5MAY

STRUCTURE OF THE LECB LECTIN FROM PSEUDOMONAS AERUGINOSA STRAIN PA14 IN COMPLEX WITH 2-Thiophenesulfonamide-N-(beta-L-fucopyranosyl methyl)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.135 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Glycomimetic, Orally Bioavailable LecB Inhibitors Block Biofilm Formation of Pseudomonas aeruginosa.

Sommer, R.Wagner, S.Rox, K.Varrot, A.Hauck, D.Wamhoff, E.C.Schreiber, J.Ryckmans, T.Brunner, T.Rademacher, C.Hartmann, R.W.Bronstrup, M.Imberty, A.Titz, A.

(2018) J. Am. Chem. Soc. 140: 2537-2545

  • DOI: 10.1021/jacs.7b11133
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The opportunistic Gram-negative bacterium Pseudomonas aeruginosa is a leading pathogen for infections of immuno-compromised patients and those suffering from cystic fibrosis. Its ability to switch from planktonic life to aggregates, forming the so-ca ...

    The opportunistic Gram-negative bacterium Pseudomonas aeruginosa is a leading pathogen for infections of immuno-compromised patients and those suffering from cystic fibrosis. Its ability to switch from planktonic life to aggregates, forming the so-called biofilms, is a front-line mechanism of antimicrobial resistance. The bacterial carbohydrate-binding protein LecB is an integral component and necessary for biofilm formation. Here, we report a new class of drug-like low molecular weight inhibitors of the lectin LecB with nanomolar affinities and excellent receptor binding kinetics and thermodynamics. This class of glycomimetic inhibitors efficiently blocked biofilm formation of P. aeruginosa in vitro while the natural monovalent carbohydrate ligands failed. Furthermore, excellent selectivity and pharmacokinetic properties were achieved. Notably, two compounds showed good oral bioavailability, and high compound concentrations in plasma and urine were achieved in vivo.


    Organizational Affiliation

    Chemical Biology of Carbohydrates and ‡Drug Design and Development, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) , D-66123 Saarbrücken, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Fucose-binding lectin PA-IIL
A, B, C, D
114Pseudomonas aeruginosa (strain UCBPP-PA14)Mutation(s): 0 
Gene Names: lecB
Find proteins for A0A0H2ZE85 (Pseudomonas aeruginosa (strain UCBPP-PA14))
Go to UniProtKB:  A0A0H2ZE85
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, B, C, D
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
PK6
Query on PK6

Download SDF File 
Download CCD File 
A, B, C, D
N-methyl-2-thiophenesulfonamide
C5 H7 N O2 S2
CTIGHRXLNNYNGU-UHFFFAOYSA-N
 Ligand Interaction
FUL
Query on FUL

Download SDF File 
Download CCD File 
A, B, C, D
BETA-L-FUCOSE
6-DEOXY-BETA-L-GALACTOSE
C6 H12 O5
SHZGCJCMOBCMKK-KGJVWPDLSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.135 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 53.089α = 90.00
b = 65.520β = 90.00
c = 109.173γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
Aimlessdata scaling
REFMACrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-12-20
    Type: Initial release
  • Version 1.1: 2018-03-14
    Type: Database references