P. aeruginosa Metabolome Database: Geranyl-PP (PAMDB000324)

Identification Taxonomy Physical Properties Biological Properties Spectra Concentrations Links References Enzymes Transporters

Proteins (3280)

Record Information

Version

1.0

Update Date

1/22/2018 12:54:54 PM

Metabolite ID

PAMDB000324

Identification

Name:

Geranyl-PP

Description:

Geranyl diphosphate is regarded as a key intermediate in the steroid, isoprene and terpene biosynthesis pathways and is used by organisms in the biosynthesis of farnesyl pyrophosphate, geranylgeranyl pyrophosphate, cholesterol, terpenes and terpenoids. (wikipedia). In E.coli, geranyl diphosphate synthase (GPPS) catalyzes the condensation of dimethylallyl diphosphate (DMAPP) and isopentenyl diphosphate (IPP) to form geranyl diphosphate. Geranyl pyrophosphate is an intermediate in the HMG-CoA reductase pathway used by organisms in the biosynthesis of terpenes and terpenoids. (Wikipedia)

Structure

🔍MOL SDF PDB SMILES InChI View Structure

Synonyms:

ω,E-geranyl diphosphate
ω,e-geranyl diphosphoric acid
(2E)-3,7-dimethylocta-2,6-dien-1-yl trihydrogen diphosphate
(2E)-3,7-Dimethylocta-2,6-dien-1-yl trihydrogen diphosphoric acid
Geranyl diphosphate
Geranyl diphosphoric acid
Geranyl pyrophosphate
Geranyl pyrophosphoric acid
Geranyl-diphosphate
Geranyl-diphosphoric acid
Geranyl-PP
Geranyl-pyrophosphate
Geranyl-pyrophosphoric acid
GPP
Monoterpenyl diphosphate
Monoterpenyl diphosphoric acid
Neryl diphosphate
Neryl diphosphoric acid
Omega,E-geranyl diphosphate
Omega,e-geranyl diphosphoric acid
Trans-Geranyl pyrophosphate
trans-Geranyl pyrophosphoric acid

Chemical Formula:

C₁₀H₂₀O₇P₂

Average Molecular Weight:

314.2091

Monoisotopic Molecular Weight:

314.068426018

InChI Key:

GVVPGTZRZFNKDS-JXMROGBWSA-N

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)/b10-7+

CAS number:

763-10-0

IUPAC Name:

[({[(2E)-3,7-dimethylocta-2,6-dien-1-yl]oxy}(hydroxy)phosphoryl)oxy]phosphonic acid

Traditional IUPAC Name:

geranyl diphosphate

SMILES:

CC(C)=CCC\C(C)=C\CO[P@@](=O)(O)OP(=O)(O)O

Chemical Taxonomy

Taxonomy Description

This compound 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.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Isoprenoid phosphates

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 phosphate
Hydrocarbon derivative
Organooxygen compound
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

polyprenol diphosphate (CHEBI:17211 )
Acyclic monoterpenoids (LMPR0102010001 )

Physical Properties

State:

Solid

Charge:

-2

Melting point:

Not Available

Experimental Properties:

Property	Value	Source

Predicted Properties

Property	Value	Source
Water Solubility	0.902 mg/mL	ALOGPS
logP	1.63	ALOGPS
logP	1.96	ChemAxon
logS	-2.5	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	8	ChemAxon
Refractivity	72.93 m³·mol^-1	ChemAxon
Polarizability	28.52 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	1	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Biological Properties

Cellular Locations:

Cytoplasm

Reactions:

Dimethylallylpyrophosphate + Isopentenyl pyrophosphate > Geranyl-PP + Pyrophosphate
Geranyl-PP + Isopentenyl pyrophosphate + Geranyl diphosphate <> Farnesyl pyrophosphate + Pyrophosphate
Geranyl-PP + Isopentenyl pyrophosphate <> Pyrophosphate + Farnesyl pyrophosphate
all-trans-Polyprenyl diphosphate + 4-Hydroxybenzoic acid + Geranyl-PP <> 4-Hydroxy-3-polyprenylbenzoate + Pyrophosphate + 4-Hydroxy-3-polyprenylbenzoate
Geranyl-PP + 1,4-Dihydroxy-2-naphthoic acid <> Demethylmenaquinol + Pyrophosphate + Carbon dioxide
Dimethylallylpyrophosphate + Isopentenyl pyrophosphate + Dimethylallylpyrophosphate + Isopentenyl pyrophosphate > Pyrophosphate + Geranyl-PP + Geranyl-PP
Geranyl-PP + Isopentenyl pyrophosphate + Geranyl-PP + Isopentenyl pyrophosphate > Pyrophosphate + Farnesyl pyrophosphate + Farnesyl pyrophosphate

Pathways:

Metabolic pathways pae01100
Terpenoid backbone biosynthesis pae00900
Ubiquinone and other terpenoid-quinone biosynthesis pae00130

Spectra

Spectra:

Spectrum Type	Description	Splash Key
GC-MS	GC-MS Spectrum - GC-MS	Not Available
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-00kr-1953000000-e5ee3340554c9ecac23e	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-000i-5910000000-82bcd2195a53b847981c	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0gc0-9400000000-f87d391f1b3c01743515	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-03di-0509000000-43083a162145718cd977	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9500000000-053b6323e620a16328a8	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-4faed4c921d605619caf	View in MoNA

References

References:

Barnard GF, Popjak G: Human liver prenyltransferase and its characterization. Biochim Biophys Acta. 1981 Sep 15;661(1):87-99. Pubmed: 7295734
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. Pubmed: 11641412
Holstein SA, Hohl RJ: Isoprenoids: remarkable diversity of form and function. Lipids. 2004 Apr;39(4):293-309. Pubmed: 15357017
Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., Tanabe, M. (2012). "KEGG for integration and interpretation of large-scale molecular data sets." Nucleic Acids Res 40:D109-D114. Pubmed: 22080510
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. Pubmed: 16684881
Keseler, I. M., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama-Castro, S., Muniz-Rascado, L., Bonavides-Martinez, C., Paley, S., Krummenacker, M., Altman, T., Kaipa, P., Spaulding, A., Pacheco, J., Latendresse, M., Fulcher, C., Sarker, M., Shearer, A. G., Mackie, A., Paulsen, I., Gunsalus, R. P., Karp, P. D. (2011). "EcoCyc: a comprehensive database of Escherichia coli biology." Nucleic Acids Res 39:D583-D590. Pubmed: 21097882
Loza-Tavera H: Monoterpenes in essential oils. Biosynthesis and properties. Adv Exp Med Biol. 1999;464:49-62. Pubmed: 10335385
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. Pubmed: 11591144
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. Pubmed: 11510819
Sagami H, Ogura K: [A new development in isoprenoid biochemistry brought by the discovery of prenylated proteins] Seikagaku. 1994 Dec;66(12):1488-501. Pubmed: 7884273
Smit A, Mushegian A: Biosynthesis of isoprenoids via mevalonate in Archaea: the lost pathway. Genome Res. 2000 Oct;10(10):1468-84. Pubmed: 11042147
van der Werf, M. J., Overkamp, K. M., Muilwijk, B., Coulier, L., Hankemeier, T. (2007). "Microbial metabolomics: toward a platform with full metabolome coverage." Anal Biochem 370:17-25. Pubmed: 17765195

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)

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Links

External Links:

Resource	Link
CHEBI ID	17211
HMDB ID	HMDB01285
Pubchem Compound ID	445995
Kegg ID	C05847
ChemSpider ID	393471
Wikipedia	Geranyl pyrophosphate
BioCyc ID	GERANYL-PP
EcoCyc ID	GERANYL-PP
Ligand Expo	GPP

Geranyl-PP (PAMDB000324)

Structure for Geranyl-PP (PAMDB000324)