MiMeDB: Showing metabocard for 3-Carboxy-2-hydroxy-4-methylpentanoate (MMDBc0049884)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-04-29 22:45:31 UTC

Update Date

2022-09-01 02:16:52 UTC

Metabolite ID

MMDBc0049884

Metabolite Identification

Common Name

3-Carboxy-2-hydroxy-4-methylpentanoate

Description

3-Carboxy-2-hydroxy-4-methylpentanoate (CAS: 16048-89-8), also known as 3-isopropylmalic acid, is an intermediate in valine, leucine, and isoleucine biosynthesis. It is a substrate for 3-isopropylmalate dehydrogenase (TT_C0867) and can be generated from the reduction of 2-isopropyl-3-oxosuccinate. Leucine biosynthesis involves a five-step conversion process starting with the valine precursor 2-keto-isovalerate. The final step in this pathway is catalyzed by two transaminases of broad specificity: branched-chain amino acid transferase (IlvE) and tyrosine aminotransferase (TyrB). This pathway is part of the super pathway of leucine, valine, and isoleucine biosynthesis that generates not only isoleucine and valine but also leucine.

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI

HEADER    PROTEIN                                 04-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-20         0                                  
HETATM    1  C   UNK     0       0.665   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -0.665  -0.764   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.995  -0.764   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.665   1.542   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -2.002   0.000   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      -0.665  -2.306   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       3.332   0.000   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       1.995  -2.306   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       2.002   2.306   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -0.672   2.306   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      -2.037   1.677   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0      -3.332  -0.771   0.000  0.00  0.00           O+0
CONECT    1    2    3    4                                                  
CONECT    2    1    5    6                                                  
CONECT    3    1    8    7                                                  
CONECT    4    1   10    9                                                  
CONECT    5    2   11   12                                                  
CONECT    6    2                                                            
CONECT    7    3                                                            
CONECT    8    3                                                            
CONECT    9    4                                                            
CONECT   10    4                                                            
CONECT   11    5                                                            
CONECT   12    5                                                            
MASTER        0    0    0    0    0    0    0    0   12    0   22    0
END

Synonyms

Value	Source
(2R,3S)-2-Hydroxy-3-isopropylsuccinic acid	ChEBI
(2R,3S)-3-Carboxy-2-hydroxy-4-methylpentanoic acid	ChEBI
2-D-Threo-hydroxy-3-carboxy-isocaproate	ChEBI
2-D-Threo-hydroxy-3-carboxyisocaproic acid	ChEBI
3-Carboxy-2-hydroxy-4-methylpentanoate	ChEBI
3-Isopropylmalate	ChEBI
(2R,3S)-2-Hydroxy-3-isopropylsuccinate	Generator
(2R,3S)-3-Carboxy-2-hydroxy-4-methylpentanoate	Generator
2-D-Threo-hydroxy-3-carboxy-isocaproic acid	Generator
2-D-Threo-hydroxy-3-carboxyisocaproate	Generator
3-Carboxy-2-hydroxy-4-methylpentanoic acid	Generator
3-Isopropylmalic acid	Generator
(2R,3S)-2-Hydroxy-3-(propan-2-yl)butanedioate	HMDB
(2R,3S)-2-Hydroxy-3-(propan-2-yl)butanedioic acid	HMDB
(2R,3S)-3-Isopropylmalate	HMDB
(2R,3S)-3-Isopropylmalic acid	HMDB
3-3-Isopropylmalic acid	HMDB
IPM	HMDB
beta-Isopropylmalate, erythro-(L)-isomer	MeSH, HMDB
beta-Isopropylmalate	MeSH, HMDB
(2R,3S)-2-Hydroxy-3-(1-methylethyl)butanedioic acid	HMDB
2-Hydroxy-3-(1-methylethyl)butanedioic acid	HMDB
Isopropylmalate	HMDB
Isopropylmalic acid	HMDB
beta-Isopropylmalic acid	HMDB
β-Isopropylmalic acid	HMDB

Molecular Formula

C₇H₁₂O₅

Average Mass

176.1672

Monoisotopic Mass

176.068473494

IUPAC Name

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

Traditional Name

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

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

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

InChI Key

RNQHMTFBUSSBJQ-CRCLSJGQSA-N

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 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

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	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0002-0920000000-4ec856cc4eb69ab95ccc	2017-09-12	View Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0002-0920000000-4ec856cc4eb69ab95ccc	2018-05-18	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-0006-9400000000-a5c729805d94db1fb7b3	2016-09-22	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (3 TMS) - 70eV, Positive	splash10-00bl-9135000000-1982df651c1931669dae	2017-10-06	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0a7i-1900000000-224a91a676e183e74333	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-06sl-7900000000-b06817c1e6edcae6d425	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-052o-9300000000-479bb2145817abc0bf1a	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0059-1900000000-acde792ba60cae65a216	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0far-9700000000-cf8f9dd2b32cfd503f42	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0a59-9100000000-138111afc561c6d0a2ec	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-03ei-3900000000-99922dc6120c0bc9d5ac	2021-09-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-000i-9300000000-6c8d0a906ce3776c4769	2021-09-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-052f-9000000000-229b51add43b0209aa10	2021-09-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-001i-1900000000-bcc925b37cd5d5f31b5a	2021-09-24	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-01q0-7900000000-222a48c445cf7526d6e6	2021-09-24	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0019-9100000000-6003ddbcaf34c522b89a	2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-09-29	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Feces

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0007074	3-Carboxy-2-hydroxy-4-methylpentanoate	3-Carboxy-4-methyl-2-oxopentanoate	Not Available		VMH	30371894
MMDBr0007075	3-Carboxy-2-hydroxy-4-methylpentanoate	2-Isopropylmaleate	Not Available		VMH	30371894

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Bacteria	Firmicutes	269	Human feces; Human pleural fluid plaque; Pig ; Human ; Human stool; Human subgingival plaque	Metabolic reconstruction
Bacteria	Proteobacteria	173	Human feces; Human sputum; Human ; Human unknown; Pig ; Human pleural fluid plaque; Human dental plaque; Human nasal swab; Human stool; Human feces; pleural fluid plaque; bal	Metabolic reconstruction
Bacteria	Actinobacteria	114	Human feces; Human pleural fluid plaque; Human dental plaque; Human sputum; Human ; Human supragingival plaque; Human mucosa; Human subgingival plaque	Metabolic reconstruction
Bacteria	Verrucomicrobia	1	Human ; Human feces	Metabolic reconstruction
Bacteria	Bacteroidetes	93	Human feces; Human appendix biopsy; Human ; Human stool; Human urine; Human gastric fluid; Human saliva	Metabolic reconstruction
Bacteria	Synergistetes	4	Human feces	Metabolic reconstruction
Bacteria	Spirochaetes	1	Human feces	Metabolic reconstruction
Archaea	Thaumarchaeota	1		Metabolic reconstruction
Bacteria	Fusobacteria	4	Human feces; Human	Metabolic reconstruction
Archaea	Euryarchaeota	5		Metabolic reconstruction
Eukaryota/Fungi	Ascomycota	1		Metabolic reconstruction
Bacteria	Planctomycetes	1	Human feces	Metabolic reconstruction
Archaea	Crenarchaeota	1		Metabolic reconstruction

Exposure Sources

Source Type	Source Sub-type	Species	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference
Human Feces	Detected but not Quantified									HMDB

External Links

HMDB ID

HMDB0012156

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

2-D-THREO-HYDROXY-3-CARBOXY-ISOCAPROATE

BiGG ID

Not Available

Wikipedia Link

Isopropylmalic acid

METLIN ID

Not Available

PubChem Compound

5462261

PDB ID

IPM

ChEBI ID

43468

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Simons K, Toomre D: Lipid rafts and signal transduction. Nat Rev Mol Cell Biol. 2000 Oct;1(1):31-9. doi: 10.1038/35036052. [PubMed:11413487 ]
Watson AD: Thematic review series: systems biology approaches to metabolic and cardiovascular disorders. Lipidomics: a global approach to lipid analysis in biological systems. J Lipid Res. 2006 Oct;47(10):2101-11. doi: 10.1194/jlr.R600022-JLR200. Epub 2006 Aug 10. [PubMed:16902246 ]
Sethi JK, Vidal-Puig AJ: Thematic review series: adipocyte biology. Adipose tissue function and plasticity orchestrate nutritional adaptation. J Lipid Res. 2007 Jun;48(6):1253-62. doi: 10.1194/jlr.R700005-JLR200. Epub 2007 Mar 20. [PubMed:17374880 ]
Lingwood D, Simons K: Lipid rafts as a membrane-organizing principle. Science. 2010 Jan 1;327(5961):46-50. doi: 10.1126/science.1174621. [PubMed:20044567 ]
Gunstone, Frank D., John L. Harwood, and Albert J. Dijkstra (2007). The lipid handbook with CD-ROM. CRC Press.

Showing metabocard for 3-Carboxy-2-hydroxy-4-methylpentanoate (MMDBc0049884)

MOL for #<Metabolite:0x00007fecb033cbe8>

3D MOL for #<Metabolite:0x00007fecb033cbe8>

3D SDF for #<Metabolite:0x00007fecb033cbe8>

3D-SDF for #<Metabolite:0x00007fecb033cbe8>

PDB for #<Metabolite:0x00007fecb033cbe8>

3D PDB for #<Metabolite:0x00007fecb033cbe8>

SMILES for #<Metabolite:0x00007fecb033cbe8>

INCHI for #<Metabolite:0x00007fecb033cbe8>

Structure for #<Metabolite:0x00007fecb033cbe8>

3D Structure for #<Metabolite:0x00007fecb033cbe8>