9BIK | pdb_00009bik

Crystal structure of inhibitor 1 bound to HPK1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 
    0.244 (Depositor), 0.245 (DCC) 
  • R-Value Work: 
    0.196 (Depositor), 0.196 (DCC) 
  • R-Value Observed: 
    0.199 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


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Literature

Discovery of GNE-6893, a Potent, Selective, Orally Bioavailable Small Molecule Inhibitor of HPK1.

Tellis, J.C.Wei, B.Siu, M.An, L.Chan, G.K.Chen, Y.Du, X.Gazzard, L.Hu, B.Kiefer, J.Kakiuchi-Kiyota, S.Lainchbury, M.Linehan, J.L.Luo, X.Malhotra, S.Mendonca, R.Pang, J.Ran, Y.Sethuraman, V.Seward, E.Sneeringer, C.Su, D.Wang, W.Wu, P.Moffat, J.G.Heffron, T.P.Choo, E.F.Chan, B.K.

(2024) ACS Med Chem Lett 15: 1606-1614

  • DOI: https://doi.org/10.1021/acsmedchemlett.4c00319
  • Primary Citation Related Structures: 
    9BI8, 9BIK, 9BJ1

  • PubMed Abstract: 

    Hematopoietic progenitor kinase 1 (HPK1) serves a key immunosuppressive role as a negative regulator of T-cell receptor (TCR) signaling. HPK1 loss-of-function is associated with augmentation of immune function and has demonstrated synergy with immune checkpoint inhibitors in syngeneic mouse cancer models. These data offer compelling evidence for the use of selective small molecule inhibitors of HPK1 in cancer immunotherapy. We identified a novel series of isoquinoline HPK1 inhibitors through fragment-based screening that displayed promising levels of biochemical potency and activity in functional cell-based assays. We used structure-based drug design to introduce key selectivity elements while simultaneously addressing pharmacokinetic liabilities. These efforts culminated in a molecule demonstrating subnanomolar biochemical inhibition of HPK1 and strong in vitro augmentation of TCR signaling in primary human T-cells. Further profiling of this molecule revealed excellent kinase selectivity (347/356 kinases <50% inhibition @ 0.1 μM), a favorable in vitro safety profile, and good projected human pharmacokinetics.


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

Macromolecule Content 

  • Total Structure Weight: 71.28 kDa 
  • Atom Count: 4,889 
  • Modeled Residue Count: 569 
  • Deposited Residue Count: 622 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Mitogen-activated protein kinase kinase kinase kinase 1
A, B
311Homo 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 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1APO
(Subject of Investigation/LOI)

Query on A1APO



Download:Ideal Coordinates CCD File
G [auth A],
M [auth B]
(1S,2S)-N-[(6P)-8-amino-6-(4-methylpyridin-3-yl)isoquinolin-3-yl]-2-cyanocyclopropane-1-carboxamide
C20 H17 N5 O
DKSAUTCUJKILFS-CABCVRRESA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
C [auth A]
D [auth A]
E [auth A]
F [auth A]
H [auth B]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
H [auth B],
I [auth B],
J [auth B],
K [auth B],
L [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free:  0.244 (Depositor), 0.245 (DCC) 
  • R-Value Work:  0.196 (Depositor), 0.196 (DCC) 
  • R-Value Observed: 0.199 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.657α = 90
b = 56.589β = 98.61
c = 84.979γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

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: 2024-10-02
    Type: Initial release