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Identification
YMDB IDYMDB00368
Name3-Isopropylmalate
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
Description3-Isopropylmalate, also known as IPM, belongs to the class of organic compounds known as hydroxy fatty acids. These are fatty acids in which the chain bears a hydroxyl group. 3-Isopropylmalate is an extremely weak basic (essentially neutral) compound (based on its pKa).
Structure
Thumb
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
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 + water3-Isopropylmalate
3-Isopropylmalate + NADNADH + hydron + (2S)-2-Isopropyl-3-oxosuccinate
KEGG Reactions
3-Isopropylmalate + S-AdenosylmethionineS-Adenosylhomocysteine + 3-hydroxy-2-isopropyl-4-methoxy-4-oxobutanoate
3-Isopropylmalatewater + 2-Isopropylmaleic acid
NAD + 3-IsopropylmalateNADH + (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 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
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 IDFDB030113
Wikipedia IDIsopropylmalic acid
BioCyc ID2-D-THREO-HYDROXY-3-CARBOXY-ISOCAPROATE

Enzymes

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.
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.
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.