Skip to main content

 9S62 | pdb_00009s62

Galectin-3 in complex with N-[4-O-(beta-d-Galactopyranosyl)-beta-d-glucopyranosyl]-N-(3-carboxyphenyl)acetamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.06 Å
  • R-Value Free: 
    0.167 (Depositor), 0.175 (DCC) 
  • R-Value Work: 
    0.151 (Depositor), 0.163 (DCC) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 9S62

Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history. 

Literature

N -Aryl- N -Lactosylamides as Potent and Highly Selective Inhibitors of Galectin-3 with Antifibrotic Activity.

Zyka, J., Kozak, J., Vanekova, L., Pimkova Polidarova, M., Prouza, V., Habanova, N., Strmen, T., Zavrel, M., Pachl, P., Choutka, J., Grantz Saskova, K., Brazdova, A., Parkan, K., Pohl, R.

(2025) J Med Chem 68: 24624-24648

  • DOI: https://doi.org/10.1021/acs.jmedchem.5c02604
  • Primary Citation Related Structures: 
    9S62

  • PubMed Abstract: 

    Galectin-3 (Gal-3) is a galactose-binding lectin involved in pathologies such as inflammation, fibrosis, heart disease, and tumor progression. Here, we report N -aryl- N -(thio)lactosylamides as a novel class of Gal-3 inhibitors. A structure-activity study identified 6-carboxyindol-4-yl amide as a key pharmacophoric motif within this series. The most potent inhibitor based on this motif, compound 11 , binds to Gal-3 with excellent affinity ( K d = 5.7 nM) and selectivity (390-fold over Gal-1). Further in vitro characterization of this compound demonstrated high metabolic stability and no cytotoxicity (CC 50 > 300 μM). Compound 11 effectively engages Gal-3 with greater activity in macrophage-like than monocyte-like THP1 cells, without affecting inflammation via LPS-induced release of TNFα. In TGFβ-stimulated LX2 hepatic stellate cells, it downregulates profibrotic signaling as assessed by the reduced expression of ACTA2 , COL1A2 , and FN1 . These findings implicate compound 11 as a promising candidate for further preclinical development in the context of fibrotic disease.


  • Organizational Affiliation: 
    • Gilead Sciences & IOCB Research Centre, Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 166 10 Prague, Czech Republic.

Macromolecule Content 

  • Total Structure Weight: 16.34 kDa 
  • Atom Count: 1,503 
  • Modeled Residue Count: 138 
  • Deposited Residue Count: 139 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Galectin-3139Homo sapiensMutation(s): 0 
Gene Names: LGALS3, MAC2
UniProt & NIH Common Fund Data Resources
Find proteins for P17931 (Homo sapiens)
Explore P17931 
Go to UniProtKB:  P17931
PHAROS:  P17931
GTEx:  ENSG00000131981 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17931
Sequence Annotations
Expand
Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-galactopyranose-(1-4)-1,5-anhydro-D-glucitolB [auth L]2N/A
Glycosylation Resources
GlyTouCan: G33271AU
GlyCosmos: G33271AU

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1JL1
(Subject of Investigation/LOI)

Query on A1JL1



Download:Ideal Coordinates CCD File
C [auth A]3-acetamidobenzoic acid
C9 H9 N O3
RGDPZMQZWZMONQ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.06 Å
  • R-Value Free:  0.167 (Depositor), 0.175 (DCC) 
  • R-Value Work:  0.151 (Depositor), 0.163 (DCC) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.824α = 90
b = 58.073β = 90
c = 63.383γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data

  • Released Date: 2025-11-19 
  • Deposition Author(s): Pachl, P.

Funding OrganizationLocationGrant Number
Ministry of Education (MoE, Czech Republic)Czech RepublicLX22NPO5103

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-19
    Type: Initial release
  • Version 1.1: 2025-12-10
    Changes: Database references