tridecaprenyl diphosphate (YMDB00639)

Identification
YMDB IDYMDB00639
Nametridecaprenyl diphosphate
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
Descriptiontridecaprenyl diphosphate belongs to the class of organic compounds known as bactoprenol diphosphates. These are polyprenyl compounds consisting of a diphosphate group substituted by a bactoprenyl moiety. tridecaprenyl diphosphate is a moderately acidic compound (based on its pKa).
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
  • all-trans-Tridecaprenyl diphosphoric acid
  • all-trans-Tridecaprenyl pyrophosphate
  • all-trans-Tridecaprenyl pyrophosphoric acid
  • Tridecaprenyl diphosphate
  • Tridecaprenyl diphosphoric acid
CAS numberNot Available
WeightAverage: 1063.4963
Monoisotopic: 1062.757028834
InChI KeyDZNALTJEOIIEJL-IBZXXNHPSA-N
InChIInChI=1S/C65H108O7P2/c1-53(2)27-15-28-54(3)29-16-30-55(4)31-17-32-56(5)33-18-34-57(6)35-19-36-58(7)37-20-38-59(8)39-21-40-60(9)41-22-42-61(10)43-23-44-62(11)45-24-46-63(12)47-25-48-64(13)49-26-50-65(14)51-52-71-74(69,70)72-73(66,67)68/h27,29,31,33,35,37,39,41,43,45,47,49,51H,15-26,28,30,32,34,36,38,40,42,44,46,48,50,52H2,1-14H3,(H,69,70)(H2,66,67,68)/b54-29+,55-31+,56-33+,57-35+,58-37+,59-39+,60-41+,61-43+,62-45+,63-47+,64-49+,65-51+
IUPAC Name({hydroxy[(3,7,11,15,19,23,27,31,35,39,43,47,51-tridecamethyldopentaconta-2,6,10,14,18,22,26,30,34,38,42,46,50-tridecaen-1-yl)oxy]phosphoryl}oxy)phosphonic acid
Traditional IUPAC Nametridecaprenyl diphosphate
Chemical FormulaC65H108O7P2
SMILES[H]C(CCC(C)=C([H])CCC(C)=C([H])CCC(C)=C([H])CCC(C)=C([H])CCC(C)=C([H])CCC(C)=C([H])CCC(C)=C([H])CCC(C)=C([H])CCC(C)=C([H])CCC(C)=C([H])CCC(C)=C([H])COP(O)(=O)OP(O)(O)=O)=C(C)CCC=C(C)C
Chemical Taxonomy
Description belongs to the class of organic compounds known as bactoprenol diphosphates. These are polyprenyl compounds consisting of a diphosphate group substituted by a bactoprenyl moiety.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassPrenol lipids
Sub ClassPolyprenols
Direct ParentBactoprenol diphosphates
Alternative Parents
Substituents
  • Polyterpenoid
  • Bactoprenol diphosphate
  • Polyprenyl diphosphate
  • Polyprenyl monophosphate
  • Organic pyrophosphate
  • Isoprenoid phosphate
  • Monoalkyl phosphate
  • Alkyl phosphate
  • Phosphoric acid ester
  • Organic phosphoric acid derivative
  • Organic oxygen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Physical Properties
StateNot Available
Charge0
Melting pointNot Available
Experimental Properties
PropertyValueReference
Water SolubilityNot AvailablePhysProp
LogPNot AvailablePhysProp
Predicted Properties
PropertyValueSource
Water Solubility0.00042 g/LALOGPS
logP9.77ALOGPS
logP20.21ChemAxon
logS-6.4ALOGPS
pKa (Strongest Acidic)1.77ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area113.29 ŲChemAxon
Rotatable Bond Count41ChemAxon
Refractivity334.76 m³·mol⁻¹ChemAxon
Polarizability133.87 ųChemAxon
Number of Rings0ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations
  • lipid particle
Organoleptic PropertiesNot Available
SMPDB PathwaysNot Available
KEGG PathwaysNot Available
SMPDB ReactionsNot Available
KEGG Reactions
Isopentenyl pyrophosphate + dodecaprenyl diphosphate ↔ Pyrophosphate + tridecaprenyl diphosphate
Isopentenyl pyrophosphate + tridecaprenyl diphosphate ↔ Pyrophosphate + tetradecaprenyl diphosphate
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0019-6101000094-23205f7a97c6a9e7703eJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-000i-1000000091-a889f1b6b9fcd70d4ed7JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-000i-0011120090-321037f45bd8577fab5dJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-03di-9400000000-3b3cd7029cd5f5da9d6fJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-056r-9800000000-a33f61213f73756d1ae2JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-0257c98f3aec5199192bJSpectraViewer
References
References:
  • Herrgard, M. J., Swainston, N., Dobson, P., Dunn, W. B., Arga, K. Y., Arvas, M., Bluthgen, N., Borger, S., Costenoble, R., Heinemann, M., Hucka, M., Le Novere, N., Li, P., Liebermeister, W., Mo, M. L., Oliveira, A. P., Petranovic, D., Pettifer, S., Simeonidis, E., Smallbone, K., Spasic, I., Weichart, D., Brent, R., Broomhead, D. S., Westerhoff, H. V., Kirdar, B., Penttila, M., Klipp, E., Palsson, B. O., Sauer, U., Oliver, S. G., Mendes, P., Nielsen, J., Kell, D. B. (2008). "A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology." Nat Biotechnol 26:1155-1160.18846089
  • Sato, M., Sato, K., Nishikawa, S., Hirata, A., Kato, J., Nakano, A. (1999). "The yeast RER2 gene, identified by endoplasmic reticulum protein localization mutations, encodes cis-prenyltransferase, a key enzyme in dolichol synthesis." Mol Cell Biol 19:471-483.9858571
  • Grabinska, K., Palamarczyk, G. (2002). "Dolichol biosynthesis in the yeast Saccharomyces cerevisiae: an insight into the regulatory role of farnesyl diphosphate synthase." FEMS Yeast Res 2:259-265.12702274
Synthesis Reference:Not Available
External Links:
ResourceLink
CHEBI ID53040
HMDB IDNot Available
Pubchem Compound ID25246091
Kegg IDNot Available
ChemSpider ID23107118
FOODB IDNot Available
Wikipedia IDNot Available
BioCyc IDNot Available

Enzymes

Protein Details
1. Putative dehydrodolichyl diphosphate synthase
General function:
Involved in transferase activity, transferring alkyl or aryl (other than methyl) groups
Specific function:
Could be a cis-prenyl transferase that adds multiple copies of isopentenyl pyrophosphate (ipp) to farnesyl pyrophosphate (FPP) to produce dehydrodolichyl diphosphate (DeDol- PP)
Gene Name:
SRT1
Uniprot ID:
Q03175
Molecular weight:
40199.69922
Reactions
Protein Details
2. Dehydrodolichyl diphosphate synthase
General function:
Involved in transferase activity, transferring alkyl or aryl (other than methyl) groups
Specific function:
Cis-prenyl transferase that adds multiple copies of isopentenyl pyrophosphate (IPP) to farnesyl pyrophosphate (FPP) to produce dehydrodolichyl diphosphate (Dedol-PP)
Gene Name:
RER2
Uniprot ID:
P35196
Molecular weight:
32693.30078
Reactions