Bovine Metabolome Database: Showing metabocard for Cytidine (BMDB0000089)

Identification Taxonomy Physical properties Pathways Spectra Concentrations Links References enzymes (2) Show 2 proteins XML

Record Information

Version

1.0

Creation Date

2016-09-30 22:19:30 UTC

Update Date

2020-06-04 20:46:47 UTC

BMDB ID

BMDB0000089

Secondary Accession Numbers

BMDB00089

Metabolite Identification

Common Name

Cytidine

Description

Cytarabine, 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

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 Weight

243.2166

Monoisotopic Molecular Weight

243.085520541

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

CAS Registry Number

65-46-3

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 Key

UHDGCWIWMRVCDJ-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.

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 )

Ontology

Status

Detected and Quantified

Origin

Endogenous

Biofunction

Not Available

Application

Not Available

Cellular locations

Lysosome
Mitochondria
Nucleus

Physical Properties

State

Solid

Experimental Properties

Property	Value	Reference
Melting Point	230.5 °C	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	-2.51	HANSCH,C ET AL. (1995)

Predicted Properties

Property	Value	Source
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	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Spectra

Spectrum Type	Description	Splash Key
GC-MS	GC-MS Spectrum - GC-MS (5 TMS)	splash10-0zfr-2951000000-7baf0e1ea8b1a34362e2	View in MoNA
GC-MS	GC-MS Spectrum - GC-MS (4 TMS)	splash10-0g4j-2980000000-9337623aef7fec22dd97	View in MoNA
GC-MS	GC-MS Spectrum - GC-MS (Non-derivatized)	splash10-0zfr-2951000000-7baf0e1ea8b1a34362e2	View in MoNA
GC-MS	GC-MS Spectrum - GC-MS (Non-derivatized)	splash10-0g4j-2980000000-9337623aef7fec22dd97	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-08ml-9320000000-b032ad2c3dbed3face55	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (3 TMS) - 70eV, Positive	splash10-0fuu-3934200000-7c3baaaffddf6aacd0f3	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	View in JSpectraViewer
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-0006-0190000000-eff861edb69ddab2c195	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-0a4i-0900000000-4b5b14f0a5467db173b6	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-0a4i-3900000000-d85ae6c771dd9206c4c2	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-06sl-9600000000-b154ca170372bcbf8a4a	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-00lu-9200000000-840df44a2d1149f4a7f7	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , positive	splash10-01ox-0790000000-270551529aa609aa9ce8	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , positive	splash10-03di-0900000000-855a7f8775ed4351b290	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , positive	splash10-03di-0900000000-50671582f88f6b4d8cee	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , positive	splash10-03di-1900000000-54269291900f80d353c3	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , positive	splash10-03di-7900000000-ae3ff52581cbe6141064	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-IT , positive	splash10-03di-0900000000-9f3ae8e87da22e4e2e82	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - 35V, Negative	splash10-0btc-3910000000-0c7172b1308a7ac699d4	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - 35V, Positive	splash10-03di-0900000000-204e273853aa2d8e09ab	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-03di-0910000000-9575881412c4c94a7eae	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-03di-5900000000-2cb5f7e3dbd7baa35b56	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-03dj-9600000000-7d281b2b2d57c8786e11	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-01ox-0960000000-db9207082a1fabf42dae	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-03xs-4910000000-c89de30dd376cbcb3b66	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-00kf-9200000000-5715839499753b91f845	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-03di-0900000000-61fe3ac4032a2baf1b89	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-03di-2900000000-230b224d4d0dd71d0a49	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-02t9-9200000000-7262e80c4fe078b890fc	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-03di-2900000000-66dec45988a096cc3483	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-01ox-9500000000-bc463e76fd8ac42ac1d0	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0006-9100000000-98e1626c7f485521a57f	View in MoNA
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, experimental)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
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 Available	View in JSpectraViewer
2D NMR	[¹H, ¹³C]-HSQC NMR Spectrum (2D, 600 MHz, H₂O, experimental)	Not Available	View in JSpectraViewer

Biological Properties

Cellular Locations

Lysosome
Mitochondria
Nucleus

Biospecimen Locations

All Tissues
Liver
Milk
Placenta
Prostate Tissue

Pathways

Name	SMPDB/Pathwhiz	KEGG
Pyrimidine Metabolism		Not Available

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
All Tissues	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Liver	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	PMID: 31873721	details
Liver	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	PMID: 31873721	details
Liver	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	PMID: 31867104	details
Milk	Detected and Quantified	15 +/- 1 uM	Not Specified	Not Specified	Normal	PMID: 30994344	details
Milk	Detected and Quantified	18 +/- 1 uM	Not Specified	Not Specified	Normal	PMID: 30994344	details
Milk	Detected and Quantified	17 +/- 2 uM	Not Specified	Not Specified	Normal	PMID: 30994344	details
Milk	Detected and Quantified	12 +/- 3 uM	Not Specified	Not Specified	Normal	PMID: 30994344	details
Milk	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Kurt J. Boudonck,...	details
Milk	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Kurt J. Boudonck,...	details
Milk	Detected and Quantified	2.4 - 11.6 uM	Not Specified	Not Specified	Normal	PMID: 11242448	details
Placenta	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Prostate Tissue	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details

Abnormal Concentrations

Not Available

External Links

HMDB ID

HMDB0015122

DrugBank ID

DB00987

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB001216

KNApSAcK ID

Not Available

Chemspider ID

6017

KEGG Compound ID

C02961

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Cytarabine

METLIN ID

Not Available

PubChem Compound

6253

PDB ID

Not Available

ChEBI ID

28680

References

Synthesis Reference

Qu, 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)

Not Available

General References

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.
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.

Enzymes

Enzyme Details

1. Single-stranded DNA cytosine deaminase

General function:: Involved in cytidine deaminase activity
Specific function:: Single-stranded DNA-specific cytidine deaminase. Involved in somatic hypermutation (SHM), gene conversion, and class-switch recombination (CSR) in B-lymphocytes by deaminating C to U during transcription of Ig-variable (V) and Ig-switch (S) region DNA. Required for several crucial steps of B-cell terminal differentiation necessary for efficient antibody responses. May also play a role in the epigenetic regulation of gene expression by participating in DNA demethylation.
Gene Name:: AICDA
Uniprot ID:: Q2PT36
Molecular weight:: 24052.0

Enzyme Details

2. Uridine-cytidine kinase 1

General function:: Nucleotide transport and metabolism
Specific function:: Phosphorylates uridine and cytidine to uridine monophosphate and cytidine monophosphate. Does not phosphorylate deoxyribonucleosides or purine ribonucleosides. Can use ATP or GTP as a phosphate donor (By similarity).
Gene Name:: UCK1
Uniprot ID:: Q0P5A4
Molecular weight:: 31195.0

Showing metabocard for Cytidine (BMDB0000089)

Structure for BMDB0000089 (Cytidine)

Enzymes