8AIJ

STRUCTURE OF THE LECB LECTIN FROM PSEUDOMONAS AERUGINOSA STRAIN PAO1 IN COMPLEX WITH N-(alpha-L-Fucopyranosyl)benzamide (6)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.138 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Discovery of N -beta-l-Fucosyl Amides as High-Affinity Ligands for the Pseudomonas aeruginosa Lectin LecB.

Mala, P.Siebs, E.Meiers, J.Rox, K.Varrot, A.Imberty, A.Titz, A.

(2022) J Med Chem 65: 14180-14200

  • DOI: https://doi.org/10.1021/acs.jmedchem.2c01373
  • Primary Citation of Related Structures:  
    8AIJ, 8AIY

  • PubMed Abstract: 

    The Gram-negative pathogen Pseudomonas aeruginosa causes severe infections mainly in immunocompromised or cystic fibrosis patients and is able to resist antimicrobial treatments. The extracellular lectin LecB plays a key role in bacterial adhesion to the host and biofilm formation. For the inhibition of LecB, we designed and synthesized a set of fucosyl amides, sulfonamides, and thiourea derivatives. Then, we analyzed their binding to LecB in competitive and direct binding assays. We identified β-fucosyl amides as unprecedented high-affinity ligands in the two-digit nanomolar range. X-ray crystallography of one α- and one β-anomer of N -fucosyl amides in complex with LecB revealed the interactions responsible for the high affinity of the β-anomer at atomic level. Further, the molecules showed good stability in murine and human blood plasma and hepatic metabolism, providing a basis for future development into antibacterial drugs.


  • Organizational Affiliation

    Chemical Biology of Carbohydrates (CBCH), Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, 66123Saarbrücken, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fucose-binding lectin PA-IILA [auth AAA],
B [auth BBB],
C [auth CCC],
D [auth DDD]
114Pseudomonas aeruginosa PAO1Mutation(s): 0 
Gene Names: lecBPA3361
UniProt
Find proteins for Q9HYN5 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9HYN5 
Go to UniProtKB:  Q9HYN5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9HYN5
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
M9I (Subject of Investigation/LOI)
Query on M9I

Download Ideal Coordinates CCD File 
G [auth AAA],
M [auth BBB],
Q [auth CCC],
T [auth DDD]
N-(alpha-L-Fucopyranosyl)benzamide
C13 H17 N O5
ZYWNMRPOYLXAAW-HTUCIKCGSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
H [auth AAA],
I [auth AAA],
J [auth AAA],
N [auth BBB]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
E [auth AAA]
F [auth AAA]
K [auth BBB]
L [auth BBB]
O [auth CCC]
E [auth AAA],
F [auth AAA],
K [auth BBB],
L [auth BBB],
O [auth CCC],
P [auth CCC],
R [auth DDD],
S [auth DDD]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.138 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.376α = 101.809
b = 51.589β = 99.474
c = 52.604γ = 115.811
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Agence Nationale de la Recherche (ANR)FranceANR-17-CE11-0048

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-02
    Type: Initial release
  • Version 1.1: 2022-11-09
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description