5AB1

Complex of the FimH lectin with a beta-cyclodextrin C-linked alpha-D-mannoside in cocrystallized orthorhombic crystals at 2.00 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.962 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The Anti-Adhesive Strategy in Crohn'S Disease: Orally Active Mannosides to Decolonize Pathogenic Escherichia Coli from the Gut.

Dorta, D.A.Sivignon, A.Chalopin, T.Dumych, T.Roos, G.Bilyy, R.Deniaud, D.Krammer, E.De Ruyck, J.Lensink, M.Bouckaert, J.Barnich, N.Gouin, S.G.

(2016) Chembiochem 17: 936

  • DOI: 10.1002/cbic.201600018

  • PubMed Abstract: 
  • Blocking the adherence of bacteria to cells is an attractive complementary approach to current antibiotic treatments, which are faced with increasing resistance. This strategy has been particularly studied in the context of urinary tract infections ( ...

    Blocking the adherence of bacteria to cells is an attractive complementary approach to current antibiotic treatments, which are faced with increasing resistance. This strategy has been particularly studied in the context of urinary tract infections (UTIs), in which the adhesion of pathogenic Escherichia coli strains to uroepithelial cells is prevented by blocking the FimH adhesin expressed at the tips of bacteria organelles called fimbriae. Recently, we extended the antiadhesive concept, showing that potent FimH antagonists can block the attachment of adherent-invasive E. coli (AIEC) colonizing the intestinal mucosa of patients with Crohn's disease (CD). In this work, we designed a small library of analogues of heptyl mannoside (HM), a previously identified nanomolar FimH inhibitor, but one that displays poor antiadhesive effects in vivo. The anomeric oxygen atom was replaced by a sulfur or a methylene group to prevent hydrolysis by intestinal glycosidases, and chemical groups were attached at the end of the alkyl tail. Importantly, a lead compound was shown to reduce AIEC levels in the feces and in the colonic and ileal mucosa after oral administration (10 mg kg(-1) ) in a transgenic mouse model of CD. The compound showed a low bioavailability, preferable in this instance, thus suggesting the possibility of setting up an innovative antiadhesive therapy, based on the water-soluble and non-cytotoxic FimH antagonists developed here, for the CD subpopulation in which AIEC plays a key role.


    Organizational Affiliation

    Danylo Halytsky Lviv National Medical University, Pekarska Str. 69, 79010, Lviv, Ukraine.,LUNAM Université, CEISAM, Chimie et Interdisciplinarité, Synthèse, Analyse, Modélisation, UMR CNRS 6230, 2, rue de la Houssinière, BP 92208, 44322, Nantes Cedex 3, France.,Structure and Function of Biological Membranes, Université Libre de Bruxelles, Boulevard du Triomphe, 1050, Brussels, Belgium.,Clermont Université, UMR 1071 Inserm/Université d'Auvergne, 63000, Clermont-Ferrand, France.,Univ. Lille, CNRS, UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, 59000, Lille, France.,LUNAM Université, CEISAM, Chimie et Interdisciplinarité, Synthèse, Analyse, Modélisation, UMR CNRS 6230, 2, rue de la Houssinière, BP 92208, 44322, Nantes Cedex 3, France. sebastien.gouin@univ-nantes.fr.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
FIMH
A, B
300Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: fimH
Find proteins for P08191 (Escherichia coli (strain K12))
Go to UniProtKB:  P08191
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TA5
Query on TA5

Download SDF File 
Download CCD File 
A, B
2H-1,2,3-TRIAZOL-4-YLMETHANOL
C3 H5 N3 O
OADYBXHYXPEGHX-UHFFFAOYSA-N
 Ligand Interaction
HP6
Query on HP6

Download SDF File 
Download CCD File 
A, B
HEPTANE
C7 H16
IMNFDUFMRHMDMM-UHFFFAOYSA-N
 Ligand Interaction
MAN
Query on MAN

Download SDF File 
Download CCD File 
A, B
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BCD
Query on BCD

Download SDF File 
Download CCD File 
A, B
BETA-CYCLODEXTRIN
CYCLO-HEPTA-AMYLOSE
C42 H70 O35
WHGYBXFWUBPSRW-FOUAGVGXSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.962 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.210 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 63.282α = 90.00
b = 68.072β = 90.00
c = 95.777γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-05-11
    Type: Initial release
  • Version 1.1: 2016-05-18
    Type: Structure summary
  • Version 1.2: 2016-05-25
    Type: Structure summary
  • Version 1.3: 2016-06-01
    Type: Database references