ECMDB: Farnesyl pyrophosphate (ECMDB00961) (M2MDB000210)

Identification Taxonomy Physical Properties Biological Properties Spectra Concentrations Links References Enzymes (4)XML

Proteins (1671)

Record Information

Version

2.0

Creation Date

2012-05-31 13:02:37 -0600

Update Date

2015-09-13 12:56:09 -0600

Secondary Accession Numbers

ECMDB00961

Identification

Name:

Farnesyl pyrophosphate

Description

Farnesyl pyrophosphate is an intermediate in the HMG-CoA reductase pathway used by organisms in the biosynthesis of terpenes and terpenoids. -- Wikipedia

Structure

MOL SDF PDB SMILES InChI

Synonyms:

ω,E,E-farnesyl diphosphate
ω,e,e-farnesyl diphosphate
ω,e,e-farnesyl diphosphoric acid
(2E,6E)-Farnesyl diphosphate
(2E,6E)-Farnesyl diphosphoric acid
(2E,6E)-Farnesyl pyrophosphate
(2E,6E)-Farnesyl pyrophosphoric acid
(E,E)-farnesyl diphosphate
(all-E)-Farnesyl diphosphate
(all-e)-Farnesyl diphosphoric acid
(E,E)-Farnesyl diphosphate
(e,e)-Farnesyl diphosphoric acid
(E,E)-Farnesyl pyrophosphate
(e,e)-Farnesyl pyrophosphoric acid
2-trans,6-trans-farnesyl diphosphate
2-trans,6-trans-Farnesyl diphosphate
2-trans,6-trans-Farnesyl diphosphoric acid
2-trans,6-trans-Farnesyl pyrophosphate
2-trans,6-trans-Farnesyl pyrophosphoric acid
all-trans-farnesyl diphosphate
trans, trans-farnesyl diphosphate
All-trans-farnesyl diphosphate
all-trans-Farnesyl diphosphoric acid
All-trans-Farnesyl pyrophosphate
all-trans-Farnesyl pyrophosphoric acid
Farnesyl diphosphate
Farnesyl diphosphoric acid
Farnesyl pyrophosphate
Farnesyl pyrophosphoric acid
Farnesyl-PP
FPP
Omega,E,E-farnesyl diphosphate
Omega,e,e-farnesyl diphosphoric acid
Trans, trans-Farnesyl diphosphate
trans, trans-Farnesyl diphosphoric acid
Trans-Farnesyl pyrophosphate
trans-Farnesyl pyrophosphoric acid
Trans-trans-Farnesyl diphosphate
trans-trans-Farnesyl diphosphoric acid
Trans-trans-Farnesyl pyrophosphate
trans-trans-Farnesyl pyrophosphoric acid

Chemical Formula:

C₁₅H₂₈O₇P₂

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+

CAS number:

13058-04-3

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

SMILES:

CC(C)=CCC\C(C)=C\CC\C(C)=C\COP(O)(=O)OP(O)(O)=O

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:

-2

Melting point:

Not Available

Experimental Properties:

Property	Value	Source

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:

Membrane

Reactions:

SMPDB Pathways:

Porphyrin metabolism	PW000936
Secondary Metabolites: Ubiquinol biosynthesis	PW000981
Secondary Metabolites: Ubiquinol biosynthesis 2	PW002036
Secondary metabolites: methylerythritol phosphate and polyisoprenoid biosynthesis	PW000958

KEGG Pathways:

Metabolic pathways eco01100
Terpenoid backbone biosynthesis ec00900

EcoCyc Pathways:

trans, trans-farnesyl diphosphate biosynthesis PWY-5123
di-trans,poly-cis-undecaprenyl phosphate biosynthesis PWY-5785
octaprenyl diphosphate biosynthesis PWY-5783

Concentrations

Not Available

Spectra

Spectra:

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

References

References:

Argmann CA, Edwards JY, Sawyez CG, O'Neil CH, Hegele RA, Pickering JG, Huff MW: Regulation of macrophage cholesterol efflux through hydroxymethylglutaryl-CoA reductase inhibition: a role for RhoA in ABCA1-mediated cholesterol efflux. J Biol Chem. 2005 Jun 10;280(23):22212-21. Epub 2005 Apr 6. Pubmed: 15817453
Fukuchi J, Song C, Ko AL, Liao S: Transcriptional regulation of farnesyl pyrophosphate synthase by liver X receptors. Steroids. 2003 Sep;68(7-8):685-91. Pubmed: 12957674
Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., Tanabe, M. (2012). "KEGG for integration and interpretation of large-scale molecular data sets." Nucleic Acids Res 40:D109-D114. Pubmed: 22080510
Keseler, I. M., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama-Castro, S., Muniz-Rascado, L., Bonavides-Martinez, C., Paley, S., Krummenacker, M., Altman, T., Kaipa, P., Spaulding, A., Pacheco, J., Latendresse, M., Fulcher, C., Sarker, M., Shearer, A. G., Mackie, A., Paulsen, I., Gunsalus, R. P., Karp, P. D. (2011). "EcoCyc: a comprehensive database of Escherichia coli biology." Nucleic Acids Res 39:D583-D590. Pubmed: 21097882
Notarnicola M, Messa C, Cavallini A, Bifulco M, Tecce MF, Eletto D, Di Leo A, Montemurro S, Laezza C, Caruso MG: Higher farnesyl diphosphate synthase activity in human colorectal cancer inhibition of cellular apoptosis. Oncology. 2004;67(5-6):351-8. Pubmed: 15713990
Reigard SA, Zahn TJ, Haworth KB, Hicks KA, Fierke CA, Gibbs RA: Interplay of isoprenoid and peptide substrate specificity in protein farnesyltransferase. Biochemistry. 2005 Aug 23;44(33):11214-23. Pubmed: 16101305
Saisho Y, Morimoto A, Umeda T: Determination of farnesyl pyrophosphate in dog and human plasma by high-performance liquid chromatography with fluorescence detection. Anal Biochem. 1997 Oct 1;252(1):89-95. Pubmed: 9324945
Sanders JM, Song Y, Chan JM, Zhang Y, Jennings S, Kosztowski T, Odeh S, Flessner R, Schwerdtfeger C, Kotsikorou E, Meints GA, Gomez AO, Gonzalez-Pacanowska D, Raker AM, Wang H, van Beek ER, Papapoulos SE, Morita CT, Oldfield E: Pyridinium-1-yl bisphosphonates are potent inhibitors of farnesyl diphosphate synthase and bone resorption. J Med Chem. 2005 Apr 21;48(8):2957-63. Pubmed: 15828834
Shellman YG, Ribble D, Miller L, Gendall J, Vanbuskirk K, Kelly D, Norris DA, Dellavalle RP: Lovastatin-induced apoptosis in human melanoma cell lines. Melanoma Res. 2005 Apr;15(2):83-9. Pubmed: 15846140
Tacer KF, Haugen TB, Baltsen M, Debeljak N, Rozman D: Tissue-specific transcriptional regulation of the cholesterol biosynthetic pathway leads to accumulation of testis meiosis-activating sterol (T-MAS). J Lipid Res. 2002 Jan;43(1):82-9. Pubmed: 11792726
van der Werf, M. J., Overkamp, K. M., Muilwijk, B., Coulier, L., Hankemeier, T. (2007). "Microbial metabolomics: toward a platform with full metabolome coverage." Anal Biochem 370:17-25. Pubmed: 17765195

Synthesis Reference:

Castillo-Bocanegra, Rafael. Synthesis and biological activity of farnesyl pyrophosphate analogs. (1977), 193 pp.

Material Safety Data Sheet (MSDS)

Download (PDF)

Links

External Links:

Resource	Link
CHEBI ID	17407
HMDB ID	HMDB00961
Pubchem Compound ID	445713
Kegg ID	C00448
ChemSpider ID	393270
Wikipedia	Farnesyl pyrophosphate
BioCyc ID	FARNESYL-PP
EcoCyc ID	FARNESYL-PP
Ligand Expo	FPP

Enzymes

Protein Details

1. Geranyltranstransferase

General function:: Involved in isoprenoid biosynthetic process
Specific function:: Geranyl diphosphate + isopentenyl diphosphate = diphosphate + trans,trans-farnesyl diphosphate
Gene Name:: ispA
Uniprot ID:: P22939
Molecular weight:: 32159

Reactions

Geranyl diphosphate + isopentenyl diphosphate = diphosphate + (2E,6E)-farnesyl diphosphate.

Protein Details

2. 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). UPP is the precursor of glycosyl carrier lipid in the biosynthesis of bacterial cell wall polysaccharide components such as peptidoglycan and lipopolysaccharide
Gene Name:: uppS
Uniprot ID:: P60472
Molecular weight:: 28444

Reactions

(2E,6E)-farnesyl diphosphate + 8 isopentenyl diphosphate = 8 diphosphate + di-trans,octa-cis-undecaprenyl diphosphate.

Protein Details

3. Octaprenyl-diphosphate synthase

General function:: Involved in isoprenoid biosynthetic process
Specific function:: Supplies octaprenyl diphosphate, the precursor for the side chain of the isoprenoid quinones ubiquinone and menaquinone
Gene Name:: ispB
Uniprot ID:: P0AD57
Molecular weight:: 35217

Reactions

(2E,6E)-farnesyl diphosphate + 5 isopentenyl diphosphate = 5 diphosphate + all-trans-octaprenyl diphosphate.

Protein Details

4. Protoheme IX farnesyltransferase

General function:: Involved in protoheme IX farnesyltransferase activity
Specific function:: Converts heme B (protoheme IX) to heme O by substitution of the vinyl group on carbon 2 of heme B porphyrin ring with a hydroxyethyl farnesyl side group
Gene Name:: cyoE
Uniprot ID:: P0AEA5
Molecular weight:: 32248

Farnesyl pyrophosphate (ECMDB00961) (M2MDB000210)

Structure for #<Compound:0x76f8ce08>

Enzymes

Reactions

Reactions

Reactions