Cytosine

Athanor · official

C₄H₅N₃O · 111.1 g/mol

IUPAC name: 6-amino-1H-pyrimidin-2-one

Also called 4-aminopyrimidin-2-one, C, pyrimidine base

Nucleic acid parts Rings RNA DNA

Open in Athanor

Drawn from its SMILES with RDKit

WarningCauses skin irritation · Causes serious eye irritation · May cause respiratory irritation

Names and identifiers

IUPAC name: 6-amino-1H-pyrimidin-2-one
Synonyms: 4-aminopyrimidin-2-one, C, pyrimidine base
+ 35 more
4-aminopyrimidin-2(1H)-one, 4-Amino-2-hydroxypyrimidine, Cytosinimine, 2(1H)-Pyrimidinone, 4-amino-, 4-Amino-2(1H)-pyrimidinone, 6-amino-1H-pyrimidin-2-one, DTXSID4044456, NSC-27787, 8J337D1HZY, CHEBI:16040, 4-amino-3h-pyrimidin-2-one, DTXCID2024456, NSC27787, 6-amino-1,2-dihydropyrimidin-2-one, RefChem:5728, 200-749-5, 4-Aminouracil, 6-Aminopyrimidin-2(1h)-One, 4-aminopyrimidin-2-ol, MFCD00006034, Cytosin, 4-amino-2-pyrimidinol, 2(1H)-pyrimidinone, 6-amino-, 4-amino-2-oxo-1,2-dihydropyrimidine, Zytosin, Cyt, AI3-52281, 6-amino-3-hydropyrimidin-2-one, pyrimidine, 4-amino-2-hydroxy-, 4-Amino-1H-pyrimidin-2-one, 4-Aminopyrimidin-2(1H)-one (Cytosine), SMR000857094, EINECS 200-749-5, Lamivudine EP Impurity E, 4-amino-1,2-dihydropyrimidin-2-one
Molecular formula: C₄H₅N₃O
Empirical formula: C₄H₅N₃O
Molecular weight: 111.1 g/mol
Exact mass: 111.04326
CAS number: 71-30-7
PubChem CID: 597
Canonical SMILES: C1=C(NC(=O)N=C1)N
Isomeric SMILES: C1=C(NC(=O)N=C1)N
InChI: InChI=1S/C4H5N3O/c5-3-1-2-6-4(8)7-3/h1-2H,(H3,5,6,7,8)
InChIKey: OPTASPLRGRRNAP-UHFFFAOYSA-N
Molfile

Names, InChI and the identifiers from PubChem, retrieved 2026-10-14.

Calculated

Heavy atoms: 8
Rings: 1
Aromatic rings: 1
Fraction sp³ carbons (Fsp3): 0
H-bond donors: 2
H-bond acceptors: 3 computed here · PubChem 2
Rotatable bonds: 0
TPSA (Å²): 71.8 computed here · PubChem 67.5
Formal charge: 0
XLogP3: -1.7 PubChem
Complexity: 170 PubChem
Stereocenters: None
Double-bond geometry: None specified
Point group: C1 of one 3D conformer with its hydrogens, by Athanor’s engine (as in the app)

Elemental analysis

C43.24%
H4.54%
N37.82%
O14.40%

Isotope pattern

Each peak is a nominal mass with its abundance-weighted exact mass, as a percentage of the tallest, from IUPAC natural isotope abundances.

Computed from the structure with RDKit 2026.09 when this page was built, beside PubChem's own computed values from its record; where the two differ, both are shown.

Predicted

log P: -0.65 Crippen (Wildman and Crippen 1999)
log S (water solubility): -0.68 ESOL (Delaney 2004), log mol/L
Synthetic accessibility: 3.3 SA score, 1 easy to 10 hard (Ertl and Schuffenhauer 2009)

Drug-likeness: Lipinski’s rule of five

Molecular weight ≤ 500: 111.1
log P ≤ 5 (Crippen): -0.65
H-bond donors ≤ 5: 2
H-bond acceptors ≤ 10: 3

Passes all four rules.

¹³C NMR shifts, predicted

Predictions, not measurements; each names its method. A measured log P, where a source reports one, is under Physical properties.

Safety

Warning

Most widely reported: 59 company reports to ECHA. Source [1].

Harmful or irritant

H315Causes skin irritation (86.4% of reports)
H319Causes serious eye irritation (86.4% of reports)
H335May cause respiratory irritation (84.7% of reports)

Precautionary statements: P261, P264, P264+P265, P271, P280, P302+P352, P304+P340, P305+P351+P338, P319, P321, P332+P317, P337+P317, P362+P364, P403+P233, P405, P501

View all classifications (2)

[1] European Chemicals Agency (ECHA)This chemical does not meet GHS hazard criteria for 13.6% (8 of 59) of reports.
[1] European Chemicals Agency (ECHA) · 59 reports · WarningH315, H319, H335

Safety data sheets on the supplier’s page: Sigma-Aldrich, LGC Standards, eMolecules.

Always read the supplier’s safety data sheet before working with it.

Spectra

Experimental spectra held by these sources; each link opens the source's own record.

Literature

Reading PubChem, OpenAlex and GSRS…

Bioactivity

Reading ChEMBL…

References

[1]European Chemicals Agency (ECHA) · ECHA legal notice: reuse with acknowledgement · via PubChem · retrieved 2026-10-14
[2]NMRShiftDB · Linked only · via PubChem · retrieved 2026-10-14
[3]Human Metabolome Database (HMDB) · Linked only · via PubChem · retrieved 2026-10-14
[4]SpectraBase · Linked only · via PubChem · retrieved 2026-10-14
[5]MassBank Europe · Linked only · via PubChem · retrieved 2026-10-14
[6]MassBank of North America (MoNA) · CC BY 4.0 · via PubChem · retrieved 2026-10-14
[7]NIST Mass Spectrometry Data Center · Linked only · via PubChem · retrieved 2026-10-14
·Calculated values: computed by Athanor with RDKit 2026.09 from the structure.
·Literature on PubChem

Data last updated 2026-10-14.