4JC1

Galectin-3 carbohydrate recognition domain in complex with thiodigalactoside


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.149 
  • R-Value Work: 0.135 
  • R-Value Observed: 0.136 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 3.1 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: https://doi.org/10.1002/cbic.201300245
  • Primary Citation of Related Structures:  
    4JC1, 4JCK

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Galectin-3143Homo 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
Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-galactopyranose-(1-1)-1-thio-beta-D-galactopyranoseB [auth C]2N/AN/A
Glycosylation Resources
GlyTouCan:  G61532BD
GlyCosmos:  G61532BD
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.149 
  • R-Value Work: 0.135 
  • R-Value Observed: 0.136 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.788α = 90
b = 58.003β = 90
c = 63.378γ = 90
Software Package:
Software NamePurpose
PROTEUM PLUSdata collection
AMoREphasing
REFMACrefinement
SAINTdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-07-31
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 3.0: 2020-08-12
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 3.1: 2023-09-20
    Changes: Data collection, Database references, Refinement description