Record Information
Version1.0
Creation date2010-04-08 22:04:53 UTC
Update date2019-11-26 02:56:07 UTC
Primary IDFDB001216
Secondary Accession NumbersNot Available
Chemical Information
FooDB NameArabinan
DescriptionCytarabine, also known as arac or cytosar, 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. Cytarabine is an extremely weak basic (essentially neutral) compound (based on its pKa). Cytarabine exists in all living species, ranging from bacteria to humans. Cytarabine has been detected, but not quantified in, several different foods, such as guava, herbs and spices, pomes, root vegetables, and sweet oranges. This could make cytarabine a potential biomarker for the consumption of these foods. Cytarabine is a potentially toxic compound.
CAS Number11078-27-6
Structure
Thumb
Synonyms
SynonymSource
1-beta-D-ArabinofuranosylcytosineChEBI
4-Amino-1-beta-D-arabinofuranosyl-2(1H)-pyrimidinoneChEBI
Ara-CChEBI
ArabinocytosineChEBI
Arabinoside CChEBI
CitarabinaChEBI
CytarabinumChEBI
Cytosine arabinosideChEBI
Cytosine-1-beta-D-arabinofuranosideChEBI
Cytosine-beta-D-arabinofuranosideChEBI
DepocytKegg
1-b-D-ArabinofuranosylcytosineGenerator
1-Β-D-arabinofuranosylcytosineGenerator
4-Amino-1-b-D-arabinofuranosyl-2(1H)-pyrimidinoneGenerator
4-Amino-1-β-D-arabinofuranosyl-2(1H)-pyrimidinoneGenerator
Cytosine-1-b-D-arabinofuranosideGenerator
Cytosine-1-β-D-arabinofuranosideGenerator
Cytosine-b-D-arabinofuranosideGenerator
Cytosine-β-D-arabinofuranosideGenerator
(beta-D-Arabinofuranosyl)cytosineHMDB
1-ArabinofuranosylcytosineHMDB
1-beta -D-ArabinofaranosylcytosineHMDB
1-beta -D-Arabinofuranosyl-4-amino-2(1H)pyrimidinoneHMDB
1-beta -D-ArabinofuranosylcytosineHMDB
1-beta-D-ArabinofaranosylcytosineHMDB
1-beta-D-Arabinofuranosyl-4-amino-2(1H)pyrimidinoneHMDB
1-beta-D-Arabinofuranosyl-cytosineHMDB
1-beta-D-Arabinofuranosylcytosine, cytosine arabinosideHMDB
1-beta-D-Arabinosyl-cytosineHMDB
1-beta-D-ArabinosylcytosineHMDB
1beta -ArabinofuranasylcytosineHMDB
1beta -D-ArabinofuranosylcytosineHMDB
1beta -D-ArabinosylcytosineHMDB
1beta-ArabinofuranasylcytosineHMDB
1beta-D-ArabinofuranosylcytosineHMDB
1beta-D-ArabinosylcytosineHMDB
2(1H)-Pyrimidinone, 4-amino-1- -D-arabinofuranosylHMDB
4-Amino-1-arabinofuranosyl-2-oxo-1,2-dihydropyrimidinHMDB
4-Amino-1-arabinofuranosyl-2-oxo-1,2-dihydropyrimidineHMDB
4-Amino-1-b-D-arabinofuranosyl-2-(1H)-pyrimidinoneHMDB
4-Amino-1-beta-D-arabinofuranosylpyrimidin-2(1H)-oneHMDB
AlexanHMDB
ArabinocytidineHMDB
ArabinofuranosylcytosineHMDB
ArabinosylcytosineHMDB
ArabitinHMDB
AraCHMDB
AracytidineHMDB
AracytinHMDB
AracytineHMDB
ArafcytHMDB
beta -ArabinosylcytosineHMDB
beta -Cytosine arabinosideHMDB
beta -D-ArabinosylcytosineHMDB
beta-Ara cHMDB
beta-ArabinosylcytosineHMDB
beta-Cytosine arabinosideHMDB
beta-D-ArabinosylcytosineHMDB
CytarabinHMDB
CytarabinaHMDB
Cytarabine liposome injectionHMDB
CytarabinosideHMDB
CytonalHMDB
CytosarHMDB
Cytosar-uHMDB
Cytosine 1-beta-D-arabinofuranosideHMDB
Cytosine arabinofuranosideHMDB
Cytosine arabinoseHMDB
Cytosine beta-D-arabinofuranosideHMDB
Cytosine beta-D-arabinosideHMDB
Cytosine, beta -D-arabinosideHMDB
Cytosine, beta-D-arabinosideHMDB
Cytosine-1-beta-D-arabinofuranoside hydrochlorideHMDB
Cytosine-beta -arabinosideHMDB
Cytosine-beta -D-arabinofuranosideHMDB
Cytosine-beta-arabinosideHMDB
CytosinearabinosideHMDB
DepocyteHMDB
ErpalfaHMDB
IretinHMDB
SpongocytidineHMDB
TarabineHMDB
UdicilHMDB
Arabinoside, cytosineHMDB
CytosarUHMDB
Hydrochloride, cytarabineHMDB
Cytarabine hydrochlorideHMDB
Cytosar uHMDB
Ara CHMDB
beta Ara CHMDB
CytarabineMeSH
2,5-Arabinanbiospider
Arabandb_source
Predicted Properties
PropertyValueSource
Water Solubility43.8 g/LALOGPS
logP-2.2ALOGPS
logP-2.8ChemAxon
logS-0.74ALOGPS
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
Polarizability22.53 ųChemAxon
Number of Rings2ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Chemical FormulaC9H13N3O5
IUPAC name4-amino-1-[(2R,3S,4S,5R)-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)/t4-,6-,7+,8-/m1/s1
InChI KeyUHDGCWIWMRVCDJ-CCXZUQQUSA-N
Isomeric SMILESNC1=NC(=O)N(C=C1)[C@@H]1O[C@H](CO)[C@@H](O)[C@@H]1O
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
Disposition

Route of exposure:

Source:

Biological location:

Role

Environmental role:

Industrial application:

Physico-Chemical Properties - Experimental
Physico-Chemical Properties - Experimental
PropertyValueReference
Physical stateNot Available
Physical DescriptionNot Available
Mass CompositionC 45.46%; H 6.10%; O 48.44%DFC
Melting PointNot Available
Boiling PointNot Available
Experimental Water SolubilityNot Available
Experimental logPNot Available
Experimental pKaNot Available
Isoelectric pointNot Available
ChargeNot Available
Optical Rotation[a]D -129 (H2O)DFC
Spectroscopic UV DataNot Available
DensityNot Available
Refractive IndexNot Available
Spectra
Spectra
EI-MS/GC-MS
TypeDescriptionSplash KeyView
GC-MSArabinan, 5 TMS, GC-MS Spectrumsplash10-0zfr-2951000000-7baf0e1ea8b1a34362e2Spectrum
GC-MSArabinan, 4 TMS, GC-MS Spectrumsplash10-0g4j-2980000000-9337623aef7fec22dd97Spectrum
GC-MSArabinan, non-derivatized, GC-MS Spectrumsplash10-0zfr-2951000000-7baf0e1ea8b1a34362e2Spectrum
GC-MSArabinan, non-derivatized, GC-MS Spectrumsplash10-0g4j-2980000000-9337623aef7fec22dd97Spectrum
Predicted GC-MSArabinan, non-derivatized, Predicted GC-MS Spectrum - 70eV, Positivesplash10-08ml-9320000000-b032ad2c3dbed3face55Spectrum
Predicted GC-MSArabinan, 3 TMS, Predicted GC-MS Spectrum - 70eV, Positivesplash10-0fuu-3934200000-7c3baaaffddf6aacd0f3Spectrum
Predicted GC-MSArabinan, non-derivatized, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
MS/MS
TypeDescriptionSplash KeyView
MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-0006-0190000000-eff861edb69ddab2c195Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-0a4i-0900000000-4b5b14f0a5467db173b6Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-0a4i-3900000000-d85ae6c771dd9206c4c2Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-06sl-9600000000-b154ca170372bcbf8a4aSpectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-00lu-9200000000-840df44a2d1149f4a7f7Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-01ox-0790000000-270551529aa609aa9ce8Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-03di-0900000000-855a7f8775ed4351b290Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-03di-0900000000-50671582f88f6b4d8ceeSpectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-03di-1900000000-54269291900f80d353c3Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-03di-7900000000-ae3ff52581cbe6141064Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-IT , positivesplash10-03di-0900000000-9f3ae8e87da22e4e2e82Spectrum
MS/MSLC-MS/MS Spectrum - 35V, Negativesplash10-0btc-3910000000-0c7172b1308a7ac699d4Spectrum
MS/MSLC-MS/MS Spectrum - 35V, Positivesplash10-03di-0900000000-204e273853aa2d8e09abSpectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-03di-0910000000-9575881412c4c94a7eaeSpectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03di-5900000000-2cb5f7e3dbd7baa35b56Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-03dj-9600000000-7d281b2b2d57c8786e11Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-01ox-0960000000-db9207082a1fabf42daeSpectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-03xs-4910000000-c89de30dd376cbcb3b66Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-00kf-9200000000-5715839499753b91f845Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-03di-0900000000-61fe3ac4032a2baf1b89Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03di-2900000000-230b224d4d0dd71d0a49Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-02t9-9200000000-7262e80c4fe078b890fcSpectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-03di-2900000000-66dec45988a096cc3483Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-01ox-9500000000-bc463e76fd8ac42ac1d0Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0006-9100000000-98e1626c7f485521a57fSpectrum
NMR
TypeDescriptionView
1D NMR1H NMR SpectrumSpectrum
1D NMR13C NMR SpectrumSpectrum
1D NMR1H NMR SpectrumSpectrum
1D NMR13C NMR SpectrumSpectrum
1D NMR1H NMR SpectrumSpectrum
1D NMR13C NMR SpectrumSpectrum
1D NMR1H NMR SpectrumSpectrum
1D NMR13C NMR SpectrumSpectrum
1D NMR1H NMR SpectrumSpectrum
1D NMR13C NMR SpectrumSpectrum
1D NMR1H NMR SpectrumSpectrum
1D NMR13C NMR SpectrumSpectrum
1D NMR1H NMR SpectrumSpectrum
1D NMR13C NMR SpectrumSpectrum
1D NMR1H NMR SpectrumSpectrum
1D NMR13C NMR SpectrumSpectrum
1D NMR1H NMR SpectrumSpectrum
1D NMR13C NMR SpectrumSpectrum
1D NMR1H NMR SpectrumSpectrum
1D NMR13C NMR SpectrumSpectrum
1D NMR1H NMR SpectrumSpectrum
2D NMR[1H,1H] 2D NMR SpectrumSpectrum
2D NMR[1H,13C] 2D NMR SpectrumSpectrum
ChemSpider IDNot Available
ChEMBL IDNot Available
KEGG Compound IDC01873
Pubchem Compound IDNot Available
Pubchem Substance IDNot Available
ChEBI IDNot Available
Phenol-Explorer IDNot Available
DrugBank IDNot Available
HMDB IDNot Available
CRC / DFC (Dictionary of Food Compounds) IDBWP79-H:BWP79-H
EAFUS IDNot Available
Dr. Duke IDARABAN
BIGG IDNot Available
KNApSAcK IDNot Available
HET IDNot Available
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
EnzymesNot Available
PathwaysNot Available
MetabolismNot Available
BiosynthesisNot Available
Organoleptic Properties
FlavoursNot Available
Files
MSDSNot Available
References
Synthesis ReferenceNot Available
General ReferenceNot Available
Content Reference— Duke, James. 'Dr. Duke's Phytochemical and Ethnobotanical Databases. United States Department of Agriculture.' Agricultural Research Service, Accessed April 27 (2004).