4CST

Crystal structure of FimH in complex with 3'-Chloro-4'-(alpha-D-mannopyranosyloxy)-biphenyl-4-carbonitrile


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 0.130 
  • R-Value Work: 0.114 
  • R-Value Observed: 0.114 

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This is version 2.0 of the entry. See complete history


Literature

Fimh Antagonists: Bioisosteres to Improve the in Vitro and in Vivo Pk/Pd Profile.

Ernst, B.Kleeb, S.Pang, L.Mayer, K.Eris, D.Sigl, A.Zihlmann, P.Preston, R.C.Sharpe, T.Jakob, R.Abgottspon, D.Hutter, A.S.Scharenberg, M.Jiang, X.Navarra, G.Rabbani, S.Smiesko, M.Ludin, N.Bezencon, J.Schwardt, O.Maier, T.

(2015) J Med Chem 58: 2221

  • DOI: 10.1021/jm501524q
  • Primary Citation of Related Structures:  
    4CST, 4CSS

  • PubMed Abstract: 
  • Urinary tract infections (UTIs), predominantly caused by uropathogenic Escherichia coli (UPEC), belong to the most prevalent infectious diseases worldwide. The attachment of UPEC to host cells is mediated by FimH, a mannose-binding adhesin at the tip of bacterial type 1 pili ...

    Urinary tract infections (UTIs), predominantly caused by uropathogenic Escherichia coli (UPEC), belong to the most prevalent infectious diseases worldwide. The attachment of UPEC to host cells is mediated by FimH, a mannose-binding adhesin at the tip of bacterial type 1 pili. To date, UTIs are mainly treated with antibiotics, leading to the ubiquitous problem of increasing resistance against most of the currently available antimicrobials. Therefore, new treatment strategies are urgently needed. Here, we describe the development of an orally available FimH antagonist. Starting from the carboxylate substituted biphenyl α-d-mannoside 9, affinity and the relevant pharmacokinetic parameters (solubility, permeability, renal excretion) were substantially improved by a bioisosteric approach. With 3'-chloro-4'-(α-d-mannopyranosyloxy)biphenyl-4-carbonitrile (10j) a FimH antagonist with an optimal in vitro PK/PD profile was identified. Orally applied, 10j was effective in a mouse model of UTI by reducing the bacterial load in the bladder by about 1000-fold.


    Organizational Affiliation

    Institute of Molecular Pharmacy, Pharmacenter, University of Basel , Klingelbergstrasse 50, CH-4056 Basel, Switzerland.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN FIMHA163Escherichia coli K-12Mutation(s): 0 
Gene Names: fimHb4320JW4283
UniProt
Find proteins for P08191 (Escherichia coli (strain K12))
Explore P08191 
Go to UniProtKB:  P08191
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CWK (Subject of Investigation/LOI)
Query on CWK

Download Ideal Coordinates CCD File 
B [auth A]3'-chloro-4'-(alpha-D-mannopyranosyloxy)biphenyl-4-carbonitrile
C19 H18 Cl N O6
NJQGFQIHQPLUNX-GFEQUFNTSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
CWK Binding MOAD:  4CST Kd: 1.3 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 0.130 
  • R-Value Work: 0.114 
  • R-Value Observed: 0.114 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.84α = 90
b = 55.89β = 90
c = 61γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2015-02-25
    Type: Initial release
  • Version 1.1: 2015-03-25
    Changes: Database references
  • Version 2.0: 2019-10-23
    Changes: Atomic model, Data collection, Other