S(8)-succinyldihydrolipoamide (YMDB00747)

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Identification

YMDB ID

YMDB00747

Name

S(8)-succinyldihydrolipoamide

Species

Saccharomyces cerevisiae

Strain

Baker's yeast

Description

S(8)-succinyldihydrolipoamide belongs to the class of organic compounds known as thia fatty acids. These are fatty acid derivatives obtained by insertion of a sulfur atom at specific positions in the chain. S(8)-succinyldihydrolipoamide is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL SDF PDB SMILES InChI

Synonyms

S-Succinyldihydrolipoamide

CAS number

Not Available

Weight

Average: 307.429
Monoisotopic: 307.091199545

InChI Key

KWKBJWYJJBQOAE-UHFFFAOYSA-N

InChI

InChI=1S/C12H21NO4S2/c13-10(14)4-2-1-3-9(18)7-8-19-12(17)6-5-11(15)16/h9,18H,1-8H2,(H2,13,14)(H,15,16)

IUPAC Name

4-[(7-carbamoyl-3-sulfanylheptyl)sulfanyl]-4-oxobutanoic acid

Traditional IUPAC Name

S(8)-succinyldihydrolipoamide

Chemical Formula

C₁₂H₂₁NO₄S₂

SMILES

NC(=O)CCCCC(S)CCSC(=O)CCC(O)=O

Chemical Taxonomy

Description

belongs to the class of organic compounds known as thia fatty acids. These are fatty acid derivatives obtained by insertion of a sulfur atom at specific positions in the chain.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Fatty Acyls

Sub Class

Fatty acids and conjugates

Direct Parent

Thia fatty acids

Alternative Parents

Substituents

Thia fatty acid
Fatty acyl thioester
Fatty amide
Carboxamide group
Primary carboxylic acid amide
Thiocarboxylic acid ester
Carbothioic s-ester
Sulfenyl compound
Thiocarboxylic acid or derivatives
Alkylthiol
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Carbonyl group
Organic oxygen compound
Organosulfur compound
Organooxygen compound
Organonitrogen compound
Organic nitrogen compound
Organopnictogen compound
Hydrocarbon derivative
Organic oxide
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

S-substituted dihydrolipoamide (CHEBI:17432 )

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	0.082 g/L	ALOGPS
logP	1.94	ALOGPS
logP	1.06	ChemAxon
logS	-3.6	ALOGPS
pKa (Strongest Acidic)	4.22	ChemAxon
pKa (Strongest Basic)	-0.58	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	97.46 Å²	ChemAxon
Rotatable Bond Count	12	ChemAxon
Refractivity	78.12 m³·mol⁻¹	ChemAxon
Polarizability	33.25 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

Not Available

SMPDB Reactions

Not Available

KEGG Reactions

Coenzyme A + S(8)-succinyldihydrolipoamide → Dihydrolipoamide + Succinyl-CoA

Oxoglutaric acid + lipoamide + hydron ↔ Carbon dioxide + S(8)-succinyldihydrolipoamide

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	splash10-0f6x-8790000000-e55ecedd6751558a3cc0	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0abc-0591000000-68ceeee1aef07ecc7bca	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-00dl-1790000000-754724dd70bfb1ccb6ca	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0mbi-8900000000-aaca13771ecaf5ee69cd	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-05fr-4493000000-9bc9b7996f912788eb1c	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0592-9450000000-05e7b3f01cf7898f1ac7	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0006-9100000000-0e7f89fa1f0d117b1aab	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:

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
Ruttkay-Nedecky, B., Subik, J. (1990). "The OGD1 gene, affecting 2-oxoglutarate dehydrogenase in S. cerevisiae, is closely linked to HIS5 on chromosome IX." Curr Genet 17:85-88.2178788
Przybyla-Zawislak, B., Gadde, D. M., Ducharme, K., McCammon, M. T. (1999). "Genetic and biochemical interactions involving tricarboxylic acid cycle (TCA) function using a collection of mutants defective in all TCA cycle genes." Genetics 152:153-166.10224250

Synthesis Reference:

Not Available

External Links:

Resource	Link
CHEBI ID	17432
HMDB ID	HMDB0060556
Pubchem Compound ID	11953795
Kegg ID	C01169
ChemSpider ID	10128096
FOODB ID	Not Available
Wikipedia ID	Not Available
BioCyc ID	Not Available

Enzymes

Protein Details

1. Dihydrolipoyl dehydrogenase, mitochondrial

General function:: Involved in oxidoreductase activity
Specific function:: Lipoamide dehydrogenase is a component of the alpha- ketoacid dehydrogenase complexes. This includes the pyruvate dehydrogenase complex, which catalyzes the overall conversion of pyruvate to acetyl-CoA and CO(2). Acts also as component of the glycine cleavage system (glycine decarboxylase complex), which catalyzes the degradation of glycine
Gene Name:: LPD1
Uniprot ID:: P09624
Molecular weight:: 54009.69922

Reactions

Protein N(6)-(dihydrolipoyl)lysine + NAD(+) → protein N(6)-(lipoyl)lysine + NADH.

Protein Details

2. 2-oxoglutarate dehydrogenase, mitochondrial

General function:: Involved in oxoglutarate dehydrogenase (succinyl-transferring) activity
Specific function:: The 2-oxoglutarate dehydrogenase complex catalyzes the overall conversion of 2-oxoglutarate to succinyl-CoA and CO(2). It contains multiple copies of three enzymatic components:2- oxoglutarate dehydrogenase (E1), dihydrolipoamide succinyltransferase (E2) and lipoamide dehydrogenase (E3)
Gene Name:: KGD1
Uniprot ID:: P20967
Molecular weight:: 114416.0

Reactions

2-oxoglutarate + [dihydrolipoyllysine-residue succinyltransferase] lipoyllysine → [dihydrolipoyllysine-residue succinyltransferase] S-succinyldihydrolipoyllysine + CO(2).

Structure for #<Compound:0xa7e28b6c>

Enzymes

Reactions

Reactions