5EXO

Crystal structure of Human galectin-3 CRD in complex with methyl 2-O-acetyl-3-O-(2H-chromene-3-yl-methyl)-a-D-galactopyranoside inhibitor

• PDB DOI: https://doi.org/10.2210/pdb5EXO/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-11-23 Released: 2016-10-05 
• Deposition Author(s): Collins, P.M., Blanchard, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.193 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.157 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.159 (Depositor) 

Starting Model: experimental

Literature

A Selective Galactose-Coumarin-Derived Galectin-3 Inhibitor Demonstrates Involvement of Galectin-3-glycan Interactions in a Pulmonary Fibrosis Model.

Rajput, V.K., MacKinnon, A., Mandal, S., Collins, P., Blanchard, H., Leffler, H., Sethi, T., Schambye, H., Mukhopadhyay, B., Nilsson, U.J.

(2016) J Med Chem 59: 8141-8147

• PubMed: 27500311 
• DOI: https://doi.org/10.1021/acs.jmedchem.6b00957
• Primary Citation of Related Structures:  
  5EXO


• PubMed Abstract: 
  

  Synthesis of doubly 3-O-coumarylmethyl-substituted thiodigalactosides from bis-3-O-propargyl-thiodigalactoside resulted in highly selective and high affinity galectin-3 inhibitors. Mutant studies, structural analysis, and molecular modeling revealed that the coumaryl substituents stack onto arginine side chains. One inhibitor displayed efficacy in a murine model of bleomycin-induced lung fibrosis similar to that of a known nonselective galectin-1/galectin-3 inhibitor, which strongly suggests that blocking galectin-3 glycan recognition is an important antifibrotic drug target.

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Organizational Affiliation: 

Indian Institute of Science Education and Research-Kolkata (IISER) Kolkata , Mohanpur Campus, P.O. BCKV Campus Main Office, Mohanpur, Nadia 741246, India.

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: 16.19 kDa 
• Atom Count: 1,339 
• Modelled Residue Count: 137 
• Deposited Residue Count: 139 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Galectin-3	A	139	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
5SY	C [auth A]	[(2~{S},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-2-methoxy-5-oxidanyl-4-[(2-oxidanylidenechromen-3-yl)methoxy]oxan-3-yl] ethanoate C19 H22 O9 CHNUXPKWFBMLRQ-RDHIYWLCSA-N
CL	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.193 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.157 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.159 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.796	α = 90
b = 58.411	β = 90
c = 63.928	γ = 90

Software Package:

Software Name	Purpose
SAINT	data reduction
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-10-05 
Deposition Author(s): Collins, P.M., Blanchard, H.

Revision History  

• Version 1.0: 2016-10-05
  Type: Initial release
  
• Version 1.1: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description