9FDC | pdb_00009fdc

Co-crystal structure of Galectin-3 with an inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 
    0.244 (Depositor), 0.201 (DCC) 
  • R-Value Work: 
    0.200 (Depositor), 0.191 (DCC) 
  • R-Value Observed: 
    0.202 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Discovery of Galactopyranose-1-carboxamides as a New Class of Small, Novel, Potent, Selective, and Orally Active Galectin-3 Inhibitors.

Zumbrunn, C.Remen, L.Sager, C.P.Grisostomi, C.Stamm, C.Krusi, D.Glutz, S.Schmidt, G.Nayler, O.Iglarz, M.Mac Sweeney, A.Chambovey, A.Muller, M.Mueller, C.Bourquin, G.Meyer, S.Huhn, E.Cattaneo, C.Vercauteren, M.Gatfield, J.Bolli, M.H.

(2025) ChemMedChem 20: e202401012-e202401012

  • DOI: https://doi.org/10.1002/cmdc.202401012
  • Primary Citation of Related Structures:  
    8RMT, 8RMU, 8RMV, 9FDB, 9FDC

  • PubMed Abstract: 

    Galectin-3 (Gal-3), a β-galactoside-binding lectin, is implicated in diverse cellular functions ranging from immune response modulation to tissue homeostasis. Notably, increased Gal-3 expression has been linked to the progression of numerous diseases, including cancer, fibrosis, and cardiovascular disorders, underscoring its potential as a therapeutic target. Small molecule inhibitors have been discovered and are valuable tools to study such diseases. We report here the discovery of novel, galactose-based, small molecule inhibitors such as compound 12 which are orally bioavailable and show efficacy in a mouse model of acute liver injury and fibrosis (CCl 4 model). The use of structure-based drug design (docking of a virtual library of amides based on acid 2) was key in the process towards potent, nanomolar inhibitors.


  • Organizational Affiliation
    • Idorsia Pharmaceuticals Ltd., Hegenheimermattweg 91, CH-4123, Allschwil, Switzerland.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Galectin-3138Homo 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
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1IB4 (Subject of Investigation/LOI)
Query on A1IB4

Download Ideal Coordinates CCD File 
C [auth A](2~{R},3~{R},4~{S},5~{R},6~{R})-~{N}-[3,5-bis(chloranyl)phenyl]-6-(hydroxymethyl)-~{N}-methyl-3,5-bis(oxidanyl)-4-[4-[3,4,5-tris(fluoranyl)phenyl]-1,2,3-triazol-1-yl]oxane-2-carboxamide
C22 H19 Cl2 F3 N4 O5
SEOMSSBVKBAYLW-OBJCFNGXSA-N
2PE
Query on 2PE

Download Ideal Coordinates CCD File 
B [auth A]NONAETHYLENE GLYCOL
C18 H38 O10
YZUUTMGDONTGTN-UHFFFAOYSA-N
SCN
Query on SCN

Download Ideal Coordinates CCD File 
D [auth A]THIOCYANATE ION
C N S
ZMZDMBWJUHKJPS-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free:  0.244 (Depositor), 0.201 (DCC) 
  • R-Value Work:  0.200 (Depositor), 0.191 (DCC) 
  • R-Value Observed: 0.202 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.59α = 90
b = 57.651β = 90
c = 63.338γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-26
    Type: Initial release
  • Version 1.1: 2025-05-28
    Changes: Database references
  • Version 1.2: 2025-06-04
    Changes: Database references