geranyl diphosphate (PAMDB110354)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes Transporters
Proteins (3280)
Record Information
Version 1.0
Update Date 1/22/2018 12:54:54 PM
Metabolite IDPAMDB110354
Identification
Name: geranyl diphosphate
Description:Trianion of geranyl diphosphate arising from deprotonation of the three OH groups of the diphosphate; major species at pH 7.3.
Structure
Thumb
🔍MOLSDFPDBSMILESInChIView Structure
Synonyms:
  • geranyl-diphosphate
  • geranyl-pyrophosphate
  • GPP
  • geranyl-PP
  • geranyl pyrophosphate
  • ω,E-geranyl diphosphate
Chemical Formula: C10H17O7P2
Average Molecular Weight: 311.19
Monoisotopic Molecular Weight: 314.0684260167
InChI Key: GVVPGTZRZFNKDS-JXMROGBWSA-K
InChI: 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)/p-3/b10-7+
CAS number: 763-10-0
IUPAC Name:(2E)-3,7-dimethylocta-2,6-dien-1-yl diphosphate
Traditional IUPAC Name: geranyl diphosphate
SMILES:CC(=CCCC(=CCOP([O-])(OP(=O)([O-])[O-])=O)C)C
Chemical Taxonomy
Taxonomy DescriptionThis compound belongs to the class of chemical entities known as isoprenoid phosphates. These are prenol lipids containing a phosphate group linked to an isoprene (2-methylbuta-1,3-diene) unit.
Kingdom Chemical entities
Super ClassOrganic compounds
Class Lipids and lipid-like molecules
Sub ClassPrenol lipids
Direct Parent Isoprenoid 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 Framework Aliphatic acyclic compounds
External Descriptors
Physical Properties
State: Solid
Charge:-3
Melting point: Not Available
Experimental Properties:
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
Water Solubility0.9 mg/mLALOGPS
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 Å2ChemAxon
Rotatable Bond Count8ChemAxon
Refractivity72.93 m3·mol-1ChemAxon
Polarizability28.52 Å3ChemAxon
Number of Rings0ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations: Not Available
Reactions:
Pathways:
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted GC-MSPredicted GC-MS Spectrum - GC-MSNot Available
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
References
References:
  • Kavanagh KL, Guo K, Dunford JE, Wu X, Knapp S, Ebetino FH, Rogers MJ, Russell RG, Oppermann U: The molecular mechanism of nitrogen-containing bisphosphonates as antiosteoporosis drugs. Proc Natl Acad Sci U S A. 2006 May 16;103(20):7829-34. Epub 2006 May 9. [16684881 ]
  • Micali E, Chehade KA, Isaacs RJ, Andres DA, Spielmann HP: Protein farnesyltransferase isoprenoid substrate discrimination is dependent on isoprene double bonds and branched methyl groups. Biochemistry. 2001 Oct 16;40(41):12254-65. [11591144 ]
  • Holstein SA, Hohl RJ: Isoprenoids: remarkable diversity of form and function. Lipids. 2004 Apr;39(4):293-309. [15357017 ]
  • Gan X, Kaplan R, Menke JG, MacNaul K, Chen Y, Sparrow CP, Zhou G, Wright SD, Cai TQ: Dual mechanisms of ABCA1 regulation by geranylgeranyl pyrophosphate. J Biol Chem. 2001 Dec 28;276(52):48702-8. Epub 2001 Oct 18. [11641412 ]
  • Sagami H, Ogura K: [A new development in isoprenoid biochemistry brought by the discovery of prenylated proteins] Seikagaku. 1994 Dec;66(12):1488-501. [7884273 ]
  • Loza-Tavera H: Monoterpenes in essential oils. Biosynthesis and properties. Adv Exp Med Biol. 1999;464:49-62. [10335385 ]
  • Barnard GF, Popjak G: Human liver prenyltransferase and its characterization. Biochim Biophys Acta. 1981 Sep 15;661(1):87-99. [7295734 ]
  • Pont F, Luciani B, Belmant C, Fournie JJ: Characterization of phosphoantigens by high-performance anion-exchange chromatography-electrospray ionization ion trap mass spectrometry and nanoelectrospray ionization ion trap mass spectrometry. Anal Chem. 2001 Aug 1;73(15):3562-9. [11510819 ]
  • Smit A, Mushegian A: Biosynthesis of isoprenoids via mevalonate in Archaea: the lost pathway. Genome Res. 2000 Oct;10(10):1468-84. [11042147 ]
Synthesis Reference: Runquist 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) Download (PDF)
External Links:
ResourceLink
ChEBI58057
ChemSpider14211068
HMDBHMDB01285
IAF126034675
KEGGC00341
KNApSAcKC00000846
MetaboLightsMTBLC58057
PubChem19379894