Human glycogen phosphorylase (tense state) in complex with the allosteric inhibitor AVE9423

Experimental Data Snapshot

  • Resolution: 2.47 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.159 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


Thermodynamic characterization of allosteric glycogen phosphorylase inhibitors.

Anderka, O.Loenze, P.Klabunde, T.Dreyer, M.K.Defossa, E.Wendt, K.U.Schmoll, D.

(2008) Biochemistry 47: 4683-4691

  • DOI: https://doi.org/10.1021/bi702397d
  • Primary Citation of Related Structures:  
    3CEH, 3CEJ, 3CEM

  • PubMed Abstract: 

    Glycogen phosphorylase (GP) is a validated target for the treatment of type 2 diabetes. Here we describe highly potent GP inhibitors, AVE5688, AVE2865, and AVE9423. The first two compounds are optimized members of the acyl urea series. The latter represents a novel quinolone class of GP inhibitors, which is introduced in this study. In the enzyme assay, both inhibitor types compete with the physiological activator AMP and act synergistically with glucose. Isothermal titration calorimetry (ITC) shows that the compounds strongly bind to nonphosphorylated, inactive GP (GPb). Binding to phosphorylated, active GP (GPa) is substantially weaker, and the thermodynamic profile reflects a coupled transition to the inactive (tense) conformation. Crystal structures confirm that the three inhibitors bind to the AMP site of tense state GP. These data provide the first direct evidence that acyl urea and quinolone compounds are allosteric inhibitors that selectively bind to and stabilize the inactive conformation of the enzyme. Furthermore, ITC reveals markedly different thermodynamic contributions to inhibitor potency that can be related to the binding modes observed in the cocrystal structures. For AVE5688, which occupies only the lower part of the bifurcated AMP site, binding to GPb (Kd = 170 nM) is exclusively enthalpic (Delta H = -9.0 kcal/mol, TDelta S = 0.3 kcal/mol). The inhibitors AVE2865 (Kd = 9 nM, Delta H = -6.8 kcal/mol, TDelta S = 4.2 kcal/mol) and AVE9423 (Kd = 24 nM, Delta H = -5.9 kcal/mol, TDelta S = 4.6 kcal/mol) fully exploit the volume of the binding pocket. Their pronounced binding entropy can be attributed to the extensive displacement of solvent molecules as well as to ionic interactions with the phosphate recognition site.

  • Organizational Affiliation

    Research and Development, Sanofi Aventis Deutschland GmbH, Frankfurt am Main, Germany. oliver.anderka@sanofi-aventis.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glycogen phosphorylase, liver form
A, B
809Homo sapiensMutation(s): 0 
Gene Names: PYGL
UniProt & NIH Common Fund Data Resources
Find proteins for P06737 (Homo sapiens)
Explore P06737 
Go to UniProtKB:  P06737
PHAROS:  P06737
GTEx:  ENSG00000100504 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06737
Sequence Annotations
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
AVD Binding MOAD:  3CEM Kd: 24 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.47 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.159 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.383α = 90
b = 124.383β = 90
c = 123.429γ = 120
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-05-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary