Record Information
Version2.0
Creation Date2012-07-30 14:55:41 -0600
Update Date2015-09-13 12:56:15 -0600
Secondary Accession Numbers
  • ECMDB21389
Identification
Name:Ribothymidine
DescriptionRibothymidine is a pyrimidine nucleoside that is also known as 5-methyluridine. (Wikipedia) It is a methylated version of uridine, one of the building blocks of RNA. It also differs from thymidine, one of the building blocks of DNA, by having an extra hydroxyl (OH group) on its ribose ring. (inferred from compound structure)
Structure
Thumb
Synonyms:
  • 1-(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl-5-methylpyrimidine-2,4-dione
  • 1-(b-D-Ribofuranosyl)thymine
  • 1-(beta-D-ribofuranosyl)thymine
  • 1-(β-D-Ribofuranosyl)thymine
  • 1-b-D-Ribofuranosylthymine
  • 1-b-delta-Ribofuranosylthymine
  • 1-b-δ-Ribofuranosylthymine
  • 1-beta-delta-Ribofuranosylthymine
  • 1-β-δ-Ribofuranosylthymine
  • 5-Methyl-1-b-D-ribofuranosyl-2,4(1H,3H)-pyrimidinedione
  • 5-Methyl-1-b-delta-ribofuranosyl-2,4(1H,3H)-pyrimidinedione
  • 5-Methyl-1-b-δ-ribofuranosyl-2,4(1H,3H)-pyrimidinedione
  • 5-methyl-1-beta-D-ribofuranosyl-2,4(1H,3H)-Pyrimidinedione
  • 5-methyl-1-beta-delta-ribofuranosyl-2,4(1H,3H)-Pyrimidinedione
  • 5-Methyl-1-β-D-ribofuranosyl-2,4(1H,3H)-pyrimidinedione
  • 5-Methyl-1-β-δ-ribofuranosyl-2,4(1H,3H)-pyrimidinedione
  • 5-methyl-Uridine
  • 5-Methyluridine
  • b-D-Ribofuranoside
  • B-D-Ribofuranoside thymine-1
  • b-delta-Ribofuranoside
  • b-delta-Ribofuranoside thymine-1
  • b-δ-Ribofuranoside
  • b-δ-Ribofuranoside thymine-1
  • Beta-D-Ribofuranoside
  • Beta-delta-Ribofuranoside
  • Beta-delta-Ribofuranoside thymine-1
  • Ribosylthymidine
  • Ribosylthymine
  • T
  • Thymine ribofuranoside
  • Thymine ribonucleoside
  • Thymine riboside
  • Thymine-1 b-D-ribofuranosylthymine
  • Thymine-1 b-delta-ribofuranosylthymine
  • Thymine-1 b-δ-ribofuranosylthymine
  • Thymine-1 beta-D-Ribofuranosylthymine
  • Thymine-1 beta-delta-Ribofuranosylthymine
  • Thymine-1 β-D-ribofuranosylthymine
  • Thymine-1 β-δ-ribofuranosylthymine
  • β-D-Ribofuranoside
  • β-δ-Ribofuranoside
  • β-δ-Ribofuranoside thymine-1
Chemical Formula:C10H14N2O6
Weight:Average: 258.228
Monoisotopic: 258.08518619
InChI Key:DWRXFEITVBNRMK-JXOAFFINSA-N
InChI: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
CAS 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 IUPAC Name:thymidin
SMILES:CC1=CN([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O)C(=O)NC1=O
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.
KingdomOrganic compounds
Super ClassNucleosides, nucleotides, and analogues
ClassPyrimidine nucleosides
Sub ClassNot Available
Direct ParentPyrimidine 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 FrameworkAromatic heteromonocyclic compounds
External Descriptors
Physical Properties
State:Solid
Charge:0
Melting point:183-187 °C
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility135 g/LALOGPS
logP-1.7ALOGPS
logP-2ChemAxon
logS-0.28ALOGPS
pKa (Strongest Acidic)9.95ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count6ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area119.33 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity56.92 m³·mol⁻¹ChemAxon
Polarizability24.1 ųChemAxon
Number of Rings2ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations:Cytoplasm
Reactions:
SMPDB Pathways:Not Available
KEGG Pathways:Not Available
EcoCyc Pathways:Not Available
Concentrations
Not Available
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-05bf-9420000000-897dab8f4bbf7b8e664cView in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (3 TMS) - 70eV, Positivesplash10-0kp0-6879400000-656a0a43be4a2cd044e7View in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)splash10-004i-0900000000-1653ad80c56ae3727f92View in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)splash10-004i-2900000000-826774188d3e78ca38f2View in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)splash10-0a6r-9800000000-f5daf31a98b364b70f8cView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-004i-0910000000-90f6da130f49fa9df29dView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-004i-5900000000-203a4367756530615ffdView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-004j-9800000000-13e51659da01285bdc7fView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0a6r-1490000000-4ba707a2228996f9f9f7View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-6920000000-a25c60ade61d6d32f0f1View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-001m-9100000000-37e601ae2d82d72111e7View in MoNA
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
2D NMR[1H,13C] 2D NMR SpectrumNot AvailableView in JSpectraViewer
References
References:
  • Avraham Y, Grossowicz N, Yashphe J: Purification and characterization of uridine and thymidine phosphorylase from Lactobacillus casei. Biochim Biophys Acta. 1990 Sep 3;1040(2):287-93. Pubmed: 2119230
  • Cho SH, Jung BH, Lee SH, Lee WY, Kong G, Chung BC: Direct determination of nucleosides in the urine of patients with breast cancer using column-switching liquid chromatography-tandem mass spectrometry. Biomed Chromatogr. 2006 Nov;20(11):1229-36. Pubmed: 16799933
  • Hacia JG, Woski SA, Fidanza J, Edgemon K, Hunt N, McGall G, Fodor SP, Collins FS: Enhanced high density oligonucleotide array-based sequence analysis using modified nucleoside triphosphates. Nucleic Acids Res. 1998 Nov 1;26(21):4975-82. Pubmed: 9776762
  • Lang TT, Selner M, Young JD, Cass CE: Acquisition of human concentrative nucleoside transporter 2 (hcnt2) activity by gene transfer confers sensitivity to fluoropyrimidine nucleosides in drug-resistant leukemia cells. Mol Pharmacol. 2001 Nov;60(5):1143-52. Pubmed: 11641443
  • Liu Z, Liu S, Xie Z, Blum W, Perrotti D, Paschka P, Klisovic R, Byrd J, Chan KK, Marcucci G: Characterization of in vitro and in vivo hypomethylating effects of decitabine in acute myeloid leukemia by a rapid, specific and sensitive LC-MS/MS method. Nucleic Acids Res. 2007;35(5):e31. Epub 2007 Jan 30. Pubmed: 17264127
  • Mori T, Guo MW, Li X, Xu JP, Mori E: Isolation and identification of apoptosis inducing nucleosides from CD57(+)HLA-DRbright natural suppressor cell line. Biochem Biophys Res Commun. 1998 Oct 20;251(2):416-22. Pubmed: 9792789
  • Morris GS, Simmonds HA, Davies PM: Use of biological fluids for the rapid diagnosis of potentially lethal inherited disorders of human purine and pyrimidine metabolism. Biomed Chromatogr. 1986 Jun;1(3):109-18. Pubmed: 3506820
  • Urbonavicius J, Durand JM, Bjork GR: Three modifications in the D and T arms of tRNA influence translation in Escherichia coli and expression of virulence genes in Shigella flexneri. J Bacteriol. 2002 Oct;184(19):5348-57. Pubmed: 12218021
  • Weisbart RH, Garrett RA, Liebling MR, Barnett EV, Paulus HE, Katz DH: Specificity of anti-nucleoside antibodies in systemic lupus erythematosus. Clin Immunol Immunopathol. 1983 Jun;27(3):403-11. Pubmed: 6603316
  • Yang TH, Hu ML: Intracellular levels of S-adenosylhomocysteine but not homocysteine are highly correlated to the expression of nm23-H1 and the level of 5-methyldeoxycytidine in human hepatoma cells with different invasion activities. Nutr Cancer. 2006;55(2):224-31. Pubmed: 17044778
Synthesis Reference:Not Available
Material Safety Data Sheet (MSDS)Download (PDF)
External Links:
ResourceLink
CHEBI ID30821
HMDB IDHMDB00884
Pubchem Compound ID445408
Kegg IDNot Available
ChemSpider ID393058
Wikipedia5-Methyluridine
BioCyc IDNot Available

Transporters

General function:
Involved in nucleoside:sodium symporter activity
Specific function:
Transports nucleosides with a high affinity except guanosine and deoxyguanosine. Driven by a proton motive force
Gene Name:
nupC
Uniprot ID:
P0AFF2
Molecular weight:
43475
General function:
Involved in nucleoside transmembrane transporter activity
Specific function:
Transports nucleosides with a high affinity. Driven by a proton motive force
Gene Name:
nupG
Uniprot ID:
P0AFF4
Molecular weight:
46389
General function:
Involved in nucleoside:sodium symporter activity
Specific function:
Nucleoside transporter
Gene Name:
nupX
Uniprot ID:
P33021
Molecular weight:
43409