Determined to realize a future in which people with cancer live longer and better than ever before 4Q18 EARNINGS PRESENTATION MARCH 2019

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Determined to realize a future in which people with cancer live longer and better than ever before 4Q18 EARNINGS PRESENTATION MARCH 2019

Forward-looking statements disclosure This presentation contains forward-looking statements within the meaning of the Private Securities Litigation Reform Act of 1995. Words such as "may," "will," "expect," "plan," "anticipate" and similar expressions (as well as other words or expressions referencing future events or circumstances) are intended to identify forward-looking statements. All statements other than statements of historical facts contained in this presentation, including statements regarding future operations, financial results and the financial condition of Syndax Pharmaceuticals, Inc. ( Syndax or the Company ), including financial position, strategy and plans, the progress, timing, clinical development and scope of clinical trials and the reporting of clinical data for Syndax s product candidates, and Syndax s expectations for liquidity and future operations, are forward-looking statements. Many factors may cause differences between current expectations and actual results, including unexpected safety or efficacy data observed during preclinical or clinical studies, clinical site activation rates or clinical trial enrollment rates that are lower than expected, changes in expected or existing competition, failure of our collaborators to support or advance collaborations or product candidates and unexpected litigation or other disputes. Moreover, Syndax operates in a very competitive and rapidly changing environment. Other factors that may cause our actual results to differ from current expectations are discussed in Syndax s filings with the U.S. Securities and Exchange Commission, including the Risk Factors sections contained therein. New risks emerge from time to time. It is not possible for Syndax s management to predict all risks, nor can Syndax assess the impact of all factors on its business or the extent to which any factor, or combination of factors, may cause actual results to differ materially from those contained in any forward-looking statement. In light of these risks, uncertainties and assumptions, the forward-looking events and circumstances discussed in this presentation may not occur and actual results could differ materially and adversely from those anticipated or implied. Except as required by law, neither Syndax nor any other person assumes responsibility for the accuracy and completeness of the forward-looking statements. Syndax undertakes no obligation to update publicly any forward-looking statements for any reason after the date of this presentation to conform these statements to actual results or to changes in Syndax s expectations. 2

2019: Portfolio prioritization to drive value Entinostat - exemestane Oral, Class I HDAC in HR+ mbc Potential positive OS data 2019 Efficacy post-cdk4,6 Tx Potential NDA filing in 2019/20 Blockbuster potential SNDX-5613 Oral, Menin inhibitor Blocks MLL-fusion protein activity IND filing 2Q, clinical data 19/ 20 Benefit expected in high need AML, ped ALL populations Blockbuster potential Entinostat - KEYTRUDA Oral, Class I HDAC, solid tumors Strong data in NSCLC and MEL 2 oral presentations at AACR Blockbuster potential Potential first combo to demonstrate survival benefit Targeted therapy provides fast to market opportunity Registration trial deferred until positive OS in E2112 NSCLC non-small cell lung cancer; MEL melanoma; AML acute myeloid leukemia; ALL acute lymphoblastic leukemia 3

Phase 3 E2112: Focused on overall survival E2112: Exemestane +/- entinostat E2112 Trial Milestones Advanced HR+ HER2- BC following SOC progression Primary endpoint: OS Exemestane + entinostat (n=300) Randomized, blinded Exemestane + placebo (n=300) 4Q18: Accrual completed (n=608), PFS and interim OS analyses shared 2Q19: Next interim OS analysis 4Q19: Additional interim OS analysis 2Q20: Final OS analysis (if needed) Expect to file NDA ~6 months after positive OS data A positive OS result allows filing for full regulatory approval 4

Blockbuster potential as 2 nd /3 rd line agent Leading treatment options HR+, HER2- advanced breast cancer 1 st line hormone Tx 2 nd /3 rd /4 th line hormone Tx Chemo-Tx Anastrozole or letrazole +/- CDK4,6 inhibitor Anastrazole, Faslodex +/- CDK4,6 inhibitor or Afinitor-exemestane Capecitabine, gemcitabine, eribulin 34,000 pts Entinostat-exemestane target population Source: DataMonitor 2016 Breast cancer: HR+/HER2- Disease Coverage Report 5

SNDX-5613 targets novel fusion protein: Fusion proteins proven to be good candidates for targeted therapies Advantages Strong target validation Precise patient selection Big effect in small studies BCR-ABL EML4-ALK Therapies targeting fusion proteins Molecular markers of disease status Rapid regulatory path NTRK Fusions RET Fusions LOXO-292 (Loxo/Lilly) entrectinib (Ignyta/Roche) BLU-667 (Blueprint) 6

In MLLr, leukemic transformation is highly dependent on the Menin-MLL interaction MLL1 Transformations Menin H 2 N Fusion partner CO 2 H MENIN H 2 N MLL1 (KMT2A) protein CO 2 H MLL peptide Conserved N-terminus Menin Binding Motif Break Point Region Inhibitor H 2 N MLL-rearrangement (KMT2A fusion) CO 2 H MLL1 fusion partner recruits oncogenic factors to transcription site 1 Menin is a scaffold protein involved in gene transcription MLL1 N-terminus binds w/in conserved pocket on Menin SNDX-5613 designed to block site of interaction Source: Yokoyama A, Cell. 2005 Oct 21;123(2):207-18; Caslini C, Cancer Res. 2007 Aug 1;67(15):7275-83. 7

Binding of Menin to MLL1 leads to upregulation of HOX gene transcription and leukemia in MLLr AML and MLLr ALL MLLr AML or MLLr ALL Inhibition with SNDX-5613 DOT1L CDK9 P-TEFb SNDX-5613 DOT1L CDK9 P-TEFb Menin MLL1 Fusion CBX8 Menin MLL1 Fusion CBX8 Leukemia Differentiation ON HOX OFF HOX Adopted from: Uckelmann HJ, et al. Presented at ASH Annual Meeting, 2018. 8

SNDX-5613: potential best-in-class, targeted, oral agent with single agent activity and fast to market potential Phase 1/2 trial population: MLLr adult, MLLr peds, NPM1 mut AML Defined fast to market pathway IND filing est. 2Q19; Phase 1 to follow PEDS MLLr ALL MLLr AML NPM1 AML ADULTS Early efficacy possible as early as year-end 2019 MLLr and NPM1 identified today with standard screening protocols No approved therapies targeting MLLr or NPM1 acute leukemias $$B commercial opportunity 9

ENCORE program testing combos across immune phenotypes Responds to PD-(L)1 Convert to inflamed with combinations Inflamed Excluded Non-Inflamed Abundance of TILs CD8+ Tcells, INFγ PD-(L)1 expression Angiogenesis MDSCs Reactive Stroma Highly proliferating tumor cells Low Tcell infiltrate ENCORE 601 ENCORE 601 ENCORE 602 ENCORE 603 NSCLC and Melanoma CRC TNBC Ovarian Source: Hedge, et al. Clin Cancer Res; 22.8 (2016): 1865-1874. 10

ENCORE clinical proof of concept program complete; positive signal observed in NSCLC and melanoma NSCLC Melanoma Strong signal in select population Strong signal in PD-1/CTLA-4 pretx pop Oral presentations on NSCLC biomarker and melanoma results at AACR 11

Update on SNDX-6352: pursuing novel indication High affinity, IgG4 (K D = 4-8 pm) CSF-1 Receptor SNDX-6352 Multiple ascending dose (MAD, solid tumors) ongoing Combination study with IMFINZI (durvalumab, AZ) commenced RP2D expected in 2Q19 Chronic graft versus host disease (cgvhd) study initiated RP2D expected in 2H19 Ligand binding Dimerisation ATP binding Kinase insert Kinase domain P P P P P CSF-1R colony stimulating factor -1 receptor; RP2D recommended Phase 2 dose. Source: Ordentlich, P. et al SITC 2016. 12

Proven ability to build the pipeline 3Q16: UCB SNDX-6352 Established relationships enhance identification and access to quality assets 4Q17: Allergan/Vitae Clinical development leadership enables competitive advantage Business development continues to be a core strength of our business Menin-MLLr inhibitors 13

2018 financial highlights and 1Q, full-year 2019 guidance Ticker SNDX (NASDAQ) Cash and short-term investments As of December 31, 2018 $80.9 million Shares Outstanding* 26.8 million 2019 1Q and full year Operating Expense Guidance 1Q 2019 2019 Research and Development $11 13 M $46-50 M Total Operating Expenses^ $15 17 M $60 64 M * Includes 24.8 million common shares and pre-funded warrants to purchase 2.0 million common shares ^ Includes $1.5 and $6 million non-cash stock compensation expense for 1Q 2019 and for 2019, respectively 14

Upcoming milestones ENTINOSTAT (Class 1 specific HDAC inhibitor) 1Q19 2Q19 3Q19 4Q19 1H20 E2112 Interim OS analysis ENCORE 601 Present final results for melanoma cohort ENCORE 601 Present biomarker analysis for NSCLC cohort SNDX-5613 (Menin inhibitor) 1Q19 2Q19 3Q19 4Q19 1H20 Investigational New Drug (IND) application Potential for early efficacy in relapsed refractory AML SNDX-6352 (anti-csf-1r mab) 1Q19 2Q19 3Q19 4Q19 1H20 Identify recommended Phase 2 dose and schedule Preliminary efficacy in chronic GVHD 15

Thank you. Questions? 16