Human Metabolome Database Version 3.5

Showing metabocard for Deoxycytidine (HMDB00014)

Record Information
Version 3.5
Creation Date 2005-11-16 08:48:42 -0700
Update Date 2013-02-08 17:07:45 -0700
HMDB ID HMDB00014
Secondary Accession Numbers None
Metabolite Identification
Common Name Deoxycytidine
Description One 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
Download: MOL | SDF | PDB | SMILES | InChI
Display: 2D Structure | 3D Structure
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 Formula C9H13N3O4
Average Molecular Weight 227.2172
Monoisotopic Molecular Weight 227.090605919
IUPAC Name 4-amino-1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2-dihydropyrimidin-2-one
Traditional IUPAC Name deoxycytidine
CAS Registry Number 951-77-9
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 Key CKTSBUTUHBMZGZ-SHYZEUOFSA-N
Chemical Taxonomy
Kingdom Organic Compounds
Super Class Nucleosides, Nucleotides, and Analogues
Class Pyrimidine Nucleosides and Analogues
Sub Class Pyrimidine 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 Parent Pyrimidine 2'-deoxyribonucleosides and Analogues
Ontology
Status Detected and Quantified
Origin
  • Endogenous
Biofunction
  • Component of Purine metabolism
  • Component of Pyrimidine metabolism
Application Not Available
Cellular locations
  • Extracellular
  • Mitochondria
  • Nucleus
  • Lysosome
Physical Properties
State Solid
Experimental Properties
Property Value Reference
Melting Point 207 - 210 °C Not Available
Boiling Point Not Available Not Available
Water Solubility 870 mg/mL Not Available
LogP -1.77 HANSCH,C ET AL. (1995)
Predicted Properties
Property Value Source
Water Solubility 15.9 g/L ALOGPS
LogP -1.93 ALOGPS
LogP -1.9 ChemAxon
LogS -1.16 ALOGPS
pKa (strongest acidic) 13.89 ChemAxon
pKa (strongest basic) -0.0012 ChemAxon
Hydrogen Acceptor Count 6 ChemAxon
Hydrogen Donor Count 3 ChemAxon
Polar Surface Area 108.38 A2 ChemAxon
Rotatable Bond Count 2 ChemAxon
Refractivity 53.03 ChemAxon
Polarizability 21.65 ChemAxon
Formal Charge 0 ChemAxon
Physiological Charge 0 ChemAxon
Spectra
1H NMR Spectrum
13C NMR Spectrum
MS/MS Spectrum Quattro_QQQ 10
MS/MS Spectrum Quattro_QQQ 25
MS/MS Spectrum Quattro_QQQ 40
MS/MS Spectrum LC-ESI-QQ (API3000, Applied Biosystems) 10
MS/MS Spectrum LC-ESI-QQ (API3000, Applied Biosystems) 20
MS/MS Spectrum LC-ESI-QQ (API3000, Applied Biosystems) 30
MS/MS Spectrum LC-ESI-QQ (API3000, Applied Biosystems) 40
MS/MS Spectrum LC-ESI-QQ (API3000, Applied Biosystems) 50
MS/MS Spectrum LC-ESI-QQ (API3000, Applied Biosystems) 10
MS/MS Spectrum LC-ESI-QQ (API3000, Applied Biosystems) 20
MS/MS Spectrum LC-ESI-QQ (API3000, Applied Biosystems) 30
MS/MS Spectrum LC-ESI-QQ (API3000, Applied Biosystems) 40
MS/MS Spectrum LC-ESI-IT (LC/MSD Trap XCT, Agilent Technologies)
MS/MS Spectrum LC-ESI-IT (LC/MSD Trap XCT, Agilent Technologies)
MS/MS Spectrum LC-ESI-QTOF (UPLC Q-Tof Premier, Waters)
[1H,13C] 2D NMR Spectrum
Biological Properties
Cellular Locations
  • Extracellular
  • Mitochondria
  • Nucleus
  • Lysosome
Biofluid Locations
  • Blood
  • Urine
Tissue Location
  • All Tissues
Pathways
Name SMPDB Link KEGG Link
Pyrimidine Metabolism SMP00046 map00240 Link_out
Normal Concentrations
Biofluid Status Value Age Sex Condition Reference
Blood Detected and Quantified
0.2 (0.0-0.5) uM Adult (>18 years old) Both Normal
Urine Detected and Quantified
0.65 +/- 0.27 umol/mmol creatinine Adult (>18 years old) Both Normal
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease References None
Associated OMIM IDs None
DrugBank ID Not Available
DrugBank Metabolite ID Not Available
Phenol Explorer Compound ID Not Available
Phenol Explorer Metabolite ID Not Available
FoodDB ID FDB021871
KNApSAcK ID Not Available
Chemspider ID 13117 Link_out
KEGG Compound ID C00881 Link_out
BioCyc ID DEOXYCYTIDINE Link_out
BiGG ID 36280 Link_out
Wikipedia Link Deoxycytidine Link_out
NuGOwiki Link HMDB00014 Link_out
Metagene Link HMDB00014 Link_out
METLIN ID 3367 Link_out
PubChem Compound 13711 Link_out
PDB ID DCZ Link_out
ChEBI ID 15698 Link_out
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 Link_out
  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 Link_out
  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 Link_out
  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 Link_out
  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 Link_out
  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
Name: 5'-nucleotidase
Reactions:
dCMP + Water unknown Deoxycytidine + Phosphoric acid details
Gene Name: NT5E
Uniprot ID: P21589 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: Cytosolic 5'-nucleotidase 1B
Reactions:
dCMP + Water unknown Deoxycytidine + Phosphoric acid details
Gene Name: NT5C1B
Uniprot ID: Q96P26 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: Cytosolic 5'-nucleotidase 1A
Reactions:
dCMP + Water unknown Deoxycytidine + Phosphoric acid details
Gene Name: NT5C1A
Uniprot ID: Q9BXI3 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: 5'(3')-deoxyribonucleotidase, cytosolic type
Reactions:
dCMP + Water unknown Deoxycytidine + Phosphoric acid details
Gene Name: NT5C
Uniprot ID: Q8TCD5 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: Deoxycytidine kinase
Reactions:
NTP + Deoxycytidine unknown NDP + dCMP details
Adenosine triphosphate + Deoxycytidine unknown ADP + dCMP details
Gene Name: DCK
Uniprot ID: P27707 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: 5'(3')-deoxyribonucleotidase, mitochondrial
Reactions:
dCMP + Water unknown Deoxycytidine + Phosphoric acid details
Gene Name: NT5M
Uniprot ID: Q9NPB1 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: AID
Reactions: Not Available
Gene Name: AID
Uniprot ID: Q546Y9 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: Cytosolic 5'-nucleotidase 3
Reactions:
dCMP + Water unknown Deoxycytidine + Phosphoric acid details
Gene Name: NT5C3
Uniprot ID: Q9H0P0 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: Cytosolic purine 5'-nucleotidase
Reactions:
dCMP + Water unknown Deoxycytidine + Phosphoric acid details
Gene Name: NT5C2
Uniprot ID: P49902 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: Cytidine deaminase
Reactions:
Deoxycytidine + Water unknown Deoxyuridine + Ammonia details
Gene Name: CDA
Uniprot ID: P32320 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: Uridine-cytidine kinase-like 1
Reactions: Not Available
Gene Name: UCKL1
Uniprot ID: Q9NWZ5 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: DNA dC->dU-editing enzyme APOBEC-3G
Reactions:
Deoxycytidine + Water unknown Deoxyuridine + Ammonia details
Gene Name: APOBEC3G
Uniprot ID: Q9HC16 Link_out
Protein Sequence: FASTA