crystal structure of Chek1 in complex with inhibitor 2

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.230 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


Development of 6-substituted indolylquinolinones as potent Chek1 kinase inhibitors.

Huang, S.Garbaccio, R.M.Fraley, M.E.Steen, J.Kreatsoulas, C.Hartman, G.Stirdivant, S.Drakas, B.Rickert, K.Walsh, E.Hamilton, K.Buser, C.A.Hardwick, J.Mao, X.Abrams, M.Beck, S.Tao, W.Lobell, R.Sepp-Lorenzino, L.Yan, Y.Ikuta, M.Murphy, J.Z.Sardana, V.Munshi, S.Kuo, L.Reilly, M.Mahan, E.

(2006) Bioorg Med Chem Lett 16: 5907-5912

  • DOI: https://doi.org/10.1016/j.bmcl.2006.08.053
  • Primary Citation of Related Structures:  
    2HXL, 2HXQ, 2HY0

  • PubMed Abstract: 

    Through a comparison of X-ray co-crystallographic data for 1 and 2 in the Chek1 active site, it was hypothesized that the affinity of the indolylquinolinone series (2) for Chek1 kinase would be improved via C6 substitution into the hydrophobic region I (HI) pocket. An efficient route to 6-bromo-3-indolyl-quinolinone (9) was developed, and this series was rapidly optimized for potency by modification at C6. A general trend was observed among these low nanomolar Chek1 inhibitors that compounds with multiple basic amines, or elevated polar surface area (PSA) exhibited poor cell potency. Minimization of these parameters (basic amines, PSA) resulted in Chek1 inhibitors with improved cell potency, and preliminary pharmacokinetic data are presented for several of these compounds.

  • Organizational Affiliation

    Department of Medicinal Chemistry, Merck Research Laboratories, West Point, PA 19486, USA. shaei_huang@merck.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase Chk1322Homo sapiensMutation(s): 0 
Gene Names: CHEK1
UniProt & NIH Common Fund Data Resources
Find proteins for O14757 (Homo sapiens)
Explore O14757 
Go to UniProtKB:  O14757
GTEx:  ENSG00000149554 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO14757
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 373

Download Ideal Coordinates CCD File 
C24 H26 N4 O
Binding Affinity Annotations 
IDSourceBinding Affinity
373 PDBBind:  2HXQ IC50: 144 (nM) from 1 assay(s)
BindingDB:  2HXQ IC50: 140 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.230 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.11α = 90
b = 66.25β = 94.61
c = 58.17γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

  • Released Date: 2007-06-19 
  • Deposition Author(s): Yan, Y.

Revision History  (Full details and data files)

  • Version 1.0: 2007-06-19
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description