Record Information
Version2.0
Creation Date2012-05-31 14:08:11 -0600
Update Date2015-06-03 15:54:51 -0600
Secondary Accession Numbers
  • ECMDB06354
Identification
Name:Deoxythymidine diphosphate-L-rhamnose
DescriptionDeoxythymidine diphosphate (dTDP)-L-rhamnose is the precursor of L-rhamnose, a saccharide required for the virulence of some pathogenic bacteria. In gram negative bacteria such as Salmonella enterica, Vibrio cholerae or Escherichia coli 075:K5, L-rhamnose is an important residue in the O-antigen of lipopolysaccharides, which are essential for resistance to serum killing and for colonization. dTDP-L-rhamnose is synthesized from glucose-1-phosphate and deoxythymidine triphosphate (dTTP) via a pathway involving four distinct enzymes. Whereas common sugars such as glucose, fructose and mannose are all D-configured, bacteria commonly utilize the L-configured carbohydrates in pharmacologically active compounds and in their cell-wall structures. The enzymes involved in dTDP-L-rhamnose synthesis are potential targets for the design of new therapeutic agents against bacteria. (PMID 10802738, 12773151)
Structure
Thumb
Synonyms:
  • Deoxythymidine diphosphoric acid-L-rhamnose
  • DTDP-6-Deoxy-L-mannose
  • DTDP-L-Rhamnose
  • DTDP-Rhamnose
  • TDP-Rhamnose
  • Thymidine diphosphate rhamnose
  • Thymidine diphosphate-L-rhamnose
  • Thymidine diphosphoric acid rhamnose
  • Thymidine diphosphoric acid-L-rhamnose
Chemical Formula:C16H26N2O15P2
Weight:Average: 548.3296
Monoisotopic: 548.080841196
InChI Key:ZOSQFDVXNQFKBY-CZRCVJRHSA-N
InChI:InChI=1S/C16H26N2O15P2/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/h4,7-13,15,19-22H,3,5H2,1-2H3,(H,25,26)(H,27,28)(H,17,23,24)/t7-,8-,9+,10+,11-,12+,13+,15?/m0/s1
CAS number:2147-59-3
IUPAC Name:{[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}({[(3R,4R,5R,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy})phosphinic acid
Traditional IUPAC Name:dtdp-L-rhamnose
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)[C@H]1O
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
  • Monosaccharide phosphate
  • Organic pyrophosphate
  • Monoalkyl phosphate
  • Pyrimidone
  • Hydropyrimidine
  • Phosphoric acid ester
  • Monosaccharide
  • Organic phosphoric acid derivative
  • Oxane
  • Alkyl phosphate
  • Pyrimidine
  • Heteroaromatic compound
  • Vinylogous amide
  • Tetrahydrofuran
  • Urea
  • Lactam
  • Secondary alcohol
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Polyol
  • Organonitrogen compound
  • Alcohol
  • Hydrocarbon derivative
  • Organic oxide
  • Organopnictogen compound
  • Organooxygen compound
  • Organic nitrogen compound
  • Organic oxygen compound
  • 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 Solubility11.6 g/LALOGPS
logP-1.1ALOGPS
logP-2.7ChemAxon
logS-1.7ALOGPS
pKa (Strongest Acidic)1.73ChemAxon
pKa (Strongest Basic)-3.2ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count12ChemAxon
Hydrogen Donor Count7ChemAxon
Polar Surface Area251.08 ŲChemAxon
Rotatable Bond Count8ChemAxon
Refractivity107.76 m³·mol⁻¹ChemAxon
Polarizability46.26 ųChemAxon
Number of Rings3ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations:Cytoplasm
Reactions:
SMPDB Pathways:
Starch and sucrose metabolismPW000941 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways:
EcoCyc Pathways:
Concentrations
Not Available
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0036-6922340000-5b7bbefa46231e0401e7View in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positivesplash10-00bc-8441509000-f72396e274d70b76dce1View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-004i-0900000000-a235a91a2d2afe7e5b0eView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-004i-3921000000-f27277a5a22d8b1a6e62View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-004i-4900000000-385a0d128de7afa0ef56View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0f6t-3303290000-8fb8bdb50a4d4dd37d52View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0ufu-5915010000-0710c988c191bfa8f10bView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0a6u-4901000000-ac82c124189fc9d5bf1dView 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:
  • Dong C, Beis K, Giraud MF, Blankenfeldt W, Allard S, Major LL, Kerr ID, Whitfield C, Naismith JH: A structural perspective on the enzymes that convert dTDP-d-glucose into dTDP-l-rhamnose. Biochem Soc Trans. 2003 Jun;31(Pt 3):532-6. Pubmed: 12773151
  • Giraud, M. F., Leonard, G. A., Field, R. A., Berlind, C., Naismith, J. H. (2000). "RmlC, the third enzyme of dTDP-L-rhamnose pathway, is a new class of epimerase." Nat Struct Biol 7:398-402. Pubmed: 10802738
  • 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
Synthesis Reference:Shibaev, V. N.; Kusov, Yu. Yu.; Eliseeva, G. I.; Petrenko, V. A. Synthesis of thymidine diphosphate rhamnose analogs. Ref. Dokl. Soobshch. - Mendeleevsk. S'ezd Obshch. Prikl. Khim., 11th (1975), 6 111. CODEN: 37MOAO CAN 88:191313 AN 1978:191313
Material Safety Data Sheet (MSDS)Not Available
External Links:
ResourceLink
CHEBI ID35452
HMDB IDHMDB06354
Pubchem Compound ID439975
Kegg IDC03319
ChemSpider ID388998
Wikipedia IDNot Available
BioCyc IDDTDP-RHAMNOSE
EcoCyc IDDTDP-RHAMNOSE

Enzymes

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.
General function:
Involved in protein binding
Specific function:
Specific function unknown
Gene Name:
rfaS
Uniprot ID:
P27126
Molecular weight:
36730