MiMeDB: Showing metabocard for (2-trans,6-trans)-Farnesol (MMDBc0032978)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-19 04:29:42 UTC

Update Date

2024-10-15 22:33:50 UTC

Metabolite ID

MMDBc0032978

Metabolite Identification

Common Name

(2-trans,6-trans)-Farnesol

Description

(2-trans,6-trans)-Farnesol, also known as farnesol, 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

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI

HMDB0004305
     RDKit          3D
Farnesol
 42 41  0  0  0  0  0  0  0  0999 V2000
   -5.6428    1.0080    0.2521 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8393   -0.2076    0.0669 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4540   -1.5328    0.3596 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5744   -0.1432   -0.3574 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9976    1.1788   -0.6377 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8468    1.5745    0.2363 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6742    0.6730    0.1625 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6656   -0.7510    0.5866 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5018    1.1642   -0.2796 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7443    0.3814   -0.4047 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8585    0.9188    0.4595 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0894    0.1230    0.3163 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3046    0.4930    1.0906 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1188   -0.9073   -0.4882 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3912   -1.6832   -0.5990 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1139   -2.9923   -0.2050 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0908    1.7753    0.8695 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6093    0.7650    0.7289 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8264    1.5298   -0.7244 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7789   -2.0279   -0.5611 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2675   -1.4268    1.1165 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6758   -2.1705    0.8267 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0210   -1.0486   -0.4992 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6153    1.1003   -1.7085 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7767    1.9815   -0.6755 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5439    2.6418    0.0171 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1875    1.5369    1.3186 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7192   -1.4666   -0.2344 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2306   -0.9680    1.2385 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5321   -0.9527    1.2750 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4951    2.2216   -0.5557 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5334   -0.6865   -0.2502 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0984    0.4531   -1.4681 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4979    0.9514    1.5101 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0809    1.9617    0.1642 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1294    1.4495    1.6560 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5947   -0.2723    1.8117 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1731    0.7126    0.4277 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2950   -1.2542   -1.0900 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7681   -1.6431   -1.6367 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1724   -1.3022    0.0839 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1477   -3.1583   -0.1110 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  2  3
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  7  9  2  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 12 14  2  0
 14 15  1  0
 15 16  1  0
  1 17  1  0
  1 18  1  0
  1 19  1  0
  3 20  1  0
  3 21  1  0
  3 22  1  0
  4 23  1  0
  5 24  1  0
  5 25  1  0
  6 26  1  0
  6 27  1  0
  8 28  1  0
  8 29  1  0
  8 30  1  0
  9 31  1  0
 10 32  1  0
 10 33  1  0
 11 34  1  0
 11 35  1  0
 13 36  1  0
 13 37  1  0
 13 38  1  0
 14 39  1  0
 15 40  1  0
 15 41  1  0
 16 42  1  0
M  END


  Mrv1652309272007342D          

 16 15  0  0  0  0            999 V2000
10002.033010002.5563    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10002.748410002.1449    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10003.463510002.5563    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10004.178710002.1449    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10004.891810002.5563    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10005.607010002.1449    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10006.322110002.5563    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10007.035210002.1449    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10004.891810003.3813    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10001.318610002.1449    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.604110002.5563    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.889710002.1449    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.175410002.5563    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.461010002.1449    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.175410003.3813    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10002.033010003.3813    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  1 10  1  0  0  0  0
  1 16  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  5  9  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
 13 14  1  0  0  0  0
 13 15  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0032978

> <DATABASE_NAME>
MIME

> <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

> <FORMULA>
C15H26O

> <MOLECULAR_WEIGHT>
222.3663

> <EXACT_MASS>
222.198365454

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
42

> <JCHEM_AVERAGE_POLARIZABILITY>
28.69644639972201

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

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

> <ALOGPS_LOGP>
4.84

> <JCHEM_LOGP>
4.1620975709999986

> <ALOGPS_LOGS>
-3.58

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
16.33002421872553

> <JCHEM_PKA_STRONGEST_BASIC>
-2.2170474067294528

> <JCHEM_POLAR_SURFACE_AREA>
20.23

> <JCHEM_REFRACTIVITY>
74.98469999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.87e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(E)-farnesol

> <JCHEM_VEBER_RULE>
1

$$$$

HMDB0004305
     RDKit          3D
Farnesol
 42 41  0  0  0  0  0  0  0  0999 V2000
   -5.6428    1.0080    0.2521 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8393   -0.2076    0.0669 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4540   -1.5328    0.3596 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5744   -0.1432   -0.3574 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9976    1.1788   -0.6377 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8468    1.5745    0.2363 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6742    0.6730    0.1625 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6656   -0.7510    0.5866 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5018    1.1642   -0.2796 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7443    0.3814   -0.4047 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8585    0.9188    0.4595 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0894    0.1230    0.3163 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3046    0.4930    1.0906 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1188   -0.9073   -0.4882 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3912   -1.6832   -0.5990 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1139   -2.9923   -0.2050 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0908    1.7753    0.8695 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6093    0.7650    0.7289 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8264    1.5298   -0.7244 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7789   -2.0279   -0.5611 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2675   -1.4268    1.1165 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6758   -2.1705    0.8267 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0210   -1.0486   -0.4992 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6153    1.1003   -1.7085 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7767    1.9815   -0.6755 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5439    2.6418    0.0171 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1875    1.5369    1.3186 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7192   -1.4666   -0.2344 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2306   -0.9680    1.2385 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5321   -0.9527    1.2750 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4951    2.2216   -0.5557 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5334   -0.6865   -0.2502 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0984    0.4531   -1.4681 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4979    0.9514    1.5101 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0809    1.9617    0.1642 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1294    1.4495    1.6560 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5947   -0.2723    1.8117 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1731    0.7126    0.4277 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2950   -1.2542   -1.0900 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7681   -1.6431   -1.6367 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1724   -1.3022    0.0839 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1477   -3.1583   -0.1110 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  2  3
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  7  9  2  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 12 14  2  0
 14 15  1  0
 15 16  1  0
  1 17  1  0
  1 18  1  0
  1 19  1  0
  3 20  1  0
  3 21  1  0
  3 22  1  0
  4 23  1  0
  5 24  1  0
  5 25  1  0
  6 26  1  0
  6 27  1  0
  8 28  1  0
  8 29  1  0
  8 30  1  0
  9 31  1  0
 10 32  1  0
 10 33  1  0
 11 34  1  0
 11 35  1  0
 13 36  1  0
 13 37  1  0
 13 38  1  0
 14 39  1  0
 15 40  1  0
 15 41  1  0
 16 42  1  0
M  END

HEADER    PROTEIN                                 27-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-SEP-20         0                                  
HETATM    1  C   UNK     0    8670.4628671.438   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0    8671.7978670.670   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0    8673.1328671.438   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0    8674.4678670.670   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0    8675.7988671.438   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0    8677.1338670.670   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0    8678.4688671.438   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0    8679.7998670.670   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0    8675.7988672.978   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0    8669.1288670.670   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0    8667.7948671.438   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0    8666.4618670.670   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0    8665.1278671.438   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0    8663.7948670.670   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0    8665.1278672.978   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0    8670.4628672.978   0.000  0.00  0.00           C+0
CONECT    1    2   10   16                                                  
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6    9                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7                                                            
CONECT    9    5                                                            
CONECT   10    1   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13                                                            
CONECT   16    1                                                            
MASTER        0    0    0    0    0    0    0    0   16    0   30    0
END

COMPND    HMDB0004305
HETATM    1  C1  UNL     1      -5.643   1.008   0.252  1.00  0.00           C  
HETATM    2  C2  UNL     1      -4.839  -0.208   0.067  1.00  0.00           C  
HETATM    3  C3  UNL     1      -5.454  -1.533   0.360  1.00  0.00           C  
HETATM    4  C4  UNL     1      -3.574  -0.143  -0.357  1.00  0.00           C  
HETATM    5  C5  UNL     1      -2.998   1.179  -0.638  1.00  0.00           C  
HETATM    6  C6  UNL     1      -1.847   1.574   0.236  1.00  0.00           C  
HETATM    7  C7  UNL     1      -0.674   0.673   0.162  1.00  0.00           C  
HETATM    8  C8  UNL     1      -0.666  -0.751   0.587  1.00  0.00           C  
HETATM    9  C9  UNL     1       0.502   1.164  -0.280  1.00  0.00           C  
HETATM   10  C10 UNL     1       1.744   0.381  -0.405  1.00  0.00           C  
HETATM   11  C11 UNL     1       2.859   0.919   0.459  1.00  0.00           C  
HETATM   12  C12 UNL     1       4.089   0.123   0.316  1.00  0.00           C  
HETATM   13  C13 UNL     1       5.305   0.493   1.091  1.00  0.00           C  
HETATM   14  C14 UNL     1       4.119  -0.907  -0.488  1.00  0.00           C  
HETATM   15  C15 UNL     1       5.391  -1.683  -0.599  1.00  0.00           C  
HETATM   16  O1  UNL     1       5.114  -2.992  -0.205  1.00  0.00           O  
HETATM   17  H1  UNL     1      -5.091   1.775   0.870  1.00  0.00           H  
HETATM   18  H2  UNL     1      -6.609   0.765   0.729  1.00  0.00           H  
HETATM   19  H3  UNL     1      -5.826   1.530  -0.724  1.00  0.00           H  
HETATM   20  H4  UNL     1      -5.779  -2.028  -0.561  1.00  0.00           H  
HETATM   21  H5  UNL     1      -6.267  -1.427   1.116  1.00  0.00           H  
HETATM   22  H6  UNL     1      -4.676  -2.171   0.827  1.00  0.00           H  
HETATM   23  H7  UNL     1      -3.021  -1.049  -0.499  1.00  0.00           H  
HETATM   24  H8  UNL     1      -2.615   1.100  -1.709  1.00  0.00           H  
HETATM   25  H9  UNL     1      -3.777   1.981  -0.675  1.00  0.00           H  
HETATM   26  H10 UNL     1      -1.544   2.642   0.017  1.00  0.00           H  
HETATM   27  H11 UNL     1      -2.188   1.537   1.319  1.00  0.00           H  
HETATM   28  H12 UNL     1      -0.719  -1.467  -0.234  1.00  0.00           H  
HETATM   29  H13 UNL     1       0.231  -0.968   1.239  1.00  0.00           H  
HETATM   30  H14 UNL     1      -1.532  -0.953   1.275  1.00  0.00           H  
HETATM   31  H15 UNL     1       0.495   2.222  -0.556  1.00  0.00           H  
HETATM   32  H16 UNL     1       1.533  -0.686  -0.250  1.00  0.00           H  
HETATM   33  H17 UNL     1       2.098   0.453  -1.468  1.00  0.00           H  
HETATM   34  H18 UNL     1       2.498   0.951   1.510  1.00  0.00           H  
HETATM   35  H19 UNL     1       3.081   1.962   0.164  1.00  0.00           H  
HETATM   36  H20 UNL     1       5.129   1.449   1.656  1.00  0.00           H  
HETATM   37  H21 UNL     1       5.595  -0.272   1.812  1.00  0.00           H  
HETATM   38  H22 UNL     1       6.173   0.713   0.428  1.00  0.00           H  
HETATM   39  H23 UNL     1       3.295  -1.254  -1.090  1.00  0.00           H  
HETATM   40  H24 UNL     1       5.768  -1.643  -1.637  1.00  0.00           H  
HETATM   41  H25 UNL     1       6.172  -1.302   0.084  1.00  0.00           H  
HETATM   42  H26 UNL     1       4.148  -3.158  -0.111  1.00  0.00           H  
CONECT    1    2   17   18   19
CONECT    2    3    4    4
CONECT    3   20   21   22
CONECT    4    5   23
CONECT    5    6   24   25
CONECT    6    7   26   27
CONECT    7    8    9    9
CONECT    8   28   29   30
CONECT    9   10   31
CONECT   10   11   32   33
CONECT   11   12   34   35
CONECT   12   13   14   14
CONECT   13   36   37   38
CONECT   14   15   39
CONECT   15   16   40   41
CONECT   16   42
END

HMDB0004305
     RDKit          3D
Farnesol
 42 41  0  0  0  0  0  0  0  0999 V2000
   -5.6428    1.0080    0.2521 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8393   -0.2076    0.0669 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4540   -1.5328    0.3596 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5744   -0.1432   -0.3574 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9976    1.1788   -0.6377 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8468    1.5745    0.2363 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6742    0.6730    0.1625 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6656   -0.7510    0.5866 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5018    1.1642   -0.2796 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7443    0.3814   -0.4047 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8585    0.9188    0.4595 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0894    0.1230    0.3163 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3046    0.4930    1.0906 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1188   -0.9073   -0.4882 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3912   -1.6832   -0.5990 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1139   -2.9923   -0.2050 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0908    1.7753    0.8695 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6093    0.7650    0.7289 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8264    1.5298   -0.7244 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7789   -2.0279   -0.5611 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2675   -1.4268    1.1165 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6758   -2.1705    0.8267 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0210   -1.0486   -0.4992 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6153    1.1003   -1.7085 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7767    1.9815   -0.6755 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5439    2.6418    0.0171 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1875    1.5369    1.3186 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7192   -1.4666   -0.2344 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2306   -0.9680    1.2385 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5321   -0.9527    1.2750 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4951    2.2216   -0.5557 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5334   -0.6865   -0.2502 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0984    0.4531   -1.4681 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4979    0.9514    1.5101 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0809    1.9617    0.1642 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1294    1.4495    1.6560 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5947   -0.2723    1.8117 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1731    0.7126    0.4277 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2950   -1.2542   -1.0900 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7681   -1.6431   -1.6367 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1724   -1.3022    0.0839 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1477   -3.1583   -0.1110 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  2  3
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  7  9  2  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 12 14  2  0
 14 15  1  0
 15 16  1  0
  1 17  1  0
  1 18  1  0
  1 19  1  0
  3 20  1  0
  3 21  1  0
  3 22  1  0
  4 23  1  0
  5 24  1  0
  5 25  1  0
  6 26  1  0
  6 27  1  0
  8 28  1  0
  8 29  1  0
  8 30  1  0
  9 31  1  0
 10 32  1  0
 10 33  1  0
 11 34  1  0
 11 35  1  0
 13 36  1  0
 13 37  1  0
 13 38  1  0
 14 39  1  0
 15 40  1  0
 15 41  1  0
 16 42  1  0
M  END

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

Molecular Formula

C₁₅H₂₆O

Average Mass

222.3663

Monoisotopic Mass

222.198365454

IUPAC Name

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

Traditional Name

(E)-farnesol

CAS Registry Number

106-28-5

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 )

Functional Ontology

Not Available

Physical Properties

State

Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.059 g/L	ALOGPS
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	No	ChemAxon

Spectra

Not Available

Biological Properties

Cellular Locations

Extracellular
Membrane

Biospecimen Locations

Blood
Epidermis
Fibroblasts
Intestine
Kidney

Tissue Locations

Epidermis
Fibroblasts
Intestine
Kidney

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species
MMDBp0193761	Retinol dehydrogenase 16	Unknown	O75452	Homo sapiens

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Eukaryota/Fungi	Ascomycota	2	Human feces; Human saliva	Unknown
Bacteria/Eubacteria	Firmicutes	1	Human feces
Bacteria/Eubacteria	Actinobacteria	1	Human

Exposure Sources

Other Exposures

Source Type	Data Source	Reference
Cosmetics	U.S. Environmental Protection Agency	CompTox
Domestics	U.S. Environmental Protection Agency	CompTox
Food Additive	U.S. Food and Drug Administration	FDA

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference
Human Blood	Detected and Quantified	0.25	0.0	0.5	uM	Adult (>18 years old)	Both	Normal	HMDB	9324945
Human Epidermis	Detected but not Quantified					Not Specified	Not Specified	Normal	HMDB	34986597
Human Fibroblasts	Detected but not Quantified					Not Specified	Not Specified	Normal	HMDB	34986597
Human Intestine	Detected but not Quantified					Not Specified	Not Specified	Normal	HMDB	34986597
Human Kidney	Detected but not Quantified					Not Specified	Not Specified	Normal	HMDB	34986597

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

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

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. doi: 10.1016/0092-8674(95)90530-8. [PubMed:7774010 ]
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. doi: 10.1172/JCI118682. [PubMed:8636420 ]
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. doi: 10.1006/bbrc.1996.6014. [PubMed:9015362 ]
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. doi: 10.1074/jbc.272.14.9197. [PubMed:9083051 ]
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. doi: 10.1097/00041433-199810000-00007. [PubMed:9812197 ]
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. doi: 10.1074/jbc.275.15.11484. [PubMed:10753967 ]
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 ]
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. doi: 10.1097/00041433-200104000-00004. [PubMed:11264982 ]
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. doi: 10.1016/j.bbalip.2004.01.003. [PubMed:15158752 ]
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. doi: 10.1042/BJ20040997. [PubMed:15320866 ]
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. doi: 10.1016/j.cbi.2005.02.006. [PubMed:15840382 ]
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. doi: 10.1002/yea.1389. [PubMed:16845684 ]

Showing metabocard for (2-trans,6-trans)-Farnesol (MMDBc0032978)

MOL for #<Metabolite:0x00007f91fcb7a030>

3D MOL for #<Metabolite:0x00007f91fcb7a030>

3D SDF for #<Metabolite:0x00007f91fcb7a030>

3D-SDF for #<Metabolite:0x00007f91fcb7a030>

PDB for #<Metabolite:0x00007f91fcb7a030>

3D PDB for #<Metabolite:0x00007f91fcb7a030>

SMILES for #<Metabolite:0x00007f91fcb7a030>

INCHI for #<Metabolite:0x00007f91fcb7a030>

Structure for #<Metabolite:0x00007f91fcb7a030>

3D Structure for #<Metabolite:0x00007f91fcb7a030>