Survey with prize
You are using an unsupported browser. Please upgrade your browser to a newer version to get the best experience on Yeast Metabolome Database.
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
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-5PADP + 5-Diphosphomevalonic acid
Adenosine triphosphate + 5-Diphosphomevalonic acidADP + phosphate + Isopentenyl pyrophosphate + Carbon dioxide
KEGG Reactions
5-Diphosphomevalonic acid + Adenosine triphosphatephosphate + Carbon dioxide + Isopentenyl pyrophosphate + ADP
Adenosine triphosphate + Mevalonic acid-5P5-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
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

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.
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).