1GGN

Structures of glycogen phosphorylase-inhibitor complexes and the implications for structure-based drug design


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.36 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Kinetic and crystallographic studies of glucopyranosylidene spirothiohydantoin binding to glycogen phosphorylase B.

Oikonomakos, N.G.Skamnaki, V.T.Osz, E.Szilagyi, L.Somsak, L.Docsa, T.Toth, B.Gergely, P.

(2002) Bioorg.Med.Chem. 10: 261-268

  • Primary Citation of Related Structures:  1HLF

  • PubMed Abstract: 
  • Glucopyranosylidene spirothiohydantoin (TH) has been identified as a potential inhibitor of both muscle and liver glycogen phosphorylase b (GPb) and a (GPa) and shown to diminish liver GPa activity in vitro. Kinetic experiments reported here show tha ...

    Glucopyranosylidene spirothiohydantoin (TH) has been identified as a potential inhibitor of both muscle and liver glycogen phosphorylase b (GPb) and a (GPa) and shown to diminish liver GPa activity in vitro. Kinetic experiments reported here show that TH inhibits muscle GPb competitively with respect to both substrates phosphate (K(i)=2.3 microM) and glycogen (K(i)=2.8 microM). The structure of the GPb-TH complex has been determined at a resolution of 2.26 A and refined to a crystallographic R value of 0.193 (R(free)=0.211). The structure of GPb-TH complex reveals that the inhibitor can be accommodated in the catalytic site of T-state GPb with very little change of the tertiary structure, and provides a basis of understanding potency and specificity of the inhibitor. The glucopyranose moiety makes the standard hydrogen bonds and van der Waals contacts as observed in the glucose complex, while the rigid thiohydantoin group is in a favourable electrostatic environment and makes additional polar contacts to the protein.


    Related Citations: 
    • N-Acetyl-Beta-D-Glucopyranosylamine: A Potent T-State Inhibitor of Glycogen Phosphorylase. A Comparison with Alpha-D-Glucose
      Oikonomakos, N.G.,Kontou, M.,Zographos, S.E.,Watson, K.A.,Johnson, L.N.,Bichard, C.J.,Fleet, G.W.,Acharya, K.R.
      (1995) Protein Sci. 4: 2469
    • Design of Inhibitors of Glycogen Phosphorylase: A Study of Alpha- and Beta-C-Glucosides and 1-Thio-Beta-D-Glucose Compounds
      Watson, K.A.,Mitchell, E.P.,Johnson, L.N.,Son, J.C.,Bichard, C.J.,Orchard, M.G.,Fleet, G.W.,Oikonomakos, N.G.,Leonidas, D.D.,Kontou, M.,Papageorgiou, A.C.
      (1994) Biochemistry 33: 5745
    • Potent Inhibition of Glycogen Phosphorylase by a Spirohydantoin of Glucopyranose: First Pyranose Analogues of Hydantocidin
      Bichard, C.J.F.,Mitchell, E.P.,Wormald, M.R.,Watson, K.A.,Johnson, L.N.,Zographos, S.E.,Koutra, D.D.,Oikonomakos, N.G.,Fleet, G.W.J.
      (1995) Tetrahedron Lett. 36: 2145
    • The Structure of a Glycogen Phosphorylase Glucopyranose Spirohydantoin Complex at 1.8 A Resolution and 100K: The Role of the Water Structure and its Contribution to Binding
      Gregoriou, M.,Noble, M.E.,Watson, K.A.,Garman, E.F.,Krulle, T.M.,de la Fuente, C.,Fleet, G.W.,Oikonomakos, N.G.,Johnson, L.N.
      (1998) Protein Sci. 7: 915


    Organizational Affiliation

    Institute of Biological Research and Biotechnology, The National Hellenic Research Foundation, 48 Vas. Constantinou Avenue, Athens 11635, Greece. ngo@eie.gr




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (GLYCOGEN PHOSPHORYLASE)
A
842Oryctolagus cuniculusGene 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
GLS
Query on GLS

Download SDF File 
Download CCD File 
A
BETA-D-GLUCOPYRANOSE SPIROHYDANTOIN
C8 H12 N2 O7
QRXBDPYWCAAAAI-WWHASAIZSA-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 %)
GLSIC50: 3100 nM (99) BINDINGDB
GLSKi: 3020 - 26000 nM (97) BINDINGDB
GLSKi: 3100 nM BINDINGMOAD
GLSKi: 3100 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.36 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.189 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 128.500α = 90.00
b = 128.500β = 90.00
c = 116.300γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
CCP4phasing
XDSdata scaling
CCP4model building
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-09-13
    Type: Initial release
  • Version 1.1: 2008-04-26
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance