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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2009-04-06 16:22:24 UTC
Update Date2021-09-14 15:45:29 UTC
HMDB IDHMDB0012289
Secondary Accession Numbers
  • HMDB12289
Metabolite Identification
Common NameTetrahydrodipicolinate
DescriptionTetrahydrodipicolinate (CAS: 2353-17-5), converted from L-aspartate, is an important intermediate in the lysine biosynthesis pathway. Several pathways are now recognized in bacteria, most algae, fungi, and higher plants for the biosynthesis of lysine. They are divided into two groups: (1) the diaminopimelate (DAP) pathways, and (2) the alpha-aminoadipate (AAA) pathways. In the pathways that belong to the DAP group, lysine is produced from aspartate (along with methionine, threonine, and isoleucine). All of these pathways share the upper segments, which include the four steps required for the conversion of L-aspartate into tetrahydrodipicolinate. They also share the last step, which is the conversion of the intermediate meso-diaminopimelate (D,L-DAP, or meso-DAP) into lysine. However, these pathways differ in the routes leading from tetrahydrodipicolinate to meso-diaminopimelate. The four variations include: (I) the succinylase variant, which involves succinylated intermediates, where tetrahydrodipicolinate is converted into meso-diaminopimelate in four enzymatic steps; (II) the acetylase variant, which involves acetylated intermediates, where tetrahydrodipicolinate is converted into meso-diaminopimelate in four enzymatic steps; (III) the dehydrogenase variant, in which tetrahydrodipicolinate is converted into meso-diaminopimelate in a single enzymatic step; and (IV) the diaminopimelate-aminotransferase variant, in which tetrahydrodipicolinate is converted into meso-diaminopimelate in two steps. In addition to lysine, the pathways in this group also produce meso-DAP, which is an important metabolite on its own.
Structure
Data?1583771011
Synonyms
ValueSource
L-2,3,4,5-Tetrahydrodipicolinic acidChEBI
Delta1-Piperidine-2,6-dicarboxylateKegg
L-2,3,4,5-TetrahydrodipicolinateKegg
(S)-2,3,4,5-Tetrahydropyridine-2,6-dicarboxylateKegg
delta1-Piperidine-2,6-dicarboxylic acidGenerator
Δ1-piperidine-2,6-dicarboxylateGenerator
Δ1-piperidine-2,6-dicarboxylic acidGenerator
(S)-2,3,4,5-Tetrahydropyridine-2,6-dicarboxylic acidGenerator
Tetrahydrodipicolinic acidGenerator
(S)-2,3,4,5-TetrahydrodipicolinateHMDB
(2S)-2,3,4,5-Tetrahydro-2,6-pyridinedicarboxylic acidHMDB
(2S)-2,3,4,5-Tetrahydropyridine-2,6-dicarboxylic acidHMDB
2,3,4,5-Tetrahydro-2,6-pyridinedicarboxylic acidHMDB
2,3,4,5-TetrahydrodipicolinateHMDB
Chemical FormulaC7H9NO4
Average Molecular Weight171.1507
Monoisotopic Molecular Weight171.053157781
IUPAC Name(2S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylic acid
Traditional Name(2S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylic acid
CAS Registry Number4226-22-6
SMILES
OC(=O)[C@@H]1CCCC(=N1)C(O)=O
InChI Identifier
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)/t4-/m0/s1
InChI KeyCXMBCXQHOXUCEO-BYPYZUCNSA-N
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
Ontology
Physiological effectNot Available
Disposition
Source
Process
RoleNot Available
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular 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
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M+H]+131.98830932474
DeepCCS[M-H]-129.14630932474
DeepCCS[M-2H]-165.37930932474
DeepCCS[M+Na]+140.88530932474
AllCCS[M+H]+136.832859911
AllCCS[M+H-H2O]+132.532859911
AllCCS[M+NH4]+140.932859911
AllCCS[M+Na]+142.032859911
AllCCS[M-H]-132.432859911
AllCCS[M+Na-2H]-133.432859911
AllCCS[M+HCOO]-134.632859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
TetrahydrodipicolinateOC(=O)[C@@H]1CCCC(=N1)C(O)=O2784.7Standard polar33892256
TetrahydrodipicolinateOC(=O)[C@@H]1CCCC(=N1)C(O)=O1372.8Standard non polar33892256
TetrahydrodipicolinateOC(=O)[C@@H]1CCCC(=N1)C(O)=O1629.2Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Tetrahydrodipicolinate,1TMS,isomer #1C[Si](C)(C)OC(=O)[C@@H]1CCCC(C(=O)O)=N11671.8Semi standard non polar33892256
Tetrahydrodipicolinate,1TMS,isomer #2C[Si](C)(C)OC(=O)C1=N[C@H](C(=O)O)CCC11687.1Semi standard non polar33892256
Tetrahydrodipicolinate,2TMS,isomer #1C[Si](C)(C)OC(=O)C1=N[C@H](C(=O)O[Si](C)(C)C)CCC11693.4Semi standard non polar33892256
Tetrahydrodipicolinate,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC(=O)[C@@H]1CCCC(C(=O)O)=N11886.3Semi standard non polar33892256
Tetrahydrodipicolinate,1TBDMS,isomer #2CC(C)(C)[Si](C)(C)OC(=O)C1=N[C@H](C(=O)O)CCC11900.1Semi standard non polar33892256
Tetrahydrodipicolinate,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC(=O)C1=N[C@H](C(=O)O[Si](C)(C)C(C)(C)C)CCC12133.6Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Tetrahydrodipicolinate GC-MS (1 TMS) - 70eV, PositiveNot Available2020-06-30Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Tetrahydrodipicolinate GC-MS (1 TMS) - 70eV, PositiveNot Available2020-06-30Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Tetrahydrodipicolinate GC-MS (2 TMS) - 70eV, PositiveNot Available2020-06-30Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Tetrahydrodipicolinate GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Tetrahydrodipicolinate 10V, Positive-QTOFsplash10-0fk9-0900000000-da720873b06552234c072019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Tetrahydrodipicolinate 20V, Positive-QTOFsplash10-004i-2900000000-795238293b624b7754b82019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Tetrahydrodipicolinate 40V, Positive-QTOFsplash10-001l-9100000000-52c53a800e3f0f4aa67f2019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Tetrahydrodipicolinate 10V, Negative-QTOFsplash10-00di-0900000000-aaae2155691750a1b4a72019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Tetrahydrodipicolinate 20V, Negative-QTOFsplash10-00fr-0900000000-29346be76a89370b70ef2019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Tetrahydrodipicolinate 40V, Negative-QTOFsplash10-003u-9300000000-2c21978c9b0481febd4b2019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Tetrahydrodipicolinate 10V, Positive-QTOFsplash10-0fi0-0900000000-115f35527d52e48ed44e2021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Tetrahydrodipicolinate 20V, Positive-QTOFsplash10-001i-9000000000-6fd7171857d8a9a1e6b12021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Tetrahydrodipicolinate 40V, Positive-QTOFsplash10-001i-9000000000-e93b7fee81fd12616b302021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Tetrahydrodipicolinate 10V, Negative-QTOFsplash10-05i0-0900000000-c27405df4a81f621a3b02021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Tetrahydrodipicolinate 20V, Negative-QTOFsplash10-00di-2900000000-669ece578275242063ef2021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Tetrahydrodipicolinate 40V, Negative-QTOFsplash10-001i-9100000000-7ac18c5b51aca55459852021-09-24Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDC00007502
Chemspider ID389168
KEGG Compound IDC03972
BioCyc IDDELTA1-PIPERIDEINE-2-6-DICARBOXYLATE
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound440179
PDB IDNot Available
ChEBI ID864
Food Biomarker OntologyNot Available
VMH IDTHDP
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available