6EOG

Human galectin-3c in complex with a galactose derivative

• PDB DOI: https://doi.org/10.2210/pdb6EOG/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: 1.20 Å
• R-Value Free: 0.146 
• R-Value Work: 0.112 
• R-Value Observed: 0.114 

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 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.

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Organizational Affiliation: 

Galecto Biotech AB, Sahlgrenska Science Park, Medicinaregatan 8A, 413 46, Gothenburg, 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: 16.42 kDa 
• Atom Count: 1,674 
• Modelled 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BKK	B [auth A]	(2~{S},3~{R},4~{S},5~{R},6~{R})-2-(3-chlorophenyl)sulfanyl-6-(hydroxymethyl)-4-[4-[3,4,5-tris(fluoranyl)phenyl]-1,2,3-triazol-1-yl]oxane-3,5-diol C20 H17 Cl F3 N3 O4 S MJHCQQXAUYYTBY-ZKIDJSGLSA-N
SCN	G [auth A]	THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M
CL	C [auth A], D [auth A], E [auth A], F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
BKK	Binding MOAD:  6EOG	Kd: 1600 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 0.146 
• R-Value Work: 0.112 
• R-Value Observed: 0.114 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.08	α = 90
b = 58.44	β = 90
c = 62.99	γ = 90

Software Package:

Software Name	Purpose
REFMAC	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