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Record Information
Version3.6
Creation Date2005-11-16 15:48:42 UTC
Update Date2016-02-11 01:03:03 UTC
HMDB IDHMDB00630
Secondary Accession NumbersNone
Metabolite Identification
Common NameCytosine
DescriptionCytosine is a pyrimidine base that is a fundamental unit of nucleic acids. The deamination of cytosine alone is apparent and the nucleotide of cytosine is the prime mutagenic nucleotide in leukaemia and cancer.
Structure
Thumb
Synonyms
ValueSource
4-amino-2(1H)-PyrimidinoneChEBI
4-amino-2-HydroxypyrimidineChEBI
CChEBI
CytChEBI
CytosinChEBI
ZytosinChEBI
4-amino-2-oxo-1,2-DihydropyrimidineHMDB
4-AminouracilHMDB
CytosinimineHMDB
Chemical FormulaC4H5N3O
Average Molecular Weight111.102
Monoisotopic Molecular Weight111.043261797
IUPAC Name6-amino-1,2-dihydropyrimidin-2-one
Traditional Name2(1H)-pyrimidinone, 6-amino-
CAS Registry Number71-30-7
SMILES
NC1=CC=NC(=O)N1
InChI Identifier
InChI=1S/C4H5N3O/c5-3-1-2-6-4(8)7-3/h1-2H,(H3,5,6,7,8)
InChI KeyInChIKey=OPTASPLRGRRNAP-UHFFFAOYSA-N
Chemical 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.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassDiazines
Sub ClassPyrimidines and pyrimidine derivatives
Direct ParentPyrimidones
Alternative Parents
Substituents
  • Pyrimidone
  • Aminopyrimidine
  • Primary aromatic amine
  • Hydropyrimidine
  • Heteroaromatic compound
  • Azacycle
  • Hydrocarbon derivative
  • Primary amine
  • Organooxygen compound
  • Organonitrogen compound
  • Amine
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Ontology
StatusDetected and Quantified
Origin
  • Endogenous
BiofunctionNot Available
ApplicationNot Available
Cellular locations
  • Extracellular
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting Point> 300 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility8.0 mg/mLNot Available
LogP-1.73HANSCH,C ET AL. (1995)
Predicted Properties
PropertyValueSource
Water Solubility30.9 mg/mLALOGPS
logP-0.94ALOGPS
logP-1.1ChemAxon
logS-0.56ALOGPS
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
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectra
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
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
2D NMR[1H,1H] 2D NMR SpectrumNot Available
2D NMR[1H,13C] 2D NMR SpectrumNot Available
Biological Properties
Cellular Locations
  • Extracellular
Biofluid Locations
  • Blood
  • Feces
  • Urine
Tissue Location
  • Fibroblasts
  • Gut
  • Muscle
  • Neuron
  • Placenta
  • Plasma
  • Prostate
  • Skeletal Muscle
  • Skin
  • Spleen
  • Testes
PathwaysNot Available
Normal Concentrations
BiofluidStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified6.4 +/- 8.5 uMAdult (>18 years old)BothNormal details
FecesDetected but not QuantifiedNot ApplicableNot SpecifiedNot Specified
Normal
details
FecesDetected but not QuantifiedNot ApplicableInfant (0-1 year old)Both
Normal
details
UrineDetected and Quantified4.1 (1.1-10.7) umol/mmol creatinineAdult (>18 years old)Both
Normal
details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
DrugBank Metabolite IDNot Available
Phenol Explorer Compound IDNot Available
Phenol Explorer Metabolite IDNot Available
FoodDB IDFDB022151
KNApSAcK IDNot Available
Chemspider ID577
KEGG Compound IDC00380
BioCyc IDCYTOSINE
BiGG ID34812
Wikipedia LinkCytosine
NuGOwiki LinkHMDB00630
Metagene LinkHMDB00630
METLIN ID283
PubChem Compound597
PDB IDCYT
ChEBI ID16040
References
Synthesis ReferenceHitchings, 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)
General References
  1. Rodriguez Ortner E, Hayes RB, Weissfeld J, Gelmann EP: Effect of homeodomain protein NKX3.1 R52C polymorphism on prostate gland size. Urology. 2006 Feb;67(2):311-5. Epub 2006 Jan 25. [16442598 ]
  2. Harvey BG, Maroni J, O'Donoghue KA, Chu KW, Muscat JC, Pippo AL, Wright CE, Hollmann C, Wisnivesky JP, Kessler PD, Rasmussen HS, Rosengart TK, Crystal RG: Safety of local delivery of low- and intermediate-dose adenovirus gene transfer vectors to individuals with a spectrum of morbid conditions. Hum Gene Ther. 2002 Jan 1;13(1):15-63. [11779412 ]
  3. Cheng JC, Yoo CB, Weisenberger DJ, Chuang J, Wozniak C, Liang G, Marquez VE, Greer S, Orntoft TF, Thykjaer T, Jones PA: Preferential response of cancer cells to zebularine. Cancer Cell. 2004 Aug;6(2):151-8. [15324698 ]
  4. Carotti D, Funiciello S, Lavia P, Caiafa P, Strom R: Different effects of histone H1 on de novo DNA methylation in vitro depend on both the DNA base composition and the DNA methyltransferase. Biochemistry. 1996 Sep 10;35(36):11660-7. [8794746 ]
  5. Tawa R, Ueno S, Yamamoto K, Yamamoto Y, Sagisaka K, Katakura R, Kayama T, Yoshimoto T, Sakurai H, Ono T: Methylated cytosine level in human liver DNA does not decline in aging process. Mech Ageing Dev. 1992 Mar 1;62(3):255-61. [1583911 ]
  6. Tsuchiya K, Tajima H, Yamada M, Takahashi H, Kuwae T, Sunaga K, Katsube N, Ishitani R: Disclosure of a pro-apoptotic glyceraldehyde-3-phosphate dehydrogenase promoter: anti-dementia drugs depress its activation in apoptosis. Life Sci. 2004 May 14;74(26):3245-58. [15094325 ]
  7. Putta MR, Zhu F, Li Y, Bhagat L, Cong Y, Kandimalla ER, Agrawal S: Novel oligodeoxynucleotide agonists of TLR9 containing N3-Me-dC or N1-Me-dG modifications. Nucleic Acids Res. 2006 Jun 23;34(11):3231-8. Print 2006. [16798912 ]
  8. Bawdon RE, Sobhi S, Dax J: The transfer of anti-human immunodeficiency virus nucleoside compounds by the term human placenta. Am J Obstet Gynecol. 1992 Dec;167(6):1570-4. [1335207 ]
  9. Sawamura D, Abe R, Goto M, Akiyama M, Hemmi H, Akira S, Shimizu H: Direct injection of plasmid DNA into the skin induces dermatitis by activation of monocytes through toll-like receptor 9. J Gene Med. 2005 May;7(5):664-71. [15655803 ]
  10. Thajeb P, Ma YS, Tzen CY, Chuang CK, Wu TY, Chen SC, Wei YH: Oculopharyngeal somatic myopathy in a patient with a novel large-scale 3,399 bp deletion and a homoplasmic T5814C transition of the mitochondrial DNA. Clin Neurol Neurosurg. 2006 Jun;108(4):407-10. [16644408 ]
  11. Sigalotti L, Coral S, Nardi G, Spessotto A, Cortini E, Cattarossi I, Colizzi F, Altomonte M, Maio M: Promoter methylation controls the expression of MAGE2, 3 and 4 genes in human cutaneous melanoma. J Immunother. 2002 Jan-Feb;25(1):16-26. [11924907 ]
  12. Costa E, Grayson DR, Mitchell CP, Tremolizzo L, Veldic M, Guidotti A: GABAergic cortical neuron chromatin as a putative target to treat schizophrenia vulnerability. Crit Rev Neurobiol. 2003;15(2):121-42. [14977367 ]
  13. Machwe A, Orren DK, Bohr VA: Accelerated methylation of ribosomal RNA genes during the cellular senescence of Werner syndrome fibroblasts. FASEB J. 2000 Sep;14(12):1715-24. [10973920 ]

Enzymes

General function:
Involved in DNA binding
Specific function:
Binds CpG islands in promoters where the DNA is methylated at position 5 of cytosine within CpG dinucleotides. Binds hemi-methylated DNA as well. Recruits histone deacetylases and DNA methyltransferases. Acts as transcriptional repressor and plays a role in gene silencing. Isoform 1 may enhance the activation of some unmethylated cAMP-responsive promoters. Reports about DNA demethylase activity of isoform 2 are contradictory
Gene Name:
MBD2
Uniprot ID:
Q9UBB5
Molecular weight:
43254.3
General function:
Involved in nucleotide binding
Specific function:
Essential component of the apolipoprotein B mRNA editing enzyme complex which is responsible for the postranscriptional editing of a CAA codon for Gln to a UAA codon for stop in APOB mRNA. Binds to APOB mRNA and is probably responsible for docking the catalytic subunit, APOBEC1, to the mRNA to allow it to deaminate its target cytosine. The complex also protects the edited APOB mRNA from nonsense-mediated decay
Gene Name:
A1CF
Uniprot ID:
Q9NQ94
Molecular weight:
65202.0
General function:
Involved in DNA binding
Specific function:
Transcriptional repressor that binds CpG islands in promoters where the DNA is methylated at position 5 of cytosine within CpG dinucleotides. Binding is abolished by the presence of 7-mG that is produced by DNA damage by methylmethanesulfonate (MMS). Acts as transcriptional repressor and plays a role in gene silencing by recruiting AFT7IP, which in turn recruits factors such as the histone methyltransferase SETDB1. Probably forms a complex with SETDB1 and ATF7IP that represses transcription and couples DNA methylation and histone 'Lys-9' trimethylation. Isoform 1 and isoform 2 can also repress transcription from unmethylated promoters
Gene Name:
MBD1
Uniprot ID:
Q9UIS9
Molecular weight:
66606.5