3H1V

Human glucokinase in complex with a synthetic activator

• PDB DOI: https://doi.org/10.2210/pdb3H1V/pdb

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


• 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 
• R-Value Observed: 0.235 

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: https://doi.org/10.1016/j.bmc.2009.05.037
• Primary Citation of Related Structures:  
  3H1V


• 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]

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: 51.29 kDa 
• Atom Count: 3,659 
• Modelled Residue Count: 446 
• Deposited Residue Count: 451 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucokinase	A [auth X]	451	Homo sapiens	Mutation(s): 0  Gene Names: GCK EC: 2.7.1.2 (PDB Primary Data), 2.7.1.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P35557 (Homo sapiens) Explore P35557  Go to UniProtKB:  P35557
PHAROS:  P35557 GTEx:  ENSG00000106633

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TK1	C [auth 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
GLC	B [auth X]	alpha-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-DVKNGEFBSA-N
NA	D [auth X]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.11 Å
• R-Value Free: 0.284 
• R-Value Work: 0.232 
• R-Value Observed: 0.235 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.793	α = 90
b = 79.793	β = 90
c = 326.124	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• 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
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.4: 2024-03-20
  Changes: Data collection, Database references, Structure summary