NP-MRD: Showing NP-Card for Geranylfarnesyl diphosphate (NP0091991)

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Record Information

Version

2.0

Created at

2022-05-11 18:54:07 UTC

Updated at

2022-05-11 18:54:07 UTC

NP-MRD ID

NP0091991

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Geranylfarnesyl diphosphate

Description

Geranylfarnesyl diphosphate, also known as geranylfarnesyl-PP or GFPP, belongs to the class of organic compounds known as polyprenyl diphosphates. These are prenol lipids in which the diphosphate group is linked to one end of the polyprenol moiety. Geranylfarnesyl diphosphate is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral. Geranylfarnesyl diphosphate exists in all eukaryotes, ranging from yeast to humans.

Structure

MOL 3D MOL SDF PDB SMILES InChI

  Mrv0541 02241203512D          

 34 33  0  0  0  0            999 V2000
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M  END

     RDKit          3D

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M  END

  Mrv0541 02241203512D          

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 27 29  1  0  0  0  0
 27 30  1  0  0  0  0
 30 31  1  0  0  0  0
 31 32  2  0  0  0  0
 31 33  1  0  0  0  0
 31 34  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0091991

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C)=CCC\C(C)=C\CC\C(C)=C\CC\C(C)=C\CC\C(C)=C\COP(O)(=O)OP(O)(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C25H44O7P2/c1-21(2)11-7-12-22(3)13-8-14-23(4)15-9-16-24(5)17-10-18-25(6)19-20-31-34(29,30)32-33(26,27)28/h11,13,15,17,19H,7-10,12,14,16,18,20H2,1-6H3,(H,29,30)(H2,26,27,28)/b22-13+,23-15+,24-17+,25-19+

> <INCHI_KEY>
JMVSBFJBMXQNJW-GIXZANJISA-N

> <FORMULA>
C25H44O7P2

> <MOLECULAR_WEIGHT>
518.5602

> <EXACT_MASS>
518.256226786

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_AVERAGE_POLARIZABILITY>
57.602275585429254

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
{[hydroxy({[(2E,6E,10E,14E)-3,7,11,15,19-pentamethylicosa-2,6,10,14,18-pentaen-1-yl]oxy})phosphoryl]oxy}phosphonic acid

> <ALOGPS_LOGP>
4.88

> <JCHEM_LOGP>
6.936161610666666

> <ALOGPS_LOGS>
-5.63

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
3.1843406094078315

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.7672186885241006

> <JCHEM_POLAR_SURFACE_AREA>
113.29000000000002

> <JCHEM_REFRACTIVITY>
144.33570000000003

> <JCHEM_ROTATABLE_BOND_COUNT>
17

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.23e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
geranylfarnesyl diphosphate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0      44.437 -13.667   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      44.437 -15.195   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      45.772 -15.964   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      43.115 -15.964   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      41.780 -15.195   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      40.447 -15.964   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      39.112 -15.195   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      39.112 -13.667   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      37.778 -15.964   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      36.443 -15.195   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      35.110 -15.964   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      33.775 -15.195   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      33.775 -13.667   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      32.442 -15.964   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      31.107 -15.195   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      29.785 -15.964   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      28.461 -15.195   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      28.461 -13.667   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      27.127 -15.964   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      25.793 -15.195   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      24.459 -15.964   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      23.125 -15.195   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      23.125 -13.667   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      21.791 -15.964   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      20.456 -15.195   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0      19.122 -15.964   0.000  0.00  0.00           O+0
HETATM   27  P   UNK     0      17.788 -15.195   0.000  0.00  0.00           P+0
HETATM   28  O   UNK     0      17.019 -16.519   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0      18.559 -13.872   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0      16.454 -14.436   0.000  0.00  0.00           O+0
HETATM   31  P   UNK     0      15.131 -15.195   0.000  0.00  0.00           P+0
HETATM   32  O   UNK     0      15.901 -16.519   0.000  0.00  0.00           O+0
HETATM   33  O   UNK     0      14.361 -13.872   0.000  0.00  0.00           O+0
HETATM   34  O   UNK     0      13.797 -15.964   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   23   24                                                  
CONECT   23   22                                                            
CONECT   24   22   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   27                                                       
CONECT   27   26   28   29   30                                             
CONECT   28   27                                                            
CONECT   29   27                                                            
CONECT   30   27   31                                                       
CONECT   31   30   32   33   34                                             
CONECT   32   31                                                            
CONECT   33   31                                                            
CONECT   34   31                                                            
MASTER        0    0    0    0    0    0    0    0   34    0   66    0
END

View in JSmol

Synonyms

Value	Source
(2E,6E,10E,14E)-Geranylfarnesyl diphosphate	ChEBI
2-trans,6-trans,10-trans,14-trans-Geranylfarnesyl diphosphate	ChEBI
all-trans-Farnesylgeranyl diphosphate	ChEBI
all-trans-Farnesylgeranyl pyrophosphate	ChEBI
all-trans-Geranylfarnesyl diphosphate	ChEBI
all-trans-Geranylfarnesyl pyrophosphate	ChEBI
(2E,6E,10E,14E)-Geranylfarnesyl diphosphoric acid	Generator
2-trans,6-trans,10-trans,14-trans-Geranylfarnesyl diphosphoric acid	Generator
all-trans-Farnesylgeranyl diphosphoric acid	Generator
all-trans-Farnesylgeranyl pyrophosphoric acid	Generator
all-trans-Geranylfarnesyl diphosphoric acid	Generator
all-trans-Geranylfarnesyl pyrophosphoric acid	Generator
Geranylfarnesyl diphosphoric acid	Generator
all-trans-Pentaprenyl diphosphate	HMDB
Geranylfarnesyl-diphosphate	HMDB
Geranylfarnesyl-PP	HMDB
GFPP	HMDB
Geranylfarnesyl diphosphate	ChEBI
all-trans-Pentaprenyl diphosphoric acid	Generator

Chemical Formula

C₂₅H₄₄O₇P₂

Average Mass

518.5602 Da

Monoisotopic Mass

518.25623 Da

IUPAC Name

{[hydroxy({[(2E,6E,10E,14E)-3,7,11,15,19-pentamethylicosa-2,6,10,14,18-pentaen-1-yl]oxy})phosphoryl]oxy}phosphonic acid

Traditional Name

geranylfarnesyl diphosphate

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C25H44O7P2/c1-21(2)11-7-12-22(3)13-8-14-23(4)15-9-16-24(5)17-10-18-25(6)19-20-31-34(29,30)32-33(26,27)28/h11,13,15,17,19H,7-10,12,14,16,18,20H2,1-6H3,(H,29,30)(H2,26,27,28)/b22-13+,23-15+,24-17+,25-19+

InChI Key

JMVSBFJBMXQNJW-GIXZANJISA-N

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Anas platyrhynchos	FooDB	FooDB
Anatidae	FooDB	FooDB
Anser anser	FooDB	FooDB
Bison bison	FooDB	FooDB
Bos taurus	FooDB	FooDB
Bos taurus X Bison bison	FooDB	FooDB
Bubalus bubalis	FooDB	FooDB
Capra aegagrus hircus	FooDB	FooDB
Cervidae	FooDB	FooDB
Cervus canadensis	FooDB	FooDB
Columba	FooDB	FooDB
Columbidae	FooDB	FooDB
Dromaius novaehollandiae	FooDB	FooDB
Equus caballus	FooDB	FooDB
Gallus gallus	FooDB	FooDB
Lagopus muta	FooDB	FooDB
Leporidae	FooDB	FooDB
Lepus timidus	FooDB	FooDB
Melanitta fusca	FooDB	FooDB
Meleagris gallopavo	FooDB	FooDB
Numida meleagris	FooDB	FooDB
Odocoileus	FooDB	FooDB
Oryctolagus	FooDB	FooDB
Ovis aries	FooDB	FooDB
Phasianidae	FooDB	FooDB
Phasianus colchicus	FooDB	FooDB
Struthio camelus	FooDB	FooDB
Sus scrofa	FooDB	FooDB
Sus scrofa domestica	FooDB	FooDB

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as polyprenyl diphosphates. These are prenol lipids in which the diphosphate group is linked to one end of the polyprenol moiety.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Polyprenols

Direct Parent

Polyprenyl diphosphates

Alternative Parents

Substituents

Polyprenyl diphosphate
Polyprenyl monophosphate
Sesterterpenoid
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

pentaprenyl diphosphate (CHEBI:16818 )
Acyclic sesterterpenoids (C04217 )
Polyterpenoids (C04217 )
Acyclic sesterterpenoids (LMPR0105010014 )

Physical Properties

State

Not Available

Experimental 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

Predicted Properties

Property	Value	Source
logP	4.88	ALOGPS
logP	6.94	ChemAxon
logS	-5.6	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	17	ChemAxon
Refractivity	144.34 m³·mol⁻¹	ChemAxon
Polarizability	57.6 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon