Hmdb loader

Showing metabocard for 2,3-Dihydroxypyridine (HMDB0245397)

Jump To Section:
IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesXML
Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-10 22:28:16 UTC
Update Date2022-09-22 17:44:19 UTC
HMDB IDHMDB0245397
Secondary Accession NumbersNone
Metabolite Identification
Common Name2,3-Dihydroxypyridine
Description2,3-Dihydroxypyridine, also known as 2,3-pyridinediol, belongs to the class of organic compounds known as pyridinones. Pyridinones are compounds containing a pyridine ring, which bears a ketone. Based on a literature review a significant number of articles have been published on 2,3-Dihydroxypyridine. This compound has been identified in human blood as reported by (PMID: 31557052 ). 2,3-dihydroxypyridine is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 2,3-Dihydroxypyridine 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
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0245397 (2,3-Dihydroxypyridine)


  Mrv1652305062021422D          

  8  8  0  0  0  0            999 V2000
    1.4289    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
    0.7145   -0.4125    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
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    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 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
  5  4  2  0  0  0  0
  6  3  2  0  0  0  0
  6  5  1  0  0  0  0
  7  4  1  0  0  0  0
  8  5  1  0  0  0  0
M  END
Download

3D MOL for HMDB0245397 (2,3-Dihydroxypyridine)

HMDB0245397
     RDKit          3D
2,3-Dihydroxypyridine
 13 13  0  0  0  0  0  0  0  0999 V2000
   -1.9705    1.1043    0.1461 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7038    0.5402    0.0625 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4225    1.2488    0.4270 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6611    0.6522    0.3289 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7282   -0.6511   -0.1374 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6071   -1.3311   -0.4911 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6127   -0.7609   -0.4007 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7606   -1.4633   -0.7651 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7976    0.6147   -0.1104 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3342    2.2657    0.7874 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5829    1.1443    0.5953 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6744   -1.1656   -0.2337 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1651   -2.1982   -0.2087 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  8  1  0
  7  2  1  0
  1  9  1  0
  3 10  1  0
  4 11  1  0
  5 12  1  0
  8 13  1  0
M  END
Download

3D SDF for HMDB0245397 (2,3-Dihydroxypyridine)


  Mrv1652305062021422D          

  8  8  0  0  0  0            999 V2000
    1.4289    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
    0.7145   -0.4125    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
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    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 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
  5  4  2  0  0  0  0
  6  3  2  0  0  0  0
  6  5  1  0  0  0  0
  7  4  1  0  0  0  0
  8  5  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0245397

> <DATABASE_NAME>
hmdb

> <SMILES>
OC1=C(O)N=CC=C1

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

> <INCHI_KEY>
GGOZGYRTNQBSSA-UHFFFAOYSA-N

> <FORMULA>
C5H5NO2

> <MOLECULAR_WEIGHT>
111.0987

> <EXACT_MASS>
111.032028409

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
13

> <JCHEM_AVERAGE_POLARIZABILITY>
10.066909096687775

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
pyridine-2,3-diol

> <ALOGPS_LOGP>
0.03

> <JCHEM_LOGP>
0.7429002756666667

> <ALOGPS_LOGS>
0.14

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.30219404722445

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.878123168771856

> <JCHEM_PKA_STRONGEST_BASIC>
2.7074570510946088

> <JCHEM_POLAR_SURFACE_AREA>
53.35000000000001

> <JCHEM_REFRACTIVITY>
28.176399999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.54e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2,3-dihydroxypyridine

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0245397 (2,3-Dihydroxypyridine)

HMDB0245397
     RDKit          3D
2,3-Dihydroxypyridine
 13 13  0  0  0  0  0  0  0  0999 V2000
   -1.9705    1.1043    0.1461 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7038    0.5402    0.0625 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4225    1.2488    0.4270 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6611    0.6522    0.3289 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7282   -0.6511   -0.1374 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6071   -1.3311   -0.4911 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6127   -0.7609   -0.4007 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7606   -1.4633   -0.7651 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7976    0.6147   -0.1104 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3342    2.2657    0.7874 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5829    1.1443    0.5953 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6744   -1.1656   -0.2337 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1651   -2.1982   -0.2087 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  8  1  0
  7  2  1  0
  1  9  1  0
  3 10  1  0
  4 11  1  0
  5 12  1  0
  8 13  1  0
M  END
Download

PDB for HMDB0245397 (2,3-Dihydroxypyridine)

HEADER    PROTEIN                                 06-MAY-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-MAY-20         0                                  
HETATM    1  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.334   2.310   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       0.000   0.000   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  O   UNK     0      -1.334   2.310   0.000  0.00  0.00           O+0
CONECT    1    2    3                                                       
CONECT    2    1    4                                                       
CONECT    3    1    6                                                       
CONECT    4    2    5    7                                                  
CONECT    5    4    6    8                                                  
CONECT    6    3    5                                                       
CONECT    7    4                                                            
CONECT    8    5                                                            
MASTER        0    0    0    0    0    0    0    0    8    0   16    0
END
Download

3D PDB for HMDB0245397 (2,3-Dihydroxypyridine)

COMPND    HMDB0245397
HETATM    1  O1  UNL     1      -1.970   1.104   0.146  1.00  0.00           O  
HETATM    2  C1  UNL     1      -0.704   0.540   0.062  1.00  0.00           C  
HETATM    3  C2  UNL     1       0.422   1.249   0.427  1.00  0.00           C  
HETATM    4  C3  UNL     1       1.661   0.652   0.329  1.00  0.00           C  
HETATM    5  C4  UNL     1       1.728  -0.651  -0.137  1.00  0.00           C  
HETATM    6  N1  UNL     1       0.607  -1.331  -0.491  1.00  0.00           N  
HETATM    7  C5  UNL     1      -0.613  -0.761  -0.401  1.00  0.00           C  
HETATM    8  O2  UNL     1      -1.761  -1.463  -0.765  1.00  0.00           O  
HETATM    9  H1  UNL     1      -2.798   0.615  -0.110  1.00  0.00           H  
HETATM   10  H2  UNL     1       0.334   2.266   0.787  1.00  0.00           H  
HETATM   11  H3  UNL     1       2.583   1.144   0.595  1.00  0.00           H  
HETATM   12  H4  UNL     1       2.674  -1.166  -0.234  1.00  0.00           H  
HETATM   13  H5  UNL     1      -2.165  -2.198  -0.209  1.00  0.00           H  
CONECT    1    2    9
CONECT    2    3    3    7
CONECT    3    4   10
CONECT    4    5    5   11
CONECT    5    6   12
CONECT    6    7    7
CONECT    7    8
CONECT    8   13
END
Download

SMILES for HMDB0245397 (2,3-Dihydroxypyridine)

OC1=C(O)N=CC=C1
Download

INCHI for HMDB0245397 (2,3-Dihydroxypyridine)

InChI=1S/C5H5NO2/c7-4-2-1-3-6-5(4)8/h1-3,7H,(H,6,8)
Download
View in JSmolView Stereo Labels
Synonyms
ValueSource
2,3-PyridinediolChEBI
3-Hydroxy-2-pyridoneChEBI
3-Hydroxy-2-pyridinoneHMDB
2,3-DihydroxypyridineChEBI
Chemical FormulaC5H5NO2
Average Molecular Weight111.0987
Monoisotopic Molecular Weight111.032028409
IUPAC Namepyridine-2,3-diol
Traditional Name2,3-dihydroxypyridine
CAS Registry NumberNot Available
SMILES
OC1=C(O)N=CC=C1
InChI Identifier
InChI=1S/C5H5NO2/c7-4-2-1-3-6-5(4)8/h1-3,7H,(H,6,8)
InChI KeyGGOZGYRTNQBSSA-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
  • Hydroxypyridine
  • 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 DescriptorsNot Available
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
logP0.03ALOGPS
logP0.74ChemAxon
logS0.14ALOGPS
pKa (Strongest Acidic)8.88ChemAxon
pKa (Strongest Basic)2.71ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area53.35 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity28.18 m³·mol⁻¹ChemAxon
Polarizability10.07 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]+122.21130932474
DeepCCS[M-H]-119.40330932474
DeepCCS[M-2H]-155.97930932474
DeepCCS[M+Na]+130.78130932474
AllCCS[M+H]+127.232859911
AllCCS[M+H-H2O]+122.532859911
AllCCS[M+NH4]+131.732859911
AllCCS[M+Na]+133.032859911
AllCCS[M-H]-118.232859911
AllCCS[M+Na-2H]-120.932859911
AllCCS[M+HCOO]-123.932859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
2,3-DihydroxypyridineOC1=C(O)N=CC=C12595.7Standard polar33892256
2,3-DihydroxypyridineOC1=C(O)N=CC=C11242.5Standard non polar33892256
2,3-DihydroxypyridineOC1=C(O)N=CC=C11224.9Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Experimental GC-MSGC-MS Spectrum - 2,3-Dihydroxypyridine GC-MS (2 TMS)splash10-0006-3970000000-8e0328c361c06bb1bc872014-06-16HMDB team, MONA, MassBankView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 2,3-Dihydroxypyridine GC-MS (Non-derivatized) - 70eV, Positivesplash10-03e9-9400000000-f3fd7df6ba8e9902d7f82021-09-23Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 2,3-Dihydroxypyridine GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 2,3-Dihydroxypyridine GC-MS (TMS_1_1) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 2,3-Dihydroxypyridine GC-MS (TMS_1_2) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 2,3-Dihydroxypyridine GC-MS (TMS_2_1) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 2,3-Dihydroxypyridine GC-MS (TBDMS_1_1) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 2,3-Dihydroxypyridine GC-MS (TBDMS_1_2) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 2,3-Dihydroxypyridine GC-MS (TBDMS_2_1) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2,3-Dihydroxypyridine 10V, Positive-QTOFsplash10-03di-0900000000-e6d973f360accf9bb3f72016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2,3-Dihydroxypyridine 20V, Positive-QTOFsplash10-03di-3900000000-22854d211d0ba9af52482016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2,3-Dihydroxypyridine 40V, Positive-QTOFsplash10-0udi-9000000000-88c2bae06f2b8802220d2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2,3-Dihydroxypyridine 10V, Negative-QTOFsplash10-03di-2900000000-24ae52591c1fcdaf29eb2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2,3-Dihydroxypyridine 20V, Negative-QTOFsplash10-03di-2900000000-90a06d69343fc267a2852016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2,3-Dihydroxypyridine 40V, Negative-QTOFsplash10-014l-9000000000-beca162360df251e02102016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2,3-Dihydroxypyridine 10V, Positive-QTOFsplash10-03e9-9800000000-577bd8a78b2122eb5c942021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2,3-Dihydroxypyridine 20V, Positive-QTOFsplash10-015l-9000000000-16836e0d61131f6f061d2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2,3-Dihydroxypyridine 40V, Positive-QTOFsplash10-0fri-9000000000-9c783b36b7e23db73e012021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2,3-Dihydroxypyridine 10V, Negative-QTOFsplash10-03di-1900000000-081cb47256adf75f80ed2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2,3-Dihydroxypyridine 20V, Negative-QTOFsplash10-0ikc-9200000000-c4e6832da32539bf65402021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2,3-Dihydroxypyridine 40V, Negative-QTOFsplash10-0f6x-9000000000-45c94990dcb18716c8dd2021-10-12Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
UrineDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedCancer patients undergoing total body irradiation details
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID26153
KEGG Compound IDNot Available
BioCyc IDCPD-14078
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound28115
PDB IDNot Available
ChEBI ID131454
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 ]