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 

wwPDB Validation   3D Report Full Report


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 Biochemistry and Molecular Biophysics , 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

View Full Validation Report



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