7CXD

Xray structure of rat Galectin-3 CRD in complex with TD-139 belonging to P121 space group


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.227 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Molecular mechanism of interspecies differences in the binding affinity of TD139 to Galectin-3.

Kumar, A.Paul, M.Panda, M.Jayaram, S.Kalidindi, N.Sale, H.Vetrichelvan, M.Gupta, A.Mathur, A.Beno, B.Regueiro-Ren, A.Cheng, D.Ramarao, M.Ghosh, K.

(2021) Glycobiology 31: 1390-1400

  • DOI: https://doi.org/10.1093/glycob/cwab072
  • Primary Citation of Related Structures:  
    7CXA, 7CXB, 7CXC, 7CXD

  • PubMed Abstract: 

    Galectin-3 (Gal-3), a β-galactoside-binding lectin, has been implicated in a plethora of pathological disorders including fibrosis, inflammation, cancer and metabolic diseases. TD139-a thio-digalactoside inhibitor developed by Galecto Biotech as a potential therapeutic for idiopathic pulmonary fibrosis-is the most advanced small-molecule Gal-3 inhibitor in clinical studies. It binds to human Gal-3 with high affinity but has lower affinity towards mouse and rat homologs, which is also manifested in the differential inhibition of Gal-3 function. Using biophysical methods and high-resolution X-ray co-crystal structures of TD139 and Gal-3 proteins, we demonstrate that a single amino acid change corresponding to A146 in human Gal-3 is sufficient for the observed reduction in the binding affinity of TD139 in rodents. Site-directed mutagenesis of A146V (in human Gal-3) and V160A (in mouse Gal-3) was sufficient to interchange the affinities, mainly by affecting the off rates of the inhibitor binding. In addition, molecular dynamics simulations of both wild-type and mutant structures revealed the sustained favorable noncovalent interactions between the fluorophenyl ring and the active site A146 (human Gal-3 and mouse V160A) that corroborate the finding from biophysical studies. Current findings have ramifications in the context of optimization of drug candidates against Gal-3.


  • Organizational Affiliation

    Discovery Biology and Translational Medicine, Biocon Bristol-Myers Squibb R&D Center, Bristol-Myers Squibb India Pvt. Ltd, Bangalore 560099, India.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Galectin-3A,
B,
C [auth D],
D [auth E]
146Rattus norvegicusMutation(s): 0 
Gene Names: Lgals3
UniProt
Find proteins for P08699 (Rattus norvegicus)
Explore P08699 
Go to UniProtKB:  P08699
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08699
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TD2 (Subject of Investigation/LOI)
Query on TD2

Download Ideal Coordinates CCD File 
F [auth A],
H [auth B],
K [auth D],
M [auth E]
3-deoxy-3-[4-(3-fluorophenyl)-1H-1,2,3-triazol-1-yl]-beta-D-galactopyranosyl 3-deoxy-3-[4-(3-fluorophenyl)-1H-1,2,3-triazol-1-yl]-1-thio-beta-D-galactopyranoside
C28 H30 F2 N6 O8 S
YGIDGBAHDZEYMT-MQFIMZJJSA-N
BR
Query on BR

Download Ideal Coordinates CCD File 
E [auth A],
G [auth B],
I [auth D],
J [auth D],
L [auth E]
BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
Binding Affinity Annotations 
IDSourceBinding Affinity
TD2 BindingDB:  7CXD IC50: min: 67, max: 300 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.227 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.241α = 90
b = 58.712β = 113.85
c = 70.773γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2021-09-01 
  • Deposition Author(s): Kumar, A.

Revision History  (Full details and data files)

  • Version 1.0: 2021-09-01
    Type: Initial release
  • Version 1.1: 2022-02-16
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description