5OAX | pdb_00005oax

Galectin-3c in complex with thiogalactoside derivate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 
    0.132 (Depositor), 0.130 (DCC) 
  • R-Value Work: 
    0.103 (Depositor), 0.100 (DCC) 
  • R-Value Observed: 
    0.104 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 9Q5Click on this verticalbar to view details

This is version 1.2 of the entry. See complete history


Literature

Systematic Tuning of Fluoro-galectin-3 Interactions Provides Thiodigalactoside Derivatives with Single-Digit nM Affinity and High Selectivity.

Peterson, K.Kumar, R.Stenstrom, O.Verma, P.Verma, P.R.Hakansson, M.Kahl-Knutsson, B.Zetterberg, F.Leffler, H.Akke, M.Logan, D.T.Nilsson, U.J.

(2018) J Med Chem 61: 1164-1175

  • DOI: https://doi.org/10.1021/acs.jmedchem.7b01626
  • Primary Citation of Related Structures:  
    5OAX, 5ODY

  • PubMed Abstract: 

    Symmetrical and asymmetrical fluorinated phenyltriazolyl-thiodigalactoside derivatives have been synthesized and evaluated as inhibitors of galectin-1 and galectin-3. Systematic tuning of the phenyltriazolyl-thiodigalactosides' fluoro-interactions with galectin-3 led to the discovery of inhibitors with exceptional affinities (K d down to 1-2 nM) in symmetrically substituted thiodigalactosides as well as unsurpassed combination of high affinity (K d 7.5 nM) and selectivity (46-fold) over galectin-1 for asymmetrical thiodigalactosides by carrying one trifluorphenyltriazole and one coumaryl moiety. Studies of the inhibitor-galectin complexes with isothermal titration calorimetry and X-ray crystallography revealed the importance of fluoro-amide interaction for affinity and for selectivity. Finally, the high affinity of the discovered inhibitors required two competitive titration assay tools to be developed: a new high affinity fluorescent probe for competitive fluorescent polarization and a competitive ligand optimal for analyzing high affinity galectin-3 inhibitors with competitive isothermal titration calorimetry.


  • Organizational Affiliation

    Centre for Analysis and Synthesis, Department of Chemistry, Lund University , Box 124, SE-221 00 Lund, Sweden.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Galectin-3138Homo 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
9Q5 (Subject of Investigation/LOI)
Query on 9Q5

Download Ideal Coordinates CCD File 
B [auth A]5,6-bis(fluoranyl)-3-[[(2~{S},3~{R},4~{S},5~{S},6~{R})-2-[(2~{S},3~{R},4~{S},5~{R},6~{R})-4-[4-(3-fluorophenyl)-1,2,3-triazol-1-yl]-6-(hydroxymethyl)-3,5-bis(oxidanyl)oxan-2-yl]sulfanyl-6-(hydroxymethyl)-3,5-bis(oxidanyl)oxan-4-yl]oxymethyl]chromen-2-one
C30 H30 F3 N3 O11 S
GCZYLGQPCXFNES-NFWFBJQFSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free:  0.132 (Depositor), 0.130 (DCC) 
  • R-Value Work:  0.103 (Depositor), 0.100 (DCC) 
  • R-Value Observed: 0.104 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.19α = 90
b = 58.15β = 90
c = 62.81γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 9Q5Click on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-02
    Type: Initial release
  • Version 1.1: 2019-10-16
    Changes: Data collection
  • Version 1.2: 2024-05-08
    Changes: Data collection, Database references