3A0I

Human glucokinase in complex with a synthetic activator


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.226 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Discovery of novel 3,6-disubstituted 2-pyridinecarboxamide derivatives as GK activators

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

(2009) Bioorg.Med.Chem.Lett. 19: 2718-2721

  • DOI: 10.1016/j.bmcl.2009.03.137
  • Primary Citation of Related Structures:  3GOI

  • PubMed Abstract: 
  • A novel class of 3,6-disubstituted 2-pyridinecarboxamide derivatives was designed based on X-ray analysis of the 2-aminobenzamide lead class. Subsequent chemical modification led to the discovery of potent GK activators which eliminate potential toxi ...

    A novel class of 3,6-disubstituted 2-pyridinecarboxamide derivatives was designed based on X-ray analysis of the 2-aminobenzamide lead class. Subsequent chemical modification led to the discovery of potent GK activators which eliminate potential toxicity concerns associated with an aniline group of the lead structure. Compound 7 demonstrated glucose lowering effect in a rat OGTT model.


    Organizational Affiliation

    Banyu Tsukuba Research Institute, Banyu Pharmaceutical Co. Ltd, Okubo, Tsukuba, Ibaraki, Japan. morihiro_mitsuya@merck.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glucokinase
X
455Homo sapiensGene 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 
X
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
GLC
Query on GLC

Download SDF File 
Download CCD File 
X
ALPHA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
 Ligand Interaction
AJI
Query on AJI

Download SDF File 
Download CCD File 
X
3-[(4-fluorophenyl)sulfanyl]-N-(4-methyl-1,3-thiazol-2-yl)-6-[(4-methyl-4H-1,2,4-triazol-3-yl)sulfanyl]pyridine-2-carboxamide
3-[(4-fluorophenyl)thio]-N-(4-methyl-1,3-thiazol-2-yl)-6-[(4-methyl-4H-1,2,4-triazol-3-yl)thio]pyridine-2-carboxamide
C19 H15 F N6 O S3
SJTQKYKXCYVFHX-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
AJIEC50: 250 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.226 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 79.732α = 90.00
b = 79.732β = 90.00
c = 321.975γ = 120.00
Software Package:
Software NamePurpose
WEISdata scaling
REFMACrefinement
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-04-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-10-11
    Type: Refinement description