Structural search and advanced query search is temporarily unavailable. We are working to fix this issue. Thank you for your support and patience.

Record Information
Version	2.0
Creation Date	2012-07-30 14:55:41 -0600
Update Date	2015-09-13 12:56:15 -0600
Secondary Accession Numbers	ECMDB21389
Identification
Name:	Ribothymidine
Description	Ribothymidine 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	MOLSDFPDBSMILESInChI × Structure for #<Compound:0xa8dab2b0> Close
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.
Kingdom	Organic compounds
Super Class	Nucleosides, nucleotides, and analogues
Class	Pyrimidine nucleosides
Sub Class	Not Available
Direct Parent	Pyrimidine nucleosides
Alternative Parents	Glycosylamines Pentoses Pyrimidones Hydropyrimidines Tetrahydrofurans Heteroaromatic compounds Vinylogous amides Ureas Lactams Secondary alcohols Oxacyclic compounds Azacyclic compounds Primary alcohols Organopnictogen compounds Organonitrogen compounds Organic oxides Hydrocarbon derivatives
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 )
Physical Properties
State:	Solid
Charge:	0
Melting point:	183-187 °C
Experimental Properties:	Property Value Source
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 Ų ChemAxon Rotatable Bond Count 2 ChemAxon Refractivity 56.92 m³·mol⁻¹ ChemAxon Polarizability 24.1 ų ChemAxon Number of Rings 2 ChemAxon Bioavailability 1 ChemAxon Rule of Five Yes ChemAxon Ghose Filter Yes ChemAxon Veber's Rule Yes ChemAxon MDDR-like Rule Yes ChemAxon
Biological Properties
Cellular Locations:	Cytoplasm
Reactions:
SMPDB Pathways:	Not Available
KEGG Pathways:	Not Available
EcoCyc Pathways:	Not Available
Concentrations
	Not Available
Spectra
Spectra:	Spectrum Type Description Splash Key Predicted GC-MS Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive splash10-05bf-9420000000-897dab8f4bbf7b8e664c View in MoNA Predicted GC-MS Predicted GC-MS Spectrum - GC-MS (3 TMS) - 70eV, Positive splash10-0kp0-6879400000-656a0a43be4a2cd044e7 View in MoNA Predicted GC-MS Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive Not Available View in JSpectraViewer Predicted GC-MS Predicted GC-MS Spectrum - GC-MS (TMS_1_1) - 70eV, Positive Not Available View in JSpectraViewer Predicted GC-MS Predicted GC-MS Spectrum - GC-MS (TMS_1_2) - 70eV, Positive Not Available View in JSpectraViewer Predicted GC-MS Predicted GC-MS Spectrum - GC-MS (TMS_1_3) - 70eV, Positive Not Available View in JSpectraViewer Predicted GC-MS Predicted GC-MS Spectrum - GC-MS (TMS_1_4) - 70eV, Positive Not Available View in JSpectraViewer Predicted GC-MS Predicted GC-MS Spectrum - GC-MS (TMS_2_1) - 70eV, Positive Not Available View in JSpectraViewer Predicted GC-MS Predicted GC-MS Spectrum - GC-MS (TMS_2_2) - 70eV, Positive Not Available View in JSpectraViewer Predicted GC-MS Predicted GC-MS Spectrum - GC-MS (TMS_2_3) - 70eV, Positive Not Available View in JSpectraViewer Predicted GC-MS Predicted GC-MS Spectrum - GC-MS (TMS_2_4) - 70eV, Positive Not Available View in JSpectraViewer Predicted GC-MS Predicted GC-MS Spectrum - GC-MS (TMS_2_5) - 70eV, Positive Not Available View in JSpectraViewer Predicted GC-MS Predicted GC-MS Spectrum - GC-MS (TMS_2_6) - 70eV, Positive Not Available View in JSpectraViewer Predicted GC-MS Predicted GC-MS Spectrum - GC-MS (TMS_3_2) - 70eV, Positive Not Available View in JSpectraViewer Predicted GC-MS Predicted GC-MS Spectrum - GC-MS (TMS_3_3) - 70eV, Positive Not Available View in JSpectraViewer Predicted GC-MS Predicted GC-MS Spectrum - GC-MS (TMS_3_4) - 70eV, Positive Not Available View in JSpectraViewer Predicted GC-MS Predicted GC-MS Spectrum - GC-MS (TBDMS_1_1) - 70eV, Positive Not Available View in JSpectraViewer Predicted GC-MS Predicted GC-MS Spectrum - GC-MS (TBDMS_1_2) - 70eV, Positive Not Available View in JSpectraViewer Predicted GC-MS Predicted GC-MS Spectrum - GC-MS (TBDMS_1_3) - 70eV, Positive Not Available View in JSpectraViewer Predicted GC-MS Predicted GC-MS Spectrum - GC-MS (TBDMS_1_4) - 70eV, Positive Not Available View in JSpectraViewer Predicted GC-MS Predicted GC-MS Spectrum - GC-MS (TBDMS_2_1) - 70eV, Positive Not Available View in JSpectraViewer Predicted GC-MS Predicted GC-MS Spectrum - GC-MS (TBDMS_2_2) - 70eV, Positive Not Available View in JSpectraViewer Predicted GC-MS Predicted GC-MS Spectrum - GC-MS (TBDMS_2_3) - 70eV, Positive Not Available View in JSpectraViewer Predicted GC-MS Predicted GC-MS Spectrum - GC-MS (TBDMS_2_4) - 70eV, Positive Not Available View in JSpectraViewer Predicted GC-MS Predicted GC-MS Spectrum - GC-MS (TBDMS_2_5) - 70eV, Positive Not Available View in JSpectraViewer LC-MS/MS LC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated) splash10-004i-0900000000-1653ad80c56ae3727f92 View in MoNA LC-MS/MS LC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated) splash10-004i-2900000000-826774188d3e78ca38f2 View in MoNA LC-MS/MS LC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated) splash10-0a6r-9800000000-f5daf31a98b364b70f8c View in MoNA LC-MS/MS LC-MS/MS Spectrum - 10V, Negative splash10-0a4i-0090000000-f186cfbb52edc03ff4de View in MoNA LC-MS/MS LC-MS/MS Spectrum - 35V, Negative splash10-004i-0900000000-9f7398feab5dd8950264 View in MoNA LC-MS/MS LC-MS/MS Spectrum - 40V, Negative splash10-0006-9100000000-893019db60499c0a9602 View in MoNA LC-MS/MS LC-MS/MS Spectrum - 20V, Negative splash10-004i-2900000000-461a9c94bf89e5b47970 View in MoNA LC-MS/MS LC-MS/MS Spectrum - 10V, Negative splash10-004i-0900000000-1db6a34eff49b044d944 View in MoNA LC-MS/MS LC-MS/MS Spectrum - 35V, Positive splash10-004i-1900000000-1c2ee21cd9d3515f7124 View in MoNA LC-MS/MS LC-MS/MS Spectrum - 10V, Positive splash10-056r-1970000000-ba6f9aa1164c365abfa2 View in MoNA LC-MS/MS LC-MS/MS Spectrum - 40V, Positive splash10-01u0-8900000000-a63ffd4c990b9c9a543a View in MoNA LC-MS/MS LC-MS/MS Spectrum - 20V, Positive splash10-004i-4900000000-71ebad0df798bf2ac282 View in MoNA LC-MS/MS LC-MS/MS Spectrum - 40V, Positive splash10-06w9-8900000000-3c0ceb68319de86fc30f View in MoNA LC-MS/MS LC-MS/MS Spectrum - 20V, Positive splash10-004i-1900000000-45b9a7b5e831351a1fe0 View in MoNA LC-MS/MS LC-MS/MS Spectrum - 10V, Positive splash10-004i-0900000000-e1eddf8b44309a38eebb View in MoNA Predicted LC-MS/MS Predicted LC-MS/MS Spectrum - 10V, Positive splash10-004i-0910000000-90f6da130f49fa9df29d View in MoNA Predicted LC-MS/MS Predicted LC-MS/MS Spectrum - 20V, Positive splash10-004i-5900000000-203a4367756530615ffd View in MoNA Predicted LC-MS/MS Predicted LC-MS/MS Spectrum - 40V, Positive splash10-004j-9800000000-13e51659da01285bdc7f View in MoNA Predicted LC-MS/MS Predicted LC-MS/MS Spectrum - 10V, Negative splash10-0a6r-1490000000-4ba707a2228996f9f9f7 View in MoNA Predicted LC-MS/MS Predicted LC-MS/MS Spectrum - 20V, Negative splash10-004i-6920000000-a25c60ade61d6d32f0f1 View in MoNA Predicted LC-MS/MS Predicted LC-MS/MS Spectrum - 40V, Negative splash10-001m-9100000000-37e601ae2d82d72111e7 View in MoNA Predicted LC-MS/MS Predicted LC-MS/MS Spectrum - 10V, Positive splash10-004i-0900000000-f08754aed5978a645b7c View in MoNA Predicted LC-MS/MS Predicted LC-MS/MS Spectrum - 20V, Positive splash10-004i-3910000000-01ae005a14dd4c188d46 View in MoNA Predicted LC-MS/MS Predicted LC-MS/MS Spectrum - 40V, Positive splash10-0a6r-9700000000-513e87b6fba58d79ef98 View in MoNA Predicted LC-MS/MS Predicted LC-MS/MS Spectrum - 10V, Negative splash10-056r-0950000000-b4a8bf9fcddaedc20b74 View in MoNA 1D NMR 1H NMR Spectrum Not Available View in JSpectraViewer 1D NMR 1H NMR Spectrum Not Available View in JSpectraViewer 1D NMR 13C NMR Spectrum Not Available View in JSpectraViewer 1D NMR 1H NMR Spectrum Not Available View in JSpectraViewer 1D NMR 13C NMR Spectrum Not Available View in JSpectraViewer 1D NMR 1H NMR Spectrum Not Available View in JSpectraViewer 1D NMR 13C NMR Spectrum Not Available View in JSpectraViewer 1D NMR 1H NMR Spectrum Not Available View in JSpectraViewer 1D NMR 13C NMR Spectrum Not Available View in JSpectraViewer 1D NMR 1H NMR Spectrum Not Available View in JSpectraViewer 1D NMR 13C NMR Spectrum Not Available View in JSpectraViewer 1D NMR 1H NMR Spectrum Not Available View in JSpectraViewer 1D NMR 13C NMR Spectrum Not Available View in JSpectraViewer 1D NMR 1H NMR Spectrum Not Available View in JSpectraViewer 1D NMR 13C NMR Spectrum Not Available View in JSpectraViewer 1D NMR 1H NMR Spectrum Not Available View in JSpectraViewer 1D NMR 13C NMR Spectrum Not Available View in JSpectraViewer 1D NMR 1H NMR Spectrum Not Available View in JSpectraViewer 1D NMR 13C NMR Spectrum Not Available View in JSpectraViewer 1D NMR 1H NMR Spectrum Not Available View in JSpectraViewer 1D NMR 13C NMR Spectrum Not Available View in JSpectraViewer 2D NMR [1H,13C] 2D NMR Spectrum Not Available View 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)
Links
External Links:	Resource Link CHEBI ID 30821 HMDB ID HMDB00884 Pubchem Compound ID 445408 Kegg ID Not Available ChemSpider ID 393058 Wikipedia 5-Methyluridine BioCyc ID Not Available

Transporters