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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2013-07-04 19:02:50 UTC

Update Date

2019-07-23 07:15:12 UTC

HMDB ID

HMDB0060840

Secondary Accession Numbers

HMDB60840

Metabolite Identification

Common Name

N-Desmethyldoxepin

Description

N-Desmethyldoxepin is a metabolite of doxepin. Doxepin is a psychotropic agent with tricyclic antidepressant and anxiolytic properties, known under many brand-names such as Aponal, the original preparation by Boehringer-Mannheim, now part of the Roche group; Adapine, Doxal, Deptran, Sinquan and Sinequan. As doxepin hydrochloride, it is the active ingredient in cream-based preparations (Zonalon and Xepin) for the treatment of dermatological itch. (Wikipedia )

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI

HMDB0060840
     RDKit          3D
N-Desmethyldoxepin
 39 41  0  0  0  0  0  0  0  0999 V2000
    4.7147   -0.7298    0.4151 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1706    0.1910   -0.5673 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.9605   -0.3405   -1.1765 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8969   -0.3609   -0.1430 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5796   -0.8698   -0.4886 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5139   -0.2414   -0.2259 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8037   -0.8888   -0.6300 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6288   -1.5717   -1.7883 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7580   -2.2474   -2.2521 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9599   -2.1893   -1.5330 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0399   -1.4618   -0.3569 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9451   -0.7757    0.1422 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2883   -0.0964    1.3846 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3103    0.6668    2.0337 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2391    1.4248    1.5357 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9795    2.6121    2.1113 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0724    3.4080    1.6444 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8636    2.9723    0.5686 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6177    1.7586   -0.0402 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4236    1.0475    0.4843 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3206   -0.5812    1.4270 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5764   -1.7592    0.0199 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8112   -0.5653    0.4564 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0369    1.1438   -0.1593 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7927    0.2344   -2.0836 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1904   -1.3683   -1.5078 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3213   -1.2805    0.4466 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0245    0.2179    0.7836 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5061   -1.8320   -0.9835 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6838   -1.5618   -2.2999 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6755   -2.8011   -3.1629 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8429   -2.7216   -1.9053 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0059   -1.4657    0.1421 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1687    0.5526    1.1982 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6514   -0.8711    2.1156 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6133    2.9228    2.9414 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2485    4.3582    2.1368 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6716    3.5938    0.2157 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1555    1.4767   -0.8992 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  2  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  2  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  2  0
 16 17  1  0
 17 18  2  0
 18 19  1  0
 19 20  2  0
 20  6  1  0
 12  7  1  0
 20 15  1  0
  1 21  1  0
  1 22  1  0
  1 23  1  0
  2 24  1  0
  3 25  1  0
  3 26  1  0
  4 27  1  0
  4 28  1  0
  5 29  1  0
  8 30  1  0
  9 31  1  0
 10 32  1  0
 11 33  1  0
 13 34  1  0
 13 35  1  0
 16 36  1  0
 17 37  1  0
 18 38  1  0
 19 39  1  0
M  END


  Mrv0541 07041312022D          

 20 22  0  0  0  0            999 V2000
    2.3747    3.6320    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3747    2.8070    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.0892    2.3945    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0892    1.5695    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8037    1.1570    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8037    0.3320    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5470   -0.0260    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7305   -0.8303    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2162   -1.4753    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3912   -1.4753    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8768   -0.8303    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0604   -0.0260    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4556    0.5352    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6673    0.2920    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4837   -0.5123    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0884   -1.0735    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5189   -1.0735    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1237   -0.5123    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9401    0.2920    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1517    0.5352    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  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
  6 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
 11 16  1  0  0  0  0
  8 17  1  0  0  0  0
 17 18  2  0  0  0  0
 18 19  1  0  0  0  0
 19 20  2  0  0  0  0
  7 20  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0060840

> <DATABASE_NAME>
hmdb

> <SMILES>
CNCC\C=C1\C2=C(COC3=C1C=CC=C3)C=CC=C2

> <INCHI_IDENTIFIER>
InChI=1S/C18H19NO/c1-19-12-6-10-16-15-8-3-2-7-14(15)13-20-18-11-5-4-9-17(16)18/h2-5,7-11,19H,6,12-13H2,1H3/b16-10-

> <INCHI_KEY>
HVKCEFHNSNZIHO-YBEGLDIGSA-N

> <FORMULA>
C18H19NO

> <MOLECULAR_WEIGHT>
265.3496

> <EXACT_MASS>
265.146664235

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_AVERAGE_POLARIZABILITY>
30.865496578317632

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
methyl({3-[(2Z)-9-oxatricyclo[9.4.0.0³,⁸]pentadeca-1(11),3(8),4,6,12,14-hexaen-2-ylidene]propyl})amine

> <ALOGPS_LOGP>
3.75

> <JCHEM_LOGP>
3.4569261373333333

> <ALOGPS_LOGS>
-4.87

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_BASIC>
10.4716084995636

> <JCHEM_POLAR_SURFACE_AREA>
21.259999999999998

> <JCHEM_REFRACTIVITY>
92.95010000000003

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.61e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
methyl({3-[(2Z)-9-oxatricyclo[9.4.0.0³,⁸]pentadeca-1(11),3(8),4,6,12,14-hexaen-2-ylidene]propyl})amine

> <JCHEM_VEBER_RULE>
1

$$$$

HMDB0060840
     RDKit          3D
N-Desmethyldoxepin
 39 41  0  0  0  0  0  0  0  0999 V2000
    4.7147   -0.7298    0.4151 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1706    0.1910   -0.5673 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.9605   -0.3405   -1.1765 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8969   -0.3609   -0.1430 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5796   -0.8698   -0.4886 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5139   -0.2414   -0.2259 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8037   -0.8888   -0.6300 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6288   -1.5717   -1.7883 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7580   -2.2474   -2.2521 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9599   -2.1893   -1.5330 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0399   -1.4618   -0.3569 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9451   -0.7757    0.1422 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2883   -0.0964    1.3846 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3103    0.6668    2.0337 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2391    1.4248    1.5357 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9795    2.6121    2.1113 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0724    3.4080    1.6444 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8636    2.9723    0.5686 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6177    1.7586   -0.0402 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4236    1.0475    0.4843 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3206   -0.5812    1.4270 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5764   -1.7592    0.0199 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8112   -0.5653    0.4564 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0369    1.1438   -0.1593 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7927    0.2344   -2.0836 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1904   -1.3683   -1.5078 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3213   -1.2805    0.4466 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0245    0.2179    0.7836 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5061   -1.8320   -0.9835 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6838   -1.5618   -2.2999 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6755   -2.8011   -3.1629 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8429   -2.7216   -1.9053 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0059   -1.4657    0.1421 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1687    0.5526    1.1982 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6514   -0.8711    2.1156 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6133    2.9228    2.9414 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2485    4.3582    2.1368 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6716    3.5938    0.2157 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1555    1.4767   -0.8992 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  2  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  2  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  2  0
 16 17  1  0
 17 18  2  0
 18 19  1  0
 19 20  2  0
 20  6  1  0
 12  7  1  0
 20 15  1  0
  1 21  1  0
  1 22  1  0
  1 23  1  0
  2 24  1  0
  3 25  1  0
  3 26  1  0
  4 27  1  0
  4 28  1  0
  5 29  1  0
  8 30  1  0
  9 31  1  0
 10 32  1  0
 11 33  1  0
 13 34  1  0
 13 35  1  0
 16 36  1  0
 17 37  1  0
 18 38  1  0
 19 39  1  0
M  END

HEADER    PROTEIN                                 04-JUL-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-JUL-13         0                                  
HETATM    1  C   UNK     0       4.433   6.780   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0       4.433   5.240   0.000  0.00  0.00           N+0
HETATM    3  C   UNK     0       5.767   4.470   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.767   2.930   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       7.100   2.160   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       7.100   0.620   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       8.488  -0.049   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       8.830  -1.550   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       7.870  -2.754   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       6.330  -2.754   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       5.370  -1.550   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       5.713  -0.049   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       4.584   0.999   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       3.112   0.545   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       2.770  -0.956   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       3.898  -2.004   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      10.302  -2.004   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      11.431  -0.956   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      11.088   0.545   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       9.617   0.999   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7   12                                                  
CONECT    7    6    8   20                                                  
CONECT    8    7    9   17                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12   16                                                  
CONECT   12   11    6   13                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   11                                                       
CONECT   17    8   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19    7                                                       
MASTER        0    0    0    0    0    0    0    0   20    0   44    0
END

COMPND    HMDB0060840
HETATM    1  C1  UNL     1       4.715  -0.730   0.415  1.00  0.00           C  
HETATM    2  N1  UNL     1       4.171   0.191  -0.567  1.00  0.00           N  
HETATM    3  C2  UNL     1       2.960  -0.340  -1.177  1.00  0.00           C  
HETATM    4  C3  UNL     1       1.897  -0.361  -0.143  1.00  0.00           C  
HETATM    5  C4  UNL     1       0.580  -0.870  -0.489  1.00  0.00           C  
HETATM    6  C5  UNL     1      -0.514  -0.241  -0.226  1.00  0.00           C  
HETATM    7  C6  UNL     1      -1.804  -0.889  -0.630  1.00  0.00           C  
HETATM    8  C7  UNL     1      -1.629  -1.572  -1.788  1.00  0.00           C  
HETATM    9  C8  UNL     1      -2.758  -2.247  -2.252  1.00  0.00           C  
HETATM   10  C9  UNL     1      -3.960  -2.189  -1.533  1.00  0.00           C  
HETATM   11  C10 UNL     1      -4.040  -1.462  -0.357  1.00  0.00           C  
HETATM   12  C11 UNL     1      -2.945  -0.776   0.142  1.00  0.00           C  
HETATM   13  C12 UNL     1      -3.288  -0.096   1.385  1.00  0.00           C  
HETATM   14  O1  UNL     1      -2.310   0.667   2.034  1.00  0.00           O  
HETATM   15  C13 UNL     1      -1.239   1.425   1.536  1.00  0.00           C  
HETATM   16  C14 UNL     1      -0.979   2.612   2.111  1.00  0.00           C  
HETATM   17  C15 UNL     1       0.072   3.408   1.644  1.00  0.00           C  
HETATM   18  C16 UNL     1       0.864   2.972   0.569  1.00  0.00           C  
HETATM   19  C17 UNL     1       0.618   1.759  -0.040  1.00  0.00           C  
HETATM   20  C18 UNL     1      -0.424   1.047   0.484  1.00  0.00           C  
HETATM   21  H1  UNL     1       4.321  -0.581   1.427  1.00  0.00           H  
HETATM   22  H2  UNL     1       4.576  -1.759   0.020  1.00  0.00           H  
HETATM   23  H3  UNL     1       5.811  -0.565   0.456  1.00  0.00           H  
HETATM   24  H4  UNL     1       4.037   1.144  -0.159  1.00  0.00           H  
HETATM   25  H5  UNL     1       2.793   0.234  -2.084  1.00  0.00           H  
HETATM   26  H6  UNL     1       3.190  -1.368  -1.508  1.00  0.00           H  
HETATM   27  H7  UNL     1       2.321  -1.281   0.447  1.00  0.00           H  
HETATM   28  H8  UNL     1       2.025   0.218   0.784  1.00  0.00           H  
HETATM   29  H9  UNL     1       0.506  -1.832  -0.984  1.00  0.00           H  
HETATM   30  H10 UNL     1      -0.684  -1.562  -2.300  1.00  0.00           H  
HETATM   31  H11 UNL     1      -2.676  -2.801  -3.163  1.00  0.00           H  
HETATM   32  H12 UNL     1      -4.843  -2.722  -1.905  1.00  0.00           H  
HETATM   33  H13 UNL     1      -5.006  -1.466   0.142  1.00  0.00           H  
HETATM   34  H14 UNL     1      -4.169   0.553   1.198  1.00  0.00           H  
HETATM   35  H15 UNL     1      -3.651  -0.871   2.116  1.00  0.00           H  
HETATM   36  H16 UNL     1      -1.613   2.923   2.941  1.00  0.00           H  
HETATM   37  H17 UNL     1       0.249   4.358   2.137  1.00  0.00           H  
HETATM   38  H18 UNL     1       1.672   3.594   0.216  1.00  0.00           H  
HETATM   39  H19 UNL     1       1.156   1.477  -0.899  1.00  0.00           H  
CONECT    1    2   21   22   23
CONECT    2    3   24
CONECT    3    4   25   26
CONECT    4    5   27   28
CONECT    5    6    6   29
CONECT    6    7   20
CONECT    7    8    8   12
CONECT    8    9   30
CONECT    9   10   10   31
CONECT   10   11   32
CONECT   11   12   12   33
CONECT   12   13
CONECT   13   14   34   35
CONECT   14   15
CONECT   15   16   16   20
CONECT   16   17   36
CONECT   17   18   18   37
CONECT   18   19   38
CONECT   19   20   20   39
END

HMDB0060840
     RDKit          3D
N-Desmethyldoxepin
 39 41  0  0  0  0  0  0  0  0999 V2000
    4.7147   -0.7298    0.4151 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1706    0.1910   -0.5673 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.9605   -0.3405   -1.1765 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8969   -0.3609   -0.1430 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5796   -0.8698   -0.4886 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5139   -0.2414   -0.2259 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8037   -0.8888   -0.6300 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6288   -1.5717   -1.7883 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7580   -2.2474   -2.2521 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9599   -2.1893   -1.5330 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0399   -1.4618   -0.3569 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9451   -0.7757    0.1422 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2883   -0.0964    1.3846 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3103    0.6668    2.0337 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2391    1.4248    1.5357 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9795    2.6121    2.1113 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0724    3.4080    1.6444 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8636    2.9723    0.5686 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6177    1.7586   -0.0402 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4236    1.0475    0.4843 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3206   -0.5812    1.4270 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5764   -1.7592    0.0199 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8112   -0.5653    0.4564 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0369    1.1438   -0.1593 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7927    0.2344   -2.0836 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1904   -1.3683   -1.5078 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3213   -1.2805    0.4466 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0245    0.2179    0.7836 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5061   -1.8320   -0.9835 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6838   -1.5618   -2.2999 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6755   -2.8011   -3.1629 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8429   -2.7216   -1.9053 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0059   -1.4657    0.1421 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1687    0.5526    1.1982 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6514   -0.8711    2.1156 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6133    2.9228    2.9414 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2485    4.3582    2.1368 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6716    3.5938    0.2157 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1555    1.4767   -0.8992 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  2  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  2  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  2  0
 16 17  1  0
 17 18  2  0
 18 19  1  0
 19 20  2  0
 20  6  1  0
 12  7  1  0
 20 15  1  0
  1 21  1  0
  1 22  1  0
  1 23  1  0
  2 24  1  0
  3 25  1  0
  3 26  1  0
  4 27  1  0
  4 28  1  0
  5 29  1  0
  8 30  1  0
  9 31  1  0
 10 32  1  0
 11 33  1  0
 13 34  1  0
 13 35  1  0
 16 36  1  0
 17 37  1  0
 18 38  1  0
 19 39  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
(Z)-N-Desmethyldoxepin	ChEBI
cis-Desmethyldoxepin	ChEBI
cis-N-Desmethyldoxepin	ChEBI
Demethyldoxepin	HMDB
Desmethyldoxepin, (e)-isomer	HMDB
Nordoxepin	HMDB
Desmethyldoxepin	HMDB
Desmethyldoxepin hydrochloride	HMDB
Desmethyldoxepin, (Z)-isomer	HMDB

Chemical Formula

C₁₈H₁₉NO

Average Molecular Weight

265.3496

Monoisotopic Molecular Weight

265.146664235

IUPAC Name

methyl({3-[(2Z)-9-oxatricyclo[9.4.0.0³,⁸]pentadeca-1(11),3(8),4,6,12,14-hexaen-2-ylidene]propyl})amine

Traditional Name

methyl({3-[(2Z)-9-oxatricyclo[9.4.0.0³,⁸]pentadeca-1(11),3(8),4,6,12,14-hexaen-2-ylidene]propyl})amine

CAS Registry Number

58534-46-6

SMILES

CNCC\C=C1\C2=C(COC3=C1C=CC=C3)C=CC=C2

InChI Identifier

InChI=1S/C18H19NO/c1-19-12-6-10-16-15-8-3-2-7-14(15)13-20-18-11-5-4-9-17(16)18/h2-5,7-11,19H,6,12-13H2,1H3/b16-10-

InChI Key

HVKCEFHNSNZIHO-YBEGLDIGSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as dibenzoxepines. Dibenzoxepines are compounds containing a dibenzoxepine moiety, which consists of two benzene connected by an oxazepine ring.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Benzoxepines

Sub Class

Dibenzoxepines

Direct Parent

Dibenzoxepines

Alternative Parents

Substituents

Dibenzoxepine
Alkyl aryl ether
Benzenoid
Oxacycle
Secondary amine
Ether
Secondary aliphatic amine
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Amine
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (HMDB: HMDB0060840)

Organ

Kidney (HMDB: HMDB0060840)
Liver (HMDB: HMDB0060840)

Excreta

Biofluid or Excreta

Urine (HMDB: HMDB0060840)

Cellular substructure

Cytoplasm (HMDB: HMDB0060840)
Membrane (HMDB: HMDB0060840)

Source

Endogenous

Endogenous (HMDB: HMDB0060840)

Process

Naturally occurring process

Biological process

Biochemical pathway

Metabolic pathway

Doxepin Metabolism Pathway (PathBank: SMP0000641)

Role

Not Available

Physical Properties

State

Not Available

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	0.0036 g/L	ALOGPS
logP	3.75	ALOGPS
logP	3.46	ChemAxon
logS	-4.9	ALOGPS
pKa (Strongest Basic)	10.47	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	21.26 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	92.95 m³·mol⁻¹	ChemAxon
Polarizability	30.87 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DarkChem	[M+H]+	164.937	31661259
DarkChem	[M-H]-	164.496	31661259
DeepCCS	[M+H]+	168.912	30932474
DeepCCS	[M-H]-	166.554	30932474
DeepCCS	[M-2H]-	199.439	30932474
DeepCCS	[M+Na]+	175.005	30932474
AllCCS	[M+H]+	162.8	32859911
AllCCS	[M+H-H2O]+	159.0	32859911
AllCCS	[M+NH4]+	166.3	32859911
AllCCS	[M+Na]+	167.3	32859911
AllCCS	[M-H]-	170.1	32859911
AllCCS	[M+Na-2H]-	169.7	32859911
AllCCS	[M+HCOO]-	169.4	32859911

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022. Predicted by Afia on May 17, 2022.	6.73 minutes	32390414
Predicted by Siyang on May 30, 2022	11.8127 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	2.88 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	1524.6 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	282.9 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	167.0 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	193.8 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	116.4 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	418.2 seconds	40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid	446.0 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	409.1 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	1038.4 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	415.4 seconds	40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid	1180.5 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	292.4 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	329.4 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	347.0 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	342.3 seconds	40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water	25.2 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
N-Desmethyldoxepin	CNCC\C=C1\C2=C(COC3=C1C=CC=C3)C=CC=C2	3310.0	Standard polar	33892256
N-Desmethyldoxepin	CNCC\C=C1\C2=C(COC3=C1C=CC=C3)C=CC=C2	2248.6	Standard non polar	33892256
N-Desmethyldoxepin	CNCC\C=C1\C2=C(COC3=C1C=CC=C3)C=CC=C2	2203.3	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
N-Desmethyldoxepin,1TMS,isomer #1	CN(CC/C=C1/C2=CC=CC=C2COC2=CC=CC=C12)[Si](C)(C)C	2514.3	Semi standard non polar	33892256
N-Desmethyldoxepin,1TMS,isomer #1	CN(CC/C=C1/C2=CC=CC=C2COC2=CC=CC=C12)[Si](C)(C)C	2442.6	Standard non polar	33892256
N-Desmethyldoxepin,1TMS,isomer #1	CN(CC/C=C1/C2=CC=CC=C2COC2=CC=CC=C12)[Si](C)(C)C	3125.4	Standard polar	33892256
N-Desmethyldoxepin,1TBDMS,isomer #1	CN(CC/C=C1/C2=CC=CC=C2COC2=CC=CC=C12)[Si](C)(C)C(C)(C)C	2726.6	Semi standard non polar	33892256
N-Desmethyldoxepin,1TBDMS,isomer #1	CN(CC/C=C1/C2=CC=CC=C2COC2=CC=CC=C12)[Si](C)(C)C(C)(C)C	2688.6	Standard non polar	33892256
N-Desmethyldoxepin,1TBDMS,isomer #1	CN(CC/C=C1/C2=CC=CC=C2COC2=CC=CC=C12)[Si](C)(C)C(C)(C)C	3223.2	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - N-Desmethyldoxepin GC-MS (Non-derivatized) - 70eV, Positive	splash10-0006-9140000000-c82077a7c3bebcc3a7e0	2017-09-20	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - N-Desmethyldoxepin GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - N-Desmethyldoxepin GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - N-Desmethyldoxepin 10V, Positive-QTOF	splash10-014r-0090000000-640c381a8a220acdd6a1	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - N-Desmethyldoxepin 20V, Positive-QTOF	splash10-00kr-3190000000-3445698d3595ed148808	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - N-Desmethyldoxepin 40V, Positive-QTOF	splash10-0f6x-9640000000-6a82b8594aa1a9414304	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - N-Desmethyldoxepin 10V, Negative-QTOF	splash10-03di-0090000000-681052c04b852a0c46fd	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - N-Desmethyldoxepin 20V, Negative-QTOF	splash10-03di-1090000000-c550628b634c6901a259	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - N-Desmethyldoxepin 40V, Negative-QTOF	splash10-053u-6190000000-5edfe7c7acd231e3e5e2	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - N-Desmethyldoxepin 10V, Positive-QTOF	splash10-014i-0090000000-2553ba0c11b34cc0d04f	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - N-Desmethyldoxepin 20V, Positive-QTOF	splash10-000i-0090000000-2e7069eda57ac81a98ea	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - N-Desmethyldoxepin 40V, Positive-QTOF	splash10-0a4u-1790000000-7dec2de1219ffc1c73d1	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - N-Desmethyldoxepin 10V, Negative-QTOF	splash10-03di-0090000000-1f4e1c77bccde6d52d61	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - N-Desmethyldoxepin 20V, Negative-QTOF	splash10-03di-0090000000-cb241f7ffb9f6ff94715	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - N-Desmethyldoxepin 40V, Negative-QTOF	splash10-014l-0390000000-030b383262d83abcb536	2021-10-12	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Cytoplasm
Membrane (predicted from logP)

Biospecimen Locations

Blood
Urine

Tissue Locations

Kidney
Liver

Pathways

Name	SMPDB/PathBank	KEGG
Doxepin Metabolism Pathway		Not Available

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Expected but not Quantified	Not Quantified	Not Available	Not Available	Normal	Not Available	details
Urine	Expected but not Quantified	Not Quantified	Not Available	Not Available	Normal	Not Available	details

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

4510230

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Nordoxepin

METLIN ID

Not Available

PubChem Compound

5353833

PDB ID

Not Available

ChEBI ID

142339

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Not Available

Showing metabocard for N-Desmethyldoxepin (HMDB0060840)

MOL for HMDB0060840 (N-Desmethyldoxepin)

3D MOL for HMDB0060840 (N-Desmethyldoxepin)

3D SDF for HMDB0060840 (N-Desmethyldoxepin)

3D-SDF for HMDB0060840 (N-Desmethyldoxepin)

PDB for HMDB0060840 (N-Desmethyldoxepin)

3D PDB for HMDB0060840 (N-Desmethyldoxepin)

SMILES for HMDB0060840 (N-Desmethyldoxepin)

INCHI for HMDB0060840 (N-Desmethyldoxepin)

Structure for HMDB0060840 (N-Desmethyldoxepin)

3D Structure for HMDB0060840 (N-Desmethyldoxepin)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra