Farnesyl pyrophosphate (YMDB00229)

You are using an unsupported browser. Please upgrade your browser to a newer version to get the best experience on Yeast Metabolome Database.

Identification

YMDB ID

YMDB00229

Name

Farnesyl pyrophosphate

Species

Saccharomyces cerevisiae

Strain

Baker's yeast

Description

Farnesyl 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

MOL SDF PDB SMILES InChI

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 number

13058-04-3

Weight

Average: 382.3261
Monoisotopic: 382.131026274

InChI Key

VWFJDQUYCIWHTN-YFVJMOTDSA-N

InChI

InChI=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 Name

farnesyl diphosphate

Chemical Formula

C₁₅H₂₈O₇P₂

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.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Sesquiterpenoids

Direct Parent

Sesquiterpenoids

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 Framework

Aliphatic acyclic compounds

External Descriptors

farnesyl diphosphate (CHEBI:17407 )
Acyclic farnesane sesquiterpenoids (C00448 )
Farnesenes (C00448 )
Acyclic farnesane sesquiterpenoids (LMPR0103010002 )

Physical Properties

State

Solid

Charge

Melting point

Not Available

Experimental Properties

Property	Value	Reference
Water Solubility	Not Available	PhysProp
LogP	Not Available	PhysProp

Predicted Properties

Property	Value	Source
Water Solubility	0.081 g/L	ALOGPS
logP	2.4	ALOGPS
logP	3.62	ChemAxon
logS	-3.7	ALOGPS
pKa (Strongest Acidic)	1.77	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	113.29 Å²	ChemAxon
Rotatable Bond Count	11	ChemAxon
Refractivity	96.73 m³·mol⁻¹	ChemAxon
Polarizability	37.94 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	1	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Biological Properties

Cellular Locations

endoplasmic reticulum
lipid particle

Organoleptic Properties

Not Available

SMPDB Pathways

Cholesterol biosynthesis and metabolism CE(10:0)	PW002545
Cholesterol biosynthesis and metabolism CE(12:0)	PW002548
Cholesterol biosynthesis and metabolism CE(14:0)	PW002544
Cholesterol biosynthesis and metabolism CE(16:0)	PW002550
Cholesterol biosynthesis and metabolism CE(18:0)	PW002551

KEGG Pathways

Steroid biosynthesis	ec00100
Terpenoid backbone biosynthesis	ec00900

SMPDB Reactions

KEGG Reactions

Farnesyl pyrophosphate + Isopentenyl pyrophosphate ↔ Pyrophosphate + geranylgeranyl diphosphate

Farnesyl pyrophosphate + protein ↔ protein

Farnesyl pyrophosphate + protein ↔ conjugated protein

Concentrations

Intracellular Concentrations

Not Available

Extracellular Concentrations

Not Available

Spectra

Spectrum Type	Description	Splash Key	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-004j-7943000000-ab6d749700f510a94133	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	JSpectraViewer
LC-MS/MS	LC-MS/MS Spectrum - n/a 26V, negative	splash10-014i-0090000000-09efa5f4e481376eae3d	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 11V, negative	splash10-001i-2009000000-b2358e50ee86b2ebccb5	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 14V, negative	splash10-004i-9004000000-b255d40b3beef0ddd16f	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 16V, negative	splash10-004i-9001000000-64cd48aa93040d775977	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 19V, negative	splash10-004i-9000000000-84a4e8d938e03661128e	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 25V, negative	splash10-004i-9000000000-eb2e768f7c19af669f74	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - n/a 26V, negative	splash10-03di-0209000000-651c59dc3e732ea880d7	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - n/a 26V, negative	splash10-0a4i-0900000000-ae4be9bde4ed56cfa99b	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - n/a 26V, positive	splash10-0002-0294000000-7019f71a6e4f542dddae	JSpectraViewer \| MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0pc0-1469000000-e3fd27c0418d0977f84e	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0a4i-6791000000-1ca128d2b96287a5b2f1	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0q29-9820000000-3277fbdf16e288ab1142	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-001i-0409000000-f8bbf786ee9d33cb48d4	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9501000000-8d060d3ceac94de45b8d	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-a265a369e6802359a7df	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-001i-0009000000-ea5bda9906940e9694b2	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-001i-2409000000-4b044bb59695723b85bd	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-056r-9600000000-a090357e0efeb6192936	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-001i-0019000000-66a0a5510c1d34aea230	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-114i-0394000000-89ab3170c9695823fb2f	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-05rs-6900000000-7b5163a81d3cbdf1feb4	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer

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:

Resource	Link
CHEBI ID	50277
HMDB ID	HMDB00961
Pubchem Compound ID	445713
Kegg ID	C00448
ChemSpider ID	23092868
FOODB ID	FDB022339
Wikipedia	Farnesyl pyrophosphate
BioCyc ID	FARNESYL-PP

Enzymes

Protein Details

1. Farnesyl pyrophosphate synthase

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.

Protein Details

2. Repressible alkaline phosphatase

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

Protein Details

3. Probable undecaprenyl pyrophosphate synthase

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.

Protein Details

4. 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

5. 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

6. 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

7. Geranylgeranyl transferase type-1 subunit beta

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.

Protein Details

8. Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha

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.

Protein Details

9. Squalene synthase

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)(+).

Protein Details

10. Protein farnesyltransferase subunit beta

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.

Structure for #<Compound:0xade11538>

Enzymes

Reactions

Reactions

Reactions

Reactions

Reactions

Reactions

Reactions

Reactions

Reactions

Reactions