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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2013-02-26 19:02:59 UTC

Update Date

2023-02-21 17:29:22 UTC

HMDB ID

HMDB0059766

Secondary Accession Numbers

HMDB59766

Metabolite Identification

Common Name

Picolinoylglycine

Description

Picolinoylglycine 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. Picolinoylglycine is a moderately basic compound (based on its pKa). These are organic compounds containing a glycine residue with the N-atom attached to another moiety through an N-ester bond.

Structure

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

2,3,4,5-tetrahydroxypentanoic acid
  Mrv0541 02261312022D          

 13 13  0  0  0  0            999 V2000
    1.9152    1.5322    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2007    1.1197    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2007    0.2946    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9152   -0.1179    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6296    0.2946    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6296    1.1197    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3441    1.5321    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3441    2.3571    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0586    1.1196    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.7731    1.5321    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4875    1.1196    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2020    1.5321    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.4875    0.2946    0.0000 O   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
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  1  6  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  7  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 11 13  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0059766

> <DATABASE_NAME>
hmdb

> <SMILES>
OC(=O)CNC(=O)C1=NC=CC=C1

> <INCHI_IDENTIFIER>
InChI=1S/C8H8N2O3/c11-7(12)5-10-8(13)6-3-1-2-4-9-6/h1-4H,5H2,(H,10,13)(H,11,12)

> <INCHI_KEY>
MNYZGNSHBPLAFN-UHFFFAOYSA-N

> <FORMULA>
C8H8N2O3

> <MOLECULAR_WEIGHT>
180.1607

> <EXACT_MASS>
180.053492132

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
16.948350477168837

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
2-(pyridin-2-ylformamido)acetic acid

> <ALOGPS_LOGP>
-0.06

> <JCHEM_LOGP>
-0.306276617

> <ALOGPS_LOGS>
-1.61

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
14.657689509724175

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.136345041135517

> <JCHEM_PKA_STRONGEST_BASIC>
1.084842425399558

> <JCHEM_POLAR_SURFACE_AREA>
79.28999999999999

> <JCHEM_REFRACTIVITY>
43.588800000000006

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.42e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(pyridin-2-ylformamido)acetic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 26-FEB-13   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: 2,3,4,5-tetrahydroxypentanoic acid                
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   26-FEB-13         0                                  
HETATM    1  N   UNK     0       3.575   2.860   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0       2.241   2.090   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.241   0.550   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       3.575  -0.220   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.909   0.550   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       4.909   2.090   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       6.242   2.860   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       6.242   4.400   0.000  0.00  0.00           O+0
HETATM    9  N   UNK     0       7.576   2.090   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0       8.910   2.860   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      10.243   2.090   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      11.577   2.860   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0      10.243   0.550   0.000  0.00  0.00           O+0
CONECT    1    2    6                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    1    7                                                  
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11                                                            
MASTER        0    0    0    0    0    0    0    0   13    0   26    0
END

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
2-{[hydroxy(pyridin-2-yl)methylidene]amino}acetate	Generator

Chemical Formula

C₈H₈N₂O₃

Average Molecular Weight

180.1607

Monoisotopic Molecular Weight

180.053492132

IUPAC Name

2-(pyridin-2-ylformamido)acetic acid

Traditional Name

(pyridin-2-ylformamido)acetic acid

CAS Registry Number

Not Available

SMILES

OC(=O)CNC(=O)C1=NC=CC=C1

InChI Identifier

InChI=1S/C8H8N2O3/c11-7(12)5-10-8(13)6-3-1-2-4-9-6/h1-4H,5H2,(H,10,13)(H,11,12)

InChI Key

MNYZGNSHBPLAFN-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 carboxylic acid or derivatives
2-heteroaryl carboxamide
Pyridine
Heteroaromatic compound
Carboxamide group
Secondary carboxylic acid amide
Azacycle
Organoheterocyclic compound
Monocarboxylic acid or derivatives
Carboxylic acid
Carbonyl group
Organopnictogen compound
Organic oxygen compound
Organooxygen compound
Organonitrogen compound
Organic nitrogen compound
Organic oxide
Hydrocarbon derivative
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

Not Available

Ontology

Not Available

Urine (PMID: 2338430)

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	4.42 g/L	ALOGPS
logP	-0.06	ALOGPS
logP	-0.31	ChemAxon
logS	-1.6	ALOGPS
pKa (Strongest Acidic)	3.14	ChemAxon
pKa (Strongest Basic)	1.08	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	3	ChemAxon
Refractivity	43.59 m³·mol⁻¹	ChemAxon
Polarizability	16.95 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	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]+	138.716	31661259
DarkChem	[M-H]-	133.004	31661259
DeepCCS	[M+H]+	136.178	30932474
DeepCCS	[M-H]-	133.695	30932474
DeepCCS	[M-2H]-	169.403	30932474
DeepCCS	[M+Na]+	144.143	30932474
AllCCS	[M+H]+	138.0	32859911
AllCCS	[M+H-H2O]+	133.7	32859911
AllCCS	[M+NH4]+	141.9	32859911
AllCCS	[M+Na]+	143.1	32859911
AllCCS	[M-H]-	136.9	32859911
AllCCS	[M+Na-2H]-	137.6	32859911
AllCCS	[M+HCOO]-	138.6	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Picolinoylglycine	OC(=O)CNC(=O)C1=NC=CC=C1	2495.0	Standard polar	33892256
Picolinoylglycine	OC(=O)CNC(=O)C1=NC=CC=C1	1604.4	Standard non polar	33892256
Picolinoylglycine	OC(=O)CNC(=O)C1=NC=CC=C1	1761.7	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Picolinoylglycine,1TMS,isomer #1	C[Si](C)(C)OC(=O)CNC(=O)C1=CC=CC=N1	1825.7	Semi standard non polar	33892256
Picolinoylglycine,1TMS,isomer #2	C[Si](C)(C)N(CC(=O)O)C(=O)C1=CC=CC=N1	1831.0	Semi standard non polar	33892256
Picolinoylglycine,2TMS,isomer #1	C[Si](C)(C)OC(=O)CN(C(=O)C1=CC=CC=N1)[Si](C)(C)C	1791.3	Semi standard non polar	33892256
Picolinoylglycine,2TMS,isomer #1	C[Si](C)(C)OC(=O)CN(C(=O)C1=CC=CC=N1)[Si](C)(C)C	1823.5	Standard non polar	33892256
Picolinoylglycine,2TMS,isomer #1	C[Si](C)(C)OC(=O)CN(C(=O)C1=CC=CC=N1)[Si](C)(C)C	2316.2	Standard polar	33892256
Picolinoylglycine,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC(=O)CNC(=O)C1=CC=CC=N1	2067.0	Semi standard non polar	33892256
Picolinoylglycine,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)N(CC(=O)O)C(=O)C1=CC=CC=N1	2051.7	Semi standard non polar	33892256
Picolinoylglycine,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC(=O)CN(C(=O)C1=CC=CC=N1)[Si](C)(C)C(C)(C)C	2237.0	Semi standard non polar	33892256
Picolinoylglycine,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC(=O)CN(C(=O)C1=CC=CC=N1)[Si](C)(C)C(C)(C)C	2197.7	Standard non polar	33892256
Picolinoylglycine,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC(=O)CN(C(=O)C1=CC=CC=N1)[Si](C)(C)C(C)(C)C	2545.5	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - Picolinoylglycine GC-MS (Non-derivatized) - 70eV, Positive	splash10-0a4i-2900000000-b58bef192623ff379046	2017-09-20	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Picolinoylglycine GC-MS (1 TMS) - 70eV, Positive	splash10-05fr-9410000000-6131cc2e3e16e8b2db60	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Picolinoylglycine 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 - Picolinoylglycine 10V, Positive-QTOF	splash10-053r-1900000000-7e132d7f2177c520686d	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Picolinoylglycine 20V, Positive-QTOF	splash10-0a6r-9600000000-65f15c67a2861b152e0a	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Picolinoylglycine 40V, Positive-QTOF	splash10-0a4i-9100000000-f37d0c935941f17d79cc	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Picolinoylglycine 10V, Negative-QTOF	splash10-004i-1900000000-d58f74540e9f7d24851b	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Picolinoylglycine 20V, Negative-QTOF	splash10-00b9-9800000000-d5ea954002400ee09f54	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Picolinoylglycine 40V, Negative-QTOF	splash10-05di-9000000000-30e8e92d2486e69aceec	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Picolinoylglycine 10V, Positive-QTOF	splash10-0a4i-0900000000-64800001f0b269655f87	2021-09-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Picolinoylglycine 20V, Positive-QTOF	splash10-0059-9100000000-46b46b5010a246620bad	2021-09-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Picolinoylglycine 40V, Positive-QTOF	splash10-004i-9000000000-c67a2e8420c923d0bd39	2021-09-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Picolinoylglycine 10V, Negative-QTOF	splash10-004i-9400000000-7a2c2ea85666805657e2	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Picolinoylglycine 20V, Negative-QTOF	splash10-004i-9000000000-0f41bbef4118ebcccefd	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Picolinoylglycine 40V, Negative-QTOF	splash10-004i-9000000000-c2850ce6846335b0374d	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)	2021-09-24	Wishart Lab	View Spectrum
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, 1000 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, 200 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, 300 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, 400 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, 500 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, 600 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, 700 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, 800 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, 900 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

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

Blood
Urine

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Urine	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	2338430	details

Abnormal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Expected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Asthma	33739820	details

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

11788622

PDB ID

Not Available

ChEBI ID

89884

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 Picolinoylglycine (HMDB0059766)

MOL for HMDB0059766 (Picolinoylglycine)

3D MOL for HMDB0059766 (Picolinoylglycine)

3D SDF for HMDB0059766 (Picolinoylglycine)

3D-SDF for HMDB0059766 (Picolinoylglycine)

PDB for HMDB0059766 (Picolinoylglycine)

3D PDB for HMDB0059766 (Picolinoylglycine)

SMILES for HMDB0059766 (Picolinoylglycine)

INCHI for HMDB0059766 (Picolinoylglycine)

Structure for HMDB0059766 (Picolinoylglycine)

3D Structure for HMDB0059766 (Picolinoylglycine)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

IR Spectra