9H8F | pdb_00009h8f

Crystal structure of HPK1 T165E/S171E in complex with pyrazine carboxamide inhibitor AZ3246 (compound 24)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.39 Å
  • R-Value Free: 
    0.246 (Depositor), 0.225 (DCC) 
  • R-Value Work: 
    0.201 (Depositor), 0.196 (DCC) 
  • R-Value Observed: 
    0.203 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Discovery and Optimization of Pyrazine Carboxamide AZ3246, a Selective HPK1 Inhibitor.

Shields, J.D.Baker, D.Balazs, A.Y.S.Bommakanti, G.Casella, R.Cao, S.Cook, S.Escobar, R.A.Fawell, S.Gibbons, F.D.Giblin, K.A.Goldberg, F.W.Gosselin, E.Grebe, T.Hariparsad, N.Hatoum-Mokdad, H.Howells, R.Hughes, S.J.Jackson, A.Karapa Reddy, I.Kettle, J.G.Lamont, G.M.Lamont, S.Li, M.Lill, S.O.N.Mele, D.A.Metrano, A.J.Mfuh, A.M.Morrill, L.A.Peng, B.Pflug, A.Proia, T.A.Rezaei, H.Richards, R.Richter, M.Robbins, K.J.San Martin, M.Schimpl, M.Schuller, A.G.Sha, L.Shen, M.Sheppeck 2nd, J.E.Singh, M.Stokes, S.Song, K.Sun, Y.Tang, H.Wagner, D.J.Wang, J.Wang, Y.Wilson, D.M.Wu, A.Wu, C.Wu, D.Wu, Y.Xu, K.Yang, Y.Yao, T.Ye, M.Zhang, A.X.Zhang, H.Zhai, X.Zhou, Y.Ziegler, R.E.Grimster, N.P.

(2025) J Med Chem 68: 4582-4595

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c02631
  • Primary Citation of Related Structures:  
    9H8D, 9H8E, 9H8F

  • PubMed Abstract: 

    Hematopoietic progenitor kinase 1 (HPK1) is a negative regulator of the T cell receptor signaling pathway and is therefore a target of interest for immunooncology. Nonselective HPK1 inhibitors may affect other kinase components of T cell activation, blunting the beneficial impact of enhanced T cell activity that results from HPK1 inhibition itself. Here, we report the discovery of pyrazine carboxamide HPK1 inhibitors and their optimization through structure-based drug design to afford a highly selective HPK1 inhibitor, compound 24 (AZ3246). This compound induces IL-2 secretion in T cells with an EC 50 of 90 nM without inhibiting antagonistic kinases, exhibits pharmacokinetic properties consistent with oral dosing, and demonstrates antitumor activity in the EMT6 syngeneic mouse model.


  • Organizational Affiliation
    • Early Oncology R&D, AstraZeneca, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mitogen-activated protein kinase kinase kinase kinase 1294Homo sapiensMutation(s): 2 
Gene Names: MAP4K1HPK1
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q92918 (Homo sapiens)
Explore Q92918 
Go to UniProtKB:  Q92918
PHAROS:  Q92918
GTEx:  ENSG00000104814 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92918
Sequence Annotations
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.39 Å
  • R-Value Free:  0.246 (Depositor), 0.225 (DCC) 
  • R-Value Work:  0.201 (Depositor), 0.196 (DCC) 
  • R-Value Observed: 0.203 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.611α = 90
b = 67.868β = 94.87
c = 63.669γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
STARANISOdata scaling
XDSdata reduction
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-19
    Type: Initial release
  • Version 1.1: 2025-03-05
    Changes: Database references