(2S,3R)-3-hydroxybutane-1,2,3-tricarboxylic acid (YMDB00535)

Identification

YMDB ID

YMDB00535

Name

(2S,3R)-3-hydroxybutane-1,2,3-tricarboxylic acid

Species

Saccharomyces cerevisiae

Strain

Baker's yeast

Description

Alpha-Methylisocitric Acid, also known as methylisocitrate, belongs to the class of organic compounds known as tricarboxylic acids and derivatives. These are carboxylic acids containing exactly three carboxyl groups. Thus, Alpha-methylisocitric Acid is considered to be a fatty acid lipid molecule. Alpha-Methylisocitric Acid is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral. Alpha-Methylisocitric Acid exists in both E. coli (prokaryote) and yeast (eukaryote).

Structure

MOL SDF 3D-SDF PDB SMILES InChI View 3D Structure

Synonyms

(2s,3r)-3-hydroxybutane-1,2,3-tricarboxylate
(2S,3R)-3-hydroxybutane-1,2,3-tricarboxylic acid
1D-myo-Inositol 1,3,4,5,6-pentakisphosphate
D-myo-Inositol 1,3,4,5,6-pentakisphosphate
Inositol 1,3,4,5,6-pentakisphosphate
Inositol 1,3,4,5,6-pentaphosphate
Inositol pentaphosphate
methylisocitrate
methylisocitric acid
myo-Inositol 1,3,4,5,6-pentakis(phosphate)
3-Carboxy-2,3-dideoxy-4-C-methyl-L-threo-pentaric acid
3-Carboxy-2,3-dideoxy-4-C-methyl-L-threo-pentarate
a-Methylisocitrate
a-Methylisocitric acid
alpha-Methylisocitrate
Α-methylisocitrate
Α-methylisocitric acid

CAS number

20298-95-7

Weight

Average: 206.1501
Monoisotopic: 206.042652674

InChI Key

HHKPKXCSHMJWCF-WVBDSBKLSA-N

InChI

InChI=1S/C7H10O7/c1-7(14,6(12)13)3(5(10)11)2-4(8)9/h3,14H,2H2,1H3,(H,8,9)(H,10,11)(H,12,13)/t3-,7-/m1/s1

IUPAC Name

(1R,2S)-1-hydroxy-1-methylpropane-1,2,3-tricarboxylic acid

Traditional IUPAC Name

methylisocitrate

Chemical Formula

C₇H₁₀O₇

SMILES

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

Chemical Taxonomy

Description

belongs to the class of organic compounds known as tricarboxylic acids and derivatives. These are carboxylic acids containing exactly three carboxyl groups.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Tricarboxylic acids and derivatives

Direct Parent

Tricarboxylic acids and derivatives

Alternative Parents

Substituents

Tricarboxylic acid or derivatives
Hydroxy acid
Alpha-hydroxy acid
Tertiary alcohol
Carboxylic acid
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Carbonyl group
Alcohol
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

tricarboxylic acid (CHEBI:15607 )
methylisocitric acid (CHEBI:15607 )

Physical Properties

State

Solid

Charge

Melting point

Not Available

Experimental Properties

Property	Value	Reference
Water Solubility	Not Available	PhysProp
LogP	-7.999	PhysProp

Predicted Properties

Property	Value	Source
Water Solubility	149 g/L	ALOGPS
logP	-0.87	ALOGPS
logP	-1	ChemAxon
logS	-0.14	ALOGPS
pKa (Strongest Acidic)	3.17	ChemAxon
pKa (Strongest Basic)	-4.1	ChemAxon
Physiological Charge	-3	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	132.13 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	40.43 m³·mol⁻¹	ChemAxon
Polarizability	17.26 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

Not Available

Organoleptic Properties

Not Available

SMPDB Pathways

Inositol Metabolism	PW002498
Inositol phosphate metabolism	PW002495

KEGG Pathways

Inositol phosphate metabolism	ec00562
Propanoate metabolism	ec00640

SMPDB Reactions

Not Available

KEGG Reactions

Not Available

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	splash10-000i-9700000000-5e955ef633a08113ea4b	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-07br-0910000000-452b302f2c220ffbdcb7	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-00xr-5900000000-09ce5fc471f12b38970e	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-01b9-6900000000-affa291e126f5947919d	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0900-2920000000-936e30fcb714056e11d0	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-014i-2900000000-01942de5aa6c81413a4f	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-00y0-9300000000-32de60d42bd02d610c8c	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer

References

References:

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
Singh, J., Kumar, D., Ramakrishnan, N., Singhal, V., Jervis, J., Garst, J. F., Slaughter, S. M., DeSantis, A. M., Potts, M., Helm, R. F. (2005). "Transcriptional response of Saccharomyces cerevisiae to desiccation and rehydration." Appl Environ Microbiol 71:8752-8763.16332871

Synthesis Reference:

Not Available

External Links:

Resource	Link
CHEBI ID	15607
HMDB ID	HMDB03529
Pubchem Compound ID	5459784
Kegg ID	C04593
ChemSpider ID	4573561
FOODB ID	Not Available
Wikipedia ID	Not Available
BioCyc ID	Not Available

Enzymes

Protein Details

1. Mitochondrial 2-methylisocitrate lyase

General function:: Involved in isocitrate lyase activity
Specific function:: Catalyzes the formation of pyruvate and succinate from 2-methylisocitrate during the metabolism of endogenous propionyl- CoA. Does not act on isocitrate
Gene Name:: ICL2
Uniprot ID:: Q12031
Molecular weight:: 64975.39844

Reactions

(2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate → pyruvate + succinate.

Protein Details

2. Probable 2-methylcitrate dehydratase

General function:: Involved in 2-methylcitrate dehydratase activity
Specific function:: Catalyzes the dehydration of 2-methylcitrate to 2- methyl-cis-aconitate
Gene Name:: PDH1
Uniprot ID:: Q12428
Molecular weight:: 57683.10156

Reactions

(2S,3S)-2-hydroxybutane-1,2,3-tricarboxylate → (Z)-but-2-ene-1,2,3-tricarboxylate + H(2)O.

(2S,3R)-3-hydroxybutane-1,2,3-tricarboxylic acid (YMDB00535)

Structure for #<Compound:0x0400982c>

Enzymes

Reactions

Reactions