2XGM

Substrate and product analogues as human O-GlcNAc transferase inhibitors.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.267 
  • R-Value Observed: 0.268 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Substrate and Product Analogues as Human O-Glcnac Transferase Inhibitors.

Dorfmueller, H.C.Borodkin, V.S.Blair, D.E.Pathak, S.Navratilova, I.Van Aalten, D.M.

(2011) Amino Acids 40: 781

  • DOI: https://doi.org/10.1007/s00726-010-0688-y
  • Primary Citation of Related Structures:  
    2XGM, 2XGO, 2XGS

  • PubMed Abstract: 

    Protein glycosylation on serine/threonine residues with N-acetylglucosamine (O-GlcNAc) is a dynamic, inducible and abundant post-translational modification. It is thought to regulate many cellular processes and there are examples of interplay between O-GlcNAc and protein phosphorylation. In metazoa, a single, highly conserved and essential gene encodes the O-GlcNAc transferase (OGT) that transfers GlcNAc onto substrate proteins using UDP-GlcNAc as the sugar donor. Specific inhibitors of human OGT would be useful tools to probe the role of this post-translational modification in regulating processes in the living cell. Here, we describe the synthesis of novel UDP-GlcNAc/UDP analogues and evaluate their inhibitory properties and structural binding modes in vitro alongside alloxan, a previously reported weak OGT inhibitor. While the novel analogues are not active on living cells, they inhibit the enzyme in the micromolar range and together with the structural data provide useful templates for further optimisation.


  • Organizational Affiliation

    Division of Molecular Microbiology, College of Life Sciences, University of Dundee, Dundee, Scotland, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
XCOGT
A, B
568Xanthomonas campestrisMutation(s): 0 
UniProt
Find proteins for Q8PC69 (Xanthomonas campestris pv. campestris (strain ATCC 33913 / DSM 3586 / NCPPB 528 / LMG 568 / P 25))
Explore Q8PC69 
Go to UniProtKB:  Q8PC69
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8PC69
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
LXN PDBBind:  2XGM Kd: 1.00e+6 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.267 
  • R-Value Observed: 0.268 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.534α = 90
b = 99.982β = 90
c = 157.196γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-08-25
    Type: Initial release
  • Version 1.1: 2011-10-12
    Changes: Database references, Version format compliance