4G16 | pdb_00004g16

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

• PDB DOI: https://doi.org/10.2210/pdb4G16/pdb

• Classification: TRANSFERASE/TRANSFERASE inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.250 (Depositor), 0.244 (DCC) 
• R-Value Work: 
  0.237 (Depositor), 0.230 (DCC) 

Starting Model: experimental

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

• PubMed: 22877629 
• DOI: https://doi.org/10.1016/j.bmcl.2012.07.046
• Primary Citation 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.

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Organizational Affiliation: 
• Medicinal Chemistry, Amgen Inc., 360 Binney Street, Cambridge, MA 02142, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 38.86 kDa 
• Atom Count: 2,734 
• Modeled Residue Count: 302 
• Deposited Residue Count: 330 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Casein kinase I isoform gamma-3	A	330	Homo sapiens	Mutation(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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0VM	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
ID	Source	Binding Affinity
0VM	BindingDB:  4G16	IC50: 6560 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.250 (Depositor), 0.244 (DCC) 
• R-Value Work:  0.237 (Depositor), 0.230 (DCC) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.153	α = 90
b = 57.153	β = 90
c = 223.431	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• 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