4RVK

CHK1 kinase domain with diazacarbazole compound 8: N-[3-(6-cyano-9H-pyrrolo[2,3-b:5,4-c']dipyridin-3-yl)phenyl]acetamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.255 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Mitigation of Acetylcholine Esterase Activity in the 1,7-Diazacarbazole Series of Inhibitors of Checkpoint Kinase 1.

Gazzard, L.Williams, K.Chen, H.Axford, L.Blackwood, E.Burton, B.Chapman, K.Crackett, P.Drobnick, J.Ellwood, C.Epler, J.Flagella, M.Gancia, E.Gill, M.Goodacre, S.Halladay, J.Hewitt, J.Hunt, H.Kintz, S.Lyssikatos, J.Macleod, C.Major, S.Medard, G.Narukulla, R.Ramiscal, J.Schmidt, S.Seward, E.Wiesmann, C.Wu, P.Yee, S.Yen, I.Malek, S.

(2015) J Med Chem 58: 5053-5074

  • DOI: 10.1021/acs.jmedchem.5b00464
  • Primary Citation of Related Structures:  
    4RVK, 4RVL, 4RVM

  • PubMed Abstract: 
  • Checkpoint kinase 1 (ChK1) plays a key role in the DNA damage response, facilitating cell-cycle arrest to provide sufficient time for lesion repair. This leads to the hypothesis that inhibition of ChK1 might enhance the effectiveness of DNA-damaging therapies in the treatment of cancer ...

    Checkpoint kinase 1 (ChK1) plays a key role in the DNA damage response, facilitating cell-cycle arrest to provide sufficient time for lesion repair. This leads to the hypothesis that inhibition of ChK1 might enhance the effectiveness of DNA-damaging therapies in the treatment of cancer. Lead compound 1 (GNE-783), the prototype of the 1,7-diazacarbazole class of ChK1 inhibitors, was found to be a highly potent inhibitor of acetylcholine esterase (AChE) and unsuitable for development. A campaign of analogue synthesis established SAR delineating ChK1 and AChE activities and allowing identification of new leads with improved profiles. In silico docking using a model of AChE permitted rationalization of the observed SAR. Compounds 19 (GNE-900) and 30 (GNE-145) were identified as selective, orally bioavailable ChK1 inhibitors offering excellent in vitro potency with significantly reduced AChE activity. In combination with gemcitabine, these compounds demonstrate an in vivo pharmacodynamic effect and are efficacious in a mouse p53 mutant xenograft model.


    Organizational Affiliation

    ∇Argenta, A Charles River Company, 8-9 Spire Green Centre, Harlow, Essex CM19 5TR, United Kingdom.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/threonine-protein kinase Chk1A298Homo 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
3XK (Subject of Investigation/LOI)
Query on 3XK

Download Ideal Coordinates CCD File 
B [auth A]N-[3-(6-cyano-9H-pyrrolo[2,3-b:5,4-c']dipyridin-3-yl)phenyl]acetamide
C19 H13 N5 O
QBZYUGXSSSASTB-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
3XK Binding MOAD:  4RVK IC50: 13.5 (nM) from 1 assay(s)
BindingDB:  4RVK IC50: 14 (nM) from 1 assay(s)
EC50: 425 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.255 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.989α = 90
b = 65.906β = 93.92
c = 57.875γ = 90
Software Package:
Software NamePurpose
JDirectordata collection
AMoREphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

  • Deposited Date: 2014-11-26 
  • Released Date: 2015-06-03 
  • Deposition Author(s): Wiesmann, C., Wu, P.

Revision History  (Full details and data files)

  • Version 1.0: 2015-06-03
    Type: Initial release
  • Version 1.1: 2015-07-08
    Changes: Database references
  • Version 1.2: 2017-11-22
    Changes: Refinement description