MolDraw › 3D molecule models › 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.
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 |
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.
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.
Open MolDraw editorFrequently 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.