2W0J

Crystal structure of Chk2 in complex with NSC 109555, a specific inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal Structure of Checkpoint Kinase 2 in Complex with Nsc 109555, a Potent and Selective Inhibitor

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

(2009) Protein Sci. 18: 92

  • DOI: 10.1002/pro.16
  • Also Cited By: 2XK9, 2YIQ, 2YIR, 2YIT

  • PubMed Abstract: 
  • Checkpoint kinase 2 (Chk2), a ser/thr kinase involved in the ATM-Chk2 checkpoint pathway, is activated by genomic instability and DNA damage and results in either arrest of the cell cycle to allow DNA repair to occur or apoptosis if the DNA damage is ...

    Checkpoint kinase 2 (Chk2), a ser/thr kinase involved in the ATM-Chk2 checkpoint pathway, is activated by genomic instability and DNA damage and results in either arrest of the cell cycle to allow DNA repair to occur or apoptosis if the DNA damage is severe. Drugs that specifically target Chk2 could be beneficial when administered in combination with current DNA-damaging agents used in cancer therapy. Recently, a novel inhibitor of Chk2, NSC 109555, was identified that exhibited high potency (IC(50) = 240 nM) and selectivity. This compound represents a new chemotype and lead for the development of novel Chk2 inhibitors that could be used as therapeutic agents for the treatment of cancer. To facilitate the discovery of new analogs of NSC 109555 with even greater potency and selectivity, we have solved the crystal structure of this inhibitor in complex with the catalytic domain of Chk2. The structure confirms that the compound is an ATP-competitive inhibitor, as the electron density clearly reveals that it occupies the ATP-binding pocket. However, the mode of inhibition differs from that of the previously studied structure of Chk2 in complex with debromohymenialdisine, a compound that inhibits both Chk1 and Chk2. A unique hydrophobic pocket in Chk2, located very close to the bound inhibitor, presents an opportunity for the rational design of compounds with higher binding affinity and greater selectivity.


    Related Citations: 
    • Identification of a Bis-Guanylhydrazone, 4,4'-Diacetyldiphenylurea-Bis(Guanylhydrazone) Nsc 109555, as a Novel Chemotype for Inhibition of Chk2 Kinase
      Jobson, A.G.,Cardellina, J.H.,Scudiero, D.,Kondapaka, S.,Zhang, H.,Kim, H.,Shoemaker, R.,Pommier, Y.
      (2007) Mol.Pharmacol. 72: 876


    Organizational Affiliation

    Macromolecular Crystallography Laboratory, National Cancer Institute at Frederick, P. O. Box B, Frederick, Maryland 21702-1201, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SERINE/THREONINE-PROTEIN KINASE CHK2
A
323Homo sapiensGene Names: CHEK2 (CDS1, CHK2, RAD53)
EC: 2.7.11.1
Find proteins for O96017 (Homo sapiens)
Go to Gene View: CHEK2
Go to UniProtKB:  O96017
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NO3
Query on NO3

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

Download SDF File 
Download CCD File 
A
4,4'-DIACETYLDIPHENYLUREA-BIS(GUANYLHYDRAZONE)
C19 H24 N10 O
HCAQGQIHBFVVIX-LYXAAFRTSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ZATIC50: 200 - 240 nM (100) BINDINGDB
ZATIC50: 240 nM BINDINGMOAD
ZATIC50: 240 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.215 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 90.847α = 90.00
b = 90.847β = 90.00
c = 93.526γ = 120.00
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
HKL-3000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-02-10
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance