3CEM

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.47 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.155 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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: 10.1021/bi702397d
  • Primary Citation of Related Structures:  

  • 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 rep ...

    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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glycogen phosphorylase, liver form
A, B
809Homo sapiensMutation(s): 0 
Gene Names: PYGL
EC: 2.4.1.1
Find proteins for P06737 (Homo sapiens)
Go to Gene View: PYGL
Go to UniProtKB:  P06737
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AVD
Query on AVD

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Download CCD File 
A, B
1-(2-carboxyphenyl)-7-chloro-6-[(2-chloro-4,6-difluorophenyl)amino]-4-oxo-1,4-dihydroquinoline-3-carboxylic acid
C23 H12 Cl2 F2 N2 O5
OEMJXSVJXPIFMA-UHFFFAOYSA-N
 Ligand Interaction
PLP
Query on PLP

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

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Download CCD File 
A, B
1-N-ACETYL-BETA-D-GLUCOSAMINE
C8 H15 N O6
IBONACLSSOLHFU-JAJWTYFOSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
AVDKd: 24 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.47 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.155 
  • Space Group: P 31
Unit Cell:
Length (Å)Angle (°)
a = 124.383α = 90.00
b = 124.383β = 90.00
c = 123.429γ = 120.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XSCALEdata scaling
XDSdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-05-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance