MiMeDB: Showing metabocard for 2,3,4,5-Tetrahydrodipicolinate (MMDBc0049956)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-04-29 22:47:03 UTC

Update Date

2024-04-30 20:41:54 UTC

Metabolite ID

MMDBc0049956

Metabolite Identification

Common Name

2,3,4,5-Tetrahydrodipicolinate

Description

Tetrahydrodipicolinate 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. Tetrahydrodipicolinate exists in all living organisms, ranging from bacteria to humans. Tetrahydrodipicolinate is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. Based on a literature review a significant number of articles have been published on Tetrahydrodipicolinate.

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI

HEADER    PROTEIN                                 04-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-20         0                                  
HETATM    1  C   UNK     0    8631.8428628.630   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0    8633.1748629.398   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0    8631.8428627.091   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0    8630.5078629.398   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0    8630.5078630.938   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0    8629.1768628.630   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0    8629.1768631.707   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0    8627.8398629.398   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0    8629.1768633.246   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0    8627.8398630.938   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0    8627.8438634.016   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0    8630.5078634.016   0.000  0.00  0.00           O+0
CONECT    1    2    3    4                                                  
CONECT    2    1                                                            
CONECT    3    1                                                            
CONECT    4    1    5    6                                                  
CONECT    5    7    4                                                       
CONECT    6    4    8                                                       
CONECT    7    9   10    5                                                  
CONECT    8    6   10                                                       
CONECT    9    7   11   12                                                  
CONECT   10    7    8                                                       
CONECT   11    9                                                            
CONECT   12    9                                                            
MASTER        0    0    0    0    0    0    0    0   12    0   24    0
END

Synonyms

Value	Source
L-2,3,4,5-Tetrahydrodipicolinic acid	ChEBI
Delta1-Piperidine-2,6-dicarboxylate	Kegg
L-2,3,4,5-Tetrahydrodipicolinate	Kegg
(S)-2,3,4,5-Tetrahydropyridine-2,6-dicarboxylate	Kegg
delta1-Piperidine-2,6-dicarboxylic acid	Generator
Δ1-piperidine-2,6-dicarboxylate	Generator
Δ1-piperidine-2,6-dicarboxylic acid	Generator
(S)-2,3,4,5-Tetrahydropyridine-2,6-dicarboxylic acid	Generator
Tetrahydrodipicolinic acid	Generator
(S)-2,3,4,5-Tetrahydrodipicolinate	HMDB
(2S)-2,3,4,5-Tetrahydro-2,6-pyridinedicarboxylic acid	HMDB
(2S)-2,3,4,5-Tetrahydropyridine-2,6-dicarboxylic acid	HMDB
2,3,4,5-Tetrahydro-2,6-pyridinedicarboxylic acid	HMDB
2,3,4,5-Tetrahydrodipicolinate	HMDB

Molecular Formula

C₇H₉NO₄

Average Mass

171.1507

Monoisotopic Mass

171.053157781

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 Number

Not Available

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 Key

CXMBCXQHOXUCEO-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.

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

2,3,4,5-tetrahydrodipicolinic acid (CHEBI:864 )

Functional Ontology

Not Available

Physical Properties

State

Expected 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 (1 TMS) - 70eV, Positive	Not Available	2020-06-30	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positive	Not Available	2020-06-30	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positive	Not Available	2020-06-30	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0fk9-0900000000-da720873b06552234c07	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-004i-2900000000-795238293b624b7754b8	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-001l-9100000000-52c53a800e3f0f4aa67f	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-00di-0900000000-aaae2155691750a1b4a7	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-00fr-0900000000-29346be76a89370b70ef	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-003u-9300000000-2c21978c9b0481febd4b	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0fi0-0900000000-115f35527d52e48ed44e	2021-09-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-001i-9000000000-6fd7171857d8a9a1e6b1	2021-09-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-001i-9000000000-e93b7fee81fd12616b30	2021-09-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-05i0-0900000000-c27405df4a81f621a3b0	2021-09-24	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-00di-2900000000-669ece578275242063ef	2021-09-24	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-001i-9100000000-7ac18c5b51aca5545985	2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-09-25	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Feces

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

Reactions

Reaction ID	Precursor	Product	Enzyme	Data Source	Reference
MMDBr0006985	LL-2,6-Diaminoheptanedioate	L-Glutamic acid	Not Available	VMH	30371894
MMDBr0006986	2,3-Dihydrodipicolinate	2,3,4,5-Tetrahydrodipicolinate	Not Available	VMH	30371894
MMDBr0007307	2,3-Dihydrodipicolinate	2,3,4,5-Tetrahydrodipicolinate	Not Available	VMH	30371894
MMDBr0007575	Succinyl-CoA	N-Succinyl-2-L-amino-6-oxoheptanedioate	Not Available	VMH	30371894
MMDBr0008087	2,3,4,5-Tetrahydrodipicolinate	N_Acetyl_L_2_amino_6_oxopimelate	Not Available	VMH	30371894
MMDBr0008516	L-Glutamic acid	LL-2,6-Diaminoheptanedioate	Not Available	VMH	30371894
MMDBr0011006	2,3,4,5-Tetrahydrodipicolinate	Meso-2,6-Diaminoheptanedioate	Not Available	VMH	30371894

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	Firmicutes	370	Human feces; Human pleural fluid plaque; Pig ; Human ; Human supragingival plaque; Human saliva; Cattle ; Human stool; Human subgingival plaque	Metabolic reconstruction
Bacteria	Proteobacteria	177	Human ; Human feces; Human sputum; Human unknown; Pig ; Human pleural fluid plaque; Human stool; Human dental plaque; Human nasal swab; Human feces; pleural fluid plaque; bal	Metabolic reconstruction
Bacteria	Actinobacteria	124	Human feces; Human sputum; Human pleural fluid plaque; Human dental plaque; Human ; Human nasopharyngeal swab; Human supragingival plaque; Human mucosa; Human subgingival plaque	Metabolic reconstruction
Bacteria	Verrucomicrobia	1	Human ; Human feces	Metabolic reconstruction
Bacteria	Bacteroidetes	129	Human feces; Human appendix biopsy; Human ; Human stool; Human urine; Human gastric fluid; Human saliva; Human subgingival plaque; Human supragingival plaque	Metabolic reconstruction
Archaea	Thaumarchaeota	1		Metabolic reconstruction
Bacteria	Fusobacteria	14	Human feces; Human	Metabolic reconstruction
Bacteria	Synergistetes	4	Human feces	Metabolic reconstruction
Archaea	Euryarchaeota	5		Metabolic reconstruction
Bacteria	Planctomycetes	1	Human feces	Metabolic reconstruction
Archaea	Crenarchaeota	1		Metabolic reconstruction
Bacteria	Tenericutes	2	Human feces	Metabolic reconstruction
Eukaryota/Fungi	Ascomycota	1		Metabolic reconstruction
Bacteria	Spirochaetes	1	Human feces	Metabolic reconstruction

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
Human Feces	Detected but not Quantified									HMDB

External Links

HMDB ID

HMDB0012289

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

C00007502

Chemspider ID

389168

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

440179

PDB ID

Not Available

ChEBI ID

864

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Noronha A, Modamio J, Jarosz Y, Guerard E, Sompairac N, Preciat G, Danielsdottir AD, Krecke M, Merten D, Haraldsdottir HS, Heinken A, Heirendt L, Magnusdottir S, Ravcheev DA, Sahoo S, Gawron P, Friscioni L, Garcia B, Prendergast M, Puente A, Rodrigues M, Roy A, Rouquaya M, Wiltgen L, Zagare A, John E, Krueger M, Kuperstein I, Zinovyev A, Schneider R, Fleming RMT, Thiele I: The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease. Nucleic Acids Res. 2019 Jan 8;47(D1):D614-D624. doi: 10.1093/nar/gky992. [PubMed:30371894 ]

Showing metabocard for 2,3,4,5-Tetrahydrodipicolinate (MMDBc0049956)

MOL for #<Metabolite:0x00007feca0537818>

3D MOL for #<Metabolite:0x00007feca0537818>

3D SDF for #<Metabolite:0x00007feca0537818>

3D-SDF for #<Metabolite:0x00007feca0537818>

PDB for #<Metabolite:0x00007feca0537818>

3D PDB for #<Metabolite:0x00007feca0537818>

SMILES for #<Metabolite:0x00007feca0537818>

INCHI for #<Metabolite:0x00007feca0537818>

Structure for #<Metabolite:0x00007feca0537818>

3D Structure for #<Metabolite:0x00007feca0537818>