1WV1

Crystallographic studies on acyl ureas, a new class of inhibitors of glycogenphosphorylase. Broad specificity of the allosteric site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 1760-1771

  • DOI: 10.1110/ps.051432405
  • Primary Citation of Related Structures:  
  • Also Cited By: 2ATI

  • PubMed Abstract: 
  • Acyl ureas were discovered as a novel class of inhibitors for glycogen phosphorylase, a molecular target to control hyperglycemia in type 2 diabetics. This series is exemplified by 6-{2,6-Dichloro- 4-[3-(2-chloro-benzoyl)-ureido]-phenoxy}-hexanoic ac ...

    Acyl ureas were discovered as a novel class of inhibitors for glycogen phosphorylase, a molecular target to control hyperglycemia in type 2 diabetics. This series is exemplified by 6-{2,6-Dichloro- 4-[3-(2-chloro-benzoyl)-ureido]-phenoxy}-hexanoic acid, which inhibits human liver glycogen phosphorylase a with an IC(50) of 2.0 microM. Here we analyze four crystal structures of acyl urea derivatives in complex with rabbit muscle glycogen phosphorylase b to elucidate the mechanism of inhibition of these inhibitors. The structures were determined and refined to 2.26 Angstroms resolution and demonstrate that the inhibitors bind at the allosteric activator site, where the physiological activator AMP binds. Acyl ureas induce conformational changes in the vicinity of the allosteric site. Our findings suggest that acyl ureas inhibit glycogen phosphorylase by direct inhibition of AMP binding and by indirect inhibition of substrate binding through stabilization of the T' state.


    Related Citations: 
    • 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-tricarbo xylate
      Oikonomakos, N.G.,Tsitsanou, K.E.,Zographos, S.E.,Skamnaki, V.T.,Goldmann, S.,Bischoff, H.
      (1999) Protein Sci. 8: 1930
    • Identification, synthesis, and characterization of new glycogen phosphorylase inhibitors binding to the allosteric AMP site
      Kristiansen, M.,Andersen, B.,Iversen, L.F.,Westergaard, N.
      (2004) J.Med.Chem. 47: 3537
    • Acyl ureas as human liver glycogen phosphorylase inhibitors for the treatment of type 2 diabetes
      Klabunde, T.,Wendt, U.K.,Kadereit, D.,Brachvogel, V.,Burger, H.J.,Herling, A.W.,Oikonomakos, N.G.,Kosmopoulou, M.N.,Schmoll, D.,Sarubbi, E.,von Roedern, E.,Schonafinger, K.,Defossa, E.
      (2005) J.Med.Chem. 48: 6178
    • 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


    Organizational Affiliation

    Institute of Organic and Pharmaceutical Chemistry, The National Hellenic Research Foundation, Athens, Greece. ngo@eie.gr




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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BN5
Query on BN5

Download SDF File 
Download CCD File 
A
5-[3-({[(2,4-DICHLOROBENZOYL)AMINO]CARBONYL}AMINO)-2-METHYLPHENOXY]PENTANOIC ACID
5-{3-[3-(2,4-DICHLORO-BENZOYL)-UREIDO]-2-METHYL-PHENOXY}-PENTANOIC ACID
C20 H20 Cl2 N2 O5
NJJIFGCFUDDBSP-UHFFFAOYSA-N
 Ligand Interaction
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
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BN5IC50: 2800 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.189 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 128.310α = 90.00
b = 128.310β = 90.00
c = 115.940γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
HKL-2000data reduction
SCALEPACKdata scaling
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-12-10
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance