dTDP-4-Dehydro-6-deoxy-L-mannose (PAMDB001729)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes Transporters
Proteins (3280)
Record Information
Version 1.0
Update Date 1/22/2018 11:54:54 AM
Metabolite IDPAMDB001729
Identification
Name: dTDP-4-Dehydro-6-deoxy-L-mannose
Description:4,6-Dideoxy-4-oxo-dTDP-D-glucose is a product of the enzyme TDP-glucose 4,6-dehydratase [EC:4.2.1.46] in the Nucleotide sugars metabolism (KEGG)
Structure
Thumb
🔍MOLSDFPDBSMILESInChIView Structure
Synonyms:
  • 4,6-Dideoxy-4-oxo-dTDP-D-glucose
  • DTDP-4-Dehydro-6-deoxy-D-glucose
  • DTDP-4-Dehydro-6-deoxy-L-mannose
  • DTDP-4-Dehydro-L-rhamnose
  • DTDP-4-Oxo-6-deoxy-D-glucose
  • DTDP-4-Oxo-6-deoxy-L-mannose
  • DTDP-4-Oxo-L-rhamnose
  • DTDP-DDMan
  • TDP-4-Keto-6-deoxy-D-glucose
  • TDP-4-Oxo-6-deoxy-D-glucose
  • Thymidine 5'-[3-(6-deoxy-L-lyxo-hexopyranosyl-4-ulose) dihydrogen diphosphate]
  • Thymidine 5'-[3-(6-deoxy-L-lyxo-hexopyranosyl-4-ulose) dihydrogen diphosphoric acid]
Chemical Formula: C16H24N2O15P2
Average Molecular Weight: 546.3137
Monoisotopic Molecular Weight: 546.065191132
InChI Key: PSXWNITXWWECNY-WPTIAVDBSA-N
InChI: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?/m0/s1
CAS number: Not Available
IUPAC Name:[({[(3R,4S,6S)-3,4-dihydroxy-6-methyl-5-oxooxan-2-yl]oxy}(hydroxy)phosphoryl)oxy]({[(2R,3S,5R)-3-hydroxy-5-(4-hydroxy-5-methyl-2-oxo-1,2-dihydropyrimidin-1-yl)oxolan-2-yl]methoxy})phosphinic acid
Traditional IUPAC Name: {[(3R,4S,6S)-3,4-dihydroxy-6-methyl-5-oxooxan-2-yl]oxy(hydroxy)phosphoryl}oxy[(2R,3S,5R)-3-hydroxy-5-(4-hydroxy-5-methyl-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxyphosphinic acid
SMILES:[H][C@]1(O)C[C@@]([H])(O[C@]1([H])COP(O)(=O)OP(O)(=O)OC1([H])O[C@@]([H])(C)C(=O)[C@@]([H])(O)[C@@]1([H])O)N1C=C(C)C(O)=NC1=O
Chemical Taxonomy
Taxonomy DescriptionThis compound 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.
Kingdom Organic compounds
Super ClassNucleosides, nucleotides, and analogues
Class Pyrimidine nucleotides
Sub ClassPyrimidine nucleotide sugars
Direct Parent Pyrimidine nucleotide sugars
Alternative Parents
Substituents
  • Pyrimidine nucleotide sugar
  • Pyrimidine 2'-deoxyribonucleoside diphosphate
  • Pyrimidine deoxyribonucleotide
  • Organic pyrophosphate
  • Hydroxypyrimidine
  • Monoalkyl phosphate
  • Pyrimidone
  • Alkyl phosphate
  • Pyrimidine
  • Phosphoric acid ester
  • Oxane
  • Organic phosphoric acid derivative
  • Organic phosphate
  • Hydropyrimidine
  • Saccharide
  • Heteroaromatic compound
  • Oxolane
  • Cyclic ketone
  • Secondary alcohol
  • Ketone
  • 1,2-diol
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organonitrogen compound
  • Carbonyl group
  • Alcohol
  • Aromatic heteromonocyclic compound
Molecular Framework Aromatic heteromonocyclic compounds
External Descriptors
Physical Properties
State: Solid
Charge:-2
Melting point: Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility16.5 mg/mLALOGPS
logP-1.1ALOGPS
logP-1.7ChemAxon
logS-1.5ALOGPS
pKa (Strongest Acidic)1.73ChemAxon
pKa (Strongest Basic)-3.2ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count13ChemAxon
Hydrogen Donor Count6ChemAxon
Polar Surface Area251.41 Å2ChemAxon
Rotatable Bond Count8ChemAxon
Refractivity107.31 m3·mol-1ChemAxon
Polarizability45.3 Å3ChemAxon
Number of Rings3ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations: Cytoplasm
Reactions:
4,6-Dideoxy-4-oxo-dTDP-D-glucose <> dTDP-4-Dehydro-6-deoxy-L-mannose
dTDP-4-Dehydro-6-deoxy-L-mannose + Hydrogen ion + NADPH <> Deoxythymidine diphosphate-L-rhamnose + NADP
Pathways:
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-004i-0900000000-829c0bbe6e6b0eebcc12View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-004i-3911000000-a11100c243372ad6a153View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-004i-4900000000-5969b778751f7221e3ebView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0udj-3702390000-eddd4cb79c27055083f3View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0fb9-4904010000-927c2bf9bd3ed82c570fView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0a6u-5900000000-f47f2109726170ad9d79View in MoNA
References
References:
  • van der Werf, M. J., Overkamp, K. M., Muilwijk, B., Coulier, L., Hankemeier, T. (2007). "Microbial metabolomics: toward a platform with full metabolome coverage." Anal Biochem 370:17-25. Pubmed: 17765195
  • Winder, C. L., Dunn, W. B., Schuler, S., Broadhurst, D., Jarvis, R., Stephens, G. M., Goodacre, R. (2008). "Global metabolic profiling of Escherichia coli cultures: an evaluation of methods for quenching and extraction of intracellular metabolites." Anal Chem 80:2939-2948. Pubmed: 18331064
Synthesis Reference: Not Available
Material Safety Data Sheet (MSDS) Not Available
External Links:
ResourceLink
CHEBI ID15744
HMDB IDHMDB01399
Pubchem Compound ID685
Kegg IDC00688
ChemSpider ID391477
Wikipedia IDNot Available
BioCyc IDNot Available