4JC1

Galectin-3 carbohydrate recognition domain in complex with thiodigalactoside


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.149 
  • R-Value Work: 0.135 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Investigation into the feasibility of thioditaloside as a novel scaffold for galectin-3-specific inhibitors.

Bum-Erdene, K.Gagarinov, I.A.Collins, P.M.Winger, M.Pearson, A.G.Wilson, J.C.Leffler, H.Nilsson, U.J.Grice, I.D.Blanchard, H.

(2013) Chembiochem 14: 1331-1342

  • DOI: 10.1002/cbic.201300245
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Galectin-3 is extensively involved in metabolic and disease processes, such as cancer metastasis, thus giving impetus for the design of specific inhibitors targeting this β-galactose-binding protein. Thiodigalactoside (TDG) presents a scaffold for co ...

    Galectin-3 is extensively involved in metabolic and disease processes, such as cancer metastasis, thus giving impetus for the design of specific inhibitors targeting this β-galactose-binding protein. Thiodigalactoside (TDG) presents a scaffold for construction of galectin inhibitors, and its inhibition of galectin-1 has already demonstrated beneficial effects as an adjuvant with vaccine immunotherapy, thereby improving the survival outcome of tumour-challenged mice. A novel approach--replacing galactose with its C2 epimer, talose--offers an alternative framework, as extensions at C2 permit exploitation of a galectin-3-specific binding groove, thereby facilitating the design of selective inhibitors. We report the synthesis of thioditaloside (TDT) and crystal structures of the galectin-3 carbohydrate recognition domain in complexes with TDT and TDG. The different abilities of galactose and talose to anchor to the protein correlate with molecular dynamics studies, likely explaining the relative disaccharide binding affinities. The feasibility of a TDT scaffold to enable access to a particular galectin-3 binding groove and the need for modifications to optimise such a scaffold for use in the design of potent and selective inhibitors are assessed.


    Organizational Affiliation

    Institute for Glycomics, Gold Coast campus, Griffith University, Queensland 4222, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Galectin-3
A
143Homo sapiensMutation(s): 0 
Gene Names: LGALS3 (MAC2)
Find proteins for P17931 (Homo sapiens)
Go to Gene View: LGALS3
Go to UniProtKB:  P17931
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TDG
Query on TDG

Download SDF File 
Download CCD File 
A
THIODIGALACTOSIDE
C12 H22 O10 S
SYKYBMOFPMXDRQ-ZFDCCPEWSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
TDGKd: 43000 - 49000 nM (100) BINDINGDB
TDGKd: 50000 nM BINDINGMOAD
TDGKd: 50000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.149 
  • R-Value Work: 0.135 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 36.788α = 90.00
b = 58.003β = 90.00
c = 63.378γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PROTEUM PLUSdata collection
AMoREphasing
SAINTdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-07-31
    Type: Initial release