7R9T | pdb_00007r9t

Crystal structure of HPK1 in complex with compound 17


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.229 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.198 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.200 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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This is version 1.2 of the entry. See complete history


Literature

Discovery of Spiro-azaindoline Inhibitors of Hematopoietic Progenitor Kinase 1 (HPK1).

Chan, B.K.Seward, E.Lainchbury, M.Brewer, T.F.An, L.Blench, T.Cartwright, M.W.Chan, G.K.Y.Choo, E.F.Drummond, J.Elliott, R.L.Gancia, E.Gazzard, L.Hu, B.Jones, G.E.Luo, X.Madin, A.Malhotra, S.Moffat, J.G.Pang, J.Salphati, L.Sneeringer, C.J.Stivala, C.E.Wei, B.Wang, W.Wu, P.Heffron, T.P.

(2022) ACS Med Chem Lett 13: 84-91

  • DOI: https://doi.org/10.1021/acsmedchemlett.1c00473
  • Primary Citation of Related Structures:  
    7R9L, 7R9N, 7R9P, 7R9T

  • PubMed Abstract: 

    Hematopoietic progenitor kinase 1 (HPK1) is implicated as a negative regulator of T-cell receptor-induced T-cell activation. Studies using HPK1 kinase-dead knock-in animals have demonstrated the loss of HPK1 kinase activity resulted in an increase in T-cell function and tumor growth inhibition in glioma models. Herein, we describe the discovery of a series of small molecule inhibitors of HPK1. Using a structure-based drug design approach, the kinase selectivity of the molecules was significantly improved by inducing and stabilizing an unusual P-loop folded binding mode. The metabolic liabilities of the initial 7-azaindole high-throughput screening hit were mitigated by addressing a key metabolic soft spot along with physicochemical property-based optimization. The resulting spiro-azaindoline HPK1 inhibitors demonstrated improved in vitro ADME properties and the ability to induce cytokine production in primary human T-cells.


  • Organizational Affiliation

    Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hematopoietic progenitor kinase
A, B
297Homo 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
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
2TR (Subject of Investigation/LOI)
Query on 2TR

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
6-amino-3-[(1S,3R)-4'-chloro-3-hydroxy-1',2'-dihydrospiro[cyclopentane-1,3'-pyrrolo[2,3-b]pyridin]-5'-yl]-2-fluoro-N,N-dimethylbenzamide
C20 H22 Cl F N4 O2
PUEWEJKMMMXQTR-CFMSYZGJSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.229 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.198 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.200 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.257α = 69.91
b = 58.272β = 66.21
c = 61.677γ = 68.21
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 2TRClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2022-01-05
    Type: Initial release
  • Version 1.1: 2022-02-09
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description