4JFW

Crystal structure of a bacterial fucosidase with iminosugar inhibitor (2S,3S,4R,5S)-2-[N-(propylferrocene)]aminoethyl-5-methylpyrrolidine-3,4-diol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

alpha-L-fucosidase inhibition by pyrrolidine-ferrocene hybrids: rationalization of ligand-binding properties by structural studies.

Hottin, A.Wright, D.W.Steenackers, A.Delannoy, P.Dubar, F.Biot, C.Davies, G.J.Behr, J.B.

(2013) Chemistry 19: 9526-9533

  • DOI: 10.1002/chem.201301001
  • Primary Citation of Related Structures:  4JFS, 4JFT, 4JFU, 4JFV

  • PubMed Abstract: 
  • Enhanced metabolism of fucose through fucosidase overexpression is a signature of some cancer types, thus suggesting that fucosidase-targetted ligands could play the role of drug-delivery vectors. Herein, we describe the synthesis of a new series of ...

    Enhanced metabolism of fucose through fucosidase overexpression is a signature of some cancer types, thus suggesting that fucosidase-targetted ligands could play the role of drug-delivery vectors. Herein, we describe the synthesis of a new series of pyrrolidine-ferrocene conjugates, consisting of a L-fuco-configured dihydroxypyrrolidine as the fucosidase ligand armed with a cytotoxic ferrocenylamine moeity. Three-dimensional structures of several of these fucosidase inhibitors reveal transition-state-mimicking (3)E conformations. Elaboration with the ferrocenyl moiety results in sub-micromolar inhibitors of both bovine and bacterial fucosidases, with the 3D structure of the latter revealing electron density indicative of highly mobile alkylferrocene compounds. The best compounds show a strong antiproliferative effect, with up to 100% inhibition of the proliferation of MDA-MB-231 cancer cells at 50 μM.


    Organizational Affiliation

    Université de Reims Champagne-Ardenne, Institut de Chimie Moléculaire de Reims, CNRS UMR 7312, UFR des Sciences Exactes et Naturelles, 51687 Reims Cedex 2, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
alpha-L-fucosidase
A, B, C, D
450Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482)N/A
Find proteins for Q8A3I4 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482))
Go to UniProtKB:  Q8A3I4
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
H58
Query on H58

Download SDF File 
Download CCD File 
A, B, C, D
(3alpha)-[3-({2-[(2S,3S,4R,5S)-3,4-dihydroxy-5-methylpyrrolidin-2-yl]ethyl}amino)propyl]ferrocene
(2S,3S,4R,5S)-2-[N-(propylferrocene)]aminoethyl-5-methylpyrrolidine-3,4-diol
C20 H30 Fe N2 O2
UONBANSHCODUCX-RDDIDZLJSA-N
 Ligand Interaction
IMD
Query on IMD

Download SDF File 
Download CCD File 
A, B, C, D
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
H58Ki: 460 nM BINDINGMOAD
H58Ki: 460 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.207 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 56.507α = 90.00
b = 189.982β = 94.09
c = 97.540γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
PDB_EXTRACTdata extraction
REFMACrefinement
MOLREPphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-09-18
    Type: Initial release
  • Version 1.1: 2014-07-02
    Type: Non-polymer description