Cytosine (YMDB00651)

Identification

YMDB ID

YMDB00651

Name

Cytosine

Species

Saccharomyces cerevisiae

Strain

Baker's yeast

Description

Cytosine, also known as C, belongs to the class of organic compounds known as pyrimidones. Pyrimidones 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. Cytosine is an extremely weak basic (essentially neutral) compound (based on its pKa). Cytosine exists in all living species, ranging from bacteria to humans.

Structure

MOL SDF 3D-SDF PDB SMILES InChI View 3D Structure

Synonyms

4-Amino-2-hydroxypyrimidine
4-Amino-2-oxo-1,2-dihydropyrimidine
4-Amino-2(1H)-pyrimidinone
4-Aminouracil
Cytosine
Cytosinimine
C
Cyt
Cytosin
Zytosin

CAS number

71-30-7

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)

IUPAC Name

6-amino-1,2-dihydropyrimidin-2-one

Traditional IUPAC Name

2(1H)-pyrimidinone, 6-amino-

Chemical Formula

C₄H₅N₃O

SMILES

NC1=NC(=O)NC=C1

Chemical Taxonomy

Description

belongs to the class of organic compounds known as pyrimidones. Pyrimidones 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 Class

Organoheterocyclic compounds

Class

Diazines

Sub Class

Pyrimidines and pyrimidine derivatives

Direct Parent

Pyrimidones

Alternative Parents

Substituents

Pyrimidone
Aminopyrimidine
Hydropyrimidine
Heteroaromatic compound
Azacycle
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Primary amine
Organooxygen compound
Organonitrogen compound
Amine
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

aminopyrimidine (CHEBI:16040 )
pyrimidone (CHEBI:16040 )
pyrimidine nucleobase (CHEBI:16040 )
pyrimidines (C00380 )
a pyrimidine-related compound (CYTOSINE )
a pyrimidine base (CYTOSINE )

Physical Properties

State

Solid

Charge

Melting point

>300 °C

Experimental Properties

Property	Value	Reference
Water Solubility	8 mg/mL at 25 oC [YALKOWSKY,SH & DANNENFELSER,RM (1992)]	PhysProp
LogP	-1.73 [HANSCH,C ET AL. (1995)]	PhysProp

Predicted Properties

Property	Value	Source
Water Solubility	30.9 g/L	ALOGPS
logP	-0.94	ALOGPS
logP	-1.1	ChemAxon
logS	-0.56	ALOGPS
pKa (Strongest Acidic)	9.83	ChemAxon
pKa (Strongest Basic)	-0.06	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	67.48 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	38.01 m³·mol⁻¹	ChemAxon
Polarizability	9.88 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	1	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Biological Properties

Cellular Locations

extracellular
cytoplasm

Organoleptic Properties

Not Available

SMPDB Pathways

Pyrimidine metabolism

PW002469

KEGG Pathways

Pyrimidine metabolism

ec00240

SMPDB Reactions

Not Available

KEGG Reactions

Cytidine monophosphate + water → Cytosine + alpha-D-ribose 5-phosphate

Cytosine + water + hydron → Uracil + Ammonium

Concentrations

Intracellular Concentrations

Not Available

Extracellular Concentrations

Not Available

Spectra

Spectrum Type	Description	Splash Key	View
GC-MS	GC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (Non-derivatized)	splash10-0udm-3970000000-a0532c16ce6140949915	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-MS (2 TMS)	splash10-0udl-4790000000-f8d777863969fe9feeee	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-MS (3 TMS)	splash10-0h6s-2914000000-5c0c43de53d8e6d5ff65	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0udm-3970000000-a0532c16ce6140949915	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-MS (Non-derivatized)	splash10-0udl-4790000000-f8d777863969fe9feeee	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-MS (Non-derivatized)	splash10-0h6s-2914000000-5c0c43de53d8e6d5ff65	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0f6w-4960000000-b053578e0f2ae00d0808	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0gxt-0914000000-bdca724db358d4bc5ccb	JSpectraViewer \| MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-03di-9400000000-109300546706ee372e62	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	JSpectraViewer
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)	splash10-03di-1900000000-ce9c385be713873945a4	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)	splash10-00kf-9100000000-5d27ff55f5080da7aaf0	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)	splash10-0006-9100000000-585d7d52c8ceb70d1b25	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive	splash10-03k9-0970000000-1491957a90e606f28d03	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive	splash10-0006-9000000000-f79bcd2133156449152c	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive	splash10-03di-0900000000-155769b79f7f2d14ee92	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive	splash10-03di-0900000000-4b1d0c842bcd05ceed1b	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive	splash10-03di-0910000000-7cd7c6a6f6e7c02ed6f1	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive	splash10-0006-9000000000-71a5fe9af8fc82824d54	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive	splash10-014i-0900000000-a210a634771936e0ffd6	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive	splash10-03di-0900000000-084e35ced5f5834ca93e	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Negative	splash10-03di-0900000000-d23ab5cfeba2d0a6ccff	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Negative	splash10-02tc-9500000000-3b81b2a441135c25b1e3	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Negative	splash10-00kf-9000000000-e57731b8ed024624cf7a	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Negative	splash10-0006-9000000000-a1679050e95cc271b8b7	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Negative	splash10-0006-9000000000-57b23eb60e1f7ce1ca97	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-03di-0900000000-d23ab5cfeba2d0a6ccff	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-02tc-9500000000-b9d5621a816bed354c10	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-00kf-9000000000-e57731b8ed024624cf7a	JSpectraViewer \| MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-03di-1900000000-4047bc076c5529ab5953	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-03dj-9600000000-4b29d871234eed6b5e40	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0uxv-9000000000-e7c1aa90d5d06c5c13b4	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-03di-2900000000-b19c12744f9718502007	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-014i-9100000000-1cf86d26f0f1d0794e0d	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0006-9000000000-51460ed94e186a6f38e0	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
2D NMR	[1H,1H] 2D NMR Spectrum	Not Available	JSpectraViewer
2D NMR	[1H,13C] 2D NMR Spectrum	Not Available	JSpectraViewer

References

References:

UniProt Consortium (2011). "Ongoing and future developments at the Universal Protein Resource." Nucleic Acids Res 39:D214-D219.21051339
Herrgard, M. J., Swainston, N., Dobson, P., Dunn, W. B., Arga, K. Y., Arvas, M., Bluthgen, N., Borger, S., Costenoble, R., Heinemann, M., Hucka, M., Le Novere, N., Li, P., Liebermeister, W., Mo, M. L., Oliveira, A. P., Petranovic, D., Pettifer, S., Simeonidis, E., Smallbone, K., Spasic, I., Weichart, D., Brent, R., Broomhead, D. S., Westerhoff, H. V., Kirdar, B., Penttila, M., Klipp, E., Palsson, B. O., Sauer, U., Oliver, S. G., Mendes, P., Nielsen, J., Kell, D. B. (2008). "A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology." Nat Biotechnol 26:1155-1160.18846089

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.

External Links:

Resource	Link
CHEBI ID	16040
HMDB ID	HMDB00630
Pubchem Compound ID	597
Kegg ID	C00380
ChemSpider ID	577
FOODB ID	FDB022151
Wikipedia	Cytosine
BioCyc ID	CYTOSINE

Enzymes

Protein Details

1. Vitamin B6 transporter TPN1

General function:: Involved in nucleobase transmembrane transporter activity
Specific function:: Thiamine-regulated, high affinity import carrier of pyridoxine, pyridoxal and pyridoxamine
Gene Name:: TPN1
Uniprot ID:: P53099
Molecular weight:: 64545.80078

Protein Details

2. Cytosine deaminase

General function:: Involved in zinc ion binding
Specific function:: Converts cytosine to uracil or 5-methylcytosine to thymine by deaminating carbon number 4
Gene Name:: FCY1
Uniprot ID:: Q12178
Molecular weight:: 17506.90039

Reactions

Cytosine + H(2)O → uracil + NH(3).

Transporters

Protein Details

1. Purine-cytosine permease FCY21

General function:: Involved in nucleobase transmembrane transporter activity
Specific function:: Probable purine-cytosine permease
Gene Name:: FCY21
Uniprot ID:: P40039
Molecular weight:: 58049.60156

Protein Details

2. Purine-cytosine permease FCY2

General function:: Involved in nucleobase transmembrane transporter activity
Specific function:: This permease has a broad specificity towards purines, and also transport cytosine and 5-methylcytosine but neither uracil nor thymine
Gene Name:: FCY2
Uniprot ID:: P17064
Molecular weight:: 58200.69922

Protein Details

3. Purine-cytosine permease FCY22

General function:: Involved in nucleobase transmembrane transporter activity
Specific function:: Probable purine-cytosine permease
Gene Name:: FCY22
Uniprot ID:: Q12119
Molecular weight:: 57326.69922

Structure for #<Compound:0xabcc3674>

Enzymes

Reactions

Transporters