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Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References XML

Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2013-07-04 18:55:04 UTC

Update Date

2023-02-21 17:30:12 UTC

HMDB ID

HMDB0060722

Secondary Accession Numbers

HMDB60722

Metabolite Identification

Common Name

2-Pyridylacetic acid

Description

2-Pyridylacetic acid, also known as 2-pyridylacetate, belongs to the class of organic compounds known as pyridines and derivatives. Pyridines and derivatives are compounds containing a pyridine ring, which is a six-member aromatic heterocycle which consists of one nitrogen atom and five carbon atoms. 2-Pyridylacetic acid is a strong basic compound (based on its pKa). 2-Pyridylacetic acid is a metabolite of betahistine. Betahistine hydrochloride (brand names Serc, Hiserk, Betaserc) is an antivertigo drug. It is commonly prescribed to patients with balance disorders or to alleviate vertigo symptoms associated with Ménière's disease. It was first registered in Europe in 1970 for the treatment of Ménière's disease.

Structure

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

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
2-Pyridylacetate	Generator
2-Pyridylacetic acid	MeSH

Chemical Formula

C₇H₇NO₂

Average Molecular Weight

137.136

Monoisotopic Molecular Weight

137.047678473

IUPAC Name

2-(pyridin-2-yl)acetic acid

Traditional Name

pyridin-2-ylacetic acid

CAS Registry Number

Not Available

SMILES

OC(=O)CC1=CC=CC=N1

InChI Identifier

InChI=1S/C7H7NO2/c9-7(10)5-6-3-1-2-4-8-6/h1-4H,5H2,(H,9,10)

InChI Key

BPSNETAIJADFTO-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyridines and derivatives. Pyridines and derivatives are compounds containing a pyridine ring, which is a six-member aromatic heterocycle which consists of one nitrogen atom and five carbon atoms.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Pyridines and derivatives

Sub Class

Not Available

Direct Parent

Pyridines and derivatives

Alternative Parents

Substituents

Pyridine
Heteroaromatic compound
Azacycle
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Carbonyl group
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (HMDB: HMDB0060722)

Organ

Kidney (HMDB: HMDB0060722)
Liver (HMDB: HMDB0060722)

Excreta

Biofluid or Excreta

Urine (HMDB: HMDB0060722)

Cellular substructure

Cytoplasm (HMDB: HMDB0060722)

Source

Endogenous

Endogenous (HMDB: HMDB0060722)

Process

Not Available

Role

Not Available

Physical Properties

State

Not Available

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	63.5 g/L	ALOGPS
logP	0.57	ALOGPS
logP	-0.24	ChemAxon
logS	-0.33	ALOGPS
pKa (Strongest Acidic)	3.35	ChemAxon
pKa (Strongest Basic)	4.67	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	50.19 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	34.84 m³·mol⁻¹	ChemAxon
Polarizability	13.28 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]+	128.413	31661259
DarkChem	[M-H]-	123.971	31661259
DeepCCS	[M+H]+	121.733	30932474
DeepCCS	[M-H]-	117.949	30932474
DeepCCS	[M-2H]-	155.234	30932474
DeepCCS	[M+Na]+	130.409	30932474
AllCCS	[M+H]+	128.1	32859911
AllCCS	[M+H-H2O]+	123.4	32859911
AllCCS	[M+NH4]+	132.5	32859911
AllCCS	[M+Na]+	133.8	32859911
AllCCS	[M-H]-	125.7	32859911
AllCCS	[M+Na-2H]-	127.3	32859911
AllCCS	[M+HCOO]-	129.0	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
2-Pyridylacetic acid	OC(=O)CC1=CC=CC=N1	2334.2	Standard polar	33892256
2-Pyridylacetic acid	OC(=O)CC1=CC=CC=N1	1260.4	Standard non polar	33892256
2-Pyridylacetic acid	OC(=O)CC1=CC=CC=N1	1292.7	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
2-Pyridylacetic acid,1TMS,isomer #1	C[Si](C)(C)OC(=O)CC1=CC=CC=N1	1318.0	Semi standard non polar	33892256
2-Pyridylacetic acid,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC(=O)CC1=CC=CC=N1	1546.3	Semi standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - 2-Pyridylacetic acid GC-MS (Non-derivatized) - 70eV, Positive	splash10-0006-9200000000-6aa4b076ec42f988041e	2017-09-20	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-Pyridylacetic acid GC-MS (1 TMS) - 70eV, Positive	splash10-006x-9300000000-afea62aab6f7ae9971f3	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-Pyridylacetic 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
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Pyridylacetic acid 10V, Positive-QTOF	splash10-00di-0900000000-aa807d19ffd3943f6760	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Pyridylacetic acid 20V, Positive-QTOF	splash10-00di-1900000000-8583a19c8c37576b2b5e	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Pyridylacetic acid 40V, Positive-QTOF	splash10-0006-9200000000-b27d2320f304c0f980f2	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Pyridylacetic acid 10V, Negative-QTOF	splash10-000i-2900000000-ce3c6fc00349bb774df2	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Pyridylacetic acid 20V, Negative-QTOF	splash10-00ko-5900000000-781b48f7224448d6d8d7	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Pyridylacetic acid 40V, Negative-QTOF	splash10-00kf-9400000000-d7af6ab0f740e5f3cc71	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Pyridylacetic acid 10V, Positive-QTOF	splash10-0079-2900000000-81dd672dbbd8d2621b36	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Pyridylacetic acid 20V, Positive-QTOF	splash10-006x-9600000000-0f6171fa5cbbdb496107	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Pyridylacetic acid 40V, Positive-QTOF	splash10-0006-9000000000-8d199fd22199d14dacbc	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Pyridylacetic acid 10V, Negative-QTOF	splash10-0006-9000000000-eef4c1f804c025cbb978	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Pyridylacetic acid 20V, Negative-QTOF	splash10-0006-9000000000-eef4c1f804c025cbb978	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Pyridylacetic acid 40V, Negative-QTOF	splash10-0296-9000000000-b30cc1f8cbbe92bb67e8	2021-10-12	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-24	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

Biospecimen Locations

Blood
Urine

Tissue Locations

Kidney
Liver

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Expected but not Quantified	Not Quantified	Not Available	Not Available	Normal	Not Available	details
Urine	Expected but not Quantified	Not Quantified	Not Available	Not Available	Normal	Not Available	details

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

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

85318

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

VMH ID

Not Available

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 2-Pyridylacetic acid (HMDB0060722)

MOL for HMDB0060722 (2-Pyridylacetic acid)

3D MOL for HMDB0060722 (2-Pyridylacetic acid)

3D SDF for HMDB0060722 (2-Pyridylacetic acid)

3D-SDF for HMDB0060722 (2-Pyridylacetic acid)

PDB for HMDB0060722 (2-Pyridylacetic acid)

3D PDB for HMDB0060722 (2-Pyridylacetic acid)

SMILES for HMDB0060722 (2-Pyridylacetic acid)

INCHI for HMDB0060722 (2-Pyridylacetic acid)

Structure for HMDB0060722 (2-Pyridylacetic acid)

3D Structure for HMDB0060722 (2-Pyridylacetic acid)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

IR Spectra