1A8I

SPIROHYDANTOIN INHIBITOR OF GLYCOGEN PHOSPHORYLASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The structure of a glycogen phosphorylase glucopyranose spirohydantoin complex at 1.8 A resolution and 100 K: 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: 915-927

  • DOI: 10.1002/pro.5560070409
  • Primary Citation of Related Structures:  2GPN
  • Also Cited By: 4CTM, 4CTN, 4CTO

  • PubMed Abstract: 
  • A glucopyranose spirohydantoin (a pyranose analogue of the potent herbicide, hydantocidin) has been identified as the highest affinity glucose analogue inhibitor of glycogen phosphorylase b (GPb). In order to elucidate the structural features that co ...

    A glucopyranose spirohydantoin (a pyranose analogue of the potent herbicide, hydantocidin) has been identified as the highest affinity glucose analogue inhibitor of glycogen phosphorylase b (GPb). In order to elucidate the structural features that contribute to the binding, the structures of GPb in the native T state conformation and in complex with glucopyranose spirohydantoin have been determined at 100 K to 2.0 A and 1.8 A resolution, respectively, and refined to crystallographic R values of 0.197 (R[free] 0.248) and 0.182 (R[free] 0.229), respectively. The low temperature structure of GPb is almost identical to that of the previously determined room temperature structure, apart from a decrease in overall atomic temperature factors ((B) room temperature GPb = 34.9 A2; (B) 100 K GPb = 23.4 A2). The glucopyranose spirohydantoin inhibitor (Ki = 3.0 microM) binds at the catalytic site and induces small changes in two key regions of the protein: the 280s loop (residues 281-286) that results in a decrease in mobility of this region, and the 380s loop (residues 377-385) that undergoes more significant shifts in order to optimize contact to the ligand. The hydantoin group, that is responsible for increasing the affinity of the glucose compound by a factor of 10(3), makes only one hydrogen bond to the protein, from one of its NH groups to the main chain oxygen of His377. The other polar groups of the hydantoin group form hydrogen bonds to five water molecules. These waters are involved in extensive networks of hydrogen bonds and appear to be an integral part of the protein structure. Analysis of the water structure at the catalytic site of the native enzyme, shows that five waters are displaced by ligand binding and that there is a significant decrease in mobility of the remaining waters on formation of the GPb-hydantoin complex. The ability of the inhibitor to exploit existing waters, to displace waters and to recruit new waters appears to be important for the high affinity of the inhibitor.


    Related Citations: 
    • Stereospecific Synthesis of Spirohydantoins of Beta-Glucopyranose: Inhibitors of Glycogen Phosphorylase
      Krulle, T.M.,De La Fuente, C.,Watson, K.A.,Gregoriou, M.,Johnson, L.N.,Tsitsanou, K.E.,Zographos, S.E.,Oikonomakos, N.G.,Fleet, G.W.J.
      (1997) Synlett --: 211
    • 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.
      (1994) Biochemistry 33: 5745
    • Acharya, K.R.,Stuart, D.I.,Varvill, K.M.,Johnson, L.N.
      (1991) Glycogen Phosphorylase B: Description of the Protein Structure --: --
    • 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
    • Glucose Analogue Inhibitors of Glycogen Phosphorylase: The Design of Potential Drugs for Diabetes
      Martin, J.L.,Veluraja, K.,Ross, K.,Johnson, L.N.,Fleet, G.W.,Ramsden, N.G.,Bruce, I.,Orchard, M.G.,Oikonomakos, N.G.,Papageorgiou, A.C.,Leonidas, D.D.,Tsitoura, H.S.
      (1991) Biochemistry 30: 10101


    Organizational Affiliation

    Laboratory of Molecular Biophysics and Oxford Centre for Molecular Sciences, University of Oxford, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GLYCOGEN PHOSPHORYLASE B
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 1 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
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
LLP
Query on LLP
A
L-PEPTIDE LINKINGC14 H22 N3 O7 PLYS
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
GLSIC50: 3100 nM (99) BINDINGDB
GLSKi: 3020 - 26000 nM (97) BINDINGDB
GLSKi: 3000 nM BINDINGMOAD
GLSKi: 3000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.182 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 127.470α = 90.00
b = 127.470β = 90.00
c = 115.800γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
CCP4phasing
CCP4model building
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-07-01
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance