| Record Information |
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| Version | 2.0 |
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| Created at | 2022-09-05 13:42:36 UTC |
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| Updated at | 2022-09-05 13:42:36 UTC |
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| NP-MRD ID | NP0214414 |
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| Secondary Accession Numbers | None |
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| Natural Product Identification |
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| Common Name | 1-[(2r,3s,4s,5r)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-hydroxy-5-methylpyrimidin-2-one |
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| Description | Spongothymidine, also known as ara-T or arabinosylthymine, 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. 1-[(2r,3s,4s,5r)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-hydroxy-5-methylpyrimidin-2-one was first documented in 2013 (PMID: 24047739). Based on a literature review a small amount of articles have been published on Spongothymidine (PMID: 34079462) (PMID: 25668560) (PMID: 29912171). |
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| Structure | CC1=CN([C@@H]2O[C@H](CO)[C@@H](O)[C@@H]2O)C(=O)N=C1O InChI=1S/C10H14N2O6/c1-4-2-12(10(17)11-8(4)16)9-7(15)6(14)5(3-13)18-9/h2,5-7,9,13-15H,3H2,1H3,(H,11,16,17)/t5-,6-,7+,9-/m1/s1 |
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| Synonyms | | Value | Source |
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| Ara-T | MeSH | | Arabinofuranosylthymine | MeSH | | Thymine arabinoside | MeSH | | 1 beta-D-Arabinofuranosylthymine | MeSH | | Arabinosylthymine | MeSH |
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| Chemical Formula | C10H14N2O6 |
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| Average Mass | 258.2300 Da |
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| Monoisotopic Mass | 258.08519 Da |
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| IUPAC Name | 1-[(2R,3S,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-hydroxy-5-methyl-1,2-dihydropyrimidin-2-one |
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| Traditional Name | 1-[(2R,3S,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-hydroxy-5-methylpyrimidin-2-one |
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| CAS Registry Number | Not Available |
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| SMILES | CC1=CN([C@@H]2O[C@H](CO)[C@@H](O)[C@@H]2O)C(=O)N=C1O |
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| InChI Identifier | InChI=1S/C10H14N2O6/c1-4-2-12(10(17)11-8(4)16)9-7(15)6(14)5(3-13)18-9/h2,5-7,9,13-15H,3H2,1H3,(H,11,16,17)/t5-,6-,7+,9-/m1/s1 |
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| InChI Key | DWRXFEITVBNRMK-JAGXHNFQSA-N |
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| Experimental Spectra |
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| Not Available | | Predicted Spectra |
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| | Spectrum Type | Description | Depositor ID | Depositor Organization | Depositor | Deposition Date | View |
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| 1D NMR | 13C NMR Spectrum (1D, 25 MHz, H2O, predicted) | Wishart Lab | Wishart Lab | David Wishart | 2021-06-20 | View Spectrum | | 1D NMR | 1H NMR Spectrum (1D, 100 MHz, H2O, predicted) | Wishart Lab | Wishart Lab | David Wishart | 2021-06-20 | View Spectrum | | 1D NMR | 13C NMR Spectrum (1D, 252 MHz, H2O, predicted) | Wishart Lab | Wishart Lab | David Wishart | 2021-06-20 | View Spectrum | | 1D NMR | 1H NMR Spectrum (1D, 1000 MHz, H2O, predicted) | Wishart Lab | Wishart Lab | David Wishart | 2021-06-20 | View Spectrum | | 1D NMR | 13C NMR Spectrum (1D, 50 MHz, H2O, predicted) | Wishart Lab | Wishart Lab | David Wishart | 2021-06-20 | View Spectrum | | 1D NMR | 1H NMR Spectrum (1D, 200 MHz, H2O, predicted) | Wishart Lab | Wishart Lab | David Wishart | 2021-06-20 | View Spectrum | | 1D NMR | 13C NMR Spectrum (1D, 75 MHz, H2O, predicted) | Wishart Lab | Wishart Lab | David Wishart | 2021-06-20 | View Spectrum | | 1D NMR | 1H NMR Spectrum (1D, 300 MHz, H2O, predicted) | Wishart Lab | Wishart Lab | David Wishart | 2021-06-20 | View Spectrum | | 1D NMR | 13C NMR Spectrum (1D, 101 MHz, H2O, predicted) | Wishart Lab | Wishart Lab | David Wishart | 2021-06-20 | View Spectrum | | 1D NMR | 1H NMR Spectrum (1D, 400 MHz, H2O, predicted) | Wishart Lab | Wishart Lab | David Wishart | 2021-06-20 | View Spectrum | | 1D NMR | 13C NMR Spectrum (1D, 126 MHz, H2O, predicted) | Wishart Lab | Wishart Lab | David Wishart | 2021-06-20 | View Spectrum | | 1D NMR | 1H NMR Spectrum (1D, 500 MHz, H2O, predicted) | Wishart Lab | Wishart Lab | David Wishart | 2021-06-20 | View Spectrum | | 1D NMR | 13C NMR Spectrum (1D, 151 MHz, H2O, predicted) | Wishart Lab | Wishart Lab | David Wishart | 2021-06-20 | View Spectrum | | 1D NMR | 1H NMR Spectrum (1D, 600 MHz, H2O, predicted) | Wishart Lab | Wishart Lab | David Wishart | 2021-06-20 | View Spectrum | | 1D NMR | 13C NMR Spectrum (1D, 176 MHz, H2O, predicted) | Wishart Lab | Wishart Lab | David Wishart | 2021-06-20 | View Spectrum | | 1D NMR | 1H NMR Spectrum (1D, 700 MHz, H2O, predicted) | Wishart Lab | Wishart Lab | David Wishart | 2021-06-20 | View Spectrum | | 1D NMR | 13C NMR Spectrum (1D, 201 MHz, H2O, predicted) | Wishart Lab | Wishart Lab | David Wishart | 2021-06-20 | View Spectrum | | 1D NMR | 1H NMR Spectrum (1D, 800 MHz, H2O, predicted) | Wishart Lab | Wishart Lab | David Wishart | 2021-06-20 | View Spectrum | | 1D NMR | 13C NMR Spectrum (1D, 226 MHz, H2O, predicted) | Wishart Lab | Wishart Lab | David Wishart | 2021-06-20 | View Spectrum | | 1D NMR | 1H NMR Spectrum (1D, 900 MHz, H2O, predicted) | Wishart Lab | Wishart Lab | David Wishart | 2021-06-20 | View Spectrum |
| | Chemical Shift Submissions |
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| Not Available | | Species |
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| Species of Origin | Not Available |
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| Chemical Taxonomy |
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| 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. |
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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 | Not Available |
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| Direct Parent | Pyrimidine nucleosides |
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| Alternative Parents | |
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| Substituents | - Pyrimidine nucleoside
- Glycosyl compound
- N-glycosyl compound
- Pentose monosaccharide
- Hydroxypyrimidine
- Pyrimidone
- Hydropyrimidine
- Monosaccharide
- Pyrimidine
- Heteroaromatic compound
- Tetrahydrofuran
- Secondary alcohol
- Azacycle
- Oxacycle
- Organoheterocyclic compound
- Alcohol
- Primary alcohol
- Hydrocarbon derivative
- Organooxygen compound
- Organonitrogen compound
- Organic oxide
- Organopnictogen compound
- Organic oxygen compound
- Organic nitrogen compound
- Aromatic heteromonocyclic compound
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| Molecular Framework | Aromatic heteromonocyclic compounds |
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| External Descriptors | |
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| Physical Properties |
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| State | Not Available |
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| Experimental Properties | | Property | Value | Reference |
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| Melting Point | Not Available | Not Available | | Boiling Point | Not Available | Not Available | | Water Solubility | Not Available | Not Available | | LogP | Not Available | Not Available |
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| Predicted Properties | |
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| General References | - Hamoda AM, Fayed B, Ashmawy NS, El-Shorbagi AA, Hamdy R, Soliman SSM: Marine Sponge is a Promising Natural Source of Anti-SARS-CoV-2 Scaffold. Front Pharmacol. 2021 May 13;12:666664. doi: 10.3389/fphar.2021.666664. eCollection 2021. [PubMed:34079462 ]
- Bertin MJ, Schwartz SL, Lee J, Korobeynikov A, Dorrestein PC, Gerwick L, Gerwick WH: Spongosine production by a Vibrio harveyi strain associated with the sponge Tectitethya crypta. J Nat Prod. 2015 Mar 27;78(3):493-9. doi: 10.1021/np5009762. Epub 2015 Feb 10. [PubMed:25668560 ]
- El-Demerdash A, Tammam MA, Atanasov AG, Hooper JNA, Al-Mourabit A, Kijjoa A: Chemistry and Biological Activities of the Marine Sponges of the Genera Mycale (Arenochalina), Biemna and Clathria. Mar Drugs. 2018 Jun 18;16(6):214. doi: 10.3390/md16060214. [PubMed:29912171 ]
- Wang LX, Takayama-Ito M, Kinoshita-Yamaguchi H, Kakiuchi S, Suzutani T, Nakamichi K, Lim CK, Kurane I, Saijo M: Characterization of DNA polymerase-associated acyclovir-resistant herpes simplex virus type 1: mutations, sensitivity to antiviral compounds, neurovirulence, and in-vivo sensitivity to treatment. Jpn J Infect Dis. 2013;66(5):404-10. doi: 10.7883/yoken.66.404. [PubMed:24047739 ]
- LOTUS database [Link]
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