4QYH

CHK1 kinase domain in complex with diazacarbazole GNE-783


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Discovery of the 1,7-diazacarbazole class of inhibitors of checkpoint kinase 1.

Gazzard, L.Appleton, B.Chapman, K.Chen, H.Clark, K.Drobnick, J.Goodacre, S.Halladay, J.Lyssikatos, J.Schmidt, S.Sideris, S.Wiesmann, C.Williams, K.Wu, P.Yen, I.Malek, S.

(2014) Bioorg Med Chem Lett 24: 5704-5709

  • DOI: 10.1016/j.bmcl.2014.10.063
  • Primary Citation of Related Structures:  
    4QYE, 4QYF, 4QYG, 4QYH

  • PubMed Abstract: 
  • Checkpoint kinase 1 (ChK1) is activated in response to DNA damage, acting to temporarily block cell cycle progression and allow for DNA repair. It is envisaged that inhibition of ChK1 will sensitize tumor cells to treatment with DNA-damaging therapies, and may enhance the therapeutic window ...

    Checkpoint kinase 1 (ChK1) is activated in response to DNA damage, acting to temporarily block cell cycle progression and allow for DNA repair. It is envisaged that inhibition of ChK1 will sensitize tumor cells to treatment with DNA-damaging therapies, and may enhance the therapeutic window. High throughput screening identified carboxylate-containing diarylpyrazines as a prominent hit series, but with limited biochemical potency and no cellular activity. Through a series of SAR investigations and X-ray crystallographic analysis the critical role of polar contacts with conserved waters in the kinase back pocket was established. Structure-based design, guided by in silico modeling, transformed the series to better satisfy these contacts and the novel 1,7-diazacarbazole class of inhibitors was discovered. Here we present the genesis of this novel series and the identification of GNE-783, a potent, selective and orally bioavailable inhibitor of ChK1.


    Organizational Affiliation

    Department of Biochemical and Cellular Pharmacology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/threonine-protein kinase Chk1A, B298Homo 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
3DX
Query on 3DX

Download Ideal Coordinates CCD File 
C [auth A], D [auth B]3-[4-(4-methylpiperazin-1-yl)phenyl]-9H-pyrrolo[2,3-b:5,4-c']dipyridine-6-carbonitrile
C22 H20 N6
PVRJSOWSQUNARV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
3DXEC50:  98   nM  BindingDB
3DXIC50:  1.2999999523162842   nM  BindingDB
3DXIC50:  1.2999999523162842   nM  Binding MOAD
3DXIC50:  98   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.078α = 90
b = 65.962β = 94.49
c = 115.682γ = 90
Software Package:
Software NamePurpose
BOSdata collection
AMoREphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2014-07-24 
  • Released Date: 2014-12-17 
  • Deposition Author(s): Wiesmann, C., Wu, P.

Revision History  (Full details and data files)

  • Version 1.0: 2014-12-17
    Type: Initial release