---
title: "Histamine Structure (C5H9N3): 3D Model, Formula & Molar Mass | MolDraw"
url: https://www.moldraw.com/molecules/histamine.html
description: "Structure of Histamine (C5H9N3, 111.15 g/mol): rotatable 3D model, 2D skeletal formula, IUPAC name, SMILES, shape, polarity, uses and FAQ."
lang: en
publisher: Scidart Academy
generated: 2026-10-26
---
[MolDraw](https://www.moldraw.com/) › [3D molecule models](https://www.moldraw.com/molecules/) › 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.

**Quick answer:** Histamine is **C5H9N3**, molar mass **111.15 g/mol**. Small, flat aromatic ring with a flexible amine tail; very polar and freely soluble in water.

Atom labels Hydrogens Spin

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](https://pubchem.ncbi.nlm.nih.gov/compound/774) |

![2D structural formula of Histamine (C5H9N3)](https://www.moldraw.com/molecules/img/histamine.svg)

2D structure (skeletal formula) · [Draw it in MolDraw](https://www.moldraw.com/)

## 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](https://www.moldraw.com/tools/free-chem-tools/molar-mass-calculator.html).

## 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.

**Drawing structures for your notes?** MolDraw is a free online chemical structure editor for molecules, reactions and lab diagrams.

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## Frequently 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.

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