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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2021-09-14 15:46:09 UTC
HMDB IDHMDB0000884
Secondary Accession Numbers
  • HMDB00884
Metabolite Identification
Common 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 ).
Structure
Data?1582752162
Synonyms
ValueSource
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
Chemical FormulaC10H14N2O6
Average Molecular Weight258.228
Monoisotopic Molecular Weight258.08518619
IUPAC Name1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-methyl-1,2,3,4-tetrahydropyrimidine-2,4-dione
Traditional Namethymidin
CAS Registry Number1463-10-1
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 KeyDWRXFEITVBNRMK-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.
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

Biological location

Source

Route of exposure

Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point183 - 187 °CNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic Properties

Experimental Collision Cross Sections

Adduct TypeData SourceCCS Value (Å2)Reference
[M-H]-MetCCS_train_neg153.52330932474
[M-H]-Not Available153.523http://allccs.zhulab.cn/database/detail?ID=AllCCS00000108
Predicted Molecular Properties
PropertyValueSource
Water Solubility135 g/LALOGPS
logP10(-1.7) g/LALOGPS
logP10(-2) g/LChemAxon
logS10(-0.28) g/LALOGPS
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
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+158.61831661259
DarkChem[M-H]-154.22931661259
AllCCS[M+H]+157.96132859911
AllCCS[M-H]-156.39332859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
RibothymidineCC1=CN([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O)C(=O)NC1=O3388.5Standard polar33892256
RibothymidineCC1=CN([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O)C(=O)NC1=O2047.8Standard non polar33892256
RibothymidineCC1=CN([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O)C(=O)NC1=O2537.8Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Ribothymidine,1TMS,isomer #1CC1=CN([C@@H]2O[C@H](CO[Si](C)(C)C)[C@@H](O)[C@H]2O)C(=O)[NH]C1=O2368.5Semi standard non polar33892256
Ribothymidine,1TMS,isomer #2CC1=CN([C@@H]2O[C@H](CO)[C@@H](O[Si](C)(C)C)[C@H]2O)C(=O)[NH]C1=O2401.8Semi standard non polar33892256
Ribothymidine,1TMS,isomer #3CC1=CN([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O[Si](C)(C)C)C(=O)[NH]C1=O2378.3Semi standard non polar33892256
Ribothymidine,1TMS,isomer #4CC1=CN([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O)C(=O)N([Si](C)(C)C)C1=O2453.2Semi standard non polar33892256
Ribothymidine,2TMS,isomer #1CC1=CN([C@@H]2O[C@H](CO[Si](C)(C)C)[C@@H](O[Si](C)(C)C)[C@H]2O)C(=O)[NH]C1=O2413.0Semi standard non polar33892256
Ribothymidine,2TMS,isomer #2CC1=CN([C@@H]2O[C@H](CO[Si](C)(C)C)[C@@H](O)[C@H]2O[Si](C)(C)C)C(=O)[NH]C1=O2410.5Semi standard non polar33892256
Ribothymidine,2TMS,isomer #3CC1=CN([C@@H]2O[C@H](CO[Si](C)(C)C)[C@@H](O)[C@H]2O)C(=O)N([Si](C)(C)C)C1=O2455.9Semi standard non polar33892256
Ribothymidine,2TMS,isomer #4CC1=CN([C@@H]2O[C@H](CO)[C@@H](O[Si](C)(C)C)[C@H]2O[Si](C)(C)C)C(=O)[NH]C1=O2424.1Semi standard non polar33892256
Ribothymidine,2TMS,isomer #5CC1=CN([C@@H]2O[C@H](CO)[C@@H](O[Si](C)(C)C)[C@H]2O)C(=O)N([Si](C)(C)C)C1=O2467.9Semi standard non polar33892256
Ribothymidine,2TMS,isomer #6CC1=CN([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O[Si](C)(C)C)C(=O)N([Si](C)(C)C)C1=O2463.6Semi standard non polar33892256
Ribothymidine,3TMS,isomer #1CC1=CN([C@@H]2O[C@H](CO[Si](C)(C)C)[C@@H](O[Si](C)(C)C)[C@H]2O[Si](C)(C)C)C(=O)[NH]C1=O2399.0Semi standard non polar33892256
Ribothymidine,3TMS,isomer #2CC1=CN([C@@H]2O[C@H](CO[Si](C)(C)C)[C@@H](O[Si](C)(C)C)[C@H]2O)C(=O)N([Si](C)(C)C)C1=O2485.9Semi standard non polar33892256
Ribothymidine,3TMS,isomer #3CC1=CN([C@@H]2O[C@H](CO[Si](C)(C)C)[C@@H](O)[C@H]2O[Si](C)(C)C)C(=O)N([Si](C)(C)C)C1=O2495.9Semi standard non polar33892256
Ribothymidine,3TMS,isomer #4CC1=CN([C@@H]2O[C@H](CO)[C@@H](O[Si](C)(C)C)[C@H]2O[Si](C)(C)C)C(=O)N([Si](C)(C)C)C1=O2489.0Semi standard non polar33892256
Ribothymidine,4TMS,isomer #1CC1=CN([C@@H]2O[C@H](CO[Si](C)(C)C)[C@@H](O[Si](C)(C)C)[C@H]2O[Si](C)(C)C)C(=O)N([Si](C)(C)C)C1=O2479.5Semi standard non polar33892256
Ribothymidine,4TMS,isomer #1CC1=CN([C@@H]2O[C@H](CO[Si](C)(C)C)[C@@H](O[Si](C)(C)C)[C@H]2O[Si](C)(C)C)C(=O)N([Si](C)(C)C)C1=O2650.7Standard non polar33892256
Ribothymidine,4TMS,isomer #1CC1=CN([C@@H]2O[C@H](CO[Si](C)(C)C)[C@@H](O[Si](C)(C)C)[C@H]2O[Si](C)(C)C)C(=O)N([Si](C)(C)C)C1=O2615.6Standard polar33892256
Ribothymidine,1TBDMS,isomer #1CC1=CN([C@@H]2O[C@H](CO[Si](C)(C)C(C)(C)C)[C@@H](O)[C@H]2O)C(=O)[NH]C1=O2650.1Semi standard non polar33892256
Ribothymidine,1TBDMS,isomer #2CC1=CN([C@@H]2O[C@H](CO)[C@@H](O[Si](C)(C)C(C)(C)C)[C@H]2O)C(=O)[NH]C1=O2661.1Semi standard non polar33892256
Ribothymidine,1TBDMS,isomer #3CC1=CN([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O[Si](C)(C)C(C)(C)C)C(=O)[NH]C1=O2647.5Semi standard non polar33892256
Ribothymidine,1TBDMS,isomer #4CC1=CN([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O)C(=O)N([Si](C)(C)C(C)(C)C)C1=O2688.7Semi standard non polar33892256
Ribothymidine,2TBDMS,isomer #1CC1=CN([C@@H]2O[C@H](CO[Si](C)(C)C(C)(C)C)[C@@H](O[Si](C)(C)C(C)(C)C)[C@H]2O)C(=O)[NH]C1=O2899.0Semi standard non polar33892256
Ribothymidine,2TBDMS,isomer #2CC1=CN([C@@H]2O[C@H](CO[Si](C)(C)C(C)(C)C)[C@@H](O)[C@H]2O[Si](C)(C)C(C)(C)C)C(=O)[NH]C1=O2899.4Semi standard non polar33892256
Ribothymidine,2TBDMS,isomer #3CC1=CN([C@@H]2O[C@H](CO[Si](C)(C)C(C)(C)C)[C@@H](O)[C@H]2O)C(=O)N([Si](C)(C)C(C)(C)C)C1=O2922.9Semi standard non polar33892256
Ribothymidine,2TBDMS,isomer #4CC1=CN([C@@H]2O[C@H](CO)[C@@H](O[Si](C)(C)C(C)(C)C)[C@H]2O[Si](C)(C)C(C)(C)C)C(=O)[NH]C1=O2894.6Semi standard non polar33892256
Ribothymidine,2TBDMS,isomer #5CC1=CN([C@@H]2O[C@H](CO)[C@@H](O[Si](C)(C)C(C)(C)C)[C@H]2O)C(=O)N([Si](C)(C)C(C)(C)C)C1=O2926.5Semi standard non polar33892256
Ribothymidine,2TBDMS,isomer #6CC1=CN([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O[Si](C)(C)C(C)(C)C)C(=O)N([Si](C)(C)C(C)(C)C)C1=O2920.9Semi standard non polar33892256
Ribothymidine,3TBDMS,isomer #1CC1=CN([C@@H]2O[C@H](CO[Si](C)(C)C(C)(C)C)[C@@H](O[Si](C)(C)C(C)(C)C)[C@H]2O[Si](C)(C)C(C)(C)C)C(=O)[NH]C1=O3113.5Semi standard non polar33892256
Ribothymidine,3TBDMS,isomer #2CC1=CN([C@@H]2O[C@H](CO[Si](C)(C)C(C)(C)C)[C@@H](O[Si](C)(C)C(C)(C)C)[C@H]2O)C(=O)N([Si](C)(C)C(C)(C)C)C1=O3125.7Semi standard non polar33892256
Ribothymidine,3TBDMS,isomer #3CC1=CN([C@@H]2O[C@H](CO[Si](C)(C)C(C)(C)C)[C@@H](O)[C@H]2O[Si](C)(C)C(C)(C)C)C(=O)N([Si](C)(C)C(C)(C)C)C1=O3131.3Semi standard non polar33892256
Ribothymidine,3TBDMS,isomer #4CC1=CN([C@@H]2O[C@H](CO)[C@@H](O[Si](C)(C)C(C)(C)C)[C@H]2O[Si](C)(C)C(C)(C)C)C(=O)N([Si](C)(C)C(C)(C)C)C1=O3126.2Semi standard non polar33892256
Ribothymidine,4TBDMS,isomer #1CC1=CN([C@@H]2O[C@H](CO[Si](C)(C)C(C)(C)C)[C@@H](O[Si](C)(C)C(C)(C)C)[C@H]2O[Si](C)(C)C(C)(C)C)C(=O)N([Si](C)(C)C(C)(C)C)C1=O3313.0Semi standard non polar33892256
Ribothymidine,4TBDMS,isomer #1CC1=CN([C@@H]2O[C@H](CO[Si](C)(C)C(C)(C)C)[C@@H](O[Si](C)(C)C(C)(C)C)[C@H]2O[Si](C)(C)C(C)(C)C)C(=O)N([Si](C)(C)C(C)(C)C)C1=O3396.8Standard non polar33892256
Ribothymidine,4TBDMS,isomer #1CC1=CN([C@@H]2O[C@H](CO[Si](C)(C)C(C)(C)C)[C@@H](O[Si](C)(C)C(C)(C)C)[C@H]2O[Si](C)(C)C(C)(C)C)C(=O)N([Si](C)(C)C(C)(C)C)C1=O3047.7Standard polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Ribothymidine GC-MS (Non-derivatized) - 70eV, Positivesplash10-05bf-9420000000-897dab8f4bbf7b8e664c2017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Ribothymidine GC-MS (3 TMS) - 70eV, Positivesplash10-0kp0-6879400000-656a0a43be4a2cd044e72017-10-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Ribothymidine GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Ribothymidine GC-MS (TMS_1_1) - 70eV, PositiveNot Available2021-11-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Ribothymidine GC-MS (TMS_1_2) - 70eV, PositiveNot Available2021-11-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Ribothymidine GC-MS (TMS_1_3) - 70eV, PositiveNot Available2021-11-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Ribothymidine GC-MS (TMS_1_4) - 70eV, PositiveNot Available2021-11-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Ribothymidine GC-MS (TMS_2_1) - 70eV, PositiveNot Available2021-11-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Ribothymidine GC-MS (TMS_2_2) - 70eV, PositiveNot Available2021-11-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Ribothymidine GC-MS (TMS_2_3) - 70eV, PositiveNot Available2021-11-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Ribothymidine GC-MS (TMS_2_4) - 70eV, PositiveNot Available2021-11-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Ribothymidine GC-MS (TMS_2_5) - 70eV, PositiveNot Available2021-11-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Ribothymidine GC-MS (TMS_2_6) - 70eV, PositiveNot Available2021-11-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Ribothymidine GC-MS (TMS_3_2) - 70eV, PositiveNot Available2021-11-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Ribothymidine GC-MS (TMS_3_3) - 70eV, PositiveNot Available2021-11-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Ribothymidine GC-MS (TMS_3_4) - 70eV, PositiveNot Available2021-11-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Ribothymidine GC-MS (TBDMS_1_1) - 70eV, PositiveNot Available2021-11-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Ribothymidine GC-MS (TBDMS_1_2) - 70eV, PositiveNot Available2021-11-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Ribothymidine GC-MS (TBDMS_1_3) - 70eV, PositiveNot Available2021-11-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Ribothymidine GC-MS (TBDMS_1_4) - 70eV, PositiveNot Available2021-11-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Ribothymidine GC-MS (TBDMS_2_1) - 70eV, PositiveNot Available2021-11-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Ribothymidine GC-MS (TBDMS_2_2) - 70eV, PositiveNot Available2021-11-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Ribothymidine GC-MS (TBDMS_2_3) - 70eV, PositiveNot Available2021-11-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Ribothymidine GC-MS (TBDMS_2_4) - 70eV, PositiveNot Available2021-11-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Ribothymidine GC-MS (TBDMS_2_5) - 70eV, PositiveNot Available2021-11-06Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Experimental LC-MS/MSLC-MS/MS Spectrum - Ribothymidine Quattro_QQQ 10V, Positive-QTOF (Annotated)splash10-004i-0900000000-1653ad80c56ae3727f922012-07-24HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Ribothymidine Quattro_QQQ 25V, Positive-QTOF (Annotated)splash10-004i-2900000000-826774188d3e78ca38f22012-07-24HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Ribothymidine Quattro_QQQ 40V, Positive-QTOF (Annotated)splash10-0a6r-9800000000-f5daf31a98b364b70f8c2012-07-24HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Ribothymidine 10V, Negative-QTOFsplash10-0a4i-0090000000-f186cfbb52edc03ff4de2021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Ribothymidine 35V, Negative-QTOFsplash10-004i-0900000000-9f7398feab5dd89502642021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Ribothymidine 40V, Negative-QTOFsplash10-0006-9100000000-893019db60499c0a96022021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Ribothymidine 20V, Negative-QTOFsplash10-004i-2900000000-461a9c94bf89e5b479702021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Ribothymidine 10V, Negative-QTOFsplash10-004i-0900000000-1db6a34eff49b044d9442021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Ribothymidine 35V, Positive-QTOFsplash10-004i-1900000000-1c2ee21cd9d3515f71242021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Ribothymidine 10V, Positive-QTOFsplash10-056r-1970000000-ba6f9aa1164c365abfa22021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Ribothymidine 40V, Positive-QTOFsplash10-01u0-8900000000-a63ffd4c990b9c9a543a2021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Ribothymidine 20V, Positive-QTOFsplash10-004i-4900000000-71ebad0df798bf2ac2822021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Ribothymidine 40V, Positive-QTOFsplash10-06w9-8900000000-3c0ceb68319de86fc30f2021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Ribothymidine 20V, Positive-QTOFsplash10-004i-1900000000-45b9a7b5e831351a1fe02021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Ribothymidine 10V, Positive-QTOFsplash10-004i-0900000000-e1eddf8b44309a38eebb2021-09-20HMDB team, MONAView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ribothymidine 10V, Positive-QTOFsplash10-004i-0910000000-90f6da130f49fa9df29d2017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ribothymidine 20V, Positive-QTOFsplash10-004i-5900000000-203a4367756530615ffd2017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ribothymidine 40V, Positive-QTOFsplash10-004j-9800000000-13e51659da01285bdc7f2017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ribothymidine 10V, Negative-QTOFsplash10-0a6r-1490000000-4ba707a2228996f9f9f72017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ribothymidine 20V, Negative-QTOFsplash10-004i-6920000000-a25c60ade61d6d32f0f12017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ribothymidine 40V, Negative-QTOFsplash10-001m-9100000000-37e601ae2d82d72111e72017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ribothymidine 10V, Positive-QTOFsplash10-004i-0900000000-f08754aed5978a645b7c2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ribothymidine 20V, Positive-QTOFsplash10-004i-3910000000-01ae005a14dd4c188d462021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ribothymidine 40V, Positive-QTOFsplash10-0a6r-9700000000-513e87b6fba58d79ef982021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ribothymidine 10V, Negative-QTOFsplash10-056r-0950000000-b4a8bf9fcddaedc20b742021-09-23Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Experimental 2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, H2O, experimental)2012-12-05Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Cytoplasm
Biospecimen Locations
  • Blood
  • Feces
  • Urine
Tissue Locations
  • Placenta
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified0.200 +/- 0.098 uMAdult (>18 years old)Not SpecifiedNormal
    • Xu, G., Enderle, ...
details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal
details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal
details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal
details
UrineDetected and Quantified0.28 +/- 0.17 umol/mmol creatinineAdult (>18 years old)FemaleNormal details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothColorectal Cancer details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Colorectal cancer
details
UrineDetected and Quantified0.51 +/- 0.53 umol/mmol creatinineAdult (>18 years old)BothBreast cancer details
UrineDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothBladder cancer details
Associated Disorders and Diseases
Disease References
Colorectal cancer
  1. Brown DG, Rao S, Weir TL, O'Malia J, Bazan M, Brown RJ, Ryan EP: Metabolomics and metabolic pathway networks from human colorectal cancers, adjacent mucosa, and stool. Cancer Metab. 2016 Jun 6;4:11. doi: 10.1186/s40170-016-0151-y. eCollection 2016. [PubMed:27275383 ]
  2. Goedert JJ, Sampson JN, Moore SC, Xiao Q, Xiong X, Hayes RB, Ahn J, Shi J, Sinha R: Fecal metabolomics: assay performance and association with colorectal cancer. Carcinogenesis. 2014 Sep;35(9):2089-96. doi: 10.1093/carcin/bgu131. Epub 2014 Jul 18. [PubMed:25037050 ]
Perillyl alcohol administration for cancer treatment
  1. Zheng YF, Kong HW, Xiong JH, Lv S, Xu GW: Clinical significance and prognostic value of urinary nucleosides in breast cancer patients. Clin Biochem. 2005 Jan;38(1):24-30. [PubMed:15607313 ]
Associated OMIM IDs
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB022298
KNApSAcK IDNot Available
Chemspider ID393058
KEGG Compound IDNot Available
BioCyc IDCPD-15123
BiGG IDNot Available
Wikipedia Link5-methyluridine
METLIN ID5843
PubChem Compound445408
PDB IDNot Available
ChEBI ID45996
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceMaruyama, Shogo; Kumon, Satoru. 5-Methyluridine manufacture with microorganism. Jpn. Kokai Tokkyo Koho (1996), 6 pp.
Material Safety Data Sheet (MSDS)Download (PDF)
General References
  1. 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 ]
  2. 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 ]
  3. 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 ]
  4. 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 ]
  5. 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 ]
  6. 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 ]
  7. 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 ]
  8. 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 ]
  9. 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 ]
  10. 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 ]
  11. Elshenawy S, Pinney SE, Stuart T, Doulias PT, Zura G, Parry S, Elovitz MA, Bennett MJ, Bansal A, Strauss JF 3rd, Ischiropoulos H, Simmons RA: The Metabolomic Signature of the Placenta in Spontaneous Preterm Birth. Int J Mol Sci. 2020 Feb 4;21(3). pii: ijms21031043. doi: 10.3390/ijms21031043. [PubMed:32033212 ]

Enzymes

General function:
Involved in RNA methyltransferase activity
Specific function:
Probable S-adenosyl-L-methionine-dependent methyltransferase that catalyzes the formation of 5-methyl-uridine at position 54 (m5U54) in all tRNA. May also have a role in tRNA stabilization or maturation (By similarity).
Gene Name:
TRMT2B
Uniprot ID:
Q96GJ1
Molecular weight:
56475.965