3FR0

Human glucokinase in complex with 2-amino benzamide activator

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 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 


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

  • DOI: 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 determine ...

    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.

    Related Citations: 
    • Structural basis for allosteric regulation of the monomeric allosteric enzyme human glucokinase
      Kamata, K., Mitsuya, M., Nishimura, T., Eiki, J., Nagata, Y.
      (2004) Structure 12: 429
    Organizational Affiliation: 

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



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GlucokinaseA455Homo sapiensMutation(s): 0 
Gene Names: GCK
EC: 2.7.1.2 (PDB Primary Data), 2.7.1.1 (UniProt)
Find proteins for P35557 (Homo sapiens)
Explore P35557 
Go to UniProtKB:  P35557
NIH Common Fund Data Resources
PHAROS  P35557
GTEx  ENSG00000106633
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AJB
Query on AJB
Download CCD File 
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		 Ligand Interaction
GLC
Query on GLC
Download CCD File 
A
alpha-D-glucopyranose
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N		 Ligand Interaction
NA
Query on NA
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
AJBKd:  440   nM  BindingDB
AJBEC50:  420   nM  BindingDB
AJBEC50:  140   nM  BindingDB
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 = 80.147α = 90
b = 80.147β = 90
c = 323.17γ = 120
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNXphasing
CNXrefinement

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2009-01-08 
  • 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