agomelatine   Click here for help

GtoPdb Ligand ID: 198

Synonyms: S20098 | Thymanax® | Valdoxan®
Approved drug PDB Ligand
agomelatine is an approved drug (EMA (2009))
Compound class: Synthetic organic
Comment: Agomelatine is a melatonergic (i.e. it acts as a a melatonin receptor agonist) antidepressant, devoid of the side-effects caused by SSRI, SNRI and tricyclic antidepressants. The drug also has low affinity for 5-HT2C receptors.
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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
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 CDK toolkit. 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 2
Hydrogen bond donors 1
Rotatable bonds 5
Topological polar surface area 38.33
Molecular weight 243.13
XLogP 2.76
No. Lipinski's rules broken 0
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.

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Canonical SMILES COc1ccc2c(c1)c(CCNC(=O)C)ccc2
Isomeric SMILES COc1ccc2c(c1)c(CCNC(=O)C)ccc2
InChI InChI=1S/C15H17NO2/c1-11(17)16-9-8-13-5-3-4-12-6-7-14(18-2)10-15(12)13/h3-7,10H,8-9H2,1-2H3,(H,16,17)
InChI Key YJYPHIXNFHFHND-UHFFFAOYSA-N
Classification Click here for help
Compound class Synthetic organic
Approved drug? Yes (EMA (2009))
IUPAC Name Click here for help
N-[2-(7-methoxynaphthalen-1-yl)ethyl]acetamide
International Nonproprietary Names Click here for help
INN number INN
7392 agomelatine
Synonyms Click here for help
S20098 | Thymanax® | Valdoxan®
Database Links Click here for help
Specialist databases
GPCRdb Ligand agomelatine
Other databases
BindingDB Ligand 50035179
CAS Registry No. 138112-76-2 (source: Scifinder)
ChEMBL Ligand CHEMBL10878
DrugBank Ligand DB06594
DrugCentral Ligand 99
GtoPdb PubChem SID 135649906
PubChem CID 82148
RCSB PDB Ligand AWY
Search Google for chemical match using the InChIKey YJYPHIXNFHFHND-UHFFFAOYSA-N
Search Google for chemicals with the same backbone YJYPHIXNFHFHND
Search PubMed clinical trials agomelatine
Search PubMed titles agomelatine
Search PubMed titles/abstracts agomelatine
UniChem Compound Search for chemical match using the InChIKey YJYPHIXNFHFHND-UHFFFAOYSA-N
UniChem Connectivity Search for chemical match using the InChIKey YJYPHIXNFHFHND-UHFFFAOYSA-N
Wikipedia Agomelatine