MiMeDB: Showing metabocard for 2,3-Dihydrodipicolinate (MMDBc0049963)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-04-29 22:47:12 UTC

Update Date

2024-04-30 20:42:00 UTC

Metabolite ID

MMDBc0049963

Metabolite Identification

Common Name

2,3-Dihydrodipicolinate

Description

L-2,3-Dihydrodipicolinate 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. L-2,3-Dihydrodipicolinate exists in all living organisms, ranging from bacteria to humans. L-2,3-Dihydrodipicolinate has been detected, but not quantified in, a few different foods, such as anatidaes (Anatidae), chickens (Gallus gallus), and domestic pigs (Sus scrofa domestica). This could make L-2,3-dihydrodipicolinate a potential biomarker for the consumption of these foods. L-2,3-Dihydrodipicolinate 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 very few articles have been published on L-2,3-Dihydrodipicolinate.

Structure

MOL 3D MOL SDF 3D SDF PDB 3D 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      29.830 -21.669   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0      29.060 -23.002   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      31.370 -21.669   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      29.060 -20.335   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      29.830 -19.002   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      29.060 -17.668   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      27.520 -17.668   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      26.750 -19.002   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0      27.520 -20.335   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0      25.210 -19.002   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      24.440 -17.668   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0      24.440 -20.335   0.000  0.00  0.00           O+0
CONECT    1    2    3    4                                                  
CONECT    2    1                                                            
CONECT    3    1                                                            
CONECT    4    1    5    9                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9   10                                                  
CONECT    9    4    8                                                       
CONECT   10    8   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10                                                            
MASTER        0    0    0    0    0    0    0    0   12    0   24    0
END

Synonyms

Value	Source
L-2,3-Dihydrodipicolinic acid	Generator
2,3-Di-H-dipicolinate	HMDB
2,3-Dihydrodipicolinate	HMDB
Dihydrodipicolinate	HMDB

Molecular Formula

C₇H₇NO₄

Average Mass

169.1348

Monoisotopic Mass

169.037507717

IUPAC Name

2,3-dihydropyridine-2,6-dicarboxylic acid

Traditional Name

2,3-dihydrodipicolinic acid

CAS Registry Number

Not Available

SMILES

OC(=O)C1CC=CC(=N1)C(O)=O

InChI Identifier

InChI=1S/C7H7NO4/c9-6(10)4-2-1-3-5(8-4)7(11)12/h1-2,5H,3H2,(H,9,10)(H,11,12)

InChI Key

UWOCFOFVIBZJGH-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
Dihydropyridinecarboxylic acid derivative
Dihydropyridine
Dicarboxylic acid or derivatives
Hydropyridine
Ketimine
Carboxylic acid
Azacycle
Propargyl-type 1,3-dipolar organic compound
Organic 1,3-dipolar compound
Organoheterocyclic compound
Organic nitrogen compound
Imine
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Organonitrogen compound
Organooxygen compound
Carbonyl group
Organic oxygen compound
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

dihydrodipicolinic acid (CHEBI:48052 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	6.84 g/L	ALOGPS
logP	0.12	ALOGPS
logP	0.66	ChemAxon
logS	-1.4	ALOGPS
pKa (Strongest Acidic)	3.17	ChemAxon
pKa (Strongest Basic)	-1.1	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	39.36 m³·mol⁻¹	ChemAxon
Polarizability	15.08 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	splash10-0077-9300000000-d72da8848d1f49469c23	2017-09-01	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positive	splash10-0002-7910000000-ae5409fbe082d4832847	2017-10-06	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, Negative	splash10-014i-0900000000-fa63cf428cc5d8471604	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-01b9-1900000000-a3ffb331ab96000a39e1	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-00bc-9400000000-35fdba6f9d56521e4e19	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-00b9-5900000000-c56aff84aa96cf6da852	2021-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-014i-5900000000-a51255d0609601301b43	2021-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0ue9-9000000000-65ec758152caf537e272	2021-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-00di-0900000000-35bd5d728d4b6335059a	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-00di-0900000000-681935e00eed4828fd0f	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0udi-9300000000-ba4f4cccfccf71d0b007	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-00di-1900000000-2698c9ffb8a4caa90c8f	2021-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-001i-9200000000-625e0679cd43f0dedb7f	2021-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0f89-9000000000-7337376b7fa4e0a9a51d	2021-09-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 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, 1000 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, 200 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, 300 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, 400 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, 500 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, 600 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, 700 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, 800 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H 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	Reaction Type	Data Source	Reference
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

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	116	Human feces; Human sputum; Human ; Human unknown; Pig ; Human pleural fluid plaque; Human stool; Human feces; pleural fluid plaque; bal	Metabolic reconstruction
Bacteria	Firmicutes	285	Pig ; Human feces; Human ; Human pleural fluid plaque; Human supragingival plaque; Human saliva; Cattle ; Human stool; Human subgingival plaque	Metabolic reconstruction
Bacteria	Actinobacteria	96	Human feces; Human sputum; Human pleural fluid plaque; Human dental plaque; Human ; Human supragingival plaque; Human mucosa; Human subgingival plaque	Metabolic reconstruction
Bacteria	Bacteroidetes	113	Human feces; Human appendix biopsy; Human stool; Human ; Human urine; Human gastric fluid; Human supragingival plaque; Human subgingival plaque; Human saliva	Metabolic reconstruction
Archaea	Thaumarchaeota	1		Metabolic reconstruction
Bacteria	Synergistetes	4	Human feces	Metabolic reconstruction
Bacteria	Fusobacteria	13	Human feces; Human	Metabolic reconstruction
Archaea	Euryarchaeota	5		Metabolic reconstruction
Bacteria	Planctomycetes	1	Human feces	Metabolic reconstruction
Bacteria	Verrucomicrobia	1	Human ; Human feces	Metabolic reconstruction
Eukaryota/Fungi	Ascomycota	1		Metabolic reconstruction

Exposure Sources

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

HMDB0012247

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB028889

KNApSAcK ID

C00007500

Chemspider ID

KEGG Compound ID

C03340

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

PDB ID

Not Available

ChEBI ID

48052

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-Dihydrodipicolinate (MMDBc0049963)

MOL for #<Metabolite:0x00007fdb1325b548>

3D MOL for #<Metabolite:0x00007fdb1325b548>

3D SDF for #<Metabolite:0x00007fdb1325b548>

3D-SDF for #<Metabolite:0x00007fdb1325b548>

PDB for #<Metabolite:0x00007fdb1325b548>

3D PDB for #<Metabolite:0x00007fdb1325b548>

SMILES for #<Metabolite:0x00007fdb1325b548>

INCHI for #<Metabolite:0x00007fdb1325b548>

Structure for #<Metabolite:0x00007fdb1325b548>

3D Structure for #<Metabolite:0x00007fdb1325b548>