5-hydroxytryptamine   Click here for help

GtoPdb Ligand ID: 5

Abbreviated name: 5-HT
Synonyms: serotonin
PDB Ligand
Compound class: Metabolite or derivative
Click here for help

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.

✖

View interactive charts of activity data across species
2D Structure
Click here for help

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.

✖
Click here for structure editor
Physico-chemical Properties
Click here for help

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.

✖
Hydrogen bond acceptors 1
Hydrogen bond donors 3
Rotatable bonds 2
Topological polar surface area 62.04
Molecular weight 176.09
XLogP 1
No. Lipinski's rules broken 0
SMILES / InChI / InChIKey
Click here for help

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.

✖
Canonical SMILES NCCc1c[nH]c2c1cc(O)cc2
Isomeric SMILES NCCc1c[nH]c2c1cc(O)cc2
InChI InChI=1S/C10H12N2O/c11-4-3-7-6-12-10-2-1-8(13)5-9(7)10/h1-2,5-6,12-13H,3-4,11H2
InChI Key QZAYGJVTTNCVMB-UHFFFAOYSA-N
Natural/Endogenous Targets
Target
5-HT1A receptor
5-HT1B receptor
5-HT1D receptor
5-ht1e receptor
5-HT1F receptor
5-HT2A receptor
5-HT2B receptor
5-HT2C receptor
5-HT3A
5-HT3A
5-HT3AB
5-HT3B
5-HT3C
5-HT3D
5-HT3E
5-HT4 receptor
5-HT5A receptor
5-ht5b receptor
5-HT6 receptor
5-HT7 receptor
D1 receptor
D5 receptor
Enzymes Catalysing Reactions with this Compound as a Substrate or Product
Enzyme EC number Reaction Reference
L-Aromatic amino-acid decarboxylase 4.1.1.28 Levodopa -> dopamine + CO2
5-hydroxy-L-tryptophan -> 5-hydroxytryptamine + CO2
Monoamine oxidase A 1.4.3.4 5-Hydroxytryptamine -> 5-hydroxyindole acetaldehyde + NH3
Monoamine oxidase B 1.4.3.4 5-Hydroxytryptamine -> 5-hydroxyindole acetaldehyde + NH3
Transporters Moving this Compound Across a Lipid Membrane
Transporter EC number Reaction Reference
SERT
Vesicular monoamine transporter 1 29
Vesicular monoamine transporter 2 29
Organic cation transporter 1
Organic cation transporter 3 86
Plasma membrane monoamine transporter 28,82
Selectivity at GPCRs
Key to terms and symbols Click column headers to sort
Target Sp. Type Action Value Parameter Concentration range (M) Reference
5-HT2A receptor Ligand is endogenous in the given species Hs Agonist Full agonist 8.9 pKd - 75
⤷ pKd 8.9 [75]
5-HT4 receptor Ligand is endogenous in the given species Hs Agonist Full agonist 8.4 – 8.8 pKd - 10
⤷ pKd 8.4 – 8.8 [10]
5-HT1F receptor Ligand is endogenous in the given species Hs Agonist Full agonist 8.0 pKd - 3
⤷ pKd 8.0 [3]
5-HT1B receptor Ligand is endogenous in the given species Hs Agonist Full agonist 7.5 – 8.4 pKd - 66,84
⤷ pKd 7.5 – 8.4 [66,84]
5-HT6 receptor Ligand is endogenous in the given species Rn Agonist Full agonist 7.9 pKd - 13
⤷ pKd 7.9 [13]
5-HT4 receptor Ligand is endogenous in the given species Rn Agonist Full agonist 7.7 pKd - 2
⤷ pKd 7.7 [2]
5-HT1A receptor Ligand is endogenous in the given species Hs Agonist Full agonist 9.1 – 9.7 pKi - 41,61-65
⤷ pKi 9.1 – 9.7 [41,61-65]
5-HT7 receptor Ligand is endogenous in the given species Rn Agonist Full agonist 8.7 – 9.2 pKi - 71,74
⤷ pKi 8.7 – 9.2 [71,74]
5-HT7 receptor Ligand is endogenous in the given species Hs Agonist Full agonist 8.1 – 9.6 pKi - 7,35,39,45,78
⤷ pKi 8.1 – 9.6 [7,35,39,45,78]
5-HT1D receptor Ligand is endogenous in the given species Hs Agonist Full agonist 8.0 – 9.0 pKi - 22,34,48,62,72,83-84
⤷ pKi 8.0 – 9.0 [22,34,48,62,72,83-84]
5-HT7 receptor Ligand is endogenous in the given species Mm Agonist Full agonist 8.3 pKi - 67
⤷ pKi 8.3 [67]
5-HT1B receptor Ligand is endogenous in the given species Hs Agonist Full agonist 7.4 – 9.0 pKi - 22,60,62,72,83-84
⤷ pKi 7.4 – 9.0 [22,60,62,72,83-84]
5-HT2B receptor Ligand is endogenous in the given species Hs Agonist Full agonist 7.9 – 8.4 pKi - 8,43,46,52,70
⤷ pKi 7.9 – 8.4 [8,43,46,52,70]
5-HT1B receptor Ligand is endogenous in the given species Mm Agonist Full agonist 8.1 pKi - 50
⤷ pKi 8.1 [50]
5-ht1e receptor Ligand is endogenous in the given species Hs Agonist Full agonist 8.0 – 8.2 pKi - 3,6,25,53
⤷ pKi 8.0 – 8.2 [3,6,25,53]
5-HT2B receptor Ligand is endogenous in the given species Rn Agonist Full agonist 8.0 pKi - 80
⤷ pKi 8.0 [80]
5-HT1F receptor Ligand is endogenous in the given species Hs Agonist Full agonist 7.7 – 8.0 pKi - 1,3,81
⤷ pKi 7.7 – 8.0 [1,3,81]
5-HT2C receptor Ligand is endogenous in the given species Hs Agonist Full agonist 6.8 – 8.6 pKi - 26,31,42-43,52
⤷ pKi 6.8 – 8.6 [26,31,42-43,52]
5-HT4 receptor Ligand is endogenous in the given species Rn Agonist Full agonist 6.7 – 8.2 pKi - 2,16,32
⤷ pKi 6.7 – 8.2 [2,16,32]
5-HT2C receptor Ligand is endogenous in the given species Rn Agonist Full agonist 6.7 – 7.9 pKi - 36,70
⤷ pKi 6.7 – 7.9 [36,70]
5-HT6 receptor Ligand is endogenous in the given species Rn Agonist Full agonist 6.6 – 7.9 pKi - 13-15,59
⤷ pKi 6.6 – 7.9 [13-15,59]
5-HT2A receptor Ligand is endogenous in the given species Hs Agonist Full agonist 6.0 – 8.4 pKi - 4,18,40,43,52,75
⤷ pKi 6.0 – 8.4 [4,18,40,43,52,75]
5-HT4 receptor Ligand is endogenous in the given species Mm Agonist Full agonist 7.2 pKi - 20
⤷ pKi 7.2 [20]
5-HT6 receptor Ligand is endogenous in the given species Hs Agonist Full agonist 6.8 – 7.5 pKi - 12,15,44
⤷ pKi 6.8 – 7.5 [12,15,44]
5-HT5A receptor Ligand is endogenous in the given species Hs Agonist Full agonist 6.7 – 6.9 pKi - 33,68
⤷ pKi 6.7 – 6.9 [33,68]
5-HT5A receptor Ligand is endogenous in the given species Rn Agonist Full agonist 6.6 pKi - 30
⤷ pKi 6.6 [30]
5-HT4 receptor Ligand is endogenous in the given species Hs Agonist Full agonist 5.9 – 7.0 pKi - 5,8,10-11,19,55-57,69,79
⤷ pKi 5.9 – 7.0 [5,8,10-11,19,55-57,69,79]
5-HT5A receptor Ligand is endogenous in the given species Mm Agonist Full agonist 6.0 – 6.6 pKi - 33,51,85
⤷ pKi 6.0 – 6.6 [33,51,85]
5-HT2A receptor Ligand is endogenous in the given species Rn Agonist Full agonist 6.0 – 6.5 pKi - 27,70,73
⤷ pKi 6.0 – 6.5 [27,70,73]
D5 receptor Ligand is endogenous in the given species Hs Agonist Full agonist 5.5 pKi - 77
⤷ pKi 5.5 [77]
D1 receptor Ligand is endogenous in the given species Hs Agonist Partial agonist 5.0 pKi - 77
⤷ pKi 5.0 [77]
5-HT1F receptor Ligand is endogenous in the given species Rn Agonist Full agonist 7.2 pIC50 - 49
⤷ pIC50 7.2 [49]
Selectivity at ion channels
Key to terms and symbols Click column headers to sort
Target Sp. Type Action Value Parameter Concentration range (M) Reference
5-HT3A Ligand is endogenous in the given species Hs Agonist Agonist 6.5 – 6.9 pKi - 17,37-38,47
⤷ pKi 6.5 – 6.9 [17,37-38,47]
5-HT3AB Ligand is endogenous in the given species Hs Agonist Agonist 6.0 pKi - 17
⤷ pKi 6.0 [17]
5-HT3A Ligand is endogenous in the given species Hs Agonist Agonist 5.5 – 6.4 pEC50 - 9,21,23-24,47,58,76
⤷ pEC50 5.5 – 6.4 [9,21,23-24,47,58,76]
5-HT3AB Ligand is endogenous in the given species Hs Agonist Agonist 4.8 – 5.8 pEC50 - 21,23-24,76
⤷ pEC50 4.8 – 5.8 [21,23-24,76]
Selectivity at transporters
Key to terms and symbols Click column headers to sort
Target Sp. Type Action Value Parameter Concentration range (M) Reference
Proton-coupled Amino acid Transporter 1 Hs Inhibitor Inhibition 2.2 pKi - 54
⤷ pKi 2.2 (Ki 5.7x10-3 M) [54]
Ligand mentioned in the following text fields
5-Hydroxytryptamine receptors overview
Monoamine transporter subfamily overview