MolDraw › 3D molecule models › Histamine structure
Histamine structure and 3D model (C5H9N3)
Histamine is an imidazole ring with a two-carbon chain ending in an NH₂ group. It is made from the amino acid histidine by removing CO₂.
Drag to rotate · pinch or scroll to zoom. 3D coordinates: computed with RDKit (ETKDG conformer, force-field optimised).
Histamine at a glance
| Formula | C5H9N3 |
|---|---|
| Molar mass | 111.15 g/mol |
| IUPAC name | 2-(1H-imidazol-5-yl)ethanamine |
| Atoms / bonds | 17 / 17 |
| H-bond donors / acceptors | 2 / 2 |
| logP (estimated) | -0.1 |
| SMILES | C1=C(NC=N1)CCN |
| InChIKey | NTYJJOPFIAHURM-UHFFFAOYSA-N |
| PubChem | 774 |
What the 3D model of Histamine shows
The model contains 17 atoms (8 heavy atoms and 9 hydrogens) joined by 17 bonds; in ball-and-stick mode every stick is one bond, and double or aromatic bonds are drawn as multiple sticks. Switch to space-filling to see the molecule as its electron cloud, scaled to van der Waals radii: this is the shape other molecules actually "feel". It can donate 2 and accept 2 hydrogen bonds, and its estimated logP of -0.1 means it is very water-loving (hydrophilic). Its topological polar surface area is 55 Ų.
Shape and bond angles
| Atom(s) | Geometry / hybridisation | Angles & lengths |
|---|---|---|
| imidazole ring atoms | Trigonal planar, sp²; aromatic 5-ring | ≈ 108° |
| CH₂ carbons | Tetrahedral, sp³ | ≈ 109.5° |
| amine N | Trigonal pyramidal, sp³ | ≈ 107° |
Is Histamine polar?
Yes, very. It has three nitrogens that take part in hydrogen bonding, and at body pH the side-chain amine is protonated.
Elemental composition of C5H9N3
| Element | Atoms | Mass (g/mol) | Mass % |
|---|---|---|---|
| Carbon (C) | 5 | 60.055 | 54.03% |
| Hydrogen (H) | 9 | 9.072 | 8.16% |
| Nitrogen (N) | 3 | 42.021 | 37.81% |
Calculated from IUPAC standard atomic weights. Check any formula with the molar mass calculator.
Uses of histamine
- Signals allergic reactions and inflammation
- Stimulates stomach acid release
- Target of antihistamine drugs
Interesting facts
- Histamine is stored in mast cells and released during allergic reactions.
- Its imidazole ring exists as two tautomers that swap the position of the N–H.
- Spoiled fish can contain enough histamine to cause scombroid food poisoning.
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Open MolDraw editorFrequently asked questions
What is the structure of Histamine?
Histamine is an imidazole ring with a two-carbon chain ending in an NH₂ group. It is made from the amino acid histidine by removing CO₂. Its SMILES is C1=C(NC=N1)CCN.
How is histamine made in the body?
The enzyme histidine decarboxylase removes CO₂ from the amino acid histidine.
What do antihistamines do?
They block histamine receptors. H1 blockers ease allergy symptoms, and H2 blockers reduce stomach acid.
What is the chemical formula and molar mass of Histamine?
Histamine is C5H9N3 with a molar mass of 111.15 g/mol. It contains 17 atoms: 5 carbon, 9 hydrogen, 3 nitrogen.
What is the IUPAC name of Histamine?
The IUPAC name is 2-(1H-imidazol-5-yl)ethanamine.
How do I draw Histamine?
Open the MolDraw editor, paste the SMILES C1=C(NC=N1)CCN or type "Histamine" in name search, and the structure is drawn for you. You can then export it as PNG, SVG, MOL or CDXML.