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Showing NP-Card for 6-(hydroxymethyl)pyridin-3-ol (NP0235113)

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Record Information
Version2.0
Created at2022-09-06 17:33:44 UTC
Updated at2022-09-06 17:33:44 UTC
NP-MRD IDNP0235113
Secondary Accession NumbersNone
Natural Product Identification
Common Name6-(hydroxymethyl)pyridin-3-ol
Description6-(Hydroxymethyl)pyridin-3-ol, also known as 5-hydroxy-2-hydroxymethylpyridine, 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. 6-(hydroxymethyl)pyridin-3-ol is found in Codonopsis pilosula and Viola mandshurica. 6-(Hydroxymethyl)pyridin-3-ol is a strong basic compound (based on its pKa).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0235113 (6-(hydroxymethyl)pyridin-3-ol)


  Mrv1533004151516382D          

  9  9  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
    0.7145   -1.2375    0.0000 O   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 N   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
  6  8  1  0  0  0  0
  8  9  2  0  0  0  0
  3  9  1  0  0  0  0
M  END
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3D MOL for NP0235113 (6-(hydroxymethyl)pyridin-3-ol)

     RDKit          3D

 16 16  0  0  0  0  0  0  0  0999 V2000
   -2.8697    1.1454    0.2367 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3096   -0.1149    0.1029 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8390   -0.0574    0.0282 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1333   -1.2271   -0.1059 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2602   -1.0999   -0.1708 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8471    0.1453   -0.1003 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2522    0.2013   -0.1717 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0914    1.2884    0.0343 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2442    1.1440    0.0946 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3966    1.7304   -0.4279 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6726   -0.5813   -0.8366 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5878   -0.8013    0.9216 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5587   -2.2062   -0.1633 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8964   -1.9692   -0.2765 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7199    0.1410    0.7449 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5444    2.2615    0.0897 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
  6  8  1  0
  8  9  2  0
  9  3  1  0
  1 10  1  0
  2 11  1  0
  2 12  1  0
  4 13  1  0
  5 14  1  0
  7 15  1  0
  8 16  1  0
M  END
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3D SDF for NP0235113 (6-(hydroxymethyl)pyridin-3-ol)


  Mrv1533004151516382D          

  9  9  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
    0.7145   -1.2375    0.0000 O   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 N   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
  6  8  1  0  0  0  0
  8  9  2  0  0  0  0
  3  9  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0235113

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OCC1=CC=C(O)C=N1

> <INCHI_IDENTIFIER>
InChI=1S/C6H7NO2/c8-4-5-1-2-6(9)3-7-5/h1-3,8-9H,4H2

> <INCHI_KEY>
NESFDGDRYVANBC-UHFFFAOYSA-N

> <FORMULA>
C6H7NO2

> <MOLECULAR_WEIGHT>
125.127

> <EXACT_MASS>
125.047678469

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
16

> <JCHEM_AVERAGE_POLARIZABILITY>
12.270370041419463

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
6-(hydroxymethyl)pyridin-3-ol

> <ALOGPS_LOGP>
-0.18

> <JCHEM_LOGP>
-0.23386980966666665

> <ALOGPS_LOGS>
-0.18

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.408153113871837

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.619889182737447

> <JCHEM_PKA_STRONGEST_BASIC>
4.821890099280311

> <JCHEM_POLAR_SURFACE_AREA>
53.35

> <JCHEM_REFRACTIVITY>
32.1757

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.34e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
6-(hydroxymethyl)pyridin-3-ol

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0235113 (6-(hydroxymethyl)pyridin-3-ol)

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PDB for NP0235113 (6-(hydroxymethyl)pyridin-3-ol)
HEADER    PROTEIN                                 15-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   15-APR-15         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  O   UNK     0       1.334  -2.310   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0       0.000   1.540   0.000  0.00  0.00           N+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    9                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9                                                       
CONECT    9    8    3                                                       
MASTER        0    0    0    0    0    0    0    0    9    0   18    0
END

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3D PDB for NP0235113 (6-(hydroxymethyl)pyridin-3-ol)
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SMILES for NP0235113 (6-(hydroxymethyl)pyridin-3-ol)
OCC1=CC=C(O)C=N1
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INCHI for NP0235113 (6-(hydroxymethyl)pyridin-3-ol)
InChI=1S/C6H7NO2/c8-4-5-1-2-6(9)3-7-5/h1-3,8-9H,4H2
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View in JSmol
Synonyms
ValueSource
5-Hydroxy-2-hydroxymethylpyridineMeSH
Chemical FormulaC6H7NO2
Average Mass125.1270 Da
Monoisotopic Mass125.04768 Da
IUPAC Name6-(hydroxymethyl)pyridin-3-ol
Traditional Name6-(hydroxymethyl)pyridin-3-ol
CAS Registry NumberNot Available
SMILES
OCC1=CC=C(O)C=N1
InChI Identifier
InChI=1S/C6H7NO2/c8-4-5-1-2-6(9)3-7-5/h1-3,8-9H,4H2
InChI KeyNESFDGDRYVANBC-UHFFFAOYSA-N
Experimental Spectra
Not Available
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Codonopsis pilosulaLOTUS Database
Viola mandshuricaLOTUS Database
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
    • 

  • 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
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP-0.18ALOGPS
logP-0.23ChemAxon
logS-0.18ALOGPS
pKa (Strongest Acidic)8.62ChemAxon
pKa (Strongest Basic)4.82ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area53.35 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity32.18 m³·mol⁻¹ChemAxon
Polarizability12.27 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound419490  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. LOTUS database [Link]