Record Information
Version1.0
Creation date2011-09-21 00:36:36 UTC
Update date2015-07-21 06:57:55 UTC
Primary IDFDB023902
Secondary Accession NumbersNot Available
Chemical Information
FooDB NameDeoxythymidine 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. In gram positive bacteria, such as streptococci, the capsule is a recognized virulence factor, for example, l-rhamnose is known to be present in the capsule of Streptococcus suis, a causative agent of meningitis in humans. In Streptococcus mutans, l-rhamnose containing polysaccharides have been implicated in tooth surface colonization and adherence to kidney, muscle and heart tissues. In mycobacteria, l-rhamnose is fundamental to the structural integrity of the cell wall since it connects the inner peptidoglycan layer to the arabinogalactan polysaccharides. 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 bacterial cell wall is unique to bacteria; neither the cell wall nor the enzymes and chemical intermediates in its formation have analogues in humans. The enzymes involved in dTDP-l-rhamnose synthesis are potential targets for the design of new therapeutic agents. (PMID: 10802738, 12773151) [HMDB]
CAS Number2147-59-3
Structure
Thumb
Synonyms
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
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
Chemical FormulaC16H26N2O15P2
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
InChI IdentifierInChI=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
InChI KeyZOSQFDVXNQFKBY-CZRCVJRHSA-N
Isomeric SMILESC[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
Average Molecular Weight548.3296
Monoisotopic Molecular Weight548.080841196
Classification
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
Ontology
Disposition

Biological location:

Source:

Physico-Chemical Properties
Physico-Chemical Properties - Experimental
Spectra
Spectra
EI-MS/GC-MS
TypeDescriptionSplash KeyView
Predicted GC-MSDeoxythymidine diphosphate-L-rhamnose, non-derivatized, Predicted GC-MS Spectrum - 70eV, Positivesplash10-0036-6922340000-5b7bbefa46231e0401e7Spectrum
Predicted GC-MSDeoxythymidine diphosphate-L-rhamnose, 2 TMS, Predicted GC-MS Spectrum - 70eV, Positivesplash10-00bc-8441509000-f72396e274d70b76dce1Spectrum
MS/MS
TypeDescriptionSplash KeyView
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-004i-0900000000-a235a91a2d2afe7e5b0e2015-09-15View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-004i-3921000000-f27277a5a22d8b1a6e622015-09-15View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-004i-4900000000-385a0d128de7afa0ef562015-09-15View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0f6t-3303290000-8fb8bdb50a4d4dd37d522015-09-15View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0ufu-5915010000-0710c988c191bfa8f10b2015-09-15View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0a6u-4901000000-ac82c124189fc9d5bf1d2015-09-15View Spectrum
NMRNot Available
ChemSpider ID388998
ChEMBL IDNot Available
KEGG Compound IDC03319
Pubchem Compound ID439975
Pubchem Substance IDNot Available
ChEBI ID35452
Phenol-Explorer IDNot Available
DrugBank IDNot Available
HMDB IDHMDB06354
CRC / DFC (Dictionary of Food Compounds) IDNot Available
EAFUS IDNot Available
Dr. Duke IDNot Available
BIGG ID41621
KNApSAcK IDNot Available
HET IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
Flavornet IDNot Available
GoodScent IDNot Available
SuperScent IDNot Available
Wikipedia IDNot Available
Phenol-Explorer Metabolite IDNot Available
Duplicate IDSNot Available
Old DFC IDSNot Available
Associated Foods
FoodContent Range AverageReference
Processing...
Biological Effects and Interactions
Health Effects / BioactivitiesNot Available
EnzymesNot Available
PathwaysNot Available
MetabolismNot Available
BiosynthesisNot Available
Organoleptic Properties
FlavoursNot Available
Files
MSDSNot Available
References
Synthesis ReferenceNot Available
General ReferenceNot Available
Content Reference