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5-(methylsulfanyl)-2,3-dioxopentyl phosphate (YMDB00024)

Identification
YMDB IDYMDB00024
Name5-(methylsulfanyl)-2,3-dioxopentyl phosphate
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
Description5-(Methylthio)-2,3-dioxopentyl phosphate, also known as 1-phospho-2,3-diketo-5-S-methylthiopentane or 2,3-diketo-5-methylthio-1-phosphopentane, belongs to the class of organic compounds known as monoalkyl phosphates. These are organic compounds containing a phosphate group that is linked to exactly one alkyl chain. 5-(Methylthio)-2,3-dioxopentyl phosphate is an extremely weak basic (essentially neutral) compound (based on its pKa). Within yeast, 5-(methylthio)-2,3-dioxopentyl phosphate participates in a number of enzymatic reactions. In particular, 5-(methylthio)-2,3-dioxopentyl phosphate can be converted into 1,2-dihydroxy-3-keto-5-methylthiopentene through the action of the enzyme 2,3-dioxomethiopentane-1-phosphate enolase/phosphatase. In addition, 5-(methylthio)-2,3-dioxopentyl phosphate can be biosynthesized from 5-methylthioribulose 1-phosphate through its interaction with the enzyme methylthioribulose-1-phosphate dehydratase. In yeast, 5-(methylthio)-2,3-dioxopentyl phosphate is involved in the metabolic pathway called the methionine metabolism and salvage pathway.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
  • 1-PDMSP
  • 1-Phospho-2,3-diketo-5-S-methylthiopentane
  • 2,3-diketo-5-methylthio-1-phosphopentane
  • 2,3-Diketo-5-methylthiopentyl-1-phosphate
  • 2,3-diketo-5-Methylthiopentyl-1-phosphoric acid
  • 5-(Methylthio)-2,3-dioxopentyl phosphate
  • 5-(methylthio)-2,3-Dioxopentyl phosphoric acid
  • 5-methylthio-1-(phosphonooxy)pentane-2,3-dione
  • 5-(Methylsulfanyl)-2,3-dioxopentyl phosphate
  • 5-(Methylsulfanyl)-2,3-dioxopentyl phosphoric acid
  • 5-(Methylsulphanyl)-2,3-dioxopentyl phosphate
  • 5-(Methylsulphanyl)-2,3-dioxopentyl phosphoric acid
  • 5-(Methylthio)-1-(phosphonooxy)-2,3-pentanedione
  • DK-MTP-1-p
CAS numberNot Available
WeightAverage: 242.187
Monoisotopic: 242.001395286
InChI KeyHKEAOVFNWRDVAJ-UHFFFAOYSA-N
InChIInChI=1S/C6H11O6PS/c1-14-3-2-5(7)6(8)4-12-13(9,10)11/h2-4H2,1H3,(H2,9,10,11)
IUPAC Name{[5-(methylsulfanyl)-2,3-dioxopentyl]oxy}phosphonic acid
Traditional IUPAC Name1-pdmsp
Chemical FormulaC6H11O6PS
SMILESCSCCC(=O)C(=O)COP(O)(O)=O
Chemical Taxonomy
Description belongs to the class of organic compounds known as monoalkyl phosphates. These are organic compounds containing a phosphate group that is linked to exactly one alkyl chain.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassOrganic phosphoric acids and derivatives
Sub ClassPhosphate esters
Direct ParentMonoalkyl phosphates
Alternative Parents
Substituents
  • Monoalkyl phosphate
  • Monosaccharide
  • Alpha-diketone
  • Ketone
  • Dialkylthioether
  • Sulfenyl compound
  • Thioether
  • Organic oxygen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organosulfur compound
  • Organooxygen compound
  • Carbonyl group
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Physical Properties
StateNot Available
Charge0
Melting pointNot Available
Experimental Properties
PropertyValueReference
Water SolubilityNot AvailablePhysProp
LogPNot AvailablePhysProp
Predicted Properties
PropertyValueSource
Water Solubility7.99 g/LALOGPS
logP-0.08ALOGPS
logP0.51ChemAxon
logS-1.5ALOGPS
pKa (Strongest Acidic)1.11ChemAxon
pKa (Strongest Basic)-9.4ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area100.9 ŲChemAxon
Rotatable Bond Count7ChemAxon
Refractivity51.2 m³·mol⁻¹ChemAxon
Polarizability21.01 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
Methionine metabolism and salvagePW002384 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways
Cysteine and methionine metabolismec00270 Map00270
SMPDB Reactions
water + 5-(methylsulfanyl)-2,3-dioxopentyl phosphate hydron + phosphate + 1,2-Dihydroxy-3-keto-5-methylthiopentene
5-Methylthioribulose 1-phosphate → 5-(methylsulfanyl)-2,3-dioxopentyl phosphate + water
KEGG Reactions
5-(methylsulfanyl)-2,3-dioxopentyl phosphate + water → hydron + 4-Methylthio-2-oxobutanoate + phosphate + Formic acid
5-Methylthioribulose 1-phosphate → 5-(methylsulfanyl)-2,3-dioxopentyl phosphate + water
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0f72-7900000000-24d819c66c14ff8aeaf4JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0007-4790000000-b3d6f7fd978638aee854JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-002b-7940000000-ea0d584390fc83528ea7JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0032-9300000000-9ea44ac5ab6994e2cbf1JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0002-9110000000-ffbac72bafb213d67f09JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004j-9000000000-3b618e15250a28020451JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-574f7e21fceca4fa56a6JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0006-2090000000-fad1b029313d537385beJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004j-9000000000-8410711e0388e8b17b92JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-a5e502a2627af2048a1fJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0f6w-1950000000-d8f80edcf3a29db22846JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0002-9400000000-8c5923edadbd9702efe0JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-01ot-9100000000-92506e54893321b61dceJSpectraViewer
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
  • Subhi, A. L., Diegelman, P., Porter, C. W., Tang, B., Lu, Z. J., Markham, G. D., Kruger, W. D. (2003). "Methylthioadenosine phosphorylase regulates ornithine decarboxylase by production of downstream metabolites." J Biol Chem 278:49868-49873.14506228
Synthesis Reference:Not Available
External Links:
ResourceLink
CHEBI ID50604
HMDB IDHMDB0059620
Pubchem Compound ID561
Kegg IDC15650
ChemSpider ID545
FOODB IDFDB030557
Wikipedia IDNot Available
BioCyc IDCPD-8999

Enzymes

Protein Details
1. Enolase-phosphatase E1
General function:
Involved in catalytic activity
Specific function:
Bifunctional enzyme that catalyzes the enolization of 2,3-diketo-5-methylthiopentyl-1-phosphate (DK-MTP-1-P) into the intermediate 2-hydroxy-3-keto-5-methylthiopentenyl-1-phosphate (HK-MTPenyl-1-P), which is then dephosphorylated to form the acireductone 1,2-dihydroxy-3-keto-5-methylthiopentene (DHK-MTPene)
Gene Name:
UTR4
Uniprot ID:
P32626
Molecular weight:
25187.19922
Reactions
5-(methylthio)-2,3-dioxopentyl phosphate + H(2)O → 1,2-dihydroxy-5-(methylthio)pent-1-en-3-one + phosphate.
2-Phosphoglycolate + H2O → glycolate + phosphate
Protein Details
2. Methylthioribulose-1-phosphate dehydratase
General function:
Involved in metal ion binding
Specific function:
Catalyzes the dehydration of methylthioribulose-1- phosphate (MTRu-1-P) into 2,3-diketo-5-methylthiopentyl-1- phosphate (DK-MTP-1-P)
Gene Name:
MDE1
Uniprot ID:
P47095
Molecular weight:
27426.59961
Reactions
S-methyl-5-thio-D-ribulose 1-phosphate → 5-(methylthio)-2,3-dioxopentyl phosphate + H(2)O.