Tetrahydrodipicolinate (ECMDB12289) (M2MDB000840)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes (2)XML
Proteins (874)
Record Information
Version2.0
Creation Date2012-05-31 14:21:40 -0600
Update Date2015-06-03 17:19:04 -0600
Secondary Accession Numbers
  • ECMDB12289
Identification
Name:Tetrahydrodipicolinate
DescriptionTetrahydrodipicolinate is involved in amino-acid biosynthesis, specifically L-lysine biosynthesis via the DAP pathway
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms:
  • Δ1-piperideine-2,6-dicarboxylate
  • Δ1-piperideine-2,6-dicarboxylic acid
  • Δ1-piperideine-2,6-dicarboxylate
  • (S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylate
  • (S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylate
  • (S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylic acid
  • 2,3,4,5-Tetrahydro-2,6-dipicolinate
  • 2,3,4,5-Tetrahydro-2,6-dipicolinic acid
  • 2,3,4,5-Tetrahydro-2,6-pyridinedicarboxylate
  • 2,3,4,5-Tetrahydro-2,6-pyridinedicarboxylic acid
  • 2,3,4,5-Tetrahydrodipicolinate
  • 2,3,4,5-Tetrahydrodipicolinic acid
  • 2,3,4,5-Tetrahydropyridine-2,6-dicarboxylate
  • 2,3,4,5-Tetrahydropyridine-2,6-dicarboxylic acid
  • 2,3,4,5-THDPA
  • Delta1-piperideine-2,6-dicarboxylate
  • Delta1-piperideine-2,6-dicarboxylic acid
  • L-2,3,4,5-Tetrahydrodipicolinate
  • L-2,3,4,5-Tetrahydrodipicolinic acid
  • Tetrahydrodipicolinate
  • Tetrahydrodipicolinic acid
  • Tetrahydropyridine-2,6-dicarboxylate
  • Tetrahydropyridine-2,6-dicarboxylic acid
  • Thdpa
  • δ1-Piperideine-2,6-dicarboxylate
  • δ1-Piperideine-2,6-dicarboxylic acid
Chemical Formula:C7H9NO4
Weight:Average: 171.1507
Monoisotopic: 171.053157781
InChI Key:CXMBCXQHOXUCEO-UHFFFAOYSA-N
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)
CAS number:2353-17-5
IUPAC Name:2,3,4,5-tetrahydropyridine-2,6-dicarboxylic acid
Traditional IUPAC Name:thdpa
SMILES:OC(=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
  • Azacycle
  • Organoheterocyclic compound
  • Organic 1,3-dipolar compound
  • Propargyl-type 1,3-dipolar organic compound
  • Carboxylic acid
  • Hydrocarbon derivative
  • Organic oxygen compound
  • Organooxygen compound
  • Organonitrogen compound
  • Imine
  • Organic nitrogen compound
  • Carbonyl group
  • Organic oxide
  • Organopnictogen compound
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Physical Properties
State:Solid
Charge:-2
Melting point:Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility6.49 g/LALOGPS
logP0.18ALOGPS
logP0.66ChemAxon
logS-1.4ALOGPS
pKa (Strongest Acidic)3.28ChemAxon
pKa (Strongest Basic)-2ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area86.96 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity38.27 m³·mol⁻¹ChemAxon
Polarizability15.74 ųChemAxon
Number of Rings1ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations:Cytoplasm
Reactions:
2,3-Dihydrodipicolinic acid + Hydrogen ion + NADPH > NADP + Tetrahydrodipicolinate
Water + Succinyl-CoA + Tetrahydrodipicolinate <> Coenzyme A + N-Succinyl-2-amino-6-ketopimelate
Tetrahydrodipicolinate + NAD <> 2,3-Dihydrodipicolinic acid + NADH + Hydrogen ion
Tetrahydrodipicolinate + NADP <> 2,3-Dihydrodipicolinic acid + NADPH + Hydrogen ion
NAD(P)<sup>+</sup> + Tetrahydrodipicolinate < NAD(P)H + 2,3-Dihydrodipicolinic acid + Hydrogen ion
Hydrogen ion + Tetrahydrodipicolinate + Water > L-&alpha;-amino-&epsilon;-keto-pimelate
Tetrahydrodipicolinate + NAD + NADP + Water <> (2S,4S)-4-Hydroxy-2,3,4,5-tetrahydrodipicolinate + NADH + NADPH + Hydrogen ion
Water + Succinyl-CoA + Tetrahydrodipicolinate <> Coenzyme A + N-Succinyl-2-amino-6-ketopimelate
2 2,3-Dihydrodipicolinic acid + Hydrogen ion + NADPH > NADP + Tetrahydrodipicolinate
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, Positivesplash10-002f-9200000000-dcc61450e37dcfd98151View in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positivesplash10-006t-9510000000-ebdd1dfd8af393e288d4View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0fk9-0900000000-c67011d10b18a0d87130View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-004i-2900000000-a7bbcc2a988fc7512c89View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-001i-9200000000-ce850c0759cdaecbf496View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-00di-0900000000-0204d30834bac9fc03e7View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-00fr-1900000000-6180db32249ad7119393View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-003u-9300000000-d4c458eb9535a9595faaView 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 ID32976
HMDB IDHMDB12289
Pubchem Compound ID632
Kegg IDC03972
ChemSpider ID612
Wikipedia IDNot Available
BioCyc IDDELTA1-PIPERIDEINE-2-6-DICARBOXYLATE
EcoCyc IDDELTA1-PIPERIDEINE-2-6-DICARBOXYLATE

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.