopag

should actually increase

•

Higher SVR rates may encourage doctors to treat more

aggressively those patients with thrombocytopenia

Eltrombopag

Clinical Studies

HepC

Studies

Eltrombopag

PII HepC

Study Design

4 wk

12 wk

PEG-IFN + ribavirin

+ eltrombopag

Pre-antiviral

Eltrombopag

4 wk

12 wk +

Eltrombopag

12 wk +

Eltrombopag

12 wk +

Eltrombopag

INITIATE

antiviral Rx if platelets

>70–100 K/µL

30 mg

50 mg

75 mg

PART 1 PART 2

4 wk

Follow-up

PLACEBO

30 mg

50 mg

75 mg

0.0007

0.0003

< 0.0001

74%

75%

95%

20%

40%

60%

80%

100%

McHutchison, NEJM 2007

Phase II: Primary Efficacy Endpoint

Platelet count

100,000/uL at Week 4

PLACEBO

30 mg

50 mg

75 mg

53%

36%

65%

20%

40%

60%

80%

100%

Phase II:

Subjects Completing 12 Weeks of PEG-IFN Therapy

Phase II:

Median Platelet Count > 200K without thrombotic events

100

150

200

250

112

Placebo

30 mg

50 mg

75 mg

INITIATION

MAINTENANCE

Study Day

McHutchison, AASLD 2006

Treatment Group, n (%)

PBO

N=18

30mg

N=14

50mg

N=19

75mg

N=23

Any AE

10 (56)

11 (79)

10 (53)

13 (57)

Headache

3 (17)

5 (36)

3 (16)

4 (17)

Dry mouth

1 (6)

2 (14)

2 (11)

2 (9)

Pruritus

2 (9)

Nausea

1 (7)

2 (11)

1 (4)

Fatigue

2 (11)

1 (4)

Upper abdominal pain

2 (14)

2 (11)

Insomnia

2 (11)

Arthralgia

2 (14)

1 (5)

No thromboembolic

or elevated LFT events of concern

Phase

II:

Adverse

Events

–

Pre-Antiviral

Phase

Phase II: Conclusions

Eltrombopag increased platelet counts in subjects in all dose groups

A significant number of subjects achieved the primary endpoint (Week 4)

in all dose groups compared to placebo

Eltrombopag enabled 45/56 subjects to initiate IFN therapy

–

31 subjects completed 12 weeks of IFN therapy

Preliminary PK findings in general indicate exposure increases with dose

with wide variability

No safety signals of concern in this initial short term study

Safety and efficacy data supports further investigation of eltrombopag in

this patient population

Two parallel global Phase III studies

ENABLE 1 and 2

peginterferon

alfa-2a

(PEGASYS)

plus

ribavirin

–

ENABLE 1

peginterferon

alfa-2b

(PEG-Intron)

plus

ribavirin

–

ENABLE 2

ltrombopag

INitiate

and

Maintain

Interferon

ntiviral

Treatment

to Benefit Subjects with Hepatitis C related Liver DiseasE

Pre-Antiviral Phase

Open-label eltrombopag

(2 –

9 weeks)

Antiviral Phase

Randomized

(up to 48 weeks)

platelets

>90,000/uL (E1)

100,000/uL (E2)

25mg>50mg>75mg>100mg

•

2:1 randomization eltrombopag:placebo

•

Dose titration of eltrombopag allowed throughout

•

Primary endpoint = proportion of patients achieving SVR (6M off –Tx)

•

N=750 dosed/675 randomized study

•

3 regions, 26 countries, >250 centres

SVR

6 months

off-Tx

Randomized Withdrawal Design

open label

eltrombopag

Eltrombopag

+ PEG-IFN/Rib

Placebo

+ PEG-IFN/Rib

Screening

Days

Platelets

<75K/µL

Pre-Antiviral Treatment Phase

Open-label eltrombopag dosed for

up to 9wks until platelet count

increases to enable initiation of

antiviral therapy.

Part 1 (2-9 Wks)

Open-Label

Platelets

90K/µL*

Platelets

90K/µL*

Platelets

90K/µL*

*Platelets

<90K/µL

*Platelets

<90K/µL

*Platelets

<90K/µL

START

*Platelets

<90K/µL

Platelets

90K/µL*

*90K/µL (ENABLE 1)

100K/µL (ENABLE 2)

2:1 Randomisation (Eltrombopag:Placebo)

Eltrombopag

plus

Antiviral Therapy

Antiviral Treatment Phase

Randomised either to

maintain dose of

eltrombopag from Part

1 or to matched

placebo.

Part 2 (

48 Wks)

Double-Blind

Placebo

plus

Antiviral Therapy

24 Week FU

Ocular/SVR

Post-last dose of

investigational

product.

ENABLE 1 and 2 Study Design

25mg

2 Weeks

50mg

1-2 Weeks

75mg

1-2 Weeks

100mg

1-3 Weeks

SVR rate defined as percentage of subjects with non-detectable

HCV-RNA at 24 weeks post-completion of the planned treatment

period

Platelet count

90-100,000/

L in Part 1

Dose modifications

Safety and tolerability

Platelet counts

RVR,

EVR and ETR

Health-related quality of life

Safety

modified

include

risk

thrombotic

events

–

both

studies

completed without DSMB concerns

Endpoints

Eltrombopag Safety Summary

ELEVATE Study and Safety

Eltrombopag in Chronic Liver Disease Patients

with Thrombocytopenia Undergoing an Elective

Invasive Procedure: Results from ELEVATE,

a Randomised Clinical Trial

Afdhal,

Giannini,²

G.N.

Tayyab,

Mohsin,

J-W.

Lee,

A. Andriulli,

L. Jeffers,

J. McHutchison,

F. Campbell,

N. Blackman,

D. Hyde,

A. Brainsky,

D. Theodore

1. Division of Gastroenterology/Liver Center, Beth Israel Deaconess Medical Center, Boston, MA, USA; 2. Gastroenterology Unit, Department of Internal

Medicine, University of Genoa, Genoa, Italy; 3. Department of Medicine, Gastroenterology and Hepatology, Post Graduate Medical Institute, and Lahore

General Hospital, Lahore, Pakistan; 4. Department of Gastroenterology, Services Hospital Lahore, Services Institute of Medical Sciences, Lahore,

Pakistan; 5. Department of Internal Medicine, Inha University Hospital and

School of Medicine, Incheon, Korea; 6. Department of Internal Medicine,

Division of Gastroenterology, Casa Sollievo Sofferenza Hospital,

San Giovanni Rotondo, Italy; 7. Center for Liver Diseases, University of Miami, Miller

School of Medicine, Miami, FL, USA; 8. Division of Gastroenterology, Duke University Medical Center, Durham, NC, USA; 9. Clinical Development,

GlaxoSmithKline, Stockley Park, Uxbridge, UK; 10. Biometrics and Epidemiology, GlaxoSmithKline, Collegeville, PA, USA; 11. Clinical Development,

GlaxoSmithKline, Collegeville, PA, USA; 12. Clinical Development, GlaxoSmithKline, Research Triangle Park, NC, USA

Difference 53% (95% CI: 43, 62)

< 0.0001

100

Placebo

(N = 147)

Eltrombopag

(N = 145)

72%

19%

n = 28

n = 104

Primary Endpoint: Avoiding Platelet

Transfusions with Elective Invasive Procedure

Placebo

(N = 145)

Eltrombopag

(N = 143)

n (%)

Bleeding

25 (17)

19 (13)

Thrombotic event

2 (1)

6 (4)

Ocular (focus on cataracts / visual

acuity decrease)

6 (4)

Malignancies*

1 (<1)

Selected Adverse Events

* Basal cell carcinoma (Grade 2) reported for one patient receiving placebo and B cell lymphoma (Grade 4) reported

for one patient receiving eltrombopag; neither was considered to be related to treatment by the investigator.

Thrombotic event

Temporal

relationship to last

dose

Temporal

relationship to

procedure

Platelet count at

event (Gi/L)

Procedure

PV / SMV thrombosis

–6 days

417

Brain tumour

resection

PV thrombosis

+4 days

288

Oesophageal

variceal

ligation

SMV thrombosis

+7 days

235

Dental extraction

SMV / mesenteric

thrombosis

+7 days

289

HCC ablation

SPV thrombosis

+14

+13 days

241

TACE

PV thrombosis

+38

+34 days

Oesophageal

variceal

ligation

Acute MI

+20

+19 days

Colon resection

Non-occlusive PV and

mesenteric thrombosis

+128

+128 days

Unknown

Oesophagoduo-

denoscopy

PV, portal vein; SMV, superior mesenteric vein; SPV, spleno-portal vein; MI, myocardial infarction

Eltrombopag

Placebo

Summary of Thrombotic Events

Platelet count >200,000/µL

YES

47 patients

(16%)

241 patients

(84%)

YES = 5 (10.6%)

NO = 42 (89.4%)

YES = 3 (1.2%)

NO = 238 (98.8%)

TEs

Thrombotic Events and Platelet Count

ELEVATE Conclusions

Eltrombopag 75 mg for 14 days

–

Reduced the need for platelet transfusions in CLD patients

with thrombocytopenia undergoing elective invasive

procedures

–

Increased platelets during treatment period and up to 2

weeks following treatment

–

Similar incidence of adverse events and serious adverse

events

–

More thrombotic events in the eltrombopag group

Relationship demonstrated for elevation of platelets

Procedure with endovascular inflammation essential feature

ENABLE studies are expected to confirm role of eltrombopag in HCV

therapy in 2011

Eltrombopag

expected

widely

used

HCV

–

increased

SVR –

increased treatment

Long term safety of eltrombopag continues to be better understood

and continued expansion of the eltrombopag franchise is warranted

Eltrombopag Summary

Financial Highlights

John Sharp

Vice President, Finance

and Chief Financial Officer

Ligand

Pharmaceuticals

Incorporated

2011 Revenue Outlook

•

Total 2011 revenue currently projected to

be $22 -

$24 million

–

$11

$12

million

from

Captisol

sales

–

$8 million from royalties

–

$3 -

$4 million from license and other

•

Potential for additional sources of

revenue and cash in 2011 above these

projections based on new license

agreements

2011 Revenue Breakdown*

License And Other

Royalties

Material Sales

*Excludes revenue from new deals, if any

~15%

~35%

~50%

Financial Guidance

2011 Guidance:

•

Revenue of $22 -

$24 million

•

Operating expenses projected to be ~$20 million

–

Average gross margin on material sales of approximately 60%

•

Projecting turning profitable on an operating basis and

having positive cash flow from operations by the 4

quarter of 2011

•

Cash at year-end projected to be ~$20 million

Low Cost Structure

$0.0

$10.0

$20.0

$30.0

$40.0

$50.0

$60.0

$70.0

$80.0

2007

2008

2009

2010

2011*

G&A

R&D

* High end of expense guidance range

•

Ligand

has significantly reduced expenses over the last several years

•

During the same period, the company closed 5 acquisitions while

significantly expanding its asset base

Pharmacopeia Acquisition

Neurogen

Acquisition

Metabasis

Acquisition

CyDex

Acquisition

IL9 Account Acquisition

Multiple Future Revenue Sources

•

8 programs currently generating royalty revenues

•

Over 50 partnered programs

•

Numerous internal programs

•

Growing Captisol

business

Expected Revenue Growth

*Excludes revenue from new deals, if any

$0.0

$5.0

$10.0

$15.0

$20.0

$25.0

$30.0

$35.0

$40.0

$45.0

2011 Guidance*

2013 Illustrative

License & Other

Material Sales

Royalty

•

Revenue could potentially double within two years on similar cost structure

•

Recurring and high-growth royalty revenue projected to drive the majority of revenue in 2013

High Quality Revenue

Future revenue drivers:

–

Increased royalties from multiple commercial products

(Promacta,Conbriza, Carfilzomib, Nexterone, etc…)

–

Steadily

increasing

Captisol

sales

–

Less

dependence

“one-time”

license/milestone

events

•

Continued potential for additional sources of revenue and cash

from new license agreements

Value of Net Operating Loss Carryforwards

(NOL)

•

Ligand

has

accumulated

substantial

NOL’s

through

our

operating

history and acquisitions

•

NOL’s

should provide significant relief on taxable income if the

company turns profitable

•

NOL’s

as of December 31, 2010 = $438 million

•

Due

tax

code,

NOL’s

are

limited

the

quantity

and

the

timing

which

they

can

used,

not

expect

get

full

offset

taxable income immediately

•

Estimated

net

present

value

NOL’s

~$100M

•

In near-term, the NOL tax should reduce federal tax rate from 34%

down to 2% (AMT)

•

Additionally, Ligand

has ~$16 million of federal R&D Tax Credits

Ligand Pharmaceuticals Incorporated

“Shots on Goal”

Portfolio

2011 Ligand Analyst Day Workshop

The “Shots on Goal”

Model at Ligand

•

The low ROI for biopharma R&D suggests that sharing the cost and

risk of R&D through partnering is a preferred route to meaningful ROI

•

Ligand has assembled the largest portfolio of partnered assets of any

company in its biopharma peer group

–

Now over 50 assets fully funded by partners

•

A focus on assembling partnered assets allows Ligand to run a very

lean cost structure without significantly high R&D costs

•

Coupled with our cost structure,

this portfolio of assets gives

Ligand a reasonable probability of

becoming a sustainably profitable

biopharma business

Industry Unique Partnered Asset Portfolio

•

Over 25 different partners

•

Over 10 different

therapeutic areas

•

Over half of the portfolio is

PII or later

•

Ligand estimates that

partners spend over

$150M per year on this

portfolio

•

Significant quarterly news

flow

Portfolio Asset Highlights

•

PIII/NDA

•

Captisol-enabled

proteasome

inhibitor for multiple

myeloma

•

Ligand eligible to

receive milestones,

royalties and

material sales

revenue

•

Potential 2012

launch

•

Beyond Promacta, there are multiple-late stage programs in the portfolio

that offer Ligand opportunities for substantial future revenue growth

Onyx

Carfilzomib

Merck

CXCR2

Pfizer

Aprela

Merck

Captisol Program

•

PII

•

Novel CXCR2

antagonist for

COPD

•

Ligand eligible to

receive milestones

and royalties

•

Potential 2015

launch

•

PIII

•

Combination of

Viviant and

Premarin for

menopausal

symptoms

•

Ligand eligible to

receive milestones

and royalties

•

Potential 2013

launch

•

PII

•

Captisol-enabled

undisclosed

program

•

Ligand eligible to

receive milestones

and material sales

revenue

•

Potential 2013

launch

Over 40 Other Programs from Preclinical to Phase III Represent

Another Potential Revenue Wave

Quality Portfolio News Flow

•

New Territory Launches

•

New Product Launches

•

NDA Approvals

•

NDA Filings

3Q11

4Q11

1Q12

2Q12

3Q12

4Q12

The

Size

the

Portfolio

Generates

Regular,

Meaningful,

Quarterly

News

Flow

•

PIII Data Releases

•

PIII Trial Initiations

•

PII Data Releases

Promacta

Nexterone

Viviant

Aprela

Carfilzomib

CXCR2

IL-9

CDK

Merck Captisol

Clopidogrel

Others

Deep Partner Relationships

•

PII CXCR2 (COPD)

•

PII CDK Inhibitor

(oncology)

•

PI BACE (Alzheimers)

•

Captisol Program

•

Promacta ITP

•

Promacta HepC

•

Promacta Oncology

•

LGD 4665/GSK 3521

•

Viviant

•

Aprela

•

Marketed Captisol

Products

Ligand has Multiple Broad and Diverse Relationships

With Premier Pharma Companies

Ligand Business Development

LIGAND

REVENUE DRIVERS

LIGAND

PROPRIETARY PIPELINE

LIGAND

BUSINESS

DEVELOPMENT

Ligand business development is the core engine that drives the shots on goal model

-Acquisitions –

Licensing –

Spin Offs -

Alliance Management-

Ligand Pharmaceuticals (LGND) 8-K/ARegulation FD Disclosure