4G17

Crystal structure of ck1g3 with 2-[(4-TERT-BUTYLPHENYL)AMINO]-1H-BENZIMIDAZOLE-6-CARBONITRILE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.219 

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:  
    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 ...

    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Casein kinase I isoform gamma-3A330Homo 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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0VN
Query on 0VN

Download Ideal Coordinates CCD File 
B [auth A]2-[(4-tert-butylphenyl)amino]-1H-benzimidazole-6-carbonitrile
C18 H18 N4
BQPYYTDDPDJCGA-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0VNIC50:  29   nM  Binding MOAD
0VNIC50:  1510   nM  BindingDB
0VNIC50 :  29   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.219 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.469α = 90
b = 57.469β = 90
c = 224.275γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
AMoREphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2012-07-10 
  • 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