8RMV | pdb_00008rmv

Galectin-3 with a bound inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 
    0.183 (Depositor), 0.187 (DCC) 
  • R-Value Work: 
    0.158 (Depositor), 0.171 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8RMV

Ligand Structure Quality Assessment 


This is version 1.3 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 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.

Macromolecule Content 

  • Total Structure Weight: 16.51 kDa 
  • Atom Count: 1,282 
  • Modeled Residue Count: 137 
  • 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: 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

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1H1X
(Subject of Investigation/LOI)

Query on A1H1X



Download:Ideal Coordinates CCD File
B [auth A](2~{R},3~{R},4~{S},5~{R},6~{R})-~{N}-[3,5-bis(chloranyl)phenyl]-6-(hydroxymethyl)-3-methoxy-5-oxidanyl-~{N}-[(1~{S},2~{S})-2-oxidanylcyclobutyl]-4-[4-[3,4,5-tris(fluoranyl)phenyl]-1,2,3-triazol-1-yl]oxane-2-carboxamide
C26 H25 Cl2 F3 N4 O6
ADYGFYLMWYMRNG-GRVGWMENSA-N
SCN

Query on SCN



Download:Ideal Coordinates CCD File
C [auth A]THIOCYANATE ION
C N S
ZMZDMBWJUHKJPS-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free:  0.183 (Depositor), 0.187 (DCC) 
  • R-Value Work:  0.158 (Depositor), 0.171 (DCC) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 34.34α = 90
b = 57.66β = 90
c = 61.11γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



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: 2025-01-29
    Type: Initial release
  • Version 1.1: 2025-03-26
    Changes: Database references
  • Version 1.2: 2025-05-28
    Changes: Database references
  • Version 1.3: 2025-06-04
    Changes: Database references