A summary of the most common chemical descriptors (InChI Key and SMILES codes) for Cytosine are summarized together with 3D and 2D structures and relevant physico-chemical properties.

What is the Cytosine?

The molecule Cytosine presents a molecular formula of C4H5N3O and its IUPAC name is 6-amino-1H-pyrimidin-2-one.

Cytosine is a nitrogenous base that is one of the four building blocks of DNA (deoxyribonucleic acid). It is a pyrimidine nucleoside, meaning that it is composed of a pyrimidine base (cytosine) bonded to a five-carbon sugar (ribose). Along with adenine, guanine, and thymine, cytosine plays a vital role in the structure and function of DNA..

In DNA, cytosine is paired with guanine through a process called hydrogen bonding. This pairing helps to stabilize the double helix structure of DNA, which is essential for the transmission of genetic information from one generation to the next..

In addition to its role in DNA, cytosine is also found in RNA (ribonucleic acid), where it is paired with uracil instead of thymine. RNA is involved in the synthesis of proteins and plays a key role in the regulation of gene expression..

Cytosine is synthesized in the body through the de novo pathway, which involves the conversion of ribose-5-phosphate and aspartate into cytosine. It can also be obtained through the diet, as it belongs in some foods, such as eggs and dairy products..

Cytosine is important for maintaining the integrity of the genome and is involved in a number of biological processes, including DNA repair and DNA methylation. It has also been the subject of research for its potential role in cancer and other diseases..


From all the above, this molecule is a nitrogenous base that is essential for the structure and function of DNA and RNA. It is involved in a number of important biological processes and has been the subject of extensive research for its potential role in diseases such as cancer..

3D structure

Cartesian coordinates

Geometry of Cytosine in x, y and z coordinates (Å units) to copy/paste elsewhere. Generated with Open Babel software.

2D drawing


Cytosine OPTASPLRGRRNAP-UHFFFAOYSA-N chemical compound 2D structure molecule svg


Molecule descriptors

IUPAC name6-amino-1H-pyrimidin-2-one
InChI codeInChI=1S/C4H5N3O/c5-3-1-2-6-4(8)7-3/h1-2H,(H3,5,6,7,8)

Other names (synonyms)

IUPAC nomenclature provides a standardized method for naming chemical compounds. Although this system is widely used in chemistry, many chemical compounds have also other names commonly used in different contexts. These synonyms can come from a variety of sources and are used for a variety of purposes.

One common source of synonyms for chemical compounds is the common or trivial names, assigned on the basis of appearance, properties, or origin of the molecule.

Another source of synonyms are historical or obsolete names employed in the past, however replaced nowadays by more modern or standardized names.

In addition to common and historical names, chemical compounds may also have synonyms that are specific to a particular field or industry.

  • 006C034
  • 107646-83-3
  • 107646-84-4
  • 134434-39-2
  • 134434-40-5
  • 2(1H)-Pyrimidinone, 3,4-dihydro-4-imino-, (E)- (9CI)
  • 2(1H)-Pyrimidinone, 3,4-dihydro-4-imino-, (Z)- (9CI)
  • 2(1H)-Pyrimidinone, 4-amino-
  • 2(1H)-Pyrimidinone, 4-amino- (9CI)
  • 2(1H)-pyrimidinone, 6-amino-
  • 2-Hydroxy-6-amino-pyrimidin
  • 2-Pyrimidinol, 1,4-dihydro-4-imino-, (Z)- (9CI)
  • 2-Pyrimidinol, 1,6-dihydro-6-imino-, (E)- (9CI)
  • 287484-45-1
  • 3h-cytosine
  • 4-Amino-1H-pyrimidin-2-one
  • 4-Amino-2(1)-pyrimidone
  • 4-Amino-2(1H)-pyrimidinone
  • 4-Amino-2(1H)-pyrimidone
  • 4-Amino-2(1H)pyrimidone
  • 4-Amino-2-hydroxypyrimidine
  • 4-Amino-2-oxypyrimidine
  • 4-Aminopyrimidin-2(1H)-one (Cytosine)
  • 4-Aminopyrimidin-2-(1H)-one
  • 4-amino-1,2-dihydropyrimidin-2-one
  • 4-amino-2-oxo-1,2-dihydropyrimidine
  • 4-amino-2-pyrimidinol
  • 4-amino-3h-pyrimidin-2-one
  • 4-amino-pyrimidin-2-ol
  • 4-aminopyrimidin-2(1H)-one
  • 4-aminopyrimidin-2-ol
  • 4-imino-3,4-dihydropyrimidin-2(1H)-one
  • 6-Aminopyrimidin-2(1h)-One
  • 6-amino-1,2-dihydropyrimidin-2-one
  • 6-amino-1H-pyrimidin-2-one
  • 6-amino-1H-pyrimidin-2-one;CYTOSINE
  • 71-30-7
  • 71C307
  • 8J337D1HZY
  • A837149
  • AC-2489
  • ACT01668
  • AI3-52281
  • AM83918
  • BCP22793
  • BCP9000005
  • BP-20183
  • C00380
  • CBA1D098-C5AB-46CE-AAC6-754572886EB2
  • CCG-266052
  • CID 5274263
  • CS-W020703
  • Cyt
  • Cytosin
  • Cytosine
  • Cytosine (8CI)
  • Cytosine-[15N2]
  • Cytosinimine
  • DB-029615
  • DSSTox_CID_24456
  • DSSTox_GSID_44456
  • DSSTox_RID_80242
  • EC 200-749-5
  • Epitope ID:167475
  • FT-0617471
  • GTPL8490
  • HMS2233N21
  • HMS3369N05
  • HY-I0626
  • Lamivudine impurity c
  • Lamivudine impurity c rs
  • MFCD00006034
  • MLS001332635
  • MLS001332636
  • NCGC00247019-01
  • NCGC00255926-01
  • NCI60_012445
  • NSC 27787
  • NSC-27787
  • NSC27787
  • Q178425
  • SMR000857094
  • SRI-2354-05
  • STK366767
  • STL455080
  • STR01426
  • SY001643
  • Z256707830
  • Zytosin
  • aminopyrimidone
  • bmse000180
  • cytosine
  • iminopyrimidinone
  • s4893

Reference codes for other databases

There exist several different chemical codes commonly used in orded to identify molecules:
  • ZINC895210
  • CAS-71-30-7
  • UNII-8J337D1HZY
  • AKOS000120336
  • AKOS005443393
  • AKOS015896942
  • ALBB-021996
  • DTXSID4044456
  • CHEMBL15913
  • CHEBI:16040
  • Tox21_302139
  • EINECS 200-749-5
  • SCHEMBL4059

Physico-Chemical properties

IUPAC name6-amino-1H-pyrimidin-2-one
Molecular formulaC4H5N3O
Molecular weight111.10
Melting point (ºC)
Boiling point (ºC)
Density (g/cm3)
Molar refractivity29.3
Topological polar surface area71.8

LogP and topological polar surface area (TPSA) values were estimated using Open Babel software.

The n-octanol/water partition coeficient (Kow) data is applied in toxicology and drug research. Kow values are used, to guess the environmental fate of persistent organic pollutants. High partition coefficients values, tend to accumulate in the fatty tissue of organisms. Molecules with a log(Kow) (or LogP) greater than 5 are considered to bioaccumulate.

TPSA values are the sum of the surface area over all polar atoms or molecules, mainly oxygen and nitrogen, also including hydrogen atoms.

In medicinal chemistry, TPSA is used to assess the ability of a drug to permeabilise cells.

For molecules to penetrate the blood-brain barrier (and act on receptors in the central nervous system), TPSA values below 90 Å2 are required. Thus, molecules with a polar surface area greater than 140 Å2 tend to be poorly permeable to cell membranes.