2ATI

Glycogen Phosphorylase Inhibitors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.232 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Acyl ureas as human liver glycogen phosphorylase inhibitors for the treatment of type 2 diabetes.

Klabunde, T.Wendt, K.U.Kadereit, D.Brachvogel, V.Burger, H.J.Herling, A.W.Oikonomakos, N.G.Kosmopoulou, M.N.Schmoll, D.Sarubbi, E.von Roedern, E.Defossa, E.

(2005) J.Med.Chem. 48: 6178-6193

  • DOI: 10.1021/jm049034y
  • Also Cited By: 1WV1, 1WV0, 1WUY

  • PubMed Abstract: 
  • Using a focused screening approach, acyl ureas have been discovered as a new class of inhibitors of human liver glycogen phosphorylase (hlGPa). The X-ray structure of screening hit 1 (IC50 = 2 microM) in a complex with rabbit muscle glycogen phosphor ...

    Using a focused screening approach, acyl ureas have been discovered as a new class of inhibitors of human liver glycogen phosphorylase (hlGPa). The X-ray structure of screening hit 1 (IC50 = 2 microM) in a complex with rabbit muscle glycogen phosphorylase b reveals that 1 binds at the AMP site, the main allosteric effector site of the dimeric enzyme. A first cycle of chemical optimization supported by X-ray structural data yielded derivative 21, which inhibited hlGPa with an IC50 of 23 +/- 1 nM, but showed only moderate cellular activity in isolated rat hepatocytes (IC50 = 6.2 microM). Further optimization was guided by (i) a 3D pharmacophore model that was derived from a training set of 24 compounds and revealed the key chemical features for the biological activity and (ii) the 1.9 angstroms crystal structure of 21 in complex with hlGPa. A second set of compounds was synthesized and led to 42 with improved cellular activity (hlGPa IC50 = 53 +/- 1 nM; hepatocyte IC50 = 380 nM). Administration of 42 to anaesthetized Wistar rats caused a significant reduction of the glucagon-induced hyperglycemic peak. These findings are consistent with the inhibition of hepatic glycogenolysis and support the use of acyl ureas for the treatment of type 2 diabetes.


    Related Citations: 
    • Activation of human liver glycogen phosphorylase by alteration of the secondary structure and packing of the catalytic core
      Rath, V.L.,Ammirati, M.,LeMotte, P.K.,Fennell, K.F.,Mansour, M.N.,Danley, D.E.,Hynes, T.R.,Schulte, G.K.,Wasilko, D.J.,Pandit, J.
      (2000) Mol.Cell 6: 139
    • Crystallographic studies on acyl ureas, a new class of glycogen phosphorylase inhibitors, as potential antidiabetic drugs
      Oikonomakos, N.G.,Kosmopoulou, M.N.,Chrysina, E.D.,Leonidas, D.D.,Kostas, I.D.,Wendt, K.U.,Klabunde, T.,Defossa, E.
      (2005) Protein Sci. 14: 1760


    Organizational Affiliation

    Sanofi-Aventis Deutschland GmbH, Scientific and Medical Affairs, D-65926 Frankfurt am Main, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glycogen phosphorylase, liver form
A, B
846Homo 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
GLC
Query on GLC

Download SDF File 
Download CCD File 
A, B
ALPHA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
 Ligand Interaction
PLP
Query on PLP

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

Download SDF File 
Download CCD File 
A, B
N-(2-CHLORO-4-FLUOROBENZOYL)-N'-(5-HYDROXY-2-METHOXYPHENYL)UREA
1-(2-CHLORO-4-FLUORO-BENZOYL)-3-(5-HYDROXY-2-METHOXY-PHENYL)-UREA
C15 H12 Cl F N2 O4
RFOBTYLRURSVJE-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
IHUIC50: 22.9 - 23 nM (100) BINDINGDB
IHUIC50: 23 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.232 
  • Space Group: P 31
Unit Cell:
Length (Å)Angle (°)
a = 124.500α = 90.00
b = 124.500β = 90.00
c = 123.200γ = 120.00
Software Package:
Software NamePurpose
XDSdata reduction
MOSFLMdata reduction
AMoREphasing
CNXrefinement
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-08-25
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance