4JFW | pdb_00004jfw

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: 2.10 Å
  • R-Value Free: 
    0.244 (Depositor), 0.249 (DCC) 
  • R-Value Work: 
    0.207 (Depositor), 0.213 (DCC) 
  • R-Value Observed: 
    0.209 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 4JFW

Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/10.1002/chem.201301001
  • Primary Citation Related Structures: 
    4JFS, 4JFT, 4JFU, 4JFV, 4JFW

  • 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 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.

Macromolecule Content 

  • Total Structure Weight: 210.82 kDa 
  • Atom Count: 14,229 
  • Modeled Residue Count: 1,755 
  • Deposited Residue Count: 1,800 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
alpha-L-fucosidase
A, B, C, D
450Bacteroides thetaiotaomicron VPI-5482Mutation(s): 0 
EC: 3.2.1.51
UniProt
Find proteins for Q8A3I4 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50))
Explore Q8A3I4 
Go to UniProtKB:  Q8A3I4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8A3I4
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
H58

Query on H58



Download:Ideal Coordinates CCD File
E [auth A],
H [auth B],
L [auth C],
P [auth D]
(3alpha)-[3-({2-[(2S,3S,4R,5S)-3,4-dihydroxy-5-methylpyrrolidin-2-yl]ethyl}amino)propyl]ferrocene
C20 H30 Fe N2 O2
UONBANSHCODUCX-RDDIDZLJSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
F [auth A]
I [auth B]
J [auth B]
M [auth C]
N [auth C]
F [auth A],
I [auth B],
J [auth B],
M [auth C],
N [auth C],
Q [auth D],
R [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
IMD

Query on IMD



Download:Ideal Coordinates CCD File
G [auth A],
K [auth B],
O [auth C],
S [auth D]
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.244 (Depositor), 0.249 (DCC) 
  • R-Value Work:  0.207 (Depositor), 0.213 (DCC) 
  • R-Value Observed: 0.209 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.507α = 90
b = 189.982β = 94.09
c = 97.54γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-09-18
    Type: Initial release
  • Version 1.1: 2014-07-02
    Changes: Non-polymer description
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description