2FFR

Crystallographic studies on N-azido-beta-D-glucopyranosylamine, an inhibitor of glycogen phosphorylase: comparison with N-acetyl-beta-D-glucopyranosylamine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystallographic studies on N-azidoacetyl-beta-d-glucopyranosylamine, an inhibitor of glycogen phosphorylase: Comparison with N-acetyl-beta-d-glucopyranosylamine.

Petsalakis, E.I.Chrysina, E.D.Tiraidis, C.Hadjiloi, T.Leonidas, D.D.Oikonomakos, N.G.Aich, U.Varghese, B.Loganathan, D.

(2006) Bioorg.Med.Chem. 14: 5316-5324

  • DOI: 10.1016/j.bmc.2006.03.044

  • PubMed Abstract: 
  • N-acetyl-beta-D-glucopyranosylamine (NAG) is a potent inhibitor (Ki=32 microM) of glycogen phosphorylase b (GPb), and has been employed as a lead compound for the structure-based design of new analogues, in an effort to utilize its potential as a hyp ...

    N-acetyl-beta-D-glucopyranosylamine (NAG) is a potent inhibitor (Ki=32 microM) of glycogen phosphorylase b (GPb), and has been employed as a lead compound for the structure-based design of new analogues, in an effort to utilize its potential as a hypoglycaemic agent. Replacement of the acetamido group by azidoacetamido group resulted in an inhibitor, N-azidoacetyl-beta-D-glucopyranosylamine (azido-NAG), with a Ki value of 48.7 microM, in the direction of glycogen synthesis. In order to elucidate the mechanism of inhibition, we determined the ligand structure in complex with GPb at 2.03 A resolution, and the structure of the fully acetylated derivative in the free form. The molecular packing of the latter is stabilized by a number of bifurcated hydrogen bonds of which the one involving a bifurcated C-H...N...H-C type hydrogen bonding is rather unique in organic azides. Azido-NAG can be accommodated in the catalytic site of T-state GPb at approximately the same position as that of NAG and stabilizes the T-state conformation of the 280 s loop by making several favourable contacts to residues of this loop. The difference observed in the Ki values of the two analogues can be interpreted in terms of desolvation effects, subtle structural changes of protein residues and changes in water structure.


    Related Citations: 
    • Crystallographic studies on two bioisosteric analogues, N-acetyl-beta-D-glucopyranosylamine and N-trifluoracetyl-beta-D-glucopyranosylamine, potent inhibitors of muscle glycogen phosphorylase
      Anagnostou, E.,Kosmopoulou, M.N.,Chrysina, E.D.,Leonidas, D.D.,Tiraidis, C.,Hadjiloi, T.,Zographos, S.E.,Gyorgydeak, Z.,Somsak, L.,Docsa, T.,Gergely, P.,Kolisis, F.N.,Oikonomakos, N.G.
      (2006) Bioorg.Med.Chem. 14: 181


    Organizational Affiliation

    Institute of Organic and Pharmaceutical Chemistry, The National Hellenic Research Foundation, 48, Vas. Constantinou Ave., 116 35 Athens, 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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DL6
Query on DL6

Download SDF File 
Download CCD File 
A
2-AZIDO-N-((2R,3R,4S,5S,6R)-3,4,5-TRIHYDROXY-6-(HYDROXYMETHYL)-TETRAHYDRO-2H-PYRAN-2-YL)ACETAMIDE
N-AZIDOACETYL-BETA-D-GLUCOPYRANOSYLAMINE
C8 H14 N4 O6
ACLUEOOMMLAETN-RHROMQPHSA-N
 Ligand Interaction
PLP
Query on PLP

Download SDF File 
Download CCD File 
A
PYRIDOXAL-5'-PHOSPHATE
VITAMIN B6 Phosphate
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DL6Ki: 49000 nM (99) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.184 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 128.626α = 90.00
b = 128.626β = 90.00
c = 116.163γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
CNSrefinement
SCALEPACKdata scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-06-20
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance