pentaprenyl diphosphate (YMDB00632)

Identification
YMDB IDYMDB00632
Namepentaprenyl diphosphate
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
DescriptionGeranylfarnesyl diphosphate belongs to the class of organic compounds known as polyprenyl diphosphates. These are prenol lipids in which the diphosphate group is linked to one end of the polyprenol moiety. Based on a literature review a significant number of articles have been published on Geranylfarnesyl diphosphate.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
  • all-trans-Pentaprenyl diphosphate
  • Geranylfarnesyl diphosphate
  • (2E,6E,10E,14E)-Geranylfarnesyl diphosphate
  • 2-trans,6-trans,10-trans,14-trans-Geranylfarnesyl diphosphate
  • all-trans-Farnesylgeranyl diphosphate
  • all-trans-Farnesylgeranyl pyrophosphate
  • all-trans-Geranylfarnesyl diphosphate
  • all-trans-Geranylfarnesyl pyrophosphate
  • (2E,6E,10E,14E)-Geranylfarnesyl diphosphoric acid
  • 2-trans,6-trans,10-trans,14-trans-Geranylfarnesyl diphosphoric acid
  • all-trans-Farnesylgeranyl diphosphoric acid
  • all-trans-Farnesylgeranyl pyrophosphoric acid
  • all-trans-Geranylfarnesyl diphosphoric acid
  • all-trans-Geranylfarnesyl pyrophosphoric acid
  • Geranylfarnesyl diphosphoric acid
  • Geranylfarnesyl-diphosphate
  • Geranylfarnesyl-PP
  • GFPP
  • all-trans-Pentaprenyl diphosphoric acid
CAS numberNot Available
WeightAverage: 518.5602
Monoisotopic: 518.256226786
InChI KeyJMVSBFJBMXQNJW-GIXZANJISA-N
InChIInChI=1S/C25H44O7P2/c1-21(2)11-7-12-22(3)13-8-14-23(4)15-9-16-24(5)17-10-18-25(6)19-20-31-34(29,30)32-33(26,27)28/h11,13,15,17,19H,7-10,12,14,16,18,20H2,1-6H3,(H,29,30)(H2,26,27,28)/b22-13+,23-15+,24-17+,25-19+
IUPAC Name{[hydroxy({[(2E,6E,10E,14E)-3,7,11,15,19-pentamethylicosa-2,6,10,14,18-pentaen-1-yl]oxy})phosphoryl]oxy}phosphonic acid
Traditional IUPAC Namegeranylfarnesyl diphosphate
Chemical FormulaC25H44O7P2
SMILES[H]C(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 polyprenyl diphosphates. These are prenol lipids in which the diphosphate group is linked to one end of the polyprenol moiety.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassPrenol lipids
Sub ClassPolyprenols
Direct ParentPolyprenyl diphosphates
Alternative Parents
Substituents
  • Polyprenyl diphosphate
  • Polyprenyl monophosphate
  • Sesterterpenoid
  • 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 Solubility0.0012 g/LALOGPS
logP4.88ALOGPS
logP6.94ChemAxon
logS-5.6ALOGPS
pKa (Strongest Acidic)1.77ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area113.29 ŲChemAxon
Rotatable Bond Count17ChemAxon
Refractivity144.34 m³·mol⁻¹ChemAxon
Polarizability57.6 ųChemAxon
Number of Rings0ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations
  • mitochondrion
  • lipid particle
  • cytoplasm
Organoleptic PropertiesNot Available
SMPDB PathwaysNot Available
KEGG PathwaysNot Available
SMPDB ReactionsNot Available
KEGG Reactions
Isopentenyl pyrophosphate + geranylgeranyl diphosphate ↔ Pyrophosphate + pentaprenyl diphosphate + hydron
pentaprenyl diphosphate + Isopentenyl pyrophosphate ↔ Pyrophosphate + hexaprenyl diphosphate
2-trans,6-trans,10-trans-geranylgeranyl diphosphate + Isopentenyl pyrophosphate → Pyrophosphate + pentaprenyl diphosphate
pentaprenyl diphosphate + Isopentenyl pyrophosphate → Pyrophosphate + hexaprenyl diphosphate
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0fvj-8897540000-8727b5480b3179b9518eJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0frl-1319560000-894aa5718fd0aa23d1a4JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0006-3429200000-52610beb1a44f351babaJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0i0c-4349100000-efc21b59b7ba7930287dJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-014i-0400190000-b7d52827f6b8fc1b2470JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-056r-7900100000-cf42494f155a7efd500eJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-3b304fd455493d238af5JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-014i-0000090000-befd6f91805f0ef51f2dJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-014i-2400290000-e7717fe9142147d4137bJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-056r-9400000000-cd37df82a8f7acbc7edaJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-014i-0203490000-a68127df024e6760e7efJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-002n-1119400000-33d1f9d47cff2aaf5fceJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-01yt-2935000000-244031b6c35d30ad5dceJSpectraViewer
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 ID53048
HMDB IDHMDB0012231
Pubchem Compound ID5280659
Kegg IDC04217
ChemSpider ID24808139
FOODB IDFDB028874
Wikipedia IDGeranylfarnesyl pyrophosphate
BioCyc IDALL-TRANS-PENTAPRENYL-DIPHOSPHATE

Enzymes

Protein Details
1. Hexaprenyl pyrophosphate synthase, mitochondrial
General function:
Involved in isoprenoid biosynthetic process
Specific function:
Assembly of polyisoprenoid side chains. The polyprenyl synthase of coenzyme Q biosynthesis catalyzes the formation from isopentenyl diphosphate of all trans-polyprenyl pyrophosphates generally ranging in length of between 6 and 10 isoprene units depending on the species
Gene Name:
COQ1
Uniprot ID:
P18900
Molecular weight:
52558.89844
Reactions
Protein Details
2. 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
3. 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