Hmdb loader

Showing metabocard for trans-3'-hydroxycotinine (HMDB0304504)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-24 10:17:30 UTC
Update Date2022-09-22 18:34:38 UTC
HMDB IDHMDB0304504
Secondary Accession NumbersNone
Metabolite Identification
Common Nametrans-3'-hydroxycotinine
DescriptionTrans-3'-hydroxycotinine, also known as 1-methyl-3-hydroxy-5-(3-pyridyl)-2-pyrrolidinone, is a member of the class of compounds known as pyrrolidinylpyridines. Pyrrolidinylpyridines are compounds containing a pyrrolidinylpyridine ring system, which consists of a pyrrolidine ring linked to a pyridine ring. Trans-3'-hydroxycotinine is soluble (in water) and a very weakly acidic compound (based on its pKa). Trans-3'-hydroxycotinine can be found in a number of food items such as annual wild rice, macadamia nut, corn salad, and radish, which makes trans-3'-hydroxycotinine a potential biomarker for the consumption of these food products.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0304504 (trans-3'-hydroxycotinine)

  Mrv1533004171521122D          

 14 15  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
    0.7145   -1.2375    0.0000 N   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
   -0.1830   -3.1745    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0470   -1.7224    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7376   -1.4675    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1665   -1.4675    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3381   -0.6605    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1227   -0.4056    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7358   -0.9576    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5642   -1.7646    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.7796   -2.0195    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
  5  7  1  0  0  0  0
  2  7  1  0  0  0  0
  7  8  2  0  0  0  0
  3  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
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
  9 14  1  0  0  0  0
M  END
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3D MOL for HMDB0304504 (trans-3'-hydroxycotinine)

HMDB0304504
     RDKit          3D
trans-3'-hydroxycotinine
 26 27  0  0  0  0  0  0  0  0999 V2000
   -1.3586    2.1759   -0.1283 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2735    0.7537    0.0898 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0369    0.0193    1.0387 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5946    0.4823    2.0633 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0766   -1.4289    0.6205 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1478   -1.5637   -0.2886 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8119   -1.5502   -0.1652 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4217   -0.1683   -0.5942 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0202    0.0212   -0.2698 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9907    0.0218   -1.2508 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3361    0.1960   -0.9725 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7058    0.3764    0.3565 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7679    0.3780    1.3252 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4492    0.2049    1.0303 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3886    2.3740   -1.2271 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5513    2.7464    0.3814 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3193    2.6072    0.2626 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1590   -2.1039    1.4712 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8570   -2.0534    0.1594 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0019   -2.2172   -1.0371 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0081   -2.0310    0.4532 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5204   -0.0395   -1.6907 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6676   -0.1204   -2.2665 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0982    0.1941   -1.7655 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7604    0.5126    0.5711 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7311    0.2125    1.8330 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
  3  5  1  0
  5  6  1  0
  5  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  2  0
 12 13  1  0
 13 14  2  0
  8  2  1  0
 14  9  1  0
  1 15  1  0
  1 16  1  0
  1 17  1  0
  5 18  1  0
  6 19  1  0
  7 20  1  0
  7 21  1  0
  8 22  1  0
 10 23  1  0
 11 24  1  0
 12 25  1  0
 14 26  1  0
M  END
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3D SDF for HMDB0304504 (trans-3'-hydroxycotinine)

  Mrv1533004171521122D          

 14 15  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
    0.7145   -1.2375    0.0000 N   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
   -0.1830   -3.1745    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0470   -1.7224    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7376   -1.4675    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1665   -1.4675    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3381   -0.6605    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1227   -0.4056    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7358   -0.9576    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5642   -1.7646    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.7796   -2.0195    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
  5  7  1  0  0  0  0
  2  7  1  0  0  0  0
  7  8  2  0  0  0  0
  3  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
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
  9 14  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0304504

> <DATABASE_NAME>
hmdb

> <SMILES>
CN1C(CC(O)C1=O)C1=CC=CN=C1

> <INCHI_IDENTIFIER>
InChI=1S/C10H12N2O2/c1-12-8(5-9(13)10(12)14)7-3-2-4-11-6-7/h2-4,6,8-9,13H,5H2,1H3

> <INCHI_KEY>
XOKCJXZZNAUIQN-UHFFFAOYSA-N

> <FORMULA>
C10H12N2O2

> <MOLECULAR_WEIGHT>
192.218

> <EXACT_MASS>
192.089877634

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
26

> <JCHEM_AVERAGE_POLARIZABILITY>
19.506098262654007

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-hydroxy-1-methyl-5-(pyridin-3-yl)pyrrolidin-2-one

> <ALOGPS_LOGP>
-0.32

> <JCHEM_LOGP>
-0.7332253989999996

> <ALOGPS_LOGS>
-0.61

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.107323140437018

> <JCHEM_PKA_STRONGEST_BASIC>
4.788748646548031

> <JCHEM_POLAR_SURFACE_AREA>
53.43

> <JCHEM_REFRACTIVITY>
50.7291

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.77e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-hydroxy-1-methyl-5-(pyridin-3-yl)pyrrolidin-2-one

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0304504 (trans-3'-hydroxycotinine)

HMDB0304504
     RDKit          3D
trans-3'-hydroxycotinine
 26 27  0  0  0  0  0  0  0  0999 V2000
   -1.3586    2.1759   -0.1283 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2735    0.7537    0.0898 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0369    0.0193    1.0387 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5946    0.4823    2.0633 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0766   -1.4289    0.6205 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1478   -1.5637   -0.2886 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8119   -1.5502   -0.1652 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4217   -0.1683   -0.5942 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0202    0.0212   -0.2698 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9907    0.0218   -1.2508 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3361    0.1960   -0.9725 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7058    0.3764    0.3565 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7679    0.3780    1.3252 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4492    0.2049    1.0303 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3886    2.3740   -1.2271 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5513    2.7464    0.3814 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3193    2.6072    0.2626 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1590   -2.1039    1.4712 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8570   -2.0534    0.1594 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0019   -2.2172   -1.0371 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0081   -2.0310    0.4532 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5204   -0.0395   -1.6907 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6676   -0.1204   -2.2665 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0982    0.1941   -1.7655 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7604    0.5126    0.5711 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7311    0.2125    1.8330 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
  3  5  1  0
  5  6  1  0
  5  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  2  0
 12 13  1  0
 13 14  2  0
  8  2  1  0
 14  9  1  0
  1 15  1  0
  1 16  1  0
  1 17  1  0
  5 18  1  0
  6 19  1  0
  7 20  1  0
  7 21  1  0
  8 22  1  0
 10 23  1  0
 11 24  1  0
 12 25  1  0
 14 26  1  0
M  END
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PDB for HMDB0304504 (trans-3'-hydroxycotinine)

HEADER    PROTEIN                                 17-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-APR-15         0                                  
HETATM    1  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0       1.334  -2.310   0.000  0.00  0.00           N+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      -0.342  -5.926   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       0.088  -3.215   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      -1.377  -2.739   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       4.044  -2.739   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       4.364  -1.233   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       5.829  -0.757   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       6.973  -1.788   0.000  0.00  0.00           C+0
HETATM   13  N   UNK     0       6.653  -3.294   0.000  0.00  0.00           N+0
HETATM   14  C   UNK     0       5.189  -3.770   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    7                                                  
CONECT    3    2    4    9                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    2    8                                                  
CONECT    8    7                                                            
CONECT    9    3   10   14                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13    9                                                       
MASTER        0    0    0    0    0    0    0    0   14    0   30    0
END
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3D PDB for HMDB0304504 (trans-3'-hydroxycotinine)

COMPND    HMDB0304504
HETATM    1  C1  UNL     1      -1.359   2.176  -0.128  1.00  0.00           C  
HETATM    2  N1  UNL     1      -1.274   0.754   0.090  1.00  0.00           N  
HETATM    3  C2  UNL     1      -2.037   0.019   1.039  1.00  0.00           C  
HETATM    4  O1  UNL     1      -2.595   0.482   2.063  1.00  0.00           O  
HETATM    5  C3  UNL     1      -2.077  -1.429   0.620  1.00  0.00           C  
HETATM    6  O2  UNL     1      -3.148  -1.564  -0.289  1.00  0.00           O  
HETATM    7  C4  UNL     1      -0.812  -1.550  -0.165  1.00  0.00           C  
HETATM    8  C5  UNL     1      -0.422  -0.168  -0.594  1.00  0.00           C  
HETATM    9  C6  UNL     1       1.020   0.021  -0.270  1.00  0.00           C  
HETATM   10  C7  UNL     1       1.991   0.022  -1.251  1.00  0.00           C  
HETATM   11  C8  UNL     1       3.336   0.196  -0.973  1.00  0.00           C  
HETATM   12  C9  UNL     1       3.706   0.376   0.357  1.00  0.00           C  
HETATM   13  N2  UNL     1       2.768   0.378   1.325  1.00  0.00           N  
HETATM   14  C10 UNL     1       1.449   0.205   1.030  1.00  0.00           C  
HETATM   15  H1  UNL     1      -1.389   2.374  -1.227  1.00  0.00           H  
HETATM   16  H2  UNL     1      -0.551   2.746   0.381  1.00  0.00           H  
HETATM   17  H3  UNL     1      -2.319   2.607   0.263  1.00  0.00           H  
HETATM   18  H4  UNL     1      -2.159  -2.104   1.471  1.00  0.00           H  
HETATM   19  H5  UNL     1      -3.857  -2.053   0.159  1.00  0.00           H  
HETATM   20  H6  UNL     1      -1.002  -2.217  -1.037  1.00  0.00           H  
HETATM   21  H7  UNL     1      -0.008  -2.031   0.453  1.00  0.00           H  
HETATM   22  H8  UNL     1      -0.520  -0.039  -1.691  1.00  0.00           H  
HETATM   23  H9  UNL     1       1.668  -0.120  -2.267  1.00  0.00           H  
HETATM   24  H10 UNL     1       4.098   0.194  -1.765  1.00  0.00           H  
HETATM   25  H11 UNL     1       4.760   0.513   0.571  1.00  0.00           H  
HETATM   26  H12 UNL     1       0.731   0.213   1.833  1.00  0.00           H  
CONECT    1    2   15   16   17
CONECT    2    3    8
CONECT    3    4    4    5
CONECT    5    6    7   18
CONECT    6   19
CONECT    7    8   20   21
CONECT    8    9   22
CONECT    9   10   10   14
CONECT   10   11   23
CONECT   11   12   12   24
CONECT   12   13   25
CONECT   13   14   14
CONECT   14   26
END
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SMILES for HMDB0304504 (trans-3'-hydroxycotinine)

CN1C(CC(O)C1=O)C1=CC=CN=C1
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INCHI for HMDB0304504 (trans-3'-hydroxycotinine)

InChI=1S/C10H12N2O2/c1-12-8(5-9(13)10(12)14)7-3-2-4-11-6-7/h2-4,6,8-9,13H,5H2,1H3
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View in JSmolView Stereo Labels
Synonyms
ValueSource
1-Methyl-3-hydroxy-5-(3-pyridyl)-2-pyrrolidinoneMeSH
3'-HydroxycotinineMeSH
3-HydroxycotinineMeSH
Chemical FormulaC10H12N2O2
Average Molecular Weight192.218
Monoisotopic Molecular Weight192.089877634
IUPAC Name3-hydroxy-1-methyl-5-(pyridin-3-yl)pyrrolidin-2-one
Traditional Name3-hydroxy-1-methyl-5-(pyridin-3-yl)pyrrolidin-2-one
CAS Registry NumberNot Available
SMILES
CN1C(CC(O)C1=O)C1=CC=CN=C1
InChI Identifier
InChI=1S/C10H12N2O2/c1-12-8(5-9(13)10(12)14)7-3-2-4-11-6-7/h2-4,6,8-9,13H,5H2,1H3
InChI KeyXOKCJXZZNAUIQN-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as pyrrolidinylpyridines. Pyrrolidinylpyridines are compounds containing a pyrrolidinylpyridine ring system, which consists of a pyrrolidine ring linked to a pyridine ring.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassPyridines and derivatives
Sub ClassPyrrolidinylpyridines
Direct ParentPyrrolidinylpyridines
Alternative Parents
Substituents
  • Pyrrolidinylpyridine
  • Alkaloid or derivatives
  • Pyrrolidone
  • 2-pyrrolidone
  • N-alkylpyrrolidine
  • Pyrrolidine
  • Tertiary carboxylic acid amide
  • Heteroaromatic compound
  • Carboxamide group
  • Lactam
  • Secondary alcohol
  • Carboxylic acid derivative
  • Azacycle
  • Organic oxide
  • Organopnictogen compound
  • Organic oxygen compound
  • Organic nitrogen compound
  • Organooxygen compound
  • Organonitrogen compound
  • Alcohol
  • Carbonyl group
  • Hydrocarbon derivative
  • 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 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
Not Available
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedCancer patients undergoing total body irradiation details
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 IDFDB031206
KNApSAcK IDNot Available
Chemspider ID401
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound414
PDB IDNot Available
ChEBI IDNot Available
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 ReferencesNot Available