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Cytidine (YMDB00051)

Identification
YMDB IDYMDB00051
NameCytidine
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
DescriptionCytarabine, also known as arac or cytosar, 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 an extremely weak basic (essentially neutral) compound (based on its pKa). Cytarabine exists in all living species, ranging from bacteria to humans. Cytarabine is a potentially toxic compound.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
  • 1-(b-D-Ribofuranosyl)-2-oxo-4-amino-1,2-dihydro-1,3-diazine
  • 1-(b-delta-Ribofuranosyl)-2-oxo-4-amino-1,2-dihydro-1,3-diazine
  • 1-b-D-Ribofuranosylcytosine
  • 1-b-D-ribosyl-Cytosine
  • 1-beta-D-ribofuranosyl-Cytosine
  • 1-beta-D-Ribofuranosylcytosine
  • 1-beta-delta-ribofuranosyl-Cytosine
  • 1-beta-delta-Ribofuranosylcytosine
  • 1-beta-delta-ribosyl-Cytosine
  • 1-β-D-ribofuranosylcytosine
  • 1b-D-Ribofuranosylcytosine
  • 1beta-D-Ribofuranosylcytosine
  • 1beta-delta-Ribofuranosylcytosine
  • 1beta-Ribofuranosylcytosine
  • 1β-D-ribofuranosylcytosine
  • 4-Amino-1-b-D-ribofuranosyl-2(1H)-pyrimidinone
  • 4-amino-1-b-D-Ribofuranosylpyrimidin-2(1H)-one
  • 4-amino-1-BETA-D-RIBOFURANOSYL-2(1H)-pyrimidinone
  • 4-amino-1-beta-D-Ribofuranosylpyrimidin-2(1H)-one
  • 4-Amino-1-beta-delta-ribofuranosyl-2(1H)-pyrimidinone
  • 4-amino-1-β-D-ribofuranosyl-2(1H)-pyrimidinone
  • 4-amino-1-β-D-ribofuranosylpyrimidin-2(1H)-one
  • 4-amino-1b-D-Ribofuranosyl-2(1H)-pyrimidinone
  • 4-amino-1beta-D-Ribofuranosyl-2(1H)-pyrimidinone
  • 4-amino-1β-D-ribofuranosyl-2(1H)-pyrimidinone
  • Cyd
  • Cytidin
  • Cytidine
  • Cytosine ribonucleoside
  • Cytosine riboside
  • cytosine-1b-D-Ribofuranoside
  • cytosine-1b-delta-Ribofuranoside
  • cytosine-1beta-D-Ribofuranoside
  • cytosine-1beta-delta-Ribofuranoside
  • Cytosine-1β-D-ribofuranoside
  • Ribonucleoside, cytosine
  • Riboside, cytosine
  • Zytidin
  • 1-beta-D-Arabinofuranosylcytosine
  • 4-Amino-1-beta-D-arabinofuranosyl-2(1H)-pyrimidinone
  • Ara-C
  • Arabinocytosine
  • Arabinoside C
  • Citarabina
  • Cytarabinum
  • Cytosine arabinoside
  • Cytosine-1-beta-D-arabinofuranoside
  • Cytosine-beta-D-arabinofuranoside
  • Depocyt
  • 1-b-D-Arabinofuranosylcytosine
  • 1-Β-D-arabinofuranosylcytosine
  • 4-Amino-1-b-D-arabinofuranosyl-2(1H)-pyrimidinone
  • 4-Amino-1-β-D-arabinofuranosyl-2(1H)-pyrimidinone
  • Cytosine-1-b-D-arabinofuranoside
  • Cytosine-1-β-D-arabinofuranoside
  • Cytosine-b-D-arabinofuranoside
  • Cytosine-β-D-arabinofuranoside
  • (beta-D-Arabinofuranosyl)cytosine
  • 1-Arabinofuranosylcytosine
  • 1-beta -D-Arabinofaranosylcytosine
  • 1-beta -D-Arabinofuranosyl-4-amino-2(1H)pyrimidinone
  • 1-beta -D-Arabinofuranosylcytosine
  • 1-beta-D-Arabinofaranosylcytosine
  • 1-beta-D-Arabinofuranosyl-4-amino-2(1H)pyrimidinone
  • 1-beta-D-Arabinofuranosyl-cytosine
  • 1-beta-D-Arabinofuranosylcytosine, cytosine arabinoside
  • 1-beta-D-Arabinosyl-cytosine
  • 1-beta-D-Arabinosylcytosine
  • 1beta -Arabinofuranasylcytosine
  • 1beta -D-Arabinofuranosylcytosine
  • 1beta -D-Arabinosylcytosine
  • 1beta-Arabinofuranasylcytosine
  • 1beta-D-Arabinofuranosylcytosine
  • 1beta-D-Arabinosylcytosine
  • 2(1H)-Pyrimidinone, 4-amino-1- -D-arabinofuranosyl
  • 4-Amino-1-arabinofuranosyl-2-oxo-1,2-dihydropyrimidin
  • 4-Amino-1-arabinofuranosyl-2-oxo-1,2-dihydropyrimidine
  • 4-Amino-1-b-D-arabinofuranosyl-2-(1H)-pyrimidinone
  • 4-Amino-1-beta-D-arabinofuranosylpyrimidin-2(1H)-one
  • Alexan
  • Arabinocytidine
  • Arabinofuranosylcytosine
  • Arabinosylcytosine
  • Arabitin
  • AraC
  • Aracytidine
  • Aracytin
  • Aracytine
  • Arafcyt
  • beta -Arabinosylcytosine
  • beta -Cytosine arabinoside
  • beta -D-Arabinosylcytosine
  • beta-Ara c
  • beta-Arabinosylcytosine
  • beta-Cytosine arabinoside
  • beta-D-Arabinosylcytosine
  • Cytarabin
  • Cytarabina
  • Cytarabine liposome injection
  • Cytarabinoside
  • Cytonal
  • Cytosar
  • Cytosar-u
  • Cytosine 1-beta-D-arabinofuranoside
  • Cytosine arabinofuranoside
  • Cytosine arabinose
  • Cytosine beta-D-arabinofuranoside
  • Cytosine beta-D-arabinoside
  • Cytosine, beta -D-arabinoside
  • Cytosine, beta-D-arabinoside
  • Cytosine-1-beta-D-arabinofuranoside hydrochloride
  • Cytosine-beta -arabinoside
  • Cytosine-beta -D-arabinofuranoside
  • Cytosine-beta-arabinoside
  • Cytosinearabinoside
  • Depocyte
  • Erpalfa
  • Iretin
  • Spongocytidine
  • Tarabine
  • Udicil
  • Arabinoside, cytosine
  • CytosarU
  • Hydrochloride, cytarabine
  • Cytarabine hydrochloride
  • Cytosar u
  • Ara C
  • beta Ara C
  • Cytarabine
CAS number65-46-3
WeightAverage: 243.2166
Monoisotopic: 243.085520541
InChI KeyUHDGCWIWMRVCDJ-XVFCMESISA-N
InChIInChI=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
IUPAC Name4-amino-1-[(2R,3S,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2-dihydropyrimidin-2-one
Traditional IUPAC Namecytarabine
Chemical FormulaC9H13N3O5
SMILES[H]OC([H])([H])[C@@]1([H])O[C@@]([H])(N2C([H])=C([H])C(=NC2=O)N([H])[H])[C@]([H])(O[H])[C@]1([H])O[H]
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 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
Physical Properties
StateSolid
Charge0
Melting point230.5 °C
Experimental Properties
PropertyValueReference
Water SolubilityNot AvailablePhysProp
LogP-2.51 [HANSCH,C ET AL. (1995)]PhysProp
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
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations
  • extracellular
  • cytoplasm
Organoleptic PropertiesNot Available
SMPDB Pathways
Pyrimidine metabolismPW002469 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways
Pyrimidine metabolismec00240 Map00240
SMPDB ReactionsNot Available
KEGG Reactions
Cytidine monophosphate + water → phosphate + Cytidine
water + hydron + Cytidine → Uridine + Ammonium
GTP + Cytidine → Cytidine monophosphate + hydron + Guanosine diphosphate
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
GC-MSGC-MS Spectrum - GC-MS (5 TMS)splash10-0zfr-2951000000-7baf0e1ea8b1a34362e2JSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-MS (4 TMS)splash10-0g4j-2980000000-9337623aef7fec22dd97JSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-MS (Non-derivatized)splash10-0zfr-2951000000-7baf0e1ea8b1a34362e2JSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-MS (Non-derivatized)splash10-0g4j-2980000000-9337623aef7fec22dd97JSpectraViewer | MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-08ml-9320000000-b032ad2c3dbed3face55JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (3 TMS) - 70eV, Positivesplash10-0fuu-3934200000-7c3baaaffddf6aacd0f3JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableJSpectraViewer
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-0006-0190000000-eff861edb69ddab2c195JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-0a4i-0900000000-4b5b14f0a5467db173b6JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-0a4i-3900000000-d85ae6c771dd9206c4c2JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-06sl-9600000000-b154ca170372bcbf8a4aJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-00lu-9200000000-840df44a2d1149f4a7f7JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-01ox-0790000000-270551529aa609aa9ce8JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-03di-0900000000-855a7f8775ed4351b290JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-03di-0900000000-50671582f88f6b4d8ceeJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-03di-1900000000-54269291900f80d353c3JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-03di-7900000000-ae3ff52581cbe6141064JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-IT , positivesplash10-03di-0900000000-9f3ae8e87da22e4e2e82JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 35V, Negativesplash10-0btc-3910000000-0c7172b1308a7ac699d4JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 35V, Positivesplash10-03di-0900000000-204e273853aa2d8e09abJSpectraViewer | MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-03di-0910000000-9575881412c4c94a7eaeJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03di-5900000000-2cb5f7e3dbd7baa35b56JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-03dj-9600000000-7d281b2b2d57c8786e11JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-01ox-0960000000-db9207082a1fabf42daeJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-03xs-4910000000-c89de30dd376cbcb3b66JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-00kf-9200000000-5715839499753b91f845JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-03di-0900000000-61fe3ac4032a2baf1b89JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03di-2900000000-230b224d4d0dd71d0a49JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-02t9-9200000000-7262e80c4fe078b890fcJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-03di-2900000000-66dec45988a096cc3483JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-01ox-9500000000-bc463e76fd8ac42ac1d0JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0006-9100000000-98e1626c7f485521a57fJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
2D NMR[1H,1H] 2D NMR SpectrumNot AvailableJSpectraViewer
2D NMR[1H,13C] 2D NMR SpectrumNot AvailableJSpectraViewer
References
References:
  • UniProt Consortium (2011). "Ongoing and future developments at the Universal Protein Resource." Nucleic Acids Res 39:D214-D219.21051339
  • Scheer, M., Grote, A., Chang, A., Schomburg, I., Munaretto, C., Rother, M., Sohngen, C., Stelzer, M., Thiele, J., Schomburg, D. (2011). "BRENDA, the enzyme information system in 2011." Nucleic Acids Res 39:D670-D676.21062828
  • Herrgard, M. J., Swainston, N., Dobson, P., Dunn, W. B., Arga, K. Y., Arvas, M., Bluthgen, N., Borger, S., Costenoble, R., Heinemann, M., Hucka, M., Le Novere, N., Li, P., Liebermeister, W., Mo, M. L., Oliveira, A. P., Petranovic, D., Pettifer, S., Simeonidis, E., Smallbone, K., Spasic, I., Weichart, D., Brent, R., Broomhead, D. S., Westerhoff, H. V., Kirdar, B., Penttila, M., Klipp, E., Palsson, B. O., Sauer, U., Oliver, S. G., Mendes, P., Nielsen, J., Kell, D. B. (2008). "A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology." Nat Biotechnol 26:1155-1160.18846089
  • Kurtz, J. E., Exinger, F., Erbs, P., Jund, R. (1999). "New insights into the pyrimidine salvage pathway of Saccharomyces cerevisiae: requirement of six genes for cytidine metabolism." Curr Genet 36:130-136.10501935
  • Nakanishi, T., Sekimizu, K. (2002). "SDT1/SSM1, a multicopy suppressor of S-II null mutant, encodes a novel pyrimidine 5'-nucleotidase." J Biol Chem 277:22103-22106.11934891
  • Hidaka, Y., Shimono, C., Ohno, M., Okumura, N., Adermann, K., Forssmann, W. G., Shimonishi, Y. (2000). "Dual function of the propeptide of prouroguanylin in the folding of the mature peptide: disulfide-coupled folding and dimerization." J Biol Chem 275:25155-25162.10827170
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.
External Links:
ResourceLink
CHEBI ID17562
HMDB IDHMDB00089
Pubchem Compound ID6175
Kegg IDC00475
ChemSpider ID5940
FOODB IDFDB001216
WikipediaCytidine
BioCyc IDCYTIDINE

Enzymes

Protein Details
1. Putative uridine kinase YDR020C
General function:
Involved in ATP binding
Specific function:
ATP + uridine = ADP + UMP
Gene Name:
Not Available
Uniprot ID:
Q12084
Molecular weight:
26594.80078
Reactions
ATP + uridine → ADP + UMP.
ATP + cytidine → ADP + CMP.
Protein Details
2. Suppressor of disruption of TFIIS
General function:
Involved in catalytic activity
Specific function:
Could be an enzyme that inactivates 6-azauracil by modifying it
Gene Name:
SDT1
Uniprot ID:
P53078
Molecular weight:
31968.40039
Reactions
Protein Details
3. Uridine kinase
General function:
Involved in ATP binding
Specific function:
Catalyzes the conversion of uridine into UMP and cytidine into CMP in the pyrimidine salvage pathway
Gene Name:
URK1
Uniprot ID:
P27515
Molecular weight:
56295.5
Reactions
ATP + uridine → ADP + UMP.
ATP + cytidine → ADP + CMP.
Protein Details
4. Cytidine deaminase
General function:
Involved in zinc ion binding
Specific function:
This enzyme scavenge exogenous and endogenous cytidine and 2'-deoxycytidine for UMP synthesis
Gene Name:
CDD1
Uniprot ID:
Q06549
Molecular weight:
15535.90039
Reactions
Cytidine + H(2)O → uridine + NH(3).

Transporters

Protein Details
1. Nucleoside transporter FUN26
General function:
Involved in nucleoside transmembrane transporter activity
Specific function:
Has broad nucleoside selectivity (uridine, ademosine and cytidine) and most likely functions to transport nucleosides across intracellular membranes
Gene Name:
FUN26
Uniprot ID:
P31381
Molecular weight:
58316.69922