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Showing metabocard for 5-(3-Pyridyl)-2-hydroxytetrahydrofuran (HMDB0062407)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2017-03-21 06:15:27 UTC
Update Date2022-03-07 03:17:54 UTC
HMDB IDHMDB0062407
Secondary Accession Numbers
  • HMDB62407
Metabolite Identification
Common Name5-(3-Pyridyl)-2-hydroxytetrahydrofuran
Description5-(3-Pyridyl)-2-hydroxytetrahydrofuran 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. 5-(3-Pyridyl)-2-hydroxytetrahydrofuran is a strong basic compound (based on its pKa).
Structure
Data?1563866307
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0062407 (5-(3-Pyridyl)-2-hydroxytetrahydrofuran)

  Mrv1652303211707152D          

 12 13  0  0  0  0            999 V2000
    0.7145   -0.4125    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
    1.3819   -1.7224    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1270   -2.5070    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3020   -2.5070    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0470   -1.7224    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1830   -3.1745    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1526   -3.9282    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3323   -4.5956    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1528   -4.5094    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4884   -3.7557    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0034   -3.0882    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  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  2  6  1  0  0  0  0
  5  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
  7 12  1  0  0  0  0
M  END
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3D MOL for HMDB0062407 (5-(3-Pyridyl)-2-hydroxytetrahydrofuran)

HMDB0062407
     RDKit          3D
5-(3-Pyridyl)-2-hydroxytetrahydrofuran
 23 24  0  0  0  0  0  0  0  0999 V2000
   -2.6192   -0.0216    1.8010 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3200   -0.7962    0.6571 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5877    0.0628   -0.5620 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2141    0.7374   -0.6836 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3603   -0.4920   -0.3825 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0243   -0.1077   -0.1170 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8736   -1.0104    0.4802 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1831   -0.6860    0.7462 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6036    0.5695    0.3923 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7727    1.4390   -0.1869 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4882    1.1440   -0.4566 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9900   -1.1332    0.6487 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9493    0.8811    1.5395 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0030   -1.6636    0.5960 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3860    0.7940   -0.4054 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7104   -0.5431   -1.4834 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0223    1.1092   -1.6901 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1658    1.4809    0.1186 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4485   -1.1390   -1.3033 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5263   -2.0171    0.7611 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8451   -1.3892    1.2116 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6246    0.8922    0.5730 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8349    1.8891   -0.9354 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  2  0
  5 12  1  0
 12  2  1  0
 11  6  1  0
  1 13  1  0
  2 14  1  0
  3 15  1  0
  3 16  1  0
  4 17  1  0
  4 18  1  0
  5 19  1  0
  7 20  1  0
  8 21  1  0
  9 22  1  0
 11 23  1  0
M  END
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3D SDF for HMDB0062407 (5-(3-Pyridyl)-2-hydroxytetrahydrofuran)

  Mrv1652303211707152D          

 12 13  0  0  0  0            999 V2000
    0.7145   -0.4125    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
    1.3819   -1.7224    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1270   -2.5070    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3020   -2.5070    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0470   -1.7224    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1830   -3.1745    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1526   -3.9282    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3323   -4.5956    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1528   -4.5094    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4884   -3.7557    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0034   -3.0882    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  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  2  6  1  0  0  0  0
  5  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
  7 12  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0062407

> <DATABASE_NAME>
hmdb

> <SMILES>
OC1CCC(O1)C1=CN=CC=C1

> <INCHI_IDENTIFIER>
InChI=1S/C9H11NO2/c11-9-4-3-8(12-9)7-2-1-5-10-6-7/h1-2,5-6,8-9,11H,3-4H2

> <INCHI_KEY>
LHGVLZHIYVKZBT-UHFFFAOYSA-N

> <FORMULA>
C9H11NO2

> <MOLECULAR_WEIGHT>
165.192

> <EXACT_MASS>
165.078978598

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
23

> <JCHEM_AVERAGE_POLARIZABILITY>
17.200697169182497

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
5-(pyridin-3-yl)oxolan-2-ol

> <ALOGPS_LOGP>
0.21

> <JCHEM_LOGP>
0.5039892543333333

> <ALOGPS_LOGS>
0.16

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.453996348905786

> <JCHEM_PKA_STRONGEST_BASIC>
4.702232796928638

> <JCHEM_POLAR_SURFACE_AREA>
42.35

> <JCHEM_REFRACTIVITY>
43.8197

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.39e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5-(pyridin-3-yl)oxolan-2-ol

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0062407 (5-(3-Pyridyl)-2-hydroxytetrahydrofuran)

HMDB0062407
     RDKit          3D
5-(3-Pyridyl)-2-hydroxytetrahydrofuran
 23 24  0  0  0  0  0  0  0  0999 V2000
   -2.6192   -0.0216    1.8010 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3200   -0.7962    0.6571 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5877    0.0628   -0.5620 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2141    0.7374   -0.6836 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3603   -0.4920   -0.3825 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0243   -0.1077   -0.1170 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8736   -1.0104    0.4802 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1831   -0.6860    0.7462 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6036    0.5695    0.3923 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7727    1.4390   -0.1869 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4882    1.1440   -0.4566 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9900   -1.1332    0.6487 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9493    0.8811    1.5395 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0030   -1.6636    0.5960 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3860    0.7940   -0.4054 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7104   -0.5431   -1.4834 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0223    1.1092   -1.6901 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1658    1.4809    0.1186 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4485   -1.1390   -1.3033 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5263   -2.0171    0.7611 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8451   -1.3892    1.2116 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6246    0.8922    0.5730 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8349    1.8891   -0.9354 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  2  0
  5 12  1  0
 12  2  1  0
 11  6  1  0
  1 13  1  0
  2 14  1  0
  3 15  1  0
  3 16  1  0
  4 17  1  0
  4 18  1  0
  5 19  1  0
  7 20  1  0
  8 21  1  0
  9 22  1  0
 11 23  1  0
M  END
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PDB for HMDB0062407 (5-(3-Pyridyl)-2-hydroxytetrahydrofuran)

HEADER    PROTEIN                                 21-MAR-17   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   21-MAR-17         0                                  
HETATM    1  O   UNK     0       1.334  -0.770   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       2.580  -3.215   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.104  -4.680   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.564  -4.680   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       0.088  -3.215   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0      -0.342  -5.926   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.285  -7.333   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0      -0.620  -8.578   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0      -2.152  -8.417   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -2.778  -7.011   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -1.873  -5.765   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    6                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6    7                                                  
CONECT    6    5    2                                                       
CONECT    7    5    8   12                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11    7                                                       
MASTER        0    0    0    0    0    0    0    0   12    0   26    0
END
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3D PDB for HMDB0062407 (5-(3-Pyridyl)-2-hydroxytetrahydrofuran)

COMPND    HMDB0062407
HETATM    1  O1  UNL     1      -2.619  -0.022   1.801  1.00  0.00           O  
HETATM    2  C1  UNL     1      -2.320  -0.796   0.657  1.00  0.00           C  
HETATM    3  C2  UNL     1      -2.588   0.063  -0.562  1.00  0.00           C  
HETATM    4  C3  UNL     1      -1.214   0.737  -0.684  1.00  0.00           C  
HETATM    5  C4  UNL     1      -0.360  -0.492  -0.382  1.00  0.00           C  
HETATM    6  C5  UNL     1       1.024  -0.108  -0.117  1.00  0.00           C  
HETATM    7  C6  UNL     1       1.874  -1.010   0.480  1.00  0.00           C  
HETATM    8  C7  UNL     1       3.183  -0.686   0.746  1.00  0.00           C  
HETATM    9  C8  UNL     1       3.604   0.569   0.392  1.00  0.00           C  
HETATM   10  N1  UNL     1       2.773   1.439  -0.187  1.00  0.00           N  
HETATM   11  C9  UNL     1       1.488   1.144  -0.457  1.00  0.00           C  
HETATM   12  O2  UNL     1      -0.990  -1.133   0.649  1.00  0.00           O  
HETATM   13  H1  UNL     1      -2.949   0.881   1.540  1.00  0.00           H  
HETATM   14  H2  UNL     1      -3.003  -1.664   0.596  1.00  0.00           H  
HETATM   15  H3  UNL     1      -3.386   0.794  -0.405  1.00  0.00           H  
HETATM   16  H4  UNL     1      -2.710  -0.543  -1.483  1.00  0.00           H  
HETATM   17  H5  UNL     1      -1.022   1.109  -1.690  1.00  0.00           H  
HETATM   18  H6  UNL     1      -1.166   1.481   0.119  1.00  0.00           H  
HETATM   19  H7  UNL     1      -0.449  -1.139  -1.303  1.00  0.00           H  
HETATM   20  H8  UNL     1       1.526  -2.017   0.761  1.00  0.00           H  
HETATM   21  H9  UNL     1       3.845  -1.389   1.212  1.00  0.00           H  
HETATM   22  H10 UNL     1       4.625   0.892   0.573  1.00  0.00           H  
HETATM   23  H11 UNL     1       0.835   1.889  -0.935  1.00  0.00           H  
CONECT    1    2   13
CONECT    2    3   12   14
CONECT    3    4   15   16
CONECT    4    5   17   18
CONECT    5    6   12   19
CONECT    6    7    7   11
CONECT    7    8   20
CONECT    8    9    9   21
CONECT    9   10   22
CONECT   10   11   11
CONECT   11   23
END
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SMILES for HMDB0062407 (5-(3-Pyridyl)-2-hydroxytetrahydrofuran)

OC1CCC(O1)C1=CN=CC=C1
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INCHI for HMDB0062407 (5-(3-Pyridyl)-2-hydroxytetrahydrofuran)

InChI=1S/C9H11NO2/c11-9-4-3-8(12-9)7-2-1-5-10-6-7/h1-2,5-6,8-9,11H,3-4H2
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View in JSmolView Stereo Labels
SynonymsNot Available
Chemical FormulaC9H11NO2
Average Molecular Weight165.192
Monoisotopic Molecular Weight165.078978598
IUPAC Name5-(pyridin-3-yl)oxolan-2-ol
Traditional Name5-(pyridin-3-yl)oxolan-2-ol
CAS Registry Number53798-73-5
SMILES
OC1CCC(O1)C1=CN=CC=C1
InChI Identifier
InChI=1S/C9H11NO2/c11-9-4-3-8(12-9)7-2-1-5-10-6-7/h1-2,5-6,8-9,11H,3-4H2
InChI KeyLHGVLZHIYVKZBT-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
  • Tetrahydrofuran
  • Hemiacetal
  • Oxacycle
  • Azacycle
  • Organic nitrogen compound
  • Organic oxygen compound
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organonitrogen compound
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Source
ProcessNot Available
RoleNot Available
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water Solubility239 g/lALOGPS
LogP0.21ALOGPS
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
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 IDNot Available
KEGG Compound IDC19578
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound179630
PDB IDNot Available
ChEBI ID82572
Food Biomarker OntologyNot Available
VMH IDM01035
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available