Record Information
Version1.0
Creation date2011-04-11 17:01:40 UTC
Update date2019-11-26 03:20:54 UTC
Primary IDFDB021809
Secondary Accession NumbersNot Available
Chemical Information
FooDB NameCytidine
DescriptionCytidine is a nucleoside that is composed of the base cytosine linked to the five-carbon sugar D-ribose. Cytidine is a pyrimidine that besides being incorporated into nucleic acids, can serve as substrate for the salvage pathway of pyrimidine nucleotide synthesis; as precursor of the cytidine triphosphate (CTP) needed in the phosphatidylcholine (PC) and phosphatidylethanolamine (PE) biosynthetic pathway. These variations probably reflect the species differences in cytidine deaminase, the enzyme that converts cytidine to uridine in the body. The transports of cytidine into the brain's extracellular fluid, and then into neurons and glia, are essential prerequisites for cytidine to be utilized in brain. An efficient mechanism mediating the brain uptake of circulating cytidine has not yet been demonstrated. The biosynthesis of PC, the most abundant phosphatide in the brain, via the Kennedy pathway requires phosphocholine and cytidine triphosphate (CTP), a cytidine nucleotide, which is involved in the rate-limiting step. The enzyme that converts CTP to endogenous CDP-choline (CTP: phosphocholine cytidylyltransferase) is unsaturated at physiological brain CTP levels. APOBEC is a family of enzymes has been discovered with the ability to deaminate cytidines on RNA or DNA. The human apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like 3G (APOBEC3G, or hA3G) protein, provides cells with an intracellular antiretroviral activity that is associated with the hypermutation of viral DNA through cytidine deamination. Indeed, hA3G belongs to a family of vertebrate proteins that contain one or two copies of a signature sequence motif unique to cytidine deaminases (CTDAs). (PMID: 16769123, 15780864, 16720547) [HMDB]. Cytidine is found in many foods, some of which are sweet potato, rocket salad (sspecies), mexican groundcherry, and cinnamon.
CAS Number65-46-3
Structure
Thumb
Synonyms
SynonymSource
ArabinosylcytosineMeSH
AracytidineMeSH
CytarabineMeSH
CytosarMeSH
Cytosar-uMeSH
CytosarUMeSH
Cytosine arabinosideMeSH
Hydrochloride, cytarabineMeSH
beta-Ara CMeSH
Ara-CMeSH
AracytineMeSH
Cytarabine hydrochlorideMeSH
Cytosar uMeSH
ArabinofuranosylcytosineMeSH
Arabinoside, cytosineMeSH
CytonalMeSH
1-(b-D-Ribofuranosyl)-2-oxo-4-amino-1,2-dihydro-1,3-diazineHMDB
1-(b-delta-Ribofuranosyl)-2-oxo-4-amino-1,2-dihydro-1,3-diazineHMDB
1-b-D-RibofuranosylcytosineGenerator
1-b-D-Ribosyl-cytosineHMDB
1-beta-D-Ribofuranosyl-cytosineHMDB
1-beta-D-RibofuranosylcytosineChEBI
1-beta-delta-Ribofuranosyl-cytosineHMDB
1-beta-delta-RibofuranosylcytosineHMDB
1-beta-delta-Ribosyl-cytosineHMDB
1-β-D-ribofuranosylcytosineGenerator
1b-D-RibofuranosylcytosineGenerator
1beta-D-RibofuranosylcytosineChEBI
1beta-delta-RibofuranosylcytosineHMDB
1beta-RibofuranosylcytosineHMDB
1β-D-ribofuranosylcytosineGenerator
4-amino-1-b-D-RIBOFURANOSYL-2(1H)-pyrimidinoneGenerator
4-amino-1-b-D-Ribofuranosylpyrimidin-2(1H)-oneGenerator
4-amino-1-BETA-D-RIBOFURANOSYL-2(1H)-pyrimidinoneChEBI
4-amino-1-beta-D-Ribofuranosylpyrimidin-2(1H)-oneChEBI
4-amino-1-beta-delta-Ribofuranosyl-2(1H)-pyrimidinoneHMDB
4-amino-1-β-D-ribofuranosyl-2(1H)-pyrimidinoneGenerator
4-amino-1-β-D-ribofuranosylpyrimidin-2(1H)-oneGenerator
4-amino-1b-D-Ribofuranosyl-2(1H)-pyrimidinoneGenerator
4-amino-1beta-D-Ribofuranosyl-2(1H)-pyrimidinoneChEBI
4-amino-1β-D-ribofuranosyl-2(1H)-pyrimidinoneGenerator
CydChEBI
CytidinChEBI
Cytosine ribosideChEBI
Cytosine-1b-D-ribofuranosideGenerator
Cytosine-1b-delta-ribofuranosideHMDB
Cytosine-1beta-D-ribofuranosideChEBI
Cytosine-1beta-delta-ribofuranosideHMDB
Cytosine-1β-D-ribofuranosideGenerator
ZytidinChEBI
Predicted Properties
PropertyValueSource
Water Solubility2.8 g/LALOGPS
logP-2ALOGPS
logP-2.8ChemAxon
logS-1.9ALOGPS
pKa (Strongest Acidic)12.55ChemAxon
pKa (Strongest Basic)-0.062ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count7ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area128.61 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity54.54 m³·mol⁻¹ChemAxon
Polarizability22.74 ųChemAxon
Number of Rings2ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Chemical FormulaC9H13N3O5
IUPAC name4-amino-1-[3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2-dihydropyrimidin-2-one
InChI IdentifierInChI=1S/C9H13N3O5/c10-5-1-2-12(9(16)11-5)8-7(15)6(14)4(3-13)17-8/h1-2,4,6-8,13-15H,3H2,(H2,10,11,16)
InChI KeyUHDGCWIWMRVCDJ-UHFFFAOYSA-N
Isomeric SMILESOCC1OC(C(O)C1O)N1C=CC(=N)N=C1O
Average Molecular Weight243.2166
Monoisotopic Molecular Weight243.085520541
Classification
Description Belongs to the class of organic compounds known as pyrimidine nucleosides. Pyrimidine nucleosides are compounds comprising a pyrimidine base attached to a ribosyl or deoxyribosyl moiety.
KingdomOrganic compounds
Super ClassNucleosides, nucleotides, and analogues
ClassPyrimidine nucleosides
Sub ClassNot Available
Direct ParentPyrimidine nucleosides
Alternative Parents
Substituents
  • Pyrimidine nucleoside
  • Glycosyl compound
  • N-glycosyl compound
  • Pentose monosaccharide
  • Aminopyrimidine
  • Pyrimidone
  • Hydropyrimidine
  • Monosaccharide
  • Pyrimidine
  • Imidolactam
  • Tetrahydrofuran
  • Heteroaromatic compound
  • Secondary alcohol
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Organic nitrogen compound
  • Primary alcohol
  • Organic oxide
  • Organooxygen compound
  • Organonitrogen compound
  • Amine
  • Alcohol
  • Organopnictogen compound
  • Organic oxygen compound
  • Primary amine
  • Hydrocarbon derivative
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Ontology
OntologyNo ontology term
Physico-Chemical Properties - Experimental
Physico-Chemical Properties - Experimental
PropertyValueReference
Physical stateSolid
Physical DescriptionNot Available
Mass CompositionNot Available
Melting PointNot Available
Boiling PointNot Available
Experimental Water SolubilityNot Available
Experimental logPNot Available
Experimental pKaNot Available
Isoelectric pointNot Available
ChargeNot Available
Optical RotationNot Available
Spectroscopic UV DataNot Available
DensityNot Available
Refractive IndexNot Available
Spectra
Spectra
EI-MS/GC-MS
TypeDescriptionSplash KeyView
Predicted GC-MSCytarabine, non-derivatized, Predicted GC-MS Spectrum - 70eV, Positivesplash10-05dl-9310000000-baa27af3867d7b2962e5Spectrum
Predicted GC-MSCytarabine, non-derivatized, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSCytarabine, TMS_1_1, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSCytarabine, TMS_1_2, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSCytarabine, TMS_1_3, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSCytarabine, TMS_1_4, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSCytarabine, TMS_1_5, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSCytarabine, TMS_2_1, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSCytarabine, TMS_2_2, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSCytarabine, TMS_2_3, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSCytarabine, TMS_2_4, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSCytarabine, TMS_2_5, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSCytarabine, TMS_2_6, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSCytarabine, TMS_2_7, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSCytarabine, TMS_2_8, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSCytarabine, TMS_2_9, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSCytarabine, TMS_2_10, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSCytarabine, TMS_3_1, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSCytarabine, TMS_3_2, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSCytarabine, TMS_3_3, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSCytarabine, TMS_3_4, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSCytarabine, TMS_3_5, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSCytarabine, TMS_3_6, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSCytarabine, TMS_3_7, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSCytarabine, TMS_3_8, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
MS/MS
TypeDescriptionSplash KeyView
MS/MSLC-MS/MS Spectrum - 40V, Positivesplash10-03di-0900000000-4d7ac7a2020f3bcdb8afSpectrum
MS/MSLC-MS/MS Spectrum - 10V, Negativesplash10-0a4l-0950000000-9d2635dbd5dba4335642Spectrum
MS/MSLC-MS/MS Spectrum - 20V, Positivesplash10-03di-0900000000-0beed630d191c3ddf484Spectrum
MS/MSLC-MS/MS Spectrum - 10V, Positivesplash10-03di-0900000000-b5174fb5250877fc4322Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-03di-0910000000-36ec7f4bb0f43c1bea01Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03di-4900000000-9df78eed4f14088c8271Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-03dj-9600000000-73e430a902e254bcf1a5Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0btd-0930000000-7dddc27b279db10b55f1Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-03dl-5920000000-ba0a861002b9566db684Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0006-9200000000-1a8e142cab2f41210227Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-03di-0910000000-ebba965cb6de7bb5887eSpectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03di-1910000000-c30c0903bd3816dc1da4Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-03di-5900000000-8cae3c9126ea35107cdeSpectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-006x-0590000000-34c91e737fe5299bafd8Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-03dl-4910000000-751c4dfb7474605dd469Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-00kf-9200000000-284eea506bf71a5900d1Spectrum
NMRNot Available
ChemSpider ID5940
ChEMBL IDCHEMBL95606
KEGG Compound IDC00475
Pubchem Compound ID6175
Pubchem Substance IDNot Available
ChEBI IDNot Available
Phenol-Explorer IDNot Available
DrugBank IDNot Available
HMDB IDHMDB00089
CRC / DFC (Dictionary of Food Compounds) IDHBQ47-Y:HBQ47-Y
EAFUS IDNot Available
Dr. Duke IDNot Available
BIGG ID35089
KNApSAcK IDNot Available
HET IDCTN
Food Biomarker OntologyNot Available
VMH IDNot Available
Flavornet IDNot Available
GoodScent IDNot Available
SuperScent IDNot Available
Wikipedia IDNot Available
Phenol-Explorer Metabolite IDNot Available
Duplicate IDSNot Available
Old DFC IDSNot Available
Associated Foods
FoodContent Range AverageReference
FoodReference
Biological Effects and Interactions
Health Effects / BioactivitiesNot Available
Enzymes
NameGene NameUniProt ID
Bifunctional UDP-N-acetylglucosamine 2-epimerase/N-acetylmannosamine kinaseGNEQ9Y223
Cytosolic 5'-nucleotidase 3NT5C3Q9H0P0
AIDAIDQ546Y9
DNA dC->dU-editing enzyme APOBEC-3HAPOBEC3HQ6NTF7
Uridine-cytidine kinase-like 1UCKL1Q9NWZ5
Pathways
NameSMPDB LinkKEGG Link
Pyrimidine MetabolismSMP00046 map00240
MetabolismNot Available
BiosynthesisNot Available
Organoleptic Properties
FlavoursNot Available
Files
MSDSshow
References
Synthesis ReferenceNot Available
General ReferenceNot Available
Content Reference