Showing metabocard for Thymidine glycol (BMDB0096158)

IdentificationTaxonomyPhysical propertiesPathwaysSpectraConcentrationsLinksReferencesXML
Record Information
Version1.0
Creation Date2020-03-10 17:02:09 UTC
Update Date2020-04-22 18:56:25 UTC
BMDB IDBMDB0096158
Secondary Accession Numbers
  • BMDB96158
Metabolite Identification
Common NameThymidine glycol
DescriptionThymidine glycol, also known as glycolthymidine, belongs to the class of organic compounds known as pyrimidine 2'-deoxyribonucleosides. Pyrimidine 2'-deoxyribonucleosides are compounds consisting of a pyrimidine linked to a ribose which lacks a hydroxyl group at position 2. Based on a literature review very few articles have been published on Thymidine glycol.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
ValueSource
Thymidine glycol, (5R,6R)-isomerHMDB
Thymidine glycol, (cis)-isomerHMDB
Thymidine glycol, (trans)-isomerHMDB
5,6-Dihydro-5,6-dihydroxythymidineHMDB
GlycolthymidineHMDB
Thymidine glycol, (5R*,6S*)-isomerHMDB
Thymidine glycol, (5R,6S)-isomerHMDB
5,6-Dihydroxy-5,6-dihydrothymidineHMDB
Thymidine glycol, (5S,6R)-isomerHMDB
Thymidine glycol, (5S,6S)-isomerHMDB
Thymidine glycolMeSH
Chemical FormulaC10H16N2O7
Average Molecular Weight276.2432
Monoisotopic Molecular Weight276.095750876
IUPAC Name4,5,6-trihydroxy-1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-methyl-1,2,5,6-tetrahydropyrimidin-2-one
Traditional Name4,5,6-trihydroxy-1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-methyl-6H-pyrimidin-2-one
CAS Registry NumberNot Available
SMILES
CC1(O)C(O)N([C@H]2C[C@H](O)[C@@H](CO)O2)C(=O)N=C1O
InChI Identifier
InChI=1S/C10H16N2O7/c1-10(18)7(15)11-9(17)12(8(10)16)6-2-4(14)5(3-13)19-6/h4-6,8,13-14,16,18H,2-3H2,1H3,(H,11,15,17)/t4-,5+,6+,8?,10?/m0/s1
InChI KeyRKEITGVZZHXKON-SKAWGCAZSA-N
Chemical Taxonomy
Description belongs to the class of organic compounds known as pyrimidine 2'-deoxyribonucleosides. Pyrimidine 2'-deoxyribonucleosides are compounds consisting of a pyrimidine linked to a ribose which lacks a hydroxyl group at position 2.
KingdomOrganic compounds
Super ClassNucleosides, nucleotides, and analogues
ClassPyrimidine nucleosides
Sub ClassPyrimidine 2'-deoxyribonucleosides
Direct ParentPyrimidine 2'-deoxyribonucleosides
Alternative Parents
Substituents
  • Pyrimidine 2'-deoxyribonucleoside
  • Pentose monosaccharide
  • Barbiturate
  • N-acyl urea
  • Pyrimidone
  • Ureide
  • 1,3-diazinane
  • Monosaccharide
  • Pyrimidine
  • Dicarboximide
  • Tetrahydrofuran
  • Tertiary alcohol
  • Carbonic acid derivative
  • Urea
  • Secondary alcohol
  • Alkanolamine
  • Organoheterocyclic compound
  • Azacycle
  • Carboxylic acid derivative
  • Oxacycle
  • Organopnictogen compound
  • Primary alcohol
  • Organic oxygen compound
  • Organooxygen compound
  • Organonitrogen compound
  • Organic oxide
  • Alcohol
  • Carbonyl group
  • Organic nitrogen compound
  • Hydrocarbon derivative
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
StatusExpected but not Quantified
Origin
  • Endogenous
BiofunctionNot Available
ApplicationNot Available
Cellular locationsNot Available
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP-2.2ALOGPS
logP-2.2ChemAxon
logS-0.5ALOGPS
pKa (Strongest Acidic)1.77ChemAxon
pKa (Strongest Basic)-2.9ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count8ChemAxon
Hydrogen Donor Count5ChemAxon
Polar Surface Area143.05 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity58.23 m³·mol⁻¹ChemAxon
Polarizability24.98 ųChemAxon
Number of Rings2ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectra
Spectrum TypeDescriptionSplash Key
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-05ts-5290000000-235e78c9d740ee21b7cfView in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (5 TMS) - 70eV, Positivesplash10-00di-1110169000-0362236d3ab9846457e5View in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-03di-0900000000-64b022d4fccc5f107a63View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-053l-8920000000-1d2c2b37a5326eb8cca3View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-03dl-1900000000-94593e549bc35d8f7d40View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0a7l-0890000000-67d9a230a9e49dc395b4View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-000i-9610000000-bac4b8dd8bd6ce35738bView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0006-9100000000-18a2a0e5278d3469af12View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-004i-0190000000-ab3d9485c704c7f50fc4View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0006-1950000000-bf8ed52ffd013dc583fdView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0a4j-9820000000-97b9b0c9bc773e2e5b66View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-056r-1190000000-7cedee041402b0ddcc6aView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0006-8940000000-e6d8221930258d6dbdc8View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0006-9300000000-78d3c140e7204d692961View in MoNA
1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
Biological Properties
Cellular LocationsNot Available
Biospecimen LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
HMDB IDHMDB0042036
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB111691
KNApSAcK IDNot Available
Chemspider ID2299366
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound3035041
PDB IDNot Available
ChEBI ID174638
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available