N-Succinyl-L,L-2,6-diaminopimelate (ECMDB12267) (M2MDB000836)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes (2)XML
Proteins (634)
Record Information
Version2.0
Creation Date2012-05-31 14:21:27 -0600
Update Date2015-06-03 17:19:04 -0600
Secondary Accession Numbers
  • ECMDB12267
Identification
Name:N-Succinyl-L,L-2,6-diaminopimelate
DescriptionN-Succinyl-L,L-2,6-diaminopimelate is an intermediate in lysine biosynthesis. It is the third to last step in the synthesis of lysine and is converted from N-Succinyl-2-amino-6-ketopimelate via the enzyme succinyldiaminopimelate transferase (EC 2.6.1.17). It is then converted to L,L-diaminopimelate via the enzyme succinyl-diaminopimelate desuccinylase (EC 3.5.1.18).
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms:
  • N-succinyl-L-2,6-diaminoheptanedioate
  • N-succinyl-LL-2,6-diaminoheptanedioate
  • L,L-Sdap
  • N-Succinyl-L,L-2,6-diaminopimelic acid
  • N-Succinyl-L-2,6-diaminoheptanedioate
  • N-Succinyl-L-2,6-diaminoheptanedioic acid
  • N-Succinyl-LL-2,6-diaminoheptanedioate
  • N-Succinyl-LL-2,6-diaminoheptanedioic acid
  • N-Succinyl-LL-2,6-diaminopimelate
  • N-Succinyl-LL-2,6-diaminopimelic acid
  • SDPA
Chemical Formula:C11H18N2O7
Weight:Average: 290.2698
Monoisotopic: 290.11140094
InChI Key:GLXUWZBUPATPBR-MLWJPKLSSA-N
InChI:InChI=1S/C11H18N2O7/c12-6(10(17)18)2-1-3-7(11(19)20)13-8(14)4-5-9(15)16/h6-7H,1-5,12H2,(H,13,14)(H,15,16)(H,17,18)(H,19,20)/t6?,7-/m0/s1
CAS number:26605-36-7
IUPAC Name:(6S)-2-amino-6-(3-carboxypropanamido)heptanedioic acid
Traditional IUPAC Name:(6S)-2-amino-6-(3-carboxypropanamido)heptanedioic acid
SMILES:NC(CCC[C@H](NC(=O)CCC(O)=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
  • Alpha-amino acid
  • Tricarboxylic acid or derivatives
  • Amino fatty acid
  • Fatty amide
  • N-acyl-amine
  • Fatty acyl
  • Carboxamide group
  • Secondary carboxylic acid amide
  • Amino acid
  • Carboxylic acid
  • Primary amine
  • Organooxygen compound
  • Organonitrogen compound
  • Organic oxide
  • Primary aliphatic amine
  • Organopnictogen compound
  • Carbonyl group
  • Organic oxygen compound
  • Organic nitrogen compound
  • Amine
  • Hydrocarbon derivative
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External DescriptorsNot Available
Physical Properties
State:Solid
Charge:-2
Melting point:Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility5.8 g/LALOGPS
logP-3.1ALOGPS
logP-3.8ChemAxon
logS-1.7ALOGPS
pKa (Strongest Acidic)1.89ChemAxon
pKa (Strongest Basic)9.53ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count8ChemAxon
Hydrogen Donor Count5ChemAxon
Polar Surface Area167.02 ŲChemAxon
Rotatable Bond Count10ChemAxon
Refractivity63.98 m³·mol⁻¹ChemAxon
Polarizability27.09 ųChemAxon
Number of Rings0ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations:Cytoplasm
Reactions:
Water + N-Succinyl-L,L-2,6-diaminopimelate <> Diaminopimelic acid + Succinic acid
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-2-amino-6-ketopimelate + L-Glutamic acid + L-Glutamate > N-Succinyl-L,L-2,6-diaminopimelate + Oxoglutaric acid
N-Succinyl-L,L-2,6-diaminopimelate + Water > Succinic acid + Diaminopimelic acid
alpha-Ketoglutarate + N-Succinyl-L,L-2,6-diaminopimelate <> L-Glutamate + N-Succinyl-2-amino-6-ketopimelate
Water + N-Succinyl-L,L-2,6-diaminopimelate <> Diaminopimelic acid + Succinic acid
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, Positivesplash10-0ukd-7980000000-e443695d136f221c8fcfView in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (3 TMS) - 70eV, Positivesplash10-006x-9303600000-53e79d2abfa0f9ef52ddView in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-00fs-0290000000-94b59924e5c6f873d3e9View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0002-1960000000-f57f28932db38b283c8cView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-054k-7900000000-66284b4cc1812fbb9f0cView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0079-0190000000-fa97ecde1f805141dc72View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-00g1-1490000000-777a3c340c9bca9df3aeView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-006y-9800000000-f1025c9e017254c3c356View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-006x-0190000000-2b72340d09586ce940a0View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0002-1910000000-e4c34aca88cb0711d6e6View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0pb9-8900000000-b3cbfc02281c4466f2deView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-000i-0090000000-39bd027060b8d3f96cffView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-000b-2970000000-0ae78022739fec47a222View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-00dl-9300000000-79f5f223496e3d1a1274View 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
Synthesis Reference:Not Available
Material Safety Data Sheet (MSDS)Not Available
External Links:
ResourceLink
CHEBI ID165894
HMDB IDHMDB12267
Pubchem Compound ID25202447
Kegg IDC04421
ChemSpider ID35032427
Wikipedia IDNot Available
BioCyc IDN-SUCCINYLLL-2-6-DIAMINOPIMELATE
EcoCyc IDN-SUCCINYLLL-2-6-DIAMINOPIMELATE

Enzymes

Protein Details
1. Succinyl-diaminopimelate desuccinylase
General function:
Involved in metallopeptidase activity
Specific function:
Catalyzes the hydrolysis of N-succinyl-L,L- diaminopimelic acid (SDAP), forming succinate and LL-2,6- diaminoheptanedioate (DAP), an intermediate involved in the bacterial biosynthesis of lysine and meso-diaminopimelic acid, an essential component of bacterial cell walls
Gene Name:
dapE
Uniprot ID:
P0AED7
Molecular weight:
41269
Reactions
N-succinyl-LL-2,6-diaminoheptanedioate + H(2)O = succinate + LL-2,6-diaminoheptanedioate.
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.