dTDP-4-Dehydro-6-deoxy-L-mannose (ECMDB21327) (M2MDB001729)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes (2)XML
Proteins (739)
Record Information
Version2.0
Creation Date2012-07-30 14:55:18 -0600
Update Date2015-06-03 17:21:10 -0600
Secondary Accession Numbers
  • ECMDB21327
Identification
Name:dTDP-4-Dehydro-6-deoxy-L-mannose
Description4,6-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
MOLSDFPDBSMILESInChI
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
Weight:Average: 546.3137
Monoisotopic: 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
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
Physical Properties
State:Solid
Charge:-2
Melting point:Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility16.5 g/LALOGPS
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 ŲChemAxon
Rotatable Bond Count8ChemAxon
Refractivity107.31 m³·mol⁻¹ChemAxon
Polarizability45.3 ųChemAxon
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
Deoxythymidine diphosphate-L-rhamnose + NADP <> dTDP-4-Dehydro-6-deoxy-L-mannose + NADPH + Hydrogen ion
dTDP-4-dehydro-6-deoxy-D-glucose > dTDP-4-Dehydro-6-deoxy-L-mannose
dTDP-6-deoxy-L-mannose + NADP > dTDP-4-Dehydro-6-deoxy-L-mannose + NADPH
dTDP-4-Dehydro-6-deoxy-L-mannose + Hydrogen ion + NADPH <> Deoxythymidine diphosphate-L-rhamnose + NADP
4 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
4 4,6-Dideoxy-4-oxo-dTDP-D-glucose <> dTDP-4-Dehydro-6-deoxy-L-mannose
SMPDB Pathways:Not Available
KEGG Pathways:
EcoCyc Pathways:Not Available
Concentrations
Not Available
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_4_32) - 70eV, PositiveNot AvailableView in JSpectraViewer
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
MSMass Spectrum (Electron Ionization)Not AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
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

Enzymes

Protein Details
1. dTDP-4-dehydrorhamnose 3,5-epimerase
General function:
Involved in dTDP-4-dehydrorhamnose 3,5-epimerase activity
Specific function:
Catalyzes the epimerization of the C3' and C5'positions of dTDP-6-deoxy-D-xylo-4-hexulose, forming dTDP-6-deoxy-L-lyxo-4- hexulose
Gene Name:
rfbC
Uniprot ID:
P37745
Molecular weight:
21270
Reactions
dTDP-4-dehydro-6-deoxy-D-glucose = dTDP-4-dehydro-6-deoxy-L-mannose.
Protein Details
2. dTDP-4-dehydrorhamnose reductase
General function:
Involved in dTDP-4-dehydrorhamnose reductase activity
Specific function:
Catalyzes the reduction of dTDP-6-deoxy-L-lyxo-4- hexulose to yield dTDP-L-rhamnose. RmlD uses NADH and NADPH nearly equally well
Gene Name:
rfbD
Uniprot ID:
P37760
Molecular weight:
32694
Reactions
dTDP-6-deoxy-L-mannose + NADP(+) = dTDP-4-dehydro-6-deoxy-L-mannose + NADPH.