Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 51519.52 
• Atom Count: 3541 
• Residue Count: 455 
• Unique protein chains: 1

3GOI

Human glucokinase in complex with a synthetic activator

• DOI: 10.2210/pdb3GOI/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli


• Deposited: 2009-03-19 Released: 2009-04-28 
• Deposition Author(s): Kamata, K., Mitsuya, M.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.52 Å
• R-Value Free: 0.282 
• R-Value Work: 0.205 

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

• PubMed: 19362831 
• DOI: 10.1016/j.bmcl.2009.03.137
• Primary Citation of Related Structures:  
  3A0I


• 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 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. [e-mail]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Glucokinase	A	455	Homo sapiens	Mutation(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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
LOI	A	2-(methylamino)-N-(4-methyl-1,3-thiazol-2-yl)-5-[(4-methyl-4H-1,2,4-triazol-3-yl)sulfanyl]benzamide C15 H16 N6 O S2 XRJAKERBMMBUGR-UHFFFAOYSA-N
GLC	A	ALPHA-D-GLUCOSE C6 H12 O6 WQZGKKKJIJFFOK-DVKNGEFBSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
LOI	EC50: 330 - 1100 nM (100) BINDINGDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.52 Å
• R-Value Free: 0.282 
• R-Value Work: 0.205 
• Space Group: P 6₅ 2 2

Unit Cell:

Length (Å)	Angle (°)
a = 80.085	α = 90.00
b = 80.085	β = 90.00
c = 323.974	γ = 120.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-03-19 
• Released Date: 2009-04-28 
• Deposition Author(s): Kamata, K., Mitsuya, M.

Revision History 

• Version 1.0: 2009-04-28
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Version format compliance
• Version 1.2: 2017-11-01
  Type: Refinement description