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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
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 acidADP + phosphate + Isopentenyl pyrophosphate + Carbon dioxide
Isopentenyl pyrophosphateDimethylallylpyrophosphate
Isopentenyl pyrophosphateDimethylallylpyrophosphate
Dimethylallylpyrophosphate + Isopentenyl pyrophosphateGeranyl-PP + Pyrophosphate
Geranyl-PP + Isopentenyl pyrophosphateFarnesyl pyrophosphate + Pyrophosphate
KEGG Reactions
Farnesyl pyrophosphate + Isopentenyl pyrophosphatePyrophosphate + geranylgeranyl diphosphate
Isopentenyl pyrophosphate + geranylgeranyl diphosphatePyrophosphate + pentaprenyl diphosphate + hydron
pentaprenyl diphosphate + Isopentenyl pyrophosphatePyrophosphate + hexaprenyl diphosphate
hexaprenyl diphosphate + Isopentenyl pyrophosphate + hydronPyrophosphate + heptaprenyl diphosphate
heptaprenyl diphosphate + Isopentenyl pyrophosphatePyrophosphate + octaprenyl 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
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
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

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.
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.
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.
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).
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.
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
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
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