1. 14th Annual BIO CEO and Investor Conference
February 13, 2012
John Higgins
President and Chief Executive 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.
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3. Ligand 2012
3 Focus Points for Investors
Unprecedented Asset
p Portfolio
f
Revenue Expansion Potential
Expansion Potential
Investment Leverage
L
3

4. Late-Stage Assets to Watch in 2012
12 in 2012
We expect these programs are either starting or ending PIII studies, filing
NDAs or hearing decisions from the FDA in 2012
Carfilzomib (Onyx) – FDA Review of NDA Delafloxacin (Rib‐X) – Initiate PIII
Promacta (GSK) – File sNDA for HepC
(GSK) File sNDA for HepC CE‐Melphalan (Ligand) – Initiate Pivotal
(Ligand) – Initiate Pivotal
Aprela (Pfizer) – File NDA Dinaciclib (Merck) – Initiate PIII
CE Carbamazepine (Lundbeck) PIII Readout
CE‐Carbamazepine (Lundbeck)– PIII Readout Merck Undisclosed CE Initiate Pivotal
Merck Undisclosed CE – Initiate Pivotal
CE‐Clopidogrel (MDCO) – Initiate Pivotal Study Lilly Undisclosed CE – Initiate PIII
Promacta (GSK) – Initiate PIII Oncology
( ) gy Hospira Undisclosed CE – Initiate Pivotal
p
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5. Illustrative Revenue Growth Potential
"Shots on Goal" 2015
Vision
Vision
Promacta
Turning into Reality Carfilzomib
2012 Avinza
Conbriza
Nexterone
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
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6. Ligand’s Partnered Portfolio
More than 50 Partnered Programs
M th 50 P t dP
Approved/
 Over 25 Different Partners
Marketed
k d
16% Over 10 Different Therapeutic Areas
Phase III/NDA  Over 50% in Phase II or Later
Phase I
Phase I 12%
35%
Phase II
30%
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7. The Value of Ligand’s Partnered Portfolio
Unprecedented Size
Unprecedented Size
Enables High Probability of Success
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8. The Value of Ligand’s Partnered Portfolio
Substantial Upside
Major News Flow
Diverse Revenue Sources
Diverse Revenue Sources
Multiple Blockbuster Programs
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9. The Value of Ligand’s Partnered Portfolio
Highly Diversified
g y
Lowers Risk
More Ways to Succeed
More Ways to Succeed
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10. The Value of Ligand’s Partnered Portfolio
Fully Funded
y
Partners Carry Majority of Risk
Allows Ligand to Run Lean Business
Allows Ligand to Run Lean Business
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11. Leveraging Partnerships
2012 Investment
E i dP E di
Estimated Partner Expenditure
>$300 M
Ligand Cash Expenses
$20 M
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12. Promacta

13. Promacta
A blockbuster driver for Ligand growth
A bl kb t d i f Li d th
Approved in all major markets for ITP
Marketed by GSK
Significant royalty interest
Major upcoming 2012 catalysts
Major upcoming 2012 catalysts
Long patent protection through 2025
Potential for major label expansion
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14. Promacta
A blockbuster driver for Ligand potential growth
A bl kb t d i f Li d t ti l th
Promacta Annual Sales ($M)
Promacta Annual Sales ($M)
$140.0
Other
EU
$120.0
$120.0
US •Dramatic Revenue Acceleration
•Dramatic Revenue Acceleration
•252% growth in 2011
$100.0
•Promacta is Gaining ITP Market Share vs. Nplate
$80.0
$80 0 •17% in 2010
•29% in 2011
$60.0
•Ligand will earn a net 8.3% royalty on $1 billion
$40.0 in annual sales
i l l
$20.0
$‐ 0
2009 2010 2011
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15. Promacta
Hepatitis C Related‐Thrombocytopenia
H titi C R l t d Th b t i
PIII ENABLE 1 and 2 studies are complete
PIII ENABLE 1 d 2 t di l t
•Primary endpoint successfully met in both studies
•Full data to be presented at 2012 EASL meeting in Barcelona (April)
GSK has stated sNDA will be filed 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
th i bilit t t t l t H C ti i l t t t
•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
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16. Promacta
The Future for Promacta i H C
Th F t f P t in HepC
Q: Will the new nucleoside inhibitors that are on the horizon eliminate the
Q: Will the new nucleoside inhibitors that are on the horizon eliminate the
need for Promacta?
A: In Ligand’s view, very unlikely
•Promacta’s target HepC patients have underlying cirrhosis,
which hepatologists suggest will require a combination
p g gg q
treatment for full cure
•These “cocktail” treatments will all likely impact platelets,
meaning Promacta will still be needed to initiate and
g
maintain anti‐viral therapy
•These new nuclease inhibitors have yet to be tested in
these very sick patients, so data is still needed to determine
their impact on platelets in these patients
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17. Promacta
Th N
The Near‐Term Future of the Promacta F
T F t f th P t Franchise
hi
Phase I Phase II Phase III Approved Clinical Studies
Approved
A d
Idiopathic Thrombocytopenia (IT) (11 Label Expansion and LT
Safety Studies Ongoing)
Hepatitis C‐Related Thrombocytopenia
l d h b 2 P-III Studies
P III
Complete
(1 Open-Label Study Ongoing)
Oncology‐Related
Thrombocytopenia 11 PI and PII St dies
Studies
• Ligand anticipates the following upcoming Promacta events
 Filing of HepC sNDA in 2012
 Initiation of Phase III oncology-related trial
 Potential start of new Phase III CLD study
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18. Captisol
Formulation
Technology

19. Captisol
The Need for an Enabling Solubility Technology
Th N d f E bli S l bilit T h l
“… between 70 and 90% of drug candidates in
pipelines are believed to have low solubility. In fact,
pipelines are believed to have low solubility In fact
poor solubility problems are considered to be the
leading challenge in drug development”
‐ Chemical Engineering News, 2010
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20. Captisol
Th S l bilit S l ti
The Solubility Solution
Patented, chemically-modified cyclodextrin
Increase drug solubility, reduce site reactions
I d l bilit d it ti
Versatile across molecule families and sizes
Type V Drug Master File
Over 100 clinical studies
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21. Captisol
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
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22. Select
Partnership
Highlights

23. Ligand Partnership Highlight
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-
g
menopausal symptoms
Conbriza, a SERM molecule, was discovered by Ligand
and licensed to Wyeth (now Pfizer) in the 1990’s
Ligand is entitled to receive milestones and royalties
from the Aprela program
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24. Ligand Partnership Highlight
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
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25. Ligand Partnership Highlight
Onyx
Carfilzomib
Onyx has filed the NDA for carfilzomib and currently has
an 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
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
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26. Ligand Partnership Highlight
Rib‐X
Delafloxacin
Rib-X has
Rib X h recently completed a PIIb program for the
tl l t d f th
delafloxacin program and anticipates starting a PIII
registration study in 2012
Delafloxacin is a novel hospital-based fluoroquinolone
antibiotic formulated with Captisol
Fluoroquinolones are a class of broad spectrum
antibiotics which kill bacteria by interfering with DNA
p
replication
Ligand is entitled to receive milestones and royalties
from the delafloxacin program
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27. Summary

28. 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 $500 million
19.7 million shares outstanding
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29. The Ligand Investment Thesis
Promacta is a blockbuster asset that can drive significant valuation
Cash‐flow positive with increasing revenue base
Uniquely large asset portfolio creates tremendous upside
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
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