3SYR

Glycogen phosphorylase b in complex with beta-D-glucopyranonucleoside 5-fluorouracil


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

3'-Axial CH(2) OH Substitution on Glucopyranose does not Increase Glycogen Phosphorylase Inhibitory Potency. QM/MM-PBSA Calculations Suggest Why.

Manta, S.Xipnitou, A.Kiritsis, C.Kantsadi, A.L.Hayes, J.M.Skamnaki, V.T.Lamprakis, C.Kontou, M.Zoumpoulakis, P.Zographos, S.E.Leonidas, D.D.Komiotis, D.

(2012) Chem.Biol.Drug Des. 79: 663-673

  • DOI: 10.1111/j.1747-0285.2012.01349.x
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Glycogen phosphorylase is a molecular target for the design of potential hypoglycemic agents. Structure-based design pinpointed that the 3'-position of glucopyranose equipped with a suitable group has the potential to form interactions with enzyme's ...

    Glycogen phosphorylase is a molecular target for the design of potential hypoglycemic agents. Structure-based design pinpointed that the 3'-position of glucopyranose equipped with a suitable group has the potential to form interactions with enzyme's cofactor, pyridoxal 5'-phosphate (PLP), thus enhancing the inhibitory potency. Hence, we have investigated the binding of two ligands, 1-(β-d-glucopyranosyl)5-fluorouracil (GlcFU) and its 3'-CH(2) OH glucopyranose derivative. Both ligands were found to be low micromolar inhibitors with K(i) values of 7.9 and 27.1 μm, respectively. X-ray crystallography revealed that the 3'-CH(2) OH glucopyranose substituent is indeed involved in additional molecular interactions with the PLP γ-phosphate compared with GlcFU. However, it is 3.4 times less potent. To elucidate this discovery, docking followed by postdocking Quantum Mechanics/Molecular Mechanics - Poisson-Boltzmann Surface Area (QM/MM-PBSA) binding affinity calculations were performed. While the docking predictions failed to reflect the kinetic results, the QM/MM-PBSA revealed that the desolvation energy cost for binding of the 3'-CH(2) OH-substituted glucopyranose derivative out-weigh the enthalpy gains from the extra contacts formed. The benefits of performing postdocking calculations employing a more accurate solvation model and the QM/MM-PBSA methodology in lead optimization are therefore highlighted, specifically when the role of a highly polar/charged binding interface is significant.


    Organizational Affiliation

    Department of Biochemistry and Biotechnology, University of Thessaly, 26 Ploutonos Str., Larissa, Greece.




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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GPK
Query on GPK

Download SDF File 
Download CCD File 
A
5-fluoro-1-(beta-D-glucopyranosyl)pyrimidine-2,4(1H,3H)-dione
C10 H13 F N2 O7
YHWGRVDTEORPPJ-XSEHCYKFSA-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 %)
GPKKi: 7900 nM BINDINGMOAD
GPKKi: 7900 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.176 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 128.556α = 90.00
b = 128.556β = 90.00
c = 116.282γ = 90.00
Software Package:
Software NamePurpose
CrysalisProdata collection
SCALAdata scaling
REFMACrefinement
MOSFLMdata reduction
REFMACphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-02-15
    Type: Initial release
  • Version 1.1: 2012-04-18
    Type: Database references
  • Version 1.2: 2017-11-08
    Type: Refinement description