Showing metabocard for 4,6-Dideoxy-4-oxo-dTDP-D-glucose (BMDB0001399)

IdentificationTaxonomyPhysical propertiesPathwaysSpectraConcentrationsLinksReferencesXML
Record Information
Version1.0
Creation Date2016-09-30 22:45:24 UTC
Update Date2020-04-22 15:08:01 UTC
BMDB IDBMDB0001399
Secondary Accession Numbers
  • BMDB01399
Metabolite Identification
Common Name4,6-Dideoxy-4-oxo-dTDP-D-glucose
Description4,6-Dideoxy-4-oxo-dTDP-D-glucose, also known as dTDP-4-oxo-6-deoxy-D-glucose or dTDP-4-dehydro-6-deoxy-L-mannose, belongs to the class of organic compounds known as pyrimidine nucleotide sugars. These are pyrimidine nucleotides bound to a saccharide derivative through the terminal phosphate group. 4,6-Dideoxy-4-oxo-dTDP-D-glucose is an extremely weak basic (essentially neutral) compound (based on its pKa). 4,6-Dideoxy-4-oxo-dTDP-D-glucose exists in all living organisms, ranging from bacteria to humans.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
ValueSource
dTDP-4-Dehydro-6-deoxy-D-glucoseHMDB
dTDP-4-Dehydro-6-deoxy-L-mannoseHMDB
dTDP-4-Dehydro-L-rhamnoseHMDB
dTDP-4-oxo-6-Deoxy-D-glucoseHMDB
dTDP-4-oxo-6-Deoxy-L-mannoseHMDB
dTDP-4-oxo-L-RhamnoseHMDB
TDP-4-Keto-6-deoxy-D-glucoseHMDB
TDP-4-oxo-6-Deoxy-D-glucoseHMDB
dTDP-6-Deoxy-4-ketoglucoseHMDB
dTDP-KDGHMDB
dTDP-6-Deoxy-D-xylo-4-hexuloseMeSH
Thymidine diphosphate-6-deoxy-xylo-4-hexulose, alpha-isomerMeSH
Thymidine diphosphate-6-deoxy-xylo-4-hexuloseMeSH
dTDP-DXHMeSH
Thymidine diphosphate-6-deoxy-D-xylo-4-hexuloseMeSH
Chemical FormulaC16H24N2O15P2
Average Molecular Weight546.3137
Monoisotopic Molecular Weight546.065191132
IUPAC Name{[(3R,4R,6R)-3,4-dihydroxy-6-methyl-5-oxooxan-2-yl]oxy}({[hydroxy({[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl)oxolan-2-yl]methoxy})phosphoryl]oxy})phosphinic acid
Traditional Name[(3R,4R,6R)-3,4-dihydroxy-6-methyl-5-oxooxan-2-yl]oxy({hydroxy[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-3H-pyrimidin-1-yl)oxolan-2-yl]methoxyphosphoryl}oxy)phosphinic acid
CAS Registry NumberNot Available
SMILES
C[C@H]1OC(OP(O)(=O)OP(O)(=O)OC[C@H]2O[C@H](C[C@@H]2O)N2C=C(C)C(=O)NC2=O)[C@H](O)[C@@H](O)C1=O
InChI Identifier
InChI=1S/C16H24N2O15P2/c1-6-4-18(16(24)17-14(6)23)10-3-8(19)9(31-10)5-29-34(25,26)33-35(27,28)32-15-13(22)12(21)11(20)7(2)30-15/h4,7-10,12-13,15,19,21-22H,3,5H2,1-2H3,(H,25,26)(H,27,28)(H,17,23,24)/t7-,8+,9-,10-,12+,13-,15?/m1/s1
InChI KeyPSXWNITXWWECNY-SRPWTXKTSA-N
Chemical Taxonomy
Description belongs to the class of organic compounds known as pyrimidine nucleotide sugars. These are pyrimidine nucleotides bound to a saccharide derivative through the terminal phosphate group.
KingdomOrganic compounds
Super ClassNucleosides, nucleotides, and analogues
ClassPyrimidine nucleotides
Sub ClassPyrimidine nucleotide sugars
Direct ParentPyrimidine nucleotide sugars
Alternative Parents
Substituents
  • Pyrimidine nucleotide sugar
  • Pyrimidine 2'-deoxyribonucleoside diphosphate
  • Pentose phosphate
  • Organic pyrophosphate
  • Pyrimidone
  • Monoalkyl phosphate
  • Hydropyrimidine
  • Organic phosphoric acid derivative
  • Pyrimidine
  • Oxane
  • Phosphoric acid ester
  • Alkyl phosphate
  • Heteroaromatic compound
  • Vinylogous amide
  • Tetrahydrofuran
  • Secondary alcohol
  • Lactam
  • Ketone
  • Urea
  • Cyclic ketone
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Organooxygen compound
  • Organonitrogen compound
  • Hydrocarbon derivative
  • Organic oxide
  • Organopnictogen compound
  • Organic oxygen compound
  • Organic nitrogen compound
  • Alcohol
  • Carbonyl group
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Ontology
StatusExpected but not Quantified
Origin
  • Endogenous
BiofunctionNot Available
ApplicationNot Available
Cellular locations
  • Cytoplasm
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP-0.93ALOGPS
logP-2ChemAxon
logS-1.7ALOGPS
pKa (Strongest Acidic)1.73ChemAxon
pKa (Strongest Basic)-3.2ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count12ChemAxon
Hydrogen Donor Count6ChemAxon
Polar Surface Area247.92 ŲChemAxon
Rotatable Bond Count8ChemAxon
Refractivity106.99 m³·mol⁻¹ChemAxon
Polarizability45.19 ųChemAxon
Number of Rings3ChemAxon
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, Positivesplash10-004i-9812620000-55c82e214c8402cb2283View in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positivesplash10-00b9-9823704000-df6af03755642135c5a0View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-004i-0900000000-5240324bf97c105ae51dView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-004i-3921000000-7e9e2dfed9a99533be0aView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-004i-4900000000-c718341e14191248128aView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0f6t-3403290000-9b28f5967f6c5a9fa675View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0fbc-5904010000-e8611fa8f8e1490b7ed1View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0a6u-5901000000-2158145d7f9abac6643eView in MoNA
1D NMR13C NMR Spectrum (1D, 100 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 100 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 1000 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 1000 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 200 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 200 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 300 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 300 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 400 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 400 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 500 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 600 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 700 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 700 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 800 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 800 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 900 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 900 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
Biological Properties
Cellular Locations
  • Cytoplasm
Biospecimen LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
HMDB IDHMDB0001399
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB022601
KNApSAcK IDNot Available
Chemspider ID391705
KEGG Compound IDC11907
BioCyc IDNot Available
BiGG ID35701
Wikipedia LinkNot Available
METLIN ID6218
PubChem Compound443496
PDB IDNot Available
ChEBI ID16620
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available