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Showing metabocard for 2-Pyridylacetic acid (HMDB0060722)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2013-07-04 18:55:04 UTC
Update Date2023-02-21 17:30:12 UTC
HMDB IDHMDB0060722
Secondary Accession Numbers
  • HMDB60722
Metabolite Identification
Common Name2-Pyridylacetic acid
Description2-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
Data?1677000612
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0060722 (2-Pyridylacetic acid)


  Mrv0541 07041311552D          

 10 10  0  0  0  0            999 V2000
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    3.3000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  2  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  6  3  2  0  0  0  0
  6  5  1  0  0  0  0
  7  5  1  0  0  0  0
  8  4  2  0  0  0  0
  8  6  1  0  0  0  0
  9  7  2  0  0  0  0
 10  7  1  0  0  0  0
M  END
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3D MOL for HMDB0060722 (2-Pyridylacetic acid)

HMDB0060722
     RDKit          3D
2-Pyridylacetic acid
 17 17  0  0  0  0  0  0  0  0999 V2000
    2.0295   -0.9121    1.3031 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3694   -0.2692    0.2767 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6930   -0.0366   -0.0568 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3382    0.2860   -0.6517 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0283   -0.0235   -0.1955 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6449    0.8674    0.6432 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9223    0.6737    1.1284 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5812   -0.4604    0.7436 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9480   -1.3563   -0.1060 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6873   -1.1269   -0.5614 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.0787    0.8769   -0.2523 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4701    1.3660   -0.6826 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4568   -0.1276   -1.6776 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1545    1.7929    0.9797 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4063    1.3856    1.7945 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5971   -0.6815    1.0883 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4657   -2.2544   -0.4127 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  2  0
 10  5  1  0
  3 11  1  0
  4 12  1  0
  4 13  1  0
  6 14  1  0
  7 15  1  0
  8 16  1  0
  9 17  1  0
M  END
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3D SDF for HMDB0060722 (2-Pyridylacetic acid)


  Mrv0541 07041311552D          

 10 10  0  0  0  0            999 V2000
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    3.3000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  2  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  6  3  2  0  0  0  0
  6  5  1  0  0  0  0
  7  5  1  0  0  0  0
  8  4  2  0  0  0  0
  8  6  1  0  0  0  0
  9  7  2  0  0  0  0
 10  7  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0060722

> <DATABASE_NAME>
hmdb

> <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

> <FORMULA>
C7H7NO2

> <MOLECULAR_WEIGHT>
137.136

> <EXACT_MASS>
137.047678473

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
13.280095434704275

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
0.57

> <JCHEM_LOGP>
-0.23663535816710152

> <ALOGPS_LOGS>
-0.33

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.346684993685088

> <JCHEM_PKA_STRONGEST_BASIC>
4.667809921777938

> <JCHEM_POLAR_SURFACE_AREA>
50.19

> <JCHEM_REFRACTIVITY>
34.83669999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.35e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
pyridin-2-ylacetic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

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

HMDB0060722
     RDKit          3D
2-Pyridylacetic acid
 17 17  0  0  0  0  0  0  0  0999 V2000
    2.0295   -0.9121    1.3031 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3694   -0.2692    0.2767 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6930   -0.0366   -0.0568 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3382    0.2860   -0.6517 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0283   -0.0235   -0.1955 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6449    0.8674    0.6432 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9223    0.6737    1.1284 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5812   -0.4604    0.7436 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9480   -1.3563   -0.1060 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6873   -1.1269   -0.5614 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.0787    0.8769   -0.2523 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4701    1.3660   -0.6826 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4568   -0.1276   -1.6776 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1545    1.7929    0.9797 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4063    1.3856    1.7945 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5971   -0.6815    1.0883 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4657   -2.2544   -0.4127 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  2  0
 10  5  1  0
  3 11  1  0
  4 12  1  0
  4 13  1  0
  6 14  1  0
  7 15  1  0
  8 16  1  0
  9 17  1  0
M  END
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PDB for HMDB0060722 (2-Pyridylacetic acid)

HEADER    PROTEIN                                 04-JUL-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-JUL-13         0                                  
HETATM    1  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+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   3.850   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.667   4.620   0.000  0.00  0.00           C+0
HETATM    8  N   UNK     0       2.667   1.540   0.000  0.00  0.00           N+0
HETATM    9  O   UNK     0       2.667   6.160   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       4.001   3.850   0.000  0.00  0.00           O+0
CONECT    1    2    3                                                       
CONECT    2    1    4                                                       
CONECT    3    1    6                                                       
CONECT    4    2    8                                                       
CONECT    5    6    7                                                       
CONECT    6    3    5    8                                                  
CONECT    7    5    9   10                                                  
CONECT    8    4    6                                                       
CONECT    9    7                                                            
CONECT   10    7                                                            
MASTER        0    0    0    0    0    0    0    0   10    0   20    0
END
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3D PDB for HMDB0060722 (2-Pyridylacetic acid)

COMPND    HMDB0060722
HETATM    1  O1  UNL     1       2.030  -0.912   1.303  1.00  0.00           O  
HETATM    2  C1  UNL     1       2.369  -0.269   0.277  1.00  0.00           C  
HETATM    3  O2  UNL     1       3.693  -0.037  -0.057  1.00  0.00           O  
HETATM    4  C2  UNL     1       1.338   0.286  -0.652  1.00  0.00           C  
HETATM    5  C3  UNL     1      -0.028  -0.023  -0.195  1.00  0.00           C  
HETATM    6  C4  UNL     1      -0.645   0.867   0.643  1.00  0.00           C  
HETATM    7  C5  UNL     1      -1.922   0.674   1.128  1.00  0.00           C  
HETATM    8  C6  UNL     1      -2.581  -0.460   0.744  1.00  0.00           C  
HETATM    9  C7  UNL     1      -1.948  -1.356  -0.106  1.00  0.00           C  
HETATM   10  N1  UNL     1      -0.687  -1.127  -0.561  1.00  0.00           N  
HETATM   11  H1  UNL     1       4.079   0.877  -0.252  1.00  0.00           H  
HETATM   12  H2  UNL     1       1.470   1.366  -0.683  1.00  0.00           H  
HETATM   13  H3  UNL     1       1.457  -0.128  -1.678  1.00  0.00           H  
HETATM   14  H4  UNL     1      -0.155   1.793   0.980  1.00  0.00           H  
HETATM   15  H5  UNL     1      -2.406   1.386   1.794  1.00  0.00           H  
HETATM   16  H6  UNL     1      -3.597  -0.682   1.088  1.00  0.00           H  
HETATM   17  H7  UNL     1      -2.466  -2.254  -0.413  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3   11
CONECT    4    5   12   13
CONECT    5    6    6   10
CONECT    6    7   14
CONECT    7    8    8   15
CONECT    8    9   16
CONECT    9   10   10   17
END
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SMILES for HMDB0060722 (2-Pyridylacetic acid)

OC(=O)CC1=CC=CC=N1
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INCHI for HMDB0060722 (2-Pyridylacetic acid)

InChI=1S/C7H7NO2/c9-7(10)5-6-3-1-2-4-8-6/h1-4H,5H2,(H,9,10)
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
2-PyridylacetateGenerator
2-Pyridylacetic acidMeSH
Chemical FormulaC7H7NO2
Average Molecular Weight137.136
Monoisotopic Molecular Weight137.047678473
IUPAC Name2-(pyridin-2-yl)acetic acid
Traditional Namepyridin-2-ylacetic acid
CAS Registry NumberNot 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 KeyBPSNETAIJADFTO-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.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassPyridines and derivatives
Sub ClassNot Available
Direct ParentPyridines 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 FrameworkAromatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
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
Water Solubility63.5 g/LALOGPS
logP0.57ALOGPS
logP-0.24ChemAxon
logS-0.33ALOGPS
pKa (Strongest Acidic)3.35ChemAxon
pKa (Strongest Basic)4.67ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area50.19 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity34.84 m³·mol⁻¹ChemAxon
Polarizability13.28 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
DarkChem[M+H]+128.41331661259
DarkChem[M-H]-123.97131661259
DeepCCS[M+H]+121.73330932474
DeepCCS[M-H]-117.94930932474
DeepCCS[M-2H]-155.23430932474
DeepCCS[M+Na]+130.40930932474
AllCCS[M+H]+128.132859911
AllCCS[M+H-H2O]+123.432859911
AllCCS[M+NH4]+132.532859911
AllCCS[M+Na]+133.832859911
AllCCS[M-H]-125.732859911
AllCCS[M+Na-2H]-127.332859911
AllCCS[M+HCOO]-129.032859911

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022. Predicted by Afia on May 17, 2022.2.8 minutes32390414
Predicted by Siyang on May 30, 20228.6954 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20223.36 minutes32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid580.9 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid317.9 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid54.8 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid195.3 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid133.8 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid286.3 seconds40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid228.2 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)595.1 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid563.8 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid37.3 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid631.1 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid199.3 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid333.7 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate608.3 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA281.4 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water338.5 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
2-Pyridylacetic acidOC(=O)CC1=CC=CC=N12334.2Standard polar33892256
2-Pyridylacetic acidOC(=O)CC1=CC=CC=N11260.4Standard non polar33892256
2-Pyridylacetic acidOC(=O)CC1=CC=CC=N11292.7Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
2-Pyridylacetic acid,1TMS,isomer #1C[Si](C)(C)OC(=O)CC1=CC=CC=N11318.0Semi standard non polar33892256
2-Pyridylacetic acid,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC(=O)CC1=CC=CC=N11546.3Semi standard non polar33892256
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm
Biospecimen Locations
  • Blood
  • Urine
Tissue Locations
  • Kidney
  • Liver
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot QuantifiedNot AvailableNot AvailableNormal
      Not Available
 details
UrineExpected but not QuantifiedNot QuantifiedNot AvailableNot AvailableNormal
      Not Available
 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 IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound85318
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 ReferencesNot Available