3T3G

Glycogen Phosphorylase b in complex with GlcBrU


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The sigma-Hole Phenomenon of Halogen Atoms Forms the Structural Basis of the Strong Inhibitory Potency of C5 Halogen Substituted Glucopyranosyl Nucleosides towards Glycogen Phosphorylase  b

Kantsadi, A.L.Hayes, J.M.Manta, S.Skamnaki, V.T.Kiritsis, C.Psarra, A.M.Koutsogiannis, Z.Dimopoulou, A.Theofanous, S.Nikoleousakos, N.Zoumpoulakis, P.Kontou, M.Papadopoulos, G.Zographos, S.E.Komiotis, D.Leonidas, D.D.

(2012) Chemmedchem 7: 722-732

  • DOI: 10.1002/cmdc.201100533
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • C5 halogen substituted glucopyranosyl nucleosides (1-(β-D-glucopyranosyl)-5-X-uracil; X=Cl, Br, I) have been discovered as some of the most potent active site inhibitors of glycogen phosphorylase (GP), with respective K(i) values of 1.02, 3.27, and 1 ...

    C5 halogen substituted glucopyranosyl nucleosides (1-(β-D-glucopyranosyl)-5-X-uracil; X=Cl, Br, I) have been discovered as some of the most potent active site inhibitors of glycogen phosphorylase (GP), with respective K(i) values of 1.02, 3.27, and 1.94 μM. The ability of the halogen atom to form intermolecular electrostatic interactions through the σ-hole phenomenon rather than through steric effects alone forms the structural basis of their improved inhibitory potential relative to the unsubstituted 1-(β-D-glucopyranosyl)uracil (K(i) =12.39 μM), as revealed by X-ray crystallography and modeling calculations exploiting quantum mechanics methods. Good agreement was obtained between kinetics results and relative binding affinities calculated by QM/MM-PBSA methodology for various substitutions at C5. Ex vivo experiments demonstrated that the most potent derivative (X=Cl) toward purified GP has no cytotoxicity and moderate inhibitory potency at the cellular level. In accordance, ADMET property predictions were performed, and suggest decreased polar surface areas as a potential means of improving activity in the cell.


    Organizational Affiliation

    Department of Biochemistry and Biotechnology, University of Thessaly, 26 Ploutonos Str., 41221 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
GPU
Query on GPU

Download SDF File 
Download CCD File 
A
5-bromo-1-(beta-D-glucopyranosyl)pyrimidine-2,4(1H,3H)-dione
C10 H13 Br N2 O7
QNNGZNNVDUDIOK-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 %)
GPUKi: 3270 nM (97) BINDINGDB
GPUKi: 3270 nM BINDINGMOAD
GPUKi: 3270 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.179 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 128.776α = 90.00
b = 128.776β = 90.00
c = 116.594γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
REFMACphasing
CrysalisProdata collection
SCALAdata scaling
MOSFLMdata reduction

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: 2013-06-26
    Type: Database references
  • Version 1.2: 2017-11-08
    Type: Refinement description