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(2S,3R)-3-hydroxybutane-1,2,3-tricarboxylic acid (YMDB00535)

Identification
YMDB IDYMDB00535
Name(2S,3R)-3-hydroxybutane-1,2,3-tricarboxylic acid
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
DescriptionAlpha-Methylisocitric Acid, also known as methylisocitrate, belongs to the class of organic compounds known as tricarboxylic acids and derivatives. These are carboxylic acids containing exactly three carboxyl groups. Thus, Alpha-methylisocitric Acid is considered to be a fatty acid lipid molecule. Alpha-Methylisocitric Acid is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral. Alpha-Methylisocitric Acid exists in both E. coli (prokaryote) and yeast (eukaryote).
Structure
Thumb
MOLSDF3D-SDFPDBSMILESInChI View 3D Structure
Synonyms
  • (2s,3r)-3-hydroxybutane-1,2,3-tricarboxylate
  • (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylic acid
  • 1D-myo-Inositol 1,3,4,5,6-pentakisphosphate
  • D-myo-Inositol 1,3,4,5,6-pentakisphosphate
  • Inositol 1,3,4,5,6-pentakisphosphate
  • Inositol 1,3,4,5,6-pentaphosphate
  • Inositol pentaphosphate
  • methylisocitrate
  • methylisocitric acid
  • myo-Inositol 1,3,4,5,6-pentakis(phosphate)
  • 3-Carboxy-2,3-dideoxy-4-C-methyl-L-threo-pentaric acid
  • 3-Carboxy-2,3-dideoxy-4-C-methyl-L-threo-pentarate
  • a-Methylisocitrate
  • a-Methylisocitric acid
  • alpha-Methylisocitrate
  • Α-methylisocitrate
  • Α-methylisocitric acid
CAS number20298-95-7
WeightAverage: 206.1501
Monoisotopic: 206.042652674
InChI KeyHHKPKXCSHMJWCF-WVBDSBKLSA-N
InChIInChI=1S/C7H10O7/c1-7(14,6(12)13)3(5(10)11)2-4(8)9/h3,14H,2H2,1H3,(H,8,9)(H,10,11)(H,12,13)/t3-,7-/m1/s1
IUPAC Name(1R,2S)-1-hydroxy-1-methylpropane-1,2,3-tricarboxylic acid
Traditional IUPAC Namemethylisocitrate
Chemical FormulaC7H10O7
SMILESC[C@@](O)([C@H](CC(O)=O)C(O)=O)C(O)=O
Chemical Taxonomy
Description belongs to the class of organic compounds known as tricarboxylic acids and derivatives. These are carboxylic acids containing exactly three carboxyl groups.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassTricarboxylic acids and derivatives
Direct ParentTricarboxylic acids and derivatives
Alternative Parents
Substituents
  • Tricarboxylic acid or derivatives
  • Hydroxy acid
  • Alpha-hydroxy acid
  • Tertiary alcohol
  • Carboxylic acid
  • Organic oxygen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Carbonyl group
  • Alcohol
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Physical Properties
StateSolid
Charge0
Melting pointNot Available
Experimental Properties
PropertyValueReference
Water SolubilityNot AvailablePhysProp
LogP-7.999PhysProp
Predicted Properties
PropertyValueSource
Water Solubility149 g/LALOGPS
logP-0.87ALOGPS
logP-1ChemAxon
logS-0.14ALOGPS
pKa (Strongest Acidic)3.17ChemAxon
pKa (Strongest Basic)-4.1ChemAxon
Physiological Charge-3ChemAxon
Hydrogen Acceptor Count7ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area132.13 ŲChemAxon
Rotatable Bond Count5ChemAxon
Refractivity40.43 m³·mol⁻¹ChemAxon
Polarizability17.26 ųChemAxon
Number of Rings0ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular LocationsNot Available
Organoleptic PropertiesNot Available
SMPDB Pathways
Inositol MetabolismPW002498 ThumbThumb?image type=greyscaleThumb?image type=simple
Inositol phosphate metabolismPW002495 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways
Inositol phosphate metabolismec00562 Map00562
Propanoate metabolismec00640 Map00640
SMPDB ReactionsNot Available
KEGG ReactionsNot Available
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-000i-9700000000-5e955ef633a08113ea4bJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-07br-0910000000-452b302f2c220ffbdcb7JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-00xr-5900000000-09ce5fc471f12b38970eJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-01b9-6900000000-affa291e126f5947919dJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0900-2920000000-936e30fcb714056e11d0JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-014i-2900000000-01942de5aa6c81413a4fJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-00y0-9300000000-32de60d42bd02d610c8cJSpectraViewer
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:
  • 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
  • Singh, J., Kumar, D., Ramakrishnan, N., Singhal, V., Jervis, J., Garst, J. F., Slaughter, S. M., DeSantis, A. M., Potts, M., Helm, R. F. (2005). "Transcriptional response of Saccharomyces cerevisiae to desiccation and rehydration." Appl Environ Microbiol 71:8752-8763.16332871
Synthesis Reference:Not Available
External Links:
ResourceLink
CHEBI ID15607
HMDB IDHMDB03529
Pubchem Compound ID5459784
Kegg IDC04593
ChemSpider ID4573561
FOODB IDNot Available
Wikipedia IDNot Available
BioCyc IDNot Available

Enzymes

Protein Details
1. Mitochondrial 2-methylisocitrate lyase
General function:
Involved in isocitrate lyase activity
Specific function:
Catalyzes the formation of pyruvate and succinate from 2-methylisocitrate during the metabolism of endogenous propionyl- CoA. Does not act on isocitrate
Gene Name:
ICL2
Uniprot ID:
Q12031
Molecular weight:
64975.39844
Reactions
(2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate → pyruvate + succinate.
Protein Details
2. Probable 2-methylcitrate dehydratase
General function:
Involved in 2-methylcitrate dehydratase activity
Specific function:
Catalyzes the dehydration of 2-methylcitrate to 2- methyl-cis-aconitate
Gene Name:
PDH1
Uniprot ID:
Q12428
Molecular weight:
57683.10156
Reactions
(2S,3S)-2-hydroxybutane-1,2,3-tricarboxylate → (Z)-but-2-ene-1,2,3-tricarboxylate + H(2)O.