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

2013-06-15 17:01:38 UTC

Update Date

2019-07-23 07:14:38 UTC

HMDB ID

HMDB0060577

Secondary Accession Numbers

HMDB60577

Metabolite Identification

Common Name

Clomipramine N-oxide

Description

Clomipramine N-oxide 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. Clomipramine N-oxide is a metabolite of clomipramine. Clomipramine N-oxide is a strong basic compound (based on its pKa). It was developed in the 1960s by the Swiss drug manufacturer Geigy (now known as Novartis) and has been in clinical use worldwide ever since. Clomipramine (trademarked as Anafranil) is a tricyclic antidepressant (TCA).

Structure

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

HMDB0060577
     RDKit          3D
Clomipramine N-oxide
 46 48  0  0  0  0  0  0  0  0999 V2000
    3.4808   -0.5403   -1.4766 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6238    0.0270   -0.1516 N   0  0  0  0  0  4  0  0  0  0  0  0
    5.0320    0.4479    0.0380 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4361   -0.9353    0.7526 O   0  0  0  0  0  1  0  0  0  0  0  0
    2.8545    1.2108    0.0136 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3841    1.0912   -0.2652 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7103    0.0725    0.6555 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6839   -0.0795    0.4793 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2343   -1.4238    0.5766 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3980   -2.2355    1.2813 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7568   -3.5496    1.4537 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9408   -4.0057    0.9153 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7683   -3.1627    0.2083 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4486   -1.8105    0.0032 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4958   -1.1003   -0.7515 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1261    0.1518   -1.4420 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5300    1.2142   -0.5900 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1413    2.4471   -0.6611 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7090    3.5370    0.0672 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6160    3.3494    0.8916 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9745    4.6701    1.8699 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   -0.9719    2.1398    0.9977 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4591    1.1094    0.2448 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8220   -1.4250   -1.4112 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1275    0.1856   -2.2166 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5042   -0.9278   -1.7561 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6078   -0.4861    0.1907 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0370    0.9758    1.0224 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3745    1.0653   -0.7921 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0589    1.6980    0.9863 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2412    1.9471   -0.7516 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9133    2.0393   -0.3823 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3623    0.6862   -1.3449 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1927   -0.8642    0.2369 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0786    0.1364    1.6815 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5164   -1.8135    1.6997 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1085   -4.1897    2.0023 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1881   -5.0603    1.0759 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6978   -3.5126   -0.2163 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9152   -1.7921   -1.5220 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3120   -0.8273   -0.0095 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0733    0.5845   -1.8562 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4951   -0.0252   -2.3582 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0094    2.5638   -1.3269 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1923    4.4828    0.0008 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1123    1.9338    1.6317 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  2  5  1  0
  5  6  1  0
  6  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
 14 15  1  0
 15 16  1  0
 16 17  1  0
 17 18  2  0
 18 19  1  0
 19 20  2  0
 20 21  1  0
 20 22  1  0
 22 23  2  0
 23  8  1  0
 14  9  1  0
 23 17  1  0
  1 24  1  0
  1 25  1  0
  1 26  1  0
  3 27  1  0
  3 28  1  0
  3 29  1  0
  5 30  1  0
  5 31  1  0
  6 32  1  0
  6 33  1  0
  7 34  1  0
  7 35  1  0
 10 36  1  0
 11 37  1  0
 12 38  1  0
 13 39  1  0
 15 40  1  0
 15 41  1  0
 16 42  1  0
 16 43  1  0
 18 44  1  0
 19 45  1  0
 22 46  1  0
M  CHG  2   2   1   4  -1
M  END


  Mrv0541 06151310012D          

 23 25  0  0  0  0            999 V2000
    1.6603   -3.7578    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7872   -4.0597    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1237   -0.0260    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9401   -0.8303    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0892   -2.1078    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5189    0.5352    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1517   -1.0735    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2162    0.9370    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3912    0.9370    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0884    0.5352    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4837   -0.0260    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8037   -1.6953    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0892   -2.9328    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4556   -1.0735    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7305    0.2920    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8768    0.2920    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6673   -0.8303    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5470   -0.5123    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0604   -0.5123    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0625   -1.3914    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    3.8037   -0.8703    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.3747   -3.3453    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.9622   -2.6308    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  4  3  2  0  0  0  0
  6  3  1  0  0  0  0
  7  4  1  0  0  0  0
  9  8  1  0  0  0  0
 11 10  2  0  0  0  0
 12  5  1  0  0  0  0
 13  5  1  0  0  0  0
 15  6  2  0  0  0  0
 15  8  1  0  0  0  0
 16  9  1  0  0  0  0
 16 10  1  0  0  0  0
 17 11  1  0  0  0  0
 17 14  2  0  0  0  0
 18  7  2  0  0  0  0
 18 15  1  0  0  0  0
 19 14  1  0  0  0  0
 19 16  2  0  0  0  0
 20 17  1  0  0  0  0
 21 12  1  0  0  0  0
 21 18  1  0  0  0  0
 21 19  1  0  0  0  0
 22  1  1  0  0  0  0
 22  2  1  0  0  0  0
 22 13  1  0  0  0  0
 23 22  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0060577

> <DATABASE_NAME>
hmdb

> <SMILES>
CN(C)(=O)CCCN1C2=CC=CC=C2CCC2=C1C=C(Cl)C=C2

> <INCHI_IDENTIFIER>
InChI=1S/C19H23ClN2O/c1-22(2,23)13-5-12-21-18-7-4-3-6-15(18)8-9-16-10-11-17(20)14-19(16)21/h3-4,6-7,10-11,14H,5,8-9,12-13H2,1-2H3

> <INCHI_KEY>
ARNOTLDVJSFYBP-UHFFFAOYSA-N

> <FORMULA>
C19H23ClN2O

> <MOLECULAR_WEIGHT>
330.852

> <EXACT_MASS>
330.149891075

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_AVERAGE_POLARIZABILITY>
36.86087204455679

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <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}-N,N-dimethylpropanamine oxide

> <ALOGPS_LOGP>
1.79

> <JCHEM_LOGP>
3.7582382873333335

> <ALOGPS_LOGS>
-5.41

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
4.124307287966347

> <JCHEM_POLAR_SURFACE_AREA>
30.12

> <JCHEM_REFRACTIVITY>
97.45529999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.29e-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}-N,N-dimethylpropanamine oxide

> <JCHEM_VEBER_RULE>
1

$$$$

HMDB0060577
     RDKit          3D
Clomipramine N-oxide
 46 48  0  0  0  0  0  0  0  0999 V2000
    3.4808   -0.5403   -1.4766 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6238    0.0270   -0.1516 N   0  0  0  0  0  4  0  0  0  0  0  0
    5.0320    0.4479    0.0380 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4361   -0.9353    0.7526 O   0  0  0  0  0  1  0  0  0  0  0  0
    2.8545    1.2108    0.0136 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3841    1.0912   -0.2652 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7103    0.0725    0.6555 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6839   -0.0795    0.4793 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2343   -1.4238    0.5766 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3980   -2.2355    1.2813 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7568   -3.5496    1.4537 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9408   -4.0057    0.9153 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7683   -3.1627    0.2083 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4486   -1.8105    0.0032 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4958   -1.1003   -0.7515 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1261    0.1518   -1.4420 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5300    1.2142   -0.5900 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1413    2.4471   -0.6611 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7090    3.5370    0.0672 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6160    3.3494    0.8916 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9745    4.6701    1.8699 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   -0.9719    2.1398    0.9977 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4591    1.1094    0.2448 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8220   -1.4250   -1.4112 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1275    0.1856   -2.2166 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5042   -0.9278   -1.7561 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6078   -0.4861    0.1907 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0370    0.9758    1.0224 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3745    1.0653   -0.7921 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0589    1.6980    0.9863 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2412    1.9471   -0.7516 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9133    2.0393   -0.3823 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3623    0.6862   -1.3449 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1927   -0.8642    0.2369 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0786    0.1364    1.6815 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5164   -1.8135    1.6997 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1085   -4.1897    2.0023 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1881   -5.0603    1.0759 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6978   -3.5126   -0.2163 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9152   -1.7921   -1.5220 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3120   -0.8273   -0.0095 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0733    0.5845   -1.8562 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4951   -0.0252   -2.3582 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0094    2.5638   -1.3269 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1923    4.4828    0.0008 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1123    1.9338    1.6317 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  2  5  1  0
  5  6  1  0
  6  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
 14 15  1  0
 15 16  1  0
 16 17  1  0
 17 18  2  0
 18 19  1  0
 19 20  2  0
 20 21  1  0
 20 22  1  0
 22 23  2  0
 23  8  1  0
 14  9  1  0
 23 17  1  0
  1 24  1  0
  1 25  1  0
  1 26  1  0
  3 27  1  0
  3 28  1  0
  3 29  1  0
  5 30  1  0
  5 31  1  0
  6 32  1  0
  6 33  1  0
  7 34  1  0
  7 35  1  0
 10 36  1  0
 11 37  1  0
 12 38  1  0
 13 39  1  0
 15 40  1  0
 15 41  1  0
 16 42  1  0
 16 43  1  0
 18 44  1  0
 19 45  1  0
 22 46  1  0
M  CHG  2   2   1   4  -1
M  END

HEADER    PROTEIN                                 15-JUN-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   15-JUN-13         0                                  
HETATM    1  C   UNK     0       3.099  -7.015   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       5.203  -7.578   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      11.431  -0.049   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      11.088  -1.550   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       5.767  -3.935   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      10.302   0.999   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       9.617  -2.004   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       7.870   1.749   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       6.330   1.749   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       3.898   0.999   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       2.770  -0.049   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       7.100  -3.165   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       5.767  -5.475   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       4.584  -2.004   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       8.830   0.545   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       5.370   0.545   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       3.112  -1.550   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       8.488  -0.956   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       5.713  -0.956   0.000  0.00  0.00           C+0
HETATM   20 Cl   UNK     0       1.983  -2.597   0.000  0.00  0.00          Cl+0
HETATM   21  N   UNK     0       7.100  -1.625   0.000  0.00  0.00           N+0
HETATM   22  N   UNK     0       4.433  -6.245   0.000  0.00  0.00           N+0
HETATM   23  O   UNK     0       3.663  -4.911   0.000  0.00  0.00           O+0
CONECT    1   22                                                            
CONECT    2   22                                                            
CONECT    3    4    6                                                       
CONECT    4    3    7                                                       
CONECT    5   12   13                                                       
CONECT    6    3   15                                                       
CONECT    7    4   18                                                       
CONECT    8    9   15                                                       
CONECT    9    8   16                                                       
CONECT   10   11   16                                                       
CONECT   11   10   17                                                       
CONECT   12    5   21                                                       
CONECT   13    5   22                                                       
CONECT   14   17   19                                                       
CONECT   15    6    8   18                                                  
CONECT   16    9   10   19                                                  
CONECT   17   11   14   20                                                  
CONECT   18    7   15   21                                                  
CONECT   19   14   16   21                                                  
CONECT   20   17                                                            
CONECT   21   12   18   19                                                  
CONECT   22    1    2   13   23                                             
CONECT   23   22                                                            
MASTER        0    0    0    0    0    0    0    0   23    0   50    0
END

COMPND    HMDB0060577
HETATM    1  C1  UNL     1       3.481  -0.540  -1.477  1.00  0.00           C  
HETATM    2  N1  UNL     1       3.624   0.027  -0.152  1.00  0.00           N1+
HETATM    3  C2  UNL     1       5.032   0.448   0.038  1.00  0.00           C  
HETATM    4  O1  UNL     1       3.436  -0.935   0.753  1.00  0.00           O1-
HETATM    5  C3  UNL     1       2.854   1.211   0.014  1.00  0.00           C  
HETATM    6  C4  UNL     1       1.384   1.091  -0.265  1.00  0.00           C  
HETATM    7  C5  UNL     1       0.710   0.073   0.655  1.00  0.00           C  
HETATM    8  N2  UNL     1      -0.684  -0.079   0.479  1.00  0.00           N  
HETATM    9  C6  UNL     1      -1.234  -1.424   0.577  1.00  0.00           C  
HETATM   10  C7  UNL     1      -0.398  -2.235   1.281  1.00  0.00           C  
HETATM   11  C8  UNL     1      -0.757  -3.550   1.454  1.00  0.00           C  
HETATM   12  C9  UNL     1      -1.941  -4.006   0.915  1.00  0.00           C  
HETATM   13  C10 UNL     1      -2.768  -3.163   0.208  1.00  0.00           C  
HETATM   14  C11 UNL     1      -2.449  -1.810   0.003  1.00  0.00           C  
HETATM   15  C12 UNL     1      -3.496  -1.100  -0.751  1.00  0.00           C  
HETATM   16  C13 UNL     1      -3.126   0.152  -1.442  1.00  0.00           C  
HETATM   17  C14 UNL     1      -2.530   1.214  -0.590  1.00  0.00           C  
HETATM   18  C15 UNL     1      -3.141   2.447  -0.661  1.00  0.00           C  
HETATM   19  C16 UNL     1      -2.709   3.537   0.067  1.00  0.00           C  
HETATM   20  C17 UNL     1      -1.616   3.349   0.892  1.00  0.00           C  
HETATM   21 CL1  UNL     1      -0.975   4.670   1.870  1.00  0.00          CL  
HETATM   22  C18 UNL     1      -0.972   2.140   0.998  1.00  0.00           C  
HETATM   23  C19 UNL     1      -1.459   1.109   0.245  1.00  0.00           C  
HETATM   24  H1  UNL     1       2.822  -1.425  -1.411  1.00  0.00           H  
HETATM   25  H2  UNL     1       3.128   0.186  -2.217  1.00  0.00           H  
HETATM   26  H3  UNL     1       4.504  -0.928  -1.756  1.00  0.00           H  
HETATM   27  H4  UNL     1       5.608  -0.486   0.191  1.00  0.00           H  
HETATM   28  H5  UNL     1       5.037   0.976   1.022  1.00  0.00           H  
HETATM   29  H6  UNL     1       5.375   1.065  -0.792  1.00  0.00           H  
HETATM   30  H7  UNL     1       3.059   1.698   0.986  1.00  0.00           H  
HETATM   31  H8  UNL     1       3.241   1.947  -0.752  1.00  0.00           H  
HETATM   32  H9  UNL     1       0.913   2.039  -0.382  1.00  0.00           H  
HETATM   33  H10 UNL     1       1.362   0.686  -1.345  1.00  0.00           H  
HETATM   34  H11 UNL     1       1.193  -0.864   0.237  1.00  0.00           H  
HETATM   35  H12 UNL     1       1.079   0.136   1.682  1.00  0.00           H  
HETATM   36  H13 UNL     1       0.516  -1.813   1.700  1.00  0.00           H  
HETATM   37  H14 UNL     1      -0.109  -4.190   2.002  1.00  0.00           H  
HETATM   38  H15 UNL     1      -2.188  -5.060   1.076  1.00  0.00           H  
HETATM   39  H16 UNL     1      -3.698  -3.513  -0.216  1.00  0.00           H  
HETATM   40  H17 UNL     1      -3.915  -1.792  -1.522  1.00  0.00           H  
HETATM   41  H18 UNL     1      -4.312  -0.827  -0.009  1.00  0.00           H  
HETATM   42  H19 UNL     1      -4.073   0.584  -1.856  1.00  0.00           H  
HETATM   43  H20 UNL     1      -2.495  -0.025  -2.358  1.00  0.00           H  
HETATM   44  H21 UNL     1      -4.009   2.564  -1.327  1.00  0.00           H  
HETATM   45  H22 UNL     1      -3.192   4.483   0.001  1.00  0.00           H  
HETATM   46  H23 UNL     1      -0.112   1.934   1.632  1.00  0.00           H  
CONECT    1    2   24   25   26
CONECT    2    3    4    5
CONECT    3   27   28   29
CONECT    5    6   30   31
CONECT    6    7   32   33
CONECT    7    8   34   35
CONECT    8    9   23
CONECT    9   10   10   14
CONECT   10   11   36
CONECT   11   12   12   37
CONECT   12   13   38
CONECT   13   14   14   39
CONECT   14   15
CONECT   15   16   40   41
CONECT   16   17   42   43
CONECT   17   18   18   23
CONECT   18   19   44
CONECT   19   20   20   45
CONECT   20   21   22
CONECT   22   23   23   46
END

HMDB0060577
     RDKit          3D
Clomipramine N-oxide
 46 48  0  0  0  0  0  0  0  0999 V2000
    3.4808   -0.5403   -1.4766 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6238    0.0270   -0.1516 N   0  0  0  0  0  4  0  0  0  0  0  0
    5.0320    0.4479    0.0380 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4361   -0.9353    0.7526 O   0  0  0  0  0  1  0  0  0  0  0  0
    2.8545    1.2108    0.0136 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3841    1.0912   -0.2652 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7103    0.0725    0.6555 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6839   -0.0795    0.4793 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2343   -1.4238    0.5766 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3980   -2.2355    1.2813 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7568   -3.5496    1.4537 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9408   -4.0057    0.9153 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7683   -3.1627    0.2083 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4486   -1.8105    0.0032 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4958   -1.1003   -0.7515 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1261    0.1518   -1.4420 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5300    1.2142   -0.5900 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1413    2.4471   -0.6611 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7090    3.5370    0.0672 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6160    3.3494    0.8916 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9745    4.6701    1.8699 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   -0.9719    2.1398    0.9977 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4591    1.1094    0.2448 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8220   -1.4250   -1.4112 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1275    0.1856   -2.2166 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5042   -0.9278   -1.7561 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6078   -0.4861    0.1907 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0370    0.9758    1.0224 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3745    1.0653   -0.7921 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0589    1.6980    0.9863 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2412    1.9471   -0.7516 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9133    2.0393   -0.3823 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3623    0.6862   -1.3449 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1927   -0.8642    0.2369 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0786    0.1364    1.6815 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5164   -1.8135    1.6997 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1085   -4.1897    2.0023 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1881   -5.0603    1.0759 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6978   -3.5126   -0.2163 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9152   -1.7921   -1.5220 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3120   -0.8273   -0.0095 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0733    0.5845   -1.8562 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4951   -0.0252   -2.3582 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0094    2.5638   -1.3269 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1923    4.4828    0.0008 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1123    1.9338    1.6317 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  2  5  1  0
  5  6  1  0
  6  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
 14 15  1  0
 15 16  1  0
 16 17  1  0
 17 18  2  0
 18 19  1  0
 19 20  2  0
 20 21  1  0
 20 22  1  0
 22 23  2  0
 23  8  1  0
 14  9  1  0
 23 17  1  0
  1 24  1  0
  1 25  1  0
  1 26  1  0
  3 27  1  0
  3 28  1  0
  3 29  1  0
  5 30  1  0
  5 31  1  0
  6 32  1  0
  6 33  1  0
  7 34  1  0
  7 35  1  0
 10 36  1  0
 11 37  1  0
 12 38  1  0
 13 39  1  0
 15 40  1  0
 15 41  1  0
 16 42  1  0
 16 43  1  0
 18 44  1  0
 19 45  1  0
 22 46  1  0
M  CHG  2   2   1   4  -1
M  END

View in JSmol View Stereo Labels

Synonyms

Not Available

Chemical Formula

C₁₉H₂₃ClN₂O

Average Molecular Weight

330.852

Monoisotopic Molecular Weight

330.149891075

IUPAC Name

3-{14-chloro-2-azatricyclo[9.4.0.0³,⁸]pentadeca-1(11),3,5,7,12,14-hexaen-2-yl}-N,N-dimethylpropanamine oxide

Traditional Name

3-{14-chloro-2-azatricyclo[9.4.0.0³,⁸]pentadeca-1(11),3,5,7,12,14-hexaen-2-yl}-N,N-dimethylpropanamine oxide

CAS Registry Number

Not Available

SMILES

CN(C)(=O)CCCN1C2=CC=CC=C2CCC2=C1C=C(Cl)C=C2

InChI Identifier

InChI=1S/C19H23ClN2O/c1-22(2,23)13-5-12-21-18-7-4-3-6-15(18)8-9-16-10-11-17(20)14-19(16)21/h3-4,6-7,10-11,14H,5,8-9,12-13H2,1-2H3

InChI Key

ARNOTLDVJSFYBP-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
Trialkyl amine oxide
Tertiary amine
Trisubstituted n-oxide
N-oxide
Azacycle
Hydrocarbon derivative
Organonitrogen compound
Organochloride
Organohalogen compound
Organic oxide
Organopnictogen compound
Organic oxygen compound
Organic nitrogen compound
Amine
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Ontology

Not Available

Kidney (HMDB: HMDB0060577)
Liver (HMDB: HMDB0060577)

Non-excretory biofluid

Biofluid or Excreta

Blood (HMDB: HMDB0060577)

Excreta

Biofluid or Excreta

Urine (HMDB: HMDB0060577)

Cellular substructure

Cytoplasm (HMDB: HMDB0060577)
Membrane (HMDB: HMDB0060577)

Process

Not Available

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	0.0013 g/L	ALOGPS
logP	1.79	ALOGPS
logP	3.76	ChemAxon
logS	-5.4	ALOGPS
pKa (Strongest Basic)	4.12	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	30.12 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	97.46 m³·mol⁻¹	ChemAxon
Polarizability	36.86 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]+	167.949	30932474
DeepCCS	[M-H]-	165.591	30932474
DeepCCS	[M-2H]-	198.689	30932474
DeepCCS	[M+Na]+	174.042	30932474
AllCCS	[M+H]+	176.4	32859911
AllCCS	[M+H-H2O]+	173.2	32859911
AllCCS	[M+NH4]+	179.4	32859911
AllCCS	[M+Na]+	180.2	32859911
AllCCS	[M-H]-	184.3	32859911
AllCCS	[M+Na-2H]-	184.3	32859911
AllCCS	[M+HCOO]-	184.3	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Clomipramine N-oxide	CN(C)(=O)CCCN1C2=CC=CC=C2CCC2=C1C=C(Cl)C=C2	3914.6	Standard polar	33892256
Clomipramine N-oxide	CN(C)(=O)CCCN1C2=CC=CC=C2CCC2=C1C=C(Cl)C=C2	2272.7	Standard non polar	33892256
Clomipramine N-oxide	CN(C)(=O)CCCN1C2=CC=CC=C2CCC2=C1C=C(Cl)C=C2	2515.6	Semi standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - Clomipramine N-oxide GC-MS (Non-derivatized) - 70eV, Positive	splash10-0006-2092000000-0b9516b1f7c51439dce5	2017-09-20	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Clomipramine N-oxide 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 - Clomipramine N-oxide 10V, Positive-QTOF	splash10-001i-0129000000-009ac0d0a7a77598909a	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Clomipramine N-oxide 20V, Positive-QTOF	splash10-0ff0-2597000000-83171f0b327887be0df7	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Clomipramine N-oxide 40V, Positive-QTOF	splash10-0f6x-9550000000-8fe1fd9ee8fed46c2256	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Clomipramine N-oxide 10V, Negative-QTOF	splash10-004i-0009000000-79ef5d7192a44513919b	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Clomipramine N-oxide 20V, Negative-QTOF	splash10-004i-1059000000-d037ac224303f5a08711	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Clomipramine N-oxide 40V, Negative-QTOF	splash10-004l-0490000000-98c439ad970b37100a18	2017-10-06	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Cytoplasm
Membrane (predicted from logP)

Biospecimen Locations

Blood
Urine

Tissue Locations

Kidney
Liver

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

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

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

29976360

PDB ID

Not Available

ChEBI ID

Not Available

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 Clomipramine N-oxide (HMDB0060577)

MOL for HMDB0060577 (Clomipramine N-oxide)

3D MOL for HMDB0060577 (Clomipramine N-oxide)

3D SDF for HMDB0060577 (Clomipramine N-oxide)

3D-SDF for HMDB0060577 (Clomipramine N-oxide)

PDB for HMDB0060577 (Clomipramine N-oxide)

3D PDB for HMDB0060577 (Clomipramine N-oxide)

SMILES for HMDB0060577 (Clomipramine N-oxide)

INCHI for HMDB0060577 (Clomipramine N-oxide)

Structure for HMDB0060577 (Clomipramine N-oxide)

3D Structure for HMDB0060577 (Clomipramine N-oxide)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

GC-MS Spectra

MS/MS Spectra