1XL1

Kinetic and crystallographic studies on 2-(beta-D-glucopyranosyl)-5-methyl-1,3,4-oxadiazole,-benzothiazole, and-benzimidazole, inhibitors of muscle glycogen phosphorylase b. Evidence for a new binding site.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Kinetic and crystallographic studies on 2-(beta-D-glucopyranosyl)-5-methyl-1, 3, 4-oxadiazole, -benzothiazole, and -benzimidazole, inhibitors of muscle glycogen phosphorylase b. Evidence for a new binding site

Chrysina, E.D.Kosmopoulou, M.N.Tiraidis, C.Kardakaris, R.Bischler, N.Leonidas, D.D.Hadady, Z.Somsak, L.Docsa, T.Gergely, P.Oikonomakos, N.G.

(2005) Protein Sci. 14: 873-888

  • DOI: 10.1110/ps.041216105
  • Primary Citation of Related Structures:  1XKX, 1XL0

  • PubMed Abstract: 
  • In an attempt to identify leads that would enable the design of inhibitors with enhanced affinity for glycogen phosphorylase (GP), that might control hyperglycaemia in type 2 diabetes, three new analogs of beta-D-glucopyranose, 2-(beta-D-glucopyranos ...

    In an attempt to identify leads that would enable the design of inhibitors with enhanced affinity for glycogen phosphorylase (GP), that might control hyperglycaemia in type 2 diabetes, three new analogs of beta-D-glucopyranose, 2-(beta-D-glucopyranosyl)-5-methyl-1, 3, 4-oxadiazole, -benzothiazole, and -benzimidazole were assessed for their potency to inhibit GPb activity. The compounds showed competitive inhibition (with respect to substrate Glc-1-P) with K(i) values of 145.2 (+/-11.6), 76 (+/-4.8), and 8.6 (+/-0.7) muM, respectively. In order to establish the mechanism of this inhibition, crystallographic studies were carried out and the structures of GPb in complex with the three analogs were determined at high resolution (GPb-methyl-oxadiazole complex, 1.92 A; GPb-benzothiazole, 2.10 A; GPb-benzimidazole, 1.93 A). The complex structures revealed that the inhibitors can be accommodated in the catalytic site of T-state GPb with very little change of the tertiary structure, and provide a rationalization for understanding variations in potency of the inhibitors. In addition, benzimidazole bound at the new allosteric inhibitor or indole binding site, located at the subunit interface, in the region of the central cavity, and also at a novel binding site, located at the protein surface, far removed (approximately 32 A) from the other binding sites, that is mostly dominated by the nonpolar groups of Phe202, Tyr203, Val221, and Phe252.


    Related Citations: 
    • Crystallographic studies on alpha and beta-D-glucopyranosyl formamide analogues, inhibitors of glycogen phosphorylase
      Chrysina, E.D.,Oikonomakos, N.G.,Zographos, S.E.,Kosmopoulou, M.,Bischler, N.,Leonidas, D.D.,Kovacs, L.,Docsa, T.,Gergely, P.
      (2003) Biocatal.Biotransfor. 21: 233
    • Binding of N-acetyl-N '-beta-D-glucopyranosyl urea and N-benzoyl-N '-beta-D-glucopyranosyl urea to glycogen phosphorylase b: kinetic and crystallographic studies
      Oikonomakos, N.G.,Kosmopoulou, M.,Zographos, S.E.,Leonidas, D.D.,Chrysina, E.D.,Somsak, L.,Nagy, V.,Praly, J.P.,Docsa, T.,Toth, B.,Gergely, P.
      (2002) Eur.J.Biochem. 269: 1684


    Organizational Affiliation

    Institute of Organic and Pharmaceutical Chemistry, The National Hellenic Research Foundation, 48 Vassileos Constantinou Avenue, 116 35 Athens, Greece.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glycogen phosphorylase, muscle form
A
842Oryctolagus cuniculusGene Names: PYGM
EC: 2.4.1.1
Find proteins for P00489 (Oryctolagus cuniculus)
Go to Gene View: PYGM
Go to UniProtKB:  P00489
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PLP
Query on PLP

Download SDF File 
Download CCD File 
A
PYRIDOXAL-5'-PHOSPHATE
VITAMIN B6 Phosphate
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
TH1
Query on TH1

Download SDF File 
Download CCD File 
A
2-(BETA-D-GLUCOPYRANOSYL)-5-METHYL-BENZOTHIAZOLE
2-(BETA-D-GLUCOPYRANOSYL)-5-METHYL-1,3,4-BENZOTHIAZOLE
C14 H17 N O5 S
WGJFWQVWYRZPEP-KABOQKQYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
TH1Ki: 76000 - 229000 nM (100) BINDINGDB
TH1Ki: 76000 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.181 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 128.114α = 90.00
b = 128.114β = 90.00
c = 115.450γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-03-15
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance