4PCS

Crystal structure of a bacterial fucosidase with iminosugar (2S,3S,4R,5S)-3,4-dihydroxy-2-[2'-phenyl]ethynyl-5-methylpyrrolidine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.226 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Exploiting the Hydrophobic Terrain in Fucosidases with Aryl-Substituted Pyrrolidine Iminosugars.

Hottin, A.Wright, D.W.Davies, G.J.Behr, J.B.

(2015) Chembiochem 16: 277-283

  • DOI: https://doi.org/10.1002/cbic.201402509
  • Primary Citation of Related Structures:  
    4PCS, 4PCT, 4PEE

  • PubMed Abstract: 

    Fucosidase inhibition shows potential in numerous therapeutic contexts. Substitution of fucose-like iminosugars with hydrophobic "aglycons" yields significant improvements in potency of fucosidase inhibition. Here we have prepared three new 2-aryl-3,4-dihydroxy-5-methylpyrrolidines featuring phenyl substituents in variable orientations with respect to the iminocyclitol core and at various distances from it to explore the key binding interactions that stabilise the enzyme-inhibitor complex. The presence of a triazole linker in one structure resulted in nanomolar inhibition of the fucosidase from bovine kidney (Ki =4.8 nM), thus giving rise to one of the most potent pyrrolidine-type inhibitors of this enzyme known to date.


  • 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Alpha-L-fucosidase
A, B, C, D
439Bacteroides thetaiotaomicron VPI-5482Mutation(s): 0 
Gene Names: BT_2970
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
2M7
Query on 2M7

Download Ideal Coordinates CCD File 
I [auth A],
N [auth B],
Q [auth C],
T [auth D]
(2S,3R,4S,5S)-2-methyl-5-(phenylethynyl)pyrrolidine-3,4-diol
C13 H15 N O2
RPIQJUPODSDSQH-SYEHKZFSSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
J [auth B]
K [auth B]
O [auth C]
E [auth A],
F [auth A],
J [auth B],
K [auth B],
O [auth C],
R [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
IMD
Query on IMD

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
L [auth B]
M [auth B]
P [auth C]
G [auth A],
H [auth A],
L [auth B],
M [auth B],
P [auth C],
S [auth D]
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.226 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.37α = 90
b = 188.28β = 94.1
c = 97.93γ = 90
Software Package:
Software NamePurpose
iMOSFLMdata reduction
PDB_EXTRACTdata extraction
REFMACrefinement
Aimlessdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-07-30
    Changes: Database references
  • Version 1.2: 2014-12-10
    Changes: Database references
  • Version 1.3: 2015-01-21
    Changes: Database references
  • Version 1.4: 2023-12-20
    Changes: Data collection, Database references, Refinement description