3ZDV

Crystal structure of the LecB lectin from Pseudomonas aeruginosa in complex with Methyl 6-(2,4,6-trimethylphenylsulfonylamido)-6-deoxy-alpha-D-mannopyranoside


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.41 Å
  • R-Value Free: 0.145 
  • R-Value Work: 0.115 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Discovery of Two Classes of Potent Glycomimetic Inhibitors of Pseudomonas Aeruginosa Lecb with Distinct Binding Modes.

Hauck, D.Joachim, I.Frommeyer, B.Varrot, A.Philipp, B.Moller, H.M.Imberty, A.Exner, T.E.Titz, A.

(2013) Acs Chem.Biol. 8: 1775

  • DOI: 10.1021/cb400371r

  • PubMed Abstract: 
  • The treatment of infections due to the opportunistic pathogen Pseudomonas aeruginosa is often difficult, as a consequence of bacterial biofilm formation. Such a protective environment shields the bacterium from host defense and antibiotic treatment a ...

    The treatment of infections due to the opportunistic pathogen Pseudomonas aeruginosa is often difficult, as a consequence of bacterial biofilm formation. Such a protective environment shields the bacterium from host defense and antibiotic treatment and secures its survival. One crucial factor for maintenance of the biofilm architecture is the carbohydrate-binding lectin LecB. Here, we report the identification of potent mannose-based LecB inhibitors from a screening of four series of mannosides in a novel competitive binding assay for LecB. Cinnamide and sulfonamide derivatives are inhibitors of bacterial adhesion with up to a 20-fold increase in affinity to LecB compared to the natural ligand methyl mannoside. Because many lectins of the host require terminal saccharides (e.g., fucosides), such capped structures as reported here may offer a beneficial selectivity profile for the pathogenic lectin. Both classes of compounds show distinct binding modes at the protein, offering the advantage of a simultaneous development of two new lead structures as anti-pseudomonadal drugs with an anti-virulence mode of action.


    Organizational Affiliation

    Department of Chemistry, University of Konstanz, D-78457 Konstanz, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
FUCOSE-BINDING LECTIN PA-IIL
A, B, C, D
115Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228)Gene Names: lecB
Find proteins for Q9HYN5 (Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228))
Go to UniProtKB:  Q9HYN5
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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Download CCD File 
D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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A, B, C, D
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

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Download CCD File 
B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MMA
Query on MMA

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Download CCD File 
A, B, C, D
O1-METHYL-MANNOSE
C7 H14 O6
HOVAGTYPODGVJG-VEIUFWFVSA-N
 Ligand Interaction
F1A
Query on F1A

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Download CCD File 
A, B, C, D
2,4,6-trimethylbenzenesulfonamide
C9 H13 N O2 S
YECJUZIGFPJWGQ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.41 Å
  • R-Value Free: 0.145 
  • R-Value Work: 0.115 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 50.530α = 90.00
b = 76.980β = 90.00
c = 99.660γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHASERphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-09-18
    Type: Initial release
  • Version 1.1: 2013-11-13
    Type: Other
  • Version 1.2: 2017-09-13
    Type: Data collection, Structure summary