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Record Information
Version3.6
Creation Date2005-11-16 15:48:42 UTC
Update Date2013-02-09 00:07:45 UTC
HMDB IDHMDB00014
Secondary Accession NumbersNone
Metabolite Identification
Common NameDeoxycytidine
DescriptionOne of the principal nucleosides of DNA composed of cytosine and deoxyribose. A nucleoside consists of only a pentose sugar linked to a purine or pyrimidine base, without a phosphate group. When N1 is linked to the C1 of deoxyribose, deoxynucleosides and nucleotides are formed from cytosine and deoxyribose; deoxycytidine monophosphate (dCMP), deoxycytidine diphosphate (dCDP), deoxycytidine triphosphate (dCTP). CTP is the source of the cytidine in RNA (ribonucleic acid) and deoxycytidine triphosphate (dCTP) is the source of the deoxycytidine in DNA (deoxyribonucleic acid).
Structure
Thumb
Synonyms
  1. 1-(2-Deoxy-b-D-ribofuranosyl)cytosine
  2. 1-(2-Deoxy-beta-D-erythro-pentofuranosyl)-Cytosine
  3. 1-(2-Deoxy-beta-D-ribofuranosyl)cytosine
  4. 1-(2-Deoxy-beta-delta-erythro-pentofuranosyl)-Cytosine
  5. 1-(2-Deoxy-beta-delta-ribofuranosyl)cytosine
  6. 2'-Deoxycytidine
  7. 2-Deoxy-Cytidine
  8. 4-Amino-1-(2-deoxy-b-D-erythro-pentofuranosyl)-2(1H)-pyrimidinone
  9. 4-Amino-1-(2-deoxy-beta-D-erythro-pentofuranosyl)-2(1H)-pyrimidinone
  10. 4-Amino-1-(2-deoxy-beta-delta-erythro-pentofuranosyl)-2(1H)-pyrimidinone
  11. Cytosine deoxyribonucleoside
  12. Cytosine deoxyriboside
  13. Deoxy-Cytidine
  14. Deoxyribose cytidine
  15. Desoxycytidine
Chemical FormulaC9H13N3O4
Average Molecular Weight227.2172
Monoisotopic Molecular Weight227.090605919
IUPAC Name4-amino-1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2-dihydropyrimidin-2-one
Traditional Namedeoxycytidine
CAS Registry Number951-77-9
SMILES
NC1=NC(=O)N(C=C1)[C@H]1C[C@H](O)[C@@H](CO)O1
InChI Identifier
InChI=1S/C9H13N3O4/c10-7-1-2-12(9(15)11-7)8-3-5(14)6(4-13)16-8/h1-2,5-6,8,13-14H,3-4H2,(H2,10,11,15)/t5-,6+,8+/m0/s1
InChI KeyCKTSBUTUHBMZGZ-SHYZEUOFSA-N
Chemical Taxonomy
KingdomOrganic Compounds
Super ClassNucleosides, Nucleotides, and Analogues
ClassPyrimidine Nucleosides and Analogues
Sub ClassPyrimidine 2'-deoxyribonucleosides and Analogues
Other Descriptors
  • Aromatic Heteropolycyclic Compounds
  • Deoxyribonucleosides(KEGG)
  • Organic Compounds
  • pyrimidine 2'-deoxyribonucleoside(ChEBI)
Substituents
  • Aminopyrimidine
  • Hydropyrimidine
  • Oxolane
  • Primary Alcohol
  • Pyrimidine
  • Pyrimidone
  • Secondary Alcohol
Direct ParentPyrimidine 2'-deoxyribonucleosides and Analogues
Ontology
StatusDetected and Quantified
Origin
  • Endogenous
Biofunction
  • Component of Purine metabolism
  • Component of Pyrimidine metabolism
ApplicationNot Available
Cellular locations
  • Extracellular
  • Mitochondria
  • Nucleus
  • Lysosome
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting Point207 - 210 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility870 mg/mLNot Available
LogP-1.77HANSCH,C ET AL. (1995)
Predicted Properties
PropertyValueSource
Water Solubility15.9 g/LALOGPS
logP-1.9ALOGPS
logP-1.9ChemAxon
logS-1.2ALOGPS
pKa (Strongest Acidic)13.89ChemAxon
pKa (Strongest Basic)-0.0012ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count6ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area108.38ChemAxon
Rotatable Bond Count2ChemAxon
Refractivity53.03ChemAxon
Polarizability21.65ChemAxon
Spectra
SpectraMS/MSLC-MS1D NMR2D NMR
Biological Properties
Cellular Locations
  • Extracellular
  • Mitochondria
  • Nucleus
  • Lysosome
Biofluid Locations
  • Blood
  • Urine
Tissue Location
  • All Tissues
Pathways
NameSMPDB LinkKEGG Link
Pyrimidine MetabolismSMP00046map00240
Normal Concentrations
BiofluidStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified0.2 (0.0-0.5) uMAdult (>18 years old)BothNormal details
UrineDetected and Quantified0.65 +/- 0.27 umol/mmol creatinineAdult (>18 years old)BothNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
DrugBank Metabolite IDNot Available
Phenol Explorer Compound IDNot Available
Phenol Explorer Metabolite IDNot Available
FoodDB IDFDB021871
KNApSAcK IDNot Available
Chemspider ID13117
KEGG Compound IDC00881
BioCyc IDDEOXYCYTIDINE
BiGG ID36280
Wikipedia LinkDeoxycytidine
NuGOwiki LinkHMDB00014
Metagene LinkHMDB00014
METLIN ID3367
PubChem Compound13711
PDB IDDCZ
ChEBI ID15698
References
Synthesis Reference Fox, Jack F.; Yung, Naishun; Wempen, Iris; Hoffer, Max. Pyrimidine nucleosides. XII. Direct synthesis of 2'-deoxycytidine and its a-anomer. Journal of the American Chemical Society (1961), 83 4066-50.
Material Safety Data Sheet (MSDS)Download (PDF)
General References
  1. van den Bosch J, Lubbert M, Verhoef G, Wijermans PW: The effects of 5-aza-2'-deoxycytidine (Decitabine) on the platelet count in patients with intermediate and high-risk myelodysplastic syndromes. Leuk Res. 2004 Aug;28(8):785-90. Pubmed: 15203276
  2. Lee SH, Jung BH, Kim SY, Chung BC: A rapid and sensitive method for quantitation of nucleosides in human urine using liquid chromatography/mass spectrometry with direct urine injection. Rapid Commun Mass Spectrom. 2004;18(9):973-7. Pubmed: 15116424
  3. Wepierre J, Marty JP, Chanal JL, Sincholle D: Percutaneous absorption of 5-iodo-2' deoxycytidine in the hairless rat and in man. Eur J Drug Metab Pharmacokinet. 1984 Jan-Mar;9(1):79-83. Pubmed: 6714272
  4. Coral S, Sigalotti L, Altomonte M, Engelsberg A, Colizzi F, Cattarossi I, Maraskovsky E, Jager E, Seliger B, Maio M: 5-aza-2'-deoxycytidine-induced expression of functional cancer testis antigens in human renal cell carcinoma: immunotherapeutic implications. Clin Cancer Res. 2002 Aug;8(8):2690-5. Pubmed: 12171902
  5. Olivares J, Verdys M: Isocratic high-performance liquid chromatographic method for studying the metabolism of blood plasma pyrimidine nucleosides and bases: concentration and radioactivity measurements. J Chromatogr. 1988 Dec 29;434(1):111-21. Pubmed: 3243806
  6. Maley, F. et al., J. Biol. Chem., 1958, 233, 1538-1543, (5-diphosphate)
  7. Charubala, R. et al., Synthesis, 1984, 965-968, (5'-(4,4'-dimethoxytrityl) 4N-benzoyl)
  8. Schaller, H. et al., J.A.C.S., 1963, 85, 3821-3827, (5'-(4,4'-dimethoxytrityl) 4N-benzoyl)
  9. Benz, E. et al., J.O.C., 1965, 30, 3067-3071, (4N-benzoyl, 5'-tosyl, 3',4N-dibenzoyl, 4N,5'-dibenzoyl, 5'-tosyl 4N-benzoyl, 5'-trityl 3',4N-dibenzoyl)
  10. Hruska, F.E. et al., Can. J. Chem., 1974, 52, 497-508, (pmr)
  11. Jones, A.J. et al., Proc. Natl. Acad. Sci. U.S.A., 1970, 65, 27-30, CA, 72, 96682j, (cmr)
  12. Miles, H.T., J.A.C.S., 1963, 85, 1007-1008, (ir, pmr)
  13. Young, D.W. et al., Acta Cryst. B, 1975, 31, 961-965, (cryst struct)
  14. Michelson, A.M. et al., J.C.S., 1954, 34-40, (phosphates, 3',4N-di-Ac, 5'-trityl, 5'-trityl 3',4N-di-Ac)
  15. Lewis, R.J., Sax's Dangerous Properties of Industrial Materials, 8th edn., Van Nostrand Reinhold, 1992, DAQ850
  16. Aldrich Library of 13C and 1H FT NMR Spectra, 1992, 3, 396A, 396C, (nmr)
  17. Stawinski, J. et al., Chem. Comm., 1976, 243-244, (3',4N,5'-tribenzoyl)
  18. Ulbricht TL. Nucleosides. 3. Synthesis of 1-methyl-2'-deoxycytidine, and comments on the N.m.r. spectra of cytosine nucleosides. J Chem Soc Perkin 1. 1965 Sep:6134-5.
  19. Wang Z, Prudhomme DR, Buck JR, Park M, Rizzo CJ. Stereocontrolled syntheses of deoxyribonucleosides via photoinduced electron-transfer deoxygenation of benzoyl-protected ribo- and arabinonucleosides. J Org Chem. 2000 Sep 22;65(19):5969-85.
  20. Saneyoshi M, Tohyama J, Nakayama C, Takiya S, Iwabuchi M. Inhibitory effects of 3'deoxycytidine 5'-triphosphate and 3'-deoxyuridine 5'-triphosphate on DNA-dependent RNA polymerases I and II purified from Dictyostelium discoideum cells. Nucleic Acids Res. 1981 Jul 10;9(13):3129-38.
  21. FOX JJ, WEMPEN I. Pyrimidine nucleosides. Adv Carbohydr Chem. 1959;14:283-380.
  22. Raffaele Saladino, Enrico Mincione, Claudia Crestini, Maurizio Mezzetti. Transformations of thiopyrimidine and thiopurine nucleosides following oxidation with dimethyldioxirane. Tetrahedron, 1996, 52, 6759-6780
  23. Aldrich Library of FT-IR Spectra, 1st edn., 1985, 2, 832B, 838D, 839C, (ir)
  24. Yang, J.T. et al., CA, 1966, 65, 12454, (ord)

Enzymes

General function:
Involved in hydrolase activity
Specific function:
Hydrolyzes extracellular nucleotides into membrane permeable nucleosides.
Gene Name:
NT5E
Uniprot ID:
P21589
Molecular weight:
57948.125
Reactions
dCMP + Water → Deoxycytidine + Phosphoric aciddetails
General function:
Involved in nucleotide binding
Specific function:
Dephosphorylates the 5' and 2'(3')-phosphates of deoxyribonucleotides. Helps to regulate adenosine levels (By similarity).
Gene Name:
NT5C1B
Uniprot ID:
Q96P26
Molecular weight:
68803.055
Reactions
dCMP + Water → Deoxycytidine + Phosphoric aciddetails
General function:
Involved in nucleotide binding
Specific function:
Dephosphorylates the 5' and 2'(3')-phosphates of deoxyribonucleotides and has a broad substrate specificity. Helps to regulate adenosine levels in heart during ischemia and hypoxia.
Gene Name:
NT5C1A
Uniprot ID:
Q9BXI3
Molecular weight:
41020.145
Reactions
dCMP + Water → Deoxycytidine + Phosphoric aciddetails
General function:
Involved in metal ion binding
Specific function:
Dephosphorylates the 5' and 2'(3')-phosphates of deoxyribonucleotides, with a preference for dUMP and dTMP, intermediate activity towards dGMP, and low activity towards dCMP and dAMP.
Gene Name:
NT5C
Uniprot ID:
Q8TCD5
Molecular weight:
Not Available
Reactions
dCMP + Water → Deoxycytidine + Phosphoric aciddetails
General function:
Involved in ATP binding
Specific function:
Required for the phosphorylation of the deoxyribonucleosides deoxycytidine (dC), deoxyguanosine (dG) and deoxyadenosine (dA). Has broad substrate specificity, and does not display selectivity based on the chirality of the substrate. It is also an essential enzyme for the phosphorylation of numerous nucleoside analogs widely employed as antiviral and chemotherapeutic agents.
Gene Name:
DCK
Uniprot ID:
P27707
Molecular weight:
30518.315
Reactions
NTP + Deoxycytidine → NDP + dCMPdetails
Adenosine triphosphate + Deoxycytidine → ADP + dCMPdetails
References
  1. Giovannetti E, Mey V, Loni L, Nannizzi S, Barsanti G, Savarino G, Ricciardi S, Del Tacca M, Danesi R: Cytotoxic activity of gemcitabine and correlation with expression profile of drug-related genes in human lymphoid cells. Pharmacol Res. 2007 Apr;55(4):343-9. Epub 2007 Jan 16. Pubmed: 17296311
General function:
Involved in phosphatase activity
Specific function:
Dephosphorylates specifically the 5' and 2'(3')-phosphates of uracil and thymine deoxyribonucleotides, and so protects mitochondrial DNA replication from excess dTTP. Has only marginal activity towards dIMP and dGMP.
Gene Name:
NT5M
Uniprot ID:
Q9NPB1
Molecular weight:
Not Available
Reactions
dCMP + Water → Deoxycytidine + Phosphoric aciddetails
General function:
Involved in zinc ion binding
Specific function:
Not Available
Gene Name:
AID
Uniprot ID:
Q546Y9
Molecular weight:
23953.3
General function:
Involved in magnesium ion binding
Specific function:
Can act both as nucleotidase and as phosphotransferase.
Gene Name:
NT5C3
Uniprot ID:
Q9H0P0
Molecular weight:
33914.91
Reactions
dCMP + Water → Deoxycytidine + Phosphoric aciddetails
General function:
Involved in 5'-nucleotidase activity
Specific function:
May have a critical role in the maintenance of a constant composition of intracellular purine/pyrimidine nucleotides in cooperation with other nucleotidases. Preferentially hydrolyzes inosine 5'-monophosphate (IMP) and other purine nucleotides.
Gene Name:
NT5C2
Uniprot ID:
P49902
Molecular weight:
64969.2
Reactions
dCMP + Water → Deoxycytidine + Phosphoric aciddetails
General function:
Involved in zinc ion binding
Specific function:
This enzyme scavenge exogenous and endogenous cytidine and 2'-deoxycytidine for UMP synthesis.
Gene Name:
CDA
Uniprot ID:
P32320
Molecular weight:
16184.545
Reactions
Deoxycytidine + Water → Deoxyuridine + Ammoniadetails
General function:
Involved in ATP binding
Specific function:
May contribute to UTP accumulation needed for blast transformation and proliferation.
Gene Name:
UCKL1
Uniprot ID:
Q9NWZ5
Molecular weight:
59465.77
General function:
Not Available
Specific function:
DNA deaminase (cytidine deaminase) that mediates a form of innate resistance to retroviral infections (at least to HIV-1 infection) by triggering G-to-A hypermutation in the newly synthesized viral DNA. The replacements C-to-U in the minus strand DNA of HIV-1 during reverse transcription, leads to G-to-A transitions in the plus strand. The inhibition of viral replication is either due to the degradation of the minus strand before its integration or to the lethality of the hypermutations. Modification of both DNA strands is not excluded. This antiviral activity is neutralized by the virion infectivity factor (VIF), that prevents the incorporation of APOBEC3G into progeny HIV-1 virions by both inhibiting its translation and/or by inducing its ubiquitination and subsequent degradation by the 26S proteasome. May also prevent the transposition of a subset of retroelements. Binds a variety of RNAs, but does not display detectable APOB, NF1 and NAT1 mRNA editing.
Gene Name:
APOBEC3G
Uniprot ID:
Q9HC16
Molecular weight:
11822.52
Reactions
Deoxycytidine + Water → Deoxyuridine + Ammoniadetails