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Showing metabocard for pyridine-3,4-diol (HMDB0256965)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 17:36:14 UTC
Update Date2021-09-26 23:13:00 UTC
HMDB IDHMDB0256965
Secondary Accession NumbersNone
Metabolite Identification
Common Namepyridine-3,4-diol
Description3-hydroxypyridin-4(1H)-one, also known as 3-hydroxy-4(1H)-pyridinone, belongs to the class of organic compounds known as hydroxypyridines. These are organic compounds containing a pyridine ring substituted at one or more positions by a hydroxyl group. Based on a literature review very few articles have been published on 3-hydroxypyridin-4(1H)-one. This compound has been identified in human blood as reported by (PMID: 31557052 ). Pyridine-3,4-diol is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically pyridine-3,4-diol 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
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0256965 (pyridine-3,4-diol)


  Mrv1533004171500392D          

  8  8  0  0  0  0            999 V2000
    0.7145    2.0625    0.0000 O   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    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 N   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    0.0000    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
   -0.7145    1.2375    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  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  2  7  1  0  0  0  0
  7  8  2  0  0  0  0
M  END
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3D MOL for HMDB0256965 (pyridine-3,4-diol)

HMDB0256965
     RDKit          3D
pyridine-3,4-diol
 13 13  0  0  0  0  0  0  0  0999 V2000
    0.6913    2.4275   -0.1066 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2223    1.2660   -0.0595 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1501    1.1185   -0.0905 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6391   -0.1738   -0.0372 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7968   -1.2390    0.0419 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5379   -1.0573    0.0701 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0968    0.2019    0.0204 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4774    0.3889    0.0496 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8305    1.9597   -0.1534 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7103   -0.3221   -0.0596 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1780   -2.2129    0.0817 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2159   -1.9233    0.1342 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0634   -0.4340    0.1089 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  7  2  1  0
  3  9  1  0
  4 10  1  0
  5 11  1  0
  6 12  1  0
  8 13  1  0
M  END
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3D SDF for HMDB0256965 (pyridine-3,4-diol)


  Mrv1533004171500392D          

  8  8  0  0  0  0            999 V2000
    0.7145    2.0625    0.0000 O   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    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 N   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    0.0000    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
   -0.7145    1.2375    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  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  2  7  1  0  0  0  0
  7  8  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0256965

> <DATABASE_NAME>
hmdb

> <SMILES>
OC1=CNC=CC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C5H5NO2/c7-4-1-2-6-3-5(4)8/h1-3,8H,(H,6,7)

> <INCHI_KEY>
ZCUUVWCJGRQCMZ-UHFFFAOYSA-N

> <FORMULA>
C5H5NO2

> <MOLECULAR_WEIGHT>
111.1

> <EXACT_MASS>
111.032028405

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
13

> <JCHEM_AVERAGE_POLARIZABILITY>
10.034514130459296

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-hydroxy-1,4-dihydropyridin-4-one

> <ALOGPS_LOGP>
-1.26

> <JCHEM_LOGP>
0.026927302666666764

> <ALOGPS_LOGS>
-0.17

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
18.68296523809031

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.837723384380743

> <JCHEM_PKA_STRONGEST_BASIC>
-2.542510661501667

> <JCHEM_POLAR_SURFACE_AREA>
49.33

> <JCHEM_REFRACTIVITY>
29.5838

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.59e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-hydroxy-4-pyridone

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0256965 (pyridine-3,4-diol)

HMDB0256965
     RDKit          3D
pyridine-3,4-diol
 13 13  0  0  0  0  0  0  0  0999 V2000
    0.6913    2.4275   -0.1066 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2223    1.2660   -0.0595 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1501    1.1185   -0.0905 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6391   -0.1738   -0.0372 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7968   -1.2390    0.0419 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5379   -1.0573    0.0701 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0968    0.2019    0.0204 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4774    0.3889    0.0496 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8305    1.9597   -0.1534 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7103   -0.3221   -0.0596 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1780   -2.2129    0.0817 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2159   -1.9233    0.1342 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0634   -0.4340    0.1089 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  7  2  1  0
  3  9  1  0
  4 10  1  0
  5 11  1  0
  6 12  1  0
  8 13  1  0
M  END
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PDB for HMDB0256965 (pyridine-3,4-diol)

HEADER    PROTEIN                                 17-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-APR-15         0                                  
HETATM    1  O   UNK     0       1.334   3.850   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0       2.667  -0.000   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      -1.334   2.310   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    7                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    2    8                                                  
CONECT    8    7                                                            
MASTER        0    0    0    0    0    0    0    0    8    0   16    0
END
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3D PDB for HMDB0256965 (pyridine-3,4-diol)

COMPND    HMDB0256965
HETATM    1  O1  UNL     1       0.691   2.427  -0.107  1.00  0.00           O  
HETATM    2  C1  UNL     1       0.222   1.266  -0.059  1.00  0.00           C  
HETATM    3  C2  UNL     1      -1.150   1.118  -0.090  1.00  0.00           C  
HETATM    4  C3  UNL     1      -1.639  -0.174  -0.037  1.00  0.00           C  
HETATM    5  N1  UNL     1      -0.797  -1.239   0.042  1.00  0.00           N  
HETATM    6  C4  UNL     1       0.538  -1.057   0.070  1.00  0.00           C  
HETATM    7  C5  UNL     1       1.097   0.202   0.020  1.00  0.00           C  
HETATM    8  O2  UNL     1       2.477   0.389   0.050  1.00  0.00           O  
HETATM    9  H1  UNL     1      -1.831   1.960  -0.153  1.00  0.00           H  
HETATM   10  H2  UNL     1      -2.710  -0.322  -0.060  1.00  0.00           H  
HETATM   11  H3  UNL     1      -1.178  -2.213   0.082  1.00  0.00           H  
HETATM   12  H4  UNL     1       1.216  -1.923   0.134  1.00  0.00           H  
HETATM   13  H5  UNL     1       3.063  -0.434   0.109  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    7
CONECT    3    4    4    9
CONECT    4    5   10
CONECT    5    6   11
CONECT    6    7    7   12
CONECT    7    8
CONECT    8   13
END
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SMILES for HMDB0256965 (pyridine-3,4-diol)

OC1=CNC=CC1=O
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INCHI for HMDB0256965 (pyridine-3,4-diol)

InChI=1S/C5H5NO2/c7-4-1-2-6-3-5(4)8/h1-3,8H,(H,6,7)
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
3-Hydroxy-4(1H)-pyridinoneChEBI
3-Hydroxy-4-pyridoneChEBI
3-Hydroxy-4H-pyrid-4-oneChEBI
3-Hydroxypyridine-4-oneChEBI
3,4-DihydroxypyridineMeSH
Chemical FormulaC5H5NO2
Average Molecular Weight111.1
Monoisotopic Molecular Weight111.032028405
IUPAC Name3-hydroxy-1,4-dihydropyridin-4-one
Traditional Name3-hydroxy-4-pyridone
CAS Registry NumberNot Available
SMILES
OC1=CNC=CC1=O
InChI Identifier
InChI=1S/C5H5NO2/c7-4-1-2-6-3-5(4)8/h1-3,8H,(H,6,7)
InChI KeyZCUUVWCJGRQCMZ-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as hydroxypyridines. These are organic compounds containing a pyridine ring substituted at one or more positions by a hydroxyl group.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassPyridines and derivatives
Sub ClassHydroxypyridines
Direct ParentHydroxypyridines
Alternative Parents
Substituents
  • Hydroxypyridine
  • Dihydropyridine
  • Hydropyridine
  • Heteroaromatic compound
  • Vinylogous amide
  • Cyclic ketone
  • 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 location
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-1.3ALOGPS
logP0.027ChemAxon
logS-0.17ALOGPS
pKa (Strongest Acidic)11.84ChemAxon
pKa (Strongest Basic)-2.5ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area49.33 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity29.58 m³·mol⁻¹ChemAxon
Polarizability10.03 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]+124.7630932474
DeepCCS[M-H]-122.16630932474
DeepCCS[M-2H]-158.41630932474
DeepCCS[M+Na]+132.93530932474
AllCCS[M+H]+122.332859911
AllCCS[M+H-H2O]+117.332859911
AllCCS[M+NH4]+127.132859911
AllCCS[M+Na]+128.432859911
AllCCS[M-H]-117.632859911
AllCCS[M+Na-2H]-120.132859911
AllCCS[M+HCOO]-122.832859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
pyridine-3,4-diolOC1=CNC=CC1=O1665.9Standard polar33892256
pyridine-3,4-diolOC1=CNC=CC1=O1114.7Standard non polar33892256
pyridine-3,4-diolOC1=CNC=CC1=O1186.8Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
pyridine-3,4-diol,2TMS,isomer #1C[Si](C)(C)OC1=CN([Si](C)(C)C)C=CC1=O1500.3Semi standard non polar33892256
pyridine-3,4-diol,2TMS,isomer #1C[Si](C)(C)OC1=CN([Si](C)(C)C)C=CC1=O1574.3Standard non polar33892256
pyridine-3,4-diol,2TMS,isomer #1C[Si](C)(C)OC1=CN([Si](C)(C)C)C=CC1=O1612.0Standard polar33892256
pyridine-3,4-diol,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC1=CN([Si](C)(C)C(C)(C)C)C=CC1=O1965.9Semi standard non polar33892256
pyridine-3,4-diol,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC1=CN([Si](C)(C)C(C)(C)C)C=CC1=O2003.1Standard non polar33892256
pyridine-3,4-diol,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC1=CN([Si](C)(C)C(C)(C)C)C=CC1=O1887.0Standard polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - pyridine-3,4-diol GC-MS (Non-derivatized) - 70eV, Positivesplash10-03e9-9300000000-d6420d4c3da8531ed92a2021-09-24Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - pyridine-3,4-diol GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - pyridine-3,4-diol GC-MS (TMS_1_1) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - pyridine-3,4-diol GC-MS (TMS_1_2) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - pyridine-3,4-diol GC-MS (TBDMS_1_1) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - pyridine-3,4-diol GC-MS (TBDMS_1_2) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-10-27Wishart 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 ID94812
KEGG Compound IDC03927
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI ID28630
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 ]