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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2009-04-06 16:21:42 UTC

Update Date

2023-02-21 17:17:46 UTC

HMDB ID

HMDB0012247

Secondary Accession Numbers

HMDB12247

Metabolite Identification

Common Name

L-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

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

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

Chemical Formula

C₇H₇NO₄

Average Molecular Weight

169.1348

Monoisotopic Molecular Weight

169.037507717

IUPAC Name

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

Traditional Name

2,3-dihydrodipicolinic acid

CAS Registry Number

16052-12-3

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 )

Ontology

Not Available

Endogenous (HMDB: HMDB0012247)

Pheasant (FooDB: FOOD00430)
Squab (FooDB: FOOD00481)
Turkey (FooDB: FOOD00494)
Quail (FooDB: FOOD00541)
Anatidae (FooDB: FOOD00576)
Rock ptarmigan (FooDB: FOOD00597)
Columbidae (Dove, Pigeon) (FooDB: FOOD00610)
Chicken (FooDB: FOOD00329)
Mallard duck (FooDB: FOOD00353)
Emu (FooDB: FOOD00360)
Greylag goose (FooDB: FOOD00368)
Guinea hen (FooDB: FOOD00373)
Ostrich (FooDB: FOOD00422)
Velvet duck (FooDB: FOOD00427)

Lagomorph

Ovis

Sheep (Mutton, Lamb) (FooDB: FOOD00473)

Bovine

Venison

Deer (FooDB: FOOD00524)
Mule deer (FooDB: FOOD00348)
Elk (FooDB: FOOD00359)

Caprae

Domestic goat (FooDB: FOOD00529)

Swine

Domestic pig (FooDB: FOOD00536)
Wild boar (FooDB: FOOD00307)

Equine

Horse (FooDB: FOOD00378)

Process

Naturally occurring process

Biological process

Biochemical pathway

Metabolic pathway

Secondary Metabolites: Threonine Biosynthesis from Aspartate (PathBank: SMP0121329)

Role

Not Available

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular 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

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DarkChem	[M+H]+	137.85	31661259
DarkChem	[M-H]-	132.708	31661259
DeepCCS	[M+H]+	131.279	30932474
DeepCCS	[M-H]-	127.452	30932474
DeepCCS	[M-2H]-	165.069	30932474
DeepCCS	[M+Na]+	140.608	30932474
AllCCS	[M+H]+	136.3	32859911
AllCCS	[M+H-H2O]+	131.9	32859911
AllCCS	[M+NH4]+	140.5	32859911
AllCCS	[M+Na]+	141.6	32859911
AllCCS	[M-H]-	130.9	32859911
AllCCS	[M+Na-2H]-	131.8	32859911
AllCCS	[M+HCOO]-	133.0	32859911

Predicted Kovats Retention Indices

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
L-2,3-Dihydrodipicolinate,1TMS,isomer #1	C[Si](C)(C)OC(=O)C1CC=CC(C(=O)O)=N1	1705.5	Semi standard non polar	33892256
L-2,3-Dihydrodipicolinate,1TMS,isomer #1	C[Si](C)(C)OC(=O)C1CC=CC(C(=O)O)=N1	1534.4	Standard non polar	33892256
L-2,3-Dihydrodipicolinate,1TMS,isomer #1	C[Si](C)(C)OC(=O)C1CC=CC(C(=O)O)=N1	2995.1	Standard polar	33892256
L-2,3-Dihydrodipicolinate,1TMS,isomer #2	C[Si](C)(C)OC(=O)C1=NC(C(=O)O)CC=C1	1743.2	Semi standard non polar	33892256
L-2,3-Dihydrodipicolinate,1TMS,isomer #2	C[Si](C)(C)OC(=O)C1=NC(C(=O)O)CC=C1	1515.7	Standard non polar	33892256
L-2,3-Dihydrodipicolinate,1TMS,isomer #2	C[Si](C)(C)OC(=O)C1=NC(C(=O)O)CC=C1	2892.1	Standard polar	33892256
L-2,3-Dihydrodipicolinate,2TMS,isomer #1	C[Si](C)(C)OC(=O)C1=NC(C(=O)O[Si](C)(C)C)CC=C1	1740.6	Semi standard non polar	33892256
L-2,3-Dihydrodipicolinate,2TMS,isomer #1	C[Si](C)(C)OC(=O)C1=NC(C(=O)O[Si](C)(C)C)CC=C1	1619.7	Standard non polar	33892256
L-2,3-Dihydrodipicolinate,2TMS,isomer #1	C[Si](C)(C)OC(=O)C1=NC(C(=O)O[Si](C)(C)C)CC=C1	2867.4	Standard polar	33892256
L-2,3-Dihydrodipicolinate,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC(=O)C1CC=CC(C(=O)O)=N1	1936.0	Semi standard non polar	33892256
L-2,3-Dihydrodipicolinate,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC(=O)C1CC=CC(C(=O)O)=N1	1757.4	Standard non polar	33892256
L-2,3-Dihydrodipicolinate,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC(=O)C1CC=CC(C(=O)O)=N1	3081.5	Standard polar	33892256
L-2,3-Dihydrodipicolinate,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC(=O)C1=NC(C(=O)O)CC=C1	1973.8	Semi standard non polar	33892256
L-2,3-Dihydrodipicolinate,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC(=O)C1=NC(C(=O)O)CC=C1	1719.3	Standard non polar	33892256
L-2,3-Dihydrodipicolinate,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC(=O)C1=NC(C(=O)O)CC=C1	3015.7	Standard polar	33892256
L-2,3-Dihydrodipicolinate,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC(=O)C1=NC(C(=O)O[Si](C)(C)C(C)(C)C)CC=C1	2178.0	Semi standard non polar	33892256
L-2,3-Dihydrodipicolinate,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC(=O)C1=NC(C(=O)O[Si](C)(C)C(C)(C)C)CC=C1	1982.8	Standard non polar	33892256
L-2,3-Dihydrodipicolinate,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC(=O)C1=NC(C(=O)O[Si](C)(C)C(C)(C)C)CC=C1	3064.1	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - L-2,3-Dihydrodipicolinate GC-MS (Non-derivatized) - 70eV, Positive	splash10-0077-9300000000-d72da8848d1f49469c23	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - L-2,3-Dihydrodipicolinate GC-MS (2 TMS) - 70eV, Positive	splash10-0002-7910000000-ae5409fbe082d4832847	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - L-2,3-Dihydrodipicolinate GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - L-2,3-Dihydrodipicolinate 10V, Negative-QTOF	splash10-014i-0900000000-fa63cf428cc5d8471604	2015-09-15	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - L-2,3-Dihydrodipicolinate 20V, Negative-QTOF	splash10-01b9-1900000000-a3ffb331ab96000a39e1	2015-09-15	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - L-2,3-Dihydrodipicolinate 40V, Negative-QTOF	splash10-00bc-9400000000-35fdba6f9d56521e4e19	2015-09-15	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - L-2,3-Dihydrodipicolinate 10V, Negative-QTOF	splash10-00b9-5900000000-c56aff84aa96cf6da852	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - L-2,3-Dihydrodipicolinate 20V, Negative-QTOF	splash10-014i-5900000000-a51255d0609601301b43	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - L-2,3-Dihydrodipicolinate 40V, Negative-QTOF	splash10-0ue9-9000000000-65ec758152caf537e272	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - L-2,3-Dihydrodipicolinate 10V, Positive-QTOF	splash10-00di-0900000000-35bd5d728d4b6335059a	2015-09-15	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - L-2,3-Dihydrodipicolinate 20V, Positive-QTOF	splash10-00di-0900000000-681935e00eed4828fd0f	2015-09-15	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - L-2,3-Dihydrodipicolinate 40V, Positive-QTOF	splash10-0udi-9300000000-ba4f4cccfccf71d0b007	2015-09-15	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - L-2,3-Dihydrodipicolinate 10V, Positive-QTOF	splash10-00di-1900000000-2698c9ffb8a4caa90c8f	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - L-2,3-Dihydrodipicolinate 20V, Positive-QTOF	splash10-001i-9200000000-625e0679cd43f0dedb7f	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - L-2,3-Dihydrodipicolinate 40V, Positive-QTOF	splash10-0f89-9000000000-7337376b7fa4e0a9a51d	2021-09-22	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum

IR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M-H]-)	2023-02-03	FELIX lab	View Spectrum
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+H]+)	2023-02-03	FELIX lab	View Spectrum
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+Na]+)	2023-02-03	FELIX lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Not Available

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

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

VMH ID

23DHDP

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Not Available

Showing metabocard for L-2,3-Dihydrodipicolinate (HMDB0012247)

MOL for HMDB0012247 (L-2,3-Dihydrodipicolinate)

3D MOL for HMDB0012247 (L-2,3-Dihydrodipicolinate)

3D SDF for HMDB0012247 (L-2,3-Dihydrodipicolinate)

3D-SDF for HMDB0012247 (L-2,3-Dihydrodipicolinate)

PDB for HMDB0012247 (L-2,3-Dihydrodipicolinate)

3D PDB for HMDB0012247 (L-2,3-Dihydrodipicolinate)

SMILES for HMDB0012247 (L-2,3-Dihydrodipicolinate)

INCHI for HMDB0012247 (L-2,3-Dihydrodipicolinate)

Structure for HMDB0012247 (L-2,3-Dihydrodipicolinate)

3D Structure for HMDB0012247 (L-2,3-Dihydrodipicolinate)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

IR Spectra