5ABH

Structure of GH84 with ligand


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

A Convenient Approach to Stereoisomeric Iminocyclitols: Generation of Potent Brain-Permeable Oga Inhibitors.

Bergeron-Brlek, M.Goodwin-Tindall, J.Cekic, N.Roth, C.Zandberg, W.F.Shan, X.Varghese, V.Chan, S.Davies, G.J.Vocadlo, D.J.Britton, R.

(2015) Angew Chem Int Ed Engl 54: 15429

  • DOI: https://doi.org/10.1002/anie.201507985
  • Primary Citation of Related Structures:  
    5ABE, 5ABF, 5ABG, 5ABH

  • PubMed Abstract: 

    Pyrrolidine-based iminocyclitols are a promising class of glycosidase inhibitors. Reported herein is a convenient epimerization strategy that provides direct access to a range of stereoisomeric iminocyclitol inhibitors of O-GlcNAcase (OGA), the enzyme responsible for catalyzing removal of O-GlcNAc from nucleocytoplasmic proteins. Structural details regarding the binding of these inhibitors to a bacterial homologue of OGA reveal the basis for potency. These compounds are orally available and permeate into rodent brain to increase O-GlcNAc, and should prove useful tools for studying the role of OGA in health and disease.


  • Organizational Affiliation

    Department of Chemistry, Simon Fraser University, Burnaby, British Columbia (Canada).


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
O-GLCNACASE BT_4395
A, B
726Bacteroides thetaiotaomicronMutation(s): 0 
EC: 3.2.1.169 (PDB Primary Data), 3.2.1.52 (PDB Primary Data)
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ89ZI2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
YWN
Query on YWN

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B]
2-[(2R,3S,4R,5R)-5-(hydroxymethyl)-3,4-bis(oxidanyl)-1-pentyl-pyrrolidin-2-yl]-N-methyl-ethanamide
C13 H26 N2 O4
NZYWNYJYZSBEBH-VCDKRKBESA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
F [auth B]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
C [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.41α = 90
b = 161.31β = 90
c = 223.2γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2015-11-18
    Type: Initial release
  • Version 1.1: 2015-11-25
    Changes: Structure summary
  • Version 1.2: 2016-01-27
    Changes: Database references
  • Version 1.3: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Other