3MSC

Glycogen phosphorylase complexed with 2-nitrobenzaldehyde-4-(beta-D-glucopyranosyl)-thiosemicarbazone


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.951 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The binding of beta-d-glucopyranosyl-thiosemicarbazone derivatives to glycogen phosphorylase: A new class of inhibitors.

Alexacou, K.M.Tenchiu Deleanu, A.C.Chrysina, E.D.Charavgi, M.D.Kostas, I.D.Zographos, S.E.Oikonomakos, N.G.Leonidas, D.D.

(2010) Bioorg.Med.Chem. 18: 7911-7922

  • DOI: 10.1016/j.bmc.2010.09.039
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Glycogen phosphorylase (GP) is a promising target for the treatment of type 2 diabetes. In the process of structure based drug design for GP, a group of 15 aromatic aldehyde 4-(β-d-glucopyranosyl)thiosemicarbazones have been synthesized and evaluated ...

    Glycogen phosphorylase (GP) is a promising target for the treatment of type 2 diabetes. In the process of structure based drug design for GP, a group of 15 aromatic aldehyde 4-(β-d-glucopyranosyl)thiosemicarbazones have been synthesized and evaluated as inhibitors of rabbit muscle glycogen phosphorylase b (GPb) by kinetic studies. These compounds are competitive inhibitors of GPb with respect to α-d-glucose-1-phosphate with IC(50) values ranging from 5.7 to 524.3μM. In order to elucidate the structural basis of their inhibition, the crystal structures of these compounds in complex with GPb at 1.95-2.23Å resolution were determined. The complex structures reveal that the inhibitors are accommodated at the catalytic site with the glucopyranosyl moiety at approximately the same position as α-d-glucose and stabilize the T conformation of the 280s loop. The thiosemicarbazone part of the studied glucosyl thiosemicarbazones possess a moiety derived from substituted benzaldehydes with NO(2), F, Cl, Br, OH, OMe, CF(3), or Me at the ortho-, meta- or para-position of the aromatic ring as well as a moiety derived from 4-pyridinecarboxaldehyde. These fit tightly into the β-pocket, a side channel from the catalytic site with no access to the bulk solvent. The differences in their inhibitory potency can be interpreted in terms of variations in the interactions of the aldehyde-derived moiety with protein residues in the β-pocket. In addition, 14 out of the 15 studied inhibitors were found bound at the new allosteric site of the enzyme.


    Organizational Affiliation

    Institute of Organic and Pharmaceutical Chemistry, National Hellenic Research Foundation, 48 Vassileos Constantinou Avenue, 11635 Athens, 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
24S
Query on 24S

Download SDF File 
Download CCD File 
A
N-({(2Z)-2-[(2-nitrophenyl)methylidene]hydrazino}carbonothioyl)-beta-D-glucopyranosylamine
2-nitrobenzaldehyde-4-(beta-D-glucopyranosyl) thiosemicarbazone
C14 H18 N4 O7 S
HIBBBAGNJNCOKR-ARDSGTFASA-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 %)
24SIC50: 484200 nM BINDINGMOAD
24SIC50: 484200 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.951 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.183 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 128.636α = 90.00
b = 128.636β = 90.00
c = 116.363γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
CNSrefinement
REFMACrefinement
HKL-3000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2010-04-29 
  • Released Date: 2011-03-16 
  • Deposition Author(s): Alexacou, K.-M.

Revision History 

  • Version 1.0: 2011-03-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance