parthenolide   Click here for help

GtoPdb Ligand ID: 12428

Synonyms: (-)-Parthenolide
PDB Ligand
Compound class: Natural product
Comment: Parthenolide is an active component of Feverfew (Tanacetum parthenium). It contains an α-methylene-γ-lactone pharmacophore that is found in many small molecules that act as inhibitors of antioxidant thioredoxin reductase enzymes (TrxR). This pharmacophore is crucial for interaction with the conserved selenocysteine (Sec) residue in the enzyme active site. Elevated expression of the TrxR1 isozyme is associated with therapy resistance and poor prognosis in a range of cancer types, so selective inhibitors are being explored for anticancer potential. Such inhibitors are proposed to elevate reactive oxygen species (ROS) generation, which induces endoplasmic reticulum stress (ERS) responses and ultimately apoptosis. Parthenolide is reported to target both the cytosolic (TrxR1) and mitochondrial (TrxR2) isozymes [1].
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Ligand Activity Visualisation Charts

These are box plot that provide a unique visualisation, summarising all the activity data for a ligand taken from ChEMBL and GtoPdb across multiple targets and species. Click on a plot to see the median, interquartile range, low and high data points. A value of zero indicates that no data are available. A separate chart is created for each target, and where possible the algorithm tries to merge ChEMBL and GtoPdb targets by matching them on name and UniProt accession, for each available species. However, please note that inconsistency in naming of targets may lead to data for the same target being reported across multiple charts.

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View interactive charts of activity data across species

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2D Structure
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2D Structure

An image of the ligand's 2D structure. For small molecules with SMILES these are drawn using the NCI/CADD Chemical Identifier Resolver. Click on the image to access the chemical structure search tool with the ligand pre-loaded in the structure editor. For other types of ligands, e.g. longer nucleotides and peptides, a manually drawn representation of the molecule may be provided.

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Physico-chemical Properties
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Physico-chemical Properties

Calculated molecular properties are available for small molecules and natural products (not peptides). Properties were generated using the Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/). All properties were selected to enable the prediction of the Lipinski Rule-of-Five profile or ‘druglikeness’ for each ligand. For more info on each category see the help pages.

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Hydrogen bond acceptors 3
Hydrogen bond donors 0
Rotatable bonds 0
Topological polar surface area 38.83
Molecular weight 248.32
XLogP 2.45
No. Lipinski's rules broken 0

Generated using the Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/)
SMILES / InChI / InChIKey
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SMILES / InChI / InChIKey

SMILES (Simplified Molecular Input Line Entry Specification) A specification for unambiguously describing the structure of chemical molecules using short ASCII strings. Canonical SMILES specify a unique representation of the 2D structure without chiral or isotopic specifications. Isomeric SMILES include chiral specification and isotopes.

Standard InChI (IUPAC International Chemical Identifier) and InChIKey InChI is a non-proprietary, standard, textual identifier for chemical substances designed to facilitate linking of information and database searching. An InChIKey is a simplified version of a full InChI, designed for easier web searching.

Generated using the Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/)

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Canonical SMILES C/C/1=C\CC[C@]2(C)[C@@H]([C@@H]3[C@@H](CC1)C(=C)C(=O)O3)O2
Isomeric SMILES C/C/1=C\CC[C@@]2([C@H](O2)[C@@H]3[C@@H](CC1)C(=C)C(=O)O3)C
InChI InChI=1S/C15H20O3/c1-9-5-4-8-15(3)13(18-15)12-11(7-6-9)10(2)14(16)17-12/h5,11-13H,2,4,6-8H2,1,3H3/b9-5+/t11-,12-,13+,15+/m0/s1
InChI Key KTEXNACQROZXEV-PVLRGYAZSA-N

Generated using the Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/)
Bioactivity Comments
Parthenolide induces ROS-mediated apoptosis of cancer cells in vitro [1].
Selectivity at GPCRs
Key to terms and symbols Click column headers to sort
Target Sp. Type Action Value Parameter Concentration range (M) Reference
TAS2R14 Hs Agonist Agonist 5.0 pEC50 - 3
⤷ pEC50 5.0 (EC50 1.027x10-5 M) [3]
TAS2R8 Hs Agonist Agonist - - - 2
⤷ [2]
Description: Threshold=100 μM
Selectivity at enzymes
Key to terms and symbols Click column headers to sort
Target Sp. Type Action Value Parameter Concentration range (M) Reference
thioredoxin reductase 1 Rn Inhibitor Inhibition ~5.5 pIC50 - 1
⤷ pIC50 ~5.5 (IC50 ~3x10-6 M) [1]