1FU7

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: 0.209 
  • R-Value Work: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Kinetic and crystallographic studies of glucopyranose spirohydantoin and glucopyranosylamine analogs inhibitors of glycogen phosphorylase.

Watson, K.A.Chrysina, E.D.Tsitsanou, K.E.Zographos, S.E.Archontis, G.Fleet, G.W.Oikonomakos, N.G.

(2005) Proteins 61: 966-983

  • DOI: 10.1002/prot.20653
  • Primary Citation of Related Structures:  1FS4, 1FTQ, 1FTW, 1FTY, 1FU4, 1FU8

  • PubMed Abstract: 
  • Glycogen phosphorylase (GP) is currently exploited as a target for inhibition of hepatic glycogenolysis under high glucose conditions. Spirohydantoin of glucopyranose and N-acetyl-beta-D-glucopyranosylamine have been identified as the most potent inh ...

    Glycogen phosphorylase (GP) is currently exploited as a target for inhibition of hepatic glycogenolysis under high glucose conditions. Spirohydantoin of glucopyranose and N-acetyl-beta-D-glucopyranosylamine have been identified as the most potent inhibitors of GP that bind at the catalytic site. Four spirohydantoin and three beta-D-glucopyranosylamine analogs have been designed, synthesized and tested for inhibition of GP in kinetic experiments. Depending on the functional group introduced, the K(i) values varied from 16.5 microM to 1200 microM. In order to rationalize the kinetic results, we determined the crystal structures of the analogs in complex with GP. All the inhibitors bound at the catalytic site of the enzyme, by making direct and water-mediated hydrogen bonds with the protein and by inducing minor movements of the side chains of Asp283 and Asn284, of the 280s loop that blocks access of the substrate glycogen to the catalytic site, and changes in the water structure in the vicinity of the site. The differences observed in the Ki values of the analogs can be interpreted in terms of variations in hydrogen bonding and van der Waals interactions, desolvation effects, ligand conformational entropy, and displacement of water molecules on ligand binding to the catalytic site.


    Related Citations: 
    • 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
    • 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
    • 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
    • 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


    Organizational Affiliation

    Laboratory of Molecular Biophysics, University of Oxford, Oxford, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
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
CR1
Query on CR1

Download SDF File 
Download CCD File 
A
1-DEOXY-1-METHOXYCARBAMIDO-BETA-D-GLUCOPYRANOSE
C8 H15 N O7
IZZJOGWXTFEDLL-XUUWZHRGSA-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 %)
CR1Ki: 85114 - 210000 nM (97) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.36 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.168 
  • 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
CCP4phasing
XDSdata reduction
X-PLORrefinement
XDSdata scaling
CCP4model building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-10-04
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance