BtGH84 in complex with FMA34

Experimental Data Snapshot

  • Resolution: 2.25 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 

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This is version 1.3 of the entry. See complete history


Molecular Basis for Inhibition of Gh84 Glycoside Hydrolases by Substituted Azepanes: Conformational Flexibility Enables Probing of Substrate Distortion.

Marcelo, F.He, Y.Yuzwa, S.A.Nieto, L.Jimenez-Barbero, J.Sollogoub, M.Vocadlo, D.J.Davies, G.J.Bleriot, Y.

(2009) J Am Chem Soc 131: 5390

  • DOI: https://doi.org/10.1021/ja809776r
  • Primary Citation of Related Structures:  
    2W66, 2W67

  • PubMed Abstract: 

    Here we report the synthesis of a series of polyhydroxylated 3- and 5-acetamido azepanes and detail the molecular basis of their inhibition of family 84 glycoside hydrolases. These family 84 enzymes include human O-GlcNAcase, an enzyme involved in post-translational processing of intracellular proteins modified by O-linked beta-N-acetylglucosamine residues. Detailed structural analysis of the binding of these azepanes to BtGH84, a bacterial homologue of O-GlcNAcase, highlights their conformational flexibility. Molecular mechanics and molecular dynamics calculations reveal that binding to the enzyme involves significant conformational distortion of these inhibitors from their preferred solution conformations. The binding of these azepanes provides structural insight into substrate distortion that likely occurs along the reaction coordinate followed by O-GlcNAcase during glycoside hydrolysis. This class of inhibitors may prove to be useful probes for evaluating the conformational itineraries of glycosidases and aid the development of more potent and specific glycosidase inhibitors.

  • Organizational Affiliation

    UPMC Univ Paris 06, Institut Parisien de Chimie Moléculaire, UMR CNRS 7201, Equipe glycochimie, C181, 4 place Jussieu, 75005 Paris, France.

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
Binding Affinity Annotations 
IDSourceBinding Affinity
F34 Binding MOAD:  2W67 Ki: 1.10e+4 (nM) from 1 assay(s)
PDBBind:  2W67 Ki: 1.10e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.25 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.248α = 103.42
b = 92.101β = 95.11
c = 98.292γ = 100.6
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-04-14
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2011-10-26
    Changes: Database references, Non-polymer description
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description