8FH4

Crystal structure of HPK1 kinase domain T165E,S171E phosphomimetic mutant in complex with 3-[6-chloro-4-(9-methyl-1-oxa-4,9-diazaspiro[5.5]undec-4-yl)-7H-pyrrolo[2,3-d]pyrimidin-5-yl]benzonitrile


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Design and Synthesis of Functionally Active 5-Amino-6-Aryl Pyrrolopyrimidine Inhibitors of Hematopoietic Progenitor Kinase 1.

Gallego, R.A.Bernier, L.Chen, H.Cho-Schultz, S.Chung, L.Collins, M.Del Bel, M.Elleraas, J.Costa Jones, C.Cronin, C.N.Edwards, M.Fang, X.Fisher, T.He, M.Hoffman, J.Huo, R.Jalaie, M.Johnson, E.Johnson, T.W.Kania, R.S.Kraus, M.Lafontaine, J.Le, P.Liu, T.Maestre, M.Matthews, J.McTigue, M.Miller, N.Mu, Q.Qin, X.Ren, S.Richardson, P.Rohner, A.Sach, N.Shao, L.Smith, G.Su, R.Sun, B.Timofeevski, S.Tran, P.Wang, S.Wang, W.Zhou, R.Zhu, J.Nair, S.K.

(2023) J Med Chem 66: 4888-4909

  • DOI: https://doi.org/10.1021/acs.jmedchem.2c02038
  • Primary Citation of Related Structures:  
    8FH4, 8FJZ, 8FKO, 8FP1, 8FP3

  • PubMed Abstract: 

    Immune activating agents represent a valuable class of therapeutics for the treatment of cancer. An area of active research is expanding the types of these therapeutics that are available to patients via targeting new biological mechanisms. Hematopoietic progenitor kinase 1 (HPK1) is a negative regulator of immune signaling and a target of high interest for the treatment of cancer. Herein, we present the discovery and optimization of novel amino-6-aryl pyrrolopyrimidine inhibitors of HPK1 starting from hits identified via virtual screening. Key components of this discovery effort were structure-based drug design aided by analyses of normalized B -factors and optimization of lipophilic efficiency.


  • Organizational Affiliation

    Oncology Medicinal Chemistry, Pfizer Worldwide Research and Development, 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
331Homo 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
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.756α = 97.66
b = 70.505β = 108.73
c = 86.042γ = 92.66
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other private--

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-05
    Type: Initial release
  • Version 1.1: 2023-04-26
    Changes: Database references
  • Version 1.2: 2023-10-25
    Changes: Data collection, Refinement description