8OJO | pdb_00008ojo

Galectin-3 in complex with 2,6-Anhydro-5-S-(beta-D-galactopyranosyl)-5-thio-D-altritol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.176 (Depositor), 0.190 (DCC) 
  • R-Value Work: 
    0.136 (Depositor), 0.149 (DCC) 
  • R-Value Observed: 
    0.138 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 8OJO

Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Strong Binding of C -Glycosylic1,2-Thiodisaccharides to Galectin-3─Enthalpy-Driven Affinity Enhancement by Water-Mediated Hydrogen Bonds.

Lazar, L.Tsagkarakou, A.S.Stravodimos, G.Kontopidis, G.Leffler, H.Nilsson, U.J.Somsak, L.Leonidas, D.D.

(2023) J Med Chem 66: 12420-12431

  • DOI: https://doi.org/10.1021/acs.jmedchem.3c00882
  • Primary Citation Related Structures: 
    8OJI, 8OJK, 8OJM, 8OJO, 8PPN

  • PubMed Abstract: 

    Galectin-3 is involved in multiple pathways of many diseases, including cancer, fibrosis, and diabetes, and it is a validated pharmaceutical target for the development of novel therapeutic agents to address unmet medical needs. Novel 1,2-thiodisaccharides with a C -glycosylic functionality were synthesized by the photoinitiated thiol-ene click reaction of O -peracylated 1-C-substituted glycals and 1-thio-glycopyranoses. Subsequent global deprotection yielded test compounds, which were studied for their binding to human galectin-3 by fluorescence polarization and isothermal titration calorimetry to show low micromolar K d values. The best inhibitor displayed a K d value of 8.0 μM. An analysis of the thermodynamic binding parameters revealed that the binding Gibbs free energy (Δ G ) of the new inhibitors was dominated by enthalpy (Δ H ). The binding mode of the four most efficient 1,2-thiodisaccharides was also studied by X-ray crystallography that uncovered the unique role of water-mediated hydrogen bonds in conferring enthalpy-driven affinity enhancement for the new inhibitors. This 1,2-thiodisaccharide-type scaffold represents a new lead for galectin-3 inhibitor discovery and offers several possibilities for further development.


  • Organizational Affiliation
    • Department of Organic Chemistry, University of Debrecen, P.O. Box 400, H-4002 Debrecen, Hungary.

Macromolecule Content 

  • Total Structure Weight: 16.13 kDa 
  • Atom Count: 1,356 
  • Modeled Residue Count: 138 
  • Deposited Residue Count: 138 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.176 (Depositor), 0.190 (DCC) 
  • R-Value Work:  0.136 (Depositor), 0.149 (DCC) 
  • R-Value Observed: 0.138 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.92α = 90
b = 58.09β = 90
c = 62.48γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not fundedGreece--

Revision History  (Full details and data files)

  • Version 1.0: 2023-09-13
    Type: Initial release
  • Version 1.1: 2023-09-20
    Changes: Database references