2W66

BtGH84 in complex with HQ602


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 10.1021/ja809776r
  • Primary Citation of Related Structures:  

  • 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 po ...

    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 Mol├ęculaire, UMR CNRS 7201, Equipe glycochimie, C181, 4 place Jussieu, 75005 Paris, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
O-GLCNACASE BT_4395
A, B
716Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482)Mutation(s): 0 
EC: 3.2.1.169
Find proteins for Q89ZI2 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482))
Go to UniProtKB:  Q89ZI2
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
HQ6
Query on HQ6

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Download CCD File 
A, B
N-[(3R,4S,5R,6R,7R)-3,5,6-trihydroxy-7-(hydroxymethyl)azepan-4-yl]acetamide
C9 H18 N2 O5
RJAFVDFBXXHCRJ-SYHAXYEDSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
HQ6Ki: 89000 nM BINDINGMOAD
HQ6Ki: 89000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.188 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 51.199α = 104.16
b = 93.465β = 94.01
c = 99.010γ = 103.02
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
REFMACrefinement
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2008-12-17 
  • Released Date: 2009-04-14 
  • Deposition Author(s): He, Y., Davies, G.J.

Revision History 

  • Version 1.0: 2009-04-14
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2011-10-26
    Type: Database references, Non-polymer description