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3-Isopropylmalate (YMDB00368)

Identification
YMDB IDYMDB00368
Name3-Isopropylmalate
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
Description3-Isopropylmalic acid, also known as 3-isopropylmalate, belongs to the class of organic compounds known as hydroxy fatty acids. These are fatty acids in which the chain bears a hydroxyl group. Based on a literature review a small amount of articles have been published on 3-Isopropylmalic acid.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
  • (2R,3S)-2-hydroxy-3-(propan-2-yl)butanedioate
  • (2R,3S)-2-hydroxy-3-(propan-2-yl)butanedioic acid
  • (2R,3S)-2-hydroxy-3-isopropylsuccinate
  • (2R,3S)-2-hydroxy-3-isopropylsuccinic acid
  • (2R,3S)-3-carboxy-2-hydroxy-4-methylpentanoate
  • (2R,3S)-3-carboxy-2-hydroxy-4-methylpentanoic acid
  • (2R,3S)-3-Isopropylmalate
  • (2R,3S)-3-isopropylmalic acid
  • 2-D-threo-Hydroxy-3-carboxy-isocaproate
  • 2-D-threo-Hydroxy-3-carboxy-isocaproic acid
  • 2-D-threo-hydroxy-3-carboxyisocaproate
  • 2-D-threo-hydroxy-3-carboxyisocaproic acid
  • 3-3-isopropylmalic acid
  • 3-Carboxy-2-hydroxy-4-methylpentanoate
  • 3-Carboxy-2-hydroxy-4-methylpentanoic acid
  • 3-Isopropylmalate
  • IPM
  • 3-Isopropylmalic acid
  • beta-Isopropylmalate, erythro-(L)-isomer
  • beta-Isopropylmalate
  • (2R,3S)-2-Hydroxy-3-(1-methylethyl)butanedioic acid
  • 2-Hydroxy-3-(1-methylethyl)butanedioic acid
  • Isopropylmalate
  • Isopropylmalic acid
  • beta-Isopropylmalic acid
  • β-Isopropylmalic acid
CAS number921-28-8
WeightAverage: 176.1672
Monoisotopic: 176.068473494
InChI KeyRNQHMTFBUSSBJQ-CRCLSJGQSA-N
InChIInChI=1S/C7H12O5/c1-3(2)4(6(9)10)5(8)7(11)12/h3-5,8H,1-2H3,(H,9,10)(H,11,12)/t4-,5+/m0/s1
IUPAC Name(2R,3S)-2-hydroxy-3-(propan-2-yl)butanedioic acid
Traditional IUPAC Name(2R,3S)-3-isopropylmalic acid
Chemical FormulaC7H12O5
SMILES[H]OC(=O)[C@]([H])(O[H])[C@@]([H])(C(=O)O[H])C([H])(C([H])([H])[H])C([H])([H])[H]
Chemical Taxonomy
Description belongs to the class of organic compounds known as hydroxy fatty acids. These are fatty acids in which the chain bears a hydroxyl group.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassFatty Acyls
Sub ClassFatty acids and conjugates
Direct ParentHydroxy fatty acids
Alternative Parents
Substituents
  • Beta-hydroxy acid
  • Branched fatty acid
  • Hydroxy fatty acid
  • Short-chain hydroxy acid
  • Methyl-branched fatty acid
  • Alpha-hydroxy acid
  • Hydroxy acid
  • Dicarboxylic acid or derivatives
  • Secondary alcohol
  • Carboxylic acid
  • Carboxylic acid derivative
  • Organooxygen compound
  • Carbonyl group
  • Alcohol
  • Hydrocarbon derivative
  • Organic oxide
  • Organic oxygen 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 Solubility83.3 g/LALOGPS
logP0.28ALOGPS
logP0.16ChemAxon
logS-0.33ALOGPS
pKa (Strongest Acidic)3.68ChemAxon
pKa (Strongest Basic)-4ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area94.83 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity38.6 m³·mol⁻¹ChemAxon
Polarizability16.47 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
Leucine BiosynthesisPW002475 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways
Valine, leucine and isoleucine biosynthesisec00290 Map00290
SMPDB Reactions
2-Isopropylmaleic acid + water → 3-Isopropylmalate
3-Isopropylmalate + NAD → NADH + hydron + (2S)-2-Isopropyl-3-oxosuccinate
KEGG Reactions
3-Isopropylmalate + S-Adenosylmethionine → S-Adenosylhomocysteine + 3-hydroxy-2-isopropyl-4-methoxy-4-oxobutanoate
3-Isopropylmalate ↔ water + 2-Isopropylmaleic acid
NAD + 3-Isopropylmalate → NADH + (2S)-2-Isopropyl-3-oxosuccinate + hydron
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-0002-0920000000-4ec856cc4eb69ab95cccJSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-0002-0920000000-4ec856cc4eb69ab95cccJSpectraViewer | MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0006-9400000000-a5c729805d94db1fb7b3JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (3 TMS) - 70eV, Positivesplash10-00bl-9135000000-1982df651c1931669daeJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0a7i-1900000000-224a91a676e183e74333JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-06sl-7900000000-b06817c1e6edcae6d425JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-052o-9300000000-479bb2145817abc0bf1aJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0059-1900000000-acde792ba60cae65a216JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0far-9700000000-cf8f9dd2b32cfd503f42JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0a59-9100000000-138111afc561c6d0a2ecJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-03ei-3900000000-99922dc6120c0bc9d5acJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-000i-9300000000-6c8d0a906ce3776c4769JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-052f-9000000000-229b51add43b0209aa10JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-001i-1900000000-bcc925b37cd5d5f31b5aJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-01q0-7900000000-222a48c445cf7526d6e6JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0019-9100000000-6003ddbcaf34c522b89aJSpectraViewer
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
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
References
References:
  • UniProt Consortium (2011). "Ongoing and future developments at the Universal Protein Resource." Nucleic Acids Res 39:D214-D219.21051339
  • 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
  • Katz, J. E., Dumlao, D. S., Wasserman, J. I., Lansdown, M. G., Jung, M. E., Faull, K. F., Clarke, S. (2004). "3-Isopropylmalate is the major endogenous substrate of the Saccharomyces cerevisiae trans-aconitate methyltransferase." Biochemistry 43:5976-5986.15147181
Synthesis Reference:Not Available
External Links:
ResourceLink
CHEBI ID43468
HMDB IDHMDB12156
Pubchem Compound ID5462261
Kegg IDC04411
ChemSpider ID4575349
FOODB IDFDB028813
Wikipedia IDIsopropylmalic acid
BioCyc ID2-D-THREO-HYDROXY-3-CARBOXY-ISOCAPROATE

Enzymes

Protein Details
1. 3-isopropylmalate dehydratase
General function:
Involved in 3-isopropylmalate dehydratase activity
Specific function:
Catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate
Gene Name:
LEU1
Uniprot ID:
P07264
Molecular weight:
85793.70313
Reactions
(2R,3S)-3-isopropylmalate → (2S)-2-isopropylmaleate + H(2)O.
(2S)-2-isopropylmaleate + H(2)O → (2S)-2-isopropylmalate.
Protein Details
2. 3-isopropylmalate dehydrogenase
General function:
Involved in magnesium ion binding
Specific function:
Catalyzes the oxidation of 3-carboxy-2-hydroxy-4- methylpentanoate (3-isopropylmalate) to 3-carboxy-4-methyl-2- oxopentanoate. The product decarboxylates to 4-methyl-2 oxopentanoate
Gene Name:
LEU2
Uniprot ID:
P04173
Molecular weight:
38952.5
Reactions
(2R,3S)-3-isopropylmalate + NAD(+) → 4-methyl-2-oxopentanoate + CO(2) + NADH.
Protein Details
3. Trans-aconitate 3-methyltransferase
General function:
Involved in methyltransferase activity
Specific function:
Catalyzes the S-adenosylmethionine monomethyl esterification of trans-aconitate and 3-isopropylmalate at high affinity and of other molecules like cis-aconitate, isocitrate, and citrate at lower velocities and affinities. The function of trans-aconitate methylation appears to be in reducing the toxicity of this spontaneous breakdown product of cis-aconitate. The role of 3-isopropylmalate methylation is unclear but may represent a metabolic branch at 3-isopropylmalate, where some of the material is taken in the pathway leading to leucine and some is taken in a pathway to the 3-isopropylmalate methyl ester, a molecule that provides a signal to switch from vegetative to invasive growth in response to amino acid starvation
Gene Name:
TMT1
Uniprot ID:
P32643
Molecular weight:
34768.0
Reactions
S-adenosyl-L-methionine + trans-aconitate → S-adenosyl-L-homocysteine + (E)-2-(methoxycarbonylmethyl)butenedioate.