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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2006-08-13 16:33:07 UTC
Update Date2022-09-22 17:43:52 UTC
HMDB IDHMDB0004305
Secondary Accession Numbers
  • HMDB04305
Metabolite Identification
Common NameFarnesol
DescriptionFarnesol is a signaling molecule that is derived from farnesyl diphosphate, an intermediate in the isoprenoid/cholesterol biosynthetic pathway. Farnesol is a 15 carbon isoprenoid alcohol is the corresponding dephosphorylated form of the isoprenoid farnesyl diphosphate. Farnesol has a potential role in controlling the degradation of 3-hydroxy-3-methylglutaryl coenzyme A (HMGCoA) reductase (EC 1.1.1.34, NADPH-hydroxymethylglutaryl-CoA reductase). The enzyme is stabilized under conditions of cellular sterol depletion (e.g. statin-treated cells) and rapidly degraded in sterol-loaded cells. In mammalian cells, this enhanced degradation is dependent on the presence of both a sterol and a non-sterol derived from the isoprenoid pathway; farnesol, the dephosphorylated form of farnesyl diphosphate, can function as the non-sterol component. Farnesol has been shown to activate the farnesoid receptor (FXR), a nuclear receptor that forms a functional heterodimer with RXR. Thus, dephosphorylation of farnesyl diphosphate, an intermediate in the cholesterol synthetic pathway, might produce an active ligand for the FXR:RXR heterodimer. The physiological ligand for FXR remains to be identified; farnesol, may simply mimic the unidentified natural ligand(s). In addition, exogenous farnesol have an effect on several other physiological processes, including inhibition of phosphatidylcholine biosynthesis, induction of apoptosis, inhibition of cell cycle progression and actin cytoskeletal disorganization. Farnesol cellular availability is an important determinant of vascular tone in animals and humans, and provides a basis for exploring farnesyl metabolism in humans with compromised vascular function as well as for using farnesyl analogues as regulators of arterial tone in vivo. A possible metabolic fate for farnesol is its conversion to farnesoic acid, and then to farnesol-derived dicarboxylic acids (FDDCAs) which would then be excreted in the urine. Farnesol can also be oxidized to a prenyl aldehyde, presumably by an alcohol dehydrogenase (ADH), and that this activity resides in the mitochondrial and peroxisomal. Liver Endoplasmic reticulum and peroxisomal fractions are able to phosphorylate farnesol to Farnesyl diphosphate in a Cytosine triphosphate dependent fashion. (PMID: 9812197 , 8636420 , 9083051 , 9015362 ). Prenol is polymerized by dehydration reactions; when there are at least four isoprene units (n in the above formula is greater than or equal to four), the polymer is called a polyprenol. Polyprenols can contain up to 100 isoprene units (n=100) linked end to end with the hydroxyl group (-OH) remaining at the end. These isoprenoid alcohols are also called terpenols These isoprenoid alcohols are important in the acylation of proteins, carotenoids, and fat-soluble vitamins A, E and K. They are also building blocks for plant oils such as farnesol and geraniol. Prenol is also a building block of cholesterol (built from six isoprene units), and thus of all steroids. Prenol has sedative properities, it is probably GABA receptor allosteric modulator.When the isoprene unit attached to the alcohol is saturated, the compound is referred to as a dolichol. Dolichols are important as glycosyl carriers in the synthesis of polysaccharides.(Wikipedia ).
Structure
Data?1582752306
Synonyms
ValueSource
(2-trans,6-trans)-3,7,11-Trimethyldodeca-2,6,10-trien-1-olChEBI
(2E,6E)-3,7,11-Trimethyl-2,6,10-dodecatrien-1-olChEBI
(2E,6E)-FarnesolChEBI
(e)-FarnesolChEBI
(e,e)-FarnesolChEBI
2-trans,6-trans-FarnesolChEBI
all-trans-FarnesolChEBI
trans,trans-alpha-FarnesolChEBI
trans,trans-FarnesolChEBI
trans-FarnesolChEBI
Ditrans,polycis-polyprenolKegg
trans,trans-a-FarnesolGenerator
trans,trans-Α-farnesolGenerator
2-cis,6-trans-FarnesolHMDB
3,7,11-Trimethyl-2,6,10-dodecatrien-1-olHMDB
Farnesyl alcoholHMDB
FCI 119aHMDB
NikkosomeHMDB
FarnesolMeSH
(E)-beta-FarnesolPhytoBank
(E)-β-FarnesolPhytoBank
(E,E)-3,7,11-Trimethyl-2,6,10-dodecatrien-1-olPhytoBank
(E,E)-Farnesyl alcoholPhytoBank
(t,t)-FarnesolPhytoBank
2,6-Di-trans-farnesolPhytoBank
2,6-trans,trans-FarnesolPhytoBank
3,7,11-Trimethyldodeca-2-trans,6-trans,10-trien-1-olPhytoBank
all-E-FarnesolPhytoBank
trans-1-Hydroxy-3,7,11-trimethyl-2,6,10-dodecatrienePhytoBank
trans-2,trans-6-FarnesolPhytoBank
3,7,11-Trimethyl-2,6,10-dodecen-1-olPhytoBank
Chemical FormulaC15H26O
Average Molecular Weight222.3663
Monoisotopic Molecular Weight222.198365454
IUPAC Name(2E,6E)-3,7,11-trimethyldodeca-2,6,10-trien-1-ol
Traditional Name(E)-farnesol
CAS Registry Number4602-84-0
SMILES
CC(C)=CCC\C(C)=C\CC\C(C)=C\CO
InChI Identifier
InChI=1S/C15H26O/c1-13(2)7-5-8-14(3)9-6-10-15(4)11-12-16/h7,9,11,16H,5-6,8,10,12H2,1-4H3/b14-9+,15-11+
InChI KeyCRDAMVZIKSXKFV-YFVJMOTDSA-N
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
  • Fatty alcohol
  • Fatty acyl
  • Organic oxygen compound
  • Hydrocarbon derivative
  • Primary alcohol
  • Organooxygen compound
  • Alcohol
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effect
Disposition
Process
Role
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point< 25 °CNot Available
Boiling Point283.00 to 284.00 °C. @ 760.00 mm HgThe Good Scents Company Information System
Water Solubility1.29 mg/L @ 25 °C (est)The Good Scents Company Information System
LogP5.314 (est)The Good Scents Company Information System
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility0.059 g/LALOGPS
logP4.84ALOGPS
logP4.16ChemAxon
logS-3.6ALOGPS
pKa (Strongest Acidic)16.33ChemAxon
pKa (Strongest Basic)-2.2ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area20.23 ŲChemAxon
Rotatable Bond Count7ChemAxon
Refractivity74.98 m³·mol⁻¹ChemAxon
Polarizability28.7 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+157.0131661259
DarkChem[M-H]-153.76131661259
DeepCCS[M+H]+157.22830932474
DeepCCS[M-H]-154.8730932474
DeepCCS[M-2H]-189.15630932474
DeepCCS[M+Na]+164.11330932474
AllCCS[M+H]+159.032859911
AllCCS[M+H-H2O]+155.432859911
AllCCS[M+NH4]+162.332859911
AllCCS[M+Na]+163.232859911
AllCCS[M-H]-159.132859911
AllCCS[M+Na-2H]-160.232859911
AllCCS[M+HCOO]-161.532859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
FarnesolCC(C)=CCC\C(C)=C\CC\C(C)=C\CO2313.6Standard polar33892256
FarnesolCC(C)=CCC\C(C)=C\CC\C(C)=C\CO1690.7Standard non polar33892256
FarnesolCC(C)=CCC\C(C)=C\CC\C(C)=C\CO1719.3Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Farnesol,1TMS,isomer #1CC(C)=CCC/C(C)=C/CC/C(C)=C/CO[Si](C)(C)C1772.6Semi standard non polar33892256
Farnesol,1TBDMS,isomer #1CC(C)=CCC/C(C)=C/CC/C(C)=C/CO[Si](C)(C)C(C)(C)C2002.7Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Experimental GC-MSGC-MS Spectrum - Farnesol GC-MS (1 TMS)splash10-000x-9800000000-0366097ae9a2af6bafce2014-06-16HMDB team, MONA, MassBankView Spectrum
Experimental GC-MSGC-MS Spectrum - Farnesol GC-MS (1 TMS)splash10-001l-9800000000-eec57a93bb5862e554f12014-06-16HMDB team, MONA, MassBankView Spectrum
Experimental GC-MSGC-MS Spectrum - Farnesol GC-MS (1 TMS)splash10-000x-8900000000-9c20df8f2d1959c137d72014-06-16HMDB team, MONA, MassBankView Spectrum
Experimental GC-MSGC-MS Spectrum - Farnesol GC-MS (Non-derivatized)splash10-000x-9800000000-0366097ae9a2af6bafce2017-09-12HMDB team, MONA, MassBankView Spectrum
Experimental GC-MSGC-MS Spectrum - Farnesol GC-MS (Non-derivatized)splash10-001l-9800000000-eec57a93bb5862e554f12017-09-12HMDB team, MONA, MassBankView Spectrum
Experimental GC-MSGC-MS Spectrum - Farnesol GC-MS (Non-derivatized)splash10-000x-8900000000-9c20df8f2d1959c137d72017-09-12HMDB team, MONA, MassBankView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Farnesol GC-MS (Non-derivatized) - 70eV, Positivesplash10-0a4u-9830000000-5e08d59a4cc2e87c99842016-09-22Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Farnesol GC-MS (1 TMS) - 70eV, Positivesplash10-05xr-9860000000-2eeca721058a47519afd2017-10-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Farnesol GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Farnesol GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
MSMass Spectrum (Electron Ionization)splash10-014l-9200000000-8e5fae6943a545e4bc0b2014-09-20Not AvailableView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Experimental LC-MS/MSLC-MS/MS Spectrum - Farnesol Linear Ion Trap , positive-QTOFsplash10-003u-0790000000-578343425424f42c9d582017-09-14HMDB team, MONAView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Farnesol 10V, Positive-QTOFsplash10-0ab9-1590000000-88a1356fe7cab31719542016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Farnesol 20V, Positive-QTOFsplash10-0avi-7930000000-81c18181dbd66735216a2016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Farnesol 40V, Positive-QTOFsplash10-0gi0-9400000000-e44ecbea8a96f84abd432016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Farnesol 10V, Negative-QTOFsplash10-00di-0390000000-9beef594142e0da5de922016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Farnesol 20V, Negative-QTOFsplash10-006x-1980000000-3b9708ac6185abaf6d962016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Farnesol 40V, Negative-QTOFsplash10-05bf-4910000000-a8db2089f5647c8532ad2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Farnesol 10V, Negative-QTOFsplash10-00di-0090000000-ab61d8a2af41e6ed2e492021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Farnesol 20V, Negative-QTOFsplash10-00di-0690000000-8a43271c10743cad1e3e2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Farnesol 40V, Negative-QTOFsplash10-00l2-4900000000-7dcaa3b1e66cfbe960c92021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Farnesol 10V, Positive-QTOFsplash10-05gi-5930000000-9f54facb49232e1c6a462021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Farnesol 20V, Positive-QTOFsplash10-05o0-9600000000-55d109ed92e3da30c7ea2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Farnesol 40V, Positive-QTOFsplash10-00l6-9100000000-bcc664ee21d185da076e2021-09-22Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, H2O, predicted)2022-08-23Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, H2O, predicted)2022-08-23Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, H2O, predicted)2022-08-23Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, H2O, predicted)2022-08-23Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, H2O, predicted)2022-08-23Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, H2O, predicted)2022-08-23Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, H2O, predicted)2022-08-23Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, H2O, predicted)2022-08-23Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, H2O, predicted)2022-08-23Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, H2O, predicted)2022-08-23Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, H2O, predicted)2022-08-23Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, predicted)2022-08-23Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, H2O, predicted)2022-08-23Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, predicted)2022-08-23Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, H2O, predicted)2022-08-23Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, H2O, predicted)2022-08-23Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, H2O, predicted)2022-08-23Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, H2O, predicted)2022-08-23Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, H2O, predicted)2022-08-23Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, H2O, predicted)2022-08-23Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Extracellular
  • Membrane (predicted from logP)
Biospecimen Locations
  • Blood
  • Urine
Tissue Locations
  • Epidermis
  • Fibroblasts
  • Intestine
  • Kidney
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified0.25 (0.0-0.5) uMAdult (>18 years old)BothNormal details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
UrineDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedCancer patients undergoing total body irradiation details
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB014891
KNApSAcK IDC00003132
Chemspider ID392816
KEGG Compound IDC06081
BioCyc ID2-TRANS6-TRANS-FARNESOL
BiGG IDNot Available
Wikipedia LinkFarnesol
METLIN ID7048
PubChem Compound445070
PDB IDNot Available
ChEBI ID16619
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1290201
References
Synthesis ReferenceImai, Kunio; Marumo, Shingo. Stereochemistry of C-1 hydrogen exchange during 2,3-double bond trans-cis isomerization of farnesol by Helminthosporium sativum. Tetrahedron Letters (1974), (49/50), 4401-4.
Material Safety Data Sheet (MSDS)Download (PDF)
General References
  1. Horn TL, Long L, Cwik MJ, Morrissey RL, Kapetanovic IM, McCormick DL: Modulation of hepatic and renal drug metabolizing enzyme activities in rats by subchronic administration of farnesol. Chem Biol Interact. 2005 Apr 15;152(2-3):79-99. [PubMed:15840382 ]
  2. Hanley K, Wood L, Ng DC, He SS, Lau P, Moser A, Elias PM, Bikle DD, Williams ML, Feingold KR: Cholesterol sulfate stimulates involucrin transcription in keratinocytes by increasing Fra-1, Fra-2, and Jun D. J Lipid Res. 2001 Mar;42(3):390-8. [PubMed:11254751 ]
  3. DeBarber AE, Bleyle LA, Roullet JB, Koop DR: Omega-hydroxylation of farnesol by mammalian cytochromes p450. Biochim Biophys Acta. 2004 Jun 1;1682(1-3):18-27. [PubMed:15158752 ]
  4. Saidi S, Luitaud C, Rouabhia M: In vitro synergistic effect of farnesol and human gingival cells against Candida albicans. Yeast. 2006 Jul 15;23(9):673-87. [PubMed:16845684 ]
  5. Hanley K, Komuves LG, Ng DC, Schoonjans K, He SS, Lau P, Bikle DD, Williams ML, Elias PM, Auwerx J, Feingold KR: Farnesol stimulates differentiation in epidermal keratinocytes via PPARalpha. J Biol Chem. 2000 Apr 14;275(15):11484-91. [PubMed:10753967 ]
  6. Forman BM, Goode E, Chen J, Oro AE, Bradley DJ, Perlmann T, Noonan DJ, Burka LT, McMorris T, Lamph WW, Evans RM, Weinberger C: Identification of a nuclear receptor that is activated by farnesol metabolites. Cell. 1995 Jun 2;81(5):687-93. [PubMed:7774010 ]
  7. Staines AG, Sindelar P, Coughtrie MW, Burchell B: Farnesol is glucuronidated in human liver, kidney and intestine in vitro, and is a novel substrate for UGT2B7 and UGT1A1. Biochem J. 2004 Dec 15;384(Pt 3):637-45. [PubMed:15320866 ]
  8. Fayard E, Schoonjans K, Auwerx J: Xol INXS: role of the liver X and the farnesol X receptors. Curr Opin Lipidol. 2001 Apr;12(2):113-20. [PubMed:11264982 ]
  9. Roullet JB, Xue H, Chapman J, McDougal P, Roullet CM, McCarron DA: Farnesyl analogues inhibit vasoconstriction in animal and human arteries. J Clin Invest. 1996 May 15;97(10):2384-90. [PubMed:8636420 ]
  10. Edwards PA, Ericsson J: Signaling molecules derived from the cholesterol biosynthetic pathway: mechanisms of action and possible roles in human disease. Curr Opin Lipidol. 1998 Oct;9(5):433-40. [PubMed:9812197 ]
  11. Bostedor RG, Karkas JD, Arison BH, Bansal VS, Vaidya S, Germershausen JI, Kurtz MM, Bergstrom JD: Farnesol-derived dicarboxylic acids in the urine of animals treated with zaragozic acid A or with farnesol. J Biol Chem. 1997 Apr 4;272(14):9197-203. [PubMed:9083051 ]
  12. Westfall D, Aboushadi N, Shackelford JE, Krisans SK: Metabolism of farnesol: phosphorylation of farnesol by rat liver microsomal and peroxisomal fractions. Biochem Biophys Res Commun. 1997 Jan 23;230(3):562-8. [PubMed:9015362 ]

Enzymes

General function:
Involved in oxidoreductase activity
Specific function:
Oxidoreductase with a preference for NAD. Oxidizes all- trans-retinol and 13-cis-retinol to the corresponding aldehydes. Has higher activity towards CRBP-bound retinol than with free retinol. Oxidizes 3-alpha-hydroxysteroids. Oxidizes androstanediol and androsterone to dihydrotestosterone and androstanedione. Can also catalyze the reverse reaction
Gene Name:
RDH16
Uniprot ID:
O75452
Molecular weight:
35673.1