4MI3

Crystal structure of Gpb in complex with SUGAR (N-{(2R)-2-METHYL-3-[4-(PROPAN-2-YL)PHENYL]PROPANOYL}-BETA-D-GLUCOPYRANOSYLAMINE) (S21)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.163 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure based inhibitor design targeting glycogen phosphorylase b. Virtual screening, synthesis, biochemical and biological assessment of novel N-acyl-beta-d-glucopyranosylamines.

Parmenopoulou, V.Kantsadi, A.L.Tsirkone, V.G.Chatzileontiadou, D.S.Manta, S.Zographos, S.E.Molfeta, C.Archontis, G.Agius, L.Hayes, J.M.Leonidas, D.D.Komiotis, D.

(2014) Bioorg.Med.Chem. 22: 4810-4825

  • DOI: 10.1016/j.bmc.2014.06.058
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Glycogen phosphorylase (GP) is a validated target for the development of new type 2 diabetes treatments. Exploiting the Zinc docking database, we report the in silico screening of 1888 N-acyl-β-d-glucopyranosylamines putative GP inhibitors differing ...

    Glycogen phosphorylase (GP) is a validated target for the development of new type 2 diabetes treatments. Exploiting the Zinc docking database, we report the in silico screening of 1888 N-acyl-β-d-glucopyranosylamines putative GP inhibitors differing only in their R groups. CombiGlide and GOLD docking programs with different scoring functions were employed with the best performing methods combined in a 'consensus scoring' approach to ranking of ligand binding affinities for the active site. Six selected candidates from the screening were then synthesized and their inhibitory potency was assessed both in vitro and ex vivo. Their inhibition constants' values, in vitro, ranged from 5 to 377μM while two of them were effective at causing inactivation of GP in rat hepatocytes at low μM concentrations. The crystal structures of GP in complex with the inhibitors were defined and provided the structural basis for their inhibitory potency and data for further structure based design of more potent inhibitors.


    Organizational Affiliation

    Laboratory of Bio-Organic Chemistry, 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
825Oryctolagus 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
26R
Query on 26R

Download SDF File 
Download CCD File 
A
N-{(2R)-2-methyl-3-[4-(propan-2-yl)phenyl]propanoyl}-beta-D-glucopyranosylamine
C19 H29 N O6
HJOFLVJJICDECE-YMZRVSMESA-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 %)
26RKi: 75290 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.163 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 128.630α = 90.00
b = 128.630β = 90.00
c = 117.040γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
REFMACrefinement
SCALAdata scaling
MAR345data collection
REFMACphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-23
    Type: Initial release
  • Version 1.1: 2014-09-10
    Type: Database references
  • Version 1.2: 2017-11-15
    Type: Data collection, Refinement description