Back to Compounds

Showing Compound Ribothymidine (FDB022298)

Record Information
Version1.0
Creation date2011-09-21 00:11:44 UTC
Update date2019-11-26 03:21:02 UTC
Primary IDFDB022298
Secondary Accession NumbersNot Available
Chemical Information
FooDB NameRibothymidine
DescriptionRibothymidine is an endogenous methylated nucleoside found in human fluids; methylated purine bases are present in higher amounts in tumor-bearing patients compared to healthy controls.DNA hypermethylation is a common finding in malignant cells and has been explored as a therapeutic target for hypomethylating agents. When chemical bonds to DNA, the DNA becomes damaged and proper and complete replication cannot occur to make the normal intended cell. A DNA adduct is an abnormal piece of DNA covalently-bonded to a cancer-causing chemical. This has shown to be the start of a cancerous cell, or carcinogenesis. DNA adducts in scientific experiments are used as bio-markers and as such are themselves measured to reflect quantitatively, for comparison, the amount of cancer in the subject. (PMID: 3506820, 17044778, 17264127, 16799933) [HMDB]
CAS Number1463-10-1
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
SynonymSource
1-(beta-D-Ribofuranosyl)thymineChEBI
RibosylthymidineChEBI
tChEBI
Thymine ribosideChEBI
1-(b-D-Ribofuranosyl)thymineGenerator
1-(Β-D-ribofuranosyl)thymineGenerator
1-b-D-RibofuranosylthymineHMDB
1-beta-delta-RibofuranosylthymineHMDB
5-Methyl-1-beta-D-ribofuranosyl-2,4(1H,3H)-pyrimidinedioneHMDB
5-Methyl-1-beta-delta-ribofuranosyl-2,4(1H,3H)-pyrimidinedioneHMDB
5-Methyl-uridineHMDB
5-MethyluridineHMDB
b-D-Ribofuranoside thymine-1HMDB
beta-D-RibofuranosideHMDB
beta-delta-RibofuranosideHMDB
beta-delta-Ribofuranoside thymine-1HMDB
RibosylthymineHMDB
Thymine ribofuranosideHMDB
Thymine ribonucleosideHMDB
Thymine-1 beta-D-ribofuranosylthymineHMDB
Thymine-1 beta-delta-ribofuranosylthymineHMDB
1-(β-D-ribofuranosyl)thymineGenerator
5-methyl-1-beta-D-ribofuranosyl-2,4(1H,3H)-Pyrimidinedionehmdb
5-methyl-1-beta-delta-ribofuranosyl-2,4(1H,3H)-Pyrimidinedionehmdb
5-methyl-Uridinehmdb
Ribothymidinehmdb
thymine-1 beta-D-Ribofuranosylthyminehmdb
thymine-1 beta-delta-Ribofuranosylthyminehmdb
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
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Chemical FormulaC10H14N2O6
IUPAC name1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-methyl-1,2,3,4-tetrahydropyrimidine-2,4-dione
InChI IdentifierInChI=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 KeyDWRXFEITVBNRMK-JXOAFFINSA-N
Isomeric SMILESCC1=CN([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O)C(=O)NC1=O
Average Molecular Weight258.228
Monoisotopic Molecular Weight258.08518619
Classification
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
Ontology
Disposition

Source:

Biological location:

Physico-Chemical Properties
Physico-Chemical Properties - Experimental
PropertyValueReference
Physical stateSolid
Physical DescriptionNot Available
Mass CompositionNot Available
Melting PointNot Available
Boiling PointNot Available
Experimental Water SolubilityNot Available
Experimental logPNot Available
Experimental pKaNot Available
Isoelectric pointNot Available
ChargeNot Available
Optical RotationNot Available
Spectroscopic UV DataNot Available
DensityNot Available
Refractive IndexNot Available
Spectra
Spectra
EI-MS/GC-MS
TypeDescriptionSplash KeyView
Predicted GC-MSRibothymidine, non-derivatized, Predicted GC-MS Spectrum - 70eV, Positivesplash10-05bf-9420000000-897dab8f4bbf7b8e664cSpectrum
Predicted GC-MSRibothymidine, 3 TMS, Predicted GC-MS Spectrum - 70eV, Positivesplash10-0kp0-6879400000-656a0a43be4a2cd044e7Spectrum
Predicted GC-MSRibothymidine, non-derivatized, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSRibothymidine, TMS_1_1, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSRibothymidine, TMS_1_2, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSRibothymidine, TMS_1_3, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSRibothymidine, TMS_1_4, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSRibothymidine, TMS_2_1, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSRibothymidine, TMS_2_2, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSRibothymidine, TMS_2_3, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSRibothymidine, TMS_2_4, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSRibothymidine, TMS_2_5, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSRibothymidine, TMS_2_6, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSRibothymidine, TMS_3_2, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSRibothymidine, TMS_3_3, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSRibothymidine, TMS_3_4, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSRibothymidine, TBDMS_1_1, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSRibothymidine, TBDMS_1_2, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSRibothymidine, TBDMS_1_3, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSRibothymidine, TBDMS_1_4, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSRibothymidine, TBDMS_2_1, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSRibothymidine, TBDMS_2_2, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSRibothymidine, TBDMS_2_3, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSRibothymidine, TBDMS_2_4, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSRibothymidine, TBDMS_2_5, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
MS/MS
TypeDescriptionSplash KeyView
MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)splash10-004i-0900000000-1653ad80c56ae3727f922012-07-24View Spectrum
MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)splash10-004i-2900000000-826774188d3e78ca38f22012-07-24View Spectrum
MS/MSLC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)splash10-0a6r-9800000000-f5daf31a98b364b70f8c2012-07-24View Spectrum
MS/MSLC-MS/MS Spectrum - 10V, Negativesplash10-0a4i-0090000000-f186cfbb52edc03ff4de2021-09-20View Spectrum
MS/MSLC-MS/MS Spectrum - 35V, Negativesplash10-004i-0900000000-9f7398feab5dd89502642021-09-20View Spectrum
MS/MSLC-MS/MS Spectrum - 40V, Negativesplash10-0006-9100000000-893019db60499c0a96022021-09-20View Spectrum
MS/MSLC-MS/MS Spectrum - 20V, Negativesplash10-004i-2900000000-461a9c94bf89e5b479702021-09-20View Spectrum
MS/MSLC-MS/MS Spectrum - 10V, Negativesplash10-004i-0900000000-1db6a34eff49b044d9442021-09-20View Spectrum
MS/MSLC-MS/MS Spectrum - 35V, Positivesplash10-004i-1900000000-1c2ee21cd9d3515f71242021-09-20View Spectrum
MS/MSLC-MS/MS Spectrum - 10V, Positivesplash10-056r-1970000000-ba6f9aa1164c365abfa22021-09-20View Spectrum
MS/MSLC-MS/MS Spectrum - 40V, Positivesplash10-01u0-8900000000-a63ffd4c990b9c9a543a2021-09-20View Spectrum
MS/MSLC-MS/MS Spectrum - 20V, Positivesplash10-004i-4900000000-71ebad0df798bf2ac2822021-09-20View Spectrum
MS/MSLC-MS/MS Spectrum - 40V, Positivesplash10-06w9-8900000000-3c0ceb68319de86fc30f2021-09-20View Spectrum
MS/MSLC-MS/MS Spectrum - 20V, Positivesplash10-004i-1900000000-45b9a7b5e831351a1fe02021-09-20View Spectrum
MS/MSLC-MS/MS Spectrum - 10V, Positivesplash10-004i-0900000000-e1eddf8b44309a38eebb2021-09-20View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-004i-0910000000-90f6da130f49fa9df29d2017-09-01View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-004i-5900000000-203a4367756530615ffd2017-09-01View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-004j-9800000000-13e51659da01285bdc7f2017-09-01View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0a6r-1490000000-4ba707a2228996f9f9f72017-09-01View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-6920000000-a25c60ade61d6d32f0f12017-09-01View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-001m-9100000000-37e601ae2d82d72111e72017-09-01View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-004i-0900000000-f08754aed5978a645b7c2021-09-22View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-004i-3910000000-01ae005a14dd4c188d462021-09-22View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0a6r-9700000000-513e87b6fba58d79ef982021-09-22View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-056r-0950000000-b4a8bf9fcddaedc20b742021-09-23View Spectrum
NMR
TypeDescriptionView
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, experimental)Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)Spectrum
2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, H2O, experimental)Spectrum
ChemSpider ID393058
ChEMBL IDCHEMBL106175
KEGG Compound IDNot Available
Pubchem Compound ID445408
Pubchem Substance IDNot Available
ChEBI ID30821
Phenol-Explorer IDNot Available
DrugBank IDNot Available
HMDB IDHMDB00884
CRC / DFC (Dictionary of Food Compounds) IDNot Available
EAFUS IDNot Available
Dr. Duke IDNot Available
BIGG IDNot Available
KNApSAcK IDNot Available
HET IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
Flavornet IDNot Available
GoodScent IDNot Available
SuperScent IDNot Available
Wikipedia ID5-Methyluridine
Phenol-Explorer Metabolite IDNot Available
Duplicate IDSNot Available
Old DFC IDSNot Available
Associated Foods
FoodContent Range AverageReference
FoodReference
Biological Effects and Interactions
Health Effects / BioactivitiesNot Available
Enzymes
NameGene NameUniProt ID
tRNA (uracil(54)-C(5))-methyltransferase homologTRMT2BQ96GJ1
PathwaysNot Available
MetabolismNot Available
BiosynthesisNot Available
Organoleptic Properties
FlavoursNot Available
Files
MSDSshow
References
Synthesis ReferenceNot Available
General ReferenceNot Available
Content Reference