Moleculium

CID 5202

C10H12N2O

Serotonin

  • C 10
  • H 12
  • N 2
  • O 1
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25 atoms, 26 bonds.
Ball-and-stick model of serotonin: 10 carbon atoms, 12 hydrogen atoms, 2 nitrogen atoms and 1 oxygen atom, 26 bonds (22 single, 4 double). Carbon is grey, hydrogen white, nitrogen blue, oxygen red.
IUPAC name
3-(2-aminoethyl)-1H-indol-5-ol
Molar mass
176.219(25) g/mol
Atoms
25
SMILES
C1=CC2=C(C=C1O)C(=CN2)CCN
InChIKey
QZAYGJVTTNCVMB-UHFFFAOYSA-N
PubChem CID
5202

Made of

C , Carbon, nonmetal H , Hydrogen, nonmetal N , Nitrogen, nonmetal O , Oxygen, nonmetal
Structural formula of serotonin. Each unlabelled corner is a carbon atom, and the eight hydrogens on carbon are not drawn. It shows which atoms are joined to which, not the shape. The model above shows the shape. Structural formula of serotonin, drawn flat from PubChem's 2D record: 10 carbon atoms, 12 hydrogen atoms, 2 nitrogen atoms and 1 oxygen atom, 26 bonds (22 single, 4 double). Each unlabelled corner is a carbon atom, and the eight hydrogens on carbon are not drawn. Symbols carry their usual colours: nitrogen blue and oxygen red. A structural formula shows how the atoms are joined, not the shape of the molecule.

Gaps separate one nerve cell from the next, and serotonin is among the chemicals that carry a signal across them. Because an electrical signal cannot cross the gap directly, the sending cell converts it into a chemical one, a neurotransmitter. More than 200 neurotransmitters have been identified since the first was found in 1921, by the count of NIGMS, the US National Institute of General Medical Sciences. Serotonin’s own signals regulate mood, emotion, appetite and sleep, according to MedlinePlus.

The US National Cancer Institute (NCI) gives it a second job, as a vasoconstrictor that narrows blood vessels, and a second name, 5-hydroxytryptamine, 5-HT for short. ChEBI (Chemical Entities of Biological Interest) defines it as the 5-hydroxy derivative of tryptamine, and its IUPAC name is 3-(2-aminoethyl)-1H-indol-5-ol. Ten carbon, twelve hydrogen, two nitrogen and one oxygen atom add up to 176.22 g/mol.

Structure and bonding

Serotonin’s 25 atoms run from an O–H group on a ring at one end to an NH2 group on a two-carbon chain at the other. Between them lie two fused flat rings, an indole system: the O–H on the six-membered ring, the chain on the five-membered. Labels shows four hydrogens on N or O, the kind that can form hydrogen bonds.

Turned edge-on in Ball-and-stick, the rings, the oxygen and the first chain carbon fall into one line. The chain’s second carbon and its nitrogen sit about 1.4 Å off that plane in PubChem’s computed model. That pose is not fixed: the chain’s single bonds can rotate. Space-filling shows a flat plate with a short arm raised off it.

Stick shows four doubled C=C bonds: three in the six-membered ring, one beside the ring nitrogen. In the real molecule those double bonds are delocalised, their electrons spread around the rings as in benzene. The drawing is also the uncharged molecule. Its amino group is a base, and ChEBI lists serotonin(1+), an ion with one more hydrogen and one positive charge.

Where it turns up

NCI places serotonin in the digestive tract, the central nervous system (the brain and spinal cord) and the platelets of the blood. In the brain’s pineal gland, serotonin is the raw material for melatonin. One 2017 study, reported by NCCIH, the US National Center for Complementary and Integrative Health, found serotonin in some of 31 shop-bought melatonin supplements.

The body builds it from the amino acid tryptophan in two steps, by MedlinePlus’s account. Tryptophan first becomes 5-hydroxytryptophan; the enzyme AADC, aromatic L-amino acid decarboxylase, then removes a carboxyl group, COOH. NICHD, the US child-health institute, names tryptophan hydroxylase as another enzyme the process needs. Monoamine oxidase A takes part in breaking serotonin down, as it does for epinephrine, norepinephrine and dopamine.

Why it matters

When signalling is no longer needed, enzymes may deactivate a neurotransmitter or the cell that released it may take it back, by NIGMS’s account. Serotonin, being highly charged, cannot pass back into cells unaided, so a transporter called SERT pumps it in to be inactivated. The gastroenterologist Kara Margolis said so at a 2022 seminar of the US National Institute of Environmental Health Sciences.

Medical Subject Headings (MeSH) lists many drugs that activate serotonin’s receptors as antidepressants, anti-anxiety medicines and migraine treatments. Drugs that block its type 3 receptor are used against nausea, vomiting and some forms of irritable bowel syndrome, NCI notes.

NIMH, the US National Institute of Mental Health, reports studies indicating reduced serotonin in seasonal affective disorder (SAD), its winter pattern especially. Shorter days may contribute, and serotonin and melatonin both help keep the body’s daily rhythm. Hannah Kinney’s team at Harvard Medical School studied brainstem tissue from infants who had died of SIDS, sudden infant death syndrome. It found less serotonin there than in infants whose unexpected deaths had other causes, NICHD reported in 2010.

Properties

Properties of serotonin Molar mass summed from IUPAC/CIAAW 2024 standard atomic weights; formula, atom and bond counts and PubChem's molecular weight from PubChem CID 5202.
Property Value Unit Source
Molecular formula (Hill order) C10H12N2O
Molar mass 176.219(25)   g/mol g/mol IUPAC/CIAAW 2024
Carbon atoms 10
Hydrogen atoms 12
Nitrogen atoms 2
Oxygen atoms 1
Bonds 26
Single bonds 22
Double bonds 4
PubChem molecular weight 176.21   g/mol g/mol PubChem

Safety

Toxic if swallowed is the hazard statement in every one of the 67 company reports on serotonin to the European Chemicals Agency (ECHA). Nearly all, 98.5%, add that it is suspected of damaging fertility or an unborn child. Inside the body too much can lead to seizures, notes NINDS, the US National Institute of Neurological Disorders and Stroke, and NCCIH warns of life-threatening serotonin toxicity. The PubChem Laboratory Chemical Safety Summary for serotonin holds the full classification.

Questions

Is serotonin a hormone or a neurotransmitter?

It is described as both. The US National Cancer Institute calls serotonin a neurotransmitter, a substance nerves use to signal one another, and also a hormone. NCCIH, the US National Center for Complementary and Integrative Health, calls it a hormone too. MeSH, the medical subject vocabulary, calls it a biochemical messenger and regulator and credits several families of receptors with its broad range of actions.

Does low serotonin cause depression?

It may be one cause. The US National Cancer Institute gives too little serotonin in the brain as a suspected cause of depression. The US National Institute of Neurological Disorders and Stroke says a shortage may bring on depression and sleep problems. The US National Institute of General Medical Sciences reports that research ties depression to unusual levels of serotonin and of dopamine. Selective serotonin reuptake inhibitors (SSRIs) leave more serotonin for the body to use.

How much of the body's serotonin is made in the gut?

Ninety-five per cent, by the figure the US National Institute of Environmental Health Sciences gave in reporting a 2022 seminar by Kara Margolis, a paediatric gastroenterologist at Columbia University. In the gut, the same report says, serotonin signals the wall to squeeze its contents onward while the stretch ahead relaxes. The medical vocabulary MeSH places serotonin in the gastrointestinal tract, the central nervous system and blood platelets.

Why is serotonin called 5-HT?

5-HT is short for 5-hydroxytryptamine, the other name the US National Cancer Institute gives it. ChEBI (Chemical Entities of Biological Interest) defines serotonin as the 5-hydroxy derivative of tryptamine: tryptamine with one O–H group added. In the 3D model that group is the lone O–H on the six-membered ring, at the opposite end from the NH2. MeSH, the medical subject vocabulary, also files serotonin under the names enteramine and hippophaine.

What is 5-HIAA?

5-HIAA, or 5-hydroxyindoleacetic acid, is what serotonin is broken down to. The US National Cancer Institute (NCI) describes it forming in the liver; the kidneys then clear it from the blood into urine. Carcinoid tumours may secrete serotonin, and measuring 5-HIAA in urine may help to diagnose and monitor them. Carcinoid syndrome, with symptoms such as facial flushing, diarrhoea and bronchial spasms, comes from serotonin and other substances released by such tumours in the gastrointestinal tract.

Made of the same elements

All 25 compounds made of carbon, hydrogen, nitrogen and oxygen

Sources

  1. PubChem CID 5202, serotonin
  2. IUPAC/CIAAW, Abridged Standard Atomic Weights 2024
  3. PubChem Laboratory Chemical Safety Summary for serotonin (CID 5202)
  4. Stephen Lower, Chem1 General Chemistry, §9.7 The Hybrid Orbital Model II (LibreTexts, CC BY 3.0)
  5. Stephen Lower, Chem1 General Chemistry, §7.3 Hydrogen-Bonding and Water (LibreTexts, CC BY 3.0)
  6. Stephen Lower, Chem1 General Chemistry, §7.9 Polymers and Plastics (LibreTexts, CC BY 3.0)
  7. Stephen Lower, Chem1 General Chemistry, §10.6 Types of Acids and Bases (LibreTexts, CC BY 3.0)
  8. National Institute of General Medical Sciences (NIGMS), Biomedical Beat: What Is a Neurotransmitter? (2024)
  9. National Cancer Institute, NCI Dictionary of Cancer Terms: serotonin
  10. National Cancer Institute, NCI Dictionary of Cancer Terms: 5-HIAA
  11. National Cancer Institute, NCI Dictionary of Cancer Terms: carcinoid tumor
  12. National Cancer Institute, NCI Dictionary of Cancer Terms: carcinoid syndrome
  13. National Cancer Institute, NCI Dictionary of Cancer Terms: type 3 serotonin receptor antagonist
  14. MedlinePlus Genetics (National Library of Medicine), DDC gene
  15. MedlinePlus Genetics (National Library of Medicine), MAOA gene
  16. NLM Medical Subject Headings (MeSH), Serotonin
  17. National Institute of Environmental Health Sciences, Environmental Factor: Mood and gut disorders linked to impaired serotonin transport (February 2022)
  18. National Institute of Mental Health (NIMH), Seasonal Affective Disorder
  19. National Institute of Neurological Disorders and Stroke (NINDS), Brain Basics: Know Your Brain
  20. NICHD (National Institutes of Health), SIDS Linked to Low Levels of Serotonin (2010)
  21. NICHD (National Institutes of Health), Researchers Discover How Melatonin Production is Switched Off (1998)
  22. NCCIH, Melatonin: What You Need To Know
  23. NCCIH, Sleep Disorders and Complementary Health Approaches: Usefulness and Safety