5-Diphosphomevalonic acid (YMDB00403)

Identification
YMDB IDYMDB00403
Name5-Diphosphomevalonic acid
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
Description(R)-5-Diphosphomevalonic acid, also known as mevalonate 5-diphosphate or mevalonic acid 5-pyrophosphate, belongs to the class of organic compounds known as organic pyrophosphates. These are organic compounds containing the pyrophosphate oxoanion, with the structure OP([O-])(=O)OP(O)([O-])=O (R)-5-Diphosphomevalonic acid is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral (R)-5-Diphosphomevalonic acid exists in all living species, ranging from bacteria to humans. Within yeast, (R)-5-diphosphomevalonic acid participates in a number of enzymatic reactions. In particular, (R)-5-diphosphomevalonic acid can be biosynthesized from mevalonic acid-5P; which is mediated by the enzyme phosphomevalonate kinase. In addition, (R)-5-diphosphomevalonic acid can be converted into isopentenyl pyrophosphate through its interaction with the enzyme diphosphomevalonate decarboxylase. In yeast, (R)-5-diphosphomevalonic acid is involved in the metabolic pathway called cholesterol biosynthesis and metabolism ce(18:0) pathway.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
  • (R)-5-Diphosphomevalonate
  • 1,1,3,7-tetrahydroxy-7-methyl-2,4-dioxa-1,3-diphosphanonan-9-oate
  • 1,1,3,7-tetrahydroxy-7-methyl-2,4-dioxa-1,3-diphosphanonan-9-oic acid
  • 1,1,3,7-tetrahydroxy-7-methyl-2,4-dioxa-1,3-diphosphanonan-9-oic acid ion(1-)1,3-dioxide
  • 5-diphosphomevalonate
  • 5-diphosphomevalonic acid
  • mevalonate 5-diphosphate
  • mevalonate pyrophosphate
  • mevalonate-diphosphate
  • (3R)-3-Hydroxy-5-[[hydroxy(phosphonooxy)phosphinyl]oxy]-3-methylpentanoic acid
  • (R)-Diphosphomevalonic acid
  • 5-Pyrophosphomevalonic acid
  • Mevalonic 5-pyrophosphate
  • Mevalonic acid 5-diphosphate
  • Mevalonic acid 5-pyrophosphate
  • Mevalonic acid pyrophosphate
  • Pyrophosphomevalonic acid
  • (3R)-3-Hydroxy-5-[[hydroxy(phosphonooxy)phosphinyl]oxy]-3-methylpentanoate
  • (R)-Diphosphomevalonate
  • 5-Pyrophosphomevalonate
  • Mevalonate 5-pyrophosphate
  • Mevalonic 5-pyrophosphic acid
  • Mevalonic acid 5-diphosphic acid
  • Mevalonic acid 5-pyrophosphic acid
  • Mevalonic acid pyrophosphic acid
  • Pyrophosphomevalonate
  • (R)-5-Diphosphomevalonic acid
  • R-Diphosphomevalonate
CAS number4872-34-8
WeightAverage: 308.1169
Monoisotopic: 308.006219692
InChI KeySIGQQUBJQXSAMW-ZCFIWIBFSA-N
InChIInChI=1S/C6H14O10P2/c1-6(9,4-5(7)8)2-3-15-18(13,14)16-17(10,11)12/h9H,2-4H2,1H3,(H,7,8)(H,13,14)(H2,10,11,12)/t6-/m1/s1
IUPAC Name(3R)-3-hydroxy-5-{[hydroxy(phosphonooxy)phosphoryl]oxy}-3-methylpentanoic acid
Traditional IUPAC Namemevalonate-diphosphate
Chemical FormulaC6H14O10P2
SMILES[H]OC(=O)C([H])([H])[C@@](O[H])(C([H])([H])[H])C([H])([H])C([H])([H])OP(=O)(O[H])OP(=O)(O[H])O[H]
Chemical Taxonomy
Description belongs to the class of organic compounds known as organic pyrophosphates. These are organic compounds containing the pyrophosphate oxoanion, with the structure OP([O-])(=O)OP(O)([O-])=O.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganic oxoanionic compounds
Sub ClassOrganic pyrophosphates
Direct ParentOrganic pyrophosphates
Alternative Parents
Substituents
  • Organic pyrophosphate
  • Monoalkyl phosphate
  • Short-chain hydroxy acid
  • Organic phosphoric acid derivative
  • Fatty acid
  • Alkyl phosphate
  • Phosphoric acid ester
  • Tertiary alcohol
  • Carboxylic acid derivative
  • Carboxylic acid
  • Monocarboxylic acid or derivatives
  • Carbonyl group
  • Alcohol
  • 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 Solubility8.26 g/LALOGPS
logP-1.2ALOGPS
logP-1.6ChemAxon
logS-1.6ALOGPS
pKa (Strongest Acidic)1.78ChemAxon
pKa (Strongest Basic)-2.9ChemAxon
Physiological Charge-3ChemAxon
Hydrogen Acceptor Count8ChemAxon
Hydrogen Donor Count5ChemAxon
Polar Surface Area170.82 ŲChemAxon
Rotatable Bond Count8ChemAxon
Refractivity56.26 m³·mol⁻¹ChemAxon
Polarizability23.46 ųChemAxon
Number of Rings0ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations
  • 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 + Mevalonic acid-5P → ADP + 5-Diphosphomevalonic acid
Adenosine triphosphate + 5-Diphosphomevalonic acid → ADP + phosphate + Isopentenyl pyrophosphate + Carbon dioxide
KEGG Reactions
5-Diphosphomevalonic acid + Adenosine triphosphate → phosphate + Carbon dioxide + Isopentenyl pyrophosphate + ADP
Adenosine triphosphate + Mevalonic acid-5P → 5-Diphosphomevalonic acid + ADP
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-004m-9820000000-7d8dd5ca92f4eb0538fdJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positivesplash10-00dv-9243200000-6d8177d69adb810da37fJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-01wf-1391000000-a8414ad19cb44452295fJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03e9-4940000000-c856f917d05bbc77ac8aJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-01sr-9840000000-db467c852b0f7d795eceJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0bt9-1494000000-7e72bc5c055d7b3e4f37JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-056r-7920000000-5c36505c154e9a3abebdJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-cbcfedc91b4fe71d5849JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0a4i-0019000000-a7e7073b139ac0acc855JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0a6r-9466000000-5ab0d4ae0def99221d8fJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-056s-9500000000-38a7f595bafdd824dd36JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0a59-0938000000-9afa28886c9f8ff753e0JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-001i-3940000000-53f4c41d4cec2fbfc65dJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-08n9-6910000000-e20806c8945d9a51ddb1JSpectraViewer
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
1D NMR1H 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
Synthesis Reference:Not Available
External Links:
ResourceLink
CHEBI ID15899
HMDB IDHMDB01090
Pubchem Compound ID516
Kegg IDC01143
ChemSpider ID388531
FOODB IDFDB031002
Wikipedia5-Diphosphomevalonic_acid
BioCyc IDCPD-641

Enzymes

Protein Details
1. Phosphomevalonate kinase
General function:
Involved in ATP binding
Specific function:
ATP + (R)-5-phosphomevalonate = ADP + (R)-5- diphosphomevalonate
Gene Name:
ERG8
Uniprot ID:
P24521
Molecular weight:
50454.39844
Reactions
ATP + (R)-5-phosphomevalonate → ADP + (R)-5-diphosphomevalonate.
Protein Details
2. 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).