6I74

Galectin-3C in complex with substituted polyfluoroaryl monothiogalactoside derivative 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.959 Å
  • R-Value Free: 0.147 
  • R-Value Work: 0.132 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Substituted polyfluoroaryl interactions with an arginine side chain in galectin-3 are governed by steric-, desolvation and electronic conjugation effects.

Kumar, R.Peterson, K.Misini Ignjatovic, M.Leffler, H.Ryde, U.Nilsson, U.J.Logan, D.T.

(2019) Org. Biomol. Chem. 17: 1081-1089

  • DOI: 10.1039/c8ob02888e
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • In the β-d-galactopyranoside-binding protein galectin-3, synthetic inhibitors substituted at the 3-position of a thiodigalactoside core cause the formation of an aglycone binding pocket through the displacement of an arginine residue (Arg144) from it ...

    In the β-d-galactopyranoside-binding protein galectin-3, synthetic inhibitors substituted at the 3-position of a thiodigalactoside core cause the formation of an aglycone binding pocket through the displacement of an arginine residue (Arg144) from its position in the apoprotein. To examine in detail the role of different molecular interactions in this pocket, we have synthesized a series of nine 3-(4-(2,3,5,6-tetrafluorophenyl)-1,2,3-triazol-1-yl)-thiogalactosides with different para substituents and measured their affinities to galectin-3 using a fluorescence polarization assay. High-resolution crystal structures (<1.3 Å) have been determined for five of the ligands in complex with the C-terminal domain of galectin-3. The binding affinities are rationalised with the help of the three-dimensional structures and quantum-mechanical calculations. Three effects seem to be involved: Firstly, the binding pocket is too small for the largest ligands with ethyl and methyl. Secondly, for the other ligands, the affinity seems to be determined mainly by desolvation effects, disfavouring the polar substituents, but this is partly counteracted by the cation-π interaction with Arg144, which stacks on top of the substituted tetrafluorophenyl group in all complexes. The results provide detailed insight into interactions of fluorinated phenyl moieties with arginine-containing protein binding sites and the complex interplay of different energetic components in defining the binding affinity.


    Organizational Affiliation

    Biochemistry and Structural Biology, Centre for Molecular Protein Science, Department of Chemistry, Lund University, Box 124, SE-221 00 Lund, Sweden. derek.logan@biochemistry.lu.se.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Galectin-3
A
138Homo 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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
H5Z
Query on H5Z

Download SDF File 
Download CCD File 
A
(2~{R},3~{R},4~{S},5~{R},6~{S})-2-(hydroxymethyl)-6-(4-methylphenyl)sulfanyl-4-[4-[2,3,4,5,6-pentakis(fluoranyl)phenyl]-1,2,3-triazol-1-yl]oxane-3,5-diol
C21 H18 F5 N3 O4 S
ZXTKEPHLSBIIAZ-WZZIOWGKSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.959 Å
  • R-Value Free: 0.147 
  • R-Value Work: 0.132 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 36.654α = 90.00
b = 57.781β = 90.00
c = 62.755γ = 90.00
Software Package:
Software NamePurpose
PHENIXphasing
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Knut and Alice Wallenberg FoundationSwedenKAW 2013.0022

Revision History 

  • Version 1.0: 2019-01-23
    Type: Initial release
  • Version 1.1: 2019-02-13
    Type: Data collection, Database references