5ABH | pdb_00005abh

Structure of GH84 with ligand

PDB DOI: https://doi.org/10.2210/pdb5ABH/pdb

Classification: HYDROLASE
Organism(s): Bacteroides thetaiotaomicron
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2015-08-05 Released: 2015-11-18
Deposition Author(s): Bergeron-Brlek, M., Goodwin-Tindall, J., Cekic, N., Varghese, V., Zandberg, W.F., Shan, X., Roth, C., Chan, S., Davies, G.J., Vocadlo, D.J., Britton, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.252 (Depositor), 0.250 (DCC)
R-Value Work:
0.212 (Depositor), 0.220 (DCC)
R-Value Observed:
0.214 (Depositor)

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

PubMed: 26545827 Search on PubMed
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).

Macromolecule Content

Total Structure Weight: 167.76 kDa
Atom Count: 11,667
Modelled Residue Count: 1,346
Deposited Residue Count: 1,452
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
O-GLCNACASE BT_4395	A, B	726	Bacteroides thetaiotaomicron	Mutation(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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q89ZI2
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
YWN Query on YWN Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth B] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B] mmCIF format, chain D [auth A] mmCIF format, chain G [auth B]	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		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B]	E [auth A], H [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain F [auth B] MOL2 format, chain F [auth B] mmCIF format, chain F [auth B]	F [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain F [auth B] Interactions & Density Focus chain F [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.252 (Depositor), 0.250 (DCC)
R-Value Work: 0.212 (Depositor), 0.220 (DCC)
R-Value Observed: 0.214 (Depositor)

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.41	α = 90
b = 161.31	β = 90
c = 223.2	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2015-11-18

Deposition Author(s):

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