Showing metabocard for Isopentenyl pyrophosphate (BMDB0001347)

IdentificationTaxonomyPhysical propertiesPathwaysSpectraConcentrationsLinksReferencesenzymes (4) Show 4 proteinsXML
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Record Information
Version1.0
Creation Date2016-09-30 22:44:30 UTC
Update Date2020-05-19 22:01:18 UTC
BMDB IDBMDB0001347
Secondary Accession Numbers
  • BMDB01347
Metabolite Identification
Common NameIsopentenyl pyrophosphate
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
Chemical FormulaC5H12O7P2
Average Molecular Weight246.0921
Monoisotopic Molecular Weight246.005825762
IUPAC Name({hydroxy[(3-methylbut-3-en-1-yl)oxy]phosphoryl}oxy)phosphonic acid
Traditional Nameisopentenyl-diphosphate
CAS Registry Number358-71-4
SMILES
CC(=C)CCOP(O)(=O)OP(O)(O)=O
InChI Identifier
InChI=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)
InChI KeyNUHSROFQTUXZQQ-UHFFFAOYSA-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
  • 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
Ontology
StatusExpected but not Quantified
Origin
  • Endogenous
BiofunctionNot Available
ApplicationNot Available
Cellular locations
  • Cell membrane
  • Cytoplasm
  • Mitochondria
  • Peroxisome
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
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
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, Positivesplash10-002b-9600000000-930df1e6e1c7e4eed108View 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 0V, negativesplash10-004i-0190000000-d2895fc0c10b183f43eeView in MoNA
LC-MS/MSLC-MS/MS Spectrum - Orbitrap 1V, negativesplash10-056r-3980000000-627cfd435c85e88822b5View in MoNA
LC-MS/MSLC-MS/MS Spectrum - Orbitrap 1V, negativesplash10-056r-3980000000-23fe88b159964959e66fView in MoNA
LC-MS/MSLC-MS/MS Spectrum - Orbitrap 5V, negativesplash10-056r-2960000000-19354ef717c66764cd68View in MoNA
LC-MS/MSLC-MS/MS Spectrum - Orbitrap 8V, negativesplash10-056r-9740000000-022ac5cb9631af8164eeView in MoNA
LC-MS/MSLC-MS/MS Spectrum - Orbitrap 10V, negativesplash10-004i-9300000000-aee23682a2c1fa358b3bView in MoNA
LC-MS/MSLC-MS/MS Spectrum - Orbitrap 11V, negativesplash10-004i-9100000000-6318f24bf41c952270c7View in MoNA
LC-MS/MSLC-MS/MS Spectrum - Orbitrap 14V, negativesplash10-004i-9000000000-84d7ad80acc22ebadc08View in MoNA
LC-MS/MSLC-MS/MS Spectrum - Orbitrap 16V, negativesplash10-004i-9000000000-52e623d1c0e3c5eec628View in MoNA
LC-MS/MSLC-MS/MS Spectrum - Orbitrap 19V, negativesplash10-004i-9000000000-71f08ee06355626ebfd6View in MoNA
LC-MS/MSLC-MS/MS Spectrum - n/a 17V, negativesplash10-0a4i-0900000000-8b768e6e6fd82a9e52fcView in MoNA
LC-MS/MSLC-MS/MS Spectrum - n/a 17V, negativesplash10-004i-9000000000-5ef060d5ec4b80c35c1aView in MoNA
LC-MS/MSLC-MS/MS Spectrum - n/a 17V, negativesplash10-00kr-0900000000-1e624fb025fa3835685bView in MoNA
LC-MS/MSLC-MS/MS Spectrum - n/a 17V, negativesplash10-014i-1900000000-2c64756ee3a8e3d9493cView in MoNA
LC-MS/MSLC-MS/MS Spectrum - Orbitrap 1V, negativesplash10-0006-0090000000-5185751820ffb8d752a3View in MoNA
LC-MS/MSLC-MS/MS Spectrum - Orbitrap 3V, negativesplash10-0006-0090000000-03743901b1bb8cf365e9View in MoNA
LC-MS/MSLC-MS/MS Spectrum - Orbitrap 4V, negativesplash10-0006-2090000000-9e4213acb94b27ef7c83View in MoNA
LC-MS/MSLC-MS/MS Spectrum - Orbitrap 5V, negativesplash10-004l-9080000000-43b0fb277b1db3562d57View in MoNA
LC-MS/MSLC-MS/MS Spectrum - Orbitrap 7V, negativesplash10-004i-9010000000-863fed72efb5d1767ed2View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-014j-9670000000-fa3d42a8ff93d345cea7View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-014i-9200000000-78e51dcb039157700c59View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-014i-9100000000-a585b43371cb54efe2ebView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0006-0490000000-391e90cfd97e6adcbb06View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9510000000-fed3169adff6f1179e01View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-5c099085cd907446a2fbView in MoNA
1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
Biological Properties
Cellular Locations
  • Cell membrane
  • Cytoplasm
  • Mitochondria
  • Peroxisome
Biospecimen Locations
  • Spleen
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
SpleenExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal
  • Not Applicable
 details
Abnormal Concentrations
Not Available
HMDB IDHMDB0001347
DrugBank IDDB04714
Phenol Explorer Compound IDNot Available
FooDB IDFDB030946
KNApSAcK IDC00000848
Chemspider ID1158
KEGG Compound IDC00129
BioCyc IDDELTA3-ISOPENTENYL-PP
BiGG ID33956
Wikipedia LinkIsopentenyl pyrophosphate
METLIN ID6181
PubChem Compound1195
PDB IDNot Available
ChEBI ID16584
References
Synthesis ReferenceKao, 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. Org Lett. 2005 Dec 8;7(25):5677-80.
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available

Enzymes

Enzyme Details
1. Diphosphomevalonate decarboxylase
General function:
Lipid transport and metabolism
Specific function:
Performs the first committed step in the biosynthesis of isoprenes.
Gene Name:
MVD
Uniprot ID:
Q0P570
Molecular weight:
43732.0
Reactions
Adenosine triphosphate + 5-Diphosphomevalonic acid → ADP + Hydrogen phosphate + Isopentenyl pyrophosphate + Carbon dioxidedetails
Enzyme Details
2. Isopentenyl-diphosphate Delta-isomerase 1
General function:
Lipid transport and metabolism
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:
Q1LZ95
Molecular weight:
26467.0
Reactions
Isopentenyl pyrophosphate → Dimethylallylpyrophosphatedetails
Enzyme Details
3. 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
4. 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