Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 51290.15 
• Atom Count: 3539 
• Residue Count: 451 
• Unique protein chains: 1

3H1V

Human glucokinase in complex with a synthetic activator

• DOI: 10.2210/pdb3H1V/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli


• Deposited: 2009-04-14 Released: 2009-10-06 
• Deposition Author(s): Kamata, K., Takahashi, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.11 Å
• R-Value Free: 0.284 
• R-Value Work: 0.232 

Literature

The design and optimization of a series of 2-(pyridin-2-yl)-1H-benzimidazole compounds as allosteric glucokinase activators.

Takahashi, K., Hashimoto, N., Nakama, C., Kamata, K., Sasaki, K., Yoshimoto, R., Ohyama, S., Hosaka, H., Maruki, H., Nagata, Y., Eiki, J., Nishimura, T.

(2009) Bioorg.Med.Chem. 17: 7042-7051

• PubMed: 19736020 
• DOI: 10.1016/j.bmc.2009.05.037


• PubMed Abstract: 
  

The optimization of a series of benzimidazole glucokinase activators is described. We identified a novel and potent achiral benzimidazole derivative as an allosteric GK activator. This activator was designed and synthesized via removal of the chiral center of the lead compound, 6-(N-acylpyrrolidin-2-yl)benzimidazole. The activator exhibited good PK profiles in rats and dogs, and significant hypoglycemic efficacy at 1 mg/kg po dosing in a rat OGTT model. The binding site and binding mode of the benzimidazole class of GKA with GK protein was confirmed by X-ray crystallographic analysis.

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Organizational Affiliation: 

Banyu Tsukuba Research Institute, Banyu Pharmaceutical Co., Ltd, 3 Okubo, Tsukuba, Ibaraki 300-2611, Japan. [e-mail]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Glucokinase	X	451	Homo sapiens	Mutation(s): 0  Gene Names: GCK EC: 2.7.1.2
Find proteins for P35557 (Homo sapiens) Go to Gene View: GCK Go to UniProtKB:  P35557

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
TK1	X	1-({5-[4-(methylsulfonyl)phenoxy]-2-pyridin-2-yl-1H-benzimidazol-6-yl}methyl)pyrrolidine-2,5-dione C24 H20 N4 O5 S IPZLCOKXDRIZBC-UHFFFAOYSA-N
NA	X	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N
GLC	X	ALPHA-D-GLUCOSE C6 H12 O6 WQZGKKKJIJFFOK-DVKNGEFBSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.11 Å
• R-Value Free: 0.284 
• R-Value Work: 0.232 
• Space Group: P 6₅ 2 2

Unit Cell:

Length (Å)	Angle (°)
a = 79.793	α = 90.00
b = 79.793	β = 90.00
c = 326.124	γ = 120.00

Software Package:

Software Name	Purpose
PDB_EXTRACT	data extraction
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-04-14 
• Released Date: 2009-10-06 
• Deposition Author(s): Kamata, K., Takahashi, K.

Revision History 

• Version 1.0: 2009-10-06
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Version format compliance
• Version 1.2: 2017-11-01
  Type: Refinement description