apigenin   Click here for help

GtoPdb Ligand ID: 4136

PDB Ligand
Compound class: Natural product
Comment: Apigenin is a plant-derived flavonoid. It has been found in coriander, celery and chili peppers.
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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 1
Hydrogen bond donors 3
Rotatable bonds 1
Topological polar surface area 90.9
Molecular weight 270.05
XLogP 3.67
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 Oc1ccc(cc1)c1cc(=O)c2c(o1)cc(cc2O)O
Isomeric SMILES Oc1ccc(cc1)c1cc(=O)c2c(o1)cc(cc2O)O
InChI InChI=1S/C15H10O5/c16-9-3-1-8(2-4-9)13-7-12(19)15-11(18)5-10(17)6-14(15)20-13/h1-7,16-18H
InChI Key KZNIFHPLKGYRTM-UHFFFAOYSA-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
Molecular docking studies show interactions with 5-HT1A and 5-HT2A receptors [1]. In vivo reductions in depressive and anxiety symptoms have been demonstrated in rodents. It can inhibit the activity of acetylcholinesterase (AChE) and reduce amyloid β aggregation in a transgenic Drosophila Alzheimer disease model [5].
Selectivity at ion channels
Key to terms and symbols Click column headers to sort
Target Sp. Type Action Value Parameter Concentration range (M) Reference
CFTR Hs Activator Potentiation - - -
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Selectivity at enzymes
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Target Sp. Type Action Value Parameter Concentration range (M) Reference
CYP1B1 Hs Inhibitor Inhibition 7.2 pKi - 3
⤷ pKi 7.2 (Ki 6.4x10-8 M) [3]
CYP1A1 Hs Inhibitor Inhibition 6.4 pKi - 3
⤷ pKi 6.4 (Ki 3.9x10-7 M) [3]
acetylcholinesterase (Yt blood group) Hs Inhibitor Inhibition 7.9 pIC50 - 2
⤷ pIC50 7.9 (IC50 1.2x10-8 M) [2]
Selectivity at other protein targets
Key to terms and symbols Click column headers to sort
Target Sp. Type Action Value Parameter Concentration range (M) Reference
transthyretin Hs None Binding 6.6 pKd - 4
⤷ pKd 6.6 (Kd 2.5x10-7 M) [4]
Targets where the ligand is described in the comment field
Target Comment
CFTR UCCF-339, UCCF-029, apigenin and genistein are examples of flavones. UCCF-853 and NS004 are examples of benzimidazolones. CBIQ is an example of a benzoquinoline. Felodipine and nimodipine are examples of 1,4-dihydropyridines. Phenylglycine-01 is an example of a phenylglycine. Sulfonamide-01 is an example of a sulfonamide. Malonic acid hydrazide conjugates are also CFTR channel blockers (see Verkman and Galietta, 2009 [6])