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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-10 22:04:29 UTC
Update Date2021-09-26 22:53:05 UTC
HMDB IDHMDB0244956
Secondary Accession NumbersNone
Metabolite Identification
Common Name2-(Pyridin-2-ylamino)acetic acid
Description2-(Pyridin-2-ylamino)acetic acid, also known as N-(2-pyridyl)glycine or NPD-glycine, 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. Based on a literature review very few articles have been published on 2-(Pyridin-2-ylamino)acetic acid. This compound has been identified in human blood as reported by (PMID: 31557052 ). 2-(pyridin-2-ylamino)acetic acid is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 2-(Pyridin-2-ylamino)acetic acid is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.
Structure
Thumb
Synonyms
ValueSource
2-(Pyridin-2-ylamino)acetateGenerator
N-(2-Pyridyl)glycineHMDB
NPD-GlycineHMDB
Chemical FormulaC7H8N2O2
Average Molecular Weight152.153
Monoisotopic Molecular Weight152.058577506
IUPAC Name2-[(pyridin-2-yl)amino]acetic acid
Traditional Name(pyridin-2-ylamino)acetic acid
CAS Registry NumberNot Available
SMILES
OC(=O)CNC1=CC=CC=N1
InChI Identifier
InChI=1S/C7H8N2O2/c10-7(11)5-9-6-3-1-2-4-8-6/h1-4H,5H2,(H,8,9)(H,10,11)
InChI KeyVWSWWWOLLQGVGN-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.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassAmino acids, peptides, and analogues
Direct ParentAlpha amino acids and derivatives
Alternative Parents
Substituents
  • Alpha-amino acid or derivatives
  • Aminopyridine
  • Secondary aliphatic/aromatic amine
  • Pyridine
  • Imidolactam
  • Heteroaromatic compound
  • Amino acid
  • Carboxylic acid
  • Monocarboxylic acid or derivatives
  • Secondary amine
  • Organoheterocyclic compound
  • Azacycle
  • Organopnictogen compound
  • Organooxygen compound
  • Organonitrogen compound
  • Amine
  • Organic nitrogen compound
  • Organic oxide
  • Organic oxygen compound
  • Hydrocarbon derivative
  • Carbonyl group
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
ProcessNot Available
RoleNot Available
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
logP-0.4ALOGPS
logP-1.4ChemAxon
logS-1.2ALOGPS
pKa (Strongest Acidic)3.65ChemAxon
pKa (Strongest Basic)6.66ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area62.22 ŲChemAxon
Rotatable Bond Count3ChemAxon
Refractivity40.49 m³·mol⁻¹ChemAxon
Polarizability14.88 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M+H]+125.68530932474
DeepCCS[M-H]-121.86530932474
DeepCCS[M-2H]-159.10230932474
DeepCCS[M+Na]+134.33430932474
AllCCS[M+H]+132.432859911
AllCCS[M+H-H2O]+127.932859911
AllCCS[M+NH4]+136.632859911
AllCCS[M+Na]+137.832859911
AllCCS[M-H]-130.632859911
AllCCS[M+Na-2H]-132.032859911
AllCCS[M+HCOO]-133.532859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
2-(Pyridin-2-ylamino)acetic acidOC(=O)CNC1=CC=CC=N12266.2Standard polar33892256
2-(Pyridin-2-ylamino)acetic acidOC(=O)CNC1=CC=CC=N11530.9Standard non polar33892256
2-(Pyridin-2-ylamino)acetic acidOC(=O)CNC1=CC=CC=N11535.1Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
2-(Pyridin-2-ylamino)acetic acid,2TMS,isomer #1C[Si](C)(C)OC(=O)CN(C1=CC=CC=N1)[Si](C)(C)C1543.1Semi standard non polar33892256
2-(Pyridin-2-ylamino)acetic acid,2TMS,isomer #1C[Si](C)(C)OC(=O)CN(C1=CC=CC=N1)[Si](C)(C)C1611.8Standard non polar33892256
2-(Pyridin-2-ylamino)acetic acid,2TMS,isomer #1C[Si](C)(C)OC(=O)CN(C1=CC=CC=N1)[Si](C)(C)C1943.5Standard polar33892256
2-(Pyridin-2-ylamino)acetic acid,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC(=O)CN(C1=CC=CC=N1)[Si](C)(C)C(C)(C)C1972.5Semi standard non polar33892256
2-(Pyridin-2-ylamino)acetic acid,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC(=O)CN(C1=CC=CC=N1)[Si](C)(C)C(C)(C)C2041.0Standard non polar33892256
2-(Pyridin-2-ylamino)acetic acid,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC(=O)CN(C1=CC=CC=N1)[Si](C)(C)C(C)(C)C2211.0Standard polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 2-(Pyridin-2-ylamino)acetic acid GC-MS (Non-derivatized) - 70eV, Positivesplash10-0a4i-1900000000-8c7604b53b2d3f00d5bd2021-09-23Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 2-(Pyridin-2-ylamino)acetic acid GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 2-(Pyridin-2-ylamino)acetic acid GC-MS (TMS_1_1) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 2-(Pyridin-2-ylamino)acetic acid GC-MS (TMS_1_2) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 2-(Pyridin-2-ylamino)acetic acid GC-MS (TBDMS_1_1) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 2-(Pyridin-2-ylamino)acetic acid GC-MS (TBDMS_1_2) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-(Pyridin-2-ylamino)acetic acid 10V, Positive-QTOFsplash10-0f79-0900000000-63a1e26e7194fd2554382021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-(Pyridin-2-ylamino)acetic acid 20V, Positive-QTOFsplash10-0a4i-1900000000-5b7a664b8e95160c2d112021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-(Pyridin-2-ylamino)acetic acid 40V, Positive-QTOFsplash10-001i-9100000000-af2f768b040ca4c5af772021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-(Pyridin-2-ylamino)acetic acid 10V, Negative-QTOFsplash10-0a4i-0900000000-e75a89fd97c681c13b2d2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-(Pyridin-2-ylamino)acetic acid 20V, Negative-QTOFsplash10-0a4i-0900000000-80c6e665a559305960eb2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-(Pyridin-2-ylamino)acetic acid 40V, Negative-QTOFsplash10-056r-9300000000-a650587917b16240abfe2021-10-12Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID168255
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound193885
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]