Record Information
Version2.0
Creation Date2012-05-31 10:28:02 -0600
Update Date2015-09-13 12:56:08 -0600
Secondary Accession Numbers
  • ECMDB00630
Identification
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.
Structure
Thumb
Synonyms:
  • 4-Amino-2(1H)-pyrimidinone
  • 4-Amino-2-hydroxypyrimidine
  • 4-Amino-2-oxo-1,2-dihydropyrimidine
  • 4-Aminouracil
  • Cytosine
  • Cytosinimine
Chemical Formula:C4H5N3O
Weight:Average: 111.102
Monoisotopic: 111.043261797
InChI Key:OPTASPLRGRRNAP-UHFFFAOYSA-N
InChI:InChI=1S/C4H5N3O/c5-3-1-2-6-4(8)7-3/h1-2H,(H3,5,6,7,8)
CAS number:71-30-7
IUPAC Name:6-amino-1,2-dihydropyrimidin-2-one
Traditional IUPAC Name:2(1H)-pyrimidinone, 6-amino-
SMILES:NC1=CC=NC(=O)N1
Chemical Taxonomy
ClassificationNot classified
Physical Properties
State:Solid
Charge:0
Melting point:>300 °C
Experimental Properties:
PropertyValueSource
Water Solubility:8.0 mg/mL [YALKOWSKY,SH & DANNENFELSER,RM (1992)]PhysProp
LogP:-1.73 [HANSCH,C ET AL. (1995)]PhysProp
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
Biological Properties
Cellular Locations:Cytoplasm
Reactions:
SMPDB Pathways:
Pyrimidine metabolismPW000942 Pw000942Pw000942 greyscalePw000942 simple
KEGG Pathways:
EcoCyc Pathways:
  • salvage pathways of pyrimidine ribonucleotides PWY0-163
Concentrations
ConcentrationStrainMediaGrowth StatusGrowth SystemTemperatureDetails
14± 0 uMK12 NCM3722Gutnick minimal complete medium (4.7 g/L KH2PO4; 13.5 g/L K2HPO4; 1 g/L K2SO4; 0.1 g/L MgSO4-7H2O; 10 mM NH4Cl) with 4 g/L glucoseMid-Log PhaseShake flask and filter culture37 oCPMID: 19561621
10± 0 uMBW2511348 mM Na2HPO4, 22 mM KH2PO4, 10 mM NaCl, 45 mM (NH4)2SO4, supplemented with 1 mM MgSO4, 1 mg/l thiamine·HCl, 5.6 mg/l CaCl2, 8 mg/l FeCl3, 1 mg/l MnCl2·4H2O, 1.7 mg/l ZnCl2, 0.43 mg/l CuCl2·2H2O, 0.6 mg/l CoCl2·2H2O and 0.6 mg/l Na2MoO4·2H2O. 4 g/L GlucoStationary Phase, glucose limitedBioreactor, pH controlled, O2 and CO2 controlled, dilution rate: 0.2/h37 oCPMID: 17379776
Find out more about how we convert literature concentrations.
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
GC-MSGC-MS Spectrum - GC-MSsplash10-03di-9400000000-109300546706ee372e62View in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOFsplash10-0udm-3970000000-a0532c16ce6140949915View in MoNA
GC-MSGC-MS Spectrum - GC-MSsplash10-0udl-4790000000-f8d777863969fe9feeeeView in MoNA
GC-MSGC-MS Spectrum - GC-MSsplash10-0h6s-2914000000-5c0c43de53d8e6d5ff65View in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOFsplash10-0f6w-4960000000-b053578e0f2ae00d0808View in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOFsplash10-0gxt-0914000000-bdca724db358d4bc5ccbView 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
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-03di-0900000000-d23ab5cfeba2d0a6ccffView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-02tc-9500000000-b9d5621a816bed354c10View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-00kf-9000000000-e57731b8ed024624cf7aView 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
References
References:
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  • Bennett, B. D., Kimball, E. H., Gao, M., Osterhout, R., Van Dien, S. J., Rabinowitz, J. D. (2009). "Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli." Nat Chem Biol 5:593-599. Pubmed: 19561621
  • 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. Pubmed: 8794746
  • 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. Pubmed: 15324698
  • 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. Pubmed: 14977367
  • 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. Pubmed: 11779412
  • Ishii, N., Nakahigashi, K., Baba, T., Robert, M., Soga, T., Kanai, A., Hirasawa, T., Naba, M., Hirai, K., Hoque, A., Ho, P. Y., Kakazu, Y., Sugawara, K., Igarashi, S., Harada, S., Masuda, T., Sugiyama, N., Togashi, T., Hasegawa, M., Takai, Y., Yugi, K., Arakawa, K., Iwata, N., Toya, Y., Nakayama, Y., Nishioka, T., Shimizu, K., Mori, H., Tomita, M. (2007). "Multiple high-throughput analyses monitor the response of E. coli to perturbations." Science 316:593-597. Pubmed: 17379776
  • Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., Tanabe, M. (2012). "KEGG for integration and interpretation of large-scale molecular data sets." Nucleic Acids Res 40:D109-D114. Pubmed: 22080510
  • Keseler, I. M., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama-Castro, S., Muniz-Rascado, L., Bonavides-Martinez, C., Paley, S., Krummenacker, M., Altman, T., Kaipa, P., Spaulding, A., Pacheco, J., Latendresse, M., Fulcher, C., Sarker, M., Shearer, A. G., Mackie, A., Paulsen, I., Gunsalus, R. P., Karp, P. D. (2011). "EcoCyc: a comprehensive database of Escherichia coli biology." Nucleic Acids Res 39:D583-D590. Pubmed: 21097882
  • 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. Pubmed: 10973920
  • 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. Pubmed: 16798912
  • 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. Pubmed: 16442598
  • 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. Pubmed: 15655803
  • 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. Pubmed: 11924907
  • 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. Pubmed: 1583911
  • 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. Pubmed: 16644408
  • 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. Pubmed: 15094325
  • van der Werf, M. J., Overkamp, K. M., Muilwijk, B., Coulier, L., Hankemeier, T. (2007). "Microbial metabolomics: toward a platform with full metabolome coverage." Anal Biochem 370:17-25. Pubmed: 17765195
  • Winder, C. L., Dunn, W. B., Schuler, S., Broadhurst, D., Jarvis, R., Stephens, G. M., Goodacre, R. (2008). "Global metabolic profiling of Escherichia coli cultures: an evaluation of methods for quenching and extraction of intracellular metabolites." Anal Chem 80:2939-2948. Pubmed: 18331064
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:
ResourceLink
CHEBI ID16040
HMDB IDHMDB00630
Pubchem Compound ID597
Kegg IDC00380
ChemSpider ID577
WikipediaCytosine
BioCyc IDCYTOSINE
EcoCyc IDCYTOSINE
Ligand ExpoCYT

Enzymes

General function:
Involved in hydrolase activity, hydrolyzing N-glycosyl compounds
Specific function:
Hydrolyzes both purine and pyrimidine ribonucleosides with a broad-substrate specificity with decreasing activity in the order uridine, xanthosine, inosine, adenosine, cytidine, guanosine
Gene Name:
rihC
Uniprot ID:
P22564
Molecular weight:
32560
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:
codA
Uniprot ID:
P25524
Molecular weight:
47591
Reactions
Cytosine + H(2)O = uracil + NH(3).
General function:
Involved in hydrolase activity, hydrolyzing N-glycosyl compounds
Specific function:
Hydrolyzes cytidine or uridine to ribose and cytosine or uracil, respectively. Has a clear preference for cytidine over uridine. Strictly specific for ribonucleosides. Has a low but significant activity for the purine nucleoside xanthosine
Gene Name:
rihB
Uniprot ID:
P33022
Molecular weight:
33748
Reactions
A pyrimidine nucleoside + H(2)O = D-ribose + a pyrimidine base.
General function:
Involved in hydrolase activity, hydrolyzing N-glycosyl compounds
Specific function:
Hydrolyzes with equal efficiency cytidine or uridine to ribose and cytosine or uracil, respectively
Gene Name:
rihA
Uniprot ID:
P41409
Molecular weight:
33823

Transporters

General function:
Involved in nucleobase transmembrane transporter activity
Specific function:
Required for cytosine transport into the cell
Gene Name:
codB
Uniprot ID:
P0AA82
Molecular weight:
43649
General function:
Involved in transporter activity
Specific function:
Non-specific porin
Gene Name:
ompN
Uniprot ID:
P77747
Molecular weight:
41220
General function:
Involved in transporter activity
Specific function:
Uptake of inorganic phosphate, phosphorylated compounds, and some other negatively charged solutes
Gene Name:
phoE
Uniprot ID:
P02932
Molecular weight:
38922
General function:
Involved in transporter activity
Specific function:
OmpF is a porin that forms passive diffusion pores which allow small molecular weight hydrophilic materials across the outer membrane. It is also a receptor for the bacteriophage T2
Gene Name:
ompF
Uniprot ID:
P02931
Molecular weight:
39333
General function:
Involved in transporter activity
Specific function:
Forms passive diffusion pores which allow small molecular weight hydrophilic materials across the outer membrane
Gene Name:
ompC
Uniprot ID:
P06996
Molecular weight:
40368