2XGS

XcOGT in complex with C-UDP

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 0.316 
  • R-Value Work: 0.257 
  • R-Value Observed: 0.258 

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Ligand Structure Quality Assessment 


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Literature

Substrate and Product Analogues as Human O-Glcnac Transferase Inhibitors.

Dorfmueller, H.C., Borodkin, V.S., Blair, D.E., Pathak, S., Navratilova, I., Van Aalten, D.M.

(2011) Amino Acids 40: 781

  • DOI: 10.1007/s00726-010-0688-y
  • Primary Citation of Related Structures:  
    2XGM, 2XGO, 2XGS

  • PubMed Abstract: 

    • Protein glycosylation on serine/threonine residues with N-acetylglucosamine (O-GlcNAc) is a dynamic, inducible and abundant post-translational modification. It is thought to regulate many cellular processes and there are examples of interplay between O-GlcNAc and protein phosphorylation ...

    Protein glycosylation on serine/threonine residues with N-acetylglucosamine (O-GlcNAc) is a dynamic, inducible and abundant post-translational modification. It is thought to regulate many cellular processes and there are examples of interplay between O-GlcNAc and protein phosphorylation. In metazoa, a single, highly conserved and essential gene encodes the O-GlcNAc transferase (OGT) that transfers GlcNAc onto substrate proteins using UDP-GlcNAc as the sugar donor. Specific inhibitors of human OGT would be useful tools to probe the role of this post-translational modification in regulating processes in the living cell. Here, we describe the synthesis of novel UDP-GlcNAc/UDP analogues and evaluate their inhibitory properties and structural binding modes in vitro alongside alloxan, a previously reported weak OGT inhibitor. While the novel analogues are not active on living cells, they inhibit the enzyme in the micromolar range and together with the structural data provide useful templates for further optimisation.

    Organizational Affiliation: 

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



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
XCOGTA, B568Xanthomonas campestrisMutation(s): 0 
UniProt
Find proteins for Q8PC69 (Xanthomonas campestris pv. campestris (strain ATCC 33913 / DSM 3586 / NCPPB 528 / LMG 568 / P 25))
Explore Q8PC69 
Go to UniProtKB:  Q8PC69
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8PC69
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
44P
Query on 44P
Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]		5'-O-[(S)-HYDROXY(PHOSPHONOMETHYL)PHOSPHORYL]URIDINE
C10 H16 N2 O11 P2
PDEGDTTUBZXACY-ZOQUXTDFSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
44P PDBBind:  2XGS Kd: 5.30e+5 (nM) from 1 assay(s)
Binding MOAD:  2XGS Kd: 5.30e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 0.316 
  • R-Value Work: 0.257 
  • R-Value Observed: 0.258 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.286α = 90
b = 94.98β = 90
c = 157.655γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-08-25
    Type: Initial release
  • Version 1.1: 2011-10-26
    Changes: Database references, Refinement description, Version format compliance