Succinyl-CoA (PAMDB000228)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes Transporters
Proteins (3280)
Record Information
Version 1.0
Update Date 1/22/2018 11:54:54 AM
Metabolite IDPAMDB000228
Identification
Name: Succinyl-CoA
Description:Succinyl-CoA is a combination of succinic acid and coenzyme A. It is an important intermediate in the citric acid cycle, where it is synthesized from alpha-Ketoglutarate by alpha-ketoglutarate dehydrogenase through decarboxylation. During the process, coenzyme A is added. It is also synthesized from propionyl CoA, the odd-numbered fatty acid, which cannot undergo beta-oxidation. Propionyl-CoA is carboxylated to D-methylmalonyl-CoA, isomerized to L-methylmalonyl-CoA, and rearranged to yield succinyl-CoA via a vitamin B12-dependent enzyme. Succinyl-CoA is an intermediate of the citric acid cycle.
Structure
Thumb
🔍MOLSDFPDBSMILESInChIView Structure
Synonyms:
  • CoA S-(hydrogen succinate)
  • CoA S-(Hydrogen succinic acid)
  • CoA S-succinate
  • CoA S-succinic acid
  • Coenzyme A S-(hydrogen succinate)
  • coenzyme A S-(Hydrogen succinic acid)
  • Coenzyme A S-succinate
  • Coenzyme A S-succinic acid
  • S-(Hydrogen butanedioate
  • S-(Hydrogen butanedioate) CoA
  • S-(Hydrogen butanedioate) Coenzyme A
  • S-(Hydrogen butanedioic acid
  • S-(Hydrogen butanedioic acid) CoA
  • S-(Hydrogen butanedioic acid) coenzyme A
  • S-Succinoylcoenzyme A
  • Suc-co-A
  • Suc-coa
  • Succ-S-CoA
  • Succ-S-coenzyme-A
  • Succ-CoA
  • Succ-Coenzyme A
  • Succ-coenzyme-A
  • Succ-S-CoA
  • Succ-S-Coenzyme A
  • Succ-S-coenzyme-A
  • Succino-1-yl-coenzyme a
  • Succinyl CoA
  • Succinyl coenzyme A
  • Succinyl-S-CoA
  • Succinyl-coenzyme A
  • Succinyl-S-CoA
  • Succinyl-S-Coenzyme A
  • Succinyl-S-coenzyme-A
  • Succinylcoenzyme A
  • Succinylcoenzyme-A
  • SucCoA
Chemical Formula: C25H40N7O19P3S
Average Molecular Weight: 867.607
Monoisotopic Molecular Weight: 867.131252359
InChI Key: VNOYUJKHFWYWIR-FZEDXVDRSA-N
InChI:InChI=1S/C25H40N7O19P3S/c1-25(2,20(38)23(39)28-6-5-14(33)27-7-8-55-16(36)4-3-15(34)35)10-48-54(45,46)51-53(43,44)47-9-13-19(50-52(40,41)42)18(37)24(49-13)32-12-31-17-21(26)29-11-30-22(17)32/h11-13,18-20,24,37-38H,3-10H2,1-2H3,(H,27,33)(H,28,39)(H,34,35)(H,43,44)(H,45,46)(H2,26,29,30)(H2,40,41,42)/t13-,18-,19-,20?,24-/m1/s1
CAS number: 604-98-8
IUPAC Name:4-[(2-{3-[(2R)-3-[({[({[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)oxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy](hydroxy)phosphoryl}oxy)methyl]-2-hydroxy-3-methylbutanamido]propanamido}ethyl)sulfanyl]-4-oxobutanoic acid
Traditional IUPAC Name: succinyl-coa
SMILES:CC(C)(COP(O)(=O)OP(O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1OP(O)(O)=O)N1C=NC2=C1N=CN=C2N)C(O)C(=O)NCCC(=O)NCCSC(=O)CCC(O)=O
Chemical Taxonomy
Taxonomy DescriptionThis compound belongs to the class of organic compounds known as acyl coas. These are organic compounds containing a coenzyme A substructure linked to an acyl chain.
Kingdom Organic compounds
Super ClassLipids and lipid-like molecules
Class Fatty Acyls
Sub ClassFatty acyl thioesters
Direct Parent Acyl CoAs
Alternative Parents
Substituents
  • Coenzyme a or derivatives
  • Purine ribonucleoside diphosphate
  • Purine ribonucleoside 3',5'-bisphosphate
  • N-glycosyl compound
  • Glycosyl compound
  • Organic pyrophosphate
  • Monosaccharide phosphate
  • 6-aminopurine
  • Purine
  • Imidazopyrimidine
  • Monoalkyl phosphate
  • Thia fatty acid
  • Aminopyrimidine
  • Imidolactam
  • Alkyl phosphate
  • Pyrimidine
  • Primary aromatic amine
  • Phosphoric acid ester
  • Organic phosphoric acid derivative
  • Organic phosphate
  • N-substituted imidazole
  • Monosaccharide
  • Saccharide
  • Heteroaromatic compound
  • Oxolane
  • Imidazole
  • Azole
  • Thiocarboxylic acid ester
  • Secondary alcohol
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Organic 1,3-dipolar compound
  • Propargyl-type 1,3-dipolar organic compound
  • Sulfenyl compound
  • Thioether
  • Thiocarboxylic acid or derivatives
  • Monocarboxylic acid or derivatives
  • Carboxylic acid
  • Carboxylic acid derivative
  • Carboximidic acid derivative
  • Carboximidic acid
  • Hydrocarbon derivative
  • Primary amine
  • Organosulfur compound
  • Organooxygen compound
  • Organonitrogen compound
  • Carbonyl group
  • Amine
  • Alcohol
  • Aromatic heteropolycyclic compound
Molecular Framework Aromatic heteropolycyclic compounds
External Descriptors
Physical Properties
State: Solid
Charge:-5
Melting point: Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility3.84 mg/mLALOGPS
logP-0.61ALOGPS
logP-7.2ChemAxon
logS-2.4ALOGPS
pKa (Strongest Acidic)0.82ChemAxon
pKa (Strongest Basic)4.98ChemAxon
Physiological Charge-5ChemAxon
Hydrogen Acceptor Count19ChemAxon
Hydrogen Donor Count10ChemAxon
Polar Surface Area400.93 Å2ChemAxon
Rotatable Bond Count23ChemAxon
Refractivity183.1 m3·mol-1ChemAxon
Polarizability76.92 Å3ChemAxon
Number of Rings3ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations: Cytoplasm
Reactions:
alpha-Ketoglutarate + Coenzyme A + NAD > Carbon dioxide + NADH + Succinyl-CoA
Adenosine triphosphate + Coenzyme A + Succinic acid <> ADP + Phosphate + Succinyl-CoA
Water + Succinyl-CoA + Tetrahydrodipicolinate <> Coenzyme A + N-Succinyl-2-amino-6-ketopimelate
Coenzyme A + 3-Oxoadipyl-CoA <> Acetyl-CoA + Succinyl-CoA
L-Arginine + Succinyl-CoA <> Coenzyme A + Hydrogen ion + N2-Succinyl-L-arginine
Succinyl-CoA > (S)-Methylmalonyl-CoA
Propionyl-CoA + Succinic acid > Propionic acid + Succinyl-CoA
L-Homoserine + Succinyl-CoA <> Coenzyme A + O-Succinyl-L-homoserine
Succinyl-CoA + L-Arginine <> Coenzyme A + N2-Succinyl-L-arginine
(R)-Methylmalonyl-CoA <> Succinyl-CoA
Succinyl-CoA + Enzyme N6-(dihydrolipoyl)lysine + Enzyme N6-(dihydrolipoyl)lysine <> Coenzyme A + [Dihydrolipoyllysine-residue succinyltransferase] S-succinyldihydrolipoyllysine
Oxoglutaric acid + Coenzyme A + NAD > Succinyl-CoA + Carbon dioxide + NADH
R-Methylmalonyl-CoA <> Succinyl-CoA
Acetoacetyl-CoA + Coenzyme A + Acetoacetyl-CoA > Acetyl-CoA + Succinyl-CoA + Succinyl-CoA
(S)-2,3,4,5-tetrahydrodipicolinate + Succinyl-CoA + Water + Succinyl-CoA > Coenzyme A + N-Succinyl-2-amino-6-ketopimelate
Oxoglutaric acid + NAD + Coenzyme A > Succinyl-CoA + NADH + Hydrogen ion + Carbon dioxide + Succinyl-CoA
Succinyl-CoA + Phosphate + Guanosine diphosphate + Succinyl-CoA <> Succinic acid + Coenzyme A + Guanosine triphosphate
Oxoglutaric acid + NAD + Coenzyme A > NADH + Carbon dioxide + Succinyl-CoA + Succinyl-CoA
Succinyl-CoA + Adenosine diphosphate + Phosphate + Succinyl-CoA + ADP > Adenosine triphosphate + Coenzyme A + Succinic acid
L-Arginine + Succinyl-CoA + Succinyl-CoA > Coenzyme A + Hydrogen ion + N2-succinyl-L-arginine + N2-succinyl-L-arginine
L-Homoserine + Succinyl-CoA + L-Homoserine + Succinyl-CoA > Coenzyme A + O-Succinyl-L-homoserine
Succinic acid + Propionyl-CoA + Propionyl-CoA > Propionic acid + Succinyl-CoA + Succinyl-CoA
Succinyl-CoA + Succinyl-CoA > Methylmalonyl-CoA
Succinyl-CoA + Dihydrolipoamide + Succinyl-CoA + Dihydrolipoamide > Coenzyme A + (S)-Succinyldihydrolipoamide
More...

Pathways:
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-000i-1912000130-5d37f85b68294f1bcd7bView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-000i-0913000000-5f3ce9a55c6b75d06990View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-000i-2911000000-d4965f3bcf572b49e153View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-017j-8921150580-9a135870fabc65b05d2eView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-003s-4910010010-1b02ce20692d0ded522eView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-057i-6900100000-44f1bfaeb10b1463a0bdView in MoNA
References
References:
  • Bennett, B. D., Kimball, E. H., Gao, M., Osterhout, R., Van Dien, S. J., Rabinowitz, J. D. (2009). "Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli." Nat Chem Biol 5:593-599. Pubmed: 19561621
  • 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
  • van der Werf, M. J., Overkamp, K. M., Muilwijk, B., Coulier, L., Hankemeier, T. (2007). "Microbial metabolomics: toward a platform with full metabolome coverage." Anal Biochem 370:17-25. Pubmed: 17765195
  • Winder, C. L., Dunn, W. B., Schuler, S., Broadhurst, D., Jarvis, R., Stephens, G. M., Goodacre, R. (2008). "Global metabolic profiling of Escherichia coli cultures: an evaluation of methods for quenching and extraction of intracellular metabolites." Anal Chem 80:2939-2948. Pubmed: 18331064
Synthesis Reference: Wollemann, M. Mechanism of the succinyl-coenzyme A synthesis in brain extracts. Acta Physiologica Academiae Scientiarum Hungaricae (1959), 16 153-4.
Material Safety Data Sheet (MSDS) Not Available
External Links:
ResourceLink
CHEBI ID15380
HMDB IDHMDB01022
Pubchem Compound ID439161
Kegg IDC00091
ChemSpider ID388307
WikipediaSuccinyl-CoA
BioCyc IDSUC-COA
EcoCyc IDSUC-COA
Ligand ExpoSCA