4KC2

Structure of the blood group glycosyltransferase AAglyB in complex with a pyridine inhibitor as a neutral pyrophosphate surrogate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Design of glycosyltransferase inhibitors: pyridine as a pyrophosphate surrogate.

Wang, S.Cuesta-Seijo, J.A.Lafont, D.Palcic, M.M.Vidal, S.

(2013) Chemistry 19: 15346-15357

  • DOI: 10.1002/chem.201301871
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • A series of ten glycosyltransferase inhibitors has been designed and synthesized by using pyridine as a pyrophosphate surrogate. The series was prepared by conjugation of carbohydrate, pyridine, and nucleoside building blocks by using a combination o ...

    A series of ten glycosyltransferase inhibitors has been designed and synthesized by using pyridine as a pyrophosphate surrogate. The series was prepared by conjugation of carbohydrate, pyridine, and nucleoside building blocks by using a combination of glycosylation, the Staudinger-Vilarrasa amide-bond formation, and azide-alkyne click chemistry. The compounds were evaluated as inhibitors of five metal-dependent galactosyltransferases. Crystallographic analyses of three inhibitors complexed in the active site of one of the enzymes confirmed that the pyridine moiety chelates the Mn(2+) ion causing a slight displacement (2 Å) from its original position. The carbohydrate head group occupies a different position than in the natural uridine diphosphate (UDP)-Gal substrate with little interaction with the enzyme.


    Organizational Affiliation

    Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, Laboratoire de Chimie Organique 2, Glycochimie, UMR 5246, CNRS and Université Claude Bernard Lyon 1, 43 Boulevard du 11 Novembre 1918, 6922 Villeurbanne (France), Fax: (+33) 472-448-109.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Fucosylglycoprotein alpha-N-acetylgalactosaminyltransferase soluble form
A
290Homo sapiensMutation(s): 0 
Gene Names: ABO
Find proteins for P16442 (Homo sapiens)
Go to Gene View: ABO
Go to UniProtKB:  P16442
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
BHE
Query on BHE

Download SDF File 
Download CCD File 
A
octyl 2-O-(6-deoxy-alpha-L-galactopyranosyl)-beta-D-galactopyranoside
H-antigen acceptor; alpha-L-Fucp-(1,2)-Beta-D-Galp-O(CH2)7CH3
C20 H38 O10
GTTDTLMUWQMDNA-ARNYJBIMSA-N
 Ligand Interaction
WS2
Query on WS2

Download SDF File 
Download CCD File 
A
6-(1-beta-D-Galactopyranosyloxymethyl)-N-(5'-deoxyluridine-5'-yl)picolinamide
C22 H28 N4 O12
KPOTWZYLDCHCIG-GBMKPDNQSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.176 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 52.880α = 90.00
b = 149.900β = 90.00
c = 80.030γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XSCALEdata scaling
XDSdata reduction
MAR345dtbdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-09-11
    Type: Initial release
  • Version 1.1: 2015-03-04
    Type: Database references
  • Version 1.2: 2017-11-15
    Type: Advisory, Database references, Refinement description