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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2012-09-11 17:54:06 UTC

Update Date

2023-02-21 17:23:10 UTC

HMDB ID

HMDB0033161

Secondary Accession Numbers

HMDB33161

Metabolite Identification

Common Name

2,6-Pyridinedicarboxylic acid

Description

2,6-Pyridinedicarboxylic acid, also known as 2,6-dicarboxypyridine or 2,6-dipicolinic acid, belongs to the class of organic compounds known as pyridinecarboxylic acids. Pyridinecarboxylic acids are compounds containing a pyridine ring bearing a carboxylic acid group. 2,6-Pyridinedicarboxylic acid is a secondary metabolite. Secondary metabolites are metabolically or physiologically non-essential metabolites that may serve a role as defense or signalling molecules. In some cases they are simply molecules that arise from the incomplete metabolism of other secondary metabolites. Based on a literature review very few articles have been published on 2,6-Pyridinedicarboxylic acid.

Structure

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

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  O   UNK     0       4.001  -2.310   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       5.335   0.000   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0       2.667   1.540   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       0.000   4.620   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       2.667   4.620   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5    9                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9   10                                                  
CONECT    9    8    4                                                       
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
2,6-Dicarboxypyridine	ChEBI
2,6-Dipicolinic acid	ChEBI
PYRIDINE-2,6-dicarboxylIC ACID	ChEBI
2,6-Dipicolinate	Generator
PYRIDINE-2,6-dicarboxylate	Generator
2,6-Pyridinedicarboxylate	Generator
2,6-Pyridine dicarboxylate	MeSH
3,4-Pyridinedicarboxylate	MeSH
Dipicolinic acid	MeSH
Dipicolinic acid, calcium salt	MeSH
Dipicolinic acid, dipotassium salt	MeSH
Dipicolinic acid, disodium salt	MeSH
Dipicolinic acid, monosodium salt	MeSH
Dipicolinic acid, zinc salt	MeSH
Zinc dipicolinate	MeSH
Dipicolinate	HMDB, Generator
2,6-Pyridinedicarboxylic acid	ChEBI

Chemical Formula

C₇H₅NO₄

Average Molecular Weight

167.1189

Monoisotopic Molecular Weight

167.021857653

IUPAC Name

pyridine-2,6-dicarboxylic acid

Traditional Name

dipicolinic acid

CAS Registry Number

499-83-2

SMILES

OC(=O)C1=CC=CC(=N1)C(O)=O

InChI Identifier

InChI=1S/C7H5NO4/c9-6(10)4-2-1-3-5(8-4)7(11)12/h1-3H,(H,9,10)(H,11,12)

InChI Key

WJJMNDUMQPNECX-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyridinecarboxylic acids. Pyridinecarboxylic acids are compounds containing a pyridine ring bearing a carboxylic acid group.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Pyridines and derivatives

Sub Class

Pyridinecarboxylic acids and derivatives

Direct Parent

Pyridinecarboxylic acids

Alternative Parents

Substituents

Pyridine carboxylic acid
Dicarboxylic acid or derivatives
Heteroaromatic compound
Azacycle
Carboxylic acid
Carboxylic acid derivative
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

pyridinedicarboxylic acid (CHEBI:46837 )

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cellular substructure

Extracellular (HMDB: HMDB0033161)
Cytoplasm (HMDB: HMDB0033161)

Excreta

Biofluid or Excreta

Feces (PMID: 27543620)

Source

Exogenous

Food

Food (HMDB: HMDB0033161)

Process

Not Available

Role

Biological role

Nutrient (HMDB: HMDB0033161)

Industrial application

Pharmaceutical industry

Pharmaceutical (HMDB: HMDB0033161)

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	252 °C	Not Available
Boiling Point	463.70 °C. @ 760.00 mm Hg (est)	The Good Scents Company Information System
Water Solubility	5 mg/mL at 25 °C	Not Available
LogP	-0.830 (est)	The Good Scents Company Information System

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	3.46 g/L	ALOGPS
logP	0.54	ALOGPS
logP	0.84	ChemAxon
logS	-1.7	ALOGPS
pKa (Strongest Acidic)	3.24	ChemAxon
pKa (Strongest Basic)	-2.5	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	87.49 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	37.67 m³·mol⁻¹	ChemAxon
Polarizability	14.57 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]+	137.075	31661259
DarkChem	[M-H]-	132.218	31661259
DeepCCS	[M+H]+	130.725	30932474
DeepCCS	[M-H]-	126.897	30932474
DeepCCS	[M-2H]-	164.41	30932474
DeepCCS	[M+Na]+	139.949	30932474
AllCCS	[M+H]+	134.5	32859911
AllCCS	[M+H-H2O]+	130.0	32859911
AllCCS	[M+NH4]+	138.7	32859911
AllCCS	[M+Na]+	139.9	32859911
AllCCS	[M-H]-	128.5	32859911
AllCCS	[M+Na-2H]-	129.3	32859911
AllCCS	[M+HCOO]-	130.4	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
2,6-Pyridinedicarboxylic acid	OC(=O)C1=CC=CC(=N1)C(O)=O	2390.7	Standard polar	33892256
2,6-Pyridinedicarboxylic acid	OC(=O)C1=CC=CC(=N1)C(O)=O	1411.4	Standard non polar	33892256
2,6-Pyridinedicarboxylic acid	OC(=O)C1=CC=CC(=N1)C(O)=O	1631.4	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
2,6-Pyridinedicarboxylic acid,1TMS,isomer #1	C[Si](C)(C)OC(=O)C1=CC=CC(C(=O)O)=N1	1782.4	Semi standard non polar	33892256
2,6-Pyridinedicarboxylic acid,2TMS,isomer #1	C[Si](C)(C)OC(=O)C1=CC=CC(C(=O)O[Si](C)(C)C)=N1	1766.2	Semi standard non polar	33892256
2,6-Pyridinedicarboxylic acid,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC(=O)C1=CC=CC(C(=O)O)=N1	2019.6	Semi standard non polar	33892256
2,6-Pyridinedicarboxylic acid,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC(=O)C1=CC=CC(C(=O)O[Si](C)(C)C(C)(C)C)=N1	2196.2	Semi standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Experimental GC-MS	GC-MS Spectrum - 2,6-Pyridinedicarboxylic acid GC-MS (2 TMS)	splash10-0f92-5970000000-e5aa4bc3f23f554c51c2	2014-06-16	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - 2,6-Pyridinedicarboxylic acid EI-B (Non-derivatized)	splash10-0kor-9400000000-4be19de76ddc678df43f	2017-09-12	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - 2,6-Pyridinedicarboxylic acid EI-B (Non-derivatized)	splash10-0kor-7900000000-48c091dd3ea56a6cad7d	2017-09-12	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - 2,6-Pyridinedicarboxylic acid EI-B (Non-derivatized)	splash10-0g29-9200000000-bbc0b97db569b40d51b6	2017-09-12	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - 2,6-Pyridinedicarboxylic acid GC-EI-TOF (Non-derivatized)	splash10-0002-1950000000-1221ab338705f508fac4	2017-09-12	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - 2,6-Pyridinedicarboxylic acid GC-MS (Non-derivatized)	splash10-0f92-5970000000-e5aa4bc3f23f554c51c2	2017-09-12	HMDB team, MONA, MassBank	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2,6-Pyridinedicarboxylic acid GC-MS (Non-derivatized) - 70eV, Positive	splash10-01ba-5900000000-32b3c0674b6807262c0a	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2,6-Pyridinedicarboxylic acid GC-MS (2 TMS) - 70eV, Positive	splash10-00di-9771000000-0b7af5e7f34fbe485102	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2,6-Pyridinedicarboxylic acid 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
Experimental LC-MS/MS	LC-MS/MS Spectrum - 2,6-Pyridinedicarboxylic acid 75V, Negative-QTOF	splash10-00di-0900000000-d1e5227c31d10a6a1429	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 2,6-Pyridinedicarboxylic acid 60V, Negative-QTOF	splash10-00di-0900000000-ed561b5a2dc4540c442f	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 2,6-Pyridinedicarboxylic acid 45V, Negative-QTOF	splash10-00di-0900000000-3d7a8f67f87e05404f07	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 2,6-Pyridinedicarboxylic acid 15V, Negative-QTOF	splash10-00di-0900000000-eac9ce6269818d6d10c4	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 2,6-Pyridinedicarboxylic acid 30V, Negative-QTOF	splash10-00di-0900000000-7fc94eff9b377b373572	2021-09-20	HMDB team, MONA	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,6-Pyridinedicarboxylic acid 10V, Positive-QTOF	splash10-014i-0900000000-f5cc3c9b53962d3c7bbf	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,6-Pyridinedicarboxylic acid 20V, Positive-QTOF	splash10-014i-0900000000-6ef5148cf9455a1681b2	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,6-Pyridinedicarboxylic acid 40V, Positive-QTOF	splash10-0udi-9200000000-a79c41271377a7dc64d1	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,6-Pyridinedicarboxylic acid 10V, Negative-QTOF	splash10-014i-0900000000-ef7d9f9d25fcfc62914a	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,6-Pyridinedicarboxylic acid 20V, Negative-QTOF	splash10-01b9-1900000000-536dbca7bed7d07b92c7	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,6-Pyridinedicarboxylic acid 40V, Negative-QTOF	splash10-0fi1-9300000000-e546b017cdf4c47c567f	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,6-Pyridinedicarboxylic acid 10V, Positive-QTOF	splash10-014i-0900000000-a863bcc891d9eaefaff0	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,6-Pyridinedicarboxylic acid 20V, Positive-QTOF	splash10-0pvi-0900000000-e4220355d21ab9eb926b	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,6-Pyridinedicarboxylic acid 40V, Positive-QTOF	splash10-0udi-9100000000-30cbef97b6d4962a5fbc	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,6-Pyridinedicarboxylic acid 10V, Negative-QTOF	splash10-00b9-9500000000-650b7bb4687fc9a07644	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,6-Pyridinedicarboxylic acid 20V, Negative-QTOF	splash10-004i-9000000000-c2850ce6846335b0374d	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,6-Pyridinedicarboxylic acid 40V, Negative-QTOF	splash10-004i-9000000000-80802babbf127fa9ad47	2021-09-25	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]-)	2023-02-04	FELIX lab	View Spectrum
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+H]+)	2023-02-04	FELIX lab	View Spectrum
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+Na]+)	2023-02-04	FELIX lab	View Spectrum

Biological Properties

Cellular Locations

Cytoplasm
Extracellular

Biospecimen Locations

Feces

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	27543620	details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	29808030	details

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

DB04267

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB011167

KNApSAcK ID

C00055308

Chemspider ID

9940

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Dipicolinic_acid

METLIN ID

Not Available

PubChem Compound

10367

PDB ID

PDC

ChEBI ID

46837

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

rw1167241

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

(). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .

Showing metabocard for 2,6-Pyridinedicarboxylic acid (HMDB0033161)

MOL for HMDB0033161 (2,6-Pyridinedicarboxylic acid)

3D MOL for HMDB0033161 (2,6-Pyridinedicarboxylic acid)

3D SDF for HMDB0033161 (2,6-Pyridinedicarboxylic acid)

3D-SDF for HMDB0033161 (2,6-Pyridinedicarboxylic acid)

PDB for HMDB0033161 (2,6-Pyridinedicarboxylic acid)

3D PDB for HMDB0033161 (2,6-Pyridinedicarboxylic acid)

SMILES for HMDB0033161 (2,6-Pyridinedicarboxylic acid)

INCHI for HMDB0033161 (2,6-Pyridinedicarboxylic acid)

Structure for HMDB0033161 (2,6-Pyridinedicarboxylic acid)

3D Structure for HMDB0033161 (2,6-Pyridinedicarboxylic acid)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

IR Spectra