CHK1 kinase domain in complex with diarylpyrazine compound 1

Experimental Data Snapshot

  • Resolution: 2.05 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 

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Discovery of the 1,7-diazacarbazole class of inhibitors of checkpoint kinase 1.

Gazzard, L.Appleton, B.Chapman, K.Chen, H.Clark, K.Drobnick, J.Goodacre, S.Halladay, J.Lyssikatos, J.Schmidt, S.Sideris, S.Wiesmann, C.Williams, K.Wu, P.Yen, I.Malek, S.

(2014) Bioorg Med Chem Lett 24: 5704-5709

  • DOI: https://doi.org/10.1016/j.bmcl.2014.10.063
  • Primary Citation of Related Structures:  
    4QYE, 4QYF, 4QYG, 4QYH

  • PubMed Abstract: 

    Checkpoint kinase 1 (ChK1) is activated in response to DNA damage, acting to temporarily block cell cycle progression and allow for DNA repair. It is envisaged that inhibition of ChK1 will sensitize tumor cells to treatment with DNA-damaging therapies, and may enhance the therapeutic window. High throughput screening identified carboxylate-containing diarylpyrazines as a prominent hit series, but with limited biochemical potency and no cellular activity. Through a series of SAR investigations and X-ray crystallographic analysis the critical role of polar contacts with conserved waters in the kinase back pocket was established. Structure-based design, guided by in silico modeling, transformed the series to better satisfy these contacts and the novel 1,7-diazacarbazole class of inhibitors was discovered. Here we present the genesis of this novel series and the identification of GNE-783, a potent, selective and orally bioavailable inhibitor of ChK1.

  • Organizational Affiliation

    Department of Discovery Chemistry, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase Chk1298Homo sapiensMutation(s): 0 
Gene Names: CHEK1CHK1
UniProt & NIH Common Fund Data Resources
Find proteins for O14757 (Homo sapiens)
Explore O14757 
Go to UniProtKB:  O14757
PHAROS:  O14757
GTEx:  ENSG00000149554 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO14757
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 3DL

Download Ideal Coordinates CCD File 
B [auth A]4-[6-(3-hydroxyphenyl)pyrazin-2-yl]benzoic acid
C17 H12 N2 O3
Binding Affinity Annotations 
IDSourceBinding Affinity
3DL Binding MOAD:  4QYE IC50: 1200 (nM) from 1 assay(s)
BindingDB:  4QYE IC50: 1200 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.05 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.85α = 90
b = 65.865β = 93.97
c = 57.742γ = 90
Software Package:
Software NamePurpose
StructureStudiodata collection
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-12-17
    Type: Initial release
  • Version 1.1: 2024-02-28
    Changes: Data collection, Database references, Derived calculations