2XPK | pdb_00002xpk

Cell-penetrant, nanomolar O-GlcNAcase inhibitors selective against lysosomal hexosaminidases

• PDB DOI: https://doi.org/10.2210/pdb2XPK/pdb

• Classification: HYDROLASE
• Organism(s): Clostridium perfringens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2010-08-26 Released: 2011-03-16 
• Deposition Author(s): Dorfmueller, H.C., Borodkin, V.S., Schimpl, M., Zheng, X., Kime, R., Read, K.D., van Aalten, D.M.F.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.242 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

Cell-Penetrant, Nanomolar O-Glcnacase Inhibitors Selective Against Lysosomal Hexosaminidases.

Dorfmueller, H.C., Borodkin, V.S., Schimpl, M., Zheng, X., Kime, R., Read, K.D., Van Aalten, D.M.F.

(2010) Chem Biol 17: 1250

• PubMed: 21095575 
• DOI: https://doi.org/10.1016/j.chembiol.2010.09.014
• Primary Citation of Related Structures:  
  2XPK


• PubMed Abstract: 
  

  Posttranslational modification of metazoan nucleocytoplasmic proteins with N-acetylglucosamine (O-GlcNAc) is essential, dynamic, and inducible and can compete with protein phosphorylation in signal transduction. Inhibitors of O-GlcNAcase, the enzyme removing O-GlcNAc, are useful tools for studying the role of O-GlcNAc in a range of cellular processes. We report the discovery of nanomolar OGA inhibitors that are up to 900,000-fold selective over the related lysosomal hexosaminidases. When applied at nanomolar concentrations on live cells, these cell-penetrant molecules shift the O-GlcNAc equilibrium toward hyper-O-GlcNAcylation with EC₅₀ values down to 3 nM and are thus invaluable tools for the study of O-GlcNAc cell biology.

---

Organizational Affiliation: 

Division of Molecular Microbiology, College of Life Sciences, University of Dundee, Dundee DD15EH, Scotland.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 134.17 kDa 
• Atom Count: 9,771 
• Modelled Residue Count: 1,170 
• Deposited Residue Count: 1,188 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
O-GLCNACASE NAGJ	A, B	594	Clostridium perfringens	Mutation(s): 1  EC: 3.2.1.52 (PDB Primary Data), 3.2.1.169 (UniProt)
UniProt
Find proteins for Q0TR53 (Clostridium perfringens (strain ATCC 13124 / DSM 756 / JCM 1290 / NCIMB 6125 / NCTC 8237 / Type A)) Explore Q0TR53  Go to UniProtKB:  Q0TR53

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
Z0M	C [auth A], D [auth B]	N-[(5R,6R,7R,8S)-6,7-DIHYDROXY-5-(HYDROXYMETHYL)-2-(2-PHENYLETHYL)-5,6,7,8-TETRAHYDROIMIDAZO[1,2-A]PYRIDIN-8-YL]-3-SULFANYLPROPANAMIDE C19 H25 N3 O4 S ZEEDRHPJCAOZKV-VDHUWJSZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.242 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: I 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 130.145	α = 90
b = 144.97	β = 90
c = 153.061	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALEPACK	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-03-16 
Deposition Author(s): Dorfmueller, H.C., Borodkin, V.S., Schimpl, M., Zheng, X., Kime, R., Read, K.D., van Aalten, D.M.F.

Revision History  

• Version 1.0: 2011-03-16
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description