2OFF

The crystal structure of Glycogen Phosphorylase b in complex with a potent allosteric inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

FR258900, a potential anti-hyperglycemic drug, binds at the allosteric site of glycogen phosphorylase

Tiraidis, C.Alexacou, K.-M.Zographos, S.E.Leonidas, D.D.Gimisis, T.Oikonomakos, N.G.

(2007) Protein Sci. 16: 1773-1782

  • DOI: 10.1110/ps.072925607

  • PubMed Abstract: 
  • FR258900 has been discovered as a novel inhibitor of human liver glycogen phosphorylase a and proved to suppress hepatic glycogen breakdown and reduce plasma glucose concentrations in diabetic mice models. To elucidate the mechanism of inhibition, we ...

    FR258900 has been discovered as a novel inhibitor of human liver glycogen phosphorylase a and proved to suppress hepatic glycogen breakdown and reduce plasma glucose concentrations in diabetic mice models. To elucidate the mechanism of inhibition, we have determined the crystal structure of the cocrystallized rabbit muscle glycogen phosphorylase b-FR258900 complex and refined it to 2.2 A resolution. The structure demonstrates that the inhibitor binds at the allosteric activator site, where the physiological activator AMP binds. The contacts from FR258900 to glycogen phosphorylase are dominated by nonpolar van der Waals interactions with Gln71, Gln72, Phe196, and Val45' (from the symmetry-related subunit), and also by ionic interactions from the carboxylate groups to the three arginine residues (Arg242, Arg309, and Arg310) that form the allosteric phosphate-recognition subsite. The binding of FR258900 to the protein promotes conformational changes that stabilize an inactive T-state quaternary conformation of the enzyme. The ligand-binding mode is different from those of the potent phenoxy-phthalate and acyl urea inhibitors, previously described, illustrating the broad specificity of the allosteric site.


    Organizational Affiliation

    Institute of Organic and Pharmaceutical Chemistry, National Hellenic Research Foundation, Athens, Greece.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glycogen phosphorylase, muscle form
A
842Oryctolagus cuniculusMutation(s): 0 
Gene 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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OFF
Query on OFF

Download SDF File 
Download CCD File 
A
2-DEOXY-3,4-BIS-O-[3-(4-HYDROXYPHENYL)PROPANOYL]-L-THREO-PENTARIC ACID
2,3-BIS((E)-3-(4-HYDROXYPHENYL)ACRYLOYLOXY)PENTANEDIOIC ACID
C23 H20 O10
VJLMRHSHSNLOGC-NOPZTHQXSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
LLP
Query on LLP
A
L-PEPTIDE LINKINGC14 H22 N3 O7 PLYS
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
OFFKi: 460 nM (100) BINDINGDB
OFFKi: 460 nM BINDINGMOAD
OFFIC50: 300 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.184 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 128.780α = 90.00
b = 128.780β = 90.00
c = 116.051γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
REFMACrefinement
ADSCdata collection
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-08-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Derived calculations, Version format compliance