Record Information
Version 1.0
Update Date 1/22/2018 11:54:54 AM
Metabolite IDPAMDB000161
Name: Cytosine
Description:Cytosine (C) is one of the four main bases found in DNA and RNA, along with adenine, guanine, and thymine (uracil in RNA). It is a pyrimidine derivative, with a heterocyclic aromatic ring and two substituents attached (an amine group at position 4 and a keto group at position 2). The nucleoside of cytosine is cytidine.
  • 4-Amino-2(1H)-pyrimidinone
  • 4-Amino-2-hydroxypyrimidine
  • 4-Amino-2-oxo-1,2-dihydropyrimidine
  • 4-Aminouracil
  • Cytosine
  • Cytosinimine
Chemical Formula: C4H5N3O
Average Molecular Weight: 111.102
Monoisotopic Molecular Weight: 111.043261797
CAS number: 71-30-7
IUPAC Name:6-amino-1,2-dihydropyrimidin-2-one
Traditional IUPAC Name: 2(1H)-pyrimidinone, 6-amino-
Chemical Taxonomy
Taxonomy DescriptionThis compound belongs to the class of organic compounds known as pyrimidones. These are compounds that contain a pyrimidine ring,which bears a ketone. Pyrimidine is a 6-membered ring consisting of four carbon atoms and two nitrogen centers at the 1- and 3- ring positions.
Kingdom Organic compounds
Super ClassOrganoheterocyclic compounds
Class Diazines
Sub ClassPyrimidines and pyrimidine derivatives
Direct Parent Pyrimidones
Alternative Parents
  • Pyrimidone
  • Aminopyrimidine
  • Primary aromatic amine
  • Hydropyrimidine
  • Heteroaromatic compound
  • Azacycle
  • Hydrocarbon derivative
  • Primary amine
  • Organooxygen compound
  • Organonitrogen compound
  • Amine
  • Aromatic heteromonocyclic compound
Molecular Framework Aromatic heteromonocyclic compounds
External Descriptors
Physical Properties
State: Solid
Melting point: >300 °C
Experimental Properties:
Water Solubility:8.0 mg/mL [YALKOWSKY,SH & DANNENFELSER,RM (1992)]PhysProp
LogP:-1.73 [HANSCH,C ET AL. (1995)]PhysProp
Predicted Properties
Water Solubility30.9 mg/mLALOGPS
pKa (Strongest Acidic)9.83ChemAxon
pKa (Strongest Basic)3.8ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area67.48 Å2ChemAxon
Rotatable Bond Count0ChemAxon
Refractivity38.01 m3·mol-1ChemAxon
Polarizability9.88 Å3ChemAxon
Number of Rings1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations: Cytoplasm
Spectrum TypeDescriptionSplash Key
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies)splash10-0udm-3970000000-a0532c16ce6140949915View in MoNA
GC-MSGC-MS Spectrum - GC-MS (2 TMS)splash10-0udl-4790000000-f8d777863969fe9feeeeView in MoNA
GC-MSGC-MS Spectrum - GC-MS (3 TMS)splash10-0h6s-2914000000-5c0c43de53d8e6d5ff65View in MoNA
GC-MSGC-MS Spectrum - GC-MSNot Available
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)splash10-03di-1900000000-ce9c385be713873945a4View in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)splash10-00kf-9100000000-5d27ff55f5080da7aaf0View in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)splash10-0006-9100000000-585d7d52c8ceb70d1b25View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positivesplash10-03k9-0970000000-1491957a90e606f28d03View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positivesplash10-0006-9000000000-f79bcd2133156449152cView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positivesplash10-03di-0900000000-155769b79f7f2d14ee92View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positivesplash10-03di-0900000000-4b1d0c842bcd05ceed1bView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positivesplash10-03di-0910000000-7cd7c6a6f6e7c02ed6f1View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positivesplash10-0006-9000000000-71a5fe9af8fc82824d54View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positivesplash10-014i-0900000000-a210a634771936e0ffd6View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positivesplash10-03di-0900000000-084e35ced5f5834ca93eView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Negativesplash10-03di-0900000000-d23ab5cfeba2d0a6ccffView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Negativesplash10-02tc-9500000000-3b81b2a441135c25b1e3View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Negativesplash10-00kf-9000000000-e57731b8ed024624cf7aView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Negativesplash10-0006-9000000000-a1679050e95cc271b8b7View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Negativesplash10-0006-9000000000-57b23eb60e1f7ce1ca97View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-03di-1900000000-4047bc076c5529ab5953View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03dj-9600000000-4b29d871234eed6b5e40View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0uxv-9000000000-e7c1aa90d5d06c5c13b4View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-03di-2900000000-b19c12744f9718502007View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-014i-9100000000-1cf86d26f0f1d0794e0dView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0006-9000000000-51460ed94e186a6f38e0View in MoNA
1D NMR13C NMR SpectrumNot Available
1D NMR1H NMR SpectrumNot Available
1D NMR1H NMR SpectrumNot Available
1D NMR13C NMR SpectrumNot Available
1D NMR1H NMR SpectrumNot Available
2D NMR[1H,1H] 2D NMR SpectrumNot Available
2D NMR[1H,13C] 2D NMR SpectrumNot Available
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Synthesis Reference: Hitchings, George H.; Elion, Gertrude B.; Falco, Elvira A.; Russell, Peter B. New synthesis of cytosine and 5-methylcytosine. Journal of Biological Chemistry (1949), 177 357-60.
Material Safety Data Sheet (MSDS) Download (PDF)
External Links:
Pubchem Compound ID597
Kegg IDC00380
ChemSpider ID577
Ligand ExpoCYT


General function:
Involved in hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds
Specific function:
Cytosine + H(2)O = uracil + NH(3)
Gene Name:
Locus Tag:
Molecular weight:
47.1 kDa
Cytosine + H(2)O = uracil + NH(3).


General function:
Involved in nucleobase transmembrane transporter activity
Specific function:
Required for cytosine transport into the cell
Gene Name:
Locus Tag:
Molecular weight:
43 kDa