---
title: "Cytosine Structure (C4H5N3O): 3D Model, Formula & Molar Mass | MolDraw"
url: https://www.moldraw.com/molecules/cytosine.html
description: "Structure of Cytosine (C4H5N3O, 111.10 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/) › Cytosine structure

# Cytosine structure and 3D model (C4H5N3O)

Cytosine is a pyrimidine base: a single six-membered ring with two nitrogens, a C=O at C2 and an NH₂ group at C4. It pairs with guanine.

**Quick answer:** Cytosine is **C4H5N3O**, molar mass **111.10 g/mol**. Small, flat ring; polar and moderately 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).

## Cytosine at a glance

| Formula | C4H5N3O |
| --- | --- |
| Molar mass | 111.10 g/mol |
| IUPAC name | 6-amino-1H-pyrimidin-2-one |
| Atoms / bonds | 13 / 13 |
| H-bond donors / acceptors | 2 / 3 |
| logP (estimated) | -0.6 |
| SMILES | `C1=C(NC(=O)N=C1)N` |
| InChIKey | `OPTASPLRGRRNAP-UHFFFAOYSA-N` |
| PubChem | [597](https://pubchem.ncbi.nlm.nih.gov/compound/597) |

![2D structural formula of Cytosine (C4H5N3O)](https://www.moldraw.com/molecules/img/cytosine.svg)

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

## What the 3D model of Cytosine shows

The model contains **13 atoms** (8 heavy atoms and 5 hydrogens) joined by **13 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 3 hydrogen bonds, and its estimated logP of -0.6 means it is very water-loving (hydrophilic). Its topological polar surface area is 72 Ų.

## Shape and bond angles

| Atom(s) | Geometry / hybridisation | Angles & lengths |
| --- | --- | --- |
| ring atoms | Trigonal planar, sp²; planar ring | ≈ 120° |
| C2 carbonyl carbon | Trigonal planar, sp² | ≈ 120° |
| exocyclic NH₂ | Near-planar, conjugated | ≈ 120° |

### Is Cytosine polar?

Yes. The NH₂, ring N–H, ring N and C=O can all take part in hydrogen bonds.

## Elemental composition of C4H5N3O

| Element | Atoms | Mass (g/mol) | Mass % |
| --- | --- | --- | --- |
| Carbon (C) | 4 | 48.044 | 43.24% |
| Hydrogen (H) | 5 | 5.040 | 4.54% |
| Nitrogen (N) | 3 | 42.021 | 37.82% |
| Oxygen (O) | 1 | 15.999 | 14.40% |

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 cytosine

- One of the bases in DNA and RNA
- Methylated cytosine (5-methylcytosine) controls which genes are switched on
- Starting point for antiviral and anticancer nucleoside drugs

## Interesting facts

- Cytosine can lose its NH₂ group to become uracil, a common form of DNA damage that cells repair.
- Methylation of cytosine is a key part of epigenetics.
- IUPAC numbering in PubChem places the NH₂ at position 6, while biochemists usually call it C4.

**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 Cytosine?

Cytosine is a pyrimidine base: a single six-membered ring with two nitrogens, a C=O at C2 and an NH₂ group at C4. It pairs with guanine. Its SMILES is C1=C(NC(=O)N=C1)N.

### Is cytosine a purine or a pyrimidine?

A pyrimidine. It has a single six-membered ring with two nitrogen atoms.

### How many hydrogen bonds does cytosine make with guanine?

Three, which makes G–C pairs more stable than A–T pairs.

### What is the chemical formula and molar mass of Cytosine?

Cytosine is C4H5N3O with a molar mass of 111.10 g/mol. It contains 13 atoms: 4 carbon, 5 hydrogen, 3 nitrogen, 1 oxygen.

### What is the IUPAC name of Cytosine?

The IUPAC name is 6-amino-1H-pyrimidin-2-one.

### How do I draw Cytosine?

Open the MolDraw editor, paste the SMILES C1=C(NC(=O)N=C1)N or type "Cytosine" 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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