5AAP

Complex of the FimH lectin with a C-linked para-biphenyl methylene alpha-D-mannoside


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.150 
  • R-Value Work: 0.122 
  • R-Value Observed: 0.123 

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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

Structures of C-Mannosylated Anti-Adhesives Bound to the Type 1 Fimbrial Fimh Adhesin

De Ruyck, J.Lensink, M.F.Bouckaert, J.

(2016) IUCrJ 3: 163

  • DOI: https://doi.org/10.1107/S2052252516002487
  • Primary Citation of Related Structures:  
    5AAL, 5AAP, 5ABZ

  • PubMed Abstract: 

    Selective inhibitors of the type 1 fimbrial adhesin FimH are recognized as attractive alternatives for antibiotic therapies and prophylaxes against Escherichia coli infections such as urinary-tract infections. To construct these inhibitors, the α-d-mannopyranoside of high-mannose N-glycans, recognized with exclusive specificity on glycoprotein receptors by FimH, forms the basal structure. A hydrophobic aglycon is then linked to the mannose by the O1 oxygen inherently present in the α-anomeric configuration. Substitution of this O atom by a carbon introduces a C-glycosidic bond, which may enhance the therapeutic potential of such compounds owing to the inability of enzymes to degrade C-glycosidic bonds. Here, the first crystal structures of the E. coli FimH adhesin in complex with C-glycosidically linked mannopyranosides are presented. These findings explain the role of the spacer in positioning biphenyl ligands for interactions by means of aromatic stacking in the tyrosine gate of FimH and how the normally hydrated C-glycosidic link is tolerated. As these new compounds can bind FimH, it can be assumed that they have the potential to serve as potent new antagonists of FimH, paving the way for the design of a new family of anti-adhesive compounds against urinary-tract infections.


  • Organizational Affiliation

    Université Lille, CNRS, UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle , 59000 Lille, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
FIMH158Escherichia coli UTI89Mutation(s): 0 
UniProt
Find proteins for Q1R2J4 (Escherichia coli (strain UTI89 / UPEC))
Explore Q1R2J4 
Go to UniProtKB:  Q1R2J4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ1R2J4
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.150 
  • R-Value Work: 0.122 
  • R-Value Observed: 0.123 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 31.18α = 90
b = 41.71β = 90
c = 97.21γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-03-09
    Type: Initial release
  • Version 1.1: 2016-03-23
    Changes: Structure summary
  • Version 1.2: 2016-05-18
    Changes: Database references
  • Version 2.0: 2019-10-23
    Changes: Atomic model, Data collection, Other
  • Version 2.1: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Refinement description