ContaminantDB: Ribothymidine

Identification Taxonomy Biological Properties Physical Properties Toxicity Profile Spectra Concentrations Links References XML

Record Information

Version

1.0

Creation Date

2016-05-25 18:08:49 UTC

Update Date

2016-11-09 01:17:20 UTC

Accession Number

CHEM021635

Identification

Common Name

Ribothymidine

Class

Small Molecule

Description

A methyluridine having a single methyl substituent at the 5-position on the uracil ring.

Contaminant Sources

FooDB Chemicals
HMDB Contaminants - Urine

Contaminant Type

Not Available

Chemical Structure

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
1-(beta-D-Ribofuranosyl)thymine	ChEBI
Ribosylthymidine	ChEBI
t	ChEBI
Thymine riboside	ChEBI
1-(b-D-Ribofuranosyl)thymine	Generator
1-(Β-D-ribofuranosyl)thymine	Generator
1-b-D-Ribofuranosylthymine	HMDB
1-beta-delta-Ribofuranosylthymine	HMDB
5-Methyl-1-beta-D-ribofuranosyl-2,4(1H,3H)-pyrimidinedione	HMDB
5-Methyl-1-beta-delta-ribofuranosyl-2,4(1H,3H)-pyrimidinedione	HMDB
5-Methyl-uridine	HMDB
5-Methyluridine	HMDB
b-D-Ribofuranoside thymine-1	HMDB
beta-D-Ribofuranoside	HMDB
beta-delta-Ribofuranoside	HMDB
beta-delta-Ribofuranoside thymine-1	HMDB
Ribosylthymine	HMDB
Thymine ribofuranoside	HMDB
Thymine ribonucleoside	HMDB
Thymine-1 beta-D-ribofuranosylthymine	HMDB
Thymine-1 beta-delta-ribofuranosylthymine	HMDB

Chemical Formula

C₁₀H₁₄N₂O₆

Average Molecular Mass

258.228 g/mol

Monoisotopic Mass

258.085 g/mol

CAS Registry Number

1463-10-1

IUPAC Name

1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-methyl-1,2,3,4-tetrahydropyrimidine-2,4-dione

Traditional Name

thymidin

SMILES

CC1=CN([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O)C(=O)NC1=O

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

InChI Key

DWRXFEITVBNRMK-JXOAFFINSA-N

Chemical Taxonomy

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.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Pyrimidine nucleosides

Sub Class

Not Available

Direct Parent

Pyrimidine nucleosides

Alternative Parents

Substituents

Pyrimidine nucleoside
Glycosyl compound
N-glycosyl compound
Pentose monosaccharide
Pyrimidone
Hydropyrimidine
Monosaccharide
Pyrimidine
Vinylogous amide
Tetrahydrofuran
Heteroaromatic compound
Urea
Secondary alcohol
Lactam
Organoheterocyclic compound
Oxacycle
Azacycle
Hydrocarbon derivative
Organopnictogen compound
Organooxygen compound
Organonitrogen compound
Primary alcohol
Alcohol
Organic oxygen compound
Organic oxide
Organic nitrogen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

methyluridine (CHEBI:45996 )

Biological Properties

Status

Detected and Not Quantified

Origin

Not Available

Cellular Locations

Not Available

Biofluid Locations

Not Available

Tissue Locations

Not Available

Pathways

Not Available

Applications

Not Available

Biological Roles

Not Available

Chemical Roles

Not Available

Physical Properties

State

Not Available

Appearance

Not Available

Experimental Properties

Property	Value
Melting Point	Not Available
Boiling Point	Not Available
Solubility	Not Available

Predicted Properties

Property	Value	Source
Water Solubility	135 g/L	ALOGPS
logP	-1.7	ALOGPS
logP	-2	ChemAxon
logS	-0.28	ALOGPS
pKa (Strongest Acidic)	9.95	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	119.33 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	56.92 m³·mol⁻¹	ChemAxon
Polarizability	24.1 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	1	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Spectrum Type	Description	Splash Key	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-05bf-9420000000-897dab8f4bbf7b8e664c	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (3 TMS) - 70eV, Positive	splash10-0kp0-6879400000-656a0a43be4a2cd044e7	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_1) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_2) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_3) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_4) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_1) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_2) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_3) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_4) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_5) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_6) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_3_2) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_3_3) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_3_4) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_2) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_3) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_4) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_2_1) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_2_2) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_2_3) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_2_4) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_2_5) - 70eV, Positive	Not Available	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)	splash10-004i-0900000000-1653ad80c56ae3727f92	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)	splash10-004i-2900000000-826774188d3e78ca38f2	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)	splash10-0a6r-9800000000-f5daf31a98b364b70f8c	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 10V, Negative	splash10-0a4i-0090000000-f186cfbb52edc03ff4de	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 35V, Negative	splash10-004i-0900000000-9f7398feab5dd8950264	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 40V, Negative	splash10-0006-9100000000-893019db60499c0a9602	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 20V, Negative	splash10-004i-2900000000-461a9c94bf89e5b47970	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 10V, Negative	splash10-004i-0900000000-1db6a34eff49b044d944	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 35V, Positive	splash10-004i-1900000000-1c2ee21cd9d3515f7124	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 10V, Positive	splash10-056r-1970000000-ba6f9aa1164c365abfa2	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 40V, Positive	splash10-01u0-8900000000-a63ffd4c990b9c9a543a	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 20V, Positive	splash10-004i-4900000000-71ebad0df798bf2ac282	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 40V, Positive	splash10-06w9-8900000000-3c0ceb68319de86fc30f	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 20V, Positive	splash10-004i-1900000000-45b9a7b5e831351a1fe0	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 10V, Positive	splash10-004i-0900000000-e1eddf8b44309a38eebb	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-004i-0910000000-90f6da130f49fa9df29d	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-004i-5900000000-203a4367756530615ffd	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-004j-9800000000-13e51659da01285bdc7f	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0a6r-1490000000-4ba707a2228996f9f9f7	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-6920000000-a25c60ade61d6d32f0f1	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-001m-9100000000-37e601ae2d82d72111e7	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-004i-0900000000-f08754aed5978a645b7c	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-004i-3910000000-01ae005a14dd4c188d46	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0a6r-9700000000-513e87b6fba58d79ef98	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-056r-0950000000-b4a8bf9fcddaedc20b74	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	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