You are using an unsupported browser. Please upgrade your browser to a newer version to get the best experience on Yeast Metabolome Database.

O-Succinyl-L-homoserine (YMDB00917)

Identification
YMDB IDYMDB00917
NameO-Succinyl-L-homoserine
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
DescriptionO-succinyl-L-homoserine belongs to the class of organic compounds known as l-alpha-amino acids. These are alpha amino acids which have the L-configuration of the alpha-carbon atom. O-succinyl-L-homoserine is a very strong basic compound (based on its pKa). selenocystathionine and O-succinyl-L-homoserine can be converted into selenocysteine and succinic acid; which is mediated by the enzyme cystathionine gamma-synthase. In yeast, O-succinyl-L-homoserine is involved in the metabolic pathway called the selenocompound metabolism pathway.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
  • O-succinyl-L-homoserine
  • O-Succinylhomoserine
  • O4-Succinyl-L-homoserine
  • O-Succinylhomoserine, (DL)-isomer
CAS number1492-23-5
WeightAverage: 219.1919
Monoisotopic: 219.074287153
InChI KeyGNISQJGXJIDKDJ-YFKPBYRVSA-N
InChIInChI=1S/C8H13NO6/c9-5(8(13)14)3-4-15-7(12)2-1-6(10)11/h5H,1-4,9H2,(H,10,11)(H,13,14)/t5-/m0/s1
IUPAC Name(2S)-2-amino-4-[(3-carboxypropanoyl)oxy]butanoic acid
Traditional IUPAC NameO-succinyl-L-homoserine
Chemical FormulaC8H13NO6
SMILESN[C@@H](CCOC(=O)CCC(O)=O)C(O)=O
Chemical Taxonomy
Description belongs to the class of organic compounds known as l-alpha-amino acids. These are alpha amino acids which have the L-configuration of the alpha-carbon atom.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassAmino acids, peptides, and analogues
Direct ParentL-alpha-amino acids
Alternative Parents
Substituents
  • L-alpha-amino acid
  • Tricarboxylic acid or derivatives
  • Fatty acid ester
  • Fatty acyl
  • Carboxylic acid ester
  • Amino acid
  • Carboxylic acid
  • Amine
  • Hydrocarbon derivative
  • Organic oxide
  • Primary amine
  • Organooxygen compound
  • Organonitrogen compound
  • Primary aliphatic amine
  • Organopnictogen compound
  • Organic oxygen compound
  • Organic nitrogen compound
  • Carbonyl group
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Physical Properties
StateNot Available
Charge0
Melting pointNot Available
Experimental Properties
PropertyValueReference
Water SolubilityNot AvailablePhysProp
LogPNot AvailablePhysProp
Predicted Properties
PropertyValueSource
Water Solubility8.69 g/LALOGPS
logP-3.3ALOGPS
logP-3.6ChemAxon
logS-1.4ALOGPS
pKa (Strongest Acidic)1.69ChemAxon
pKa (Strongest Basic)9.46ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count6ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area126.92 ŲChemAxon
Rotatable Bond Count8ChemAxon
Refractivity46.95 m³·mol⁻¹ChemAxon
Polarizability20.51 ųChemAxon
Number of Rings0ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations
  • cytoplasm
Organoleptic PropertiesNot Available
SMPDB Pathways
Selenocompound metabolismPW002472 ThumbThumb?image type=greyscaleThumb?image type=simple
Sulfur metabolismPW002483 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways
Cysteine and methionine metabolismec00270 Map00270
Selenocompound metabolismec00450 Map00450
Sulfur metabolismec00920 Map00920
SMPDB Reactions
Selenocystathionine + O-Succinyl-L-homoserine ↔ Selenocysteine + Succinic acid
KEGG Reactions
O-Succinyl-L-homoserine + water ↔ hydron + Ammonium + 2-Ketobutyric acid + Succinic acid
O-Succinyl-L-homoserine + L-Cysteine → L-Cystathionine + hydron + Succinic acid
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0uk9-9600000000-0ee701fa496e19e3d173JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0uk9-1950000000-5b18c68cf76a73eb1d8fJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0pi0-7900000000-3331dd355814be8ede11JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0a6r-9400000000-146c8b009d4e75570320JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-014j-7690000000-0163fcb4afd466414db2JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-01ba-9720000000-dd9470ad7562bdf591b1JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-05tb-9200000000-ae21c8bfb909ac97af60JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
References
References:
  • UniProt Consortium (2011). "Ongoing and future developments at the Universal Protein Resource." Nucleic Acids Res 39:D214-D219.21051339
  • 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
  • Ono, B., Ishii, N., Naito, K., Miyoshi, S., Shinoda, S., Yamamoto, S., Ohmori, S. (1993). "Cystathionine gamma-lyase of Saccharomyces cerevisiae: structural gene and cystathionine gamma-synthase activity." Yeast 9:389-397.8511969
Synthesis Reference:Not Available
External Links:
ResourceLink
CHEBI ID16160
HMDB IDNot Available
Pubchem Compound ID439406
Kegg IDC01118
ChemSpider ID388523
FOODB IDFDB031067
Wikipedia IDNot Available
BioCyc IDNot Available

Enzymes

Protein Details
1. Putative cystathionine gamma-synthase YML082W
General function:
Involved in pyridoxal phosphate binding
Specific function:
O(4)-succinyl-L-homoserine + L-cysteine = L- cystathionine + succinate
Gene Name:
Not Available
Uniprot ID:
Q04533
Molecular weight:
74312.70313
Reactions
O(4)-succinyl-L-homoserine + L-cysteine → L-cystathionine + succinate.
Protein Details
2. Putative cystathionine gamma-synthase YLL058W
General function:
Involved in pyridoxal phosphate binding
Specific function:
O(4)-succinyl-L-homoserine + L-cysteine = L- cystathionine + succinate
Gene Name:
Not Available
Uniprot ID:
Q12198
Molecular weight:
64222.80078
Reactions
O(4)-succinyl-L-homoserine + L-cysteine → L-cystathionine + succinate.
Protein Details
3. Cystathionine gamma-synthase
General function:
Involved in pyridoxal phosphate binding
Specific function:
O(4)-succinyl-L-homoserine + L-cysteine = L- cystathionine + succinate
Gene Name:
STR2
Uniprot ID:
P47164
Molecular weight:
72349.89844
Reactions
O(4)-succinyl-L-homoserine + L-cysteine → L-cystathionine + succinate.