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Showing metabocard for 3-Pyridinemethanol (HMDB0245980)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-10 23:01:28 UTC
Update Date2022-09-22 17:44:20 UTC
HMDB IDHMDB0245980
Secondary Accession NumbersNone
Metabolite Identification
Common Name3-Pyridinemethanol
DescriptionNicotinyl alcohol, also known as 3-pyridinylcarbinol or 3-pyridylmethanol, 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. Based on a literature review a small amount of articles have been published on Nicotinyl alcohol. This compound has been identified in human blood as reported by (PMID: 31557052 ). 3-pyridinemethanol is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 3-Pyridinemethanol 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 HMDB0245980 (3-Pyridinemethanol)

  Mrv0541 02231217282D          

  8  8  0  0  0  0            999 V2000
    0.0000    2.4750    0.0000 O   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    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   -0.4125    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
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  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
  7  8  2  0  0  0  0
  3  8  1  0  0  0  0
M  END
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3D MOL for HMDB0245980 (3-Pyridinemethanol)

HMDB0245980
     RDKit          3D
3-Pyridinemethanol
 15 15  0  0  0  0  0  0  0  0999 V2000
   -2.4865    0.4725    0.8414 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8410   -0.3316   -0.1144 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3624   -0.2205   -0.0148 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3597    0.7218   -0.7216 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7238    0.7483   -0.5652 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4116   -0.1174    0.2614 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6877   -1.0240    0.9375 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.3482   -1.0745    0.8048 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8247    1.2761    0.3912 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1860   -1.3679    0.0868 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2130   -0.0847   -1.1416 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1813    1.3996   -1.3692 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3046    1.4815   -1.1126 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5039   -0.0605    0.3563 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2446   -1.8187    1.3600 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
  8  3  1  0
  1  9  1  0
  2 10  1  0
  2 11  1  0
  4 12  1  0
  5 13  1  0
  6 14  1  0
  8 15  1  0
M  END
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3D SDF for HMDB0245980 (3-Pyridinemethanol)

  Mrv0541 02231217282D          

  8  8  0  0  0  0            999 V2000
    0.0000    2.4750    0.0000 O   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    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   -0.4125    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
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  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
  7  8  2  0  0  0  0
  3  8  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0245980

> <DATABASE_NAME>
hmdb

> <SMILES>
OCC1=CC=CN=C1

> <INCHI_IDENTIFIER>
InChI=1S/C6H7NO/c8-5-6-2-1-3-7-4-6/h1-4,8H,5H2

> <INCHI_KEY>
MVQVNTPHUGQQHK-UHFFFAOYSA-N

> <FORMULA>
C6H7NO

> <MOLECULAR_WEIGHT>
109.1259

> <EXACT_MASS>
109.052763851

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_AVERAGE_POLARIZABILITY>
11.227756199860899

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
pyridin-3-ylmethanol

> <ALOGPS_LOGP>
-0.13

> <JCHEM_LOGP>
-0.011776378333333407

> <ALOGPS_LOGS>
0.46

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.690153284532908

> <JCHEM_PKA_STRONGEST_BASIC>
4.728595177886644

> <JCHEM_POLAR_SURFACE_AREA>
33.120000000000005

> <JCHEM_REFRACTIVITY>
30.716999999999995

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.12e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
β pyridylcarbinol

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0245980 (3-Pyridinemethanol)

HMDB0245980
     RDKit          3D
3-Pyridinemethanol
 15 15  0  0  0  0  0  0  0  0999 V2000
   -2.4865    0.4725    0.8414 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8410   -0.3316   -0.1144 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3624   -0.2205   -0.0148 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3597    0.7218   -0.7216 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7238    0.7483   -0.5652 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4116   -0.1174    0.2614 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6877   -1.0240    0.9375 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.3482   -1.0745    0.8048 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8247    1.2761    0.3912 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1860   -1.3679    0.0868 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2130   -0.0847   -1.1416 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1813    1.3996   -1.3692 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3046    1.4815   -1.1126 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5039   -0.0605    0.3563 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2446   -1.8187    1.3600 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
  8  3  1  0
  1  9  1  0
  2 10  1  0
  2 11  1  0
  4 12  1  0
  5 13  1  0
  6 14  1  0
  8 15  1  0
M  END
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PDB for HMDB0245980 (3-Pyridinemethanol)

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  O   UNK     0       0.000   4.620   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.334   2.310   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       2.667   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    8                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    3                                                       
MASTER        0    0    0    0    0    0    0    0    8    0   16    0
END
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3D PDB for HMDB0245980 (3-Pyridinemethanol)

COMPND    HMDB0245980
HETATM    1  O1  UNL     1      -2.487   0.472   0.841  1.00  0.00           O  
HETATM    2  C1  UNL     1      -1.841  -0.332  -0.114  1.00  0.00           C  
HETATM    3  C2  UNL     1      -0.362  -0.221  -0.015  1.00  0.00           C  
HETATM    4  C3  UNL     1       0.360   0.722  -0.722  1.00  0.00           C  
HETATM    5  C4  UNL     1       1.724   0.748  -0.565  1.00  0.00           C  
HETATM    6  C5  UNL     1       2.412  -0.117   0.261  1.00  0.00           C  
HETATM    7  N1  UNL     1       1.688  -1.024   0.938  1.00  0.00           N  
HETATM    8  C6  UNL     1       0.348  -1.075   0.805  1.00  0.00           C  
HETATM    9  H1  UNL     1      -2.825   1.276   0.391  1.00  0.00           H  
HETATM   10  H2  UNL     1      -2.186  -1.368   0.087  1.00  0.00           H  
HETATM   11  H3  UNL     1      -2.213  -0.085  -1.142  1.00  0.00           H  
HETATM   12  H4  UNL     1      -0.181   1.400  -1.369  1.00  0.00           H  
HETATM   13  H5  UNL     1       2.305   1.481  -1.113  1.00  0.00           H  
HETATM   14  H6  UNL     1       3.504  -0.060   0.356  1.00  0.00           H  
HETATM   15  H7  UNL     1      -0.245  -1.819   1.360  1.00  0.00           H  
CONECT    1    2    9
CONECT    2    3   10   11
CONECT    3    4    4    8
CONECT    4    5   12
CONECT    5    6    6   13
CONECT    6    7   14
CONECT    7    8    8
CONECT    8   15
END
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SMILES for HMDB0245980 (3-Pyridinemethanol)

OCC1=CC=CN=C1
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INCHI for HMDB0245980 (3-Pyridinemethanol)

InChI=1S/C6H7NO/c8-5-6-2-1-3-7-4-6/h1-4,8H,5H2
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
Chemical FormulaC6H7NO
Average Molecular Weight109.1259
Monoisotopic Molecular Weight109.052763851
IUPAC Namepyridin-3-ylmethanol
Traditional Nameβ pyridylcarbinol
CAS Registry NumberNot Available
SMILES
OCC1=CC=CN=C1
InChI Identifier
InChI=1S/C6H7NO/c8-5-6-2-1-3-7-4-6/h1-4,8H,5H2
InChI KeyMVQVNTPHUGQQHK-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
  • Organic nitrogen compound
  • Organic oxygen compound
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Aromatic alcohol
  • Primary alcohol
  • Organooxygen compound
  • Organonitrogen compound
  • Alcohol
  • 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
Predicted Chromatographic Properties
Spectra
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 IDDB04145
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID7229
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNicotinyl_alcohol
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI ID45213
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1193151
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 ]