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TDP-Rhamnose (M2MDB001344)

Record Information
Version2.0
Creation Date2012-05-31 14:49:34 -0600
Update Date2015-06-03 17:20:11 -0600
Secondary Accession Numbers
  • ECMDB20537
Identification
Name:TDP-Rhamnose
DescriptionTDP-rhamnose is a member of the chemical class known as Mixed Pentose/Hexose Disaccharides. These are disaccharides containing both an hexose and a pentose. dTDP-rhamnose is an important precursor of cell wall polysaccharides and rhamnose-containing exopolysaccharides (EPS) in E. coli. (PMID 14973085)
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms:
  • DTDP-6-Deoxy-L-mannose
  • DTDP-L-Rhamnose
  • DTDP-Rhamnose
  • TDP-rhamnose
Chemical Formula:C17H26N2O14P2
Weight:Average: 544.3409
Monoisotopic: 544.085926574
InChI Key:NQGLMWQXKRELIQ-AYDVIBIJSA-N
InChI:InChI=1S/C17H26N2O14P2/c1-7-6-19(17(25)18-15(7)24)11-5-9(20)10(31-11)3-4-34(26,27)33-35(28,29)32-16-14(23)13(22)12(21)8(2)30-16/h6,8-14,16,20-23H,3-5H2,1-2H3,(H-2,18,24,25,26,27,28,29)/t8-,9-,10-,11-,12+,13+,14+,16+/m0/s1
CAS number:Not Available
IUPAC Name:4-hydroxy-1-[(2S,4S,5S)-4-hydroxy-5-[2-({[(2R,3R,4R,5S,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl phosphonato]oxy}phosphinato)ethyl]oxolan-2-yl]-5-methyl-2-oxo-2,5-dihydro-1λ⁵-pyrimidine-1,5-bis(ylium)
Traditional IUPAC Name:4-hydroxy-1-[(2S,4S,5S)-4-hydroxy-5-(2-{[(2R,3R,4R,5S,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl phosphonato]oxyphosphinato}ethyl)oxolan-2-yl]-5-methyl-2-oxo-5H-1λ⁵-pyrimidine-1,5-bis(ylium)
SMILES:[H][C@]1(O)C[C@]([H])(O[C@@]1([H])CCP([O-])(=O)OP([O-])(=O)O[C@@]1([H])O[C@@]([H])(C)[C@@]([H])(O)[C@@]([H])(O)[C@@]1([H])O)[N+]1=C[C+](C)C(O)=NC1=O
Chemical Taxonomy
Description belongs to the class of organic compounds known as monosaccharide phosphates. These are monosaccharides comprising a phosphated group linked to the carbohydrate unit.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbohydrates and carbohydrate conjugates
Direct ParentMonosaccharide phosphates
Alternative Parents
Substituents
  • Monosaccharide phosphate
  • Pyrimidone
  • Alkyl phosphate
  • Pyrimidine
  • Phosphoric acid ester
  • Oxane
  • Organic phosphoric acid derivative
  • 2,5-dihydropyrimidine
  • Hydropyrimidine
  • Tetrahydrofuran
  • Organophosphonic acid derivative
  • Organophosphonic acid
  • Secondary alcohol
  • Carbonic acid derivative
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Organic 1,3-dipolar compound
  • Propargyl-type 1,3-dipolar organic compound
  • Polyol
  • Organic nitrogen compound
  • Organopnictogen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organic zwitterion
  • Organophosphorus compound
  • Organonitrogen compound
  • Carbonyl group
  • Alcohol
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External DescriptorsNot Available
Physical Properties
State:Not Available
Charge:-1
Melting point:Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility9.33 g/LALOGPS
logP0.32ALOGPS
logP-7.3ChemAxon
logS-1.8ALOGPS
pKa (Strongest Acidic)-6.8ChemAxon
pKa (Strongest Basic)-3.3ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count13ChemAxon
Hydrogen Donor Count5ChemAxon
Polar Surface Area250.77 ŲChemAxon
Rotatable Bond Count8ChemAxon
Refractivity108.28 m³·mol⁻¹ChemAxon
Polarizability47.31 ųChemAxon
Number of Rings3ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations:Cytoplasm
Reactions:
dTDP-4-dehydro-beta-L-rhamnose + NADH + Hydrogen ion > NADP + TDP-Rhamnose
SMPDB Pathways:Not Available
KEGG Pathways:Not Available
EcoCyc Pathways:
Concentrations
Not Available
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-004i-0900000000-a61fed63da985429a3afView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-004i-2932000000-00053e7daf36e782ee6aView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-054k-8910000000-766c30a5c264a2357c63View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-004i-1302190000-94527e411abfb00cf94bView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0h0r-6935140000-e6f9febc06291233d81dView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-00di-9101000000-a8d559c16a5fca2d6bccView in MoNA
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:
  • Boels, I. C., Beerthuyzen, M. M., Kosters, M. H., Van Kaauwen, M. P., Kleerebezem, M., De Vos, W. M. (2004). "Identification and functional characterization of the Lactococcus lactis rfb operon, required for dTDP-rhamnose Biosynthesis." J Bacteriol 186:1239-1248. Pubmed: 14973085
  • 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
Synthesis Reference:Not Available
Material Safety Data Sheet (MSDS)Not Available
External Links:
ResourceLink
CHEBI IDNot Available
HMDB IDNot Available
Pubchem Compound ID25200574
Kegg IDNot Available
ChemSpider IDNot Available
Wikipedia IDNot Available
BioCyc IDDTDP-RHAMNOSE
EcoCyc IDDTDP-RHAMNOSE

Enzymes

Protein Details
1. 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.