9D00

HPK1 kinase domain T165E,S171E phosphomimetic mutant in complex with compound 53


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.247 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Discovery of PF-07265028, A Selective Small Molecule Inhibitor of Hematopoietic Progenitor Kinase 1 (HPK1) for the Treatment of Cancer.

Gallego, R.A.Cho-Schultz, S.Del Bel, M.Dechert-Schmitt, A.M.Donaldson, J.S.He, M.Jalaie, M.Kania, R.Matthews, J.McTigue, M.Tuttle, J.B.Risley, H.Zhou, D.Zhou, R.Ahmad, O.K.Bernier, L.Berritt, S.Braganza, J.Chen, Z.Cianfrogna, J.A.Collins, M.Costa Jones, C.Cronin, C.N.Davis, C.Dress, K.Edwards, M.Farrell, W.France, S.P.Grable, N.Johnson, E.Johnson, T.W.Jones, R.Knauber, T.Lafontaine, J.Loach, R.P.Maestre, M.Miller, N.Moen, M.Monfette, S.Morse, P.Nager, A.R.Niosi, M.Richardson, P.Rohner, A.K.Sach, N.W.Timofeevski, S.Tucker, J.W.Vetelino, B.Zhang, L.Nair, S.K.

(2024) J Med Chem 

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c01930
  • Primary Citation of Related Structures:  
    9CZT, 9CZU, 9CZW, 9CZX, 9D00

  • PubMed Abstract: 

    Hematopoietic progenitor kinase 1 (HPK1/MAP4K1) represents a high interest target for the treatment of cancer through an immune-mediated mechanism. Herein we present highlights of the drug discovery campaign within the lactam/azalactam series of inhibitors that yielded a small molecule ( 21 , PF-07265028), which was advanced to a phase 1 clinical trial (NCT05233436). Key components of the discovery effort included optimization of potency through mitigation of ligand strain as guided by the use of cocrystal structures, mitigation of ADME liabilities (plasma instability and fraction metabolism by CYP2D6), and optimization of kinase selectivity, particularly over immune-modulating kinases with high homology to HPK1. Structure-based drug design via leveraging cocrystal structures and lipophilic efficiency analysis proved to be valuable tools that ultimately enabled the delivery of a clinical-quality small molecule inhibitor of HPK1.


  • Organizational Affiliation

    Oncology Medicinal Chemistry Worldwide Research and Development, Pfizer, Inc., 10770 Science Center Drive, La Jolla, California 92121, 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 1
A, B, C, D
309Homo sapiensMutation(s): 0 
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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.247 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.78α = 103.45
b = 80.33β = 106.49
c = 84.09γ = 103.18
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
STARANISOdata scaling
BUSTERphasing

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: 2024-12-18
    Type: Initial release
  • Version 1.1: 2024-12-25
    Changes: Database references