Showing Compound Thymine 2-desoxyriboside (FDB012757)

Record Information

Version

1.0

Creation date

2010-04-08 22:10:20 UTC

Update date

2019-11-26 03:07:32 UTC

Primary ID

FDB012757

Secondary Accession Numbers

Not Available

Chemical Information

FooDB Name

Thymine 2-desoxyriboside

Description

Isolated from seedlings of Phaseolus vulgaris (kidney bean) Deoxythymidine is non-toxic and as part of one of the four nucleotides in DNA it is a naturally occurring compound that exists in all living organisms and DNA viruses. RNA has uridine (uracil joined to ribose) instead. Uracil is chemically very similar to thymine, the latter being 5-methyluracil. Since thymine nucleotides are precursors of DNA, not RNA, the prefix "deoxy" is often left out, i.e., deoxythymidine is often just called thymidine.; In its composition, deoxythymidine is a nucleoside composed of deoxyribose (a pentose sugar) joined to the pyrimidine base thymine.; Iododeoxyuridine is a radiosensitizer and increases the amount of DNA damage received from ionizing radiation.; Thymidine (more precisely called deoxythymidine; can also be labelled deoxyribosylthymine, and thymine deoxyriboside) is a chemical compound, more precisely a pyrimidine deoxynucleoside. Deoxythymidine is the DNA nucleoside T, which pairs with deoxyadenosine (A) in double-stranded DNA. In cell biology it is used to synchronize the cells in S phase.; Thymidine is non-toxic and is a naturally occurring compound that exists in all living organisms and DNA viruses. 25% of DNA is composed of thymidine. RNA does not have thymidine and has uridine instead. Thymidine is a chemical compound which is a pyrimidine nucleoside. Thymidine is the DNA base T, which pairs with adenosine in double stranded DNA. Thymine 2-desoxyriboside is found in pulses, yellow wax bean, and green bean.

CAS Number

50-89-5

Structure

MOL SDF PDB SMILES InChI

Synonyms

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Search:

Synonym	Source
(3H)Thymidine	biospider
1-(2-Deoxy-b-D-erythro-pentofuranosyl)-5-methyl-2,4(1H,3H)-pyrimidinedione	HMDB
1-(2-Deoxy-b-D-erythro-pentofuranosyl)-5-methyl-2,4(1H,3H)-pyrimidinedione, 9CI	db_source
1-(2-Deoxy-b-D-erythro-pentofuranosyl)-5-methylpyrimidine-2,4(1H,3H)-dione	Generator
1-(2-Deoxy-b-D-ribofuranosyl)-5-methyluracil	db_source
1-(2-Deoxy-beta-D-erythro-pentofuranosyl)-5-methylpyrimidine-2,4(1H,3H)-dione	ChEBI
1-(2-Deoxy-beta-D-ribofuranosyl)-5-methyluracil	biospider
1-(2-Deoxy-beta-D-ribofuranosyl)thymine	biospider
1-(2-Deoxy-beta-delta-erythro-pentofuranosyl)-5-methyl-2,4(1H,3H)-pyrimidinedione	HMDB
1-(2-Deoxy-beta-ribofuranosyl)-5-methyluracil	biospider

Showing 1 to 10 of 49 entries

Predicted Properties

Property	Value	Source
Water Solubility	19.8 g/L	ALOGPS
logP	-1.7	ALOGPS
logP	-0.75	ChemAxon
logS	-1.1	ALOGPS
pKa (Strongest Acidic)	7.52	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	102.59 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	55.73 m³·mol⁻¹	ChemAxon
Polarizability	23.08 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Chemical Formula

C10H14N2O5

IUPAC name

4-hydroxy-1-[4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-methyl-1,2-dihydropyrimidin-2-one

InChI Identifier

InChI=1S/C10H14N2O5/c1-5-3-12(10(16)11-9(5)15)8-2-6(14)7(4-13)17-8/h3,6-8,13-14H,2,4H2,1H3,(H,11,15,16)

InChI Key

IQFYYKKMVGJFEH-UHFFFAOYSA-N

Isomeric SMILES

CC1=CN(C2CC(O)C(CO)O2)C(=O)N=C1O

Average Molecular Weight

242.2286

Monoisotopic Molecular Weight

242.090271568

Classification

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.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Pyrimidine nucleosides

Sub Class

Pyrimidine 2'-deoxyribonucleosides

Direct Parent

Pyrimidine 2'-deoxyribonucleosides

Alternative Parents

Substituents

Pyrimidine 2'-deoxyribonucleoside
Pyrimidone
Hydropyrimidine
Pyrimidine
Heteroaromatic compound
Tetrahydrofuran
Vinylogous amide
Lactam
Secondary alcohol
Urea
Oxacycle
Azacycle
Organoheterocyclic compound
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Primary alcohol
Organooxygen compound
Organonitrogen compound
Organic oxygen compound
Alcohol
Organic nitrogen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

a pyrimidine-related compound (THYMIDINE )
a deoxynucleoside (THYMIDINE )

Ontology

No ontology term

Physico-Chemical Properties

Physico-Chemical Properties - Experimental

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Search:

Property	Value	Reference
Boiling Point	Not Available
Charge	0
Density	Not Available
Experimental logP	-0.93	SANGSTER (1993)
Experimental pKa	pKa2 12.9 (25°)	DFC
Experimental Water Solubility	Not Available
Isoelectric point	Not Available
Mass Composition	C 49.58%; H 5.83%; N 11.56%; O 33.03%	DFC
Melting Point	Mp 186-187°	DFC
Optical Rotation	[a]25D +30.6 (c, 1.0 in H2O)	DFC

Showing 1 to 10 of 14 entries

Spectra

EI-MS/GC-MS

Type	Description	Splash Key	View
EI-MS	Mass Spectrum (Electron Ionization)	splash10-01dj-9300000000-6e24b5b6d36e07dd73d0	2014-09-20	View Spectrum
Predicted GC-MS	Thymine 2-desoxyriboside, non-derivatized, Predicted GC-MS Spectrum - 70eV, Positive	splash10-0006-9520000000-4f5fdf466b2300e3cc3e	Spectrum
Predicted GC-MS	Thymine 2-desoxyriboside, non-derivatized, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Thymine 2-desoxyriboside, TMS_1_1, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Thymine 2-desoxyriboside, TMS_1_2, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Thymine 2-desoxyriboside, TMS_1_3, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Thymine 2-desoxyriboside, TMS_2_1, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Thymine 2-desoxyriboside, TMS_2_2, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Thymine 2-desoxyriboside, TMS_2_3, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Thymine 2-desoxyriboside, TMS_3_1, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Thymine 2-desoxyriboside, TBDMS_1_1, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Thymine 2-desoxyriboside, TBDMS_1_2, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Thymine 2-desoxyriboside, TBDMS_1_3, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Thymine 2-desoxyriboside, TBDMS_2_1, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Thymine 2-desoxyriboside, TBDMS_2_2, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Thymine 2-desoxyriboside, TBDMS_2_3, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Thymine 2-desoxyriboside, TBDMS_3_1, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum

MS/MS

Type	Description	Splash Key	View
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-004i-0900000000-9c9e9e6d7f74fb1f2757	2015-05-27	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-004i-4900000000-3b1e6c50c2450e123648	2015-05-27	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-004i-6900000000-b04537b00f6e00caad37	2015-05-27	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-052g-1940000000-8fce8753136d1a1982ae	2015-05-27	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0ufu-3920000000-1a2bd5708f88b9808da6	2015-05-27	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-000x-9200000000-d9db5a1484e9c4936d30	2015-05-27	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-004i-1900000000-bcb24421d7b0162d607d	2021-10-12	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-057j-7900000000-ddd5f450835af7ef5edf	2021-10-12	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0a4i-5900000000-c6ee0c9772bd68aa7c3f	2021-10-12	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-002f-1980000000-a20f517efa944c15889c	2021-10-12	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-002f-9400000000-0daaa361f245163aeaec	2021-10-12	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0006-9400000000-de7ded95723d9abbf35f	2021-10-12	View Spectrum

NMR

Type	Description	View
1D NMR	¹H NMR Spectrum (1D, 400 MHz, DMSO-d6, experimental)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 25.16 MHz, D₂O, experimental)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Spectrum