Safe Harbor Statement

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1 September 2007

2 Safe Harbor Statement During the course of this presentation we will make forward-looking statements that involve risks and uncertainties associated with a developing pharmaceutical company. Actual results could differ materially from those projected in the forward-looking statements as a result of the risk factors discussed in SuperGen s filings with the U.S. Securities and Exchange Commission, including but not limited to, our most recent Form 10-K and Form 10-Q, as well as our reports on Form 8-K. These documents contain and identify important factors that could cause results to differ materially from those contained in any forwardlooking statements.

3 Mission To build a global sustainable business by discovering, developing and commercializing new drugs for oncologists, hematologists and their patients

4 Experienced Oncology Management Team James S. Manuso, Ph.D. Michael Molkentin, C.P.A. Gregory Berk, M.D. David Bearss, Ph.D. Timothy L. Enns Mark Lewis Michael McCullar, Ph.D. Joi Ninomoto, PharmD. Sanjeev Redkar, Ph.D. President & CEO CFO & Corporate Secretary Chief Medical Officer VP, Chief Scientist SVP, Corporate Communications & Bus. Development Managing Director, EuroGen VP, Drug Discovery Operations VP, Medical Research & Communications VP, Manufacturing & Pre-Clinical Development David Smith, Ph.D. VP, Regulatory and Quality Affairs

5 Scientific Advisory Board Allan R. Goldberg, Ph.D., Chairman of the Scientific Advisory Board SuperGen Board of Directors David J. Bearss, Ph.D., VP and Chief Scientist of SuperGen Inc. Roger D. Kornberg, Ph.D. Winzer Professor of Medicine, Stanford University Nobel Prize in Chemistry, 2006 Daniel Von Hoff, M.D. Chief Physician and Director of Translational Research, Translational Genomics Research Institute Member, National Cancer Advisory Board Robert A. Weinberg, Ph.D. Co-Founder, Whitehead Institute for Biomedical Research First Director of the Ludwig Cancer Center at MIT Ludwig Professor for Cancer Research at MIT

6 Business Highlights Revenue Generating Products: Dacogen and Nipent Significant Commercial Partners: MGI PHARMA JNJ Hospira, Inc. Five Regulatory Approvals Including Dacogen NDA Innovative Discovery Process & Diverse Oncology Pipeline 70 Total Employees (~ 70% in R&D) Strong Financial Position: $86 M in Cash (*) Debt Free FY 2007 Income from Operations Guidance (**): > $6 M * nd quarter unrestricted cash, cash equivalents and marketable securities ** Guidance provided at nd quarter earnings call 8/2/07

7 Marketed & Development-Stage Products Development Preclinical Phase 1 Phase 2 Phase 3 Approved Marketed Dacogen (decitabine) for Injection MGI PHARMA N. America, JNJ Rest of World Nipent (pentostatin for injection) Hospira, Inc. MP470 TK Inhibitor MP529 Aurora A Inhibitor S110 DNMT1 Inhibitor PIM JAK2 Signal Transduction & DNA Repair Prevention GBM, NSCLC, SCLC, GIST Mitotic Failure Induction Pancreatic, Colorectal, Breast DNA Hypomethylation MDS, AML, Solid Tumors Potent Apoptosis Induction - Lymphomas, AML, Prostate Cytokine Signal Inhibition Myeloproliferative Disorders, Solid Tumors

8 Marketed & Development-Stage Products Development Preclinical Phase 1 Phase 2 Phase 3 Approved Marketed Dacogen (decitabine) for Injection MGI PHARMA N. America, JNJ Rest of World Nipent (pentostatin for injection) Hospira, Inc. MP470 TK Inhibitor MP529 Aurora A Inhibitor S110 DNMT1 Inhibitor PIM JAK2

9 Dacogen (decitabine) for Injection FDA Approved Indication: Myelodysplastic Syndrome (MDS) All FAB Classifications IPSS (Int-1, Int-2 & High Risk) de novo & secondary MDS Additional Development MDS Survival Phase III EORTC JNJ Guided to EMEA submission in 2008 Elderly AML Phase III Licensed to MGI Pharma Worldwide $100 M Upfront Payments, Equity Investment & Milestones 20% 30% royalty on all worldwide sales Sublicensed to JNJ outside of North America

10 Hypomethylators in MDS Labeled Indication (MDS) All FAB, HR, Int- 1, Int-2, de novo, previous treated All FAB Registration Trials (# of Patients) Overall Response Rate 17 & 21% 15.7% Schedule & Cycles 3 day: 3-4 cycles 7 day: 9 cycles Additional MDS Trial (MDACC) #pts Overall Response Rate (5 day-5 cyc) 49% - Phase III Survival Data 1H 2008 December 2007 Schedule & Cycle 3 day: 4-8 cycles 7 day: 9 cycles Q2 07 Sales - North American $30.2 M $32.5 M

11 Hypomethylation & Survival in MDS Dacogen US Phase III trial (Median survival)* Responders 23.5 mo. vs non-responders 13.7 mo. Dacogen 5 day study (n=115) vs Historical controls (n=115)** Dacogen 22 mo. vs Historical Controls 12 mo. EORTC Dacogen Phase III survival data expected in 2008 * Decitabine Improves Patient Outcomes in Myelodysplastic Syndromes Cancer: April 15, 2006 Vol. 106 p ** Survival Advantage with Decitabine Versus Intensive Chemotherapy in Patients with Higher Risk Myelodysplastic Syndrome Cancer: March 15, 2007, Vol. 109 P

12 Dacogen Market U.S. MDS market estimated to exceed $1 B MGI 2007 Revenue Guidance of $115 M YTD 2007 $53.3 M Q $30.2 M 31% Quarter over Quarter growth MGI Guidance: $250 M peak year US sales Global Sales Estimate: 2-3x peak year US sales

13 CLIMB TM : Parallel Processing Drug Discovery Target Modeling and Mining Hit Identification Lead Selection Disease and Animal Model Testing Target Selection Lead Development Optimization CLIMB Total Time = 2.0 Years

14 Marketed & Development-Stage Products Development Preclinical Phase 1 Phase 2 Phase 3 Approved Marketed Dacogen (decitabine) for Injection MGI PHARMA N. America, JNJ Rest of World Nipent (pentostatin for injection) Hospira, Inc. MP470 TK Inhibitor Signal Transduction & DNA Repair Prevention GBM, NSCLC, SCLC, GIST MP529 Aurora A Inhibitor S110 DNMT1 Inhibitor PIM JAK2

15 MP470 Preclinical Summary Oral, multi-targeted tyrosine kinase inhibitor DNA repair modulation Broad therapeutic potential Efficacy established in multiple tumor models Single agent Combination therapies Preclinical toxicology suggests wide therapeutic window

16 MP470 Targeted Pathways Kit PDGFR FLT3 DNA Repair Proliferation Survival Adhesion and chemotaxis Stimulation of angiogenesis Prevention of differentiation DNA damage leads to upregulation of repair mechanisms Rad51 Creates resistance to treatment

17 MP470 Targeted Pathways Kit PDGFR FLT3 DNA Repair MP470 Inhibition of these pathways leads to: Increased accumulation of DNA damage Decreased cell proliferation Decreased resistance to apoptosis Tumor Cell Death

18 MP470 Enhances the Efficacy of Carboplatin & Paclitaxel In NSCLC Xenografts Effect of MP470.HCl in Combination with Carboplatin and Taxol on A549 Xenograft Tumor Growth Average Tumor Volume, mm Vehicle MP470.HCl, 50mg/kg Carboplatin/Taxol Carboplatin/Taxol/MP470.HCl Day

19 MP470 Clinical Development Phase 1 Single Agent Trial Solid Tumors and Lymphomas Dose escalation to MTD (n=24-30) Pharmacokinetics Biomarkers: CTC, FDG-PET, perk, Rad51 Trial is enrolling at two centers

20 MP470 Phase 1b Combination Trial MP470 administered in combination with: Carboplatin/Paclitaxel NSCLC, Ovarian Carboplatin/Etoposide SCLC Docetaxel NSCLC, Breast, Gastric, Prostate, H&N Erlotinib NSCLC, Pancreatic Gemcitabine NSCLC, Breast, Pancreatic, Ovarian

21 Marketed & Development-Stage Products Development Preclinical Phase 1 Phase 2 Phase 3 Approved Marketed Dacogen (decitabine) for Injection MGI PHARMA N. America, JNJ Rest of World Nipent (pentostatin for injection) Hospira, Inc. MP470 TK Inhibitor MP529 Aurora A Inhibitor Mitotic Failure Induction Pancreatic, Colorectal, Breast S110 DNMT1 Inhibitor PIM JAK2

22 MP529: Selective Aurora A Kinase Inhibitor 1,000-fold selectivity for Aurora A versus Aurora B Rapid onset of irreversible apoptosis Significant activity in human tumor xenograft models Prostate Colorectal Pancreatic Highly stable Long half-life Pre IND meeting - Q4 07

23 Marketed & Development-Stage Products Development Preclinical Phase 1 Phase 2 Phase 3 Approved Marketed Dacogen (decitabine) for Injection MGI PHARMA N. America, JNJ Rest of World Nipent (pentostatin for injection) Hospira, Inc. MP470 TK Inhibitor MP529 Aurora A Inhibitor S110 DNMT1 Inhibitor PIM DNA Hypomethylation MDS, AML, Solid Tumors JAK2

24 S110: A potent inhibitor of DNA Methylation S110 acts as a prodrug of Decitabine NH 2 NH 2 N N N N N O HO O N O O HO O N NH H H OH O H H H O P O ONa OH O N N NH 2 Decitabine S110

25 S110: A More Stable Decitabine Longer Half Life Extended Exposure to Methylated DNA Decitabine S110 % Initial Absorbance Time (Hr)

26 Marketed & Development-Stage Products Development Preclinical Phase 1 Phase 2 Phase 3 Approved Marketed Dacogen (decitabine) for Injection MGI PHARMA N. America, JNJ Rest of World Nipent (pentostatin for injection) Hospira, Inc. MP470 TK Inhibitor MP529 Aurora A Inhibitor S110 DNMT1 Inhibitor PIM JAK2 Potent Apoptosis Induction - Lymphomas, AML, Prostate

27 PIM Kinase Inhibitor Inhibits PIM 1, 2 & 3 in nanomolar concentrations Modulates growth signals and transcription Activity in human xenograft models Solid Tumors Leukemia & Lymphoma IND submission planned for 2008

28 Marketed & Development-Stage Products Development Preclinical Phase 1 Phase 2 Phase 3 Approved Marketed Dacogen (decitabine) for Injection MGI PHARMA N. America, JNJ Rest of World Nipent (pentostatin for injection) Hospira, Inc. MP470 TK Inhibitor MP529 Aurora A Inhibitor S110 DNMT1 Inhibitor PIM JAK2 Cytokine Signal Inhibition Myeloproliferative Disorders, Solid Tumors

29 JAK2 Kinase Inhibitor Inhibits V617F JAK2 mutant kinase V617F JAK2 mutant plays a causal role in myeloproliferative disorders Potency in low nanomolar concentrations

30 Marketed & Development-Stage Products Development Preclinical Phase 1 Phase 2 Phase 3 Approved Marketed Dacogen (decitabine) for Injection MGI PHARMA N. America, JNJ Rest of World Nipent (pentostatin for injection) Hospira, Inc. MP470 TK Inhibitor MP529 Aurora A Inhibitor S110 DNMT1 Inhibitor PIM JAK2 Signal Transduction & DNA Repair Prevention GBM, NSCLC, SCLC, GIST Mitotic Failure Induction Pancreatic, Colorectal, Breast DNA Hypomethylation MDS, AML, Solid Tumors Potent Apoptosis Induction - Lymphomas, AML, Prostate Cytokine Signal Inhibition Myeloproliferative Disorders, Solid Tumors

31 Balance Sheet Highlights June 30, 2007 Amount (In $ 000 s) Cash, Cash Equivalents & Marketable Securities $86,556 Total Assets $96,476 Stockholders Equity $88,467 Debt None

32 Capital Structure June 30, 2007 Amount Common Stock Options Warrants Yield Potential = $21.3 M Fully Diluted Shares 57.5 M 7.8 M 3.1 M 68.4 M

33 2007 Revised Financial Guidance 8/2/07 Earnings Call Description (In $ 000 s) Low High Net product revenue $ 621 $ 621 Other revenue / gains: Gain on sale of products 33,700 33,700 Royalty revenue (Dacogen) 20,000 21,000 Costs and operating expenses (*): Cost of product revenue R&D 23,000 24,500 Acquired in-process R&D expense 9,967 9,967 SG&A 14,500 14,500 Total costs and operating expenses 47,688 49,188 Net income from operations $ 6,133 $ 6,633 *Includes estimated stock option expense $ 4,000 $ 4,500 Estimated average shares outstanding 57,500 57,500

34 Milestones Events When MP470 Phase 1b Trial Initiation Q4 07 Data Release & Presentations (EORTC-AACR-NCI & ASH) Q4 07 Dacogen data on ADOPT trial Q4 07 EORTC Phase III Dacogen Survival 1H 08 IND for MP529 1H 08

35 Investment Highlights Two Marketed Products Generating Revenue Substantial Commercial Partners Strong Financial Position Innovative & Diverse Oncology Pipeline Novel Discovery Capabilities

36

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