5F3F | pdb_00005f3f

Crystal structure of para-biphenyl-2-methyl-3'-methyl amide mannoside bound to FimH lectin domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 
    0.172 (Depositor), 0.173 (DCC) 
  • R-Value Work: 
    0.135 (Depositor), 0.138 (DCC) 
  • R-Value Observed: 
    0.137 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Antivirulence C-Mannosides as Antibiotic-Sparing, Oral Therapeutics for Urinary Tract Infections.

Mydock-McGrane, L.Cusumano, Z.Han, Z.Binkley, J.Kostakioti, M.Hannan, T.Pinkner, J.S.Klein, R.Kalas, V.Crowley, J.Rath, N.P.Hultgren, S.J.Janetka, J.W.

(2016) J Med Chem 59: 9390-9408

  • DOI: https://doi.org/10.1021/acs.jmedchem.6b00948
  • Primary Citation Related Structures: 
    5F3F

  • PubMed Abstract: 

    Gram-negative uropathogenic Escherichia coli (UPEC) bacteria are a causative pathogen of urinary tract infections (UTIs). Previously developed antivirulence inhibitors of the type 1 pilus adhesin, FimH, demonstrated oral activity in animal models of UTI but were found to have limited compound exposure due to the metabolic instability of the O-glycosidic bond (O-mannosides). Herein, we disclose that compounds having the O-glycosidic bond replaced with carbon linkages had improved stability and inhibitory activity against FimH. We report on the design, synthesis, and in vivo evaluation of this promising new class of carbon-linked C-mannosides that show improved pharmacokinetic (PK) properties relative to O-mannosides. Interestingly, we found that FimH binding is stereospecifically modulated by hydroxyl substitution on the methylene linker, where the R-hydroxy isomer has a 60-fold increase in potency. This new class of C-mannoside antagonists have significantly increased compound exposure and, as a result, enhanced efficacy in mouse models of acute and chronic UTI.


  • Organizational Affiliation
    • Fimbrion Therapeutics, Inc. , Saint Louis, Missouri 63108 United States.

Macromolecule Content 

  • Total Structure Weight: 17.32 kDa 
  • Atom Count: 1,504 
  • Modeled Residue Count: 158 
  • Deposited Residue Count: 158 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein FimH158Escherichia coli J96Mutation(s): 0 
Gene Names: fimH
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
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
5US

Query on 5US



Download:Ideal Coordinates CCD File
B [auth A]3-[4-[(2~{R},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-3-methyl-phenyl]-~{N}-methyl-benzamide
C21 H25 N O7
LECOXVSYFKTZFV-AGRFSFNASA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free:  0.172 (Depositor), 0.173 (DCC) 
  • R-Value Work:  0.135 (Depositor), 0.138 (DCC) 
  • R-Value Observed: 0.137 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.97α = 90
b = 55.66β = 90
c = 60.89γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
MOSFLMdata reduction
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: 2016-12-07
    Type: Initial release
  • Version 1.1: 2023-09-27
    Changes: Data collection, Database references, Refinement description
  • Version 1.2: 2024-01-03
    Changes: Database references
  • Version 1.3: 2024-10-30
    Changes: Structure summary