3FR0

Human glucokinase in complex with 2-amino benzamide activator

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.211 

wwPDB Validation 3D Report Full Report


This is version 1.1 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

  • 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glucokinase
A
455Homo sapiensMutation(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
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA
Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
AJB
Query on AJB
Download SDF File 
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
2-amino-5-(4-methyl-4H-[1,2,4]triazole-3-yl-sulfanyl)-N-(4-methyl-thiazole-2-yl)benzamide
C14 H14 N6 O S2
JEBOJMQHVUEKBE-UHFFFAOYSA-N
 Ligand Interaction
GLC
Query on GLC
Download SDF File 
Download CCD File 
A
ALPHA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
AJBKd: 440 nM (100) BINDINGDB
AJBEC50: 140 - 420 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.211 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 80.147α = 90.00
b = 80.147β = 90.00
c = 323.170γ = 120.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data collection
CNXphasing
HKL-2000data scaling
CNSrefinement
CNXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots


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
    Type: Version format compliance