1C50

IDENTIFICATION AND STRUCTURAL CHARACTERIZATION OF A NOVEL ALLOSTERIC BINDING SITE OF GLYCOGEN PHOSPHORYLASE B


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A new allosteric site in glycogen phosphorylase b as a target for drug interactions.

Oikonomakos, N.G.Skamnaki, V.T.Tsitsanou, K.E.Gavalas, N.G.Johnson, L.N.

(2000) Structure Fold.Des. 8: 575-584

  • Also Cited By: 1H5U, 1WUT

  • PubMed Abstract: 
  • In muscle and liver, glycogen concentrations are regulated by the coordinated activities of glycogen phosphorylase (GP) and glycogen synthase. GP exists in two forms: the dephosphorylated low-activity form GPb and the phosphorylated high-activity for ...

    In muscle and liver, glycogen concentrations are regulated by the coordinated activities of glycogen phosphorylase (GP) and glycogen synthase. GP exists in two forms: the dephosphorylated low-activity form GPb and the phosphorylated high-activity form GPa. In both forms, allosteric effectors can promote equilibrium between a less active T state and a more active R state. GP is a possible target for drugs that aim to prevent unwanted glycogen breakdown and to stimulate glycogen synthesis in non-insulin-dependent diabetes. As a result of a data bank search, 5-chloro-1H-indole-2-carboxylic acid (1-(4-fluorobenzyl)-2-(4-hydroxypiperidin-1-yl)-2-oxoethy l)amide, CP320626, was identified as a potent inhibitor of human liver GP. Structural studies have been carried out in order to establish the mechanism of this unusual inhibitor.


    Related Citations: 
    • The Structure of Glycogen Phosphorylase b with an Alkyldihydropyridine-Dicarboxylic Acid Compound, A Novel and Potent Inhibitor
      Zographos, S.E.,Oikonomakos, N.G.,Tsitsanou, K.E.,Leonidas, D.D.,Chrysina, E.D.,Skamnaki, V.T.,Bischoff, H.,Goldmann, S.,Watson, K.A.,Johnson, L.N.
      (1997) Structure 5: 1413
    • Allosteric Inhibition of Glycogen Phosphorylase a by the Potential Antidiabetic Drug 3-Isopropyl 4-(2-Chlorophenyl)-1,4-Dihydro-1-Ethyl-2-Methyl-Pyridine-3,5,6-Tricarboxylate
      Oikonomakos, N.G.,Tsitsanou, K.E.,Zographos, S.E.,Skamnaki, V.T.,Goldmann, S.,Bischoff, H.
      (1999) Protein Sci. 8: 1930


    Organizational Affiliation

    Institute of Biological Research and Biotechnology, The National Hellenic Research Foundation, Athens, 11635, Greece. nikos@krokees. eie.gr.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (GLYCOGEN PHOSPHORYLASE)
A
830Oryctolagus 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
CHI
Query on CHI

Download SDF File 
Download CCD File 
A
5-CHLORO-1H-INDOLE-2-CARBOXYLIC ACID [1-(4-FLUOROBENZYL)-2-(4-HYDROXYPIPERIDIN-1YL)-2-OXOETHYL]AMIDE
C23 H23 Cl F N3 O3
YDCGVASFVACWKF-NRFANRHFSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
CHIIC50: 500 nM (97) BINDINGDB
CHIIC50: 334 nM BINDINGMOAD
CHIIC50: 334 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.199 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 129.174α = 90.00
b = 127.174β = 90.00
c = 116.220γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-12-23
    Type: Initial release
  • Version 1.1: 2007-10-16
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance