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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 01:58:37 UTC
Update Date2021-09-26 22:58:53 UTC
HMDB IDHMDB0248553
Secondary Accession NumbersNone
Metabolite Identification
Common NameArabinofuranosylcytosine
Description This compound has been identified in human blood as reported by (PMID: 31557052 ). Arabinofuranosylcytosine is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Arabinofuranosylcytosine is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.
Structure
Thumb
Synonyms
ValueSource
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
Chemical FormulaC9H13N3O5
Average Molecular Weight243.2166
Monoisotopic Molecular Weight243.085520541
IUPAC Name4-amino-1-[3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2-dihydropyrimidin-2-one
Traditional Namecytidine
CAS Registry NumberNot Available
SMILES
OCC1OC(C(O)C1O)N1C=CC(=N)N=C1O
InChI Identifier
InChI=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
Chemical Taxonomy
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
Physiological effectNot Available
Disposition
ProcessNot Available
RoleNot Available
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
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
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
AllCCS[M+H]+155.532859911
AllCCS[M+H-H2O]+151.732859911
AllCCS[M+NH4]+159.032859911
AllCCS[M+Na]+160.032859911
AllCCS[M-H]-152.532859911
AllCCS[M+Na-2H]-152.532859911
AllCCS[M+HCOO]-152.632859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
ArabinofuranosylcytosineOCC1OC(C(O)C1O)N1C=CC(=N)N=C1O4119.4Standard polar33892256
ArabinofuranosylcytosineOCC1OC(C(O)C1O)N1C=CC(=N)N=C1O2563.7Standard non polar33892256
ArabinofuranosylcytosineOCC1OC(C(O)C1O)N1C=CC(=N)N=C1O2580.9Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Arabinofuranosylcytosine,5TMS,isomer #1C[Si](C)(C)N=C1C=CN(C2OC(CO[Si](C)(C)C)C(O[Si](C)(C)C)C2O[Si](C)(C)C)C(O[Si](C)(C)C)=N12369.8Semi standard non polar33892256
Arabinofuranosylcytosine,5TMS,isomer #1C[Si](C)(C)N=C1C=CN(C2OC(CO[Si](C)(C)C)C(O[Si](C)(C)C)C2O[Si](C)(C)C)C(O[Si](C)(C)C)=N12580.8Standard non polar33892256
Arabinofuranosylcytosine,5TMS,isomer #1C[Si](C)(C)N=C1C=CN(C2OC(CO[Si](C)(C)C)C(O[Si](C)(C)C)C2O[Si](C)(C)C)C(O[Si](C)(C)C)=N12802.6Standard polar33892256
Arabinofuranosylcytosine,5TBDMS,isomer #1CC(C)(C)[Si](C)(C)N=C1C=CN(C2OC(CO[Si](C)(C)C(C)(C)C)C(O[Si](C)(C)C(C)(C)C)C2O[Si](C)(C)C(C)(C)C)C(O[Si](C)(C)C(C)(C)C)=N13319.6Semi standard non polar33892256
Arabinofuranosylcytosine,5TBDMS,isomer #1CC(C)(C)[Si](C)(C)N=C1C=CN(C2OC(CO[Si](C)(C)C(C)(C)C)C(O[Si](C)(C)C(C)(C)C)C2O[Si](C)(C)C(C)(C)C)C(O[Si](C)(C)C(C)(C)C)=N13484.7Standard non polar33892256
Arabinofuranosylcytosine,5TBDMS,isomer #1CC(C)(C)[Si](C)(C)N=C1C=CN(C2OC(CO[Si](C)(C)C(C)(C)C)C(O[Si](C)(C)C(C)(C)C)C2O[Si](C)(C)C(C)(C)C)C(O[Si](C)(C)C(C)(C)C)=N13214.0Standard polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 2-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)-5-(hydroxymethyl)oxolane-3,4-diol GC-MS (Non-derivatized) - 70eV, Positivesplash10-05dl-9310000000-baa27af3867d7b2962e52018-04-09Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 2-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)-5-(hydroxymethyl)oxolane-3,4-diol GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 2-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)-5-(hydroxymethyl)oxolane-3,4-diol GC-MS (TMS_1_1) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 2-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)-5-(hydroxymethyl)oxolane-3,4-diol GC-MS (TMS_1_2) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 2-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)-5-(hydroxymethyl)oxolane-3,4-diol GC-MS (TMS_1_3) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 2-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)-5-(hydroxymethyl)oxolane-3,4-diol GC-MS (TMS_1_4) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 2-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)-5-(hydroxymethyl)oxolane-3,4-diol GC-MS (TMS_1_5) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 2-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)-5-(hydroxymethyl)oxolane-3,4-diol GC-MS (TMS_2_1) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 2-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)-5-(hydroxymethyl)oxolane-3,4-diol GC-MS (TMS_2_2) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 2-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)-5-(hydroxymethyl)oxolane-3,4-diol GC-MS (TMS_2_3) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 2-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)-5-(hydroxymethyl)oxolane-3,4-diol GC-MS (TMS_2_4) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 2-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)-5-(hydroxymethyl)oxolane-3,4-diol GC-MS (TMS_2_5) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 2-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)-5-(hydroxymethyl)oxolane-3,4-diol GC-MS (TMS_2_6) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 2-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)-5-(hydroxymethyl)oxolane-3,4-diol GC-MS (TMS_2_7) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 2-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)-5-(hydroxymethyl)oxolane-3,4-diol GC-MS (TMS_2_8) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 2-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)-5-(hydroxymethyl)oxolane-3,4-diol GC-MS (TMS_2_9) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 2-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)-5-(hydroxymethyl)oxolane-3,4-diol GC-MS (TMS_2_10) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 2-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)-5-(hydroxymethyl)oxolane-3,4-diol GC-MS (TMS_3_1) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 2-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)-5-(hydroxymethyl)oxolane-3,4-diol GC-MS (TMS_3_2) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 2-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)-5-(hydroxymethyl)oxolane-3,4-diol GC-MS (TMS_3_3) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 2-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)-5-(hydroxymethyl)oxolane-3,4-diol GC-MS (TMS_3_4) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 2-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)-5-(hydroxymethyl)oxolane-3,4-diol GC-MS (TMS_3_5) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 2-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)-5-(hydroxymethyl)oxolane-3,4-diol GC-MS (TMS_3_6) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 2-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)-5-(hydroxymethyl)oxolane-3,4-diol GC-MS (TMS_3_7) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 2-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)-5-(hydroxymethyl)oxolane-3,4-diol GC-MS (TMS_3_8) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Experimental LC-MS/MSLC-MS/MS Spectrum - Arabinofuranosylcytosine 40V, Positive-QTOFsplash10-03di-0900000000-4d7ac7a2020f3bcdb8af2021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Arabinofuranosylcytosine 10V, Negative-QTOFsplash10-0a4l-0950000000-9d2635dbd5dba43356422021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Arabinofuranosylcytosine 20V, Positive-QTOFsplash10-03di-0900000000-0beed630d191c3ddf4842021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Arabinofuranosylcytosine 10V, Positive-QTOFsplash10-03di-0900000000-b5174fb5250877fc43222021-09-20HMDB team, MONAView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Arabinofuranosylcytosine 10V, Positive-QTOFsplash10-03di-0910000000-36ec7f4bb0f43c1bea012015-05-26Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Arabinofuranosylcytosine 20V, Positive-QTOFsplash10-03di-4900000000-9df78eed4f14088c82712015-05-26Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Arabinofuranosylcytosine 40V, Positive-QTOFsplash10-03dj-9600000000-73e430a902e254bcf1a52015-05-26Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Arabinofuranosylcytosine 10V, Negative-QTOFsplash10-0btd-0930000000-7dddc27b279db10b55f12015-05-27Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Arabinofuranosylcytosine 20V, Negative-QTOFsplash10-03dl-5920000000-ba0a861002b9566db6842015-05-27Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Arabinofuranosylcytosine 40V, Negative-QTOFsplash10-0006-9200000000-1a8e142cab2f412102272015-05-27Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Arabinofuranosylcytosine 10V, Positive-QTOFsplash10-03di-0910000000-ebba965cb6de7bb5887e2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Arabinofuranosylcytosine 20V, Positive-QTOFsplash10-03di-1910000000-c30c0903bd3816dc1da42021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Arabinofuranosylcytosine 40V, Positive-QTOFsplash10-03di-5900000000-8cae3c9126ea35107cde2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Arabinofuranosylcytosine 10V, Negative-QTOFsplash10-006x-0590000000-34c91e737fe5299bafd82021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Arabinofuranosylcytosine 20V, Negative-QTOFsplash10-03dl-4910000000-751c4dfb7474605dd4692021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Arabinofuranosylcytosine 40V, Negative-QTOFsplash10-00kf-9200000000-284eea506bf71a5900d12021-10-12Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB001979
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkCytarabine
METLIN IDNot Available
PubChem Compound596
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]