2J47

Bacteroides thetaiotaomicron GH84 O-GlcNAcase in complex with a imidazole-pugnac hybrid inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.193 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Inhibition of O-Glcnacase by a Gluco-Configured Nagstatin and a Pugnac-Imidazole Hybrid Inhibitor

Shanmugasundaram, B.Debowski, A.W.Dennis, R.J.Davies, G.J.Vocadlo, D.J.Vasella, A.

(2006) Chem Commun (Camb) 42: 4372

  • DOI: 10.1039/b612154c
  • Primary Citation of Related Structures:  
    2J47

  • PubMed Abstract: 
  • Synthesis of a PUGNAc-imidazole hybrid and its characterization as an inhibitor of human O-GlcNAcase through enzyme kinetics and X-ray structural analysis.


    Related Citations: 
    • Structure and Mechanism of a Bacterial Beta-Glucosaminidase Having O-Glcnacsae Activity
      Dennis, R.J., Taylor, E.J., Macauley, M.S., Stubbs, K.A., Turkenburg, J.P., Hart, S.J., Black, G.N., Vocadlo, D.J., Davies, G.J.
      (2006) Nat Struct Mol Biol 13: 365

    Organizational Affiliation

    Laboratorium für Organische Chemie, HCI H 317, ETH Zürich, CH-8093 Zürich, Switzerland. vasella@org.chem.ethz.ch



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GLUCOSAMINIDASEA716Bacteroides thetaiotaomicron VPI-5482Mutation(s): 0 
Gene Names: BT_4395
EC: 3.2.1.52 (PDB Primary Data), 3.2.1.169 (UniProt)
UniProt
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDV (Subject of Investigation/LOI)
Query on GDV

Download Ideal Coordinates CCD File 
B [auth A](5R,6R,7R,8S)-8-(ACETYLAMINO)-6,7-DIHYDROXY-5-(HYDROXYMETHYL)-N-PHENYL-1,5,6,7,8,8A-HEXAHYDROIMIDAZO[1,2-A]PYRIDINE-2-CARBOXAMIDE
C17 H21 N4 O5
WWSQBPPKQTUEDT-KBUPBQIOSA-O
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
GDV Binding MOAD:  2J47 Ki: 3900 (nM) from 1 assay(s)
PDBBind:  2J47 Ki: 3900 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.193 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 188.426α = 90
b = 51.34β = 100.22
c = 85.474γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-10-03
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance