4,6-Dideoxy-4-oxo-dTDP-D-glucose (PAMDB000370)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes Transporters
Proteins (3280)
Record Information
Version 1.0
Update Date 1/22/2018 11:54:54 AM
Metabolite IDPAMDB000370
Identification
Name: 4,6-Dideoxy-4-oxo-dTDP-D-glucose
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:
  • DTDP-4-dehydro-6-deoxy-α-D-glucopyranose
  • dTDP-4-dehydro-6-Deoxy-a-D-galactose
  • dTDP-4-dehydro-6-Deoxy-a-D-glucopyranose
  • dTDP-4-dehydro-6-Deoxy-a-D-glucose
  • DTDP-4-Dehydro-6-deoxy-alpha-D-galactose
  • DTDP-4-Dehydro-6-deoxy-alpha-D-glucopyranose
  • DTDP-4-Dehydro-6-deoxy-alpha-D-glucose
  • DTDP-4-Dehydro-6-deoxy-D-galactose
  • DTDP-4-Dehydro-6-deoxy-D-glucose
  • DTDP-4-dehydro-6-deoxy-L-mannose
  • dTDP-4-dehydro-6-Deoxy-α-D-galactose
  • dTDP-4-dehydro-6-Deoxy-α-D-glucopyranose
  • dTDP-4-dehydro-6-Deoxy-α-D-glucose
  • DTDP-4-dehydro-L-rhamnose
  • DTDP-4-oxo-6-deoxy--α-D-glucose
  • dTDP-4-oxo-6-Deoxy--a-D-glucose
  • DTDP-4-Oxo-6-deoxy--alpha-D-glucose
  • dTDP-4-oxo-6-Deoxy--α-D-glucose
  • dTDP-4-oxo-6-Deoxy-a-D-glucose
  • DTDP-4-Oxo-6-deoxy-alpha-D-glucose
  • DTDP-4-Oxo-6-deoxy-D-glucose
  • DTDP-4-oxo-6-deoxy-L-mannose
  • dTDP-4-oxo-6-Deoxy-α-D-glucose
  • DTDP-4-oxo-L-rhamnose
  • DTDP-6-deoxy-α-D-xylo-4-hexosulose
  • dTDP-6-Deoxy-α-D-xylo-4-hexosulose
  • DTDP-6-deoxy-α-D-xylohex-4-ulose
  • dTDP-6-Deoxy-a-D-xylo-4-hexosulose
  • dTDP-6-Deoxy-a-D-xylohex-4-ulose
  • DTDP-6-Deoxy-alpha-D-xylo-4-hexosulose
  • DTDP-6-Deoxy-alpha-D-xylohex-4-ulose
  • dTDP-6-Deoxy-α-D-xylo-4-hexosulose
  • dTDP-6-Deoxy-α-D-xylohex-4-ulose
  • DTDP-DDGlc
  • TDP-4-keto-6-deoxy--α-D-glucose
  • TDP-4-keto-6-Deoxy--a-D-glucose
  • TDP-4-Keto-6-deoxy--alpha-D-glucose
  • TDP-4-keto-6-Deoxy--α-D-glucose
  • TDP-4-keto-6-deoxy-D-glucose
  • TDP-4-oxo-6-deoxy--α-D-glucose
  • TDP-4-oxo-6-Deoxy--a-D-glucose
  • TDP-4-Oxo-6-deoxy--alpha-D-glucose
  • TDP-4-oxo-6-Deoxy--α-D-glucose
  • TDP-4-oxo-6-deoxy-D-glucose
  • Thymidine 5'-[3-(D-xylo-hexopyranosyl-4-ulose) dihydrogen diphosphate]
  • Thymidine 5'-[3-(D-xylo-hexopyranosyl-4-ulose) dihydrogen diphosphoric acid]
Chemical Formula: C16H24N2O15P2
Average Molecular Weight: 546.3137
Monoisotopic Molecular Weight: 546.065191132
InChI Key: PSXWNITXWWECNY-SRPWTXKTSA-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?/m1/s1
CAS number: Not Available
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 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-3H-pyrimidin-1-yl)oxolan-2-yl]methoxyphosphoryl}oxy)phosphinic acid
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
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
  • Monoalkyl phosphate
  • Pyrimidone
  • Alkyl phosphate
  • Pyrimidine
  • Phosphoric acid ester
  • Oxane
  • Organic phosphoric acid derivative
  • Organic phosphate
  • Hydropyrimidine
  • Saccharide
  • Heteroaromatic compound
  • Vinylogous amide
  • Oxolane
  • Cyclic ketone
  • Urea
  • Secondary alcohol
  • Lactam
  • 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 Solubility11.3 mg/mLALOGPS
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 Å2ChemAxon
Rotatable Bond Count8ChemAxon
Refractivity106.99 m3·mol-1ChemAxon
Polarizability45.19 Å3ChemAxon
Number of Rings3ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations: Cytoplasm
Reactions:
dTDP-D-Glucose <> 4,6-Dideoxy-4-oxo-dTDP-D-glucose + Water
4,6-Dideoxy-4-oxo-dTDP-D-glucose <> dTDP-4-Dehydro-6-deoxy-L-mannose
4,6-Dideoxy-4-oxo-dTDP-D-glucose + L-Glutamate > alpha-Ketoglutarate + dTDP-D-Fucosamine
4,6-Dideoxy-4-oxo-dTDP-D-glucose + NADH + Hydrogen ion <> Deoxythymidine diphosphate-L-rhamnose + NAD
4,6-Dideoxy-4-oxo-dTDP-D-glucose <> dTDP-4-dehydro-6-deoxy-&beta;-L-mannose
4,6-Dideoxy-4-oxo-dTDP-D-glucose + L-Glutamate <> dTDP-D-Fucosamine + Oxoglutaric acid
Pathways:
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
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
References
References:
  • Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., Tanabe, M. (2012). "KEGG for integration and interpretation of large-scale molecular data sets." Nucleic Acids Res 40:D109-D114. Pubmed: 22080510
  • Keseler, I. M., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama-Castro, S., Muniz-Rascado, L., Bonavides-Martinez, C., Paley, S., Krummenacker, M., Altman, T., Kaipa, P., Spaulding, A., Pacheco, J., Latendresse, M., Fulcher, C., Sarker, M., Shearer, A. G., Mackie, A., Paulsen, I., Gunsalus, R. P., Karp, P. D. (2011). "EcoCyc: a comprehensive database of Escherichia coli biology." Nucleic Acids Res 39:D583-D590. Pubmed: 21097882
  • 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 ID16620
HMDB IDHMDB01399
Pubchem Compound ID443496
Kegg IDC11907
ChemSpider ID391705
Wikipedia IDNot Available
BioCyc IDDTDP-DEOH-DEOXY-GLUCOSE
EcoCyc IDDTDP-DEOH-DEOXY-GLUCOSE

Enzymes

Protein Details
• 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
Locus Tag:
PA5164
Molecular weight:
20.8 kDa
Reactions
dTDP-4-dehydro-6-deoxy-D-glucose = dTDP-4-dehydro-6-deoxy-L-mannose.
Protein Details
• dTDP-glucose 4,6-dehydratase 1
General function:
Involved in dTDP-glucose 4,6-dehydratase activity
Specific function:
Catalyzes the dehydration of dTDP-D-glucose to form dTDP-6-deoxy-D-xylo-4-hexulose via a three-step process involving oxidation, dehydration and reduction
Gene Name:
rfbB
Locus Tag:
PA5161
Molecular weight:
kDa
Reactions
dTDP-glucose = dTDP-4-dehydro-6-deoxy-D-glucose + H(2)O.