4JCK

Galectin-3 carbohydrate recognition domain in complex with thioditaloside


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.138 
  • R-Value Observed: 0.139 

wwPDB Validation   3D Report Full Report


This is version 3.0 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:  
    4JCK, 4JC1

  • 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 ...

    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Galectin-3A143Homo sapiensMutation(s): 0 
Gene Names: LGALS3MAC2
Find proteins for P17931 (Homo sapiens)
Explore P17931 
Go to UniProtKB:  P17931
NIH Common Fund Data Resources
PHAROS:  P17931
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
beta-D-talopyranose-(1-1)-1-thio-beta-D-talopyranoseB [auth C]2 N/A N/A Oligosaccharides Interaction
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download Ideal Coordinates CCD File 
C [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
1LLKd :  4300000   nM  PDBBind
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900109
Query on PRD_900109
B [auth C]thioditalosideOligosaccharide /  Inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.138 
  • R-Value Observed: 0.139 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.78α = 90
b = 57.855β = 90
c = 62.65γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
AMoREphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



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