Record Information |
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Version | 4.0 |
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Status | Detected and Quantified |
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Creation Date | 2005-11-16 15:48:42 UTC |
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Update Date | 2020-02-26 21:21:47 UTC |
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HMDB ID | HMDB0000014 |
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Secondary Accession Numbers | |
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Metabolite Identification |
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Common Name | Deoxycytidine |
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Description | Deoxycytidine, also known as dC, belongs to the class of organic compounds known as pyrimidine 2'-deoxyribonucleosides. Pyrimidine 2'-deoxyribonucleosides are compounds consisting of a pyrimidine linked to a ribose which lacks a hydroxyl group at position 2. Deoxycytidine is an extremely weak basic (essentially neutral) compound (based on its pKa). Deoxycytidine exists in all living species, ranging from bacteria to humans. Within humans, deoxycytidine participates in a number of enzymatic reactions. In particular, deoxycytidine can be biosynthesized from dCMP through the action of the enzyme cytosolic purine 5'-nucleotidase. In addition, deoxycytidine can be converted into dCMP; which is mediated by the enzyme uridine-cytidine kinase-like 1. 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). A nucleoside consists of only a pentose sugar linked to a purine or pyrimidine base, without a phosphate group. In humans, deoxycytidine is involved in the metabolic disorder called ump synthase deficiency (orotic aciduria). Outside of the human body, Deoxycytidine has been detected, but not quantified in, several different foods, such as bilberries, lentils, swamp cabbages, evergreen huckleberries, and horseradish tree. This could make deoxycytidine a potential biomarker for the consumption of these foods. 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). One of the principal nucleosides of DNA composed of cytosine and deoxyribose. |
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Structure | |
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Synonyms | Value | Source |
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4-Amino-1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl]pyrimidin-2(1H)-one | ChEBI | dC | ChEBI | DCYD | ChEBI | 2'-Deoxycytidine | Kegg | 1-(2-Deoxy-b-D-ribofuranosyl)cytosine | HMDB | 1-(2-Deoxy-beta-D-erythro-pentofuranosyl)-cytosine | HMDB | 1-(2-Deoxy-beta-D-ribofuranosyl)cytosine | HMDB | 1-(2-Deoxy-beta-delta-erythro-pentofuranosyl)-cytosine | HMDB | 1-(2-Deoxy-beta-delta-ribofuranosyl)cytosine | HMDB | 2-Deoxy-cytidine | HMDB | 4-Amino-1-(2-deoxy-b-D-erythro-pentofuranosyl)-2(1H)-pyrimidinone | HMDB | 4-Amino-1-(2-deoxy-beta-D-erythro-pentofuranosyl)-2(1H)-pyrimidinone | HMDB | 4-Amino-1-(2-deoxy-beta-delta-erythro-pentofuranosyl)-2(1H)-pyrimidinone | HMDB | Cytosine deoxyribonucleoside | HMDB | Cytosine deoxyriboside | HMDB | Deoxy-cytidine | HMDB | Deoxyribose cytidine | HMDB | Desoxycytidine | HMDB | Deoxyribonucleoside, cytosine | HMDB | Deoxyriboside, cytosine | HMDB | Deoxycytidine | ChEBI |
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Chemical Formula | C9H13N3O4 |
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Average Molecular Weight | 227.2172 |
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Monoisotopic Molecular Weight | 227.090605919 |
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IUPAC Name | 4-amino-1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2-dihydropyrimidin-2-one |
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Traditional Name | 2'-deoxycytidine |
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CAS Registry Number | 951-77-9 |
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SMILES | NC1=NC(=O)N(C=C1)[C@H]1C[C@H](O)[C@@H](CO)O1 |
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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 |
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InChI Key | CKTSBUTUHBMZGZ-SHYZEUOFSA-N |
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Chemical Taxonomy |
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Description | belongs to the class of organic compounds known as pyrimidine 2'-deoxyribonucleosides. Pyrimidine 2'-deoxyribonucleosides are compounds consisting of a pyrimidine linked to a ribose which lacks a hydroxyl group at position 2. |
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Kingdom | Organic compounds |
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Super Class | Nucleosides, nucleotides, and analogues |
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Class | Pyrimidine nucleosides |
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Sub Class | Pyrimidine 2'-deoxyribonucleosides |
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Direct Parent | Pyrimidine 2'-deoxyribonucleosides |
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Alternative Parents | |
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Substituents | - Pyrimidine 2'-deoxyribonucleoside
- Aminopyrimidine
- Pyrimidone
- Hydropyrimidine
- Pyrimidine
- Imidolactam
- Heteroaromatic compound
- Tetrahydrofuran
- Secondary alcohol
- Azacycle
- Oxacycle
- Organoheterocyclic compound
- Alcohol
- Hydrocarbon derivative
- Organic oxide
- Organopnictogen compound
- Primary amine
- Primary alcohol
- Organooxygen compound
- Organonitrogen compound
- Organic oxygen compound
- Organic nitrogen compound
- Amine
- Aromatic heteromonocyclic compound
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Molecular Framework | Aromatic heteromonocyclic compounds |
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External Descriptors | |
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Ontology |
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Disposition | Route of exposure: Source: Biological location: |
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Process | Naturally occurring process: |
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Role | Industrial application: |
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Physical Properties |
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State | Solid |
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Experimental Properties | Property | Value | Reference |
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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) |
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Predicted Properties | |
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| Spectrum Type | Description | Splash Key | View |
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Predicted GC-MS | Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive | splash10-0006-9510000000-43f83823bd8a63669514 | Spectrum | Predicted GC-MS | Predicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positive | splash10-0gb9-4912000000-fef878d78b0000e850bb | Spectrum | LC-MS/MS | LC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated) | splash10-03di-0900000000-27431bdd2327f6f2b886 | Spectrum | LC-MS/MS | LC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated) | splash10-03di-1900000000-0ea85f3f3940843e385b | Spectrum | LC-MS/MS | LC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated) | splash10-03dl-9500000000-569e473eba0b700f5b6e | Spectrum | LC-MS/MS | LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Negative | splash10-004i-0090000000-5c8c0fde4f2163fbc335 | Spectrum | LC-MS/MS | LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Negative | splash10-0006-9420000000-28279714b575d59761ce | Spectrum | LC-MS/MS | LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Negative | splash10-0006-9200000000-df7c76b755c9fac5267b | Spectrum | LC-MS/MS | LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Negative | splash10-0006-9100000000-acbd1d7557be6d716a19 | Spectrum | LC-MS/MS | LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Negative | splash10-00kf-9100000000-056ef35d3aa743e0d5cf | Spectrum | LC-MS/MS | LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Positive | splash10-03di-0910000000-52e9d173bb94576f7d9e | Spectrum | LC-MS/MS | LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Positive | splash10-03di-0900000000-e06e5a9f19c4162aa24f | Spectrum | LC-MS/MS | LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Positive | splash10-03di-0900000000-551d8ee9679ef3fb65fa | Spectrum | LC-MS/MS | LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Positive | splash10-03di-3900000000-4c62633283ba566dbee0 | Spectrum | LC-MS/MS | LC-MS/MS Spectrum - LC-ESI-IT (LC/MSD Trap XCT, Agilent Technologies) , Positive | splash10-03di-0900000000-bac3656523b118a2c1bc | Spectrum | LC-MS/MS | LC-MS/MS Spectrum - LC-ESI-IT (LC/MSD Trap XCT, Agilent Technologies) , Positive | splash10-03dj-6900000000-dfa8435d3dd8b8981621 | Spectrum | LC-MS/MS | LC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Positive | splash10-01t9-0690000000-72302b09c51553dde169 | Spectrum | LC-MS/MS | LC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) 30V, Positive | splash10-03fr-0930000000-f5c80400a73719f6211f | Spectrum | LC-MS/MS | LC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Negative | splash10-0006-9130000000-c7f95a478d22e3cc83f4 | Spectrum | LC-MS/MS | LC-MS/MS Spectrum - LC-ESI-QQ , negative | splash10-004i-0090000000-af75883dba546c82e7bc | Spectrum | LC-MS/MS | LC-MS/MS Spectrum - LC-ESI-QQ , negative | splash10-0006-9420000000-562a675c6278a4ae2bc4 | Spectrum | Predicted LC-MS/MS | Predicted LC-MS/MS Spectrum - 10V, Positive | splash10-03di-0900000000-e9d4ffd1148d792f5132 | Spectrum | Predicted LC-MS/MS | Predicted LC-MS/MS Spectrum - 20V, Positive | splash10-03di-4900000000-b2a5f419f882d45f6ae7 | Spectrum | Predicted LC-MS/MS | Predicted LC-MS/MS Spectrum - 40V, Positive | splash10-03di-8900000000-0bbcfd7be44c4f38c4fc | Spectrum | Predicted LC-MS/MS | Predicted LC-MS/MS Spectrum - 10V, Negative | splash10-004i-1890000000-395ff33971fbc8368eca | Spectrum | Predicted LC-MS/MS | Predicted LC-MS/MS Spectrum - 20V, Negative | splash10-0016-4910000000-2dc8aa3aad2b1c83316f | Spectrum | Predicted LC-MS/MS | Predicted LC-MS/MS Spectrum - 40V, Negative | splash10-0006-9200000000-cc82bf3d145faf0a6ca3 | Spectrum | 1D NMR | 1H NMR Spectrum | Not Available | Spectrum | 1D NMR | 13C NMR Spectrum | Not Available | Spectrum | 2D NMR | [1H,13C] 2D NMR Spectrum | Not Available | Spectrum |
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General References | - 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 ]
- 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 ]
- 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 ]
- 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 ]
- 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 ]
- (). Maley, F. et al., J. Biol. Chem., 1958, 233, 1538-1543, (5-diphosphate). .
- (). Charubala, R. et al., Synthesis, 1984, 965-968, (5'-(4,4'-dimethoxytrityl) 4N-benzoyl). .
- (). Schaller, H. et al., J.A.C.S., 1963, 85, 3821-3827, (5'-(4,4'-dimethoxytrityl) 4N-benzoyl). .
- (). 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). .
- (). Hruska, F.E. et al., Can. J. Chem., 1974, 52, 497-508, (pmr). .
- (). Jones, A.J. et al., Proc. Natl. Acad. Sci. U.S.A., 1970, 65, 27-30, CA, 72, 96682j, (cmr). .
- (). Miles, H.T., J.A.C.S., 1963, 85, 1007-1008, (ir, pmr). .
- (). Young, D.W. et al., Acta Cryst. B, 1975, 31, 961-965, (cryst struct). .
- (). Michelson, A.M. et al., J.C.S., 1954, 34-40, (phosphates, 3',4N-di-Ac, 5'-trityl, 5'-trityl 3',4N-di-Ac). .
- (). Lewis, R.J., Sax's Dangerous Properties of Industrial Materials, 8th edn., Van Nostrand Reinhold, 1992, DAQ850. .
- (). Aldrich Library of 13C and 1H FT NMR Spectra, 1992, 3, 396A, 396C, (nmr). .
- (). Stawinski, J. et al., Chem. Comm., 1976, 243-244, (3',4N,5'-tribenzoyl). .
- (). 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.. .
- (). 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. . .
- (). 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.. .
- (). FOX JJ, WEMPEN I. Pyrimidine nucleosides. Adv Carbohydr Chem. 1959;14:283-380.. .
- (). Raffaele Saladino, Enrico Mincione, Claudia Crestini, Maurizio Mezzetti. Transformations of thiopyrimidine and thiopurine nucleosides following oxidation with dimethyldioxirane. Tetrahedron, 1996, 52, 6759-6780. .
- (). Aldrich Library of FT-IR Spectra, 1st edn., 1985, 2, 832B, 838D, 839C, (ir). .
- (). Yang, J.T. et al., CA, 1966, 65, 12454, (ord). .
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