3JVR

Characterization of the Chk1 allosteric inhibitor binding site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.202 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Characterization of the CHK1 allosteric inhibitor binding site.

Vanderpool, D.Johnson, T.O.Ping, C.Bergqvist, S.Alton, G.Phonephaly, S.Rui, E.Luo, C.Deng, Y.L.Grant, S.Quenzer, T.Margosiak, S.Register, J.Brown, E.Ermolieff, J.

(2009) Biochemistry 48: 9823-9830

  • DOI: 10.1021/bi900258v
  • Primary Citation of Related Structures:  
    3JVR, 3JVS

  • PubMed Abstract: 
  • Checkpoint kinase 1 (CHK1) is a key element in the DNA damage response pathway and plays a crucial role in the S-G(2)-phase checkpoint. Inhibiting CHK1 is a therapeutic strategy involving abrogation of the G2/M mitotic checkpoint defense of tumor cells toward lethal damage induced by DNA-directed chemotherapeutic agents ...

    Checkpoint kinase 1 (CHK1) is a key element in the DNA damage response pathway and plays a crucial role in the S-G(2)-phase checkpoint. Inhibiting CHK1 is a therapeutic strategy involving abrogation of the G2/M mitotic checkpoint defense of tumor cells toward lethal damage induced by DNA-directed chemotherapeutic agents. To date, most CHK1 inhibition approaches have involved targeting the ATP site of this kinase. In this study, we provide crystallographic and kinetic characterization of two small molecule inhibitors that bind to an allosteric site in the proximity of the CHK1 substrate site. Analysis of kinetic and biophysical data has led to the conclusion that these small molecule allosteric site inhibitors of CHK1 are reversible and are neither ATP- nor peptide substrate-competitive. K(i) values of 1.89 and 0.15 microM, respectively, have been determined for these compounds using a mixed inhibitor kinetic analysis. Cocrystal structures of the inhibitors bound to CHK1 reveal an allosteric site, unique to CHK1, located in the C-terminal domain and consisting of a shallow groove linked to a small hydrophobic pocket. The pocket displays induced fit characteristics in the presence of the two inhibitors. These findings establish the potential for the development of highly selective CHK1 inhibitors.


    Organizational Affiliation

    Department of Biochemistry and Primary Screening, Pfizer, La Jolla, San Diego 92121, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/threonine-protein kinase Chk1A271Homo sapiensMutation(s): 0 
Gene Names: CHEK1CHK1
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for O14757 (Homo sapiens)
Explore O14757 
Go to UniProtKB:  O14757
PHAROS:  O14757
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AGX (Subject of Investigation/LOI)
Query on AGX

Download Ideal Coordinates CCD File 
B [auth A](1S)-1-(1H-benzimidazol-2-yl)ethyl (3,4-dichlorophenyl)carbamate
C16 H13 Cl2 N3 O2
MVMZWHAHBIJEDT-VIFPVBQESA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
AGX BindingDB:  3JVR Ki: 1890 (nM) from 1 assay(s)
Binding MOAD:  3JVR Ki: 1890 (nM) from 1 assay(s)
PDBBind:  3JVR Ki: 1890 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.202 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.763α = 90
b = 65.362β = 93.67
c = 57.916γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
CNXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNXphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

  • Deposited Date: 2009-09-17 
  • Released Date: 2009-10-06 
  • Deposition Author(s): Chen, P.

Revision History  (Full details and data files)

  • Version 1.0: 2009-10-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-06-07
    Changes: Source and taxonomy