4A6S

Structure of the PAIL lectin from Pseudomonas aeruginosa in complex with 2-Naphtyl-1-thio-beta-D-galactopyranoside


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Aromatic Thioglycoside Inhibitors Against the Virulence Factor Leca from Pseudomonas Aeruginosa.

Rodrigue, J.Ganne, G.Blanchard, B.Saucier, C.Giguere, D.Shiao, T.C.Varrot, A.Imberty, A.Roy, R.

(2013) Org Biomol Chem 11: 6906

  • DOI: 10.1039/c3ob41422a
  • Primary Citation of Related Structures:  
    4A6S

  • PubMed Abstract: 
  • Three small families of hydrolytically stable thioaryl glycosides were prepared as inhibitors of the LecA (PA-IL) virulence factor corresponding to the carbohydrate binding lectin from the bacterial pathogen Pseudomonas aeruginosa. The monosaccharidic arylthio β-d-galactopyranosides served as a common template for the major series that was also substituted at the O-3 position ...

    Three small families of hydrolytically stable thioaryl glycosides were prepared as inhibitors of the LecA (PA-IL) virulence factor corresponding to the carbohydrate binding lectin from the bacterial pathogen Pseudomonas aeruginosa. The monosaccharidic arylthio β-d-galactopyranosides served as a common template for the major series that was also substituted at the O-3 position. Arylthio disaccharides from lactose and from melibiose constituted the other two series members. In spite of the fact that the natural ligand for LecA is a glycolipid of the globotriaosylceramide having an α-d-galactopyranoside epitope, this study illustrated that the β-d-galactopyranoside configuration having a hydrophobic aglycon could override the requirement toward the anomeric configuration of the natural sugar. The enzyme linked lectin assay together with isothermal titration microcalorimetry established that naphthyl 1-thio-β-d-galactopyranoside () gave the best inhibition with an IC50 twenty-three times better than that of the reference methyl α-d-galactopyranoside. In addition it showed a KD of 6.3 μM which was ten times better than that of the reference compound. The X-ray crystal structure of LecA with was also obtained.


    Organizational Affiliation

    PharmaQAM - Department of Chemistry, Université du Québec à Montréal, P.O. Box 8888, Succ. Centre-ville, Montréal, Québec, Canada H3C 3P8. roy.rene@uqam.ca.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PA-I GALACTOPHILIC LECTINABCD121Pseudomonas aeruginosa PAO1Mutation(s): 0 
Gene Names: lecApa1LPA2570
Find proteins for Q05097 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q05097 
Go to UniProtKB:  Q05097
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GS9
Query on GS9

Download CCD File 
A, B, C, D
naphthalen-2-yl 1-thio-beta-D-galactopyranoside
C16 H18 O5 S
UTPJJZURVZIAID-CWVYHPPDSA-N
 Ligand Interaction
CA
Query on CA

Download CCD File 
A, B, C, D
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
GS9Kd :  6300   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.217 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.334α = 90
b = 54.334β = 90
c = 390.501γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-10-17
    Type: Initial release
  • Version 1.1: 2012-11-14
    Changes: Atomic model, Other
  • Version 1.2: 2013-10-02
    Changes: Database references
  • Version 1.3: 2013-10-09
    Changes: Database references
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Derived calculations, Other, Structure summary