Showing Compound Cytarabine (FDB001979)

Record Information

Version

1.0

Creation date

2010-04-08 22:05:11 UTC

Update date

2019-11-26 02:56:50 UTC

Primary ID

FDB001979

Secondary Accession Numbers

Not Available

Chemical Information

FooDB Name

Cytarabine

Description

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. 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 Number

147-94-4

Structure

MOL SDF PDB SMILES InChI

Synonyms

Synonym	Source
Arabinosylcytosine	MeSH
Aracytidine	MeSH
Cytarabine	MeSH
Cytosar	MeSH
Cytosar-u	MeSH
CytosarU	MeSH
Cytosine arabinoside	MeSH
Hydrochloride, cytarabine	MeSH
beta-Ara C	MeSH
Ara-C	MeSH
Aracytine	MeSH
Cytarabine hydrochloride	MeSH
Cytosar u	MeSH
Arabinofuranosylcytosine	MeSH
Arabinoside, cytosine	MeSH
Cytonal	MeSH
(beta-d-arabinofuranosyl)cytosine	biospider
β-arabinosylcytosine	biospider
β-cytosine arabinoside	biospider
β-d-arabinosylcytosine	biospider
1-β-D-Arabinofaranosylcytosine	biospider
1-β-D-Arabinofuranosyl-4-amino-2(1H)pyrimidinone	biospider
1-β-D-Arabinofuranosylcytosine	biospider
1-Arabinofuranosylcytosine	biospider
1-b-D-Arabinofuranosylcytosine	Generator
1-beta -D-Arabinofaranosylcytosine	HMDB
1-beta -D-Arabinofuranosyl-4-amino-2(1H)pyrimidinone	HMDB
1-beta -D-Arabinofuranosylcytosine	HMDB
1-beta-D-Arabinofaranosylcytosine	biospider
1-beta-D-Arabinofuranosyl-4-amino-2(1H)pyrimidinone	biospider
1-beta-D-Arabinofuranosyl-cytosine	HMDB
1-beta-D-arabinofuranosylcytosine	biospider
1-beta-D-Arabinofuranosylcytosine, Cytosine Arabinoside	biospider
1-beta-D-Arabinosyl-cytosine	HMDB
1-beta-D-Arabinosylcytosine	biospider
1-β-D-arabinofuranosylcytosine	Generator
1β-Arabinofuranasylcytosine	biospider
1β-D-Arabinofuranosylcytosine	biospider
1β-D-Arabinosylcytosine	biospider
147-94-4 (FREE BASE)	biospider
1beta -Arabinofuranasylcytosine	HMDB
1beta -D-Arabinofuranosylcytosine	HMDB
1beta -D-Arabinosylcytosine	HMDB
1beta-Arabinofuranasylcytosine	biospider
1beta-D-Arabinofuranosylcytosine	biospider
1beta-D-Arabinosylcytosine	biospider
2(1H)-Pyrimidinone, 4-amino-1- -D-arabinofuranosyl	HMDB
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-dihydropyrimidin	biospider
4-Amino-1-arabinofuranosyl-2-oxo-1,2-dihydropyrimidine	biospider
4-Amino-1-b-D-arabinofuranosyl-2-(1H)-pyrimidinone	biospider
4-amino-1-b-D-Arabinofuranosyl-2(1H)-pyrimidinone	Generator
4-Amino-1-beta-D-arabinofuranosyl-2(1H)-pyrimidinon	biospider
4-Amino-1-beta-D-arabinofuranosyl-2(1H)-pyrimidinone	biospider
4-amino-1-beta-D-arabinofuranosylpyrimidin-2(1H)-one	biospider
4-amino-1-β-D-arabinofuranosyl-2(1H)-pyrimidinone	Generator
Alexan	db_source
Arabinocytidine	biospider
Arabitin	biospider
ARAC	biospider
Aracytin	db_source
Arafcyt	biospider
beta -Arabinosylcytosine	HMDB
beta -Cytosine arabinoside	HMDB
beta -D-Arabinosylcytosine	HMDB
Beta-ara c	biospider
Beta-arabinosylcytosine	biospider
Beta-cytosine arabinoside	biospider
Beta-d-arabinosylcytosine	biospider
Citarabina	biospider
Cytarabin	biospider
Cytarabina	biospider
Cytarabine - Pws 1gn/Vial	biospider
Cytarabine - Pws 2gm/Vial	biospider
Cytarabine - Pws 500mg/Vial	biospider
Cytarabine (JP15/USP/INN)	biospider
CYTARABINE (SEE ALSO CYTARABINE HYDROCHLORIDE 69-74-9)	biospider
Cytarabine [usan:inn:ban:jan]	biospider
Cytarabine liposome injection	HMDB
Cytarabine-Pws 100mg/Vial	biospider
Cytarabine, BAN, INN, JAN, USAN	db_source
Cytarabine(usan)	biospider
Cytarabinoside	biospider
Cytarabinum	biospider
Cytosar-U	db_source
Cytosine 1-beta-D-arabinofuranoside	biospider
Cytosine arabinofuranoside	biospider
Cytosine arabinose	biospider
Cytosine arabinoside (van)	biospider
Cytosine beta-d-arabinofuranoside	biospider
Cytosine beta-d-arabinoside	biospider
Cytosine-β-arabinoside	biospider
Cytosine-β-d-arabinofuranoside	biospider
Cytosine-1-b-D-arabinofuranoside	Generator
Cytosine-1-beta-D-arabinofuranoside	biospider
Cytosine-1-beta-D-arabinofuranoside hydrochloride	biospider
Cytosine-1-β-D-arabinofuranoside	Generator
Cytosine-b-D-arabinofuranoside	Generator
Cytosine-beta -arabinoside	HMDB
Cytosine-beta -D-arabinofuranoside	HMDB
Cytosine-beta-arabinoside	biospider
Cytosine-beta-d-arabinofuranoside	biospider
Cytosine-β-D-arabinofuranoside	Generator
Cytosine, β-d-arabinoside	biospider
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-arabinoside	HMDB
Cytosine, beta-d-arabinoside	biospider
Cytosinearabinoside	biospider
Depocyt	biospider
Depocyt (liposomal)	biospider
Depocyt (TN)	biospider
Depocyte	biospider
Erpalfa	biospider
Intrathecal (injected into the spinal fluid) depocyt	biospider
Intrathecal cytarabine (also known as ara-c)	biospider
Iretin	biospider
NSC 63878	db_source
Spongocytidine	biospider
Tarabine	db_source
U 19920	db_source
Udicil	biospider

Predicted Properties

Property	Value	Source
Water Solubility	2.8 g/L	ALOGPS
logP	-2	ALOGPS
logP	-2.8	ChemAxon
logS	-1.9	ALOGPS
pKa (Strongest Acidic)	12.55	ChemAxon
pKa (Strongest Basic)	-0.062	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	128.61 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	54.54 m³·mol⁻¹	ChemAxon
Polarizability	22.74 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Chemical Formula

C9H13N3O5

IUPAC name

4-amino-1-[3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2-dihydropyrimidin-2-one

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 Key

UHDGCWIWMRVCDJ-UHFFFAOYSA-N

Isomeric SMILES

OCC1OC(C(O)C1O)N1C=CC(=N)N=C1O

Average Molecular Weight

243.2166

Monoisotopic Molecular Weight

243.085520541

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.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Pyrimidine nucleosides

Sub Class

Not Available

Direct Parent

Pyrimidine 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 Framework

Aromatic heteromonocyclic compounds

External Descriptors

a pyrimidine ribonucleoside (CYTIDINE )

Ontology

No ontology term

Physico-Chemical Properties

Physico-Chemical Properties - Experimental

Property	Value	Reference
Physical state	Solid
Physical Description	Not Available
Mass Composition	C 44.45%; H 5.39%; N 17.28%; O 32.89%	DFC
Melting Point	Mp 223-224°	DFC
Boiling Point	Not Available
Experimental Water Solubility	Not Available
Experimental logP	Not Available
Experimental pKa	Not Available
Isoelectric point	Not Available
Charge	Not Available
Optical Rotation	[a]25D +155.2 (c, 0.7 in H2O)	DFC
Spectroscopic UV Data	272 (e 12020) (H2O) (Berdy)	DFC
Density	Not Available
Refractive Index	Not Available

Spectra

EI-MS/GC-MS

Type	Description	Splash Key	View
Predicted GC-MS	Cytarabine, non-derivatized, Predicted GC-MS Spectrum - 70eV, Positive	splash10-05dl-9310000000-baa27af3867d7b2962e5	Spectrum
Predicted GC-MS	Cytarabine, non-derivatized, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Cytarabine, TMS_1_1, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Cytarabine, TMS_1_2, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Cytarabine, TMS_1_3, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Cytarabine, TMS_1_4, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Cytarabine, TMS_1_5, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Cytarabine, TMS_2_1, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Cytarabine, TMS_2_2, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Cytarabine, TMS_2_3, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Cytarabine, TMS_2_4, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Cytarabine, TMS_2_5, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Cytarabine, TMS_2_6, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Cytarabine, TMS_2_7, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Cytarabine, TMS_2_8, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Cytarabine, TMS_2_9, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Cytarabine, TMS_2_10, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Cytarabine, TMS_3_1, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Cytarabine, TMS_3_2, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Cytarabine, TMS_3_3, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Cytarabine, TMS_3_4, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Cytarabine, TMS_3_5, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Cytarabine, TMS_3_6, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Cytarabine, TMS_3_7, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Cytarabine, TMS_3_8, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum

MS/MS

Type	Description	Splash Key	View
MS/MS	LC-MS/MS Spectrum - 40V, Positive	splash10-03di-0900000000-4d7ac7a2020f3bcdb8af	2021-09-20	View Spectrum
MS/MS	LC-MS/MS Spectrum - 10V, Negative	splash10-0a4l-0950000000-9d2635dbd5dba4335642	2021-09-20	View Spectrum
MS/MS	LC-MS/MS Spectrum - 20V, Positive	splash10-03di-0900000000-0beed630d191c3ddf484	2021-09-20	View Spectrum
MS/MS	LC-MS/MS Spectrum - 10V, Positive	splash10-03di-0900000000-b5174fb5250877fc4322	2021-09-20	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-03di-0910000000-36ec7f4bb0f43c1bea01	2015-05-26	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-03di-4900000000-9df78eed4f14088c8271	2015-05-26	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-03dj-9600000000-73e430a902e254bcf1a5	2015-05-26	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0btd-0930000000-7dddc27b279db10b55f1	2015-05-27	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-03dl-5920000000-ba0a861002b9566db684	2015-05-27	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0006-9200000000-1a8e142cab2f41210227	2015-05-27	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-03di-0910000000-ebba965cb6de7bb5887e	2021-10-12	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-03di-1910000000-c30c0903bd3816dc1da4	2021-10-12	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-03di-5900000000-8cae3c9126ea35107cde	2021-10-12	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-006x-0590000000-34c91e737fe5299bafd8	2021-10-12	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-03dl-4910000000-751c4dfb7474605dd469	2021-10-12	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-00kf-9200000000-284eea506bf71a5900d1	2021-10-12	View Spectrum