ContaminantDB: Cytidine

Identification Taxonomy Biological Properties Physical Properties Toxicity Profile Spectra Concentrations Links References XML

Record Information

Version

1.0

Creation Date

2016-05-25 18:09:44 UTC

Update Date

2016-11-09 01:17:20 UTC

Accession Number

CHEM021675

Identification

Common Name

Cytidine

Class

Small Molecule

Description

A pyrimidine nucleoside analog that is used mainly in the treatment of leukemia, especially acute non-lymphoblastic 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. It also has antiviral and immunosuppressant properties. (From Martindale, The Extra Pharmacopoeia, 30th ed, p472)

Contaminant Sources

FooDB Chemicals
HMDB Contaminants - Urine

Contaminant Type

Not Available

Chemical Structure

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
1-beta-D-Arabinofuranosylcytosine	ChEBI
4-Amino-1-beta-D-arabinofuranosyl-2(1H)-pyrimidinone	ChEBI
Ara-C	ChEBI
Arabinocytosine	ChEBI
Arabinoside C	ChEBI
Citarabina	ChEBI
Cytarabinum	ChEBI
Cytosine arabinoside	ChEBI
Cytosine-1-beta-D-arabinofuranoside	ChEBI
Cytosine-beta-D-arabinofuranoside	ChEBI
Depocyt	Kegg
1-b-D-Arabinofuranosylcytosine	Generator
1-Β-D-arabinofuranosylcytosine	Generator
4-Amino-1-b-D-arabinofuranosyl-2(1H)-pyrimidinone	Generator
4-Amino-1-β-D-arabinofuranosyl-2(1H)-pyrimidinone	Generator
Cytosine-1-b-D-arabinofuranoside	Generator
Cytosine-1-β-D-arabinofuranoside	Generator
Cytosine-b-D-arabinofuranoside	Generator
Cytosine-β-D-arabinofuranoside	Generator
(beta-D-Arabinofuranosyl)cytosine	HMDB
1-Arabinofuranosylcytosine	HMDB
1-beta -D-Arabinofaranosylcytosine	HMDB
1-beta -D-Arabinofuranosyl-4-amino-2(1H)pyrimidinone	HMDB
1-beta -D-Arabinofuranosylcytosine	HMDB
1-beta-D-Arabinofaranosylcytosine	HMDB
1-beta-D-Arabinofuranosyl-4-amino-2(1H)pyrimidinone	HMDB
1-beta-D-Arabinofuranosyl-cytosine	HMDB
1-beta-D-Arabinofuranosylcytosine, cytosine arabinoside	HMDB
1-beta-D-Arabinosyl-cytosine	HMDB
1-beta-D-Arabinosylcytosine	HMDB
1beta -Arabinofuranasylcytosine	HMDB
1beta -D-Arabinofuranosylcytosine	HMDB
1beta -D-Arabinosylcytosine	HMDB
1beta-Arabinofuranasylcytosine	HMDB
1beta-D-Arabinofuranosylcytosine	HMDB
1beta-D-Arabinosylcytosine	HMDB
2(1H)-Pyrimidinone, 4-amino-1- -D-arabinofuranosyl	HMDB
4-Amino-1-arabinofuranosyl-2-oxo-1,2-dihydropyrimidin	HMDB
4-Amino-1-arabinofuranosyl-2-oxo-1,2-dihydropyrimidine	HMDB
4-Amino-1-b-D-arabinofuranosyl-2-(1H)-pyrimidinone	HMDB
4-Amino-1-beta-D-arabinofuranosylpyrimidin-2(1H)-one	HMDB
Alexan	HMDB
Arabinocytidine	HMDB
Arabinofuranosylcytosine	HMDB
Arabinosylcytosine	HMDB
Arabitin	HMDB
AraC	HMDB
Aracytidine	HMDB
Aracytin	HMDB
Aracytine	HMDB
Arafcyt	HMDB
beta -Arabinosylcytosine	HMDB
beta -Cytosine arabinoside	HMDB
beta -D-Arabinosylcytosine	HMDB
beta-Ara c	HMDB
beta-Arabinosylcytosine	HMDB
beta-Cytosine arabinoside	HMDB
beta-D-Arabinosylcytosine	HMDB
Cytarabin	HMDB
Cytarabina	HMDB
Cytarabine liposome injection	HMDB
Cytarabinoside	HMDB
Cytonal	HMDB
Cytosar	HMDB
Cytosar-u	HMDB
Cytosine 1-beta-D-arabinofuranoside	HMDB
Cytosine arabinofuranoside	HMDB
Cytosine arabinose	HMDB
Cytosine beta-D-arabinofuranoside	HMDB
Cytosine beta-D-arabinoside	HMDB
Cytosine, beta -D-arabinoside	HMDB
Cytosine, beta-D-arabinoside	HMDB
Cytosine-1-beta-D-arabinofuranoside hydrochloride	HMDB
Cytosine-beta -arabinoside	HMDB
Cytosine-beta -D-arabinofuranoside	HMDB
Cytosine-beta-arabinoside	HMDB
Cytosinearabinoside	HMDB
Depocyte	HMDB
Erpalfa	HMDB
Iretin	HMDB
Spongocytidine	HMDB
Tarabine	HMDB
Udicil	HMDB
Arabinoside, cytosine	HMDB
CytosarU	HMDB
Hydrochloride, cytarabine	HMDB
Cytarabine hydrochloride	HMDB
Cytosar u	HMDB
Ara C	HMDB
beta Ara C	HMDB
Cytarabine	MeSH

Chemical Formula

C₉H₁₃N₃O₅

Average Molecular Mass

243.217 g/mol

Monoisotopic Mass

243.086 g/mol

CAS Registry Number

65-46-3

IUPAC Name

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

Traditional Name

cytarabine

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 Key

UHDGCWIWMRVCDJ-XVFCMESISA-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.

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

monosaccharide derivative (CHEBI:28680 )
beta-D-arabinoside (CHEBI:28680 )
pyrimidine nucleoside (CHEBI:28680 )

Biological Properties

Status

Detected and Not Quantified

Origin

Not Available

Cellular Locations

Not Available

Biofluid Locations

Not Available

Tissue Locations

Not Available

Pathways

Not Available

Applications

Not Available

Biological Roles

Not Available

Chemical Roles

Not Available

Physical Properties

State

Not Available

Appearance

Not Available

Experimental Properties

Property	Value
Melting Point	Not Available
Boiling Point	Not Available
Solubility	Not Available

Predicted Properties

Property	Value	Source
Water Solubility	43.8 g/L	ALOGPS
logP	-2.2	ALOGPS
logP	-2.8	ChemAxon
logS	-0.74	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	22.53 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	1	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Spectrum Type	Description	Splash Key	View
GC-MS	GC-MS Spectrum - GC-MS (5 TMS)	splash10-0zfr-2951000000-7baf0e1ea8b1a34362e2	Spectrum
GC-MS	GC-MS Spectrum - GC-MS (4 TMS)	splash10-0g4j-2980000000-9337623aef7fec22dd97	Spectrum
GC-MS	GC-MS Spectrum - GC-MS (Non-derivatized)	splash10-0zfr-2951000000-7baf0e1ea8b1a34362e2	Spectrum
GC-MS	GC-MS Spectrum - GC-MS (Non-derivatized)	splash10-0g4j-2980000000-9337623aef7fec22dd97	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-08ml-9320000000-b032ad2c3dbed3face55	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (3 TMS) - 70eV, Positive	splash10-0fuu-3934200000-7c3baaaffddf6aacd0f3	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-0006-0190000000-eff861edb69ddab2c195	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-0a4i-0900000000-4b5b14f0a5467db173b6	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-0a4i-3900000000-d85ae6c771dd9206c4c2	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-06sl-9600000000-b154ca170372bcbf8a4a	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-00lu-9200000000-840df44a2d1149f4a7f7	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , positive	splash10-01ox-0790000000-270551529aa609aa9ce8	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , positive	splash10-03di-0900000000-855a7f8775ed4351b290	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , positive	splash10-03di-0900000000-50671582f88f6b4d8cee	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , positive	splash10-03di-1900000000-54269291900f80d353c3	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , positive	splash10-03di-7900000000-ae3ff52581cbe6141064	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-IT , positive	splash10-03di-0900000000-9f3ae8e87da22e4e2e82	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 35V, Negative	splash10-0btc-3910000000-0c7172b1308a7ac699d4	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 35V, Positive	splash10-03di-0900000000-204e273853aa2d8e09ab	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-03di-0910000000-9575881412c4c94a7eae	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-03di-5900000000-2cb5f7e3dbd7baa35b56	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-03dj-9600000000-7d281b2b2d57c8786e11	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-01ox-0960000000-db9207082a1fabf42dae	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-03xs-4910000000-c89de30dd376cbcb3b66	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-00kf-9200000000-5715839499753b91f845	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-03di-0900000000-61fe3ac4032a2baf1b89	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-03di-2900000000-230b224d4d0dd71d0a49	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-02t9-9200000000-7262e80c4fe078b890fc	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-03di-2900000000-66dec45988a096cc3483	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-01ox-9500000000-bc463e76fd8ac42ac1d0	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0006-9100000000-98e1626c7f485521a57f	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
2D NMR	[1H,1H] 2D NMR Spectrum	Not Available	Spectrum
2D NMR	[1H,13C] 2D NMR Spectrum	Not Available	Spectrum