2-Isopropylmalic acid (YMDB00106)

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Identification

YMDB ID

YMDB00106

Name

2-Isopropylmalic acid

Species

Saccharomyces cerevisiae

Strain

Baker's yeast

Description

2-Isopropylmalic acid, also known as (2S)-2-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. 2-Isopropylmalic acid is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral.

Structure

MOL SDF PDB SMILES InChI

Synonyms

(2S)-2-hydroxy-2-(propan-2-yl)butanedioic acid
(2S)-2-Hydroxy-2-isopropylsuccinic acid
(2S)-2-Isopropylmalate
(3S)-3-carboxy-3-hydroxy-4-methylpentanoic acid
(3S)-3-carboxy-3-hydroxyisocaproic acid
2-Hydroxy-2-isopropylsuccinate
2-Hydroxy-2-isopropylsuccinic acid
2-Isopropyl-2-hydroxybutanedioate
2-Isopropyl-2-hydroxybutanedioic acid
2-isopropyl-Malic acid
2-Isopropylmalate
2-Isopropylmalic acid
3-Carboxy-3-hydroxy-4-methylpentanoate
3-Carboxy-3-hydroxyisocaproate
3-Carboxy-3-hydroxyisocaproic acid
3-hydroxy-4-methyl-3-carboxypentanoate
a-Isopropylmalate
a-Isopropylmalic acid
alpha-Isopropylmalate
alpha-Isopropylmalic acid
(S)-2-Hydroxy-2-(isopropyl)succinic acid
(2S)-2-Hydroxy-2-isopropylsuccinate
(2S)-2-Isopropylmalic acid
(3S)-3-Carboxy-3-hydroxy-4-methylpentanoate
(3S)-3-Carboxy-3-hydroxyisocaproate
(S)-2-Hydroxy-2-(isopropyl)succinate
3-Carboxy-3-hydroxy-4-methylpentanoic acid

CAS number

49601-06-1

Weight

Average: 176.1672
Monoisotopic: 176.068473494

InChI Key

BITYXLXUCSKTJS-ZETCQYMHSA-N

InChI

InChI=1S/C7H12O5/c1-4(2)7(12,6(10)11)3-5(8)9/h4,12H,3H2,1-2H3,(H,8,9)(H,10,11)/t7-/m0/s1

IUPAC Name

(2S)-2-hydroxy-2-(propan-2-yl)butanedioic acid

Traditional IUPAC Name

2-isopropyl-malic acid

Chemical Formula

C₇H₁₂O₅

SMILES

[H]OC(=O)C([H])([H])[C@@](O[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.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Fatty Acyls

Sub Class

Fatty acids and conjugates

Direct Parent

Hydroxy fatty acids

Alternative Parents

Substituents

Branched fatty acid
Methyl-branched fatty acid
Short-chain hydroxy acid
Hydroxy fatty acid
Alpha-hydroxy acid
Dicarboxylic acid or derivatives
Hydroxy acid
Tertiary alcohol
Carboxylic acid
Carboxylic acid derivative
Alcohol
Hydrocarbon derivative
Carbonyl group
Organic oxide
Organic oxygen compound
Organooxygen compound
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

2-isopropylmalic acid (CHEBI:35128 )
Dicarboxylic acids (LMFA01170083 )

Physical Properties

State

Solid

Charge

Melting point

144-146 °C

Experimental Properties

Property	Value	Reference
Water Solubility	Not Available	PhysProp
LogP	Not Available	PhysProp

Predicted Properties

Property	Value	Source
Water Solubility	181 g/L	ALOGPS
logP	-0.29	ALOGPS
logP	0.21	ChemAxon
logS	0.01	ALOGPS
pKa (Strongest Acidic)	3.63	ChemAxon
pKa (Strongest Basic)	-4.1	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	94.83 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	38.58 m³·mol⁻¹	ChemAxon
Polarizability	16.37 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	1	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Biological Properties

Cellular Locations

Cytoplasm
Extracellular
Mitochondrion

Organoleptic Properties

Not Available

SMPDB Pathways

Leucine Biosynthesis	PW002475
Pyruvate metabolism	PW002447

KEGG Pathways

Pyruvate metabolism	ec00620
Valine, leucine and isoleucine biosynthesis	ec00290

SMPDB Reactions

2-Isopropylmalic acid + Coenzyme A ↔ Acetyl-CoA + water + Alpha-Ketoisovaleric acid

(S)-3-methyl-2-oxovaleric acid + water + Acetyl-CoA → Coenzyme A + hydron + 2-Isopropylmalic acid

2-Isopropylmalic acid → water + 2-Isopropylmaleic acid

KEGG Reactions

water + 2-Isopropylmaleic acid ↔ 2-Isopropylmalic acid

Acetyl-CoA + Alpha-Ketoisovaleric acid + water → 2-Isopropylmalic acid + hydron + Coenzyme A

Concentrations

Intracellular Concentrations

Not Available

Extracellular Concentrations

Not Available

Spectra

Spectrum Type	Description	Splash Key	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-0006-9400000000-1c869c73651e7e4e5dda	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (3 TMS) - 70eV, Positive	splash10-00bl-9134000000-30fabfd0c26c38444fff	JSpectraViewer
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 10V, Negative (Annotated)	splash10-004i-0900000000-1bb48f5ddadbf88b8f6c	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 25V, Negative (Annotated)	splash10-00kr-9400000000-5df8f3f29d2e8a962cac	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 40V, Negative (Annotated)	splash10-05n0-9200000000-c62b1543d0e6a41388f1	JSpectraViewer \| MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0690-1900000000-3b83300261e0daab2ef1	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0006-9700000000-2652db028b01706ac042	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-00di-9300000000-808bda4307e96bcfcc83	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-003r-2900000000-9fa33cd594a81b5d67cd	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-055r-9700000000-8ab90438d0e6c9b7d0be	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0a4r-9100000000-41e1c40b755f8bfaf000	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
2D NMR	[1H,13C] 2D NMR Spectrum	Not Available	JSpectraViewer

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
Kobayashi, A., Edo, H., Furihata, K., Yoshimura, E. (2005). "Secretion of an aluminum chelator, 2-isopropylmalic acid, by the budding yeast, Saccharomyces cerevisiae." J Inorg Biochem 99:1260-1263.15833351
Yannai S. Dictionary of food compounds with CD-ROM: additives, flavors, and ingredients. Chapman & Hall/CRC; 2004.
Chang, L. F., Cunningham, T. S., Gatzek, P. R., Chen, W. J., Kohlhaw, G. B. (1984). "Cloning and characterization of yeast Leu4, one of two genes responsible for alpha-isopropylmalate synthesis." Genetics 108:91-106.6090272
Suzuki, T., Tamura, S., Nakanishi, H., Tashiro, M., Nishizawa, N. K., Yoshimura, E. (2007). "Reduction of aluminum toxicity by 2-isopropylmalic acid in the budding yeast Saccharomyces cerevisiae." Biol Trace Elem Res 120:257-263.17916978
Castrillo, J. I., Zeef, L. A., Hoyle, D. C., Zhang, N., Hayes, A., Gardner, D. C., Cornell, M. J., Petty, J., Hakes, L., Wardleworth, L., Rash, B., Brown, M., Dunn, W. B., Broadhurst, D., O'Donoghue, K., Hester, S. S., Dunkley, T. P., Hart, S. R., Swainston, N., Li, P., Gaskell, S. J., Paton, N. W., Lilley, K. S., Kell, D. B., Oliver, S. G. (2007). "Growth control of the eukaryote cell: a systems biology study in yeast." J Biol 6:4.17439666

Synthesis Reference:

Schloss J V; Magolda R; Emptage M Synthesis of alpha-isopropylmalate, beta-isopropylmalate, and dimethylcitraconate. Methods in enzymology (1988), 166 92-6.

External Links:

Resource	Link
CHEBI ID	35128
HMDB ID	HMDB00402
Pubchem Compound ID	5280523
Kegg ID	C02504
ChemSpider ID	4444155
FOODB ID	FDB011983
Wikipedia ID	Isopropylmalic acid
BioCyc ID	Not Available

Enzymes

Protein Details

1. 2-isopropylmalate synthase 2, mitochondrial

General function:: Involved in 2-isopropylmalate synthase activity
Specific function:: Catalyzes the condensation of the acetyl group of acetyl-CoA with 3-methyl-2-oxobutanoate (2-oxoisovalerate) to form 3-carboxy-3-hydroxy-4-methylpentanoate (2-isopropylmalate). Redundant to LEU4, responsible of about 20% of alpha-IPMS activity. Involved in leucine synthesis
Gene Name:: LEU9
Uniprot ID:: Q12166
Molecular weight:: 67199.60156

Reactions

Acetyl-CoA + 3-methyl-2-oxobutanoate + H(2)O → (2S)-2-isopropylmalate + CoA.

Protein Details

2. 2-isopropylmalate synthase

General function:: Involved in 2-isopropylmalate synthase activity
Specific function:: Catalyzes the condensation of the acetyl group of acetyl-CoA with 3-methyl-2-oxobutanoate (2-oxoisovalerate) to form 3-carboxy-3-hydroxy-4-methylpentanoate (2-isopropylmalate)
Gene Name:: LEU4
Uniprot ID:: P06208
Molecular weight:: 68408.29688

Reactions

Acetyl-CoA + 3-methyl-2-oxobutanoate + H(2)O → (2S)-2-isopropylmalate + CoA.

Protein Details

3. 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.

Structure for #<Compound:0xae6f3ef8>

Enzymes

Reactions

Reactions

Reactions