Bacteroides thetaiotaomicron GH84 O-GlcNAcase in complex with 2- Acetylamino-2-deoxy-1-epivalienamine

Experimental Data Snapshot

  • Resolution: 1.95 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 

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This is version 1.3 of the entry. See complete history


A 1-Acetamido Derivative of 6-Epi-Valienamine: An Inhibitor of a Diverse Group of Beta-N-Acetylglucosaminidases.

Scaffidi, A.Stubbs, K.A.Dennis, R.J.Taylor, E.J.Davies, G.J.Vocadlo, D.J.Stick, R.V.

(2007) Org Biomol Chem 5: 3013

  • DOI: https://doi.org/10.1039/b709681j
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The synthesis of an analogue of 6-epi-valienamine bearing an acetamido group and its characterisation as an inhibitor of beta-N-acetylglucosaminidases are described. The compound is a good inhibitor of both human O-GlcNAcase and human beta-hexosaminidase, as well as two bacterial beta-N-acetylglucosaminidases. A 3-D structure of the complex of Bacteroides thetaiotaomicron BtGH84 with the inhibitor shows the unsaturated ring is surprisingly distorted away from its favoured solution phase conformation and reveals potential for improved inhibitor potency.

  • Organizational Affiliation

    Chemistry M313, School of Biomedical, Biomolecular and Chemical Sciences, The University of Western Australia, 35 Stirling Hwy, Crawley, WA, Australia.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
716Bacteroides thetaiotaomicron VPI-5482Mutation(s): 0 
Find proteins for Q89ZI2 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50))
Explore Q89ZI2 
Go to UniProtKB:  Q89ZI2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ89ZI2
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on BEU

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
C9 H16 N2 O4
Binding Affinity Annotations 
IDSourceBinding Affinity
BEU PDBBind:  2JIW Ki: 2.60e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.95 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.398α = 104.97
b = 94.131β = 94.09
c = 99.808γ = 102.48
Software Package:
Software NamePurpose

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-08-07
    Type: Initial release
  • Version 1.1: 2011-05-07
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-05-08
    Changes: Data collection, Database references, Other