2X0Y

Screening-based discovery of drug-like O-GlcNAcase inhibitor scaffolds


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.204 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Screening-Based Discovery of Drug-Like O-Glcnacase Inhibitor Scaffolds

Dorfmueller, H.C.Van Aalten, D.M.F.

(2010) FEBS Lett 584: 694

  • DOI: https://doi.org/10.1016/j.febslet.2009.12.020
  • Primary Citation of Related Structures:  
    2X0Y

  • PubMed Abstract: 

    O-GlcNAcylation is an essential posttranslational modification in metazoa. Modulation of O-GlcNAc levels with small molecule inhibitors of O-GlcNAc hydrolase (OGA) is a useful strategy to probe the role of this modification in a range of cellular processes. Here we report the discovery of novel, low molecular weight and drug-like O-GlcNAcase inhibitor scaffolds by high-throughput screening. Kinetic and X-ray crystallographic analyses of the binding modes with human/bacterial O-GlcNAcases identify some of these as competitive inhibitors. Comparative kinetic experiments with the mechanistically related human lysosomal hexosaminidases reveal that three of the inhibitor scaffolds show selectivity towards human OGA. These scaffolds provide attractive starting points for the development of non-carbohydrate, drug-like OGA inhibitors.


  • 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
O-GLCNACASE NAGJ
A, B
594Clostridium perfringensMutation(s): 0 
EC: 3.2.1.52 (PDB Primary Data), 3.2.1.169 (UniProt)
UniProt
Find proteins for Q0TR53 (Clostridium perfringens (strain ATCC 13124 / DSM 756 / JCM 1290 / NCIMB 6125 / NCTC 8237 / Type A))
Explore Q0TR53 
Go to UniProtKB:  Q0TR53
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ0TR53
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
X0T
Query on X0T

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
7-[(2S)-2,3-DIHYDROXYPROPYL]-1,3-DIMETHYL-3,7-DIHYDRO-1H-PURINE-2,6-DIONE
C10 H14 N4 O4
KSCFJBIXMNOVSH-LURJTMIESA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
X0T PDBBind:  2X0Y Ki: 2.50e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.204 
  • Space Group: I 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 130.405α = 90
b = 148.549β = 90
c = 151.97γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-01-12
    Type: Initial release
  • Version 1.1: 2011-06-02
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description