1. 24th ROTH Conference
March 12, 2012
John Higgins
President and Chief Executive Officer
P id d Chi f E i Offi
Matt Foehr
EVP and Chief Operating Officer

2. 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 2012 or thereafter.
The forward-looking statements made in the presentation are subject to several risk factors, including, but not
limited to, statements regarding intent, belief or current expectations of the Ligand its internal and partnered
to intent belief, Ligand,
programs, including Promacta, Ligand’s reliance on collaborative partners for milestone and royalty
payments, regulatory hurdles facing Ligand's and partner's product candidates, uncertainty regarding Ligand's
and partner's product development costs, the possibility that Ligand'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
forward-looking 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.
2

3. Ligand 2012
3 Focus Points for Investors
Unprecedented Asset Portfolio
Revenue Expansion Potential
p
Investment
Investment Leverage
3

4. Ligand 2012
Growth Investment with Biotech Upside
G th I t t ith Bi t h U id
M j tf li i
Major portfolio expansion
Ligand Royalties in potential blockbuster programs
2012
Significant reduction in operating expenses
Focused on recurring quarterly revenue
Focused on recurring quarterly revenue
Acquisition strategy to fuel future growth
Reward
Ligand
2006
Risk
4

5. The Value of Ligand’s Partnered Portfolio
More than 50 Partnered Programs
M th 50 P t dP
Highly Diversified
More Ways to Succeed
More Ways to Succeed
Fully Funded
Partners Carry Majority of Risk
f k
Allows Ligand to Run Lean Business
5

6. Ligand’s Partnered Portfolio
Over 25
Different Partners
6

7. Ligand’s Partnered Portfolio
O 25 Diff P
Over 25 Different Partners
Big Pharma
Big Biotech
Specialty Pharma
Biotech
7

8. Ligand’s Partnered Portfolio
Over 10
Different
Therapeutic Areas
8

9. Ligand’s Partnered Portfolio
Over 10 Different Therapeutic Areas
Over 10 Different Therapeutic Areas
CNS Anti-F ngal
Anti-Fungal
Infectious
Diabetes
Disease
Inflammation
Osteoporosis
Oncology Blood
Disorders
Di d
Women’s
Health Pain
9
Arthritis

10. Ligand’s Partnered Portfolio
Over 50%in
Phase 2 or Later
10

11. Ligand’s Partnered Portfolio
Over 50% in Phase 2 or Later
O 50% i Ph 2 L t
Approved/
Marketed
16%
Phase 3/NDA
Phase 1
Phase 1 12%
35%
Phase 2
30%
11

12. Late-Stage Programs Expected in 2012
12 in 2012
Twelve “Phase 3 Stage” Programs in 2012
Carfilzomib (Onyx) – FDA Review of NDA Delafloxacin (Rib‐X) – Initiate Phase 3
Promacta (GSK) File sNDA for HepC
Promacta® (GSK) – File sNDA for HepC CE‐Melphalan (Ligand) – Initiate Pivotal
(Ligand) – Initiate Pivotal
Aprela® (Pfizer) – File NDA Dinaciclib (Merck) – Initiate Phase 3
CE Carbamazepine (Lundbeck) Phase 3 Readout
CE‐Carbamazepine (Lundbeck)– Phase 3 Readout Merck Undisclosed CE Initiate Pivotal
Merck Undisclosed CE – Initiate Pivotal
CE‐Clopidogrel (MDCO) – Initiate Pivotal Study Lilly Undisclosed CE – Initiate Phase 3
Promacta (GSK) – Initiate Phase 3 Oncology
( ) gy Hospira Undisclosed CE – Initiate Pivotal
p
12

13. Illustrative Revenue Growth Potential
"Shots on Goal" 2015
Vision
Vision
Promacta
Turning into Reality Avinza®
2012 Conbriza
Nexterone
Carfilzomib
Promacta
Aprela
Avinza
Dinaciclib
Conbriza®
CE‐Clopidogrel
p g
Nexterone®
N t ®
CE‐Melphalan
Captisol Material Sales
CE‐Carbamazepine
License/Milestone Fees
Lilly CE Program
Hospira CE Program
p g
$30M Captisol Material Sales
License/Milestone Fees
$150 200M
$150-200M
13

14. Leveraging Partnerships
2012 Investment
Estimated Partner Expenditure
E i dP E di
>$300 M
Ligand Cash Expenses
$20 M
$20 M
14

15. Promacta

16. Promacta
A potential blockbuster driver for Ligand growth
A t ti l bl kb t d i f Li d th
Oral medicine that boosts platelets to treat thrombocytopenia
Marketed by GSK for ITP
Significant royalty interest
Major upcoming 2012 catalysts
Major upcoming 2012 catalysts
Long patent protection through 2025
Potential for major label expansion
16

17. Promacta
A potential blockbuster driver for Ligand growth
A t ti l bl kb t d i f Li d th
Promacta Annual Sales ($M)
Promacta Annual Sales ($M)
$140
Other
EU
$120
$120
US • Dramatic Revenue Acceleration
Dramatic Revenue Acceleration
• 252% growth in 2011
$100
• Promacta is Gaining ITP Market Share vs. Nplate
$80
$80 • 17% in 2010
$ millions
• 29% in 2011
$60
• Ligand is entitled to a net 8.3% royalty on $1
$40 billion in annual sales
billi i l l
$20
$‐ 0
2009 2010 2011
17

18. Promacta
Hepatitis C Related‐Thrombocytopenia
H titi C R l t d Th b t i
Next big potential indication for Promacta is HepC
Phase 3 ENABLE 1 and 2 data expected at EASL in Barcelona, April 18‐22
• Primary endpoint successfully met in both studies
GSK has committed to filing an sNDA in 2012
Potential blockbuster market opportunity for HepC indication alone
• 8‐10% of all HepC patients world‐wide have thrombocytopenia that limits
their ability to start or complete a HepC anti‐viral treatment1
• Third party sell‐side analysts project major sales potential for Promacta in
HepC
1Thrombocytopenia in Hepatitis C: Impact on Patient Management
http://www.clinicaloptions.com/Hepatitis/Treatment%20Updates/Thrombocytopenia.aspx
18

19. Promacta
Franchise Expansion Beyond HepC
F hi E i B dH C
Oncology-Related Thrombocytopenia
gy y p
Oncology‐related thrombocytopenia (ORT) is currently in Phase 2 development at GSK
ORT is comprised of two separate patient populations
• Chemotherapy‐induced thrombocytopenia
• Cancers of the blood such as myelodysplastic syndrome (MDS) or acute
myeloid leukemia (AML)
Excess bleeding results in severe
complications or death for nearly 25% of
these patients1
Another potential blockbuster indication
for Promacta as total worldwide patients
approaches 100K annually
1Expert Opinion: Thrombocytopenia and Myelodysplastic Syndrome
http://www.medscape.org/viewarticle/565023
19

20. Formulation
Technology

21. The Need for an Enabling Solubility Technology
Th N d f E bli S l bilit T h l
4 out of 5
Drug candidates i R&D pipelines
D did in i li
believed to have poor solubility
Chemical & Engineering News, 2010
21

22. The Need for an Enabling Solubility Technology
Th N d f E bli S l bilit T h l
2 out of 5
Currently marketed d
C l k d drugs have
h
poor solubility
American Pharmaceutical Review ‐ Solubility Roundtable, 2011
22

23. Increasing Needs in Our Industry
I i N d i O I d t
Solubility publications
10,000
8,000
ns
r of publication
6,000
Number
4,000
2,000
2 000
0
1980 1985 1990 1995 2000 2005 2010
Year
American Pharmaceutical Review, 2012

24. Increasing Needs in Our Industry
I i N d i O I d t
Solubility publications
10,000
8,000
ns
r of publication
6,000
Number
4,000
2,000
2 000
0
1980 1985 1990 1995 2000 2005 2010
Year
American Pharmaceutical Review, 2012

25. Increasing Needs in Our Industry
I i N d i O I d t
Solubility publications
10,000
High‐throughput screening publications
8,000
ns
r of publication
6,000
Number
4,000
2,000
2 000
0
1980 1985 1990 1995 2000 2005 2010
Year
American Pharmaceutical Review, 2012

26. Increasing Needs in Our Industry
I i N d i O I d t
Solubility publications
10,000
High‐throughput screening publications
8,000 Introduction of HT screening in the mid 1990's
accelerated drug discovery and the need for solubility
ns
r of publication
technologies
6,000
Number
4,000
2,000
2 000
0
1980 1985 1990 1995 2000 2005 2010
Year
American Pharmaceutical Review, 2012

27. Th S l bilit S l ti
The Solubility Solution
Patented, chemically‐modified cyclodextrin
Increase drug solubility, reduce site reactions
d l bl d
Highly versatile across drug families
Highly versatile across drug families
Major safety database with Type V Drug Master File
Over 100 clinical studies
27

28. The Solubility Solution
Th S l bilit S l ti
RATIONALLY ENGINEERED
Not all Cyclodextrins are created equally.
28

29. The Solubility Solution
Th S l bilit S l ti
A CLEAR ADVANTAGE
Solving problems. Enabling products to market.
29

30. The Solubility Solution
Th S l bilit S l ti
PARTNERING
Valued technology. Globally recognized experts.
30

31. 2011 D l E di th P t B
2011 Deals Expanding the Partner Base
Merck
Undisclosed Captisol program
The Medicines Company
Captisol‐enabled clopidogrel
Sage Therapeutics
Captisol‐enabled CNS
Lilly
Captisol platform relationship
Hospira
Undisclosed Captisol program
31

33. 12 in 2012
Highlights

34. 12 in 2012 Highlight Initiate Pivotal
Study
The Medicines Company
Captisol‐enabled clopidogrel
MEDCO has announced they plan to initiate a pivotal
registration study in 2012 for CE-clopidogrel, with
potential NDA filing in 2013
l is h i ingrediant in Plavix®, currently
Clopidogrel i the active i
Cl id di i Pl i l
only available orally
This program offers the first intravenous formulation of
clopidogrel to doctors and patients
Ligand is entitled to receive milestones and royalties,
and Captisol material sales from the clopidogrel
p g
program
34

35. 12 in 2012 Highlight NDA
Action
Onyx
Carfilzomib
Onyx has filed the NDA for carfilzomib and currently has
a PDUFA date of July, 27, 2012 for an FDA decision
Carfilzomib is Captisol-enabled and has shown strong
efficacy and safety to date in patients with multiple
ffi d f t t d t i ti t ith lti l
myeloma
Third party analysts predict over $1 billion in peak
sales for carfilzomib
Ligand is entitled to receive milestones and royalties, and
Captisol material sales from the carfilzomib program
35

36. 12 in 2012 Highlight NDA
Submission
Pfizer
Aprela
Pfizer has recently announced they will be filing an
NDA in 2012 for Aprela
Aprela is the combination of Conbriza® (bazedoxifene)
and Premarin® and is designed as a therapeutic for
post-menopausal symptoms
Conbriza, a SERM molecule, was discovered by Ligand
and licensed to Wyeth (now Pfizer) in the 1990 s
1990’s
Ligand is entitled to receive milestones and royalties
from the Aprela program
36

37. Summary

38. Projected Financial Highlights
2012 Fi i l G id
2012 Financial Guidance 2012 R
2012 Revenue Composition
C iti
• $30M in total revenue
• $25M in operating expenses ~25%
%
‐ Includes $6M non‐cash expense Material
• COGS at 30‐35% of material sales Sales
~ 50%
Royalty
~ 25%
~ 25%
License
Fees
NOLs exceed $450 million
19.7 million shares outstanding
38

39. Ligand Royalty Revenue Growth
• Ligand revenue model focused on
$16
RQR (recurring quarterly revenue)
Other
$14 Avinza • Revenue sharing from licensee
Promacta product revenue
$12 • RQR has 100% gross margin
$ millions
$10 • RQR projected to increase by over
RQR j d i b
50% in 2012
$8
• Promacta expected to be a major
p j
$6 growth driver in 2012 AND has 13
years remaining patent life
$4
• Several potential new sources of
Several potential new sources of
$2 RQR to come on line within
the next several years with potential
$‐0 new product launches by licensees
2010 2011 2012
Actual Actual Projected
39

40. The Ligand Investment Thesis
Large asset portfolio creates tremendous upside
Cash‐flow positive with increasing revenue base
Promacta is a potential blockbuster asset that can drive significant valuation
Innovative internal R&D with focus on ROI
Innovative internal R&D with focus on ROI
12 in 2012 ‐ potential for major late‐stage news flow this year
40

41. Ligand 2012
Growth Investment with Biotech Upside
G th I t t ith Bi t h U id
M j tf li i
Major portfolio expansion
Ligand Royalties in potential blockbuster programs
2012
Significant reduction in operating expenses
Focused on recurring quarterly revenue
Focused on recurring quarterly revenue
Acquisition strategy to fuel future growth
Reward
Ligand
2006
Risk
41