Bovine Metabolome Database: Showing metabocard for Farnesol (BMDB0004305)

Identification Taxonomy Physical properties Pathways Spectra Concentrations Links References enzymes (1) Show 1 protein XML

Record Information

Version

1.0

Creation Date

2016-09-30 23:09:08 UTC

Update Date

2020-05-11 20:15:19 UTC

BMDB ID

BMDB0004305

Secondary Accession Numbers

BMDB04305

Metabolite Identification

Common Name

Farnesol

Description

Farnesol, also known as (2E,6E)-farnesol or trans-farnesol, belongs to the class of organic compounds known as sesquiterpenoids. These are terpenes with three consecutive isoprene units. Thus, farnesol is considered to be an isoprenoid. Based on a literature review a significant number of articles have been published on Farnesol.

Structure

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
(2-trans,6-trans)-3,7,11-Trimethyldodeca-2,6,10-trien-1-ol	ChEBI
(2E,6E)-3,7,11-Trimethyl-2,6,10-dodecatrien-1-ol	ChEBI
(2E,6E)-Farnesol	ChEBI
(e)-Farnesol	ChEBI
(e,e)-Farnesol	ChEBI
2-trans,6-trans-Farnesol	ChEBI
all-trans-Farnesol	ChEBI
trans,trans-alpha-Farnesol	ChEBI
trans,trans-Farnesol	ChEBI
trans-Farnesol	ChEBI
Ditrans,polycis-polyprenol	Kegg
trans,trans-a-Farnesol	Generator
trans,trans-Α-farnesol	Generator
2-cis,6-trans-Farnesol	HMDB
3,7,11-Trimethyl-2,6,10-dodecatrien-1-ol	HMDB
Farnesyl alcohol	HMDB
FCI 119a	HMDB
Nikkosome	HMDB
Farnesol	MeSH
(E)-beta-Farnesol	PhytoBank
(E)-β-Farnesol	PhytoBank
(E,E)-3,7,11-Trimethyl-2,6,10-dodecatrien-1-ol	PhytoBank
(E,E)-Farnesyl alcohol	PhytoBank
(t,t)-Farnesol	PhytoBank
2,6-Di-trans-farnesol	PhytoBank
2,6-trans,trans-Farnesol	PhytoBank
3,7,11-Trimethyldodeca-2-trans,6-trans,10-trien-1-ol	PhytoBank
all-E-Farnesol	PhytoBank
trans-1-Hydroxy-3,7,11-trimethyl-2,6,10-dodecatriene	PhytoBank
trans-2,trans-6-Farnesol	PhytoBank
3,7,11-Trimethyl-2,6,10-dodecen-1-ol	PhytoBank

Chemical Formula

C₁₅H₂₆O

Average Molecular Weight

222.3663

Monoisotopic Molecular Weight

222.198365454

IUPAC Name

(2E,6E)-3,7,11-trimethyldodeca-2,6,10-trien-1-ol

Traditional Name

(E)-farnesol

CAS Registry Number

4602-84-0

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 Key

CRDAMVZIKSXKFV-YFVJMOTDSA-N

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
Fatty alcohol
Fatty acyl
Organic oxygen compound
Hydrocarbon derivative
Primary alcohol
Organooxygen compound
Alcohol
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

farnesol (CHEBI:16619 )
Other Prenol lipids (C06081 )
Acyclic farnesane sesquiterpenoids (LMPR0103010001 )

Ontology

Status

Expected but not Quantified

Origin

Endogenous

Exogenous

Biofunction

Not Available

Application

Not Available

Cellular locations

Cell membrane
Cytoplasm
Membrane

Physical Properties

State

Solid

Experimental Properties

Property	Value	Reference
Melting Point	< 25 °C	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
logP	4.84	ALOGPS
logP	4.16	ChemAxon
logS	-3.6	ALOGPS
pKa (Strongest Acidic)	16.33	ChemAxon
pKa (Strongest Basic)	-2.2	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	1	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	20.23 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	74.98 m³·mol⁻¹	ChemAxon
Polarizability	28.7 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Spectra

Spectrum Type	Description	Splash Key
GC-MS	GC-MS Spectrum - GC-MS (1 TMS)	splash10-000x-9800000000-0366097ae9a2af6bafce	View in MoNA
GC-MS	GC-MS Spectrum - GC-MS (1 TMS)	splash10-001l-9800000000-eec57a93bb5862e554f1	View in MoNA
GC-MS	GC-MS Spectrum - GC-MS (1 TMS)	splash10-000x-8900000000-9c20df8f2d1959c137d7	View in MoNA
GC-MS	GC-MS Spectrum - GC-MS (Non-derivatized)	splash10-000x-9800000000-0366097ae9a2af6bafce	View in MoNA
GC-MS	GC-MS Spectrum - GC-MS (Non-derivatized)	splash10-001l-9800000000-eec57a93bb5862e554f1	View in MoNA
GC-MS	GC-MS Spectrum - GC-MS (Non-derivatized)	splash10-000x-8900000000-9c20df8f2d1959c137d7	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-0a4u-9830000000-5e08d59a4cc2e87c9984	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positive	splash10-05xr-9860000000-2eeca721058a47519afd	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	View in JSpectraViewer
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 - Linear Ion Trap , positive	splash10-003u-0790000000-578343425424f42c9d58	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0ab9-1590000000-88a1356fe7cab3171954	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0avi-7930000000-81c18181dbd66735216a	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0gi0-9400000000-e44ecbea8a96f84abd43	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-00di-0390000000-9beef594142e0da5de92	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-006x-1980000000-3b9708ac6185abaf6d96	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-05bf-4910000000-a8db2089f5647c8532ad	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-00di-0090000000-ab61d8a2af41e6ed2e49	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-00di-0690000000-8a43271c10743cad1e3e	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-00l2-4900000000-7dcaa3b1e66cfbe960c9	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-05gi-5930000000-9f54facb49232e1c6a46	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-05o0-9600000000-55d109ed92e3da30c7ea	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-00l6-9100000000-bcc664ee21d185da076e	View in MoNA
MS	Mass Spectrum (Electron Ionization)	splash10-014l-9200000000-8e5fae6943a545e4bc0b	View in MoNA
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)	Not Available	View in JSpectraViewer

Biological Properties

Cellular Locations

Cell membrane
Cytoplasm
Membrane

Biospecimen Locations

Epidermis
Fibroblasts
Intestine
Kidney

Pathways

Not Available

Name	SMPDB/Pathwhiz	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Epidermis	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Fibroblasts	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Intestine	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Kidney	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details

Abnormal Concentrations

Not Available

External Links

HMDB ID

HMDB0004305

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

2-TRANS6-TRANS-FARNESOL

BiGG ID

Not Available

Wikipedia Link

Farnesol

METLIN ID

7048

PubChem Compound

445070

PDB ID

Not Available

ChEBI ID

16619

References

Synthesis Reference

Imai, 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)

Not Available

General References

Not Available

Enzymes

Enzyme Details

1. Bile acid receptor

General function:: Involved in sequence-specific DNA binding
Specific function:: Ligand-activated transcription factor. Receptor for bile acids (BAs) such as chenodeoxycholic acid (CDCA), lithocholic acid, deoxycholic acid (DCA) and allocholic acid (ACA). Plays a essential role in BA homeostasis through the regulation of genes involved in BA synthesis, conjugation and enterohepatic circulation. Also regulates lipid and glucose homeostasis and is involved innate immune response. The FXR-RXR heterodimer binds predominantly to farnesoid X receptor response elements (FXREs) containing two inverted repeats of the consensus sequence 5'-AGGTCA-3' in which the monomers are spaced by 1 nucleotide (IR-1) but also to tandem repeat DR1 sites with lower affinity, and can be activated by either FXR or RXR-specific ligands. It is proposed that monomeric nuclear receptors such as NR5A2/LRH-1 bound to coregulatory nuclear responsive element (NRE) halfsites located in close proximity to FXREs modulate transcriptional activity. In the liver activates transcription of the corepressor NR0B2 thereby indirectly inhibiting CYP7A1 and CYP8B1 (involved in BA synthesis) implicating at least in part histone demethylase KDM1A resulting in epigenomic repression, and SLC10A1/NTCP (involved in hepatic uptake of conjugated BAs). Activates transcription of the repressor MAFG (involved in regulation of BA synthesis). Activates transcription of SLC27A5/BACS and BAAT (involved in BA conjugation), ABCB11/BSEP (involved in bile salt export) by directly recruiting histone methyltransferase CARM1, and ABCC2/MRP2 (involved in secretion of conjugated BAs) and ABCB4 (involved in secretion of phosphatidylcholine in the small intestine). Activates transcription of SLC27A5/BACS and BAAT (involved in BA conjugation), ABCB11/BSEP (involved in bile salt export) by directly recruiting histone methyltransferase CARM1, and ABCC2/MRP2 (involved in secretion of conjugated BAs) and ABCB4 (involved in secretion of phosphatidylcholine in the small intestine). In the intestine activates FGF19 expression and secretion leading to hepatic CYP7A1 repression. The function also involves the coordinated induction of hepatic KLB/beta-klotho expression. Regulates transcription of liver UGT2B4 and SULT2A1 involved in BA detoxification; binding to the UGT2B4 promoter seems to imply a monomeric transactivation independent of RXRA. Modulates lipid homeostasis by activating liver NR0B2/SHP-mediated repression of SREBF1 (involved in de novo lipogenesis), expression of PLTP (involved in HDL formation), SCARB1 (involved in HDL hepatic uptake), APOE, APOC1, APOC4, PPARA (involved in beta-oxidation of fatty acids), VLDLR and SDC1 (involved in the hepatic uptake of LDL and IDL remnants), and inhibiting expression of MTTP (involved in VLDL assembly). Increases expression of APOC2 (promoting lipoprotein lipase activity implicated in triglyceride clearance). Transrepresses APOA1 involving a monomeric competition with NR2A1 for binding to a DR1 element. Also reduces triglyceride clearance by inhibiting expression of ANGPTL3 and APOC3 (both involved in inhibition of lipoprotein lipase). Involved in glucose homeostasis by modulating hepatic gluconeogenesis through activation of NR0B2/SHP-mediated repression of respective genes. Modulates glycogen synthesis (inducing phosphorylation of glycogen synthase kinase-3). Modulates glucose-stimulated insulin secretion and is involved in insulin resistance. Involved in intestinal innate immunity. Plays a role in protecting the distal small intestine against bacterial overgrowth and preservation of the epithelial barrier. Down-regulates inflammatory cytokine expression in several types of immune cells including macrophages and mononuclear cells. Mediates trans-repression of TLR4-induced cytokine expression; the function seems to require its sumoylation and prevents N-CoR nuclear receptor corepressor clearance from target genes such as IL1B and NOS2. Involved in the TLR9-mediated protective mechanism in intestinal inflammation. Plays an anti-inflammatory role in liver inflammation; proposed to inhibit proinflammatory (but not antiapoptotic) NF-kappa-B signaling.
Gene Name:: NR1H4
Uniprot ID:: Q3SZL0
Molecular weight:: 55460.0

Showing metabocard for Farnesol (BMDB0004305)

Structure for BMDB0004305 (Farnesol)

Enzymes