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

Experimental Data Snapshot

  • Resolution: 2.10 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.186 

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

  • 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, 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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SERINE/THREONINE-PROTEIN KINASE CHK1297Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for O14757 (Homo sapiens)
Explore O14757 
Go to UniProtKB:  O14757
PHAROS:  O14757
GTEx:  ENSG00000149554 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO14757
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on DBQ

Download Ideal Coordinates CCD File 
C11 H11 N5 O2
Query on SO3

Download Ideal Coordinates CCD File 
O3 S
Binding Affinity Annotations 
IDSourceBinding Affinity
DBQ Binding MOAD:  2C3J Ki: 659 (nM) from 1 assay(s)
PDBBind:  2C3J Ki: 659 (nM) from 1 assay(s)
BindingDB:  2C3J IC50: min: 725, max: 3000 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.10 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.186 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.039α = 90
b = 65.853β = 102.53
c = 54.582γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Other, Refinement description