6Q0Q

Crystal structure of Human galectin-3 CRD in complex with Methyl 3-O-(1-{3-O-[1-(b-D-galactopyranosyl)-1,2,3-triazol-4-yl]-methyl-b-D-galactopyranosyl}-1,2,3-triazol-4-yl)-methyl-b-D-galactopyranoside


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Linear triazole-linked pseudo oligogalactosides as scaffolds for galectin inhibitor development.

Dussouy, C.Kishor, C.Lambert, A.Lamoureux, C.Blanchard, H.Grandjean, C.

(2020) Chem Biol Drug Des 96: 1123-1133

  • DOI: https://doi.org/10.1111/cbdd.13683
  • Primary Citation of Related Structures:  
    6Q0Q, 6Q17

  • PubMed Abstract: 

    Galectins play key roles in numerous biological processes. Their mode of action depends on their localization which can be extracellular, cytoplasmic, or nuclear and is partly mediated through interactions with β-galactose containing glycans. Galectins have emerged as novel therapeutic targets notably for the treatment of inflammatory disorders and cancers. This has stimulated the design of carbohydrate-based inhibitors targeting the carbohydrate recognition domains (CRDs) of the galectins. Pursuing this approach, we reasoned that linear oligogalactosides obtained by straightforward iterative click chemistry could mimic poly-lactosamine motifs expressed at eukaryote cell surfaces which the extracellular form of galectin-3, a prominent member of the galectin family, specifically recognizes. Affinities toward galectin-3 consistently increased with the length of the representative oligogalactosides but without reaching that of oligo-lactosamines. Elucidation of the X-ray crystal structures of the galectin-3 CRD in complex with a synthesized di- and tri-galactoside confirmed that the compounds bind within the carbohydrate-binding site. The atomic structures revealed that binding interactions mainly occur with the galactose moiety at the non-reducing end, primarily with subsites C and D of the CRD, differing from oligo-lactosamine which bind more consistently across the whole groove formed by the five subsites (A-E) of the galectin-3 CRD.


  • Organizational Affiliation

    Unité Fonctionnalité et Ingénierie des Protéines (UFIP), CNRS, UMR 6286, Université de Nantes, Nantes, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Galectin-3139Homo 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
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
P8G (Subject of Investigation/LOI)
Query on P8G

Download Ideal Coordinates CCD File 
C [auth A](2~{R},3~{R},4~{S},5~{R},6~{R})-2-(hydroxymethyl)-6-[4-[[(2~{R},3~{S},4~{S},5~{R},6~{R})-2-(hydroxymethyl)-6-[4-[[(2~{R},3~{S},4~{S},5~{R},6~{R})-2-(hydroxymethyl)-6-methoxy-3,5-bis(oxidanyl)oxan-4-yl]oxymethyl]-1,2,3-triazol-1-yl]-3,5-bis(oxidanyl)oxan-4-yl]oxymethyl]-1,2,3-triazol-1-yl]oxane-3,4,5-triol
C25 H40 N6 O16
ZQXDLGAORGHMLS-LZGLEUEQSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
B [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.95α = 90
b = 57.86β = 90
c = 62.34γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentAustraliaCancer Council Queensland Grant ID180845

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-29
    Type: Initial release
  • Version 1.1: 2020-12-23
    Changes: Database references
  • Version 1.2: 2024-03-13
    Changes: Data collection, Database references