2X0Y | pdb_00002x0y

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

• PDB DOI: https://doi.org/10.2210/pdb2X0Y/pdb

• Classification: HYDROLASE
• Organism(s): Clostridium perfringens
• Mutation(s): No 


• Deposited: 2009-12-18 Released: 2010-01-12 
• Deposition Author(s): Dorfmueller, H.C., van Aalten, D.M.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.246 (Depositor), 0.241 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Starting Model: experimental

Literature

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

Dorfmueller, H.C., Van Aalten, D.M.F.

(2010) FEBS Lett 584: 694

• PubMed: 20026047 
• DOI: https://doi.org/10.1016/j.febslet.2009.12.020
• Primary Citation 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.

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Organizational Affiliation: 
• Division of Molecular Microbiology, College of Life Sciences, University of Dundee, Dundee, Scotland, UK.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 133.89 kDa 
• Atom Count: 10,123 
• Modeled Residue Count: 1,169 
• Deposited Residue Count: 1,188 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
O-GLCNACASE NAGJ	A, B	594	Clostridium perfringens	Mutation(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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
X0T	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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.246 (Depositor), 0.241 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: I 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 130.405	α = 90
b = 148.549	β = 90
c = 151.97	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-01-12 
Deposition Author(s): Dorfmueller, H.C., van Aalten, D.M.F.

Revision History  

• 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