(S)-2,3,4,5-tetrahydrodipicolinate (ECMDB24187) (M2MDB006304)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes (2)XML
Proteins (2)
Record Information
Version2.0
Creation Date2015-09-08 17:49:58 -0600
Update Date2015-09-14 16:46:30 -0600
Secondary Accession Numbers
  • ECMDB24187
Identification
Name:(S)-2,3,4,5-tetrahydrodipicolinate
Description(S)-2,3,4,5-tetrahydrodipicolinate is an intermediate in L-lysine biosynthesis I pathway in E.coli. It is a substrate for the enzyme tetrahydrodipicolinate succinylase which catalyzes the reaction (S)-2,3,4,5-tetrahydrodipicolinate + succinyl-CoA + H2O -> N-succinyl-2-amino-6-ketopimelate + coenzyme A. It is also a product for enzyme 4-hydroxy-tetrahydrodipicolinate reductase which catalyzes reaction (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + NADPH + H+ -> (S)-2,3,4,5-tetrahydrodipicolinate + NADP+ + H2O (BioCyc compound: DELTA1-PIPERIDEINE-2-6-DICARBOXYLATE).
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms:
  • (S)-2,3,4,5-Tetrahydrodipicolinic acid
Chemical Formula:C7H7NO4
Weight:Average: 169.137
Monoisotopic: 169.038604869
InChI Key:CXMBCXQHOXUCEO-UHFFFAOYSA-L
InChI:InChI=1S/C7H9NO4/c9-6(10)4-2-1-3-5(8-4)7(11)12/h4H,1-3H2,(H,9,10)(H,11,12)/p-2
CAS number:Not Available
IUPAC Name:2,3,4,5-tetrahydropyridine-2,6-dicarboxylate
Traditional IUPAC Name:2,3,4,5-tetrahydrodipicolinate
SMILES:[O-]C(=O)C1CCCC(=N1)C([O-])=O
Chemical Taxonomy
Description belongs to the class of organic compounds known as alpha amino acids and derivatives. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon), or a derivative thereof.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassAmino acids, peptides, and analogues
Direct ParentAlpha amino acids and derivatives
Alternative Parents
Substituents
  • Alpha-amino acid or derivatives
  • Tetrahydropyridine
  • Dicarboxylic acid or derivatives
  • Hydropyridine
  • Ketimine
  • Carboxylic acid
  • Organoheterocyclic compound
  • Azacycle
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organonitrogen compound
  • Organic oxide
  • Imine
  • Organopnictogen compound
  • Organic oxygen compound
  • Organic nitrogen compound
  • Carbonyl group
  • Organic anion
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Physical Properties
State:Not Available
Charge:-2
Melting point:Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility6.42 g/LALOGPS
logP0.02ALOGPS
logP0.66ChemAxon
logS-1.5ALOGPS
pKa (Strongest Acidic)3.28ChemAxon
pKa (Strongest Basic)-2ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area92.62 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity59.94 m³·mol⁻¹ChemAxon
Polarizability14.84 ųChemAxon
Number of Rings1ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations:Cytoplasm
Reactions:
(2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + Hydrogen ion + NADPH + (2S,4S)-4-Hydroxy-2,3,4,5-tetrahydrodipicolinate + NADPH > Water + NADP + (S)-2,3,4,5-tetrahydrodipicolinate
(S)-2,3,4,5-tetrahydrodipicolinate + Succinyl-CoA + Water + Succinyl-CoA > Coenzyme A + N-Succinyl-2-amino-6-ketopimelate
SMPDB Pathways:
Lysine biosynthesisPW000771 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways:
EcoCyc Pathways:Not Available
Concentrations
Not Available
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-00di-0900000000-3bbcafe91a30720bb736View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-00di-0900000000-1347c32500acf52bc79dView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0006-9100000000-c32da1dc7cc3fafb5fc0View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-014i-0900000000-643f36ee3510b74a2eb3View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-014i-1900000000-d8305875fe20207dff59View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-001l-9300000000-36365a0fe19d6e926f92View 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:Not Available
Synthesis Reference:Not Available
Material Safety Data Sheet (MSDS)Not Available
External Links:
ResourceLink
CHEBI ID11408
HMDB IDHMDB0303994
Pubchem Compound IDNot Available
Kegg IDNot Available
ChemSpider ID4574219
Wikipedia IDNot Available
BioCyc IDNot Available

Enzymes

Protein Details
1. Dihydrodipicolinate reductase
General function:
Involved in dihydrodipicolinate reductase activity
Specific function:
2,3,4,5-tetrahydrodipicolinate + NAD(P)(+) = 2,3-dihydrodipicolinate + NAD(P)H
Gene Name:
dapB
Uniprot ID:
P04036
Molecular weight:
28756
Reactions
(S)-2,3,4,5-tetrahydrodipicolinate + NAD(P)(+) = (S)-2,3-dihydrodipicolinate + NAD(P)H.
Protein Details
2. 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.