2YIT

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

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: 10.1016/j.febslet.2011.08.050
  • Structures With Same Primary Citation

  • 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 ...

    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.


    Related Citations: 
    • 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

    Organizational Affiliation

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



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SERINE/THREONINE-PROTEIN KINASE CHK2A323Homo 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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
YIT
Query on YIT

Download CCD File 
A
N-{4-[(1E)-N-carbamimidoylbutanehydrazonoyl]phenyl}-5-methoxy-1H-indole-2-carboxamide
C21 H24 N6 O2
IFLKHYHIUCIDRM-NLRVBDNBSA-N
 Ligand Interaction
NO3
Query on NO3

Download CCD File 
A
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
YITIC50 :  0.28999999165534973   nM  PDBBind
YITIC50:  0.28999999165534973   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
REFMACrefinement
HKL-3000data reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-09-07
    Type: Initial release
  • Version 1.1: 2011-10-26
    Changes: Database references