ECMDB: 3-Isopropylmalate (ECMDB04158) (M2MDB000641)

Identification Taxonomy Physical Properties Biological Properties Spectra Concentrations Links References Enzymes (4)XML

Proteins (1320)

Record Information

Version

2.0

Creation Date

2012-05-31 14:06:45 -0600

Update Date

2015-06-03 15:54:48 -0600

Secondary Accession Numbers

ECMDB04158

Identification

Name:

3-Isopropylmalate

Description

3-Isopropylmalate is an intermediate in valine, leucine and isoleucine biosynthesis. It is a substrate for 3-isopropylmalate dehydrogenase (TT_C0867)

Structure

MOL SDF PDB SMILES InChI

Synonyms:

β-isopropylmalate
β-isopropylmalic acid
(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-Isopropylmalate
3-3-Isopropylmalic acid
3-Carboxy-2-hydroxy-4-methylpentanoate
3-Carboxy-2-hydroxy-4-methylpentanoic acid
3-isopropylmalate
3-Isopropylmalic acid
3IPMA
b-Isopropylmalate
b-Isopropylmalic acid
Beta-Isopropylmalate
Beta-Isopropylmalic acid
IPM
β-Isopropylmalate
β-Isopropylmalic acid

Chemical Formula:

C₇H₁₂O₅

Weight:

Average: 176.1672
Monoisotopic: 176.068473494

InChI Key:

RNQHMTFBUSSBJQ-CRCLSJGQSA-N

InChI:

InChI=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

CAS number:

921-28-8

IUPAC Name:

(2R,3S)-2-hydroxy-3-(propan-2-yl)butanedioic acid

Traditional IUPAC Name:

(2R,3S)-3-isopropylmalic acid

SMILES:

CC(C)[C@@H]([C@@H](O)C(O)=O)C(O)=O

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

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 Framework

Aliphatic acyclic compounds

External Descriptors

3-isopropylmalic acid (CHEBI:43468 )

Physical Properties

State:

Solid

Charge:

-2

Melting point:

Not Available

Experimental Properties:

Property	Value	Source

Predicted Properties

Property	Value	Source
Water Solubility	83.3 g/L	ALOGPS
logP	0.28	ALOGPS
logP	0.16	ChemAxon
logS	-0.33	ALOGPS
pKa (Strongest Acidic)	3.68	ChemAxon
pKa (Strongest Basic)	-4	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	38.6 m³·mol⁻¹	ChemAxon
Polarizability	16.47 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

Reactions:

3-Isopropylmalate <> Isopropylmaleate + Water
3-Isopropylmalate + NAD > 2-Isopropyl-3-oxosuccinate + Hydrogen ion + NADH
3-Isopropylmalate + NAD <> 2-Isopropyl-3-oxosuccinate + NADH + Hydrogen ion
3-Isopropylmalate < Isopropylmaleate + Water
3-Isopropylmalate + NAD > Ketoleucine + Carbon dioxide + NADH
3-Isopropylmalate > Isopropylmaleate + Water
3-Isopropylmalate + Isopropylmaleate + Water <> 2-Isopropylmalic acid
3-Isopropylmalate + NAD + 2-Isopropyl-3-oxosuccinate <> Ketoleucine + Carbon dioxide + NADH + Hydrogen ion
Isopropylmaleate + Water > 3-Isopropylmalate
3 3-Isopropylmalate + NAD >2 2-Isopropyl-3-oxosuccinate + Hydrogen ion + NADH
3 3-Isopropylmalate <> Isopropylmaleate + Water
3 3-Isopropylmalate + NAD >2 2-Isopropyl-3-oxosuccinate + Hydrogen ion + NADH
3 3-Isopropylmalate <> Isopropylmaleate + Water

SMPDB Pathways:

Leucine Biosynthesis	PW000811
Secondary Metabolite: Leucine biosynthesis	PW000980
Secondary Metabolites: Valine and I-leucine biosynthesis from pyruvate	PW000978

KEGG Pathways:

C5-Branched dibasic acid metabolism ec00660
Metabolic pathways eco01100
Valine, leucine and isoleucine biosynthesis ec00290

EcoCyc Pathways:

isoleucine biosynthesis I (from threonine) LEUSYN-PWY

Concentrations

Not Available

Spectra

Spectra:

Spectrum Type	Description	Splash Key
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0002-0920000000-4ec856cc4eb69ab95ccc	View in MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0002-0920000000-4ec856cc4eb69ab95ccc	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-0006-9400000000-a5c729805d94db1fb7b3	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (3 TMS) - 70eV, Positive	splash10-00bl-9135000000-1982df651c1931669dae	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0a7i-1900000000-224a91a676e183e74333	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-06sl-7900000000-b06817c1e6edcae6d425	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-052o-9300000000-479bb2145817abc0bf1a	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0059-1900000000-acde792ba60cae65a216	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0far-9700000000-cf8f9dd2b32cfd503f42	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0a59-9100000000-138111afc561c6d0a2ec	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-03ei-3900000000-99922dc6120c0bc9d5ac	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-000i-9300000000-6c8d0a906ce3776c4769	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-052f-9000000000-229b51add43b0209aa10	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-001i-1900000000-bcc925b37cd5d5f31b5a	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-01q0-7900000000-222a48c445cf7526d6e6	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0019-9100000000-6003ddbcaf34c522b89a	View in MoNA
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer

References

References:

Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., Tanabe, M. (2012). "KEGG for integration and interpretation of large-scale molecular data sets." Nucleic Acids Res 40:D109-D114. Pubmed: 22080510
Keseler, I. M., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama-Castro, S., Muniz-Rascado, L., Bonavides-Martinez, C., Paley, S., Krummenacker, M., Altman, T., Kaipa, P., Spaulding, A., Pacheco, J., Latendresse, M., Fulcher, C., Sarker, M., Shearer, A. G., Mackie, A., Paulsen, I., Gunsalus, R. P., Karp, P. D. (2011). "EcoCyc: a comprehensive database of Escherichia coli biology." Nucleic Acids Res 39:D583-D590. Pubmed: 21097882

Synthesis Reference:

Not Available

Material Safety Data Sheet (MSDS)

Not Available

Links

External Links:

Resource	Link
CHEBI ID	35114
HMDB ID	HMDB12156
Pubchem Compound ID	5462261
Kegg ID	C04411
ChemSpider ID	4575349
Wikipedia ID	Isopropylmalic acid
BioCyc ID	2-D-THREO-HYDROXY-3-CARBOXY-ISOCAPROATE
EcoCyc ID	2-D-THREO-HYDROXY-3-CARBOXY-ISOCAPROATE
Ligand Expo	IPM

Enzymes

Protein Details

1. 3-isopropylmalate dehydratase large subunit

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:: leuC
Uniprot ID:: P0A6A6
Molecular weight:: 49882

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:: leuB
Uniprot ID:: P30125
Molecular weight:: 39517

Reactions

(2R,3S)-3-isopropylmalate + NAD(+) = 4-methyl-2-oxopentanoate + CO(2) + NADH.

Protein Details

3. 3-isopropylmalate dehydratase small subunit

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:: leuD
Uniprot ID:: P30126
Molecular weight:: 22487

Reactions

(2R,3S)-3-isopropylmalate = (2S)-2-isopropylmaleate + H(2)O.
(2S)-2-isopropylmaleate + H(2)O = (2S)-2-isopropylmalate.

Protein Details

4. D-malate dehydrogenase [decarboxylating]

General function:: Involved in magnesium ion binding
Specific function:: Catalyzes the NAD(+)-dependent oxidative decarboxylation of D-malate into pyruvate. Is essential for aerobic growth on D- malate as the sole carbon source. But is not required for anaerobic D-malate utilization, although DmlA is expressed and active in those conditions. Appears to be not able to use L- tartrate as a substrate for dehydrogenation instead of D-malate
Gene Name:: dmlA
Uniprot ID:: P76251
Molecular weight:: 40315

Reactions

(R)-malate + NAD(+) = pyruvate + CO(2) + NADH.

3-Isopropylmalate (ECMDB04158) (M2MDB000641)

Structure for #<Compound:0xa92bfc88>

Enzymes

Reactions

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