4G16

Crystal structure of ck1g3 with 2-[(4-{[3-(TRIFLUOROMETHYL)PYRIDIN2-YL]OXY}PHENYL)AMINO]-1H-BENZIMIDAZOLE-6-CARBONITRILE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.237 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

2-Phenylamino-6-cyano-1H-benzimidazole-based isoform selective casein kinase 1 gamma (CK1g)inhibitors

Hua, Z.Huang, X.Bregman, H.Chakka, N.DiMauro, E.F.Doherty, E.M.Goldstein, J.Gunaydin, H.Huang, H.Mercede, S.Newcomb, J.Patel, V.F.Turci, S.M.Yan, J.Wilson, C.Martin, M.W.

(2012) Bioorg Med Chem Lett 22: 5392-5395

  • DOI: https://doi.org/10.1016/j.bmcl.2012.07.046
  • Primary Citation of Related Structures:  
    4G16, 4G17

  • PubMed Abstract: 

    Screening of the Amgen compound library led to the identification of 2-phenylamino-6-cyano-1H-benzimidazole 1a as a potent CK1 gamma inhibitor with excellent kinase selectivity and unprecedented CK1 isoform selectivity. Further structure-based optimization of this series resulted in the discovery of 1h which possessed good enzymatic and cellular potency, excellent CK1 isoform and kinase selectivity, and acceptable pharmacokinetic properties.


  • Organizational Affiliation

    Medicinal Chemistry, Amgen Inc., 360 Binney Street, Cambridge, MA 02142, USA. zihao.hua@amgen.com


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Casein kinase I isoform gamma-3330Homo sapiensMutation(s): 0 
Gene Names: CSNK1G3
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y6M4 (Homo sapiens)
Explore Q9Y6M4 
Go to UniProtKB:  Q9Y6M4
PHAROS:  Q9Y6M4
GTEx:  ENSG00000151292 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y6M4
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
0VM
Query on 0VM

Download Ideal Coordinates CCD File 
B [auth A]2-[(4-{[3-(trifluoromethyl)pyridin-2-yl]oxy}phenyl)amino]-1H-benzimidazole-6-carbonitrile
C20 H12 F3 N5 O
GAHCTGQCJXQYNK-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
0VM BindingDB:  4G16 IC50: 6560 (nM) from 1 assay(s)
PDBBind:  4G16 IC50: 140 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.237 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.153α = 90
b = 57.153β = 90
c = 223.431γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
AMoREphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2013-05-22 
  • Deposition Author(s): Huang, X.

Revision History  (Full details and data files)

  • Version 1.0: 2013-05-22
    Type: Initial release
  • Version 1.1: 2018-01-24
    Changes: Structure summary
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description