N-Succinyl-2-amino-6-ketopimelate (ECMDB12266) (M2MDB000835)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes (2)XML
Proteins (530)
Record Information
Version2.0
Creation Date2012-05-31 14:21:24 -0600
Update Date2015-06-03 17:19:04 -0600
Secondary Accession Numbers
  • ECMDB12266
Identification
Name:N-Succinyl-2-amino-6-ketopimelate
DescriptionN-Succinyl-2-amino-6-ketopimelate is an intermediate in lysine biosynthesis. It is the fourth to last step in n the synthesis of lysine and is converted from tetrahydrodipicolinate via the enzyme tetrahydrodipicolinate N-succinyltransferase (EC 2.3.1.117). It is then converted to N-succinyl-L,L-2,6-diaminopimelate via the enzyme Succinyldiaminopimelate transferase (EC 2.6.1.17).
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms:
  • (2S)-2-(3-carboxypropanamido)-6-oxoheptanedioate
  • (2S)-2-(3-carboxypropanamido)-6-oxoheptanedioic acid
  • (S)-2-(Succinylamino)-6-oxoheptanedioate
  • (S)-2-(Succinylamino)-6-oxoheptanedioic acid
  • N-succinyl-L-2-amino-6-oxoheptanedioate
  • L-2-Succinylamino-6-oxoheptanedioate
  • L-2-Succinylamino-6-oxoheptanedioic acid
  • N-Succinyl-2-amino-6-ketopimelic acid
  • N-Succinyl-2-amino-6-oxo-L-pimelate
  • N-Succinyl-2-amino-6-oxo-L-pimelic acid
  • N-Succinyl-2-L-amino-6-oxoheptanedioate
  • N-Succinyl-2-L-amino-6-oxoheptanedioic acid
  • N-Succinyl-epsilon-keto-L-aminopimelate
  • N-Succinyl-epsilon-keto-L-aminopimelic acid
  • N-Succinyl-L-2-amino-6-oxoheptanedioate
  • N-Succinyl-L-2-amino-6-oxoheptanedioic acid
  • N-Succinyl-L-2-amino-6-oxopimelate
  • N-Succinyl-L-2-amino-6-oxopimelic acid
  • SAKPA
  • Succinyl-ε-keto-α-aminopimelate
  • Succinyl-ε-keto-α-aminopimelic acid
  • Succinyl-epsilon-keto-a-aminopimelate
  • Succinyl-epsilon-keto-a-aminopimelic acid
  • Succinyl-epsilon-keto-alpha-aminopimelate
  • Succinyl-epsilon-keto-alpha-aminopimelic acid
  • Succinyl-epsilon-keto-α-aminopimelate
  • Succinyl-epsilon-keto-α-aminopimelic acid
Chemical Formula:C11H15NO8
Weight:Average: 289.2387
Monoisotopic: 289.079766461
InChI Key:SDVXSCSNVVZWDD-LURJTMIESA-N
InChI:InChI=1S/C11H15NO8/c13-7(11(19)20)3-1-2-6(10(17)18)12-8(14)4-5-9(15)16/h6H,1-5H2,(H,12,14)(H,15,16)(H,17,18)(H,19,20)/t6-/m0/s1
CAS number:Not Available
IUPAC Name:(2S)-2-(3-carboxypropanamido)-6-oxoheptanedioic acid
Traditional IUPAC Name:(2S)-2-(3-carboxypropanamido)-6-oxoheptanedioic acid
SMILES:OC(=O)CCC(=O)N[C@@H](CCCC(=O)C(O)=O)C(O)=O
Chemical Taxonomy
Description belongs to the class of organic compounds known as n-acyl-l-alpha-amino acids. These are n-acylated 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 ParentN-acyl-L-alpha-amino acids
Alternative Parents
Substituents
  • N-acyl-l-alpha-amino acid
  • Tricarboxylic acid or derivatives
  • Alpha-keto acid
  • Fatty amide
  • Keto acid
  • Fatty acyl
  • N-acyl-amine
  • Alpha-hydroxy ketone
  • Carboxamide group
  • Secondary carboxylic acid amide
  • Ketone
  • Carboxylic acid
  • Organooxygen compound
  • Hydrocarbon derivative
  • Organic oxide
  • Organopnictogen compound
  • Carbonyl group
  • Organic oxygen compound
  • Organic nitrogen compound
  • Organonitrogen compound
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Physical Properties
State:Solid
Charge:-3
Melting point:Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility1.41 g/LALOGPS
logP-0.78ALOGPS
logP-0.55ChemAxon
logS-2.3ALOGPS
pKa (Strongest Acidic)2.78ChemAxon
pKa (Strongest Basic)-1.5ChemAxon
Physiological Charge-3ChemAxon
Hydrogen Acceptor Count8ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area158.07 ŲChemAxon
Rotatable Bond Count10ChemAxon
Refractivity61.57 m³·mol⁻¹ChemAxon
Polarizability25.89 ųChemAxon
Number of Rings0ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations:Cytoplasm
Reactions:
Water + Succinyl-CoA + Tetrahydrodipicolinate <> Coenzyme A + N-Succinyl-2-amino-6-ketopimelate
alpha-Ketoglutarate + N-Succinyl-L,L-2,6-diaminopimelate <> L-Glutamate + N-Succinyl-2-amino-6-ketopimelate
Oxoglutaric acid + N-Succinyl-L,L-2,6-diaminopimelate <> L-Glutamate + N-Succinyl-2-amino-6-ketopimelate
N-succinyl-L-2,6-diaminoheptanedioate + Oxoglutaric acid > N-Succinyl-2-amino-6-ketopimelate + L-Glutamate
Succinyl-CoA + (S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylate + Water > CoA + N-Succinyl-2-amino-6-ketopimelate
(S)-2,3,4,5-tetrahydrodipicolinate + Succinyl-CoA + Water + Succinyl-CoA > Coenzyme A + N-Succinyl-2-amino-6-ketopimelate
N-Succinyl-2-amino-6-ketopimelate + L-Glutamic acid + L-Glutamate > N-Succinyl-L,L-2,6-diaminopimelate + Oxoglutaric acid
alpha-Ketoglutarate + N-Succinyl-L,L-2,6-diaminopimelate <> L-Glutamate + N-Succinyl-2-amino-6-ketopimelate
Water + Succinyl-CoA + Tetrahydrodipicolinate <> Coenzyme A + N-Succinyl-2-amino-6-ketopimelate
SMPDB Pathways:
Lysine biosynthesisPW000771 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways:
EcoCyc Pathways:
Concentrations
Not Available
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0006-9880000000-0f0ff4f7e373c0b3162cView in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (3 TMS) - 70eV, Positivesplash10-00du-9408600000-fd466a0230c24aa5db92View in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0fkc-0290000000-2cf1a6c8c873c44c176aView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0fdo-1970000000-e6da5433a70177935dddView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-05i3-7900000000-a6e1749a519577b39b0bView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-007c-0190000000-cfcf85c3db41c68abca2View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-009g-1590000000-73abaab210b9727b9f16View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0006-5910000000-b01ea1042bed0446bc1cView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0006-0790000000-d2b9c6f92d7b00453793View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0abc-4930000000-f2f2e3269f8edd762cf8View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0pb9-9700000000-787d11c10df4c3cb6d65View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-000l-0590000000-2961efd3a4f8e021c893View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-002g-0960000000-6adfe9927596ba357d75View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0006-9500000000-70678263ddcfe89f4fb6View in MoNA
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
References
References:
  • 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
Synthesis Reference:Not Available
Material Safety Data Sheet (MSDS)Not Available
External Links:
ResourceLink
CHEBI ID35266
HMDB IDHMDB12266
Pubchem Compound ID440349
Kegg IDC04462
ChemSpider ID389314
Wikipedia IDNot Available
BioCyc IDN-SUCCINYL-2-AMINO-6-KETOPIMELATE
EcoCyc IDN-SUCCINYL-2-AMINO-6-KETOPIMELATE

Enzymes

Protein Details
1. 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase
General function:
Involved in 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase activity
Specific function:
Succinyl-CoA + (S)-2,3,4,5-tetrahydropyridine- 2,6-dicarboxylate + H(2)O = CoA + N-succinyl-L-2-amino-6- oxoheptanedioate
Gene Name:
dapD
Uniprot ID:
P0A9D8
Molecular weight:
29892
Reactions
Succinyl-CoA + (S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylate + H(2)O = CoA + N-succinyl-L-2-amino-6-oxoheptanedioate.
Protein Details
2. Acetylornithine/succinyldiaminopimelate aminotransferase
General function:
Involved in transaminase activity
Specific function:
Involved in both the arginine and lysine biosynthetic pathways
Gene Name:
argD
Uniprot ID:
P18335
Molecular weight:
43767
Reactions
N(2)-acetyl-L-ornithine + 2-oxoglutarate = N-acetyl-L-glutamate 5-semialdehyde + L-glutamate.
N-succinyl-L-2,6-diaminoheptanedioate + 2-oxoglutarate = N-succinyl-2-L-amino-6-oxoheptanedioate + L-glutamate.