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Identification
YMDB IDYMDB00229
NameFarnesyl pyrophosphate
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
DescriptionFarnesyl pyrophosphate, also known as farnesyl diphosphoric acid or farnesyl-PP, belongs to the class of organic compounds known as sesquiterpenoids. These are terpenes with three consecutive isoprene units. Farnesyl pyrophosphate is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral.
Structure
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Synonyms
  • (2E,6E)-Farnesyl diphosphate
  • (2E,6E)-Farnesyl pyrophosphate
  • (all-E)-Farnesyl diphosphate
  • (E,E)-Farnesyl diphosphate
  • (E,E)-Farnesyl pyrophosphate
  • 2-trans,6-trans-Farnesyl diphosphate
  • 2-trans,6-trans-Farnesyl pyrophosphate
  • all-trans-Farnesyl pyrophosphate
  • Farnesyl diphosphate
  • Farnesyl pyrophosphate
  • Farnesyl pyrophosphic acid
  • Farnesyl-PP
  • trans-Farnesyl pyrophosphate
  • trans-trans-Farnesyl diphosphate
  • trans-trans-Farnesyl pyrophosphate
  • (2E,6E)-Farnesol diphosphate
  • trans,trans-Farnesyl diphosphate
  • (2E,6E)-Farnesol diphosphoric acid
  • (2E,6E)-Farnesyl diphosphoric acid
  • (2E,6E)-Farnesyl pyrophosphoric acid
  • (all-e)-Farnesyl diphosphoric acid
  • (e,e)-Farnesyl pyrophosphoric acid
  • 2-trans,6-trans-Farnesyl pyrophosphoric acid
  • all-trans-Farnesyl pyrophosphoric acid
  • Farnesyl diphosphoric acid
  • trans,trans-Farnesyl diphosphoric acid
  • trans-trans-Farnesyl diphosphoric acid
  • 2-trans,6-trans-Farnesyl diphosphoric acid
  • Farnesyl pyrophosphoric acid
  • Farnesyl pyrophosphate, (e,e)-isomer
  • Farnesyl pyrophosphate, (e,Z)-isomer
  • Farnesyl pyrophosphate, (Z,e)-isomer
  • Farnesyl pyrophosphate, (Z,Z)-isomer
  • Farnesylpyrophosphate
CAS number13058-04-3
WeightAverage: 382.3261
Monoisotopic: 382.131026274
InChI KeyVWFJDQUYCIWHTN-YFVJMOTDSA-N
InChIInChI=1S/C15H28O7P2/c1-13(2)7-5-8-14(3)9-6-10-15(4)11-12-21-24(19,20)22-23(16,17)18/h7,9,11H,5-6,8,10,12H2,1-4H3,(H,19,20)(H2,16,17,18)/b14-9+,15-11+
IUPAC Name{[hydroxy({[(2E,6E)-3,7,11-trimethyldodeca-2,6,10-trien-1-yl]oxy})phosphoryl]oxy}phosphonic acid
Traditional IUPAC Namefarnesyl diphosphate
Chemical FormulaC15H28O7P2
SMILES[H]OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H]
Chemical Taxonomy
Description belongs to the class of organic compounds known as sesquiterpenoids. These are terpenes with three consecutive isoprene units.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassPrenol lipids
Sub ClassSesquiterpenoids
Direct ParentSesquiterpenoids
Alternative Parents
Substituents
  • Farsesane sesquiterpenoid
  • Sesquiterpenoid
  • 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
StateSolid
Charge0
Melting pointNot Available
Experimental Properties
PropertyValueReference
Water SolubilityNot AvailablePhysProp
LogPNot AvailablePhysProp
Predicted Properties
PropertyValueSource
Water Solubility0.081 g/LALOGPS
logP2.4ALOGPS
logP3.62ChemAxon
logS-3.7ALOGPS
pKa (Strongest Acidic)1.77ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area113.29 ŲChemAxon
Rotatable Bond Count11ChemAxon
Refractivity96.73 m³·mol⁻¹ChemAxon
Polarizability37.94 ųChemAxon
Number of Rings0ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations
  • endoplasmic reticulum
  • lipid particle
Organoleptic PropertiesNot Available
SMPDB Pathways
Cholesterol biosynthesis and metabolism CE(10:0)PW002545 ThumbThumb?image type=greyscaleThumb?image type=simple
Cholesterol biosynthesis and metabolism CE(12:0)PW002548 ThumbThumb?image type=greyscaleThumb?image type=simple
Cholesterol biosynthesis and metabolism CE(14:0)PW002544 ThumbThumb?image type=greyscaleThumb?image type=simple
Cholesterol biosynthesis and metabolism CE(16:0)PW002550 ThumbThumb?image type=greyscaleThumb?image type=simple
Cholesterol biosynthesis and metabolism CE(18:0)PW002551 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways
Steroid biosynthesisec00100 Map00100
Terpenoid backbone biosynthesisec00900 Map00900
SMPDB Reactions
Heme + Farnesyl pyrophosphateHeme O
Geranyl-PP + Isopentenyl pyrophosphateFarnesyl pyrophosphate + Pyrophosphate
Farnesyl pyrophosphate + Isopentenyl pyrophosphatePyrophosphate + 2-trans,6-trans,10-trans-geranylgeranyl diphosphate
Farnesyl pyrophosphate + NADPHsqualene + NADP + Pyrophosphate
Farnesyl pyrophosphate + Isopentenyl pyrophosphatehexaprenyl diphosphate + Pyrophosphate
KEGG Reactions
Farnesyl pyrophosphate + Isopentenyl pyrophosphatePyrophosphate + geranylgeranyl diphosphate
Farnesyl pyrophosphate + protein ↔ protein
Farnesyl pyrophosphate + protein ↔ conjugated protein
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-004j-7943000000-ab6d749700f510a94133JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0pc0-1469000000-e3fd27c0418d0977f84eJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0a4i-6791000000-1ca128d2b96287a5b2f1JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0q29-9820000000-3277fbdf16e288ab1142JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-001i-0409000000-f8bbf786ee9d33cb48d4JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9501000000-8d060d3ceac94de45b8dJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-a265a369e6802359a7dfJSpectraViewer
References
References:
  • UniProt Consortium (2011). "Ongoing and future developments at the Universal Protein Resource." Nucleic Acids Res 39:D214-D219.21051339
  • 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
  • He, B., Chen, P., Chen, S. Y., Vancura, K. L., Michaelis, S., Powers, S. (1991). "RAM2, an essential gene of yeast, and RAM1 encode the two polypeptide components of the farnesyltransferase that prenylates a-factor and Ras proteins." Proc Natl Acad Sci U S A 88:11373-11377.1763050
  • 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:Castillo-Bocanegra, Rafael. Synthesis and biological activity of farnesyl pyrophosphate analogs. (1977), 193 pp.
External Links:
ResourceLink
CHEBI ID50277
HMDB IDHMDB00961
Pubchem Compound ID445713
Kegg IDC00448
ChemSpider ID23092868
FOODB IDFDB022339
WikipediaFarnesyl pyrophosphate
BioCyc IDFARNESYL-PP

Enzymes

General function:
Involved in isoprenoid biosynthetic process
Specific function:
Catalyzes the sequential condensation of isopentenyl pyrophosphate with the allylic pyrophosphates, dimethylallyl pyrophosphate, and then with the resultant geranylpyrophosphate to the ultimate product farnesyl pyrophosphate
Gene Name:
ERG20
Uniprot ID:
P08524
Molecular weight:
40483.0
Reactions
Dimethylallyl diphosphate + isopentenyl diphosphate → diphosphate + geranyl diphosphate.
Geranyl diphosphate + isopentenyl diphosphate → diphosphate + (2E,6E)-farnesyl diphosphate.
General function:
Involved in catalytic activity
Specific function:
A phosphate monoester + H(2)O = an alcohol + phosphate
Gene Name:
PHO8
Uniprot ID:
P11491
Molecular weight:
63003.60156
Reactions
A phosphate monoester + H(2)O → an alcohol + phosphate.
(2E,6E)-farnesyl diphosphate + H(2)O → (2E,6E)-farnesol + diphosphate.
beta-D-fructose 2,6-bisphosphate + H2O → beta-D-fructofuranose 2-phosphate + phosphate
General function:
Involved in transferase activity, transferring alkyl or aryl (other than methyl) groups
Specific function:
Generates undecaprenyl pyrophosphate (UPP) from isopentenyl pyrophosphate (IPP)
Gene Name:
NUS1
Uniprot ID:
Q12063
Molecular weight:
42556.69922
Reactions
(2E,6E)-farnesyl diphosphate + 8 isopentenyl diphosphate → 8 diphosphate + di-trans,octa-cis-undecaprenyl diphosphate.
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
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
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
General function:
Involved in catalytic activity
Specific function:
Catalyzes the transfer of a geranyl-geranyl moiety from geranyl-geranyl pyrophosphate to proteins having the C-terminal sequence Cys-Ile-Ile-Leu or Cys-Val-Leu-Leu. Acts, among other substrates, on Rho1 and Rho2 and CDC42 proteins. Participates in a RAS-like C-terminal modification of proteins involved in nuclear division and bud growth. It is involved in bud positioning and cell polarity
Gene Name:
CDC43
Uniprot ID:
P18898
Molecular weight:
42689.10156
Reactions
Geranylgeranyl diphosphate + protein-cysteine → S-geranylgeranyl-protein + diphosphate.
General function:
Involved in protein prenyltransferase activity
Specific function:
Catalyzes the transfer of a farnesyl or geranyl-geranyl moiety from farnesyl or geranyl-geranyl pyrophosphate to a cysteine at the fourth position from the C-terminus of several proteins having the C-terminal sequence Cys-aliphatic-aliphatic-X. The alpha subunit is thought to participate in a stable complex with the substrate. The beta subunit binds the peptide substrate
Gene Name:
RAM2
Uniprot ID:
P29703
Molecular weight:
37507.30078
Reactions
Farnesyl diphosphate + protein-cysteine → S-farnesyl protein + diphosphate.
Geranylgeranyl diphosphate + protein-cysteine → S-geranylgeranyl-protein + diphosphate.
General function:
Involved in transferase activity
Specific function:
May regulate the flux of isoprene intermediates through the sterol pathway. Squalene synthase is crucial for balancing the incorporation of farnesyl diphosphate (FPP) into sterol and nonsterol isoprene synthesis. ERG9 is also essential for cell growth in yeast
Gene Name:
ERG9
Uniprot ID:
P29704
Molecular weight:
51719.39844
Reactions
2 farnesyl diphosphate → diphosphate + presqualene diphosphate.
Presqualene diphosphate + NAD(P)H → squalene + diphosphate + NAD(P)(+).
General function:
Involved in catalytic activity
Specific function:
Catalyzes the transfer of a farnesyl moiety from farnesyl pyrophosphate to a cysteine at the fourth position from the C-terminus of several proteins such as a-factor and RAS. The beta subunit is responsible for peptide-binding
Gene Name:
RAM1
Uniprot ID:
P22007
Molecular weight:
48189.39844
Reactions
Farnesyl diphosphate + protein-cysteine → S-farnesyl protein + diphosphate.