Showing metabocard for Geranyl-PP (BMDB0001285)

IdentificationTaxonomyPhysical propertiesPathwaysSpectraConcentrationsLinksReferencesenzymes (2) Show 2 proteinsXML
Record Information
Version1.0
Creation Date2016-09-30 22:43:36 UTC
Update Date2020-04-22 15:07:28 UTC
BMDB IDBMDB0001285
Secondary Accession Numbers
  • BMDB01285
Metabolite Identification
Common NameGeranyl-PP
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
ValueSource
Geranyl pyrophosphateChEBI
PolyisopentenylpyrophosphateKegg
PolyisopentenyldiphosphateKegg
trans-PolyisopentenyldiphosphateKegg
Polyprenyl diphosphateKegg
Geranyl pyrophosphoric acidGenerator
Polyisopentenylpyrophosphoric acidGenerator
Polyisopentenyldiphosphoric acidGenerator
trans-Polyisopentenyldiphosphoric acidGenerator
Polyprenyl diphosphoric acidGenerator
(2E)-3,7-Dimethylocta-2,6-dien-1-yl trihydrogen diphosphateHMDB
Geranyl diphosphateHMDB
Geranyl-diphosphateHMDB
Geranyl-pyrophosphateHMDB
Monoterpenyl diphosphateHMDB
Neryl diphosphateHMDB
trans-Geranyl pyrophosphateHMDB
P-[(2E)-3,7-Dimethyl-2,6-octadien-1-yl]diphosphoric acidHMDB
trans-geranyl-PPHMDB
Chemical FormulaC10H20O7P2
Average Molecular Weight314.2091
Monoisotopic Molecular Weight314.068426018
IUPAC Name[({[(2E)-3,7-dimethylocta-2,6-dien-1-yl]oxy}(hydroxy)phosphoryl)oxy]phosphonic acid
Traditional Namegeranyl diphosphate
CAS Registry Number763-10-0
SMILES
CC(C)=CCC\C(C)=C\CO[P@@](=O)(O)OP(=O)(O)O
InChI Identifier
InChI=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+
InChI KeyGVVPGTZRZFNKDS-JXMROGBWSA-N
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
Ontology
StatusExpected but not Quantified
Origin
  • Endogenous
BiofunctionNot Available
ApplicationNot Available
Cellular locations
  • Cell membrane
  • Cytoplasm
  • Mitochondria
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
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
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectra
Spectrum TypeDescriptionSplash Key
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-004j-9640000000-9ce32c835bdcfa97fa15View in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableView in JSpectraViewer
LC-MS/MSLC-MS/MS Spectrum - Orbitrap 6V, negativesplash10-0002-0090000000-b5ca864b0ba8818ad627View in MoNA
LC-MS/MSLC-MS/MS Spectrum - Orbitrap 8V, negativesplash10-0002-0090000000-c7f7c5c529a56d532304View in MoNA
LC-MS/MSLC-MS/MS Spectrum - Orbitrap 11V, negativesplash10-0002-3390000000-010bee66d1e4bd685e95View in MoNA
LC-MS/MSLC-MS/MS Spectrum - Orbitrap 14V, negativesplash10-004i-9440000000-13e525f66230aae586a2View in MoNA
LC-MS/MSLC-MS/MS Spectrum - Orbitrap 17V, negativesplash10-004i-9200000000-a9da8f03edb73eec50bfView in MoNA
LC-MS/MSLC-MS/MS Spectrum - Orbitrap 20V, negativesplash10-004i-9100000000-fe3060700600ee72f8ddView in MoNA
LC-MS/MSLC-MS/MS Spectrum - Orbitrap 23V, negativesplash10-004i-9000000000-15de26c097afd86b7007View in MoNA
LC-MS/MSLC-MS/MS Spectrum - Orbitrap 27V, negativesplash10-004i-9000000000-bcc45bf0bf3bbb46af13View in MoNA
LC-MS/MSLC-MS/MS Spectrum - Orbitrap 33V, negativesplash10-004i-9000000000-b8b56dc9ea06c2ce52b5View in MoNA
LC-MS/MSLC-MS/MS Spectrum - n/a 21V, negativesplash10-0a4i-0900000000-f2685d197409ed952f02View in MoNA
LC-MS/MSLC-MS/MS Spectrum - n/a 21V, negativesplash10-004i-9000000000-5ef060d5ec4b80c35c1aView in MoNA
LC-MS/MSLC-MS/MS Spectrum - n/a 21V, negativesplash10-0a4i-0900000000-60b9e910670cbc6ebe0cView in MoNA
LC-MS/MSLC-MS/MS Spectrum - n/a 21V, negativesplash10-0bt9-0390000000-6532032bbb594aa54d9cView in MoNA
LC-MS/MSLC-MS/MS Spectrum - Orbitrap 5V, negativesplash10-03di-0009000000-3bcab8c3688c96a4cec5View in MoNA
LC-MS/MSLC-MS/MS Spectrum - Orbitrap 7V, negativesplash10-03di-2009000000-42fa98db20ae4d6f687eView in MoNA
LC-MS/MSLC-MS/MS Spectrum - Orbitrap 9V, negativesplash10-01t9-9005000000-44618200345aed481b48View in MoNA
LC-MS/MSLC-MS/MS Spectrum - Orbitrap 12V, negativesplash10-004i-9000000000-befed7a961a777eb5f66View in MoNA
LC-MS/MSLC-MS/MS Spectrum - Orbitrap 15V, negativesplash10-004i-9000000000-8afaaf750b51acbd1a01View in MoNA
LC-MS/MSLC-MS/MS Spectrum - Orbitrap 18V, negativesplash10-004i-9000000000-b5b3b346fecad6ae473dView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-00kr-1953000000-e5ee3340554c9ecac23eView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-000i-5910000000-82bcd2195a53b847981cView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0gc0-9400000000-f87d391f1b3c01743515View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-03di-0509000000-43083a162145718cd977View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9500000000-053b6323e620a16328a8View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-4faed4c921d605619cafView in MoNA
1D NMR13C NMR Spectrum (1D, 100 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 100 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 1000 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 1000 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 200 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 200 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 300 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 300 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 400 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 400 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 500 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 600 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 700 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 700 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 800 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 800 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 900 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 900 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
Biological Properties
Cellular Locations
  • Cell membrane
  • Cytoplasm
  • Mitochondria
Biospecimen LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
HMDB IDHMDB0001285
DrugBank IDDB02552
Phenol Explorer Compound IDNot Available
FooDB IDFDB001463
KNApSAcK IDC00000846
Chemspider ID393471
KEGG Compound IDC05847
BioCyc IDGERANYL-PP
BiGG ID34712
Wikipedia LinkGeranyl_pyrophosphate
METLIN ID6134
PubChem Compound445995
PDB IDNot Available
ChEBI ID17211
References
Synthesis ReferenceRunquist M; Ericsson J; Thelin A; Chojnacki T; Dallner G Biosynthesis of trans,trans,trans-geranylgeranyl diphosphate by the cytosolic fraction from rat tissues. Biochemical and biophysical research communications (1992), 186(1), 157-65.
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available

Enzymes

Enzyme Details
1. Farnesyl pyrophosphate synthase
General function:
Coenzyme transport and metabolism
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 (By similarity).
Gene Name:
FDPS
Uniprot ID:
Q8WMY2
Molecular weight:
40510.0
Enzyme Details
2. Geranylgeranyl pyrophosphate synthase
General function:
Coenzyme transport and metabolism
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:
P56966
Molecular weight:
34900.0