2CGW

Identification of chemically diverse Chk1 inhibitors by receptor- based virtual screening


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Identification of Chemically Diverse Chk1 Inhibitors by Receptor-Based Virtual Screening.

Foloppe, N.Fisher, L.M.Howes, R.Potter, A.Robertson, A.G.S.Surgenor, A.E.

(2006) Bioorg.Med.Chem. 14: 4792

  • DOI: 10.1016/j.bmc.2006.03.021
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Inhibition of the Chk1 kinase by small molecules is of great therapeutic interest for oncology and in understanding the cellular regulation of the G2/M checkpoint. We report how computational docking of a large electronic catalogue of compounds to an ...

    Inhibition of the Chk1 kinase by small molecules is of great therapeutic interest for oncology and in understanding the cellular regulation of the G2/M checkpoint. We report how computational docking of a large electronic catalogue of compounds to an X-ray structure of the Chk1 ATP-binding site allowed prioritisation of a small subset of these compounds for assay. This led to the discovery of 10 novel Chk1 inhibitors, distributed among nine new and clearly different chemical scaffolds. Several of these scaffolds have promising lead-like properties. All these ligands act by competitive binding to the targeted ATP site. The crystal structures of four of these compounds bound to this site are presented, and reasonable modelled docking modes are suggested for the 5 other scaffolds. This structural context is used to assess the potential of these scaffolds for further medicinal chemistry efforts, suggesting that several of them could be elaborated to make additional interactions with the buried part of the ATP site. Some unusual interactions with the conserved kinase backbone motif are pointed out. The ligand-binding modes are also used to discuss their medicinal chemistry potential with respect to undesirable chemical functionalities, whether these functionalities bind directly to the protein or not. Overall, this work illustrates how virtual screening can identify a diverse set of ligands which bind to the targeted site. The structural models for these ligands in the Chk1 ATP-binding site will facilitate further medicinal chemistry efforts targeting this kinase.


    Organizational Affiliation

    Vernalis (R&D) Ltd, Granta Park, Abington, Cambridge CB1 6GB, UK. n.foloppe@vernalis.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SERINE/THREONINE-PROTEIN KINASE CHK1
A
297Homo sapiensMutation(s): 0 
Gene Names: CHEK1 (CHK1)
EC: 2.7.11.1
Find proteins for O14757 (Homo sapiens)
Go to Gene View: CHEK1
Go to UniProtKB:  O14757
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3C3
Query on 3C3

Download SDF File 
Download CCD File 
A
4,4'-(1-PROPYL-1H-1,2,4-TRIAZOLE-3,5-DIYL)BIS(2,5-DIHYDRO-1,2,5-OXADIAZOL-3-AMINE)
C9 H15 N9 O2
AZHWQKVREXJRBF-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
3C3IC50: 17300 nM BINDINGMOAD
3C3IC50: 17300 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.186 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 45.130α = 90.00
b = 65.695β = 101.75
c = 54.680γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
REFMACrefinement
AMoREphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-04-05
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance