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Showing metabocard for Cytidine (BMDB0000089)

IdentificationTaxonomyPhysical propertiesSpectraConcentrationsLinksReferencesXML
Record Information
Version1.0
Creation Date2016-09-30 22:19:30 UTC
Update Date2020-06-04 20:46:47 UTC
MCDB ID BMDB0000089
Secondary Accession Numbers
  • BMDB00089
Metabolite Identification
Common NameCytidine
DescriptionCytarabine, also known as cytosar or aracytine, 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 a drug which is used for the treatment of acute non-lymphocytic leukemia, acute lymphocytic leukemia and blast phase of chronic myelocytic leukemia. Cytarabine exists as a solid, possibly soluble (in water), and an extremely weak basic (essentially neutral) compound (based on its pKa) molecule. Cytarabine exists in all living species, ranging from bacteria to humans. Cytarabine is a potentially toxic compound.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
ValueSource
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
Chemical FormulaC9H13N3O5
Average Molecular Weight243.2166
Monoisotopic Molecular Weight243.085520541
IUPAC Name4-amino-1-[(2R,3S,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2-dihydropyrimidin-2-one
Traditional Namecytarabine
CAS Registry Number65-46-3
SMILES
NC1=NC(=O)N(C=C1)[C@@H]1O[C@H](CO)[C@@H](O)[C@@H]1O
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)/t4-,6-,7+,8-/m1/s1
InChI KeyUHDGCWIWMRVCDJ-CCXZUQQUSA-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
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting Point230.5 °CNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogP-2.51HANSCH,C ET AL. (1995)
Predicted Properties
PropertyValueSource
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
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Spectra
Spectrum TypeDescriptionSplash KeyDeposition DateView
GC-MSGC-MS Spectrum - GC-MS (5 TMS)splash10-0zfr-2951000000-7baf0e1ea8b1a34362e22018-05-25View Spectrum
GC-MSGC-MS Spectrum - GC-MS (4 TMS)splash10-0g4j-2980000000-9337623aef7fec22dd972018-05-25View Spectrum
GC-MSGC-MS Spectrum - GC-MS (Non-derivatized)splash10-0zfr-2951000000-7baf0e1ea8b1a34362e22018-05-25View Spectrum
GC-MSGC-MS Spectrum - GC-MS (Non-derivatized)splash10-0g4j-2980000000-9337623aef7fec22dd972018-05-25View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-08ml-9320000000-b032ad2c3dbed3face552017-09-01View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (3 TMS) - 70eV, Positivesplash10-0fuu-3934200000-7c3baaaffddf6aacd0f32017-10-06View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12View Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-0006-0190000000-eff861edb69ddab2c1952017-09-14View Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-0a4i-0900000000-4b5b14f0a5467db173b62017-09-14View Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-0a4i-3900000000-d85ae6c771dd9206c4c22017-09-14View Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-06sl-9600000000-b154ca170372bcbf8a4a2017-09-14View Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-00lu-9200000000-840df44a2d1149f4a7f72017-09-14View Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-01ox-0790000000-270551529aa609aa9ce82017-09-14View Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-03di-0900000000-855a7f8775ed4351b2902017-09-14View Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-03di-0900000000-50671582f88f6b4d8cee2017-09-14View Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-03di-1900000000-54269291900f80d353c32017-09-14View Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-03di-7900000000-ae3ff52581cbe61410642017-09-14View Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-IT , positivesplash10-03di-0900000000-9f3ae8e87da22e4e2e822017-09-14View Spectrum
LC-MS/MSLC-MS/MS Spectrum - 35V, Negativesplash10-0btc-3910000000-0c7172b1308a7ac699d42021-09-20View Spectrum
LC-MS/MSLC-MS/MS Spectrum - 35V, Positivesplash10-03di-0900000000-204e273853aa2d8e09ab2021-09-20View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-03di-0910000000-9575881412c4c94a7eae2016-06-03View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03di-5900000000-2cb5f7e3dbd7baa35b562016-06-03View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-03dj-9600000000-7d281b2b2d57c8786e112016-06-03View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-01ox-0960000000-db9207082a1fabf42dae2016-08-03View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-03xs-4910000000-c89de30dd376cbcb3b662016-08-03View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-00kf-9200000000-5715839499753b91f8452016-08-03View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-03di-0900000000-61fe3ac4032a2baf1b892021-10-11View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03di-2900000000-230b224d4d0dd71d0a492021-10-11View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-02t9-9200000000-7262e80c4fe078b890fc2021-10-11View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-03di-2900000000-66dec45988a096cc34832021-10-11View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-01ox-9500000000-bc463e76fd8ac42ac1d02021-10-11View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0006-9100000000-98e1626c7f485521a57f2021-10-11View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, experimental)Not Available2018-05-25View Spectrum
1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)Not Available2021-09-25View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)Not Available2021-09-25View Spectrum
1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)Not Available2021-09-25View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)Not Available2021-09-25View Spectrum
1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)Not Available2021-09-25View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)Not Available2021-09-25View Spectrum
1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)Not Available2021-09-25View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)Not Available2021-09-25View Spectrum
1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)Not Available2021-09-25View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)Not Available2021-09-25View Spectrum
1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)Not Available2021-09-25View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)Not Available2021-09-25View Spectrum
1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)Not Available2021-09-25View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)Not Available2021-09-25View Spectrum
1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)Not Available2021-09-25View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)Not Available2021-09-25View Spectrum
1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)Not Available2021-09-25View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)Not Available2021-09-25View Spectrum
1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)Not Available2021-09-25View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)Not Available2021-09-25View Spectrum
2D NMR[1H, 1H]-TOCSY. Unexported temporarily by An Chi on Oct 15, 2021 until json or nmrML file is generated. 2D NMR Spectrum (experimental)Not Available2018-05-25View Spectrum
2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, H2O, experimental)Not Available2018-05-25View Spectrum
Concentrations
StatusValueReferenceDetails
Detected and Quantified2.4 - 12 uM details
Detected but not QuantifiedNot Applicable
  • Kurt J. Boudonck,...
 details
Detected but not QuantifiedNot Applicable
  • Kurt J. Boudonck,...
 details
Detected and Quantified15 +/- 1 uM details
Detected and Quantified18 +/- 1 uM details
Detected and Quantified17 +/- 2 uM details
Detected and Quantified12 +/- 3 uM details
HMDB IDHMDB0015122
DrugBank IDDB00987
Phenol Explorer Compound IDNot Available
FoodDB IDFDB001216
KNApSAcK IDNot Available
Chemspider ID6017
KEGG Compound IDC02961
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkCytarabine
METLIN IDNot Available
PubChem Compound6253
PDB IDNot Available
ChEBI ID28680
References
Synthesis ReferenceQu, Guirong; Yang, Xining; Shen, Yanhong; Dong, Chunhong; Guo, Haiming; Wang, Xiuqiang; Wang, Dongchao. Synthesis of cytidine. Faming Zhuanli Shenqing Gongkai Shuomingshu (2007), 11pp.
Material Safety Data Sheet (MSDS)Download (PDF)
General References
  1. Kurt J. Boudonck, Matthew W. Mitchell, Jacob Wulff and John A. Ryals (2009). Kurt J. Boudonck, Matthew W. Mitchell, Jacob Wulff and John A. Ryals. Characterization of the biochemical variability of bovine milk using metabolomics. Metabolomics (2009) 5:375?386. Metabolomics.
  2. A. Foroutan et al. (2019). A. Foroutan et al. The Chemical Composition of Commercial Cow's Milk (in preparation). Journal of Agricultural and Food Chemistry.