Homoisocitric acid (YMDB00144)

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Identification

YMDB ID

YMDB00144

Name

Homoisocitric acid

Species

Saccharomyces cerevisiae

Strain

Baker's yeast

Description

Homoisocitric acid, also known as homoisocitrate, belongs to the class of organic compounds known as tricarboxylic acids and derivatives. These are carboxylic acids containing exactly three carboxyl groups. Homoisocitric acid is an extremely weak basic (essentially neutral) compound (based on its pKa). Homoisocitric acid exists in both E. coli (prokaryote) and yeast (eukaryote).

Structure

MOL SDF PDB SMILES InChI

Synonyms

(-)-1-Hydroxy-1,2,4-butanetricarboxylate
(1R,2S)-1-Hydroxybutane-1,2,4-tricarboxylate
1-Hydroxybutane-1,2,4-tricarboxylate
3-Carboxy-2-hydroxyadipate
Homoisocitrate
(-)-Threo-homoisocitrate
3-Carboxy-2-hydroxyadipic acid
(-)-1-Hydroxy-1,2,4-butanetricarboxylic acid
(1R,2S)-1-Hydroxybutane-1,2,4-tricarboxylic acid
(-)-Threo-homoisocitric acid
Homoisocitric acid
1-Hydroxy-1,2,4-butanetricarboxylic acid

CAS number

Not Available

Weight

Average: 206.1501
Monoisotopic: 206.042652674

InChI Key

OEJZZCGRGVFWHK-WVZVXSGGSA-N

InChI

InChI=1S/C7H10O7/c8-4(9)2-1-3(6(11)12)5(10)7(13)14/h3,5,10H,1-2H2,(H,8,9)(H,11,12)(H,13,14)/t3-,5+/m0/s1

IUPAC Name

(1R,2S)-1-hydroxybutane-1,2,4-tricarboxylic acid

Traditional IUPAC Name

(-)-homoisocitric acid

Chemical Formula

C₇H₁₀O₇

SMILES

O[C@H]([C@H](CCC(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
Beta-hydroxy acid
Monosaccharide
Hydroxy acid
Alpha-hydroxy acid
Secondary 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

homoisocitric acid (CHEBI:30903 )

Physical Properties

State

Not Available

Charge

Melting point

Not Available

Experimental Properties

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

Predicted Properties

Property	Value	Source
Water Solubility	26.2 g/L	ALOGPS
logP	-0.54	ALOGPS
logP	-1	ChemAxon
logS	-0.9	ALOGPS
pKa (Strongest Acidic)	3.12	ChemAxon
pKa (Strongest Basic)	-4	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	6	ChemAxon
Refractivity	40.32 m³·mol⁻¹	ChemAxon
Polarizability	17.63 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

Mitochondrion

Organoleptic Properties

Not Available

SMPDB Pathways

Not Available

KEGG Pathways

Lysine biosynthesis

ec00300

SMPDB Reactions

Not Available

KEGG Reactions

but-1-ene-1,2,4-tricarboxylic acid + water ↔ Homoisocitric acid

NAD + Homoisocitric acid ↔ NADH + 2-Oxaloglutaric acid + hydron

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	splash10-040c-4900000000-245ee743f483524a8b03	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-06yc-0910000000-5c3dafa2c882be609ea5	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-044u-3900000000-844b0dbd7ceda195cc3c	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0079-9500000000-a9250a420bcaa09a94ec	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0bt9-1930000000-53a9e446f7ec93873520	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-090r-3900000000-9b3c3bafb9f9e3cfbfdd	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0aor-9500000000-7e7a6c4a5222720a30e9	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:

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
Strassman, M., Ceci, L. N. (1965). "Enzymatic formation of alpha-ketoadipic acid from homoisocitric acid." J Biol Chem 240:4357-4361.4284830
Zabriskie, T. M., Jackson, M. D. (2000). "Lysine biosynthesis and metabolism in fungi." Nat Prod Rep 17:85-97.10714900

Synthesis Reference:

Not Available

External Links:

Resource	Link
CHEBI ID	30903
HMDB ID	Not Available
Pubchem Compound ID	5460287
Kegg ID	C05662
ChemSpider ID	21865262
FOODB ID	Not Available
Wikipedia ID	Homoisocitric acid
BioCyc ID	Not Available

Enzymes

Protein Details

1. Homoisocitrate dehydrogenase, mitochondrial

General function:: Involved in magnesium ion binding
Specific function:: Catalyzes the NAD(+)-dependent conversion of homoisocitrate to alpha-ketoadipate
Gene Name:: LYS12
Uniprot ID:: P40495
Molecular weight:: 40068.60156

Reactions

(1R,2S)-1-hydroxybutane-1,2,4-tricarboxylate + NAD(+) → 2-oxoadipate + CO(2) + NADH.

Protein Details

2. Homoaconitase, mitochondrial

General function:: Involved in metabolic process
Specific function:: Responsible for the dehydration of cis-homoaconitate to homoisocitric acid
Gene Name:: LYS4
Uniprot ID:: P49367
Molecular weight:: 75150.10156

Reactions

(1R,2S)-1-hydroxybutane-1,2,4-tricarboxylate → (Z)-but-1-ene-1,2,4-tricarboxylate + H(2)O.

Structure for #<Compound:0xa79d31ac>

Enzymes

Reactions

Reactions