3A0I | pdb_00003a0i

Human glucokinase in complex with a synthetic activator

• PDB DOI: https://doi.org/10.2210/pdb3A0I/pdb

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


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.277 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.226 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.229 (Depositor) 

Starting Model: experimental

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: https://doi.org/10.1016/j.bmcl.2009.03.137
• Primary Citation Related Structures: 
  3A0I, 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 toxicity concerns associated with an aniline group of the lead structure. Compound 7 demonstrated glucose lowering effect in a rat OGTT model.

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Organizational Affiliation: 
• Banyu Tsukuba Research Institute, Banyu Pharmaceutical Co. Ltd, Okubo, Tsukuba, Ibaraki, Japan. [e-mail]

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: 51.64 kDa 
• Atom Count: 3,685 
• Modeled Residue Count: 448 
• Deposited Residue Count: 455 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucokinase	A [auth X]	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
AJI	C [auth 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 C19 H15 F N6 O S3 SJTQKYKXCYVFHX-UHFFFAOYSA-N
GLC	B [auth X]	alpha-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-DVKNGEFBSA-N
NA	D [auth X]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
AJI	BindingDB:  3A0I	EC50: 250 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.277 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.226 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.229 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.732	α = 90
b = 79.732	β = 90
c = 321.975	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
WEIS	data scaling
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• 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
  Changes: Version format compliance
• Version 1.2: 2017-10-11
  Changes: Refinement description
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.4: 2023-11-01
  Changes: Data collection, Database references, Refinement description, Structure summary