9H0Q | pdb_00009h0q

N terminal domain of BC2L-C lectin in complex with N-(beta-L-Fucopyranosyl)-biphenyl-3-carboxamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 
    0.222 (Depositor), 0.227 (DCC) 
  • R-Value Work: 
    0.179 (Depositor), 0.186 (DCC) 

Starting Models: experimental
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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 of 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lectin
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J
134Burkholderia cenocepacia J2315Mutation(s): 0 
Gene Names: BCAM0185
UniProt
Find proteins for B4EH86 (Burkholderia cenocepacia (strain ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610))
Explore B4EH86 
Go to UniProtKB:  B4EH86
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB4EH86
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MJO (Subject of Investigation/LOI)
Query on MJO

Download Ideal Coordinates CCD File 
AA [auth J]
K [auth A]
N [auth B]
P [auth C]
R [auth D]
AA [auth J],
K [auth A],
N [auth B],
P [auth C],
R [auth D],
S [auth E],
U [auth F],
W [auth G],
Y [auth H],
Z [auth I]
N-(beta-L-Fucopyranosyl)-biphenyl-3-carboxamide
C19 H21 N O5
KFRIUGARMXQWFO-QFFBLRJASA-N
1PE
Query on 1PE

Download Ideal Coordinates CCD File 
O [auth B]PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
PG4
Query on PG4

Download Ideal Coordinates CCD File 
BA [auth J]
L [auth A]
M [auth A]
Q [auth C]
T [auth E]
BA [auth J],
L [auth A],
M [auth A],
Q [auth C],
T [auth E],
V [auth F],
X [auth G]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free:  0.222 (Depositor), 0.227 (DCC) 
  • R-Value Work:  0.179 (Depositor), 0.186 (DCC) 
Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 169.506α = 90
b = 169.506β = 90
c = 344.036γ = 120
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