8BZ3

Structure od the carbohydrate reconition domain of Gal3 in comples with SAF-2-010


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.31 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.157 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Selectively Modified Lactose and N -Acetyllactosamine Analogs at Three Key Positions to Afford Effective Galectin-3 Ligands.

Abdullayev, S.Kadav, P.Bandyopadhyay, P.Medrano, F.J.Rabinovich, G.A.Dam, T.K.Romero, A.Roy, R.

(2023) Int J Mol Sci 24

  • DOI: https://doi.org/10.3390/ijms24043718
  • Primary Citation of Related Structures:  
    8BZ3

  • PubMed Abstract: 

    Galectins constitute a family of galactose-binding lectins overly expressed in the tumor microenvironment as well as in innate and adaptive immune cells, in inflammatory diseases. Lactose ((β-D-galactopyranosyl)-(1→4)-β-D-glucopyranose, Lac) and N -Acetyllactosamine (2-acetamido-2-deoxy-4- O -β-D-galactopyranosyl-D-glucopyranose, LacNAc) have been widely exploited as ligands for a wide range of galectins, sometimes with modest selectivity. Even though several chemical modifications at single positions of the sugar rings have been applied to these ligands, very few examples combined the simultaneous modifications at key positions known to increase both affinity and selectivity. We report herein combined modifications at the anomeric position, C-2, and O -3' of each of the two sugars, resulting in a 3'- O -sulfated LacNAc analog having a Kd of 14.7 µM against human Gal-3 as measured by isothermal titration calorimetry (ITC). This represents a six-fold increase in affinity when compared to methyl β-D-lactoside having a Kd of 91 µM. The three best compounds contained sulfate groups at the O -3' position of the galactoside moieties, which were perfectly in line with the observed highly cationic character of the human Gal-3 binding site shown by the co-crystal of one of the best candidates of the LacNAc series.


  • Organizational Affiliation

    Glycosciences and Nanomaterials Laboratory, Université du Québec à Montréal, Succ. Centre-Ville, P.O. Box 8888, Montréal, QC H3C 3P8, Canada.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Galectin-3145Homo 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
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SQR (Subject of Investigation/LOI)
Query on SQR

Download Ideal Coordinates CCD File 
B [auth A][(2~{S},3~{R},4~{S},5~{S},6~{R})-2-[(2~{R},3~{S},4~{R},5~{R},6~{S})-5-acetamido-2-(hydroxymethyl)-6-(4-nitrophenoxy)-4-oxidanyl-oxan-3-yl]oxy-6-(hydroxymethyl)-3,5-bis(oxidanyl)oxan-4-yl] hydrogen sulfate
C20 H28 N2 O16 S
RWBHCBGHSHJQOQ-MRHFAZSRSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.31 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.157 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.764α = 90
b = 57.983β = 90
c = 63.389γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentSpain--

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-01
    Type: Initial release
  • Version 1.1: 2023-03-08
    Changes: Database references
  • Version 1.2: 2024-06-19
    Changes: Data collection