---
title: "Thymine Structure (C5H6N2O2): 3D Model, Formula & Molar Mass | MolDraw"
url: https://www.moldraw.com/molecules/thymine.html
description: "Structure of Thymine (C5H6N2O2, 126.11 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/) › Thymine structure

# Thymine structure and 3D model (C5H6N2O2)

Thymine is a pyrimidine base with two C=O groups and a methyl group at C5. It is found in DNA, where it pairs with adenine.

**Quick answer:** Thymine is **C5H6N2O2**, molar mass **126.11 g/mol**. Flat ring with a methyl group; polar and sparingly soluble in cold water.

Atom labels Hydrogens Spin

Drag to rotate · pinch or scroll to zoom. 3D coordinates: computed with RDKit (ETKDG conformer, force-field optimised).

## Thymine at a glance

| Formula | C5H6N2O2 |
| --- | --- |
| Molar mass | 126.11 g/mol |
| IUPAC name | 5-methyl-1H-pyrimidine-2,4-dione |
| Atoms / bonds | 15 / 15 |
| H-bond donors / acceptors | 2 / 2 |
| logP (estimated) | -0.6 |
| SMILES | `CC1=CNC(=O)NC1=O` |
| InChIKey | `RWQNBRDOKXIBIV-UHFFFAOYSA-N` |
| PubChem | [1135](https://pubchem.ncbi.nlm.nih.gov/compound/1135) |

![2D structural formula of Thymine (C5H6N2O2)](https://www.moldraw.com/molecules/img/thymine.svg)

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

## What the 3D model of Thymine shows

The model contains **15 atoms** (9 heavy atoms and 6 hydrogens) joined by **15 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 -0.6 means it is very water-loving (hydrophilic). Its topological polar surface area is 66 Ų.

## Shape and bond angles

| Atom(s) | Geometry / hybridisation | Angles & lengths |
| --- | --- | --- |
| ring atoms | Trigonal planar, sp²; planar ring | ≈ 120° |
| C=O carbons | Trigonal planar, sp² | ≈ 120° |
| methyl carbon | Tetrahedral, sp³ | ≈ 109.5° |

### Is Thymine polar?

Yes. Two N–H donors and two C=O acceptors make it polar, but the solid is strongly hydrogen-bonded so it dissolves only slowly in cold water.

## Elemental composition of C5H6N2O2

| Element | Atoms | Mass (g/mol) | Mass % |
| --- | --- | --- | --- |
| Carbon (C) | 5 | 60.055 | 47.62% |
| Hydrogen (H) | 6 | 6.048 | 4.80% |
| Nitrogen (N) | 2 | 28.014 | 22.21% |
| Oxygen (O) | 2 | 31.998 | 25.37% |

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 thymine

- One of the four bases in DNA
- Thymidine analogues are used as antiviral drugs
- Used to study UV damage to DNA

## Interesting facts

- Thymine is also called 5-methyluracil; RNA uses uracil instead.
- UV light can join two neighbouring thymines into a thymine dimer, which damages DNA.
- It was first isolated from calf thymus glands, which gave it its name.

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## Frequently asked questions

### What is the structure of Thymine?

Thymine is a pyrimidine base with two C=O groups and a methyl group at C5. It is found in DNA, where it pairs with adenine. Its SMILES is CC1=CNC(=O)NC1=O.

### What is the difference between thymine and uracil?

Thymine has a methyl group at C5; uracil has a hydrogen there. DNA uses thymine and RNA uses uracil.

### Is thymine in RNA?

Normally no. RNA uses uracil, although many transfer RNAs contain one modified nucleoside (ribothymidine) that carries thymine.

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

Thymine is C5H6N2O2 with a molar mass of 126.11 g/mol. It contains 15 atoms: 5 carbon, 6 hydrogen, 2 nitrogen, 2 oxygen.

### What is the IUPAC name of Thymine?

The IUPAC name is 5-methyl-1H-pyrimidine-2,4-dione.

### How do I draw Thymine?

Open the MolDraw editor, paste the SMILES CC1=CNC(=O)NC1=O or type "Thymine" 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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