3FR0

Human glucokinase in complex with 2-amino benzamide activator

• PDB DOI: https://doi.org/10.2210/pdb3FR0/pdb

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


• Deposited: 2009-01-08 Released: 2009-02-17 
• Deposition Author(s): Kamata, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.274 
• R-Value Work: 0.211 
• R-Value Observed: 0.214 

Starting Model: experimental

Literature

Identification of novel and potent 2-amino benzamide derivatives as allosteric glucokinase activators

Nishimura, T., Iino, T., Mitsuya, M., Bamba, M., Watanabe, H., Tsukahara, D., Kamata, K., Sasaki, K., Ohyama, S., Hosaka, H., Futamura, M., Nagata, Y., Eiki, J.

(2009) Bioorg Med Chem Lett 19: 1357-1360

• PubMed: 19188063 
• DOI: https://doi.org/10.1016/j.bmcl.2009.01.053
• Primary Citation of Related Structures:  
  3FR0


• PubMed Abstract: 
  

  The identification and structure-activity-relationships (SARs) of novel 2-amino benzamide glucokinase activators are described. Compounds in this series were developed to be potent GK activators, and their binding mode to the GK protein was determined by crystal structure analysis. In vivo pharmacokinetic and acute in vivo efficacy studies of compound 18 are also described.

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Organizational Affiliation: 

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

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: 51.53 kDa 
• Atom Count: 3,675 
• Modelled Residue Count: 448 
• Deposited Residue Count: 455 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucokinase	A	455	Homo sapiens	Mutation(s): 0  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
AJB	C [auth A]	2-amino-N-(4-methyl-1,3-thiazol-2-yl)-5-[(4-methyl-4H-1,2,4-triazol-3-yl)sulfanyl]benzamide C14 H14 N6 O S2 JEBOJMQHVUEKBE-UHFFFAOYSA-N
GLC	B [auth A]	alpha-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-DVKNGEFBSA-N
NA	D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
AJB	BindingDB:  3FR0	Kd: 440 (nM) from 1 assay(s)
		EC50: min: 140, max: 420 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.274 
• R-Value Work: 0.211 
• R-Value Observed: 0.214 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.147	α = 90
b = 80.147	β = 90
c = 323.17	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CNX	phasing
CNX	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-02-17 
Deposition Author(s): Kamata, K.

Revision History  

• Version 1.0: 2009-02-17
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.3: 2023-11-01
  Changes: Data collection, Database references, Refinement description, Structure summary