6G2S

Crystal structure of FimH in complex with a pentaflourinated biphenyl alpha D-mannoside


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.198 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Improvement of Aglycone pi-Stacking Yields Nanomolar to Sub-nanomolar FimH Antagonists.

Schonemann, W.Cramer, J.Muhlethaler, T.Fiege, B.Silbermann, M.Rabbani, S.Datwyler, P.Zihlmann, P.Jakob, R.P.Sager, C.P.Smiesko, M.Schwardt, O.Maier, T.Ernst, B.

(2019) ChemMedChem 14: 749-757

  • DOI: https://doi.org/10.1002/cmdc.201900051
  • Primary Citation of Related Structures:  
    6G2R, 6G2S

  • PubMed Abstract: 

    Antimicrobial resistance has become a serious concern for the treatment of urinary tract infections. In this context, an anti-adhesive approach targeting FimH, a bacterial lectin enabling the attachment of E. coli to host cells, has attracted considerable interest. FimH can adopt a low/medium-affinity state in the absence and a high-affinity state in the presence of shear forces. Until recently, mostly the high-affinity state has been investigated, despite the fact that a therapeutic antagonist should bind predominantly to the low-affinity state. In this communication, we demonstrate that fluorination of biphenyl α-d-mannosides leads to compounds with perfect π-π stacking interactions with the tyrosine gate of FimH, yielding low nanomolar to sub-nanomolar K D values for the low- and high-affinity states, respectively. The face-to-face alignment of the perfluorinated biphenyl group of FimH ligands and Tyr48 was confirmed by crystal structures as well as 1 H, 15 N-HSQC NMR analysis. Finally, fluorination improves pharmacokinetic parameters predictive for oral availability.


  • Organizational Affiliation

    Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056, Basel, Switzerland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Type 1 fimbrin D-mannose specific adhesin
A, B, C, D, E
A, B, C, D, E, F, G, H, I
158Escherichia coli K-12Mutation(s): 0 
Gene Names: fimHb4320JW4283
UniProt
Find proteins for P08191 (Escherichia coli (strain K12))
Explore P08191 
Go to UniProtKB:  P08191
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08191
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EJN
Query on EJN

Download Ideal Coordinates CCD File 
AA [auth I]
J [auth A]
L [auth B]
O [auth C]
Q [auth D]
AA [auth I],
J [auth A],
L [auth B],
O [auth C],
Q [auth D],
T [auth E],
V [auth F],
X [auth G],
Z [auth H]
(2~{R},3~{S},4~{S},5~{S},6~{R})-2-(hydroxymethyl)-6-[4-[2,3,4,5,6-pentakis(fluoranyl)phenyl]phenoxy]oxane-3,4,5-triol
C18 H15 F5 O6
WCSHODXKNWBNJL-VYMSMKAZSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
K [auth A]
M [auth B]
N [auth B]
P [auth C]
R [auth D]
K [auth A],
M [auth B],
N [auth B],
P [auth C],
R [auth D],
S [auth D],
U [auth E],
W [auth F],
Y [auth G]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.198 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.01α = 90
b = 86.01β = 90
c = 203.14γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2019-03-20
    Type: Initial release
  • Version 1.1: 2019-04-17
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description