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
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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 of 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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Galectin-3139Homo sapiensMutation(s): 0 
Gene Names: LGALS3MAC2
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
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D 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

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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