4BUQ

Crystal structure of wild type FimH lectin domain in complex with heptyl alpha-D-mannopyrannoside


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.199 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.1 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.Bouckaert, 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, B
158Escherichia coliMutation(s): 0 
Gene Names: fimH
Find proteins for A2IC68 (Escherichia coli)
Go to UniProtKB:  A2IC68
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
KGM
Query on KGM

Download SDF File 
Download CCD File 
A, B
Heptyl Alpha-D-mannopyrannoside
C13 H26 O6
NIDYWHLDTIVRJT-BNDIWNMDSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
KGMKd: 7.3 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.199 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.202 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 60.305α = 90.00
b = 68.070β = 90.00
c = 95.607γ = 90.00
Software Package:
Software NamePurpose
SCALESdata scaling
XDSdata reduction
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-02-19
    Type: Initial release
  • Version 1.1: 2014-06-18
    Type: Database references