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Record Information
Version1.0
Created at2012-09-06 15:16:51 UTC
Updated at2021-08-19 20:22:30 UTC
NP-MRD IDNP0000033
Secondary Accession NumbersNone
Natural Product Identification
Common NameCytarabine
DescriptionCytarabine, or cytosine arabinoside, a pyrimidine nucleoside analog, is found in mushrooms. Cytarabine is isolated 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. Cytarabine is an antimetabolite antineoplastic agent that inhibits the synthesis of DNA. Its actions are specific for the S phase of the cell cycle to stop normal cell 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 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
Structure
Thumb
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
AracytidineMeSH
Arabinoside, cytosineMeSH
CytonalMeSH
Ara CMeSH
ArabinofuranosylcytosineMeSH
ArabinosylcytosineMeSH
CytosarMeSH
Cytosar-uMeSH
beta Ara CMeSH
AracytineMeSH
Cytarabine hydrochlorideMeSH
Cytosar uMeSH
beta-Ara CMeSH
(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
ArabitinHMDB
AraCHMDB
AracytinHMDB
ArafcytHMDB
beta -ArabinosylcytosineHMDB
beta -Cytosine arabinosideHMDB
beta -D-ArabinosylcytosineHMDB
beta-ArabinosylcytosineHMDB
beta-Cytosine arabinosideHMDB
beta-D-ArabinosylcytosineHMDB
CytarabinHMDB
CytarabinaHMDB
Cytarabine liposome injectionHMDB
CytarabinosideHMDB
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
CytosarUMeSH, HMDB
Hydrochloride, cytarabineMeSH, HMDB
CytarabineMeSH
Chemical FormulaC9H13N3O5
Average Mass243.2166 Da
Monoisotopic Mass243.08552 Da
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 Number147-94-4
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
Spectra
Spectrum TypeDescriptionDepositor IDDeposition DateView
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, experimental)Wishart Lab2021-06-20View Spectrum
2D NMR[1H, 1H] 2D NMR Spectrum (experimental)Wishart Lab2021-06-20View Spectrum
2D NMR[1H, 13C] NMR Spectrum (2D, 600 MHz, H2O, experimental)Wishart Lab2021-06-20View Spectrum
Species
Species of Origin
  • Animalia
  • Plantae
  • 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 ParentsNot Available
    SubstituentsNot Available
    Molecular FrameworkAromatic heteromonocyclic compounds
    External DescriptorsNot Available
    Physical Properties
    StateSolid
    Experimental Properties
    PropertyValueReference
    Melting Point212 - 213 °CNot Available
    Boiling Point545.68 °C. @ 760.00 mm Hg (est)The Good Scents Company Information System
    Water Solubility43.8 g/LNot Available
    LogP-2.8Not Available
    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
    External Links
    HMDB IDHMDB0155273
    DrugBank IDDB00987
    Phenol Explorer Compound IDNot Available
    FoodDB IDFDB001216
    KNApSAcK IDC00054108
    Chemspider ID6017
    KEGG Compound IDC02961
    BioCyc IDNot Available
    BiGG IDNot Available
    Wikipedia LinkCytarabine
    METLIN IDNot Available
    PubChem Compound6253
    PDB IDNot Available
    ChEBI ID28680
    Good Scents IDrw1380091
    References
    General References
    1. Zaky DA, Betts RF, Douglas RG Jr, Bengali K, Neil GL: Varicella-zoster virus and subcutaneous cytarabine: correlation of in vitro sensitivities to blood levels. Antimicrob Agents Chemother. 1975 Mar;7(3):229-32. [PubMed:166610 ]
    2. Relling MV, Mulhern RK, Fairclough D, Baker D, Pui CH: Chlorpromazine with and without lorazepam as antiemetic therapy in children receiving uniform chemotherapy. J Pediatr. 1993 Nov;123(5):811-6. [PubMed:8229497 ]
    3. Mallick KS, Hajek AS, Parrish RK 2nd: Fluorouracil (5-FU) and cytarabine (ara-C) inhibition of corneal epithelial cell and conjunctival fibroblast proliferation. Arch Ophthalmol. 1985 Sep;103(9):1398-402. [PubMed:4038134 ]
    4. Bursztyn J, Boccara JF, Paillassou B, Bavoux F: [Corneal toxicity of cytarabine. Apropos of a case]. Ophtalmologie. 1989 Jun-Aug;3(3):229-30. [PubMed:2641118 ]
    5. Ohta T, Hori H, Ogawa M, Miyahara M, Kawasaki H, Taniguchi N, Komada Y: Impact of cytidine deaminase activity on intrinsic resistance to cytarabine in carcinoma cells. Oncol Rep. 2004 Nov;12(5):1115-20. [PubMed:15492802 ]
    6. (). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .