CHK1 kinase domain with diazacarbazole compound 19

Experimental Data Snapshot

  • Resolution: 1.86 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.3 of the entry. See complete history


Mitigation of Acetylcholine Esterase Activity in the 1,7-Diazacarbazole Series of Inhibitors of Checkpoint Kinase 1.

Gazzard, L.Williams, K.Chen, H.Axford, L.Blackwood, E.Burton, B.Chapman, K.Crackett, P.Drobnick, J.Ellwood, C.Epler, J.Flagella, M.Gancia, E.Gill, M.Goodacre, S.Halladay, J.Hewitt, J.Hunt, H.Kintz, S.Lyssikatos, J.Macleod, C.Major, S.Medard, G.Narukulla, R.Ramiscal, J.Schmidt, S.Seward, E.Wiesmann, C.Wu, P.Yee, S.Yen, I.Malek, S.

(2015) J Med Chem 58: 5053-5074

  • DOI: https://doi.org/10.1021/acs.jmedchem.5b00464
  • Primary Citation of Related Structures:  
    4RVK, 4RVL, 4RVM

  • PubMed Abstract: 

    Checkpoint kinase 1 (ChK1) plays a key role in the DNA damage response, facilitating cell-cycle arrest to provide sufficient time for lesion repair. This leads to the hypothesis that inhibition of ChK1 might enhance the effectiveness of DNA-damaging therapies in the treatment of cancer. Lead compound 1 (GNE-783), the prototype of the 1,7-diazacarbazole class of ChK1 inhibitors, was found to be a highly potent inhibitor of acetylcholine esterase (AChE) and unsuitable for development. A campaign of analogue synthesis established SAR delineating ChK1 and AChE activities and allowing identification of new leads with improved profiles. In silico docking using a model of AChE permitted rationalization of the observed SAR. Compounds 19 (GNE-900) and 30 (GNE-145) were identified as selective, orally bioavailable ChK1 inhibitors offering excellent in vitro potency with significantly reduced AChE activity. In combination with gemcitabine, these compounds demonstrate an in vivo pharmacodynamic effect and are efficacious in a mouse p53 mutant xenograft model.

  • Organizational Affiliation

    ∇Argenta, A Charles River Company, 8-9 Spire Green Centre, Harlow, Essex CM19 5TR, United Kingdom.

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 3X7

Download Ideal Coordinates CCD File 
B [auth A]3-[4-(piperidin-1-ylmethyl)phenyl]-9H-pyrrolo[2,3-b:5,4-c']dipyridine-6-carbonitrile
C23 H21 N5
Binding Affinity Annotations 
IDSourceBinding Affinity
3X7 BindingDB:  4RVM IC50: 1 (nM) from 1 assay(s)
EC50: 53 (nM) from 1 assay(s)
Binding MOAD:  4RVM IC50: 1 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.86 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.123α = 90
b = 65.93β = 94.63
c = 58.117γ = 90
Software Package:
Software NamePurpose
JDirectordata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2015-06-03
    Type: Initial release
  • Version 1.1: 2015-08-26
    Changes: Database references
  • Version 1.2: 2017-11-22
    Changes: Refinement description
  • Version 1.3: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description