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 
  • R-Value Observed: 0.136 

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Ligand Structure Quality Assessment 


This is version 1.2 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:  
    5MAY, 5MB1

  • 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-called biofilms, is a front-line mechanism of antimicrobial resistance ...

    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

    Department of Pharmacy, Saarland University , D-66123 Saarbrücken, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Fucose-binding lectin PA-IILA, B, C, D114Pseudomonas aeruginosa UCBPP-PA14Mutation(s): 0 
Gene Names: lecBPA14_20610
UniProt
Find proteins for A0A0H2ZE85 (Pseudomonas aeruginosa (strain UCBPP-PA14))
Explore A0A0H2ZE85 
Go to UniProtKB:  A0A0H2ZE85
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PK6 (Subject of Investigation/LOI)
Query on PK6

Download Ideal Coordinates CCD File 
H [auth A], L [auth B], P [auth C], T [auth D]N-methyl-2-thiophenesulfonamide
C5 H7 N O2 S2
CTIGHRXLNNYNGU-UHFFFAOYSA-N
 Ligand Interaction
FUL (Subject of Investigation/LOI)
Query on FUL

Download Ideal Coordinates CCD File 
G [auth A], K [auth B], O [auth C], S [auth D]beta-L-fucopyranose
C6 H12 O5
SHZGCJCMOBCMKK-KGJVWPDLSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
E [auth A], F [auth A], I [auth B], J [auth B], M [auth C], N [auth C], Q [auth D], R [auth D]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-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 
  • R-Value Observed: 0.136 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.089α = 90
b = 65.52β = 90
c = 109.173γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-20
    Type: Initial release
  • Version 1.1: 2018-03-14
    Changes: Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary