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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2013-01-09 12:11:23 UTC

Update Date

2023-02-21 17:29:16 UTC

HMDB ID

HMDB0059723

Secondary Accession Numbers

HMDB59723

Metabolite Identification

Common Name

Pyridylacetylglycine

Description

Pyridylacetylglycine belongs to the class of organic compounds known as n-acyl-alpha amino acids. N-acyl-alpha amino acids are compounds containing an alpha amino acid which bears an acyl group at its terminal nitrogen atom. Pyridylacetylglycine is a strong basic compound (based on its pKa). Pyridylacetylglycine is a metabolite of nicotine, an alkaloid found in the nightshade family of plants (Solanaceae) that acts as a nicotinic acetylcholine receptor agonist.

Structure

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


  Mrv0541 01091312052D          

 14 14  0  0  0  0            999 V2000
    1.4289   -4.1250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -3.7125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -4.9500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1447   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1447   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302   -5.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158   -4.9500    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  6  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
  9 14  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0059723

> <DATABASE_NAME>
hmdb

> <SMILES>
OC(=O)CNC(=O)CC1=CC=CC=N1

> <INCHI_IDENTIFIER>
InChI=1S/C9H10N2O3/c12-8(11-6-9(13)14)5-7-3-1-2-4-10-7/h1-4H,5-6H2,(H,11,12)(H,13,14)

> <INCHI_KEY>
CWRPZJWABUTVME-UHFFFAOYSA-N

> <FORMULA>
C9H10N2O3

> <MOLECULAR_WEIGHT>
194.1873

> <EXACT_MASS>
194.069142196

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
18.478799333275095

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-[2-(pyridin-2-yl)acetamido]acetic acid

> <ALOGPS_LOGP>
0.04

> <JCHEM_LOGP>
-1.397800587549767

> <ALOGPS_LOGS>
-1.77

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
15.069801934112252

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.382584774341868

> <JCHEM_PKA_STRONGEST_BASIC>
4.38023127821011

> <JCHEM_POLAR_SURFACE_AREA>
79.29

> <JCHEM_REFRACTIVITY>
47.6402

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.29e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[2-(pyridin-2-yl)acetamido]acetic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 09-JAN-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   09-JAN-13         0                                  
HETATM    1  O   UNK     0       2.667  -7.700   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       4.001  -6.930   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       4.001  -5.390   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       5.335  -7.700   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0       6.668  -6.930   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0       8.002  -7.700   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       8.002  -9.240   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       9.336  -6.930   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      10.669  -7.700   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      12.003  -6.930   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      13.337  -7.700   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      13.337  -9.240   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      12.003 -10.010   0.000  0.00  0.00           C+0
HETATM   14  N   UNK     0      10.669  -9.240   0.000  0.00  0.00           N+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9                                                       
CONECT    9    8   10   14                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13    9                                                       
MASTER        0    0    0    0    0    0    0    0   14    0   28    0
END

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Not Available

Chemical Formula

C₉H₁₀N₂O₃

Average Molecular Weight

194.1873

Monoisotopic Molecular Weight

194.069142196

IUPAC Name

2-[2-(pyridin-2-yl)acetamido]acetic acid

Traditional Name

[2-(pyridin-2-yl)acetamido]acetic acid

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C9H10N2O3/c12-8(11-6-9(13)14)5-7-3-1-2-4-10-7/h1-4H,5-6H2,(H,11,12)(H,13,14)

InChI Key

CWRPZJWABUTVME-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as n-acyl-alpha amino acids. N-acyl-alpha amino acids are compounds containing an alpha amino acid which bears an acyl group at its terminal nitrogen atom.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

N-acyl-alpha amino acids

Alternative Parents

Substituents

N-acyl-alpha-amino acid
Pyridine
Heteroaromatic compound
Carboxamide group
Secondary carboxylic acid amide
Carboxylic acid
Monocarboxylic acid or derivatives
Organoheterocyclic compound
Azacycle
Organopnictogen compound
Organooxygen compound
Organonitrogen compound
Organic oxygen compound
Carbonyl group
Organic oxide
Organic nitrogen compound
Hydrocarbon derivative
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

pyridines (CHEBI:68456 )
N-acylglycine (CHEBI:68456 )

Ontology

Not Available

Not Available

Not Available

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	3.29 g/L	ALOGPS
logP	0.04	ALOGPS
logP	-1.4	ChemAxon
logS	-1.8	ALOGPS
pKa (Strongest Acidic)	3.38	ChemAxon
pKa (Strongest Basic)	4.38	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	79.29 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	47.64 m³·mol⁻¹	ChemAxon
Polarizability	18.48 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]+	143.753	31661259
DarkChem	[M-H]-	138.982	31661259
DeepCCS	[M+H]+	132.868	30932474
DeepCCS	[M-H]-	129.038	30932474
DeepCCS	[M-2H]-	166.611	30932474
DeepCCS	[M+Na]+	142.15	30932474
AllCCS	[M+H]+	141.4	32859911
AllCCS	[M+H-H2O]+	137.3	32859911
AllCCS	[M+NH4]+	145.3	32859911
AllCCS	[M+Na]+	146.4	32859911
AllCCS	[M-H]-	142.1	32859911
AllCCS	[M+Na-2H]-	142.7	32859911
AllCCS	[M+HCOO]-	143.4	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Pyridylacetylglycine	OC(=O)CNC(=O)CC1=CC=CC=N1	2885.0	Standard polar	33892256
Pyridylacetylglycine	OC(=O)CNC(=O)CC1=CC=CC=N1	1575.5	Standard non polar	33892256
Pyridylacetylglycine	OC(=O)CNC(=O)CC1=CC=CC=N1	1887.9	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Pyridylacetylglycine,1TMS,isomer #1	C[Si](C)(C)OC(=O)CNC(=O)CC1=CC=CC=N1	1907.0	Semi standard non polar	33892256
Pyridylacetylglycine,1TMS,isomer #2	C[Si](C)(C)N(CC(=O)O)C(=O)CC1=CC=CC=N1	1888.8	Semi standard non polar	33892256
Pyridylacetylglycine,2TMS,isomer #1	C[Si](C)(C)OC(=O)CN(C(=O)CC1=CC=CC=N1)[Si](C)(C)C	1868.4	Semi standard non polar	33892256
Pyridylacetylglycine,2TMS,isomer #1	C[Si](C)(C)OC(=O)CN(C(=O)CC1=CC=CC=N1)[Si](C)(C)C	1924.9	Standard non polar	33892256
Pyridylacetylglycine,2TMS,isomer #1	C[Si](C)(C)OC(=O)CN(C(=O)CC1=CC=CC=N1)[Si](C)(C)C	2391.6	Standard polar	33892256
Pyridylacetylglycine,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC(=O)CNC(=O)CC1=CC=CC=N1	2145.6	Semi standard non polar	33892256
Pyridylacetylglycine,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)N(CC(=O)O)C(=O)CC1=CC=CC=N1	2126.4	Semi standard non polar	33892256
Pyridylacetylglycine,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC(=O)CN(C(=O)CC1=CC=CC=N1)[Si](C)(C)C(C)(C)C	2340.7	Semi standard non polar	33892256
Pyridylacetylglycine,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC(=O)CN(C(=O)CC1=CC=CC=N1)[Si](C)(C)C(C)(C)C	2338.5	Standard non polar	33892256
Pyridylacetylglycine,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC(=O)CN(C(=O)CC1=CC=CC=N1)[Si](C)(C)C(C)(C)C	2607.8	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - Pyridylacetylglycine GC-MS (Non-derivatized) - 70eV, Positive	splash10-006x-7900000000-05562e1f20f9c793aa3e	2017-09-20	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Pyridylacetylglycine GC-MS (1 TMS) - 70eV, Positive	splash10-00dm-9800000000-80681ef863db88caff58	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Pyridylacetylglycine 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 - Pyridylacetylglycine 10V, Negative-QTOF	splash10-0006-0900000000-ed3936bee2145a1f3e6b	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Pyridylacetylglycine 20V, Negative-QTOF	splash10-006x-4900000000-1e33f6f50b01b19816aa	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Pyridylacetylglycine 40V, Negative-QTOF	splash10-05fu-9100000000-ebbfcb654e8836ef4760	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Pyridylacetylglycine 10V, Negative-QTOF	splash10-00dl-9000000000-ffe606835c41d304dd67	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Pyridylacetylglycine 20V, Negative-QTOF	splash10-006x-9000000000-a6674ff598dec550f69d	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Pyridylacetylglycine 40V, Negative-QTOF	splash10-00dl-9000000000-3a6fee0450aca506a22f	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Pyridylacetylglycine 10V, Positive-QTOF	splash10-002b-2900000000-d927e34ca15fd62dcf90	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Pyridylacetylglycine 20V, Positive-QTOF	splash10-056s-9500000000-70aa3f7b65e55ab9d6c9	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Pyridylacetylglycine 40V, Positive-QTOF	splash10-0a6u-9100000000-bb3a714a017ba0e5aa1c	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Pyridylacetylglycine 10V, Positive-QTOF	splash10-00b9-8900000000-953114ef97d3f14a7b54	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Pyridylacetylglycine 20V, Positive-QTOF	splash10-0596-9700000000-265ee590c151315f3903	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Pyridylacetylglycine 40V, Positive-QTOF	splash10-0006-9100000000-8829116fe8b20f78afc5	2021-09-24	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

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

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

22501452

PDB ID

Not Available

ChEBI ID

68456

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

Roux A, Xu Y, Heilier JF, Olivier MF, Ezan E, Tabet JC, Junot C: Annotation of the human adult urinary metabolome and metabolite identification using ultra high performance liquid chromatography coupled to a linear quadrupole ion trap-Orbitrap mass spectrometer. Anal Chem. 2012 Aug 7;84(15):6429-37. doi: 10.1021/ac300829f. Epub 2012 Jul 17. [PubMed:22770225 ]

Showing metabocard for Pyridylacetylglycine (HMDB0059723)

MOL for HMDB0059723 (Pyridylacetylglycine)

3D MOL for HMDB0059723 (Pyridylacetylglycine)

3D SDF for HMDB0059723 (Pyridylacetylglycine)

3D-SDF for HMDB0059723 (Pyridylacetylglycine)

PDB for HMDB0059723 (Pyridylacetylglycine)

3D PDB for HMDB0059723 (Pyridylacetylglycine)

SMILES for HMDB0059723 (Pyridylacetylglycine)

INCHI for HMDB0059723 (Pyridylacetylglycine)

Structure for HMDB0059723 (Pyridylacetylglycine)

3D Structure for HMDB0059723 (Pyridylacetylglycine)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

IR Spectra