Structural analysis of checkpoint kinase 2 in complex with PV1162, a novel inhibitor

Experimental Data Snapshot

  • Resolution: 2.20 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.196 

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X-Ray Structures of Checkpoint Kinase 2 in Complex with Inhibitors that Target its Gatekeeper-Dependent Hydrophobic Pocket.

Lountos, G.T.Jobson, A.G.Tropea, J.E.Self, C.R.Zhang, G.Pommier, Y.Shoemaker, R.H.Waugh, D.S.

(2011) FEBS Lett 585: 3245

  • DOI: https://doi.org/10.1016/j.febslet.2011.08.050
  • Primary Citation of Related Structures:  
    2YIQ, 2YIR, 2YIT

  • PubMed Abstract: 

    The serine/threonine checkpoint kinase 2 (Chk2) is an attractive molecular target for the development of small molecule inhibitors to treat cancer. Here, we report the rational design of Chk2 inhibitors that target the gatekeeper-dependent hydrophobic pocket located behind the adenine-binding region of the ATP-binding site. These compounds exhibit IC(50) values in the low nanomolar range and are highly selective for Chk2 over Chk1. X-ray crystallography was used to determine the structures of the inhibitors in complex with the catalytic kinase domain of Chk2 to verify their modes of binding.

  • Organizational Affiliation

    Basic Science Program, SAIC-Frederick, Frederick, MD 21702-1201, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SERINE/THREONINE-PROTEIN KINASE CHK2323Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for O96017 (Homo sapiens)
Explore O96017 
Go to UniProtKB:  O96017
PHAROS:  O96017
GTEx:  ENSG00000183765 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO96017
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on YIT

Download Ideal Coordinates CCD File 
B [auth A]N-{4-[(1E)-N-carbamimidoylbutanehydrazonoyl]phenyl}-5-methoxy-1H-indole-2-carboxamide
C21 H24 N6 O2
Query on NO3

Download Ideal Coordinates CCD File 
N O3
Binding Affinity Annotations 
IDSourceBinding Affinity
YIT Binding MOAD:  2YIT IC50: 0.29 (nM) from 1 assay(s)
PDBBind:  2YIT IC50: 0.29 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.20 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.196 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.208α = 90
b = 91.208β = 90
c = 93.465γ = 120
Software Package:
Software NamePurpose
HKL-3000data 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: 2011-09-07
    Type: Initial release
  • Version 1.1: 2011-10-26
    Changes: Database references
  • Version 1.2: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description