Jump To Section:

Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References XML

Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2013-07-09 16:08:55 UTC

Update Date

2019-07-23 07:15:26 UTC

HMDB ID

HMDB0060947

Secondary Accession Numbers

HMDB60947

Metabolite Identification

Common Name

desmethylclomipramine

Description

desmethylclomipramine belongs to the class of organic compounds known as dibenzazepines. Dibenzazepines are compounds with two benzene rings connected by an azepine ring. Azepine is an unsaturated seven-member heterocycle with one nitrogen atom replacing a carbon atom. Based on a literature review a significant number of articles have been published on desmethylclomipramine.

Structure

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

HMDB0060947
     RDKit          3D
desmethylclomipramine
 42 44  0  0  0  0  0  0  0  0999 V2000
    5.0586   -1.3030    1.1813 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6608   -1.3083    0.7914 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.5146   -0.3639   -0.2805 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0441   -0.3086   -0.7572 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1238    0.0938    0.3038 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2741    0.2136    0.1080 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1111   -0.9266    0.3826 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125   -2.0992    0.4172 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0485   -3.2898    0.6838 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4063   -3.3373    0.9238 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1345   -2.1584    0.8936 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4895   -0.9795    0.6269 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4027    0.1624    0.6297 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3655    0.9307   -0.6484 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1431    1.7732   -0.6979 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4402    3.0484   -1.1529 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4308    3.9592   -1.2785 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1387    3.6786   -0.9784 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1753    4.7968   -1.1207 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    0.1604    2.3882   -0.5181 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8115    1.4381   -0.3731 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1141   -1.5630    2.2574 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5586   -2.0851    0.5475 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4738   -0.2973    0.9752 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3664   -2.2528    0.4448 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6770    0.6573    0.1776 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2159   -0.4504   -1.0957 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9536   -1.2713   -1.2729 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9826    0.4325   -1.6155 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6149    0.9326    0.8962 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2352   -0.6286    1.2306 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6045   -2.0907    0.2450 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4849   -4.2410    0.7123 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9074   -4.2498    1.1306 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1810   -2.2156    1.0814 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4583   -0.1940    0.7712 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2013    0.8744    1.4618 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2493    1.6023   -0.6626 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4596    0.2839   -1.5425 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4736    3.2667   -1.3912 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6771    4.9505   -1.6345 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1674    2.1307   -0.2821 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  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
 18 20  1  0
 20 21  2  0
 21  6  1  0
 12  7  1  0
 21 15  1  0
  1 22  1  0
  1 23  1  0
  1 24  1  0
  2 25  1  0
  3 26  1  0
  3 27  1  0
  4 28  1  0
  4 29  1  0
  5 30  1  0
  5 31  1  0
  8 32  1  0
  9 33  1  0
 10 34  1  0
 11 35  1  0
 13 36  1  0
 13 37  1  0
 14 38  1  0
 14 39  1  0
 16 40  1  0
 17 41  1  0
 20 42  1  0
M  END


  Mrv0541 07091309082D          

 21 23  0  0  0  0            999 V2000
    1.8649    2.3229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.3285    1.1483    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5401    0.9052    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0083    2.7354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.5120    1.9527    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9354    1.4663    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2087    3.2818    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7962    3.9962    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7968    4.9235    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0085    5.1667    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2939    2.3229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7228    2.3229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5873    3.8012    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9073    2.5138    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9804    4.1192    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4037    4.6055    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1189    2.2706    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3756    3.5581    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6154    4.8487    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    2.5794    2.7354    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.4373    2.7354    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  2  0  0  0  0
  5  2  1  0  0  0  0
  6  3  1  0  0  0  0
  8  7  1  0  0  0  0
 10  9  2  0  0  0  0
 11  4  1  0  0  0  0
 12  4  1  0  0  0  0
 14  5  2  0  0  0  0
 14  7  1  0  0  0  0
 15  8  1  0  0  0  0
 15  9  1  0  0  0  0
 16 10  1  0  0  0  0
 16 13  2  0  0  0  0
 17  6  2  0  0  0  0
 17 14  1  0  0  0  0
 18 13  1  0  0  0  0
 18 15  2  0  0  0  0
 19 16  1  0  0  0  0
 20  1  1  0  0  0  0
 20 11  1  0  0  0  0
 21 12  1  0  0  0  0
 21 17  1  0  0  0  0
 21 18  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0060947

> <DATABASE_NAME>
hmdb

> <SMILES>
CNCCCN1C2=CC=CC=C2CCC2=C1C=C(Cl)C=C2

> <INCHI_IDENTIFIER>
InChI=1S/C18H21ClN2/c1-20-11-4-12-21-17-6-3-2-5-14(17)7-8-15-9-10-16(19)13-18(15)21/h2-3,5-6,9-10,13,20H,4,7-8,11-12H2,1H3

> <INCHI_KEY>
VPIXQGUBUKFLRF-UHFFFAOYSA-N

> <FORMULA>
C18H21ClN2

> <MOLECULAR_WEIGHT>
300.826

> <EXACT_MASS>
300.139326389

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_AVERAGE_POLARIZABILITY>
34.34936707244567

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(3-{14-chloro-2-azatricyclo[9.4.0.0³,⁸]pentadeca-1(11),3,5,7,12,14-hexaen-2-yl}propyl)(methyl)amine

> <ALOGPS_LOGP>
4.43

> <JCHEM_LOGP>
4.499565533333333

> <ALOGPS_LOGS>
-4.51

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_BASIC>
10.018711765100768

> <JCHEM_POLAR_SURFACE_AREA>
15.27

> <JCHEM_REFRACTIVITY>
90.11569999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
9.33e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(3-{14-chloro-2-azatricyclo[9.4.0.0³,⁸]pentadeca-1(11),3,5,7,12,14-hexaen-2-yl}propyl)(methyl)amine

> <JCHEM_VEBER_RULE>
1

$$$$

HMDB0060947
     RDKit          3D
desmethylclomipramine
 42 44  0  0  0  0  0  0  0  0999 V2000
    5.0586   -1.3030    1.1813 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6608   -1.3083    0.7914 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.5146   -0.3639   -0.2805 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0441   -0.3086   -0.7572 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1238    0.0938    0.3038 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2741    0.2136    0.1080 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1111   -0.9266    0.3826 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125   -2.0992    0.4172 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0485   -3.2898    0.6838 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4063   -3.3373    0.9238 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1345   -2.1584    0.8936 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4895   -0.9795    0.6269 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4027    0.1624    0.6297 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3655    0.9307   -0.6484 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1431    1.7732   -0.6979 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4402    3.0484   -1.1529 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4308    3.9592   -1.2785 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1387    3.6786   -0.9784 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1753    4.7968   -1.1207 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    0.1604    2.3882   -0.5181 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8115    1.4381   -0.3731 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1141   -1.5630    2.2574 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5586   -2.0851    0.5475 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4738   -0.2973    0.9752 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3664   -2.2528    0.4448 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6770    0.6573    0.1776 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2159   -0.4504   -1.0957 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9536   -1.2713   -1.2729 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9826    0.4325   -1.6155 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6149    0.9326    0.8962 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2352   -0.6286    1.2306 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6045   -2.0907    0.2450 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4849   -4.2410    0.7123 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9074   -4.2498    1.1306 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1810   -2.2156    1.0814 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4583   -0.1940    0.7712 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2013    0.8744    1.4618 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2493    1.6023   -0.6626 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4596    0.2839   -1.5425 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4736    3.2667   -1.3912 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6771    4.9505   -1.6345 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1674    2.1307   -0.2821 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  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
 18 20  1  0
 20 21  2  0
 21  6  1  0
 12  7  1  0
 21 15  1  0
  1 22  1  0
  1 23  1  0
  1 24  1  0
  2 25  1  0
  3 26  1  0
  3 27  1  0
  4 28  1  0
  4 29  1  0
  5 30  1  0
  5 31  1  0
  8 32  1  0
  9 33  1  0
 10 34  1  0
 11 35  1  0
 13 36  1  0
 13 37  1  0
 14 38  1  0
 14 39  1  0
 16 40  1  0
 17 41  1  0
 20 42  1  0
M  END

HEADER    PROTEIN                                 09-JUL-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   09-JUL-13         0                                  
HETATM    1  C   UNK     0       3.481   4.336   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      13.680   2.143   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      12.208   1.690   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       7.482   5.106   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      14.022   3.645   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      11.079   2.737   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      13.456   6.126   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      12.686   7.460   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      10.821   9.191   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       9.349   9.645   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       6.149   4.336   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       8.816   4.336   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       8.563   7.096   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      12.894   4.692   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      11.163   7.689   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       8.220   8.597   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      11.422   4.238   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      10.034   6.642   0.000  0.00  0.00           C+0
HETATM   19 Cl   UNK     0       6.749   9.051   0.000  0.00  0.00          Cl+0
HETATM   20  N   UNK     0       4.815   5.106   0.000  0.00  0.00           N+0
HETATM   21  N   UNK     0      10.150   5.106   0.000  0.00  0.00           N+0
CONECT    1   20                                                            
CONECT    2    3    5                                                       
CONECT    3    2    6                                                       
CONECT    4   11   12                                                       
CONECT    5    2   14                                                       
CONECT    6    3   17                                                       
CONECT    7    8   14                                                       
CONECT    8    7   15                                                       
CONECT    9   10   15                                                       
CONECT   10    9   16                                                       
CONECT   11    4   20                                                       
CONECT   12    4   21                                                       
CONECT   13   16   18                                                       
CONECT   14    5    7   17                                                  
CONECT   15    8    9   18                                                  
CONECT   16   10   13   19                                                  
CONECT   17    6   14   21                                                  
CONECT   18   13   15   21                                                  
CONECT   19   16                                                            
CONECT   20    1   11                                                       
CONECT   21   12   17   18                                                  
MASTER        0    0    0    0    0    0    0    0   21    0   46    0
END

COMPND    HMDB0060947
HETATM    1  C1  UNL     1       5.059  -1.303   1.181  1.00  0.00           C  
HETATM    2  N1  UNL     1       3.661  -1.308   0.791  1.00  0.00           N  
HETATM    3  C2  UNL     1       3.515  -0.364  -0.281  1.00  0.00           C  
HETATM    4  C3  UNL     1       2.044  -0.309  -0.757  1.00  0.00           C  
HETATM    5  C4  UNL     1       1.124   0.094   0.304  1.00  0.00           C  
HETATM    6  N2  UNL     1      -0.274   0.214   0.108  1.00  0.00           N  
HETATM    7  C5  UNL     1      -1.111  -0.927   0.383  1.00  0.00           C  
HETATM    8  C6  UNL     1      -0.413  -2.099   0.417  1.00  0.00           C  
HETATM    9  C7  UNL     1      -1.049  -3.290   0.684  1.00  0.00           C  
HETATM   10  C8  UNL     1      -2.406  -3.337   0.924  1.00  0.00           C  
HETATM   11  C9  UNL     1      -3.135  -2.158   0.894  1.00  0.00           C  
HETATM   12  C10 UNL     1      -2.490  -0.980   0.627  1.00  0.00           C  
HETATM   13  C11 UNL     1      -3.403   0.162   0.630  1.00  0.00           C  
HETATM   14  C12 UNL     1      -3.366   0.931  -0.648  1.00  0.00           C  
HETATM   15  C13 UNL     1      -2.143   1.773  -0.698  1.00  0.00           C  
HETATM   16  C14 UNL     1      -2.440   3.048  -1.153  1.00  0.00           C  
HETATM   17  C15 UNL     1      -1.431   3.959  -1.278  1.00  0.00           C  
HETATM   18  C16 UNL     1      -0.139   3.679  -0.978  1.00  0.00           C  
HETATM   19 CL1  UNL     1       1.175   4.797  -1.121  1.00  0.00          CL  
HETATM   20  C17 UNL     1       0.160   2.388  -0.518  1.00  0.00           C  
HETATM   21  C18 UNL     1      -0.811   1.438  -0.373  1.00  0.00           C  
HETATM   22  H1  UNL     1       5.114  -1.563   2.257  1.00  0.00           H  
HETATM   23  H2  UNL     1       5.559  -2.085   0.547  1.00  0.00           H  
HETATM   24  H3  UNL     1       5.474  -0.297   0.975  1.00  0.00           H  
HETATM   25  H4  UNL     1       3.366  -2.253   0.445  1.00  0.00           H  
HETATM   26  H5  UNL     1       3.677   0.657   0.178  1.00  0.00           H  
HETATM   27  H6  UNL     1       4.216  -0.450  -1.096  1.00  0.00           H  
HETATM   28  H7  UNL     1       1.954  -1.271  -1.273  1.00  0.00           H  
HETATM   29  H8  UNL     1       1.983   0.433  -1.615  1.00  0.00           H  
HETATM   30  H9  UNL     1       1.615   0.933   0.896  1.00  0.00           H  
HETATM   31  H10 UNL     1       1.235  -0.629   1.231  1.00  0.00           H  
HETATM   32  H11 UNL     1       0.604  -2.091   0.245  1.00  0.00           H  
HETATM   33  H12 UNL     1      -0.485  -4.241   0.712  1.00  0.00           H  
HETATM   34  H13 UNL     1      -2.907  -4.250   1.131  1.00  0.00           H  
HETATM   35  H14 UNL     1      -4.181  -2.216   1.081  1.00  0.00           H  
HETATM   36  H15 UNL     1      -4.458  -0.194   0.771  1.00  0.00           H  
HETATM   37  H16 UNL     1      -3.201   0.874   1.462  1.00  0.00           H  
HETATM   38  H17 UNL     1      -4.249   1.602  -0.663  1.00  0.00           H  
HETATM   39  H18 UNL     1      -3.460   0.284  -1.542  1.00  0.00           H  
HETATM   40  H19 UNL     1      -3.474   3.267  -1.391  1.00  0.00           H  
HETATM   41  H20 UNL     1      -1.677   4.951  -1.635  1.00  0.00           H  
HETATM   42  H21 UNL     1       1.167   2.131  -0.282  1.00  0.00           H  
CONECT    1    2   22   23   24
CONECT    2    3   25
CONECT    3    4   26   27
CONECT    4    5   28   29
CONECT    5    6   30   31
CONECT    6    7   21
CONECT    7    8    8   12
CONECT    8    9   32
CONECT    9   10   10   33
CONECT   10   11   34
CONECT   11   12   12   35
CONECT   12   13
CONECT   13   14   36   37
CONECT   14   15   38   39
CONECT   15   16   16   21
CONECT   16   17   40
CONECT   17   18   18   41
CONECT   18   19   20
CONECT   20   21   21   42
END

HMDB0060947
     RDKit          3D
desmethylclomipramine
 42 44  0  0  0  0  0  0  0  0999 V2000
    5.0586   -1.3030    1.1813 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6608   -1.3083    0.7914 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.5146   -0.3639   -0.2805 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0441   -0.3086   -0.7572 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1238    0.0938    0.3038 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2741    0.2136    0.1080 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1111   -0.9266    0.3826 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125   -2.0992    0.4172 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0485   -3.2898    0.6838 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4063   -3.3373    0.9238 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1345   -2.1584    0.8936 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4895   -0.9795    0.6269 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4027    0.1624    0.6297 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3655    0.9307   -0.6484 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1431    1.7732   -0.6979 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4402    3.0484   -1.1529 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4308    3.9592   -1.2785 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1387    3.6786   -0.9784 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1753    4.7968   -1.1207 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    0.1604    2.3882   -0.5181 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8115    1.4381   -0.3731 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1141   -1.5630    2.2574 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5586   -2.0851    0.5475 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4738   -0.2973    0.9752 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3664   -2.2528    0.4448 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6770    0.6573    0.1776 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2159   -0.4504   -1.0957 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9536   -1.2713   -1.2729 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9826    0.4325   -1.6155 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6149    0.9326    0.8962 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2352   -0.6286    1.2306 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6045   -2.0907    0.2450 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4849   -4.2410    0.7123 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9074   -4.2498    1.1306 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1810   -2.2156    1.0814 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4583   -0.1940    0.7712 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2013    0.8744    1.4618 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2493    1.6023   -0.6626 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4596    0.2839   -1.5425 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4736    3.2667   -1.3912 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6771    4.9505   -1.6345 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1674    2.1307   -0.2821 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  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
 18 20  1  0
 20 21  2  0
 21  6  1  0
 12  7  1  0
 21 15  1  0
  1 22  1  0
  1 23  1  0
  1 24  1  0
  2 25  1  0
  3 26  1  0
  3 27  1  0
  4 28  1  0
  4 29  1  0
  5 30  1  0
  5 31  1  0
  8 32  1  0
  9 33  1  0
 10 34  1  0
 11 35  1  0
 13 36  1  0
 13 37  1  0
 14 38  1  0
 14 39  1  0
 16 40  1  0
 17 41  1  0
 20 42  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
N-Demethylclomipramine	HMDB
Desmethylclomipramine hydrochloride	HMDB
Demethylchlorimipramine	HMDB
Desmethylchlorimipramine	HMDB

Chemical Formula

C₁₈H₂₁ClN₂

Average Molecular Weight

300.826

Monoisotopic Molecular Weight

300.139326389

IUPAC Name

(3-{14-chloro-2-azatricyclo[9.4.0.0³,⁸]pentadeca-1(11),3,5,7,12,14-hexaen-2-yl}propyl)(methyl)amine

Traditional Name

(3-{14-chloro-2-azatricyclo[9.4.0.0³,⁸]pentadeca-1(11),3,5,7,12,14-hexaen-2-yl}propyl)(methyl)amine

CAS Registry Number

303-48-0

SMILES

CNCCCN1C2=CC=CC=C2CCC2=C1C=C(Cl)C=C2

InChI Identifier

InChI=1S/C18H21ClN2/c1-20-11-4-12-21-17-6-3-2-5-14(17)7-8-15-9-10-16(19)13-18(15)21/h2-3,5-6,9-10,13,20H,4,7-8,11-12H2,1H3

InChI Key

VPIXQGUBUKFLRF-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as dibenzazepines. Dibenzazepines are compounds with two benzene rings connected by an azepine ring. Azepine is an unsaturated seven-member heterocycle with one nitrogen atom replacing a carbon atom.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Benzazepines

Sub Class

Dibenzazepines

Direct Parent

Dibenzazepines

Alternative Parents

Substituents

Dibenzazepine
Alkyldiarylamine
Tertiary aliphatic/aromatic amine
Azepine
Aryl chloride
Aryl halide
Benzenoid
Tertiary amine
Secondary amine
Secondary aliphatic amine
Azacycle
Hydrocarbon derivative
Organonitrogen compound
Organochloride
Organohalogen compound
Organopnictogen compound
Organic nitrogen 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: HMDB0060947)

Organ

Kidney (HMDB: HMDB0060947)
Liver (HMDB: HMDB0060947)

Excreta

Biofluid or Excreta

Urine (HMDB: HMDB0060947)

Cellular substructure

Cytoplasm (HMDB: HMDB0060947)
Membrane (HMDB: HMDB0060947)

Source

Endogenous

Endogenous (HMDB: HMDB0060947)

Process

Naturally occurring process

Biological process

Biochemical pathway

Metabolic pathway

Clomipramine Metabolism Pathway (PathBank: SMP0000639)

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	0.0093 g/L	ALOGPS
logP	4.43	ALOGPS
logP	4.5	ChemAxon
logS	-4.5	ALOGPS
pKa (Strongest Basic)	10.02	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	15.27 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	90.12 m³·mol⁻¹	ChemAxon
Polarizability	34.35 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
DeepCCS	[M+H]+	166.626	30932474
DeepCCS	[M-H]-	164.268	30932474
DeepCCS	[M-2H]-	197.153	30932474
DeepCCS	[M+Na]+	172.719	30932474
AllCCS	[M+H]+	170.3	32859911
AllCCS	[M+H-H2O]+	166.8	32859911
AllCCS	[M+NH4]+	173.5	32859911
AllCCS	[M+Na]+	174.4	32859911
AllCCS	[M-H]-	176.3	32859911
AllCCS	[M+Na-2H]-	176.0	32859911
AllCCS	[M+HCOO]-	175.8	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.	6.72 minutes	32390414
Predicted by Siyang on May 30, 2022	13.3375 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	2.75 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	1612.0 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	331.7 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	179.2 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	196.1 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	134.4 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	459.9 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	425.8 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	221.4 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	1265.6 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	509.2 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	1335.6 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	339.0 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	354.5 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	300.1 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	128.2 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	7.9 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
desmethylclomipramine	CNCCCN1C2=CC=CC=C2CCC2=C1C=C(Cl)C=C2	3641.7	Standard polar	33892256
desmethylclomipramine	CNCCCN1C2=CC=CC=C2CCC2=C1C=C(Cl)C=C2	2448.7	Standard non polar	33892256
desmethylclomipramine	CNCCCN1C2=CC=CC=C2CCC2=C1C=C(Cl)C=C2	2421.6	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
desmethylclomipramine,1TMS,isomer #1	CN(CCCN1C2=CC=CC=C2CCC2=CC=C(Cl)C=C21)[Si](C)(C)C	2587.9	Semi standard non polar	33892256
desmethylclomipramine,1TMS,isomer #1	CN(CCCN1C2=CC=CC=C2CCC2=CC=C(Cl)C=C21)[Si](C)(C)C	2797.9	Standard non polar	33892256
desmethylclomipramine,1TMS,isomer #1	CN(CCCN1C2=CC=CC=C2CCC2=CC=C(Cl)C=C21)[Si](C)(C)C	3242.9	Standard polar	33892256
desmethylclomipramine,1TBDMS,isomer #1	CN(CCCN1C2=CC=CC=C2CCC2=CC=C(Cl)C=C21)[Si](C)(C)C(C)(C)C	2805.8	Semi standard non polar	33892256
desmethylclomipramine,1TBDMS,isomer #1	CN(CCCN1C2=CC=CC=C2CCC2=CC=C(Cl)C=C21)[Si](C)(C)C(C)(C)C	3095.9	Standard non polar	33892256
desmethylclomipramine,1TBDMS,isomer #1	CN(CCCN1C2=CC=CC=C2CCC2=CC=C(Cl)C=C21)[Si](C)(C)C(C)(C)C	3348.1	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - desmethylclomipramine GC-MS (Non-derivatized) - 70eV, Positive	splash10-0006-6090000000-9eed19a2ef45fc520c90	2017-09-20	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - desmethylclomipramine GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - desmethylclomipramine 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 - desmethylclomipramine 10V, Positive-QTOF	splash10-0uk9-1069000000-86dede74ad37de04b372	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - desmethylclomipramine 20V, Positive-QTOF	splash10-00dl-6093000000-595de34abeb5c6686672	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - desmethylclomipramine 40V, Positive-QTOF	splash10-0006-9240000000-ac7e79f4ac427320c754	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - desmethylclomipramine 10V, Negative-QTOF	splash10-0002-0090000000-f1e765f5a26c70ab77d7	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - desmethylclomipramine 20V, Negative-QTOF	splash10-002b-1090000000-1ddc75254b4387dae329	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - desmethylclomipramine 40V, Negative-QTOF	splash10-0fbc-2390000000-bb1e61bf6aeb82c055f0	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - desmethylclomipramine 10V, Positive-QTOF	splash10-0udi-2009000000-c20e525f00993d151f84	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - desmethylclomipramine 20V, Positive-QTOF	splash10-0fk9-4095000000-6701457843879edd44f4	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - desmethylclomipramine 40V, Positive-QTOF	splash10-0096-9040000000-fdf055a6b5c0574ca702	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - desmethylclomipramine 10V, Negative-QTOF	splash10-0002-0090000000-228c0f7f447a837fde13	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - desmethylclomipramine 20V, Negative-QTOF	splash10-002b-0090000000-0c7b194f8eae2f796bbd	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - desmethylclomipramine 40V, Negative-QTOF	splash10-004i-2090000000-e19659de1a99730937fb	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
Clomipramine 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

540947

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Norclomipramine

METLIN ID

Not Available

PubChem Compound

622606

PDB ID

Not Available

ChEBI ID

124969

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 desmethylclomipramine (HMDB0060947)

MOL for HMDB0060947 (desmethylclomipramine)

3D MOL for HMDB0060947 (desmethylclomipramine)

3D SDF for HMDB0060947 (desmethylclomipramine)

3D-SDF for HMDB0060947 (desmethylclomipramine)

PDB for HMDB0060947 (desmethylclomipramine)

3D PDB for HMDB0060947 (desmethylclomipramine)

SMILES for HMDB0060947 (desmethylclomipramine)

INCHI for HMDB0060947 (desmethylclomipramine)

Structure for HMDB0060947 (desmethylclomipramine)

3D Structure for HMDB0060947 (desmethylclomipramine)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra