MiMeDB: Showing metabocard for Tetrahydrodipicolinate (MMDBc0029933)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-17 23:47:22 UTC

Update Date

2022-08-31 17:37:42 UTC

Metabolite ID

MMDBc0029933

Metabolite Identification

Common Name

Tetrahydrodipicolinate

Description

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

Structure

MOL SDF PDB SMILES InChI

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0      24.007 -15.877   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      22.467 -15.877   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      24.777 -17.211   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      21.697 -17.211   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      24.007 -18.544   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      20.158 -17.211   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      24.777 -19.878   0.000  0.00  0.00           C+0
HETATM    8  N   UNK     0      22.467 -18.544   0.000  0.00  0.00           N+0
HETATM    9  O   UNK     0      19.388 -15.877   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0      19.388 -18.544   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0      24.007 -21.211   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0      26.317 -19.878   0.000  0.00  0.00           O+0
CONECT    1    2    3                                                       
CONECT    2    1    4                                                       
CONECT    3    1    5                                                       
CONECT    4    2    6    8                                                  
CONECT    5    3    8    7                                                  
CONECT    6    4    9   10                                                  
CONECT    7    5   11   12                                                  
CONECT    8    4    5                                                       
CONECT    9    6                                                            
CONECT   10    6                                                            
CONECT   11    7                                                            
CONECT   12    7                                                            
MASTER        0    0    0    0    0    0    0    0   12    0   24    0
END

Synonyms

Value	Source
2,3,4,5-Tetrahydro-2,6-pyridinedicarboxylic acid	ChEBI
THDPA	ChEBI
2,3,4,5-Tetrahydro-2,6-pyridinedicarboxylate	Generator
Tetrahydrodipicolinic acid	Generator
(S)-2,3,4,5-Tetrahydropyridine-2,6-dicarboxylate	HMDB
2,3,4,5-Tetrahydro-2,6-dipicolinate	HMDB
2,3,4,5-Tetrahydrodipicolinate	HMDB
2,3,4,5-Tetrahydrodipicolinic acid	HMDB
2,3,4,5-Tetrahydropyridine-2,6-dicarboxylic acid	HMDB
Delta1-Piperideine-2,6-dicarboxylate	HMDB
L-2,3,4,5-Tetrahydrodipicolinate	HMDB

Molecular Formula

C₇H₉NO₄

Average Mass

171.1507

Monoisotopic Mass

171.053157781

IUPAC Name

2,3,4,5-tetrahydropyridine-2,6-dicarboxylic acid

Traditional Name

thdpa

CAS Registry Number

2353-17-5

SMILES

OC(=O)C1CCCC(=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)

InChI Key

CXMBCXQHOXUCEO-UHFFFAOYSA-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.

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
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

amino dicarboxylic acid (CHEBI:32976 )
tetrahydropyridine (CHEBI:32976 )

Functional Ontology

Not Available

Physical Properties

State

Solid

Predicted Properties

Property	Value	Source
Water Solubility	6.49 g/L	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	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-002f-9200000000-dcc61450e37dcfd98151	2017-09-01	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positive	splash10-006t-9510000000-ebdd1dfd8af393e288d4	2017-10-06	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0fk9-0900000000-c67011d10b18a0d87130	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-004i-2900000000-a7bbcc2a988fc7512c89	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-001i-9200000000-ce850c0759cdaecbf496	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-00di-0900000000-0204d30834bac9fc03e7	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-00fr-1900000000-6180db32249ad7119393	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-003u-9300000000-d4c458eb9535a9595faa	2015-09-15	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-22	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Not Available

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Bacteria	Proteobacteria	1	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human stool	Unknown

Exposure Sources

Source Type	Source Sub-type	Species	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference

External Links

HMDB ID

HMDB0012289

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB028918

KNApSAcK ID

Not Available

Chemspider ID

612

KEGG Compound ID

C03972

BioCyc ID

DELTA1-PIPERIDEINE-2-6-DICARBOXYLATE

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

632

PDB ID

Not Available

ChEBI ID

32976

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

van der Werf MJ, Overkamp KM, Muilwijk B, Coulier L, Hankemeier T: Microbial metabolomics: toward a platform with full metabolome coverage. Anal Biochem. 2007 Nov 1;370(1):17-25. doi: 10.1016/j.ab.2007.07.022. Epub 2007 Aug 1. [PubMed:17765195 ]
Keseler IM, 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 AG, Mackie A, Paulsen I, Gunsalus RP, Karp PD: EcoCyc: a comprehensive database of Escherichia coli biology. Nucleic Acids Res. 2011 Jan;39(Database issue):D583-90. doi: 10.1093/nar/gkq1143. Epub 2010 Nov 21. [PubMed:21097882 ]
Kanehisa M, Goto S, Sato Y, Furumichi M, Tanabe M: KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res. 2012 Jan;40(Database issue):D109-14. doi: 10.1093/nar/gkr988. Epub 2011 Nov 10. [PubMed:22080510 ]

Showing metabocard for Tetrahydrodipicolinate (MMDBc0029933)

MOL for #<Metabolite:0x00007fecfcae5218>

3D MOL for #<Metabolite:0x00007fecfcae5218>

3D SDF for #<Metabolite:0x00007fecfcae5218>

3D-SDF for #<Metabolite:0x00007fecfcae5218>

PDB for #<Metabolite:0x00007fecfcae5218>

3D PDB for #<Metabolite:0x00007fecfcae5218>

SMILES for #<Metabolite:0x00007fecfcae5218>

INCHI for #<Metabolite:0x00007fecfcae5218>

Structure for #<Metabolite:0x00007fecfcae5218>

3D Structure for #<Metabolite:0x00007fecfcae5218>