2C3K

Identification of a buried pocket for potent and selective inhibition of Chk1: prediction and verification

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.202 

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This is version 1.2 of the entry. See complete history. 


Literature

Identification of a Buried Pocket for Potent and Selective Inhibition of Chk1: Prediction and Verification.

Foloppe, N., Fisher, L.M., Francis, G., Howes, R., Kierstan, P., Potter, A.

(2006) Bioorg Med Chem 14: 1792

  • DOI: 10.1016/j.bmc.2005.10.022
  • Primary Citation of Related Structures:  
    2C3L, 2C3K, 2C3J

  • PubMed Abstract: 

    • Inhibition of the Chk1 kinase by small molecules binding to its active site is a strategy of great therapeutic interest for oncology. We report how computational modelling predicted the binding mode of ligands of special interest to the Chk1 ATP site, fo ...

    Inhibition of the Chk1 kinase by small molecules binding to its active site is a strategy of great therapeutic interest for oncology. We report how computational modelling predicted the binding mode of ligands of special interest to the Chk1 ATP site, for representatives of an indazole series and debromohymenialdisine. These binding modes were subsequently confirmed by X-ray crystallography. The binding mode of a potent indazole derivative involves non-conventional C-H...O and N-H...pi-aromatic interactions with the protein. These interactions are formed in a buried pocket at the periphery of the ATP-binding site, the importance of which has previously been overlooked for ligand design against Chk1. It is demonstrated that filling this pocket can confer ligands with dramatically enhanced affinity for Chk1. Structural arguments in conjunction with assay data explain why targeting this pocket is also advantageous for selective binding to Chk1. Structural overlays of known inhibitors complexed with Chk1 show that only the indazole series utilizes the pocket of interest. Therefore, the analysis presented here should prove helpful in guiding future structure-based ligand design efforts against Chk1.

    Organizational Affiliation: 

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



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SERINE/THREONINE-PROTEIN KINASE CHK1 A297Homo sapiensMutation(s): 0 
Gene Names: CHEK1, CHK1
EC: 2.7.1.37 (PDB Primary Data), 2.7.11.1 (UniProt)
Find proteins for O14757 (Homo sapiens)
Explore O14757 
Go to UniProtKB:  O14757
NIH Common Fund Data Resources
PHAROS:  O14757
GTEx:  ENSG00000149554
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ABO
Query on ABO
Download Ideal Coordinates CCD File 
A
4-[3-(1H-BENZIMIDAZOL-2-YL)-1H-INDAZOL-6-YL]-2-METHOXYPHENOL
C21 H16 N4 O2
GYPHGCGOSZJXOT-UHFFFAOYSA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ABOKi :  26   nM  PDBBind
ABOIC50:  42   nM  BindingDB
ABOKi:  26   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.202 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.057α = 90
b = 65.891β = 102.01
c = 54.584γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-11-23
    Type: Initial release
  • Version 1.1: 2011-05-07
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance