9G3K | pdb_00009g3k

LecB from PA01 in complex with synthetic beta - fucosylamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 
    0.168 (Depositor), 0.168 (DCC) 
  • R-Value Work: 
    0.137 (Depositor), 0.137 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9G3K

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Toward Dual-Target Glycomimetics against Two Bacterial Lectins to Fight Pseudomonas aeruginosa - Burkholderia cenocepacia Infections: A Biophysical Study.

Antonini, G.Fares, M.Hauck, D.Mala, P.Gillon, E.Belvisi, L.Bernardi, A.Titz, A.Varrot, A.Mazzotta, S.

(2025) J Med Chem 68: 9681-9693

  • DOI: https://doi.org/10.1021/acs.jmedchem.5c00405
  • Primary Citation Related Structures: 
    9G3K, 9G3L, 9H0Q

  • PubMed Abstract: 

    Chronic lung infections caused by Pseudomonas aeruginosa and Burkholderia cenocepacia pose a severe threat to immunocompromised patients, particularly those with cystic fibrosis. These pathogens often infect the respiratory tract, and available treatments are limited due to antibiotic resistance. Targeting bacterial lectins involved in biofilm formation and host-pathogen interactions represents a promising therapeutic strategy. In this study, we evaluate the potential of synthetic fucosylamides as inhibitors of the two lectins LecB ( P. aeruginosa ) and BC2L-C-Nt ( B. cenocepacia ). Using a suite of biophysical assays, we assessed their binding affinities, identifying three β-fucosylamides as promising dual-target ligands, while crystallography studies revealed the atomic basis of these ligands to interact with both bacterial lectins. The emerged classes of compounds represent a solid starting point for the necessary hit-to-lead optimization for future dual inhibitors aiming at the treatment of coinfections with these two bacterial pathogens.


  • Organizational Affiliation
    • Dipartimento di Chimica, Università degli Studi di Milano, Via Golgi 19, 20133 Milan, Italy.

Macromolecule Content 

  • Total Structure Weight: 48.1 kDa 
  • Atom Count: 4,035 
  • Modeled Residue Count: 456 
  • Deposited Residue Count: 456 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Fucose-binding lectin PA-IIL
A, B, C, D
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
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
R7E
(Subject of Investigation/LOI)

Query on R7E



Download:Ideal Coordinates CCD File
Q [auth D]5-[3-(aminomethyl)phenyl]-~{N}-[(2~{S},3~{S},4~{R},5~{S},6~{S})-6-methyl-3,4,5-tris(oxidanyl)oxan-2-yl]furan-2-carboxamide
C18 H22 N2 O6
NOVNWDXRBIJEJE-GUJIERIFSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
G [auth A],
J [auth B],
M [auth C],
N [auth C],
R [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CA
(Subject of Investigation/LOI)

Query on CA



Download:Ideal Coordinates CCD File
E [auth A]
F [auth A]
H [auth B]
I [auth B]
K [auth C]
E [auth A],
F [auth A],
H [auth B],
I [auth B],
K [auth C],
L [auth C],
O [auth D],
P [auth D]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free:  0.168 (Depositor), 0.168 (DCC) 
  • R-Value Work:  0.137 (Depositor), 0.137 (DCC) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.351α = 90
b = 80.166β = 109.361
c = 52.406γ = 90
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
European Union (EU)European Union765581

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-16
    Type: Initial release
  • Version 1.1: 2025-05-07
    Changes: Database references
  • Version 1.2: 2025-05-21
    Changes: Database references