6EOL | pdb_00006eol

Human galectin-3c in complex with a galactose derivative

• PDB DOI: https://doi.org/10.2210/pdb6EOL/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-10-09 Released: 2018-08-22 
• Deposition Author(s): Hakansson, M., Nilsson, U.J., Zetterberg, F., Logan, D.T.
• Funding Organization(s): Swedish Research Council, Knut and Alice Wallenberg Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.218 (Depositor), 0.215 (DCC) 
• R-Value Work: 
  0.170 (Depositor), 0.173 (DCC) 
• R-Value Observed: 
  0.172 (Depositor) 

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

• PubMed: 29194992 
• DOI: https://doi.org/10.1002/cmdc.201700744
• Primary Citation 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.

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Organizational Affiliation: 
• Galecto Biotech AB, Sahlgrenska Science Park, Medicinaregatan 8A, 413 46, Gothenburg, Sweden.
Centre for Analysis and Synthesis, Department of Chemistry, Lund University, Box 124, 221 00, Lund, Sweden.
Red Glead Discovery AB, Medicon Village, 223 63, Lund, Sweden.
SARomics Biostructures AB, Medicon Village, 223 63, Lund, Sweden.
Biochemistry and Structural Biology, Center for Molecular Protein Science, Department of Chemistry, Lund University, Box 124, 221 00, Lund, Sweden.
Department of Laboratory Medicine, Section MIG, Lund University BMC-C1228b, Klinikgatan 28, 221 84, Lund, Sweden.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 16.37 kDa 
• Atom Count: 1,538 
• Modeled Residue Count: 138 
• Deposited Residue Count: 138 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Galectin-3	A	138	Homo sapiens	Mutation(s): 0  Gene Names: LGALS3, MAC2
UniProt & NIH Common Fund Data Resources
Find proteins for P17931 (Homo sapiens) Explore P17931  Go to UniProtKB:  P17931
PHAROS:  P17931 GTEx:  ENSG00000131981

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BKH	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	B [auth A], C [auth A]	THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.218 (Depositor), 0.215 (DCC) 
• R-Value Work:  0.170 (Depositor), 0.173 (DCC) 
• R-Value Observed: 0.172 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.152	α = 90
b = 58.26	β = 90
c = 62.797	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
XSCALE	data scaling
REFMAC	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-08-22 
Deposition Author(s): Hakansson, M., Nilsson, U.J., Zetterberg, F., Logan, D.T.

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Funding Organization	Location	Grant Number
Swedish Research Council	Sweden	621-2012-2978
Knut and Alice Wallenberg Foundation	Sweden	2013.0022

Revision History  

• Version 1.0: 2018-08-22
  Type: Initial release
  
• Version 1.1: 2019-10-16
  Changes: Data collection
• Version 1.2: 2024-05-08
  Changes: Data collection, Database references