Crystal structure of chk1 kinase in complex with inhibitor 38

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 

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This is version 1.2 of the entry. See complete history


Development of thioquinazolinones, allosteric Chk1 kinase inhibitors.

Converso, A.Hartingh, T.Garbaccio, R.M.Tasber, E.Rickert, K.Fraley, M.E.Yan, Y.Kreatsoulas, C.Stirdivant, S.Drakas, B.Walsh, E.S.Hamilton, K.Buser, C.A.Mao, X.Abrams, M.T.Beck, S.C.Tao, W.Lobell, R.Sepp-Lorenzino, L.Zugay-Murphy, J.Sardana, V.Munshi, S.K.Jezequel-Sur, S.M.Zuck, P.D.Hartman, G.D.

(2009) Bioorg Med Chem Lett 19: 1240-1244

  • DOI: https://doi.org/10.1016/j.bmcl.2008.12.076
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    A high throughput screening campaign was designed to identify allosteric inhibitors of Chk1 kinase by testing compounds at high concentration. Activity was then observed at K(m) for ATP and at near-physiological concentrations of ATP. This strategy led to the discovery of a non-ATP competitive thioquinazolinone series which was optimized for potency and stability. An X-ray crystal structure for the complex of our best inhibitor bound to Chk1 was solved, indicating that it binds to an allosteric site approximately 13A from the ATP binding site. Preliminary data is presented for several of these compounds.

  • Organizational Affiliation

    Department of Medicinal Chemistry, Merck Research Laboratories, Merck & Co., PO Box 4, West Point, PA 19486, USA. antonella_converso@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: CHEK1CHK1
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 38M

Download Ideal Coordinates CCD File 
B [auth A]3-(3-chlorophenyl)-2-({(1S)-1-[(6S)-2,8-diazaspiro[5.5]undec-2-ylcarbonyl]pentyl}sulfanyl)quinazolin-4(3H)-one
C29 H35 Cl N4 O2 S
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
O4 S
Binding Affinity Annotations 
IDSourceBinding Affinity
38M PDBBind:  3F9N IC50: 1300 (nM) from 1 assay(s)
Binding MOAD:  3F9N IC50: 1300 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.06α = 90
b = 65.75β = 96.24
c = 58.41γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data 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: 2009-01-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description