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decaprenyl diphosphate (YMDB00636)

Identification
YMDB IDYMDB00636
Namedecaprenyl diphosphate
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
Descriptionall-trans-Decaprenyl 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. all-trans-Decaprenyl diphosphate is a moderately acidic compound (based on its pKa).
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
  • di-trans,poly-cis-Decaprenyl diphosphate
  • ditrans,heptacis-Decaprenyl diphosphate
  • all-trans-Decaprenyl diphosphoric acid
  • Decaprenyl diphosphoric acid
CAS numberNot Available
WeightAverage: 859.1453
Monoisotopic: 858.569228066
InChI KeyFSCYHDCTHRVSKN-CMVHWAPMSA-N
InChIInChI=1S/C50H84O7P2/c1-41(2)21-12-22-42(3)23-13-24-43(4)25-14-26-44(5)27-15-28-45(6)29-16-30-46(7)31-17-32-47(8)33-18-34-48(9)35-19-36-49(10)37-20-38-50(11)39-40-56-59(54,55)57-58(51,52)53/h21,23,25,27,29,31,33,35,37,39H,12-20,22,24,26,28,30,32,34,36,38,40H2,1-11H3,(H,54,55)(H2,51,52,53)/b42-23+,43-25+,44-27+,45-29+,46-31+,47-33+,48-35+,49-37+,50-39+
IUPAC Name({[(3,7,11,15,19,23,27,31,35,39-decamethyltetraconta-2,6,10,14,18,22,26,30,34,38-decaen-1-yl)oxy](hydroxy)phosphoryl}oxy)phosphonic acid
Traditional IUPAC Namedecaprenyl diphosphate
Chemical FormulaC50H84O7P2
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])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 Solubility0.00032 g/LALOGPS
logP8.9ALOGPS
logP15.23ChemAxon
logS-6.4ALOGPS
pKa (Strongest Acidic)1.77ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area113.29 ŲChemAxon
Rotatable Bond Count32ChemAxon
Refractivity263.35 m³·mol⁻¹ChemAxon
Polarizability103.91 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
nonaprenyl diphosphate + Isopentenyl pyrophosphate ↔ Pyrophosphate + decaprenyl diphosphate
Isopentenyl pyrophosphate + decaprenyl diphosphate ↔ Pyrophosphate + undecaprenyl diphosphate
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0560-0200009460-3b1abcb01c8d9f4817fbJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-001i-1111109200-bceb19e3f40f2424887bJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0f89-0232339000-5cde4543c96f6f88ff18JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0a4i-0400000090-d5f49448e5726abd3a0aJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-056r-7900000010-c51f65f9878cace4fa01JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-0d9fac3c81a88e14dad1JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0a4i-0000000090-093ecf1c976d87a41f65JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0a4i-2400010290-bb5f10b91d3bd86a3e46JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-056r-9400000000-c9258da5f7e1bcf30955JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0a4i-0100001490-59124ee62549de39e9ecJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-00m0-0001007910-81a39312a6e8bb7dee6dJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-00pi-0219555310-5c4773b5eb03f35064e4JSpectraViewer
References
References:
  • Scheer, M., Grote, A., Chang, A., Schomburg, I., Munaretto, C., Rother, M., Sohngen, C., Stelzer, M., Thiele, J., Schomburg, D. (2011). "BRENDA, the enzyme information system in 2011." Nucleic Acids Res 39:D670-D676.21062828
  • 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 ID53043
HMDB IDHMDB0059616
Pubchem Compound ID46173330
Kegg IDC04509
ChemSpider ID4575322
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
Protein Details
3. Para-hydroxybenzoate--polyprenyltransferase, mitochondrial
General function:
Involved in prenyltransferase activity
Specific function:
Catalyzes the prenylation of para-hydroxybenzoate (PHB) with an all-trans polyprenyl group. Mediates the second step in the final reaction sequence of coenzyme Q (CoQ) biosynthesis, which is the condensation of the polyisoprenoid side chain with PHB
Gene Name:
COQ2
Uniprot ID:
P32378
Molecular weight:
41001.0
Reactions
A polyprenyl diphosphate + 4-hydroxybenzoate → diphosphate + a 4-hydroxy-3-polyprenylbenzoate.