7M0M

HPK1 IN COMPLEX WITH COMPOUND 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Discovery of Diaminopyrimidine Carboxamide HPK1 Inhibitors as Preclinical Immunotherapy Tool Compounds.

Vara, B.A.Levi, S.M.Achab, A.Candito, D.A.Fradera, X.Lesburg, C.A.Kawamura, S.Lacey, B.M.Lim, J.Methot, J.L.Xu, Z.Xu, H.Smith, D.M.Piesvaux, J.A.Miller, J.R.Bittinger, M.Ranganath, S.H.Bennett, D.J.DiMauro, E.F.Pasternak, A.

(2021) ACS Med Chem Lett 12: 653-661

  • DOI: https://doi.org/10.1021/acsmedchemlett.1c00096
  • Primary Citation of Related Structures:  
    7M0K, 7M0L, 7M0M

  • PubMed Abstract: 

    Hematopoietic progenitor kinase 1 (HPK1), a serine/threonine kinase, is a negative immune regulator of T cell receptor (TCR) and B cell signaling that is primarily expressed in hematopoietic cells. Accordingly, it has been reported that HPK1 loss-of-function in HPK1 kinase-dead syngeneic mouse models shows enhanced T cell signaling and cytokine production as well as tumor growth inhibition in vivo , supporting its value as an immunotherapeutic target. Herein, we present the structurally enabled discovery of novel, potent, and selective diaminopyrimidine carboxamide HPK1 inhibitors. The key discovery of a carboxamide moiety was essential for enhanced enzyme inhibitory potency and kinome selectivity as well as sustained elevation of cellular IL-2 production across a titration range in human peripheral blood mononuclear cells. The elucidation of structure-activity relationships using various pendant amino ring systems allowed for the identification of several small molecule type-I inhibitors with promising in vitro profiles.


  • Organizational Affiliation

    Discovery Chemistry, Computational and Structural Chemistry, Quantitative Biosciences, Pharmacokinetics and Drug Metabolism, Oncology Early Discovery, Merck & Co., Inc., Boston, Massachusetts 02115, 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
293Homo 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
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
YK1 (Subject of Investigation/LOI)
Query on YK1

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
4-[2-fluoro-6-(trifluoromethyl)anilino]-2-[(6-methoxy-2-methyl-1,2,3,4-tetrahydroisoquinolin-7-yl)amino]pyrimidine-5-carboxamide
C23 H22 F4 N6 O2
RZLXOEIALAVGKH-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.168α = 86.73
b = 56.994β = 86.63
c = 63.459γ = 67.06
Software Package:
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-04-07
    Type: Initial release
  • Version 1.1: 2021-05-05
    Changes: Database references
  • Version 1.2: 2024-03-06
    Changes: Advisory, Data collection, Database references, Refinement description
  • Version 1.3: 2024-04-03
    Changes: Refinement description