6MAW

F9 Pilus Adhesin FmlH Lectin Domain from E. coli UTI89 in Complex with Galactoside N-[(2S,3R,4R,5R,6R)-4,5-dihydroxy-6-(hydroxymethyl)-2-{[S-methyl-6-(trifluoromethyl)-[1,1'-biphenyl]-3'-yl]oxy}oxan-3-yl]acetamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.162 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Biphenyl Gal and GalNAc FmlH Lectin Antagonists of Uropathogenic E. coli (UPEC): Optimization through Iterative Rational Drug Design.

Maddirala, A.R.Klein, R.Pinkner, J.S.Kalas, V.Hultgren, S.J.Janetka, J.W.

(2019) J Med Chem 62: 467-479

  • DOI: https://doi.org/10.1021/acs.jmedchem.8b01561
  • Primary Citation of Related Structures:  
    6MAP, 6MAQ, 6MAW

  • PubMed Abstract: 

    The F9/Yde/Fml pilus, tipped with the FmlH adhesin, has been shown to provide uropathogenic Escherichia coli (UPEC) a fitness advantage in urinary tract infections (UTIs). Here, we used X-ray structure guided design to optimize our previously described ortho-biphenyl Gal and GalNAc FmlH antagonists such as compound 1 by replacing the carboxylate with a sulfonamide as in 50. Other groups which can accept H-bonds were also tolerated. We pursued further modifications to the biphenyl aglycone resulting in significantly improved activity. Two of the most potent compounds, 86 (IC 50 = 0.051 μM) and 90 (IC 50 = 0.034 μM), exhibited excellent metabolic stability in mouse plasma and liver microsomes but showed only limited oral bioavailability (<1%) in rats. Compound 84 also showed a good pharmacokinetic (PK) profile in mice after IP dosing with compound exposure above the IC 50 for 6 h. These new FmlH antagonists represent new antivirulence drugs for UTIs.


  • Organizational Affiliation

    Department of Molecular Microbiology , Washington University School of Medicine , St. Louis , Missouri 63110 , United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fimbrial adhesin FmlD166Escherichia coli UTI89Mutation(s): 0 
Gene Names: 
UniProt
Find proteins for P77588 (Escherichia coli (strain K12))
Explore P77588 
Go to UniProtKB:  P77588
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP77588
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
JC7 (Subject of Investigation/LOI)
Query on JC7

Download Ideal Coordinates CCD File 
B [auth A]N-[2'-{[2-(acetylamino)-2-deoxy-beta-D-galactopyranosyl]oxy}-6'-(trifluoromethyl)[1,1'-biphenyl]-3-yl]methanesulfonamide
C22 H25 F3 N2 O8 S
RPOJFLNPFLSKOB-QNDFHXLGSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.162 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.445α = 90
b = 110.212β = 90
c = 90.195γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI048689

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-04
    Type: Initial release
  • Version 1.1: 2019-12-18
    Changes: Author supporting evidence
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2023-12-13
    Changes: Database references