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: 2.3 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.237 

wwPDB Validation 3D Report Full Report


This is version 1.0 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: 10.1016/j.bmcl.2012.07.046
  • Primary Citation of Related Structures:  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 optimi ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Casein kinase I isoform gamma-3
A
330Homo sapiensGene Names: CSNK1G3
EC: 2.7.11.1
Find proteins for Q9Y6M4 (Homo sapiens)
Go to Gene View: CSNK1G3
Go to UniProtKB:  Q9Y6M4
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0VM
Query on 0VM

Download SDF File 
Download CCD File 
A
2-[(4-{[3-(trifluoromethyl)pyridin-2-yl]oxy}phenyl)amino]-1H-benzimidazole-6-carbonitrile
C20 H12 F3 N5 O
GAHCTGQCJXQYNK-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0VMIC50: 6560 nM (88) BINDINGDB
0VMIC50: 140 nM BINDINGMOAD
0VMIC50: 140 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 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 = 90.00
b = 57.153β = 90.00
c = 223.431γ = 120.00
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
HKL-2000data collection
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2012-07-10 
  • Released Date: 2013-05-22 
  • Deposition Author(s): Huang., X.

Revision History 

  • Version 1.0: 2013-05-22
    Type: Initial release