2C3L

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.3 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:  

  • 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 ...

    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: 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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
IDZ
Query on IDZ

Download SDF File 
Download CCD File 
A
3-(1H-BENZIMIDAZOL-2-YL)-1H-INDAZOLE
C14 H10 N4
JTKFRFMSUBOCIQ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
IDZKi: 8580 nM (98) BINDINGDB
IDZIC50: 6296 nM (98) BINDINGDB
IDZKi: 26 nM BINDINGMOAD
IDZKi: 8580 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.185 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 44.980α = 90.00
b = 65.862β = 94.63
c = 58.086γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-11-23
    Type: Initial release
  • Version 1.1: 2011-05-07
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-07-12
    Type: Data collection