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Showing metabocard for Pyrithione (HMDB0256986)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 17:37:37 UTC
Update Date2022-11-23 22:29:18 UTC
HMDB IDHMDB0256986
Secondary Accession NumbersNone
Metabolite Identification
Common NamePyrithione
Descriptionpyrithione belongs to the class of organic compounds known as dihydropyridines. Dihydropyridines are compounds containing a dihydropyridine moiety, which is a semi-saturated pyridine derivative with two double bonds. Based on a literature review very few articles have been published on pyrithione. This compound has been identified in human blood as reported by (PMID: 31557052 ). Pyrithione is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Pyrithione 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 HMDB0256986 (Pyrithione)


  Mrv1652306031606562D          

  8  8  0  0  0  0            999 V2000
    0.7145   -0.4125    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
   -0.0000    0.0000    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
    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 N   0  0  0  0  0  0  0  0  0  0  0  0
    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 S   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  1  2  0  0  0  0
  4  2  2  0  0  0  0
  5  3  1  0  0  0  0
  6  4  1  0  0  0  0
  6  5  1  0  0  0  0
  7  6  1  0  0  0  0
  8  5  2  0  0  0  0
M  END
Download

3D MOL for HMDB0256986 (Pyrithione)

HMDB0256986
     RDKit          3D
pyrithione
 13 13  0  0  0  0  0  0  0  0999 V2000
    2.4024   -0.4545   -0.3240 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0432   -0.2244   -0.1815 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.1755   -1.2412   -0.1397 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1817   -1.0177    0.0022 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7006    0.2541    0.1066 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7935    1.3000    0.0622 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5727    1.0299   -0.0826 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6714    2.2392   -0.1389 S   0  0  0  0  0  0  0  0  0  0  0  0
    2.9768   -0.5540    0.5280 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5622   -2.2695   -0.2209 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8503   -1.8627    0.0318 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7661    0.4551    0.2192 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1121    2.3458    0.1376 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  2  0
  7  2  1  0
  1  9  1  0
  3 10  1  0
  4 11  1  0
  5 12  1  0
  6 13  1  0
M  END
Download

3D SDF for HMDB0256986 (Pyrithione)


  Mrv1652306031606562D          

  8  8  0  0  0  0            999 V2000
    0.7145   -0.4125    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
   -0.0000    0.0000    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
    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 N   0  0  0  0  0  0  0  0  0  0  0  0
    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 S   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  1  2  0  0  0  0
  4  2  2  0  0  0  0
  5  3  1  0  0  0  0
  6  4  1  0  0  0  0
  6  5  1  0  0  0  0
  7  6  1  0  0  0  0
  8  5  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0256986

> <DATABASE_NAME>
hmdb

> <SMILES>
ON1C=CC=CC1=S

> <INCHI_IDENTIFIER>
InChI=1S/C5H5NOS/c7-6-4-2-1-3-5(6)8/h1-4,7H

> <INCHI_KEY>
YBBJKCMMCRQZMA-UHFFFAOYSA-N

> <FORMULA>
C5H5NOS

> <MOLECULAR_WEIGHT>
127.16

> <EXACT_MASS>
127.009184959

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
13

> <JCHEM_AVERAGE_POLARIZABILITY>
12.225373470132656

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1-hydroxy-1,2-dihydropyridine-2-thione

> <ALOGPS_LOGP>
0.28

> <JCHEM_LOGP>
0.9035497583333333

> <ALOGPS_LOGS>
-1.47

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.240917561570157

> <JCHEM_PKA_STRONGEST_BASIC>
-5.755222658569214

> <JCHEM_POLAR_SURFACE_AREA>
23.47

> <JCHEM_REFRACTIVITY>
37.800799999999995

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.32e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
pyrithione

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0256986 (Pyrithione)

HMDB0256986
     RDKit          3D
pyrithione
 13 13  0  0  0  0  0  0  0  0999 V2000
    2.4024   -0.4545   -0.3240 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0432   -0.2244   -0.1815 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.1755   -1.2412   -0.1397 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1817   -1.0177    0.0022 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7006    0.2541    0.1066 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7935    1.3000    0.0622 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5727    1.0299   -0.0826 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6714    2.2392   -0.1389 S   0  0  0  0  0  0  0  0  0  0  0  0
    2.9768   -0.5540    0.5280 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5622   -2.2695   -0.2209 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8503   -1.8627    0.0318 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7661    0.4551    0.2192 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1121    2.3458    0.1376 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  2  0
  7  2  1  0
  1  9  1  0
  3 10  1  0
  4 11  1  0
  5 12  1  0
  6 13  1  0
M  END
Download

PDB for HMDB0256986 (Pyrithione)

HEADER    PROTEIN                                 03-JUN-16   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   03-JUN-16         0                                  
HETATM    1  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.000   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0       1.334   2.310   0.000  0.00  0.00           N+0
HETATM    7  O   UNK     0       1.334   3.850   0.000  0.00  0.00           O+0
HETATM    8  S   UNK     0      -1.334   2.310   0.000  0.00  0.00           S+0
CONECT    1    2    3                                                       
CONECT    2    1    4                                                       
CONECT    3    1    5                                                       
CONECT    4    2    6                                                       
CONECT    5    3    6    8                                                  
CONECT    6    4    5    7                                                  
CONECT    7    6                                                            
CONECT    8    5                                                            
MASTER        0    0    0    0    0    0    0    0    8    0   16    0
END
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3D PDB for HMDB0256986 (Pyrithione)

COMPND    HMDB0256986
HETATM    1  O1  UNL     1       2.402  -0.455  -0.324  1.00  0.00           O  
HETATM    2  N1  UNL     1       1.043  -0.224  -0.182  1.00  0.00           N  
HETATM    3  C1  UNL     1       0.176  -1.241  -0.140  1.00  0.00           C  
HETATM    4  C2  UNL     1      -1.182  -1.018   0.002  1.00  0.00           C  
HETATM    5  C3  UNL     1      -1.701   0.254   0.107  1.00  0.00           C  
HETATM    6  C4  UNL     1      -0.794   1.300   0.062  1.00  0.00           C  
HETATM    7  C5  UNL     1       0.573   1.030  -0.083  1.00  0.00           C  
HETATM    8  S1  UNL     1       1.671   2.239  -0.139  1.00  0.00           S  
HETATM    9  H1  UNL     1       2.977  -0.554   0.528  1.00  0.00           H  
HETATM   10  H2  UNL     1       0.562  -2.269  -0.221  1.00  0.00           H  
HETATM   11  H3  UNL     1      -1.850  -1.863   0.032  1.00  0.00           H  
HETATM   12  H4  UNL     1      -2.766   0.455   0.219  1.00  0.00           H  
HETATM   13  H5  UNL     1      -1.112   2.346   0.138  1.00  0.00           H  
CONECT    1    2    9
CONECT    2    3    7
CONECT    3    4    4   10
CONECT    4    5   11
CONECT    5    6    6   12
CONECT    6    7   13
CONECT    7    8    8
END
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SMILES for HMDB0256986 (Pyrithione)

ON1C=CC=CC1=S
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INCHI for HMDB0256986 (Pyrithione)

InChI=1S/C5H5NOS/c7-6-4-2-1-3-5(6)8/h1-4,7H
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
1-Hydroxy-2-pyridinethioneChEBI
1-Hydroxyl-1H-pyridine-2-thioneChEBI
1-Hydroxypyridine-2-thioneChEBI
2-HPT CPDMeSH
2-Mercaptopyridine-N-oxideMeSH
2-Pyridinethiol 1-oxideMeSH
67Ga-mpoMeSH
68Ga-mercaptopyridine-N-oxideMeSH
N-Hydroxypyridine-2-thioneMeSH
OmadineMeSH
Indium 111-2-mercaptopyridine-1-oxideMeSH
Pyridine-2-thiol N-oxideMeSH
Pyrithione barium (2:1) saltMeSH
Pyrithione calcium (2:1) saltMeSH
Pyrithione magnesium saltMeSH
Pyrithione potassium saltMeSH
Pyrithione sodium saltMeSH
Sodium pyridinethioneMeSH
Chemical FormulaC5H5NOS
Average Molecular Weight127.16
Monoisotopic Molecular Weight127.009184959
IUPAC Name1-hydroxy-1,2-dihydropyridine-2-thione
Traditional Namepyrithione
CAS Registry NumberNot Available
SMILES
ON1C=CC=CC1=S
InChI Identifier
InChI=1S/C5H5NOS/c7-6-4-2-1-3-5(6)8/h1-4,7H
InChI KeyYBBJKCMMCRQZMA-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as dihydropyridines. Dihydropyridines are compounds containing a dihydropyridine moiety, which is a semi-saturated pyridine derivative with two double bonds.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassPyridines and derivatives
Sub ClassHydropyridines
Direct ParentDihydropyridines
Alternative Parents
Substituents
  • Dihydropyridine
  • Heteroaromatic compound
  • Thiolactam
  • Azacycle
  • Organic nitrogen compound
  • Organic oxygen compound
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Organosulfur 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
logP0.28ALOGPS
logP0.9ChemAxon
logS-1.5ALOGPS
pKa (Strongest Acidic)8.24ChemAxon
pKa (Strongest Basic)-5.8ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area23.47 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity37.8 m³·mol⁻¹ChemAxon
Polarizability12.23 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
DeepCCS[M+H]+125.44530932474
DeepCCS[M-H]-123.45730932474
DeepCCS[M-2H]-158.94330932474
DeepCCS[M+Na]+133.1630932474
AllCCS[M+H]+124.032859911
AllCCS[M+H-H2O]+119.032859911
AllCCS[M+NH4]+128.632859911
AllCCS[M+Na]+129.932859911
AllCCS[M-H]-118.932859911
AllCCS[M+Na-2H]-121.432859911
AllCCS[M+HCOO]-124.132859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
pyrithioneON1C=CC=CC1=S2127.0Standard polar33892256
pyrithioneON1C=CC=CC1=S1230.1Standard non polar33892256
pyrithioneON1C=CC=CC1=S1412.4Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Pyrithione GC-MS (Non-derivatized) - 70eV, Positivesplash10-004i-9200000000-0ff5787d54b5ad3be61d2021-09-24Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Pyrithione GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pyrithione 10V, Positive-QTOFsplash10-004i-1900000000-536a0bfe9e80cd8713692019-02-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pyrithione 20V, Positive-QTOFsplash10-005d-9300000000-6f324b0a4554bec67cd32019-02-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pyrithione 40V, Positive-QTOFsplash10-0udi-9000000000-bf04db702e047e5c8f452019-02-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pyrithione 10V, Negative-QTOFsplash10-004i-0900000000-3415c7e9196fb3c470522019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pyrithione 20V, Negative-QTOFsplash10-004i-3900000000-6fb23e3facdcc96387122019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pyrithione 40V, Negative-QTOFsplash10-007k-9100000000-a53a4bedbe0f84fb30eb2019-02-23Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 100 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, 1000 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 NMR1H 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 NMR13C NMR Spectrum (1D, 400 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, 500 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 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 ID1514
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkPyrithione
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI ID36578
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 ]