8ITZ | pdb_00008itz

Crystal structure of human Galectin-3 in complex with small molecule inhibitor

• PDB DOI: https://doi.org/10.2210/pdb8ITZ/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2023-03-23 Released: 2024-03-27 
• Deposition Author(s): Jinal, S., Amit, K., Ghosh, K.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.22 Å
• R-Value Free: 
  0.173 (Depositor), 0.170 (DCC) 
• R-Value Work: 
  0.147 (Depositor), 0.140 (DCC) 
• R-Value Observed: 
  0.148 (Depositor) 

Starting Model: experimental

Literature

Discovery and Exploration of Monosaccharide Linked Dimers to Target Fibrosis

Swidorski, J.J., Beno, B.B., Liu, C., Yoon, D., Ghosh, K., Sale, H., Shah, D., Acharya, K., Yanchunas, J., Ellsworth, B., Cheng, D., Regueiro-Ren, A.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: light scattering

Macromolecule Content

• Total Structure Weight: 19.99 kDa 
• Atom Count: 1,341 
• Modelled Residue Count: 138 
• Deposited Residue Count: 179 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Galectin-3	A	179	Homo sapiens	Mutation(s): 2  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
QB2 (Subject of Investigation/LOI)	C [auth A]	2-[(2R,3R,4S,5R,6R)-2-(3,4-dichlorophenyl)sulfanyl-6-(hydroxymethyl)-5-oxidanyl-4-[4-[3,4,5-tris(fluoranyl)phenyl]-1,2,3-triazol-1-yl]oxan-3-yl]oxyethanoic acid C22 H18 Cl2 F3 N3 O6 S RROCGPVSGSQEET-WIXLDOGYSA-N
CL	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
QB2	BindingDB:  8ITZ	IC50: 46 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.22 Å
• R-Value Free:  0.173 (Depositor), 0.170 (DCC) 
• R-Value Work:  0.147 (Depositor), 0.140 (DCC) 
• R-Value Observed: 0.148 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.51	α = 90
b = 57.241	β = 90
c = 61.257	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
REFMAC	refinement
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-03-27 
Deposition Author(s): Jinal, S., Amit, K., Ghosh, K.

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Funding Organization	Location	Grant Number
Other private		--

Revision History  

• Version 1.0: 2024-03-27
  Type: Initial release