6W4Z | pdb_00006w4z

Galectin-8N terminal domain in complex with Methyl 3-O-[3-O-benzyloxy]-malonyl-beta-D-galactopyranoside


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free: 
    0.226 (Depositor), 0.233 (DCC) 
  • R-Value Work: 
    0.193 (Depositor), 0.201 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Rational Design and Synthesis of Methyl-beta-d-galactomalonyl Phenyl Esters as Potent Galectin-8 N Antagonists.

Patel, B.Kishor, C.Houston, T.A.Shatz-Azoulay, H.Zick, Y.Vinik, Y.Blanchard, H.

(2020) J Med Chem 63: 11573-11584

  • DOI: https://doi.org/10.1021/acs.jmedchem.0c00602
  • Primary Citation Related Structures: 
    6W4Z

  • PubMed Abstract: 

    Galectin-8 is a β-galactoside-recognizing protein having an important role in the regulation of bone remodeling and cancer progression and metastasis. Methyl β-d-galactopyranoside malonyl aromatic esters have been designed to target and engage with particular amino acid residues of the galectin-8 N extended carbohydrate-binding site. The chemically synthesized compounds had in vitro binding affinity toward galectin-8 N in the range of 5-33 μM, as evaluated by isothermal titration calorimetry. This affinity directly correlated with the compounds' ability to inhibit galectin-8-induced expression of chemokines and proinflammatory cytokines in the SUM159 breast cancer cell line. X-ray crystallographic structure determination revealed that these monosaccharide-based compounds bind galectin-8 N by engaging its unique arginine (Arg59) and simultaneously cross-linking to another arginine (Arg45) located across the carbohydrate-binding site. This structure-based drug design approach has led to the discovery of novel monosaccharide galactose-based antagonists, with the strongest-binding compound ( K d 5.72 μM) holding 7-fold tighter than the disaccharide lactose.


  • Organizational Affiliation
    • Institute for Glycomics, Griffith University, Gold Coast Campus, Southport, Queensland 4222, Australia.

Macromolecule Content 

  • Total Structure Weight: 35.68 kDa 
  • Atom Count: 2,690 
  • Modeled Residue Count: 305 
  • Deposited Residue Count: 306 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Galectin-8
A, B
153Homo sapiensMutation(s): 1 
Gene Names: LGALS8
UniProt & NIH Common Fund Data Resources
Find proteins for O00214 (Homo sapiens)
Explore O00214 
Go to UniProtKB:  O00214
PHAROS:  O00214
GTEx:  ENSG00000116977 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO00214
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SZS
(Subject of Investigation/LOI)

Query on SZS



Download:Ideal Coordinates CCD File
C [auth A],
F [auth B]
methyl 3-O-[3-(benzyloxy)-3-oxopropanoyl]-beta-D-galactopyranoside
C17 H22 O9
NMJLHFMLSWSVNI-GNXUOLQESA-N
PG4

Query on PG4



Download:Ideal Coordinates CCD File
G [auth B]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
E [auth A],
H [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
D [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Binding Affinity Annotations 
IDSourceBinding Affinity
SZS BindingDB:  6W4Z Kd: 9170 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free:  0.226 (Depositor), 0.233 (DCC) 
  • R-Value Work:  0.193 (Depositor), 0.201 (DCC) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.391α = 90
b = 40.003β = 98.222
c = 70.324γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Cancer Council WAAustralia1080845

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-02
    Type: Initial release
  • Version 1.1: 2020-11-04
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Database references, Derived calculations, Refinement description