4AUJ

FimH lectin domain co-crystal with a alpha-D-mannoside O-linked to para hydroxypropargyl phenyl


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.527 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.160 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Validation of Reactivity Descriptors to Assess the Aromatic Stacking within the Tyrosine Gate of Fimh.

Roos, G.Wellens, A.Touaibia, M.Yamakawa, N.Geerlings, P.Roy, R.Wyns, L.Bouchaert, J.

(2013) Acs Med.Chem.Lett. 4: 1085

  • DOI: 10.1021/ml400269v
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Antagonists of the FimH adhesin, a protein almost universally present at the extremity of type-1 fimbriae expressed by Escherichia coli, have been abundantly in the spotlight as alternative treatments of urinary tract infections. The antagonists func ...

    Antagonists of the FimH adhesin, a protein almost universally present at the extremity of type-1 fimbriae expressed by Escherichia coli, have been abundantly in the spotlight as alternative treatments of urinary tract infections. The antagonists function as bacterial antiadhesives through highly specific α-d-mannose binding in a charged and polar pocket at the tip of the FimH lectin domain and by the stacking of alkyl or aromatic moieties substituted on the mannose with two tyrosine residues (Tyr48 and Tyr137) at the entrance of the mannose-binding pocket. Using high-resolution crystal data, interaction energies are calculated for the different observed aromatic stacking modes between the tyrosines and the antagonist. The dispersion component of the interaction energy correlates with the observed electron density. The quantum chemical reactivity descriptors local hardness and polarizability were successfully validated as prediction tools for ligand affinity in the tyrosine gate of FimH and therefore have potential for rapid drug screening.


    Organizational Affiliation

    Unité de Glycobiologie Structurale et Fonctionnelle, UMR8576 du CNRS, Université Lille 1 , 59655 Villeneuve d'Ascq, France.,General Chemistry, Vrije Universiteit Brussel, Structural Biology Brussels, VIB and Vrije Universiteit Brussel, and Brussels Center for Redox Biology, Pleinlaan 2, 1050 Brussels, Belgium ; General Chemistry, Vrije Universiteit Brussel, Structural Biology Brussels, VIB and Vrije Universiteit Brussel, and Brussels Center for Redox Biology, Pleinlaan 2, 1050 Brussels, Belgium ; General Chemistry, Vrije Universiteit Brussel, Structural Biology Brussels, VIB and Vrije Universiteit Brussel, and Brussels Center for Redox Biology, Pleinlaan 2, 1050 Brussels, Belgium.,Department of Chemistry, Université du Québec à Montréal , Montréal, QC H3C 3P8, Canada ; Department of Chemistry and Biochemistry, Université de Moncton , Moncton, NB E1A 3E9, Canada.,General Chemistry, Vrije Universiteit Brussel, Structural Biology Brussels, VIB and Vrije Universiteit Brussel, and Brussels Center for Redox Biology, Pleinlaan 2, 1050 Brussels, Belgium ; Unité de Glycobiologie Structurale et Fonctionnelle, UMR8576 du CNRS, Université Lille 1 , 59655 Villeneuve d'Ascq, France.,General Chemistry, Vrije Universiteit Brussel, Structural Biology Brussels, VIB and Vrije Universiteit Brussel, and Brussels Center for Redox Biology, Pleinlaan 2, 1050 Brussels, Belgium.,Department of Chemistry, Université du Québec à Montréal , Montréal, QC H3C 3P8, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
FIMH
A
158Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: fimH
Find proteins for P08191 (Escherichia coli (strain K12))
Go to UniProtKB:  P08191
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HNW
Query on HNW

Download SDF File 
Download CCD File 
A
D-MANNOSE ALPHA1O P-HYDROXYPROPYNYL-PHENYL
C15 H18 O7
GNTPQQUJBAFHOR-MRLBHPIUSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
HNWKd: 18.3 nM BINDINGMOAD
HNWKd: 18.3 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.527 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.160 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 32.920α = 90.00
b = 42.290β = 90.00
c = 96.340γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
XSCALEdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-05-29
    Type: Initial release
  • Version 1.1: 2013-12-25
    Type: Database references
  • Version 1.2: 2014-06-18
    Type: Database references