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
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