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Showing metabocard for 2-Hydroxypyridine (HMDB0013751)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2012-05-18 14:35:50 UTC
Update Date2023-02-21 17:18:02 UTC
HMDB IDHMDB0013751
Secondary Accession Numbers
  • HMDB13751
Metabolite Identification
Common Name2-Hydroxypyridine
DescriptionThis colourless crystalline solid is used in peptide synthesis. It is well known to form hydrogen bonded structures somewhat related to the base-pairing mechanism found in RNA and DNA. It is also a classic case of a molecule that exists as tautomers. Some publications only focus one of the two possible patterns, and neglect the influence of the other. For example, to calculation of the energy difference of the two tautomers in a non-polar solution will lead to a wrong result if a large quantity of the substance is on the side of the dimer in an equilibrium. The direct tautomerisation is not energetically favoured, but a dimerisation followed by a double proton transfer and dissociation of the dimer is a self catalytic path from one tautomer to the other. Protic solvents also mediate the proton transfer during the tautomerisation.
Structure
Data?1676999882
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0013751 (2-Hydroxypyridine)

 
  Mrv1652304202019402D          
 
  7  7  0  0  0  0            999 V2000
   11.1938   -9.1195    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.1938   -8.2945    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.4743   -9.5413    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   11.9018   -9.5299    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.4743   -7.8838    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.7661   -9.1195    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.7661   -8.2945    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  0  0  0  0
  2  5  1  0  0  0  0
  3  6  2  0  0  0  0
  5  7  2  0  0  0  0
  6  7  1  0  0  0  0
M  END
Download

3D MOL for HMDB0013751 (2-Hydroxypyridine)

HMDB0013751
     RDKit          3D
2-Hydroxypyridine
 12 12  0  0  0  0  0  0  0  0999 V2000
    2.5645    0.1441   -0.3099 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1773    0.1626   -0.1902 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4939   -1.0285   -0.0076 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8829   -1.0550    0.1159 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5714    0.1380    0.0533 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8871    1.3141   -0.1279 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4624    1.3057   -0.2453 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.0735    0.6108    0.4405 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0568   -1.9585    0.0389 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4133   -2.0083    0.2606 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6508    0.1193    0.1498 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4228    2.2556   -0.1780 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  2  0
  7  2  1  0
  1  8  1  0
  3  9  1  0
  4 10  1  0
  5 11  1  0
  6 12  1  0
M  END
Download

3D SDF for HMDB0013751 (2-Hydroxypyridine)

 
  Mrv1652304202019402D          
 
  7  7  0  0  0  0            999 V2000
   11.1938   -9.1195    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.1938   -8.2945    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.4743   -9.5413    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   11.9018   -9.5299    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.4743   -7.8838    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.7661   -9.1195    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.7661   -8.2945    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  0  0  0  0
  2  5  1  0  0  0  0
  3  6  2  0  0  0  0
  5  7  2  0  0  0  0
  6  7  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0013751

> <DATABASE_NAME>
hmdb

> <SMILES>
OC1=CC=CC=N1

> <INCHI_IDENTIFIER>
InChI=1S/C5H5NO/c7-5-3-1-2-4-6-5/h1-4H,(H,6,7)

> <INCHI_KEY>
UBQKCCHYAOITMY-UHFFFAOYSA-N

> <FORMULA>
C5H5NO

> <MOLECULAR_WEIGHT>
95.0993

> <EXACT_MASS>
95.037113787

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
12

> <JCHEM_AVERAGE_POLARIZABILITY>
9.200287283659224

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
pyridin-2-ol

> <ALOGPS_LOGP>
0.64

> <JCHEM_LOGP>
1.0464655973333332

> <ALOGPS_LOGS>
0.53

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.700690095151401

> <JCHEM_PKA_STRONGEST_BASIC>
2.429271976905061

> <JCHEM_POLAR_SURFACE_AREA>
33.120000000000005

> <JCHEM_REFRACTIVITY>
26.195499999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.20e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-pyridone

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0013751 (2-Hydroxypyridine)

HMDB0013751
     RDKit          3D
2-Hydroxypyridine
 12 12  0  0  0  0  0  0  0  0999 V2000
    2.5645    0.1441   -0.3099 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1773    0.1626   -0.1902 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4939   -1.0285   -0.0076 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8829   -1.0550    0.1159 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5714    0.1380    0.0533 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8871    1.3141   -0.1279 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4624    1.3057   -0.2453 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.0735    0.6108    0.4405 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0568   -1.9585    0.0389 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4133   -2.0083    0.2606 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6508    0.1193    0.1498 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4228    2.2556   -0.1780 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  2  0
  7  2  1  0
  1  8  1  0
  3  9  1  0
  4 10  1  0
  5 11  1  0
  6 12  1  0
M  END
Download

PDB for HMDB0013751 (2-Hydroxypyridine)

HEADER    PROTEIN                                 20-APR-20   NONE
TITLE     NULL                                                        
COMPND    MOLECULE:                                                   
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   20-APR-20         0                                  
HETATM    1  C   UNK     0      20.895 -17.023   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      20.895 -15.483   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0      19.552 -17.810   0.000  0.00  0.00           N+0
HETATM    4  O   UNK     0      22.217 -17.789   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0      19.552 -14.716   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      18.230 -17.023   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      18.230 -15.483   0.000  0.00  0.00           C+0
CONECT    1    2    3    4                                                  
CONECT    2    1    5                                                       
CONECT    3    1    6                                                       
CONECT    4    1                                                            
CONECT    5    2    7                                                       
CONECT    6    3    7                                                       
CONECT    7    5    6                                                       
MASTER        0    0    0    0    0    0    0    0    7    0   14    0
END
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3D PDB for HMDB0013751 (2-Hydroxypyridine)

COMPND    HMDB0013751
HETATM    1  O1  UNL     1       2.565   0.144  -0.310  1.00  0.00           O  
HETATM    2  C1  UNL     1       1.177   0.163  -0.190  1.00  0.00           C  
HETATM    3  C2  UNL     1       0.494  -1.028  -0.008  1.00  0.00           C  
HETATM    4  C3  UNL     1      -0.883  -1.055   0.116  1.00  0.00           C  
HETATM    5  C4  UNL     1      -1.571   0.138   0.053  1.00  0.00           C  
HETATM    6  C5  UNL     1      -0.887   1.314  -0.128  1.00  0.00           C  
HETATM    7  N1  UNL     1       0.462   1.306  -0.245  1.00  0.00           N  
HETATM    8  H1  UNL     1       3.073   0.611   0.440  1.00  0.00           H  
HETATM    9  H2  UNL     1       1.057  -1.958   0.039  1.00  0.00           H  
HETATM   10  H3  UNL     1      -1.413  -2.008   0.261  1.00  0.00           H  
HETATM   11  H4  UNL     1      -2.651   0.119   0.150  1.00  0.00           H  
HETATM   12  H5  UNL     1      -1.423   2.256  -0.178  1.00  0.00           H  
CONECT    1    2    8
CONECT    2    3    3    7
CONECT    3    4    9
CONECT    4    5    5   10
CONECT    5    6   11
CONECT    6    7    7   12
END
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SMILES for HMDB0013751 (2-Hydroxypyridine)

OC1=CC=CC=N1
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INCHI for HMDB0013751 (2-Hydroxypyridine)

InChI=1S/C5H5NO/c7-5-3-1-2-4-6-5/h1-4H,(H,6,7)
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View in JSmolView Stereo Labels
Synonyms
ValueSource
2-PyridinolChEBI
2-PyridoneChEBI
1-Hydroxy-2-pyridineHMDB
1H-Pyridin-2-oneHMDB
2(1H)-PyridinoneHMDB
2(1H)-PyridoneHMDB
2-OxopyridineHMDB
2-Pyridinol (acd/name 4.0)HMDB
2-PyridinoneHMDB
2-PyridolHMDB
alpha -PyridoneHMDB
alpha-PyridoneHMDB
Pyridin-2-olHMDB
Pyridone-2HMDB
2-Hydroxypyridine sodium saltHMDB
2-HydroxypyridineChEBI
Chemical FormulaC5H5NO
Average Molecular Weight95.0993
Monoisotopic Molecular Weight95.037113787
IUPAC Namepyridin-2-ol
Traditional Name2-pyridone
CAS Registry Number142-08-5
SMILES
OC1=CC=CC=N1
InChI Identifier
InChI=1S/C5H5NO/c7-5-3-1-2-4-6-5/h1-4H,(H,6,7)
InChI KeyUBQKCCHYAOITMY-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as pyridinones. Pyridinones are compounds containing a pyridine ring, which bears a ketone.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassPyridines and derivatives
Sub ClassHydropyridines
Direct ParentPyridinones
Alternative Parents
Substituents
  • Pyridinone
  • Dihydropyridine
  • Heteroaromatic compound
  • Lactam
  • Azacycle
  • Organic nitrogen compound
  • Organic oxygen compound
  • Organopnictogen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organonitrogen compound
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
ProcessNot Available
RoleNot Available
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point107.8 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility1000 mg/mL at 20 °CNot Available
LogPNot AvailableNot Available
Experimental Chromatographic Properties

Experimental Collision Cross Sections

Adduct TypeData SourceCCS Value (Å2)Reference
[M+H]+Not Available115.8http://allccs.zhulab.cn/database/detail?ID=AllCCS00002167
Predicted Molecular Properties
PropertyValueSource
Water Solubility320 g/LALOGPS
logP0.64ALOGPS
logP1.05ChemAxon
logS0.53ALOGPS
pKa (Strongest Acidic)11.7ChemAxon
pKa (Strongest Basic)2.43ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area33.12 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity26.2 m³·mol⁻¹ChemAxon
Polarizability9.2 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+115.65931661259
DarkChem[M-H]-111.30831661259
DeepCCS[M+H]+120.98530932474
DeepCCS[M-H]-118.18630932474
DeepCCS[M-2H]-154.46530932474
DeepCCS[M+Na]+129.21630932474
AllCCS[M+H]+118.432859911
AllCCS[M+H-H2O]+113.232859911
AllCCS[M+NH4]+123.332859911
AllCCS[M+Na]+124.732859911
AllCCS[M-H]-116.132859911
AllCCS[M+Na-2H]-119.132859911
AllCCS[M+HCOO]-122.432859911

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, 2022.1.94 minutes32390414
Predicted by Siyang on May 30, 20229.2936 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20223.55 minutes32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid113.8 seconds40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid874.0 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid355.5 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid95.9 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid232.3 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid67.0 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid269.6 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 Acid276.7 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)184.5 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid666.5 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid39.1 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid802.0 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid214.7 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid290.0 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate518.3 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA264.7 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water141.2 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
2-HydroxypyridineOC1=CC=CC=N12206.5Standard polar33892256
2-HydroxypyridineOC1=CC=CC=N11023.5Standard non polar33892256
2-HydroxypyridineOC1=CC=CC=N11014.4Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
2-Hydroxypyridine,1TMS,isomer #1C[Si](C)(C)OC1=CC=CC=N11037.5Semi standard non polar33892256
2-Hydroxypyridine,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC1=CC=CC=N11288.6Semi standard non polar33892256
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
UrineDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothBladder cancer details
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB112195
KNApSAcK IDC00007405
Chemspider ID8537
KEGG Compound IDC02502
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia Link2-Pyridone
METLIN IDNot Available
PubChem Compound8871
PDB IDNot Available
ChEBI ID16540
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Download (PDF)
General References
  1. Nhan DD, Carvalho FP, Nam BQ: Fate of 14C-chlorpyrifos in the tropical estuarine environment. Environ Technol. 2002 Nov;23(11):1229-34. [PubMed:12472153 ]
  2. Menon R, Tolbert D, Cefali E: The comparative bioavailability of an extended-release niacin and lovastatin fixed dose combination tablet versus extended-release niacin tablet, lovastatin tablet and a combination of extended-release niacin tablet and lovastatin tablet. Biopharm Drug Dispos. 2007 Sep;28(6):297-306. [PubMed:17571283 ]