You are using an unsupported browser. Please upgrade your browser to a newer version to get the best experience on Yeast Metabolome Database.

Isopentenyl pyrophosphate (YMDB00200)

Identification
YMDB IDYMDB00200
NameIsopentenyl pyrophosphate
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
DescriptionIsopentenyl pyrophosphate, also known as IPP or delta(3)-isopentenyl-PP, 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. Isopentenyl pyrophosphate is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
  • 3-Methyl-3-butenyl pyrophosphate
  • delta-3-Isopentenyl pyrophosphat
  • Delta(3)-isopentenyl-PP
  • delta3-isopentenyl diphosphate
  • delta3-methyl-3-butenyl diphosphate
  • Diphosphoric acid mono(3-methyl-3-butenyl) ester
  • IPP
  • IPR
  • isopentenyl diphosphate
  • Isopentenyl pyrophosphate
  • Isopentenyl pyrophosphic acid
  • isopentenyl-pp
  • Mono(3-methyl-3-butenyl) diphosphate
  • 3-Methylbut-3-en-1-yl trihydrogen diphosphate
  • 3-Methylbut-3-enyl phosphono hydrogen phosphate
  • delta-3-Isopentenyl pyrophosphate
  • IPPP
  • 3-Methyl-3-butenyl pyrophosphoric acid
  • 3-Methylbut-3-en-1-yl trihydrogen diphosphoric acid
  • 3-Methylbut-3-enyl phosphono hydrogen phosphoric acid
  • delta-3-Isopentenyl pyrophosphoric acid
  • Δ-3-isopentenyl pyrophosphate
  • Δ-3-isopentenyl pyrophosphoric acid
  • delta3-Isopentenyl diphosphoric acid
  • Δ3-isopentenyl diphosphate
  • Δ3-isopentenyl diphosphoric acid
  • delta3-Methyl-3-butenyl diphosphoric acid
  • Δ3-methyl-3-butenyl diphosphate
  • Δ3-methyl-3-butenyl diphosphoric acid
  • Diphosphate mono(3-methyl-3-butenyl) ester
  • mono(3-Methyl-3-butenyl) diphosphoric acid
  • Isopentenyl pyrophosphoric acid
  • Isopentenyl pyrophosphate, 4-(14)C-labeled
CAS number358-71-4
WeightAverage: 246.0921
Monoisotopic: 246.005825762
InChI KeyNUHSROFQTUXZQQ-UHFFFAOYSA-N
InChIInChI=1S/C5H12O7P2/c1-5(2)3-4-11-14(9,10)12-13(6,7)8/h1,3-4H2,2H3,(H,9,10)(H2,6,7,8)
IUPAC Name({hydroxy[(3-methylbut-3-en-1-yl)oxy]phosphoryl}oxy)phosphonic acid
Traditional IUPAC Nameisopentenyl-diphosphate
Chemical FormulaC5H12O7P2
SMILES[H]OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C([H])([H])C(=C([H])[H])C([H])([H])[H]
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
  • 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 FrameworkAliphatic acyclic compounds
External Descriptors
Physical Properties
StateSolid
Charge0
Melting pointNot Available
Experimental Properties
PropertyValueReference
Water SolubilityNot AvailablePhysProp
LogPNot AvailablePhysProp
Predicted Properties
PropertyValueSource
Water Solubility6.69 g/LALOGPS
logP0.04ALOGPS
logP0.2ChemAxon
logS-1.6ALOGPS
pKa (Strongest Acidic)1.78ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area113.29 ŲChemAxon
Rotatable Bond Count6ChemAxon
Refractivity48.21 m³·mol⁻¹ChemAxon
Polarizability19.01 ųChemAxon
Number of Rings0ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations
  • mitochondrion
  • lipid particle
  • cytoplasm
Organoleptic PropertiesNot Available
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
SMPDB Reactions
Adenosine triphosphate + 5-Diphosphomevalonic acid → ADP + phosphate + Isopentenyl pyrophosphate + Carbon dioxide
Isopentenyl pyrophosphate ↔ Dimethylallylpyrophosphate
Isopentenyl pyrophosphate → Dimethylallylpyrophosphate
Dimethylallylpyrophosphate + Isopentenyl pyrophosphate → Geranyl-PP + Pyrophosphate
Geranyl-PP + Isopentenyl pyrophosphate → Farnesyl pyrophosphate + Pyrophosphate
KEGG Reactions
octaprenyl diphosphate + Isopentenyl pyrophosphate ↔ nonaprenyl diphosphate + Pyrophosphate
nonaprenyl diphosphate + Isopentenyl pyrophosphate ↔ Pyrophosphate + decaprenyl diphosphate
Isopentenyl pyrophosphate + decaprenyl diphosphate ↔ Pyrophosphate + undecaprenyl diphosphate
Isopentenyl pyrophosphate + undecaprenyl diphosphate ↔ Pyrophosphate + dodecaprenyl diphosphate
Isopentenyl pyrophosphate + dodecaprenyl diphosphate ↔ Pyrophosphate + tridecaprenyl diphosphate
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-002b-9600000000-930df1e6e1c7e4eed108JSpectraViewer
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 0V, negativesplash10-004i-0190000000-d2895fc0c10b183f43eeJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Orbitrap 1V, negativesplash10-056r-3980000000-627cfd435c85e88822b5JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Orbitrap 1V, negativesplash10-056r-3980000000-23fe88b159964959e66fJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Orbitrap 5V, negativesplash10-056r-2960000000-19354ef717c66764cd68JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Orbitrap 8V, negativesplash10-056r-9740000000-022ac5cb9631af8164eeJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Orbitrap 10V, negativesplash10-004i-9300000000-aee23682a2c1fa358b3bJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Orbitrap 11V, negativesplash10-004i-9100000000-6318f24bf41c952270c7JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Orbitrap 14V, negativesplash10-004i-9000000000-84d7ad80acc22ebadc08JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Orbitrap 16V, negativesplash10-004i-9000000000-52e623d1c0e3c5eec628JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Orbitrap 19V, negativesplash10-004i-9000000000-71f08ee06355626ebfd6JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - n/a 17V, negativesplash10-0a4i-0900000000-8b768e6e6fd82a9e52fcJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - n/a 17V, negativesplash10-004i-9000000000-5ef060d5ec4b80c35c1aJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - n/a 17V, negativesplash10-00kr-0900000000-1e624fb025fa3835685bJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - n/a 17V, negativesplash10-014i-1900000000-2c64756ee3a8e3d9493cJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Orbitrap 1V, negativesplash10-0006-0090000000-5185751820ffb8d752a3JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Orbitrap 3V, negativesplash10-0006-0090000000-03743901b1bb8cf365e9JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Orbitrap 4V, negativesplash10-0006-2090000000-9e4213acb94b27ef7c83JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Orbitrap 5V, negativesplash10-004l-9080000000-43b0fb277b1db3562d57JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Orbitrap 7V, negativesplash10-004i-9010000000-863fed72efb5d1767ed2JSpectraViewer | MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-014j-9670000000-fa3d42a8ff93d345cea7JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-014i-9200000000-78e51dcb039157700c59JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-014i-9100000000-a585b43371cb54efe2ebJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0006-0490000000-391e90cfd97e6adcbb06JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9510000000-fed3169adff6f1179e01JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-5c099085cd907446a2fbJSpectraViewer
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
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
References
References:
  • UniProt Consortium (2011). "Ongoing and future developments at the Universal Protein Resource." Nucleic Acids Res 39:D214-D219.21051339
  • Scheer, M., Grote, A., Chang, A., Schomburg, I., Munaretto, C., Rother, M., Sohngen, C., Stelzer, M., Thiele, J., Schomburg, D. (2011). "BRENDA, the enzyme information system in 2011." Nucleic Acids Res 39:D670-D676.21062828
  • 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
  • Sato, M., Sato, K., Nishikawa, S., Hirata, A., Kato, J., Nakano, A. (1999). "The yeast RER2 gene, identified by endoplasmic reticulum protein localization mutations, encodes cis-prenyltransferase, a key enzyme in dolichol synthesis." Mol Cell Biol 19:471-483.9858571
  • 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
  • Hsu, A. Y., Do, T. Q., Lee, P. T., Clarke, C. F. (2000). "Genetic evidence for a multi-subunit complex in the O-methyltransferase steps of coenzyme Q biosynthesis." Biochim Biophys Acta 1484:287-297.10760477
Synthesis Reference:Kao, Chai-Lin; Kittleman, William; Zhang, Hua; Seto, Haruo; Liu, Hung-Wen. Stereochemical Analysis of Isopentenyl Diphosphate Isomerase Type II from Staphylococcus aureus Using Chemically Synthesized (S)- and (R)-[2-2H]Isopentenyl Diphosphates.Organic Let
External Links:
ResourceLink
CHEBI ID16584
HMDB IDHMDB01347
Pubchem Compound ID1195
Kegg IDC00129
ChemSpider ID1158
FOODB IDFDB030946
WikipediaIsopentenyl pyrophosphate
BioCyc IDDELTA3-ISOPENTENYL-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.
Protein Details
2. Geranylgeranyl pyrophosphate synthase
General function:
Involved in isoprenoid biosynthetic process
Specific function:
Catalyzes the trans-addition of the 3 molecules of IPP onto DMAPP to form geranylgeranyl pyrophosphate. Required for the membrane attachment of YPT1 and SEC4. May be involved in vesicle trafficking and protein sorting
Gene Name:
BTS1
Uniprot ID:
Q12051
Molecular weight:
38651.0
Reactions
Dimethylallyl diphosphate + isopentenyl diphosphate → diphosphate + geranyl diphosphate.
Geranyl diphosphate + isopentenyl diphosphate → diphosphate + (2E,6E)-farnesyl diphosphate.
Trans,trans-farnesyl diphosphate + isopentenyl diphosphate → diphosphate + geranylgeranyl diphosphate.
Protein Details
3. Isopentenyl-diphosphate Delta-isomerase
General function:
Involved in isopentenyl-diphosphate delta-isomerase activity
Specific function:
Catalyzes the 1,3-allylic rearrangement of the homoallylic substrate isopentenyl (IPP) to its highly electrophilic allylic isomer, dimethylallyl diphosphate (DMAPP)
Gene Name:
IDI1
Uniprot ID:
P15496
Molecular weight:
33351.30078
Reactions
Isopentenyl diphosphate → dimethylallyl diphosphate.
Protein Details
4. Diphosphomevalonate decarboxylase
General function:
Involved in ATP binding
Specific function:
ATP + (R)-5-diphosphomevalonate = ADP + phosphate + isopentenyl diphosphate + CO(2)
Gene Name:
MVD1
Uniprot ID:
P32377
Molecular weight:
44115.5
Reactions
ATP + (R)-5-diphosphomevalonate → ADP + phosphate + isopentenyl diphosphate + CO(2).
Protein Details
5. Probable undecaprenyl pyrophosphate synthase
General function:
Involved in transferase activity, transferring alkyl or aryl (other than methyl) groups
Specific function:
Generates undecaprenyl pyrophosphate (UPP) from isopentenyl pyrophosphate (IPP)
Gene Name:
NUS1
Uniprot ID:
Q12063
Molecular weight:
42556.69922
Reactions
(2E,6E)-farnesyl diphosphate + 8 isopentenyl diphosphate → 8 diphosphate + di-trans,octa-cis-undecaprenyl diphosphate.
Protein Details
6. Hexaprenyl pyrophosphate synthase, mitochondrial
General function:
Involved in isoprenoid biosynthetic process
Specific function:
Assembly of polyisoprenoid side chains. The polyprenyl synthase of coenzyme Q biosynthesis catalyzes the formation from isopentenyl diphosphate of all trans-polyprenyl pyrophosphates generally ranging in length of between 6 and 10 isoprene units depending on the species
Gene Name:
COQ1
Uniprot ID:
P18900
Molecular weight:
52558.89844
Reactions
Protein Details
7. Putative dehydrodolichyl diphosphate synthase
General function:
Involved in transferase activity, transferring alkyl or aryl (other than methyl) groups
Specific function:
Could be a cis-prenyl transferase that adds multiple copies of isopentenyl pyrophosphate (ipp) to farnesyl pyrophosphate (FPP) to produce dehydrodolichyl diphosphate (DeDol- PP)
Gene Name:
SRT1
Uniprot ID:
Q03175
Molecular weight:
40199.69922
Reactions
Protein Details
8. Dehydrodolichyl diphosphate synthase
General function:
Involved in transferase activity, transferring alkyl or aryl (other than methyl) groups
Specific function:
Cis-prenyl transferase that adds multiple copies of isopentenyl pyrophosphate (IPP) to farnesyl pyrophosphate (FPP) to produce dehydrodolichyl diphosphate (Dedol-PP)
Gene Name:
RER2
Uniprot ID:
P35196
Molecular weight:
32693.30078
Reactions