1

Joseph A. Mollica, Chairman of the Board,

Interim President & CEO

Pharmacopeia

John L. Higgins, President & CEO

Ligand Pharmaceuticals

The Oppenheimer 19th Annual Healthcare Conference

New York City, November 3, 2008

Filed by

Ligand

Pharmaceuticals

Incorporated

Pursuant to Rule 425

under the Securities Act of 1933 and

deemed filed pursuant to Rule 14a-6 under

the Securities Exchange Act of 1934, as amended

Subject Company: Pharmacopeia, Inc.

Commission File No: 0-50523

Joseph A. Mollica, Chairman of the Board,

Interim President & CEO

Discovering excellence, driving clinical success

TM

3

This presentation, and oral statements made with respect to information contained in this

presentation, constitute forward-looking statements within the meaning of the Private Securities

Litigation Reform Act of 1995. Such forward-looking statements include those which express

plan, anticipation, intent, goal, contingency or future development and/or otherwise are not

statements of historical fact. These statements are based upon management's current

expectations and are subject to risks and uncertainties, known and unknown, which could

cause actual results and developments to differ materially from those expressed or implied in

such statements. These forward-looking statements include, but are not limited to, statements

about the successful implementation of Pharmacopeia's strategic plans and the merger

transaction between Pharmacopeia and Ligand Pharmaceuticals.  Further information about

these

and

other

relevant

risks

and

uncertainties

may

be

found

in

Pharmacopeia’s

Reports

on

Form 8-K, 10-Q and 10-K filed with the U.S. Securities and Exchange Commission.

Pharmacopeia urges you to carefully review and consider the disclosures found in its filings

which

are

available

in

the

SEC

EDGAR

database

at

http://www.sec.gov

and

from

Pharmacopeia at http://www.pharmacopeia.com. All forward-looking statements in this

presentation and oral statements made with respect to information contained in this

presentation

are

qualified

entirely

by

the

cautionary

statements

included

in

this

presentation

and such filings. These risks and uncertainties could cause actual results to differ materially

from results expressed or implied by such forward-looking statements. These forward-looking

statements speak only as of the date of this presentation. Pharmacopeia undertakes no

obligation to (and expressly disclaims any such obligation to) publicly update or revise the

statements made herein or the risk factors that may relate thereto whether as a result of new

information, future events, or otherwise.

Forward-Looking Statements

4

Pharmacopeia/Ligand Merger

•

Merger announced on September 24, 2008

•

Expected to close Q4 2008/January 2009

•

Pharmacopeia shareholders benefit from any growth of

combined company

•

Exciting combined portfolio with significant royalty potential

•

Premium over Pharmacopeia stock price, including further

upside through CVR if DARA is partnered

•

Pharmacopeia financing risk removed

5

Combined Product Pipeline

Stage of Development

Product

Indication

Partner

Preclinical

Phase I

Phase II

Phase III / NDA

Marketed

AVINZA ®

Chronic pain

King Pharmaceuticals

PROMACTA™

ITP, Hep C, CLD, CIT

GlaxoSmithKline

VIVIANT™

/ APRELA™

Osteoporosis

Wyeth

FABLYN®

Osteoporosis

Pfizer

PS433540

DARA / Cardiovascular

NA

PS291822

COPD (CXCR2)

Schering-Plough

PS540446

Psoriasis / RA (p38)

Bristol-Myers Squibb

LGD-4665

Thrombocytopenia

NA

PS178990

Muscle Wasting (SARM)

NA

PS095760

Oncology

Schering-Plough

PS386113

Inflammation

Schering-Plough

PS948115

Respiratory

Schering-Plough

PS248288

Metabolic Diseases

Schering-Plough

PS873266

Inflammation

Celgene

LGD-4033

Muscle Wasting (SARM)

NA

Erythropoietin (EPO)

Anemia

NA

AIPC

Prostate Cancer

NA

PS031291

Arthritis/MS (CCR1)

NA

Ligand Products

PS015146

Undisclosed

Schering-Plough

Pharmacopeia Products

SGRM

Inflammation & Cancer

NA

John L. Higgins, President & CEO

Ligand Pharmaceuticals

7

Safe Harbor Statement

•

The following presentation contains forward-looking statements regarding the proposed

acquisition of Pharmacopeia by Ligand, including projections regarding expectations for

potential research and development payments, savings in operational costs, cash burn rates,

timing of achieving positive cash flow, and potential revenue and profits of a combined

company.

•

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

including, but not limited to the reliance on collaborative partners for milestone and royalty

payments, regulatory hurdles facing product candidates, uncertain product development

costs, disputes regarding ownership of intellectual property, the commercial success of

approved products. The failure of Pharmacopeia’s stockholders to approve the merger,

Ligand’s

or

Pharmacopeia’s

inability

to

satisfy

the

conditions

of

the

merger,

or

that

the

merger

is otherwise delayed or ultimately not consummated, and a failure of the combined

businesses to be integrated successfully.  Additional risks may apply to forward looking

statements made in this presentation.

•

The

risk

factors

facing

Ligand

and

Pharmacopeia

are

explained

in

greater

detail

in

the

Company’s and Pharmacopeia’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.

8

Additional Information and Where to Find It

•

Ligand filed on October 20, 2008, the SEC a preliminary Registration Statement on Form S-4, which includes a proxy

statement of Pharmacopeia and other relevant materials in connection with the proposed transaction. Once, finalized, the

proxy statement will be mailed to the stockholders of Pharmacopeia. Investors and security holders of Pharmacopeia are

urged to read the proxy statement and the other relevant materials when they become available because they will contain

important information about Ligand, Pharmacopeia and the proposed transaction. The proxy statement and other relevant

materials (when they become available), and any other documents filed by Ligand or Pharmacopeia with the SEC, may be

obtained free of charge at the SEC's web site at www.sec.gov. In addition, investors and security holders may obtain free

copies

of

the

documents

filed

with

the

SEC

by

Ligand

by

going

to

Ligand’s

Investor

Relations

website

at

www.ligand.com.

Investors and security holders may obtain free copies of the documents filed with the SEC by Pharmacopeia by going to

Pharmacopeia’s Investor Relations page on its corporate website at www.pharmacopeia.com. Investors and security holders

of Pharmacopeia are urged to read the proxy statement and the other relevant materials when they become available before

making any voting or investment decision with respect to the proposed transaction.

•

Ligand and its respective directors and executive officers may be deemed to be participants in the solicitation of proxies from

the

stockholders

of

Pharmacopeia

in

favor

of

the

proposed

transaction.

Information

concerning

Ligand’s

directors

and

executive

officers

is

set

forth

in

Ligand’s

proxy

statement

for

its

2008

annual

meeting

of

shareholders,

which

was

filed

with

the SEC on April 29, 2008, and annual report on Form 10-K filed with the SEC on March 5, 2008.

•

Pharmacopeia

and

its

respective

directors

and

executive

officers

may

be

deemed

to

be

participants

in

the

solicitation

of

proxies from the stockholders of Pharmacopeia in favor of the proposed transaction. Information about Pharmacopeia’s

executive officers and directors and their ownership of Pharmacopeia common stock is set forth in the proxy statement for

the Pharmacopeia 2008 annual meeting of shareholders, which was filed with the SEC on March 24, 2008. Investors and

security holders may obtain more detailed information regarding the direct and indirect interests of Pharmacopeia and its

respective executive officers and directors in the acquisition by reading the proxy statement regarding the merger, which will

be filed with the SEC.

9

Why are we Acquiring Pharmacopeia?

•

Royalty partnerships

•

Drug discovery platform

•

Partnerable

assets

•

Cash and tax assets

10

Vision for the Combined Companies

•

Consolidated operations with strong fundamentals

Strong balance sheet

Cost-efficient R&D business with spending discipline

Robust product pipeline 

Diverse royalty partnerships with promising potential revenue and profits

•

Leverage highly successful drug discovery capabilities of both companies

Focus on early stage drug discovery and development

Partner pipeline assets at earliest value inflection point

•

Leadership

focused

on

shareholders,

market

credibility

and

solid

foundation

•

Commitment to driving shareholder value and to transparency on the business with

goal to drive strong cash flow and earnings

11

Combined Revenue Sources

•

AVINZA royalties

•

Potential royalties from three pending NDA’s and future registrations in

expanded indications

PROMACTA (GSK)

FABLYN (Pfizer)

VIVIANT (Wyeth)

APRELA NDA submission expected in 2009 (Wyeth)

•

Milestone and Research Payments from existing Pharmacopeia

partnerships

$6.5 to $25 million potential in 2009

•

Potential new license payments from pipeline assets

SARM, TPO, Oral EPO, SGRM, DARA, CCR1, JAK3

12

Combined company will have one of the strongest, most diverse royalty

partnership rosters in the small cap biotech universe

Significant Value in Royalty Partnerships

•

Numerous deals with nine pharmaceutical companies

•

Over 15 programs in various stages of research and development

in partnership portfolio

•

More than 20 different therapeutic indications being pursued including the largest

untapped markets

Muscle wasting, COPD, thrombocytopenia, asthma

•

More than $400 million in potential R&D and milestone payments from existing

deals

13

Ligand’s

Plan for DARA

•

Current 2009 plan

Finish Phase

IIb

trial;

spend

minimal

amount

to

complete

study

•

Evaluate partnerability

of DARA by focusing on:

Quality of data

Time and cost to develop drug and get it to market

Patent extension options

Terms of DARA agreement with BMS

Interest level conveyed by

past partnering discussions

14

Pro Forma Financial Forecast

•

Given our current outlook on the combined businesses, 2009 pro forma operating

cash burn rate is expected to be $20 million

•

Potential for additional revenue and cash infusion from new license agreements

•

More than $350 million in potential Net Operating Loss carry-forwards before any

limitations

Robustly capitalized company that has sufficient cash

to make it to profitability without additional financings

15

Strong Research Platforms

Mainly GPCR, kinase, ion channel, other

targets

Exclusively nuclear and cytokine

receptor targets

Targets

Combinatorial chemistry compound library

Over 7 million compound screening deck

Discrete compounds

100,000 compound library

Chemistry

Broad approach similar to Big Pharma:

-High-throughput & Ultra-HTS Screening

Focused expertise:

-Cell-based assays

-Gene transcription

Screening

Pharmacopeia

Ligand

•

Highly complementary research technology  

•

Transaction combines two successful discovery platforms and

integrates strong biology and chemistry capabilities

16

Opportunities

and Benefits to Shareholders

•

Ligand shareholders gain access to:

Numerous royalty partnerships

Pipeline assets

Drug discovery assets

Cash and NOLs

•

Pharmacopeia shareholders will participate in:

Lucrative potential near-term royalties

Well capitalized company with no anticipated financing needs

Expanded product pipeline

Financial liquidity

17

Overview of Ligand’s

Partnerships

18

Major Collaborations

•

1997 drug discovery collaboration resulted in

eltrombopag

(PROMACTA) –

small molecule

TPO mimetic

•

ITP: Numerous clinical studies tested, data

published in NEJM, NDA pending approval

(16-0 panel vote in favor of drug)

•

Hepatitis C: Two Phase III trials were initiated

in 4Q:07, Phase II Hep C data published in

the NEJM

•

CIT: Chemotherapy-induced

thrombocytopenia Phase II ongoing

•

Sarcoma: Phase I trial

&

19

Thrombocytopenia -

Causes of Disease

•

Decreased production of platelets

Myelodysplastic syndrome

Hepatitis C

Cancer in the bone marrow (leukemia)

Aplastic anemia

•

Increased destruction of platelets

Autoimmune, such as ITP

Sequestration in the spleen

•

Drug-induced

Myelosuppression by chemotherapy regimens

Anti-virals in Hep C therapies

Thrombocytopenia is a condition in which there is an abnormally low level of

platelets in the blood. 

Regardless of the underlying cause, thrombocytopenia leads to decreased platelet counts,

which puts patients at greater risk for bleeding and serious adverse events.

20

Medical Significance of Thrombocytopenia (US)

(Estimated markets)

Potential

Treatable

Patients

ITP

~100,000

Hepatitis C

~120,000

Myelodysplastic syndrome

~20,000

Leukemia / lymphoma

~50,000

Chemotherapy induced thrombocytopenia

~140,000

Intensive

care

unit

–

acquired

~500,000

Bone marrow transplants

~50,000

Lupus

~100,000

Cirrhosis

~113,000

HIV/other

~600,000

~ 2 million platelet transfusions per year

21

Illustrative Cost for Blood-Related Treatments

Annual

Cost

of

Care

Pharmaceuticals

~$15,000 (annual cost of care)

Splenectomy

$48,000 (procedure and medical management)

Platelet Transfusion

Single Course

$4,000

Leukemia

$84,000 (2 to 4 weeks daily)

Bone Marrow Transplant

$140,000 (4 to 6 weeks daily)

Chemotherapy

$20,000 (5 cycles)

NPlate

*$55,000

References: USRDS, 2005. DrugStore.com, Blood 108:481B-482B, 2006

American Red Cross, Transfusion of Plateles: Current Issues, Medical and Scientific Updates, No 98-6.

*Cost of therapy will be significantly higher if increased dose is needed; Cowen & Company Analyst Report,

August 29, 2008

22

SERM Collaborations

•

Ligand has two partnerships around

Selective Estrogen Receptor Modulators (SERMs):

Wyeth

Pfizer

•

SERMs bind with estrogen receptors in a tissue-specific manner:

Exhibit estrogen action in some tissues and anti-estrogen

action in other tissues

Deliver benefits of estrogen in desirable tissues without

the negative side effects

•

Potential target markets: osteoporosis, vaginal atrophy and

vasomotor symptoms of menopause

23

SERM Collaborations

&

•

Bazedoxifene (VIVIANT) Monotherapy:   

Received third FDA approvable letter for osteoporosis

in May 2008

•

Expects to file complete response with FDA by year-end

Submitted NDA for osteoporosis treatment in 3Q:07 

Submitted MAA for osteoporosis prevention &             

treatment in 3Q:07

•

Bazedoxifene in Combination with Premarin CE (APRELA):

FDA Meeting in February 2008 discussed product

formulation, bioequivalence and clinical study

efforts to support the planned NDA filing.

NDA planned by 2H:09

24

SERM Collaborations

•

Lasofoxifene (FABLYN) for osteoporosis

treatment

•

NDA pending approval; FDA Extended Review

through January 2009

•

FDA Panel had positive vote (9-3) on

September 8, 2008 that benefits could

outweigh its risks, including blood clots and

vaginal bleeding for the osteoporosis treatment

indication for FABLYN

&

25

SARM

Selective Androgen Receptor Modulators

26

SARM Program

•

Androgens (e.g. testosterone) are steroids that play key roles in bone,

skeletal muscle and libido

•

Current androgenic drugs have disadvantages that significantly limit their

use

Non-selective stimulation of all androgen receptors

Inconvenient formulations –

injectable or topical

Available oral drugs have potential for hepatotoxicity

•

Ligand’s lead SARMs LGD-3303 and LGD-4033:

Tissue-selective for bone and muscle while sparing the prostate

Orally active

In preclinical development and expected IND filing in 4Q08

•

Target Indications:

osteoporosis, frailty, hypogonadism,                        

sexual dysfunction, cachexia

Market Need

•

Convenient, prostate-sparing androgen receptor modulator with activity

in bone, muscle and CNS

27

BMD

Muscle

Mass

SARMs Address a Major Unmet Need

Approximately 1/3 of Older Adults

have low muscle mass and

low bone mineral density

Revue de Medecine Interne 2000; 21:608,

Molecular Aspects Med. 2005; 26:818

Healthy Elderly

Elderly with

Serious Disease

Epidemiology of Aging

Ligand SARM Repletes

Muscle and Bone Loss

Increased falls

Increased risk of fractures

Normal Level

Hormone Deficient

28

EPO Mimetic Program

29

Oral EPO Mimetics Will Provide New Therapeutic Options

to Patients

•

Research-stage program to discover non-peptide, small molecule oral agonists

•

Builds upon our recent success in discovering TPO mimetic drugs

•

Current recombinant EPO proteins and the EPO receptor synthetic peptides in

development

All require injection

Minimal differentiation of products results in limited therapeutic option

•

Oral HIF Prolyl Hydroxylase inhibitors in development have the potential for

mechanism-based toxicity

HIF-induced angiogenesis is a risk

•

Oral EPO mimetics will potentially provide targeted activation of the EPO

signaling pathway with an oral dosing route

30

TPO Mimetic Program

31

Ligand TPO Mimetic Program

•

The goal to develop best-in-class molecules to stimulate the

production of platelets focused on:

Potency

Onset of action

Safety

Oral dosing flexibility

•

Ligand’s lead molecule, LGD-4665 has a promising efficacy and

safety profile

•

Ligand is developing a robust library of next generation

compounds

32

LGD-4665 Summary

•

LGD-4665 is approximately 10 times more potent than

eltrombopag based on published data

•

The drug was safe and well tolerated in Phase I studies

•

The strong efficacy, good safety and long half-life may permit

weekly dosing regimen

•

Conducting numerous pharmacology studies, to establish drug

activity and differentiate drug profile from other TPO mimetic drug

candidates

•

Conducting Phase II ITP trial

33

Combined Product Pipeline

Stage of Development

Product

Indication

Partner

Preclinical

Phase I

Phase II

Phase III / NDA

Marketed

AVINZA ®

Chronic pain

King Pharmaceuticals

PROMACTA™

ITP, Hep C, CLD, CIT

GlaxoSmithKline

VIVIANT™

/ APRELA™

Osteoporosis

Wyeth

FABLYN®

Osteoporosis

Pfizer

PS433540

DARA / Cardiovascular

NA

PS291822

COPD (CXCR2)

Schering-Plough

PS540446

Psoriasis / RA (p38)

Bristol-Myers Squibb

LGD-4665

Thrombocytopenia

NA

PS178990

Muscle Wasting (SARM)

NA

PS095760

Oncology

Schering-Plough

PS386113

Inflammation

Schering-Plough

PS948115

Respiratory

Schering-Plough

PS248288

Metabolic Diseases

Schering-Plough

PS873266

Inflammation

Celgene

LGD-4033

Muscle Wasting (SARM)

NA

Erythropoietin (EPO)

Anemia

NA

AIPC

Prostate Cancer

NA

PS031291

Arthritis/MS (CCR1)

NA

Ligand Products

PS015146

Undisclosed

Schering-Plough

Pharmacopeia Products

SGRM

Inflammation & Cancer

NA

34

Near-Term Milestone and Events Calendar

1Q 09

FABLYN FDA Action

1Q 09

Phase IIb

DARA

4Q 08

Completion of SP CXCR2 Trial in COPD

1Q 09

VIVIANT FDA Action

4Q 08

Phase II ITP Interim Data

Projected Timing

Development and Regulatory Events

Ligand SARM IND Submission

PROMACTA FDA Action

4Q 08

Anytime?