geranyl diphosphate (YMDB00670)

Identification
YMDB IDYMDB00670
Namegeranyl diphosphate
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
DescriptionGeranyl-PP, also known as neryl diphosphate, belongs to the class of organic compounds known as isoprenoid phosphates. These are prenol lipids containing a phosphate group linked to an isoprene (2-methylbuta-1,3-diene) unit. Thus, geranyl-PP is considered to be an isoprenoid lipid molecule. Geranyl-PP is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
  • (2E)-3,7-dimethylocta-2,6-dien-1-yl trihydrogen diphosphate
  • Geranyl diphosphate
  • geranyl pyrophosphate
  • Geranyl pyrophosphic acid
  • geranyl-diphosphate
  • geranyl-PP
  • geranyl-pyrophosphate
  • Monoterpenyl diphosphate
  • Neryl diphosphate
  • trans-geranyl pyrophosphate
  • Polyisopentenylpyrophosphate
  • Polyisopentenyldiphosphate
  • trans-Polyisopentenyldiphosphate
  • Polyprenyl diphosphate
  • Geranyl pyrophosphoric acid
  • Polyisopentenylpyrophosphoric acid
  • Polyisopentenyldiphosphoric acid
  • trans-Polyisopentenyldiphosphoric acid
  • Polyprenyl diphosphoric acid
  • P-[(2E)-3,7-Dimethyl-2,6-octadien-1-yl]diphosphoric acid
  • trans-geranyl-PP
CAS number763-10-0
WeightAverage: 314.2091
Monoisotopic: 314.068426018
InChI KeyGVVPGTZRZFNKDS-JXMROGBWSA-N
InChIInChI=1S/C10H20O7P2/c1-9(2)5-4-6-10(3)7-8-16-19(14,15)17-18(11,12)13/h5,7H,4,6,8H2,1-3H3,(H,14,15)(H2,11,12,13)/b10-7+
IUPAC Name[({[(2E)-3,7-dimethylocta-2,6-dien-1-yl]oxy}(hydroxy)phosphoryl)oxy]phosphonic acid
Traditional IUPAC Namegeranyl diphosphate
Chemical FormulaC10H20O7P2
SMILESCC(C)=CCC\C(C)=C\COP(O)(=O)OP(O)(O)=O
Chemical Taxonomy
Description belongs to the class of organic compounds known as isoprenoid phosphates. These are prenol lipids containing a phosphate group linked to an isoprene (2-methylbuta-1,3-diene) unit.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassPrenol lipids
Sub ClassIsoprenoid phosphates
Direct ParentIsoprenoid phosphates
Alternative Parents
Substituents
  • Organic pyrophosphate
  • Monoterpenoid
  • Isoprenoid phosphate
  • Acyclic monoterpenoid
  • Monoalkyl phosphate
  • Alkyl phosphate
  • Phosphoric acid ester
  • Organic phosphoric acid derivative
  • Organic oxygen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Physical Properties
StateSolid
Charge0
Melting pointNot Available
Experimental Properties
PropertyValueReference
Water SolubilityNot AvailablePhysProp
LogPNot AvailablePhysProp
Predicted Properties
PropertyValueSource
Water Solubility0.9 g/LALOGPS
logP1.63ALOGPS
logP1.96ChemAxon
logS-2.5ALOGPS
pKa (Strongest Acidic)1.77ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area113.29 ŲChemAxon
Rotatable Bond Count8ChemAxon
Refractivity72.93 m³·mol⁻¹ChemAxon
Polarizability28.52 ųChemAxon
Number of Rings0ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations
  • Cytoplasm
Organoleptic Properties
Flavour/OdourSource
AppleFDB001463
FruityFDB001463
RoseFDB001463
SMPDB Pathways
Cholesterol biosynthesis and metabolism CE(10:0)PW002545 ThumbThumb?image type=greyscaleThumb?image type=simple
Cholesterol biosynthesis and metabolism CE(12:0)PW002548 ThumbThumb?image type=greyscaleThumb?image type=simple
Cholesterol biosynthesis and metabolism CE(14:0)PW002544 ThumbThumb?image type=greyscaleThumb?image type=simple
Cholesterol biosynthesis and metabolism CE(16:0)PW002550 ThumbThumb?image type=greyscaleThumb?image type=simple
Cholesterol biosynthesis and metabolism CE(18:0)PW002551 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways
Steroid biosynthesisec00100 Map00100
Terpenoid backbone biosynthesisec00900 Map00900
Ubiquinone and other terpenoid-quinone biosynthesisec00130 Map00130
SMPDB ReactionsNot Available
KEGG ReactionsNot Available
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-004j-9640000000-9ce32c835bdcfa97fa15JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableJSpectraViewer
LC-MS/MSLC-MS/MS Spectrum - Orbitrap 6V, negativesplash10-0002-0090000000-b5ca864b0ba8818ad627JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Orbitrap 8V, negativesplash10-0002-0090000000-c7f7c5c529a56d532304JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Orbitrap 11V, negativesplash10-0002-3390000000-010bee66d1e4bd685e95JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Orbitrap 14V, negativesplash10-004i-9440000000-13e525f66230aae586a2JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Orbitrap 17V, negativesplash10-004i-9200000000-a9da8f03edb73eec50bfJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Orbitrap 20V, negativesplash10-004i-9100000000-fe3060700600ee72f8ddJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Orbitrap 23V, negativesplash10-004i-9000000000-15de26c097afd86b7007JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Orbitrap 27V, negativesplash10-004i-9000000000-bcc45bf0bf3bbb46af13JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Orbitrap 33V, negativesplash10-004i-9000000000-b8b56dc9ea06c2ce52b5JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - n/a 21V, negativesplash10-0a4i-0900000000-f2685d197409ed952f02JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - n/a 21V, negativesplash10-004i-9000000000-5ef060d5ec4b80c35c1aJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - n/a 21V, negativesplash10-0a4i-0900000000-60b9e910670cbc6ebe0cJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - n/a 21V, negativesplash10-0bt9-0390000000-6532032bbb594aa54d9cJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Orbitrap 5V, negativesplash10-03di-0009000000-3bcab8c3688c96a4cec5JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Orbitrap 7V, negativesplash10-03di-2009000000-42fa98db20ae4d6f687eJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Orbitrap 9V, negativesplash10-01t9-9005000000-44618200345aed481b48JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Orbitrap 12V, negativesplash10-004i-9000000000-befed7a961a777eb5f66JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Orbitrap 15V, negativesplash10-004i-9000000000-8afaaf750b51acbd1a01JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Orbitrap 18V, negativesplash10-004i-9000000000-b5b3b346fecad6ae473dJSpectraViewer | MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-00kr-1953000000-e5ee3340554c9ecac23eJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-000i-5910000000-82bcd2195a53b847981cJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0gc0-9400000000-f87d391f1b3c01743515JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-03di-0509000000-43083a162145718cd977JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9500000000-053b6323e620a16328a8JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-4faed4c921d605619cafJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
References
References:
  • Herrgard, M. J., Swainston, N., Dobson, P., Dunn, W. B., Arga, K. Y., Arvas, M., Bluthgen, N., Borger, S., Costenoble, R., Heinemann, M., Hucka, M., Le Novere, N., Li, P., Liebermeister, W., Mo, M. L., Oliveira, A. P., Petranovic, D., Pettifer, S., Simeonidis, E., Smallbone, K., Spasic, I., Weichart, D., Brent, R., Broomhead, D. S., Westerhoff, H. V., Kirdar, B., Penttila, M., Klipp, E., Palsson, B. O., Sauer, U., Oliver, S. G., Mendes, P., Nielsen, J., Kell, D. B. (2008). "A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology." Nat Biotechnol 26:1155-1160.18846089
  • Grabinska, K., Palamarczyk, G. (2002). "Dolichol biosynthesis in the yeast Saccharomyces cerevisiae: an insight into the regulatory role of farnesyl diphosphate synthase." FEMS Yeast Res 2:259-265.12702274
  • Song, L. (2006). "A soluble form of phosphatase in Saccharomyces cerevisiae capable of converting farnesyl diphosphate into E,E-farnesol." Appl Biochem Biotechnol 128:149-158.16484724
Synthesis Reference:Not Available
External Links:
ResourceLink
CHEBI ID17211
HMDB IDHMDB01285
Pubchem Compound ID445995
Kegg IDC00341
ChemSpider ID24785181
FOODB IDFDB001463
WikipediaGeranyl_pyrophosphate
BioCyc IDGERANYL-PP

Enzymes

Protein Details
1. Farnesyl pyrophosphate synthase
General function:
Involved in isoprenoid biosynthetic process
Specific function:
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:
ERG20
Uniprot ID:
P08524
Molecular weight:
40483.0
Reactions
Dimethylallyl diphosphate + isopentenyl diphosphate → diphosphate + geranyl diphosphate.
Geranyl diphosphate + isopentenyl diphosphate → diphosphate + (2E,6E)-farnesyl diphosphate.