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Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References enzymes (9) Show 9 proteins XML

Record Information

Version

5.0

Status

Detected and Quantified

Creation Date

2005-11-16 15:48:42 UTC

Update Date

2022-03-07 02:49:07 UTC

HMDB ID

HMDB0000961

Secondary Accession Numbers

HMDB0004201
HMDB00961
HMDB04201

Metabolite Identification

Common Name

Farnesyl pyrophosphate

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


  Mrv1652306222023512D          

 26 25  0  0  0  0            999 V2000
   -5.3625   -3.5724    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3625   -2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8875   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7125   -2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2375   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1250   -2.8579    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8875   -2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6500   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9500   -2.8579    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4750   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    4.2868    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    3.9849    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    3.1599    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    1.7309    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    2.5559    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500    2.8579    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    3.5724    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    2.1434    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2375   -2.1434    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.7145    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  7  5  1  0  0  0  0
  8  5  1  0  0  0  0
  9  6  1  0  0  0  0
 10  6  1  0  0  0  0
 12 11  1  0  0  0  0
 13  1  1  0  0  0  0
 13  2  1  0  0  0  0
 13  7  2  0  0  0  0
 14  3  1  0  0  0  0
 14  8  1  0  0  0  0
 14  9  2  0  0  0  0
 15  4  1  0  0  0  0
 15 10  1  0  0  0  0
 15 11  2  0  0  0  0
 21 12  1  0  0  0  0
 23 16  1  0  0  0  0
 23 17  1  0  0  0  0
 23 18  2  0  0  0  0
 23 22  1  0  0  0  0
 24 19  1  0  0  0  0
 24 20  2  0  0  0  0
 24 21  1  0  0  0  0
 24 22  1  0  0  0  0
 25  9  1  0  0  0  0
 26 11  1  0  0  0  0
M  END

HMDB0000961
     RDKit          3D
Farnesyl pyrophosphate
 52 51  0  0  0  0  0  0  0  0999 V2000
    6.4230    0.1068    2.1179 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8021    0.6763    0.8043 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.2477    0.9937    0.5106 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9122    0.9278   -0.1512 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4791    0.6271    0.1045 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0071   -0.3726   -0.9087 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5547   -0.7155   -0.6961 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8734   -1.6898   -1.5874 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8503   -0.1638    0.2818 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4205   -0.5451    0.4377 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3990    0.7068    0.2875 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8424    0.5019    0.4157 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5093   -0.0389    1.6139 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6084    0.8303   -0.6323 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0843    0.6507   -0.5778 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5011   -0.2336   -1.5922 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1560   -0.4622   -1.5647 P   0  0  0  0  0  5  0  0  0  0  0  0
   -6.5541   -1.5528   -0.5842 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7524   -0.9186   -3.0826 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9556    0.9883   -1.1511 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.9336    0.7780    0.2040 P   0  0  0  0  0  5  0  0  0  0  0  0
   -7.4179   -0.2590    1.1490 O   0  0  0  0  0  0  0  0  0  0  0  0
   -8.0774    2.2827    1.0034 O   0  0  0  0  0  0  0  0  0  0  0  0
   -9.4855    0.2767   -0.3086 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.9058    0.9026    2.7188 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7913   -0.8053    2.0244 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.3494   -0.2290    2.6404 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.4145    1.0482   -0.5717 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.9067    0.2229    0.9256 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.4674    1.9452    1.0444 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1898    1.3413   -1.1040 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3054    0.2569    1.1163 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9265    1.5870   -0.0927 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5674   -1.3165   -0.8025 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1908   -0.0094   -1.9398 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5095   -2.5829   -1.0295 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0402   -1.2015   -2.1644 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6081   -2.0394   -2.3412 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2926    0.5463    0.9550 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1125   -1.2625   -0.3500 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2741   -1.0505    1.4015 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1224    1.1978   -0.6626 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0937    1.4305    1.0934 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7276   -0.2485    2.4004 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2070    0.6783    2.0885 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0561   -0.9909    1.4217 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1606    1.2385   -1.5515 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5466    1.6403   -0.7923 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3659    0.2330    0.3944 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0256   -0.7905   -3.7414 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.8420    3.0130    0.3519 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.9975   -0.0772    0.4737 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
 16 17  1  0
 17 18  2  0
 17 19  1  0
 17 20  1  0
 20 21  1  0
 21 22  2  0
 21 23  1  0
 21 24  1  0
  1 25  1  0
  1 26  1  0
  1 27  1  0
  3 28  1  0
  3 29  1  0
  3 30  1  0
  4 31  1  0
  5 32  1  0
  5 33  1  0
  6 34  1  0
  6 35  1  0
  8 36  1  0
  8 37  1  0
  8 38  1  0
  9 39  1  0
 10 40  1  0
 10 41  1  0
 11 42  1  0
 11 43  1  0
 13 44  1  0
 13 45  1  0
 13 46  1  0
 14 47  1  0
 15 48  1  0
 15 49  1  0
 19 50  1  0
 23 51  1  0
 24 52  1  0
M  END


  Mrv1652306222023512D          

 26 25  0  0  0  0            999 V2000
   -5.3625   -3.5724    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3625   -2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8875   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7125   -2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2375   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1250   -2.8579    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8875   -2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6500   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9500   -2.8579    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4750   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    4.2868    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    3.9849    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    3.1599    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    1.7309    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    2.5559    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500    2.8579    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    3.5724    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    2.1434    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2375   -2.1434    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.7145    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  7  5  1  0  0  0  0
  8  5  1  0  0  0  0
  9  6  1  0  0  0  0
 10  6  1  0  0  0  0
 12 11  1  0  0  0  0
 13  1  1  0  0  0  0
 13  2  1  0  0  0  0
 13  7  2  0  0  0  0
 14  3  1  0  0  0  0
 14  8  1  0  0  0  0
 14  9  2  0  0  0  0
 15  4  1  0  0  0  0
 15 10  1  0  0  0  0
 15 11  2  0  0  0  0
 21 12  1  0  0  0  0
 23 16  1  0  0  0  0
 23 17  1  0  0  0  0
 23 18  2  0  0  0  0
 23 22  1  0  0  0  0
 24 19  1  0  0  0  0
 24 20  2  0  0  0  0
 24 21  1  0  0  0  0
 24 22  1  0  0  0  0
 25  9  1  0  0  0  0
 26 11  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0000961

> <DATABASE_NAME>
hmdb

> <SMILES>
[H]\C(CC\C(C)=C(/[H])COP(O)(=O)OP(O)(O)=O)=C(\C)CCC=C(C)C

> <INCHI_IDENTIFIER>
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+

> <INCHI_KEY>
VWFJDQUYCIWHTN-YFVJMOTDSA-N

> <FORMULA>
C15H28O7P2

> <MOLECULAR_WEIGHT>
382.33

> <EXACT_MASS>
382.131027238

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
52

> <JCHEM_AVERAGE_POLARIZABILITY>
37.94192720134606

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
{[hydroxy({[(2E,6E)-3,7,11-trimethyldodeca-2,6,10-trien-1-yl]oxy})phosphoryl]oxy}phosphonic acid

> <ALOGPS_LOGP>
2.40

> <JCHEM_LOGP>
3.6167330606666663

> <ALOGPS_LOGS>
-3.68

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
3.2043406094078315

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.7672186885241006

> <JCHEM_POLAR_SURFACE_AREA>
113.28999999999999

> <JCHEM_REFRACTIVITY>
96.73049999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
11

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.07e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
farnesyl diphosphate

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0000961
     RDKit          3D
Farnesyl pyrophosphate
 52 51  0  0  0  0  0  0  0  0999 V2000
    6.4230    0.1068    2.1179 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8021    0.6763    0.8043 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.2477    0.9937    0.5106 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9122    0.9278   -0.1512 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4791    0.6271    0.1045 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0071   -0.3726   -0.9087 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5547   -0.7155   -0.6961 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8734   -1.6898   -1.5874 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8503   -0.1638    0.2818 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4205   -0.5451    0.4377 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3990    0.7068    0.2875 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8424    0.5019    0.4157 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5093   -0.0389    1.6139 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6084    0.8303   -0.6323 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0843    0.6507   -0.5778 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5011   -0.2336   -1.5922 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1560   -0.4622   -1.5647 P   0  0  0  0  0  5  0  0  0  0  0  0
   -6.5541   -1.5528   -0.5842 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7524   -0.9186   -3.0826 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9556    0.9883   -1.1511 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.9336    0.7780    0.2040 P   0  0  0  0  0  5  0  0  0  0  0  0
   -7.4179   -0.2590    1.1490 O   0  0  0  0  0  0  0  0  0  0  0  0
   -8.0774    2.2827    1.0034 O   0  0  0  0  0  0  0  0  0  0  0  0
   -9.4855    0.2767   -0.3086 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.9058    0.9026    2.7188 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7913   -0.8053    2.0244 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.3494   -0.2290    2.6404 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.4145    1.0482   -0.5717 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.9067    0.2229    0.9256 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.4674    1.9452    1.0444 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1898    1.3413   -1.1040 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3054    0.2569    1.1163 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9265    1.5870   -0.0927 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5674   -1.3165   -0.8025 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1908   -0.0094   -1.9398 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5095   -2.5829   -1.0295 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0402   -1.2015   -2.1644 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6081   -2.0394   -2.3412 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2926    0.5463    0.9550 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1125   -1.2625   -0.3500 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2741   -1.0505    1.4015 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1224    1.1978   -0.6626 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0937    1.4305    1.0934 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7276   -0.2485    2.4004 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2070    0.6783    2.0885 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0561   -0.9909    1.4217 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1606    1.2385   -1.5515 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5466    1.6403   -0.7923 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3659    0.2330    0.3944 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0256   -0.7905   -3.7414 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.8420    3.0130    0.3519 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.9975   -0.0772    0.4737 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
 16 17  1  0
 17 18  2  0
 17 19  1  0
 17 20  1  0
 20 21  1  0
 21 22  2  0
 21 23  1  0
 21 24  1  0
  1 25  1  0
  1 26  1  0
  1 27  1  0
  3 28  1  0
  3 29  1  0
  3 30  1  0
  4 31  1  0
  5 32  1  0
  5 33  1  0
  6 34  1  0
  6 35  1  0
  8 36  1  0
  8 37  1  0
  8 38  1  0
  9 39  1  0
 10 40  1  0
 10 41  1  0
 11 42  1  0
 11 43  1  0
 13 44  1  0
 13 45  1  0
 13 46  1  0
 14 47  1  0
 15 48  1  0
 15 49  1  0
 19 50  1  0
 23 51  1  0
 24 52  1  0
M  END

HEADER    PROTEIN                                 22-JUN-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   22-JUN-20         0                                  
HETATM    1  C   UNK     0     -10.010  -6.668   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0     -10.010  -4.001   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -5.390  -1.334   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.770   1.334   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -6.930  -4.001   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -2.310  -1.334   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -7.700  -5.335   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -5.390  -4.001   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -3.080  -2.667   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -0.770  -1.334   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       2.310   1.334   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -9.240  -5.335   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -4.620  -2.667   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       1.540   8.002   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       3.644   7.438   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       0.976   5.898   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       3.644   3.231   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       0.976   4.771   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0       1.540   2.667   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0       3.080   5.335   0.000  0.00  0.00           O+0
HETATM   23  P   UNK     0       2.310   6.668   0.000  0.00  0.00           P+0
HETATM   24  P   UNK     0       2.310   4.001   0.000  0.00  0.00           P+0
HETATM   25  H   UNK     0      -2.310  -4.001   0.000  0.00  0.00           H+0
HETATM   26  H   UNK     0       2.310  -1.334   0.000  0.00  0.00           H+0
CONECT    1   13                                                            
CONECT    2   13                                                            
CONECT    3   14                                                            
CONECT    4   15                                                            
CONECT    5    7    8                                                       
CONECT    6    9   10                                                       
CONECT    7    5   13                                                       
CONECT    8    5   14                                                       
CONECT    9    6   14   25                                                  
CONECT   10    6   15                                                       
CONECT   11   12   15   26                                                  
CONECT   12   11   21                                                       
CONECT   13    1    2    7                                                  
CONECT   14    3    8    9                                                  
CONECT   15    4   10   11                                                  
CONECT   16   23                                                            
CONECT   17   23                                                            
CONECT   18   23                                                            
CONECT   19   24                                                            
CONECT   20   24                                                            
CONECT   21   12   24                                                       
CONECT   22   23   24                                                       
CONECT   23   16   17   18   22                                             
CONECT   24   19   20   21   22                                             
CONECT   25    9                                                            
CONECT   26   11                                                            
MASTER        0    0    0    0    0    0    0    0   26    0   50    0
END

COMPND    HMDB0000961
HETATM    1  C1  UNL     1       6.423   0.107   2.118  1.00  0.00           C  
HETATM    2  C2  UNL     1       6.802   0.676   0.804  1.00  0.00           C  
HETATM    3  C3  UNL     1       8.248   0.994   0.511  1.00  0.00           C  
HETATM    4  C4  UNL     1       5.912   0.928  -0.151  1.00  0.00           C  
HETATM    5  C5  UNL     1       4.479   0.627   0.104  1.00  0.00           C  
HETATM    6  C6  UNL     1       4.007  -0.373  -0.909  1.00  0.00           C  
HETATM    7  C7  UNL     1       2.555  -0.716  -0.696  1.00  0.00           C  
HETATM    8  C8  UNL     1       1.873  -1.690  -1.587  1.00  0.00           C  
HETATM    9  C9  UNL     1       1.850  -0.164   0.282  1.00  0.00           C  
HETATM   10  C10 UNL     1       0.420  -0.545   0.438  1.00  0.00           C  
HETATM   11  C11 UNL     1      -0.399   0.707   0.288  1.00  0.00           C  
HETATM   12  C12 UNL     1      -1.842   0.502   0.416  1.00  0.00           C  
HETATM   13  C13 UNL     1      -2.509  -0.039   1.614  1.00  0.00           C  
HETATM   14  C14 UNL     1      -2.608   0.830  -0.632  1.00  0.00           C  
HETATM   15  C15 UNL     1      -4.084   0.651  -0.578  1.00  0.00           C  
HETATM   16  O1  UNL     1      -4.501  -0.234  -1.592  1.00  0.00           O  
HETATM   17  P1  UNL     1      -6.156  -0.462  -1.565  1.00  0.00           P  
HETATM   18  O2  UNL     1      -6.554  -1.553  -0.584  1.00  0.00           O  
HETATM   19  O3  UNL     1      -6.752  -0.919  -3.083  1.00  0.00           O  
HETATM   20  O4  UNL     1      -6.956   0.988  -1.151  1.00  0.00           O  
HETATM   21  P2  UNL     1      -7.934   0.778   0.204  1.00  0.00           P  
HETATM   22  O5  UNL     1      -7.418  -0.259   1.149  1.00  0.00           O  
HETATM   23  O6  UNL     1      -8.077   2.283   1.003  1.00  0.00           O  
HETATM   24  O7  UNL     1      -9.485   0.277  -0.309  1.00  0.00           O  
HETATM   25  H1  UNL     1       5.906   0.903   2.719  1.00  0.00           H  
HETATM   26  H2  UNL     1       5.791  -0.805   2.024  1.00  0.00           H  
HETATM   27  H3  UNL     1       7.349  -0.229   2.640  1.00  0.00           H  
HETATM   28  H4  UNL     1       8.414   1.048  -0.572  1.00  0.00           H  
HETATM   29  H5  UNL     1       8.907   0.223   0.926  1.00  0.00           H  
HETATM   30  H6  UNL     1       8.467   1.945   1.044  1.00  0.00           H  
HETATM   31  H7  UNL     1       6.190   1.341  -1.104  1.00  0.00           H  
HETATM   32  H8  UNL     1       4.305   0.257   1.116  1.00  0.00           H  
HETATM   33  H9  UNL     1       3.926   1.587  -0.093  1.00  0.00           H  
HETATM   34  H10 UNL     1       4.567  -1.316  -0.803  1.00  0.00           H  
HETATM   35  H11 UNL     1       4.191  -0.009  -1.940  1.00  0.00           H  
HETATM   36  H12 UNL     1       1.510  -2.583  -1.029  1.00  0.00           H  
HETATM   37  H13 UNL     1       1.040  -1.201  -2.164  1.00  0.00           H  
HETATM   38  H14 UNL     1       2.608  -2.039  -2.341  1.00  0.00           H  
HETATM   39  H15 UNL     1       2.293   0.546   0.955  1.00  0.00           H  
HETATM   40  H16 UNL     1       0.113  -1.263  -0.350  1.00  0.00           H  
HETATM   41  H17 UNL     1       0.274  -1.050   1.401  1.00  0.00           H  
HETATM   42  H18 UNL     1      -0.122   1.198  -0.663  1.00  0.00           H  
HETATM   43  H19 UNL     1      -0.094   1.430   1.093  1.00  0.00           H  
HETATM   44  H20 UNL     1      -1.728  -0.249   2.400  1.00  0.00           H  
HETATM   45  H21 UNL     1      -3.207   0.678   2.088  1.00  0.00           H  
HETATM   46  H22 UNL     1      -3.056  -0.991   1.422  1.00  0.00           H  
HETATM   47  H23 UNL     1      -2.161   1.238  -1.552  1.00  0.00           H  
HETATM   48  H24 UNL     1      -4.547   1.640  -0.792  1.00  0.00           H  
HETATM   49  H25 UNL     1      -4.366   0.233   0.394  1.00  0.00           H  
HETATM   50  H26 UNL     1      -6.026  -0.790  -3.741  1.00  0.00           H  
HETATM   51  H27 UNL     1      -7.842   3.013   0.352  1.00  0.00           H  
HETATM   52  H28 UNL     1      -9.998  -0.077   0.474  1.00  0.00           H  
CONECT    1    2   25   26   27
CONECT    2    3    4    4
CONECT    3   28   29   30
CONECT    4    5   31
CONECT    5    6   32   33
CONECT    6    7   34   35
CONECT    7    8    9    9
CONECT    8   36   37   38
CONECT    9   10   39
CONECT   10   11   40   41
CONECT   11   12   42   43
CONECT   12   13   14   14
CONECT   13   44   45   46
CONECT   14   15   47
CONECT   15   16   48   49
CONECT   16   17
CONECT   17   18   18   19   20
CONECT   19   50
CONECT   20   21
CONECT   21   22   22   23   24
CONECT   23   51
CONECT   24   52
END

HMDB0000961
     RDKit          3D
Farnesyl pyrophosphate
 52 51  0  0  0  0  0  0  0  0999 V2000
    6.4230    0.1068    2.1179 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8021    0.6763    0.8043 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.2477    0.9937    0.5106 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9122    0.9278   -0.1512 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4791    0.6271    0.1045 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0071   -0.3726   -0.9087 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5547   -0.7155   -0.6961 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8734   -1.6898   -1.5874 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8503   -0.1638    0.2818 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4205   -0.5451    0.4377 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3990    0.7068    0.2875 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8424    0.5019    0.4157 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5093   -0.0389    1.6139 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6084    0.8303   -0.6323 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0843    0.6507   -0.5778 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5011   -0.2336   -1.5922 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1560   -0.4622   -1.5647 P   0  0  0  0  0  5  0  0  0  0  0  0
   -6.5541   -1.5528   -0.5842 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7524   -0.9186   -3.0826 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9556    0.9883   -1.1511 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.9336    0.7780    0.2040 P   0  0  0  0  0  5  0  0  0  0  0  0
   -7.4179   -0.2590    1.1490 O   0  0  0  0  0  0  0  0  0  0  0  0
   -8.0774    2.2827    1.0034 O   0  0  0  0  0  0  0  0  0  0  0  0
   -9.4855    0.2767   -0.3086 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.9058    0.9026    2.7188 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7913   -0.8053    2.0244 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.3494   -0.2290    2.6404 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.4145    1.0482   -0.5717 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.9067    0.2229    0.9256 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.4674    1.9452    1.0444 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1898    1.3413   -1.1040 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3054    0.2569    1.1163 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9265    1.5870   -0.0927 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5674   -1.3165   -0.8025 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1908   -0.0094   -1.9398 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5095   -2.5829   -1.0295 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0402   -1.2015   -2.1644 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6081   -2.0394   -2.3412 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2926    0.5463    0.9550 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1125   -1.2625   -0.3500 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2741   -1.0505    1.4015 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1224    1.1978   -0.6626 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0937    1.4305    1.0934 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7276   -0.2485    2.4004 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2070    0.6783    2.0885 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0561   -0.9909    1.4217 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1606    1.2385   -1.5515 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5466    1.6403   -0.7923 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3659    0.2330    0.3944 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0256   -0.7905   -3.7414 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.8420    3.0130    0.3519 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.9975   -0.0772    0.4737 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
 16 17  1  0
 17 18  2  0
 17 19  1  0
 17 20  1  0
 20 21  1  0
 21 22  2  0
 21 23  1  0
 21 24  1  0
  1 25  1  0
  1 26  1  0
  1 27  1  0
  3 28  1  0
  3 29  1  0
  3 30  1  0
  4 31  1  0
  5 32  1  0
  5 33  1  0
  6 34  1  0
  6 35  1  0
  8 36  1  0
  8 37  1  0
  8 38  1  0
  9 39  1  0
 10 40  1  0
 10 41  1  0
 11 42  1  0
 11 43  1  0
 13 44  1  0
 13 45  1  0
 13 46  1  0
 14 47  1  0
 15 48  1  0
 15 49  1  0
 19 50  1  0
 23 51  1  0
 24 52  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
(2E,6E)-Farnesol diphosphate	ChEBI
(2E,6E)-Farnesyl diphosphate	ChEBI
(2E,6E)-Farnesyl pyrophosphate	ChEBI
(all-e)-Farnesyl diphosphate	ChEBI
(e,e)-Farnesyl pyrophosphate	ChEBI
2-trans,6-trans-Farnesyl pyrophosphate	ChEBI
all-trans-Farnesyl pyrophosphate	ChEBI
Farnesyl diphosphate	ChEBI
trans,trans-Farnesyl diphosphate	ChEBI
trans-trans-Farnesyl diphosphate	ChEBI
2-trans,6-trans-Farnesyl diphosphate	Kegg
(2E,6E)-Farnesol diphosphoric acid	Generator
(2E,6E)-Farnesyl diphosphoric acid	Generator
(2E,6E)-Farnesyl pyrophosphoric acid	Generator
(all-e)-Farnesyl diphosphoric acid	Generator
(e,e)-Farnesyl pyrophosphoric acid	Generator
2-trans,6-trans-Farnesyl pyrophosphoric acid	Generator
all-trans-Farnesyl pyrophosphoric acid	Generator
Farnesyl diphosphoric acid	Generator
trans,trans-Farnesyl diphosphoric acid	Generator
trans-trans-Farnesyl diphosphoric acid	Generator
2-trans,6-trans-Farnesyl diphosphoric acid	Generator
Farnesyl pyrophosphoric acid	Generator
(e,e)-Farnesyl diphosphate	HMDB
Farnesyl-PP	HMDB
trans-Farnesyl pyrophosphate	HMDB
trans-trans-Farnesyl pyrophosphate	HMDB
Farnesyl pyrophosphate, (e,e)-isomer	HMDB
Farnesyl pyrophosphate, (e,Z)-isomer	HMDB
Farnesyl pyrophosphate, (Z,e)-isomer	HMDB
Farnesyl pyrophosphate, (Z,Z)-isomer	HMDB
Farnesylpyrophosphate	HMDB

Chemical Formula

C₁₅H₂₈O₇P₂

Average Molecular Weight

382.33

Monoisotopic Molecular Weight

382.131027238

IUPAC Name

{[hydroxy({[(2E,6E)-3,7,11-trimethyldodeca-2,6,10-trien-1-yl]oxy})phosphoryl]oxy}phosphonic acid

Traditional Name

farnesyl diphosphate

CAS Registry Number

13058-04-3

SMILES

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

InChI Identifier

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+

InChI Key

VWFJDQUYCIWHTN-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
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 )

Ontology

Not Available

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Experimental Collision Cross Sections

Adduct Type	Data Source	CCS Value (Å²)	Reference
[M-H]-	MetCCS_train_neg	183.852	30932474
[M-H]-	Not Available	183.852	http://allccs.zhulab.cn/database/detail?ID=AllCCS00000232

Predicted Molecular 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	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DarkChem	[M+H]+	192.591	31661259
DarkChem	[M-H]-	185.192	31661259
AllCCS	[M+H]+	195.566	32859911
AllCCS	[M-H]-	187.85	32859911
DeepCCS	[M+H]+	168.21	30932474
DeepCCS	[M-H]-	164.757	30932474
DeepCCS	[M-2H]-	200.258	30932474
DeepCCS	[M+Na]+	176.551	30932474
AllCCS	[M+H]+	195.6	32859911
AllCCS	[M+H-H2O]+	193.0	32859911
AllCCS	[M+NH4]+	197.9	32859911
AllCCS	[M+Na]+	198.6	32859911
AllCCS	[M-H]-	187.8	32859911
AllCCS	[M+Na-2H]-	189.1	32859911
AllCCS	[M+HCOO]-	190.6	32859911

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022. Predicted by Afia on May 17, 2022.	8.14 minutes	32390414
Predicted by Siyang on May 30, 2022	11.2194 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	2.37 minutes	32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid	214.9 seconds	40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	2108.1 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	182.3 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	139.3 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	167.5 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	83.9 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	472.4 seconds	40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid	599.7 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	114.0 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	867.2 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	527.0 seconds	40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid	538.9 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	355.7 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	279.6 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	471.8 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	208.5 seconds	40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water	33.3 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Farnesyl pyrophosphate	CC(C)=CCC\C(C)=C\CC\C(C)=C\COP(O)(=O)OP(O)(O)=O	4064.9	Standard polar	33892256
Farnesyl pyrophosphate	CC(C)=CCC\C(C)=C\CC\C(C)=C\COP(O)(=O)OP(O)(O)=O	2391.3	Standard non polar	33892256
Farnesyl pyrophosphate	CC(C)=CCC\C(C)=C\CC\C(C)=C\COP(O)(=O)OP(O)(O)=O	2820.4	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Farnesyl pyrophosphate,1TMS,isomer #1	CC(C)=CCC/C(C)=C/CC/C(C)=C/COP(=O)(O[Si](C)(C)C)OP(=O)(O)O	2733.9	Semi standard non polar	33892256
Farnesyl pyrophosphate,1TMS,isomer #1	CC(C)=CCC/C(C)=C/CC/C(C)=C/COP(=O)(O[Si](C)(C)C)OP(=O)(O)O	2329.2	Standard non polar	33892256
Farnesyl pyrophosphate,1TMS,isomer #1	CC(C)=CCC/C(C)=C/CC/C(C)=C/COP(=O)(O[Si](C)(C)C)OP(=O)(O)O	3598.0	Standard polar	33892256
Farnesyl pyrophosphate,1TMS,isomer #2	CC(C)=CCC/C(C)=C/CC/C(C)=C/COP(=O)(O)OP(=O)(O)O[Si](C)(C)C	2724.8	Semi standard non polar	33892256
Farnesyl pyrophosphate,1TMS,isomer #2	CC(C)=CCC/C(C)=C/CC/C(C)=C/COP(=O)(O)OP(=O)(O)O[Si](C)(C)C	2332.2	Standard non polar	33892256
Farnesyl pyrophosphate,1TMS,isomer #2	CC(C)=CCC/C(C)=C/CC/C(C)=C/COP(=O)(O)OP(=O)(O)O[Si](C)(C)C	3630.0	Standard polar	33892256
Farnesyl pyrophosphate,2TMS,isomer #1	CC(C)=CCC/C(C)=C/CC/C(C)=C/COP(=O)(O[Si](C)(C)C)OP(=O)(O)O[Si](C)(C)C	2738.4	Semi standard non polar	33892256
Farnesyl pyrophosphate,2TMS,isomer #1	CC(C)=CCC/C(C)=C/CC/C(C)=C/COP(=O)(O[Si](C)(C)C)OP(=O)(O)O[Si](C)(C)C	2395.4	Standard non polar	33892256
Farnesyl pyrophosphate,2TMS,isomer #1	CC(C)=CCC/C(C)=C/CC/C(C)=C/COP(=O)(O[Si](C)(C)C)OP(=O)(O)O[Si](C)(C)C	3235.9	Standard polar	33892256
Farnesyl pyrophosphate,2TMS,isomer #2	CC(C)=CCC/C(C)=C/CC/C(C)=C/COP(=O)(O)OP(=O)(O[Si](C)(C)C)O[Si](C)(C)C	2739.1	Semi standard non polar	33892256
Farnesyl pyrophosphate,2TMS,isomer #2	CC(C)=CCC/C(C)=C/CC/C(C)=C/COP(=O)(O)OP(=O)(O[Si](C)(C)C)O[Si](C)(C)C	2379.3	Standard non polar	33892256
Farnesyl pyrophosphate,2TMS,isomer #2	CC(C)=CCC/C(C)=C/CC/C(C)=C/COP(=O)(O)OP(=O)(O[Si](C)(C)C)O[Si](C)(C)C	3235.6	Standard polar	33892256
Farnesyl pyrophosphate,3TMS,isomer #1	CC(C)=CCC/C(C)=C/CC/C(C)=C/COP(=O)(O[Si](C)(C)C)OP(=O)(O[Si](C)(C)C)O[Si](C)(C)C	2746.2	Semi standard non polar	33892256
Farnesyl pyrophosphate,3TMS,isomer #1	CC(C)=CCC/C(C)=C/CC/C(C)=C/COP(=O)(O[Si](C)(C)C)OP(=O)(O[Si](C)(C)C)O[Si](C)(C)C	2465.7	Standard non polar	33892256
Farnesyl pyrophosphate,3TMS,isomer #1	CC(C)=CCC/C(C)=C/CC/C(C)=C/COP(=O)(O[Si](C)(C)C)OP(=O)(O[Si](C)(C)C)O[Si](C)(C)C	2863.8	Standard polar	33892256
Farnesyl pyrophosphate,1TBDMS,isomer #1	CC(C)=CCC/C(C)=C/CC/C(C)=C/COP(=O)(O[Si](C)(C)C(C)(C)C)OP(=O)(O)O	2952.4	Semi standard non polar	33892256
Farnesyl pyrophosphate,1TBDMS,isomer #1	CC(C)=CCC/C(C)=C/CC/C(C)=C/COP(=O)(O[Si](C)(C)C(C)(C)C)OP(=O)(O)O	2486.4	Standard non polar	33892256
Farnesyl pyrophosphate,1TBDMS,isomer #1	CC(C)=CCC/C(C)=C/CC/C(C)=C/COP(=O)(O[Si](C)(C)C(C)(C)C)OP(=O)(O)O	3719.4	Standard polar	33892256
Farnesyl pyrophosphate,1TBDMS,isomer #2	CC(C)=CCC/C(C)=C/CC/C(C)=C/COP(=O)(O)OP(=O)(O)O[Si](C)(C)C(C)(C)C	2941.7	Semi standard non polar	33892256
Farnesyl pyrophosphate,1TBDMS,isomer #2	CC(C)=CCC/C(C)=C/CC/C(C)=C/COP(=O)(O)OP(=O)(O)O[Si](C)(C)C(C)(C)C	2506.6	Standard non polar	33892256
Farnesyl pyrophosphate,1TBDMS,isomer #2	CC(C)=CCC/C(C)=C/CC/C(C)=C/COP(=O)(O)OP(=O)(O)O[Si](C)(C)C(C)(C)C	3747.7	Standard polar	33892256
Farnesyl pyrophosphate,2TBDMS,isomer #1	CC(C)=CCC/C(C)=C/CC/C(C)=C/COP(=O)(O[Si](C)(C)C(C)(C)C)OP(=O)(O)O[Si](C)(C)C(C)(C)C	3128.2	Semi standard non polar	33892256
Farnesyl pyrophosphate,2TBDMS,isomer #1	CC(C)=CCC/C(C)=C/CC/C(C)=C/COP(=O)(O[Si](C)(C)C(C)(C)C)OP(=O)(O)O[Si](C)(C)C(C)(C)C	2709.6	Standard non polar	33892256
Farnesyl pyrophosphate,2TBDMS,isomer #1	CC(C)=CCC/C(C)=C/CC/C(C)=C/COP(=O)(O[Si](C)(C)C(C)(C)C)OP(=O)(O)O[Si](C)(C)C(C)(C)C	3378.4	Standard polar	33892256
Farnesyl pyrophosphate,2TBDMS,isomer #2	CC(C)=CCC/C(C)=C/CC/C(C)=C/COP(=O)(O)OP(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C	3138.3	Semi standard non polar	33892256
Farnesyl pyrophosphate,2TBDMS,isomer #2	CC(C)=CCC/C(C)=C/CC/C(C)=C/COP(=O)(O)OP(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C	2671.2	Standard non polar	33892256
Farnesyl pyrophosphate,2TBDMS,isomer #2	CC(C)=CCC/C(C)=C/CC/C(C)=C/COP(=O)(O)OP(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C	3398.4	Standard polar	33892256
Farnesyl pyrophosphate,3TBDMS,isomer #1	CC(C)=CCC/C(C)=C/CC/C(C)=C/COP(=O)(O[Si](C)(C)C(C)(C)C)OP(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C	3299.3	Semi standard non polar	33892256
Farnesyl pyrophosphate,3TBDMS,isomer #1	CC(C)=CCC/C(C)=C/CC/C(C)=C/COP(=O)(O[Si](C)(C)C(C)(C)C)OP(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C	2890.4	Standard non polar	33892256
Farnesyl pyrophosphate,3TBDMS,isomer #1	CC(C)=CCC/C(C)=C/CC/C(C)=C/COP(=O)(O[Si](C)(C)C(C)(C)C)OP(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C	3094.2	Standard polar	33892256

Spectra

Biological Properties

Cellular Locations

Cytoplasm
Extracellular
Membrane
Endoplasmic reticulum
Peroxisome

Biospecimen Locations

Blood

Tissue Locations

Neuron
Testis

Pathways

Name	SMPDB/PathBank	KEGG
Porphyrin Metabolism
Steroid Biosynthesis
Smith-Lemli-Opitz Syndrome (SLOS)		Not Available
CHILD Syndrome		Not Available
Desmosterolosis		Not Available

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected and Quantified	0.0086 (0.0000-0.0170) uM	Adult (>18 years old)	Not Specified	Normal	9324945	details

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

DB07780

Phenol Explorer Compound ID

Not Available

FooDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

BiGG ID

Wikipedia Link

Farnesyl pyrophosphate

METLIN ID

403

PubChem Compound

445713

PDB ID

Not Available

ChEBI ID

17407

Food Biomarker Ontology

Not Available

VMH ID

FRDP

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Castillo-Bocanegra, Rafael. Synthesis and biological activity of farnesyl pyrophosphate analogs. University of California, San Francisco., 1977 - Farnesol p.364

Material Safety Data Sheet (MSDS)

Download (PDF)

General References

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 ]
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 ]
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 ]
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 ]
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 ]
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 ]
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 ]

Enzymes

Enzyme Details

1. Squalene synthase

General function:: Involved in transferase activity
Specific function:: Not Available
Gene Name:: FDFT1
Uniprot ID:: P37268
Molecular weight:: 48114.87

Reactions

Farnesyl pyrophosphate + NAD(P)H → Squalene + Pyrophosphate + NAD(P)(+)	details
Farnesyl pyrophosphate → Pyrophosphate + Presqualene diphosphate	details
Farnesyl pyrophosphate + NADPH + Hydrogen Ion → Squalene + Pyrophosphate + NADP	details

Enzyme Details

2. Geranylgeranyl pyrophosphate synthase

General function:: Involved in isoprenoid biosynthetic process
Specific function:: Catalyzes the trans-addition of the three molecules of IPP onto DMAPP to form geranylgeranyl pyrophosphate, an important precursor of carotenoids and geranylated proteins.
Gene Name:: GGPS1
Uniprot ID:: O95749
Molecular weight:: 34870.625

Reactions

Geranyl-PP + Isopentenyl pyrophosphate → Pyrophosphate + Farnesyl pyrophosphate	details
Farnesyl pyrophosphate + Isopentenyl pyrophosphate → Pyrophosphate + Geranylgeranyl-PP	details

Enzyme Details

3. Farnesyl pyrophosphate synthase

General function:: Involved in isoprenoid biosynthetic process
Specific function:: Key enzyme in isoprenoid biosynthesis which catalyzes the formation of farnesyl diphosphate (FPP), a precursor for several classes of essential metabolites including sterols, dolichols, carotenoids, and ubiquinones. FPP also serves as substrate for protein farnesylation and geranylgeranylation. 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:: FDPS
Uniprot ID:: P14324
Molecular weight:: 48275.03

Reactions

Geranyl-PP + Isopentenyl pyrophosphate → Pyrophosphate + Farnesyl pyrophosphate	details

Enzyme Details

4. Protoheme IX farnesyltransferase, mitochondrial

General function:: Involved in protoheme IX farnesyltransferase activity
Specific function:: Converts protoheme IX and farnesyl diphosphate to heme O (By similarity).
Gene Name:: COX10
Uniprot ID:: Q12887
Molecular weight:: Not Available

Reactions

Heme + Water + Farnesyl pyrophosphate → Heme O + Pyrophosphate	details

Enzyme Details

5. 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. Through RAC1 prenylation and activation may positively regulate neuromuscular junction development downstream of MUSK (By similarity).
Gene Name:: FNTA
Uniprot ID:: P49354
Molecular weight:: 44408.32

Reactions

Farnesyl pyrophosphate + protein-cysteine → S-farnesyl protein + Pyrophosphate	details
Farnesyl pyrophosphate + Protein-cysteine → S-Farnesyl protein + Pyrophosphate	details

Enzyme Details

6. Dehydrodolichyl diphosphate synthase

General function:: Involved in transferase activity, transferring alkyl or aryl (other than methyl) groups
Specific function:: Catalyzes cis-prenyl chain elongation to produce the polyprenyl backbone of dolichol, a glycosyl carrier-lipid required for the biosynthesis of several classes of glycoprotein.
Gene Name:: DHDDS
Uniprot ID:: Q86SQ9
Molecular weight:: Not Available

Reactions

Farnesyl pyrophosphate + → Dehydrodolichol diphosphate +	details

Enzyme Details

7. 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. The beta subunit is responsible for peptide-binding.
Gene Name:: FNTB
Uniprot ID:: P49356
Molecular weight:: 48773.2

Reactions

Farnesyl pyrophosphate + protein-cysteine → S-farnesyl protein + Pyrophosphate	details
Farnesyl pyrophosphate + Protein-cysteine → S-Farnesyl protein + Pyrophosphate	details

Enzyme Details

8. Decaprenyl-diphosphate synthase subunit 2

General function:: Not Available
Specific function:: Supplies decaprenyl diphosphate, the precursor for the side chain of the isoprenoid quinones ubiquinone-10.
Gene Name:: PDSS2
Uniprot ID:: Q86YH6
Molecular weight:: 44128.17

Reactions

Farnesyl pyrophosphate + Isopentenyl pyrophosphate → Pyrophosphate + all-trans-Decaprenyl diphosphate	details

Enzyme Details

9. Decaprenyl-diphosphate synthase subunit 1

General function:: Not Available
Specific function:: Supplies decaprenyl diphosphate, the precursor for the side chain of the isoprenoid quinones ubiquinone-10.
Gene Name:: PDSS1
Uniprot ID:: Q5T2R2
Molecular weight:: 46260.6

Reactions

Farnesyl pyrophosphate + Isopentenyl pyrophosphate → Pyrophosphate + all-trans-Decaprenyl diphosphate	details

Showing metabocard for Farnesyl pyrophosphate (HMDB0000961)

MOL for HMDB0000961 (Farnesyl pyrophosphate)

3D MOL for HMDB0000961 (Farnesyl pyrophosphate)

3D SDF for HMDB0000961 (Farnesyl pyrophosphate)

3D-SDF for HMDB0000961 (Farnesyl pyrophosphate)

PDB for HMDB0000961 (Farnesyl pyrophosphate)

3D PDB for HMDB0000961 (Farnesyl pyrophosphate)

SMILES for HMDB0000961 (Farnesyl pyrophosphate)

INCHI for HMDB0000961 (Farnesyl pyrophosphate)

Structure for HMDB0000961 (Farnesyl pyrophosphate)

3D Structure for HMDB0000961 (Farnesyl pyrophosphate)

Experimental Collision Cross Sections

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

Enzymes

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