7RH3

Co-crystallization of human galectin-3 CRD complex with Methyl 2-O-(2-nitro-4-chloro)-benzoyl-3-O-toluoyl-b-D-talopyranoside


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.05 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.157 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Novel Selective Galectin-3 Antagonists Are Cytotoxic to Acute Lymphoblastic Leukemia.

Bum-Erdene, K.Collins, P.M.Hugo, M.W.Tarighat, S.S.Fei, F.Kishor, C.Leffler, H.Nilsson, U.J.Groffen, J.Grice, I.D.Heisterkamp, N.Blanchard, H.

(2022) J Med Chem 65: 5975-5989

  • DOI: https://doi.org/10.1021/acs.jmedchem.1c01296
  • Primary Citation of Related Structures:  
    7RGX, 7RGY, 7RGZ, 7RH0, 7RH1, 7RH3, 7RH4

  • PubMed Abstract: 

    Galectin-3 is a β-galactoside-specific, carbohydrate-recognizing protein (lectin) that is strongly implicated in cancer development, metastasis, and drug resistance. Galectin-3 promotes migration and ability to withstand drug treatment of B-cell precursor acute lymphoblastic leukemia (BCP-ALL) cells. Due to high amino acid conservation among galectins and the shallow nature of their glycan-binding site, the design of selective potent antagonists targeting galectin-3 is challenging. Herein, we report the design and synthesis of novel taloside-based antagonists of galectin-3 with enhanced affinity and selectivity. The molecules were optimized by in silico docking, selectivity was established against four galectins, and the binding modes were confirmed by elucidation of X-ray crystal structures. Critically, the specific inhibition of galectin-3-induced BCP-ALL cell agglutination was demonstrated. The compounds decreased the viability of ALL cells even when grown in the presence of protective stromal cells. We conclude that these compounds are promising leads for therapeutics, targeting the tumor-supportive activities of galectin-3 in cancer.


  • Organizational Affiliation

    Institute for Glycomics, Griffith University, Gold Coast Campus, Queensland 4222, Australia.


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
59O (Subject of Investigation/LOI)
Query on 59O

Download Ideal Coordinates CCD File 
C [auth A]methyl 2-O-(4-chloro-2-nitrobenzoyl)-3-O-(4-methylbenzoyl)-beta-D-talopyranoside
C22 H22 Cl N O10
FSBFERQGFVBNEJ-NOYKIMNZSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
B [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Binding Affinity Annotations 
IDSourceBinding Affinity
59O BindingDB:  7RH3 Kd: 5300 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.05 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.157 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.201α = 90
b = 57.814β = 90
c = 62.098γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-13
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Refinement description