6EOL

Human galectin-3c in complex with a galactose derivative


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.172 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Monosaccharide Derivatives with Low-Nanomolar Lectin Affinity and High Selectivity Based on Combined Fluorine-Amide, Phenyl-Arginine, Sulfur-pi , and Halogen Bond Interactions.

Zetterberg, F.R.Peterson, K.Johnsson, R.E.Brimert, T.Hakansson, M.Logan, D.T.Leffler, H.Nilsson, U.J.

(2018) ChemMedChem 13: 133-137

  • DOI: https://doi.org/10.1002/cmdc.201700744
  • Primary Citation of Related Structures:  
    6EOG, 6EOL

  • PubMed Abstract: 

    The design of small and high-affinity lectin inhibitors remains a major challenge because the natural ligand binding sites of lectin are often shallow and have polar character. Herein we report that derivatizing galactose with un-natural structural elements that form multiple non-natural lectin-ligand interactions (orthogonal multipolar fluorine-amide, phenyl-arginine, sulfur-π, and halogen bond) can provide inhibitors with extraordinary affinity (low nanomolar) for the model lectin, galectin-3, which is more than five orders of magnitude higher than the parent galactose; moreover, is selective over other galectins.


  • Organizational Affiliation

    Department of Laboratory Medicine, Section MIG, Lund University BMC-C1228b, Klinikgatan 28, 221 84, 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
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BKH
Query on BKH

Download Ideal Coordinates CCD File 
D [auth A](2~{R},3~{R},4~{S},5~{R},6~{R})-2-(3,4-dichlorophenyl)sulfanyl-6-(hydroxymethyl)-4-[4-[3,4,5-tris(fluoranyl)phenyl]-1,2,3-triazol-1-yl]oxane-3,5-diol
C20 H16 Cl2 F3 N3 O4 S
CSGJIUAIYDKFPC-DABHTEOTSA-N
SCN
Query on SCN

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
THIOCYANATE ION
C N S
ZMZDMBWJUHKJPS-UHFFFAOYSA-M
Binding Affinity Annotations 
IDSourceBinding Affinity
BKH Binding MOAD:  6EOL Kd: 37 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.172 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.152α = 90
b = 58.26β = 90
c = 62.797γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Research CouncilSweden621-2012-2978
Knut and Alice Wallenberg FoundationSweden2013.0022

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-22
    Type: Initial release
  • Version 1.1: 2019-10-16
    Changes: Data collection