4A9U

CRYSTAL STRUCTURE OF HUMAN CHK2 IN COMPLEX WITH BENZIMIDAZOLE CARBOXAMIDE INHIBITOR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.48 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Benzimidazole Inhibitors of the Protein Kinase Chk2: Clarification of the Binding Mode by Flexible Side Chain Docking and Protein-Ligand Crystallography

Matijssen, C.Silva-Santisteban, M.C.Westwood, I.M.Siddique, S.Choi, V.Sheldrake, P.Van Montfort, R.L.M.Blagg, J.

(2012) Bioorg Med Chem 20: 6630

  • DOI: 10.1016/j.bmc.2012.09.024
  • Primary Citation of Related Structures:  
    4A9T, 4A9U, 4A9R, 4A9S

  • PubMed Abstract: 
  • Two closely related binding modes have previously been proposed for the ATP-competitive benzimidazole class of checkpoint kinase 2 (CHK2) inhibitors; however, neither binding mode is entirely consistent with the reported SAR. Unconstrained rigid dock ...

    Two closely related binding modes have previously been proposed for the ATP-competitive benzimidazole class of checkpoint kinase 2 (CHK2) inhibitors; however, neither binding mode is entirely consistent with the reported SAR. Unconstrained rigid docking of benzimidazole ligands into representative CHK2 protein crystal structures reveals an alternative binding mode involving a water-mediated interaction with the hinge region; docking which incorporates protein side chain flexibility for selected residues in the ATP binding site resulted in a refinement of the water-mediated hinge binding mode that is consistent with observed SAR. The flexible docking results are in good agreement with the crystal structures of four exemplar benzimidazole ligands bound to CHK2 which unambiguously confirmed the binding mode of these inhibitors, including the water-mediated interaction with the hinge region, and which is significantly different from binding modes previously postulated in the literature.


    Organizational Affiliation

    Cancer Research UK Cancer Therapeutics Unit, Division of Cancer Therapeutics, Institute of Cancer Research, Haddow Laboratories, Sutton, Surrey, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SERINE/THREONINE-PROTEIN KINASE CHK2A329Homo sapiensMutation(s): 0 
Gene Names: CHEK2CDS1CHK2RAD53
EC: 2.7.11.1
Find proteins for O96017 (Homo sapiens)
Explore O96017 
Go to UniProtKB:  O96017
NIH Common Fund Data Resources
PHAROS  O96017
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
A9U
Query on A9U

Download CCD File 
A
2-{4-[(1-BENZYLPIPERIDIN-4-YL)METHOXY]PHENYL}-1H-BENZIMIDAZOLE-6-CARBOXAMIDE
C27 H28 N4 O2
LTUJRTNXSJGLBT-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download CCD File 
A
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
NO3
Query on NO3

Download CCD File 
A
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
A9UIC50:  70   nM  BindingDB
A9UIC50:  231   nM  BindingDB
A9UIC50 :  60   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.48 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.185 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.07α = 90
b = 91.07β = 90
c = 93.41γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-10-10
    Type: Initial release
  • Version 1.1: 2012-10-24
    Changes: Database references
  • Version 1.2: 2012-11-07
    Changes: Database references