3A0I

Human glucokinase in complex with a synthetic activator


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
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted AJIClick on this verticalbar to view detailsBest fitted GLCClick on this verticalbar to view details

This is version 1.4 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: https://doi.org/10.1016/j.bmcl.2009.03.137
  • Primary Citation of 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.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GlucokinaseA [auth X]455Homo sapiensMutation(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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP35557
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AJI
Query on AJI

Download Ideal Coordinates CCD File 
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
Query on GLC

Download Ideal Coordinates CCD File 
B [auth X]alpha-D-glucopyranose
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
D [auth X]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding 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 = 79.732α = 90
b = 79.732β = 90
c = 321.975γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
WEISdata scaling
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted AJIClick on this verticalbar to view detailsBest fitted GLCClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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