Record Information
Version 1.0
Update Date 1/22/2018 12:54:54 PM
Metabolite IDPAMDB110167
Identification
Name: (S)-2,3,4,5-tetrahydrodipicolinate
Description:Tetrahydrodipicolinate, converted from L-aspartate, is an important intermediate in 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 - the diaminopimelate (DAP) pathways, and the α-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 conversion of L-aspartate to tetrahydrodipicolinate. They also share the last step, which is the conversion of the intermediate meso-diaminopimelate (D,L-DAP, or meso-DAP) to 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. In this route tetrahydrodipicolinate is coverted to meso-diaminopimelate in four enzymatic steps; (II) the acetylase variant, which involves acetylated intermediates. This route also involves four enzymatic steps for the conversion of tetrahydrodipicolinate to meso-diaminopimelate; (III) the dehydrogenase variant, in which tetrahydrodipicolinate is converted to meso-diaminopimelate in a single enzymatic step; (IV) the diaminopimelate-aminotransferase variant, in which tetrahydrodipicolinate is converted to 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
Thumb
Synonyms:
  • 2,3,4,5-tetrahydrodipicolinate
  • (S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylate
  • Δ1-piperideine-2,6-dicarboxylate
  • tetrahydrodipicolinate
  • tetrahydropyridine-2,6-dicarboxylate
  • L-2,3,4,5-tetrahydrodipicolinate
Chemical Formula: C7H7NO4
Average Molecular Weight: 169.14
Monoisotopic Molecular Weight: 171.0531577825
InChI Key: CXMBCXQHOXUCEO-BYPYZUCNSA-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/t4-/m0/s1
CAS number: 2353-17-5
IUPAC Name:(2S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylate
Traditional IUPAC Name: thdpa
SMILES:C1(CC(=NC(C1)C([O-])=O)C([O-])=O)
Chemical Taxonomy
Taxonomy DescriptionThis compound belongs to the class of chemical entities 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.
Kingdom Chemical entities
Super ClassOrganic compounds
Class Organic acids and derivatives
Sub ClassCarboxylic acids and derivatives
Direct Parent Alpha 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 Framework Aliphatic heteromonocyclic compounds
External Descriptors
Physical Properties
State: Solid
Charge:-2
Melting point: Not Available
Experimental Properties:
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
Water Solubility6.49 mg/mLALOGPS
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 Å2ChemAxon
Rotatable Bond Count2ChemAxon
Refractivity38.27 m3·mol-1ChemAxon
Polarizability15.74 Å3ChemAxon
Number of Rings1ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations: Not Available
Reactions:
Pathways:
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
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
References
References: Not Available
Synthesis Reference: Not Available
Material Safety Data Sheet (MSDS) Not Available
External Links:
ResourceLink
CAS52-52-8
ChEBI16845
ChemSpider4573939
HMDBHMDB12289
IAF126042888
KEGGC03972
PubChem5460405