Record Information
Version1.0
Creation date2010-04-08 22:05:11 UTC
Update date2019-11-27 17:05:47 UTC
Primary IDFDB001979
Secondary Accession NumbersNot Available
Chemical Information
FooDB NameCytarabine
DescriptionIsolated from the mushroom Xerocomus nigromaculatus of unknown palatability Cytarabine is an antineoplastic anti-metabolite used in the treatment of several forms of leukemia including acute myelogenous leukemia and meningeal leukemia. Anti-metabolites masquerade as purine or pyrimidine - which become the building blocks of DNA. They prevent these substances becoming incorporated in to DNA during the "S" phase (of the cell cycle), stopping normal development and division. Cytarabine is metabolized intracellularly into its active triphosphate form (cytosine arabinoside triphosphate). This metabolite then damages DNA by multiple mechanisms, including the inhibition of alpha-DNA polymerase, inhibition of DNA repair through an effect on beta-DNA polymerase, and incorporation into DNA. The latter mechanism is probably the most important. Cytotoxicity is highly specific for the S phase of the cell cycle.; Cytarabine, or cytosine arabinoside, is a chemotherapy agent used mainly in the treatment of hematological malignancies such as acute myeloid leukemia (AML) and non-Hodgkin lymphoma. It is also known as ara C.; Cytosine arabinoside is an antimetabolic agent with the chemical name of 1?-arabinofuranosylcytosine. Its mode of action is due to its rapid conversion into cytosine arabinoside triphosphate, which damages DNA when the cell cycle holds in the S phase (synthesis of DNA). Rapidly dividing cells, which require DNA replication for mitosis, are therefore most affected. Cytosine arabinoside also inhibits both DNA and RNA polymerases and nucleotide reductase enzymes needed for DNA synthesis. Cytarabine is found in mushrooms.
CAS Number147-94-4
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
(beta-d-arabinofuranosyl)cytosinebiospider
β-arabinosylcytosinebiospider
β-cytosine arabinosidebiospider
β-d-arabinosylcytosinebiospider
1-β-D-Arabinofaranosylcytosinebiospider
1-β-D-Arabinofuranosyl-4-amino-2(1H)pyrimidinonebiospider
1-β-D-Arabinofuranosylcytosinebiospider
1-Arabinofuranosylcytosinebiospider
1-b-D-ArabinofuranosylcytosineGenerator
1-beta -D-ArabinofaranosylcytosineHMDB
1-beta -D-Arabinofuranosyl-4-amino-2(1H)pyrimidinoneHMDB
1-beta -D-ArabinofuranosylcytosineHMDB
1-beta-D-Arabinofaranosylcytosinebiospider
1-beta-D-Arabinofuranosyl-4-amino-2(1H)pyrimidinonebiospider
1-beta-D-Arabinofuranosyl-cytosineHMDB
1-beta-D-arabinofuranosylcytosinebiospider
1-beta-D-Arabinofuranosylcytosine, Cytosine Arabinosidebiospider
1-beta-D-Arabinosyl-cytosineHMDB
1-beta-D-Arabinosylcytosinebiospider
1-β-D-arabinofuranosylcytosineGenerator
1β-Arabinofuranasylcytosinebiospider
1β-D-Arabinofuranosylcytosinebiospider
1β-D-Arabinosylcytosinebiospider
147-94-4 (FREE BASE)biospider
1beta -ArabinofuranasylcytosineHMDB
1beta -D-ArabinofuranosylcytosineHMDB
1beta -D-ArabinosylcytosineHMDB
1beta-Arabinofuranasylcytosinebiospider
1beta-D-Arabinofuranosylcytosinebiospider
1beta-D-Arabinosylcytosinebiospider
2(1H)-Pyrimidinone, 4-amino-1- -D-arabinofuranosylHMDB
2(1H)-Pyrimidinone, 4-amino-1- -D-arabinofuranosyl- [CAS]biospider
2(1H)-Pyrimidinone, 4-amino-1-β-D-arabinofuranosyl-biospider
2(1H)-Pyrimidinone, 4-amino-1-beta-D-arabinofuranosyl-biospider
2(1H)-Pyrimidinone, 4-amino-1β-D-arabinofuranosyl-biospider
4-Amino-1-arabinofuranosyl-2-oxo-1,2-dihydropyrimidinbiospider
4-Amino-1-arabinofuranosyl-2-oxo-1,2-dihydropyrimidinebiospider
4-Amino-1-b-D-arabinofuranosyl-2-(1H)-pyrimidinonebiospider
4-amino-1-b-D-Arabinofuranosyl-2(1H)-pyrimidinoneGenerator
4-Amino-1-beta-D-arabinofuranosyl-2(1H)-pyrimidinonbiospider
4-Amino-1-beta-D-arabinofuranosyl-2(1H)-pyrimidinonebiospider
4-amino-1-beta-D-arabinofuranosylpyrimidin-2(1H)-onebiospider
4-amino-1-β-D-arabinofuranosyl-2(1H)-pyrimidinoneGenerator
Alexandb_source
Arabinocytidinebiospider
Arabitinbiospider
ARACbiospider
Aracytindb_source
Arafcytbiospider
beta -ArabinosylcytosineHMDB
beta -Cytosine arabinosideHMDB
beta -D-ArabinosylcytosineHMDB
Beta-ara cbiospider
Beta-arabinosylcytosinebiospider
Beta-cytosine arabinosidebiospider
Beta-d-arabinosylcytosinebiospider
Citarabinabiospider
Cytarabinbiospider
Cytarabinabiospider
Cytarabine - Pws 1gn/Vialbiospider
Cytarabine - Pws 2gm/Vialbiospider
Cytarabine - Pws 500mg/Vialbiospider
Cytarabine (JP15/USP/INN)biospider
CYTARABINE (SEE ALSO CYTARABINE HYDROCHLORIDE 69-74-9)biospider
Cytarabine [usan:inn:ban:jan]biospider
Cytarabine liposome injectionHMDB
Cytarabine-Pws 100mg/Vialbiospider
Cytarabine, BAN, INN, JAN, USANdb_source
Cytarabine(usan)biospider
Cytarabinosidebiospider
Cytarabinumbiospider
Cytosar-Udb_source
Cytosine 1-beta-D-arabinofuranosidebiospider
Cytosine arabinofuranosidebiospider
Cytosine arabinosebiospider
Cytosine arabinoside (van)biospider
Cytosine beta-d-arabinofuranosidebiospider
Cytosine beta-d-arabinosidebiospider
Cytosine-β-arabinosidebiospider
Cytosine-β-d-arabinofuranosidebiospider
Cytosine-1-b-D-arabinofuranosideGenerator
Cytosine-1-beta-D-arabinofuranosidebiospider
Cytosine-1-beta-D-arabinofuranoside hydrochloridebiospider
Cytosine-1-β-D-arabinofuranosideGenerator
Cytosine-b-D-arabinofuranosideGenerator
Cytosine-beta -arabinosideHMDB
Cytosine-beta -D-arabinofuranosideHMDB
Cytosine-beta-arabinosidebiospider
Cytosine-beta-d-arabinofuranosidebiospider
Cytosine-β-D-arabinofuranosideGenerator
Cytosine, β-d-arabinosidebiospider
Cytosine, 1-β-D-arabinofuranosyl-biospider
Cytosine, 1-β-D-arabinosyl-biospider
Cytosine, 1-beta-D-arabinofuranosyl-biospider
Cytosine, 1-beta-D-arabinosyl-biospider
Cytosine, beta -D-arabinosideHMDB
Cytosine, beta-d-arabinosidebiospider
Cytosinearabinosidebiospider
Depocytbiospider
Depocyt (liposomal)biospider
Depocyt (TN)biospider
Depocytebiospider
Erpalfabiospider
Intrathecal (injected into the spinal fluid) depocytbiospider
Intrathecal cytarabine (also known as ara-c)biospider
Iretinbiospider
NSC 63878db_source
Spongocytidinebiospider
Tarabinedb_source
U 19920db_source
Udicilbiospider
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
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
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 CompositionC 44.45%; H 5.39%; N 17.28%; O 32.89%DFC
Melting PointMp 223-224°DFC
Boiling PointNot Available
Experimental Water SolubilityNot Available
Experimental logPNot Available
Experimental pKaNot Available
Isoelectric pointNot Available
ChargeNot Available
Optical Rotation[a]25D +155.2 (c, 0.7 in H2O)DFC
Spectroscopic UV Data272 (e 12020) (H2O) (Berdy)DFC
DensityNot Available
Refractive IndexNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash Key
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-05dl-9310000000-baa27af3867d7b2962e5View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-03di-0910000000-36ec7f4bb0f43c1bea01View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03di-4900000000-9df78eed4f14088c8271View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-03dj-9600000000-73e430a902e254bcf1a5View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0btd-0930000000-7dddc27b279db10b55f1View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-03dl-5920000000-ba0a861002b9566db684View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0006-9200000000-1a8e142cab2f41210227View in MoNA
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
ChemSpider ID6017
ChEMBL IDCHEMBL803
KEGG Compound IDC02961
Pubchem Compound ID6253
Pubchem Substance IDNot Available
ChEBI ID28680
Phenol-Explorer IDNot Available
DrugBank IDDB00987
HMDB IDHMDB15122
CRC / DFC (Dictionary of Food Compounds) IDHDV37-I:CBW05-L
EAFUS IDNot Available
Dr. Duke IDNot Available
BIGG IDNot Available
KNApSAcK IDNot Available
HET IDAR3
Food Biomarker OntologyNot Available
VMH IDNot Available
Flavornet IDNot Available
GoodScent IDNot Available
SuperScent IDNot Available
Wikipedia IDCytarabine
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
Deoxycytidine kinaseDCKP27707
PathwaysNot Available
MetabolismNot Available
BiosynthesisNot Available
Organoleptic Properties
FlavoursNot Available
Files
MSDSshow
References
Synthesis ReferenceNot Available
General ReferenceNot Available
Content Reference