6QLO

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.18 Å
  • R-Value Free: 0.153 
  • R-Value Work: 0.133 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structure and energetics of ligand-fluorine interactions with galectin-3 backbone and side-chain amides - insight into solvation effects and multipolar interactions.

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

(2019) Chemmedchem --: --

  • DOI: 10.1002/cmdc.201900293
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Multipolar fluorine-amide interactions with backbone and side-chain amides have been described as important for protein-ligand interactions and have been used to improve the potency of synthetic inhibitors. In this study, fluorine interactions within ...

    Multipolar fluorine-amide interactions with backbone and side-chain amides have been described as important for protein-ligand interactions and have been used to improve the potency of synthetic inhibitors. In this study, fluorine interactions within a well-defined binding pocket on galectin-3 are investigated systematically using phenyltriazolyl-thiogalactosides fluorinated singly or multiply at different positions on the phenyl ring. X-ray structures of the C-terminal domain of galectin-3 in complex with eight of these ligands revealed potential orthogonal fluorine-amide interactions with backbone amides and one with a side-chain amide. The two interactions involving main chain amides seem to have a strong influence on affinity as determined by fluorescence anisotropy. In contrast, the interaction with the side-chain amide did not influence affinity. Quantum mechanics calculations were used to analyse the relative contributions of these interactions to the binding energies. No clear correlation could be found between the relative energies of the fluorine-main chain amide interactions and the overall binding energy. Instead, dispersion and desolvation effects play a larger role. The results confirm that the contribution of fluorine-amide interactions to protein-ligand interactions cannot simply be predicted, on geometrical considerations alone, but require careful consideration of the energetic components.


    Organizational Affiliation

    Lund University, Chemistry / Biochemistry & Structural Biology, Box 124, 221 00, Lund, SWEDEN.,Lund University, Laboratory Medicine, SWEDEN.,Lund University, Theoretical Chemistry, Box 124, 221 00, Lund, SWEDEN.,Lund University, Centre for Analysis and Synthesis, Box 124, 221 00, Lund, SWEDEN.,Lund University, Biochemistry & Structural Biology, Box 124, 221 00, Lund, SWEDEN.




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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
J5E
Query on J5E

Download SDF File 
Download CCD File 
A
(2~{R},3~{R},4~{S},5~{R},6~{S})-4-[4-[3,4-bis(fluoranyl)phenyl]-1,2,3-triazol-1-yl]-2-(hydroxymethyl)-6-(4-methylphenyl)sulfanyl-oxane-3,5-diol
C21 H21 F2 N3 O4 S
DWZCKGAEDMIIIZ-IFLJBQAJSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.18 Å
  • R-Value Free: 0.153 
  • R-Value Work: 0.133 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 36.392α = 90.00
b = 57.790β = 90.00
c = 62.858γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
XDSdata reduction
PHENIXphasing

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: 2019-07-10
    Type: Initial release