P. aeruginosa Metabolome Database: Tetrahydrodipicolinate (PAMDB000840)

Identification Taxonomy Physical Properties Biological Properties Spectra Concentrations Links References Enzymes Transporters

Proteins (3280)

Record Information

Version

1.0

Update Date

1/22/2018 12:54:54 PM

Metabolite ID

PAMDB000840

Identification

Name:

Tetrahydrodipicolinate

Description:

Tetrahydrodipicolinate is involved in amino-acid biosynthesis, specifically L-lysine biosynthesis via the DAP pathway

Structure

🔍MOL SDF PDB SMILES InChI View Structure

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

Average Molecular Weight:

171.1507

Monoisotopic Molecular Weight:

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

Taxonomy Description

This compound 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.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Alpha amino acids and derivatives

Alternative Parents

Substituents

Alpha-amino acid or derivatives
Tetrahydropyridine
Hydropyridine
Dicarboxylic acid or derivatives
Ketimine
Azacycle
Organoheterocyclic compound
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Carboxylic acid
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Imine
Carbonyl group
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

Not Available

Physical Properties

State:

Solid

Charge:

-2

Melting point:

Not Available

Experimental Properties:

Property	Value	Source

Predicted Properties

Property	Value	Source
Water Solubility	6.49 mg/mL	ALOGPS
logP	0.18	ALOGPS
logP	0.66	ChemAxon
logS	-1.4	ALOGPS
pKa (Strongest Acidic)	3.28	ChemAxon
pKa (Strongest Basic)	-2	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	86.96 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	38.27 m³·mol^-1	ChemAxon
Polarizability	15.74 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	1	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	Yes	ChemAxon

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
NAD(P)<sup>+</sup> + Tetrahydrodipicolinate < NAD(P)H + 2,3-Dihydrodipicolinic acid + Hydrogen ion
Hydrogen ion + Tetrahydrodipicolinate + Water > L-α-amino-ε-keto-pimelate
Tetrahydrodipicolinate + NAD + NADP + Water <> (2S,4S)-4-Hydroxy-2,3,4,5-tetrahydrodipicolinate + NADH + NADPH + Hydrogen ion

Pathways:

Lysine biosynthesis pae00300
Metabolic pathways pae01100
Microbial metabolism in diverse environments pae01120
Monobactam biosynthesis pae00261

Spectra

Spectra:

Spectrum Type	Description	Splash Key
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0fk9-0900000000-c67011d10b18a0d87130	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-004i-2900000000-a7bbcc2a988fc7512c89	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-001i-9200000000-ce850c0759cdaecbf496	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-00di-0900000000-0204d30834bac9fc03e7	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-00fr-1900000000-6180db32249ad7119393	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-003u-9300000000-d4c458eb9535a9595faa	View in MoNA

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

Links

External Links:

Resource	Link
CHEBI ID	32976
HMDB ID	HMDB12289
Pubchem Compound ID	632
Kegg ID	C03972
ChemSpider ID	612
Wikipedia ID	Not Available
BioCyc ID	DELTA1-PIPERIDEINE-2-6-DICARBOXYLATE
EcoCyc ID	DELTA1-PIPERIDEINE-2-6-DICARBOXYLATE

Tetrahydrodipicolinate (PAMDB000840)

Structure for Tetrahydrodipicolinate (PAMDB000840)