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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2013-07-09 16:06:05 UTC

Update Date

2019-07-23 07:15:20 UTC

HMDB ID

HMDB0060900

Secondary Accession Numbers

HMDB60900

Metabolite Identification

Common Name

Clozapine N-oxide

Description

Clozapine N-oxide is a metabolite of clozapine. Clozapine (sold as Clozaril, Gen-Clozapine in Canada, Azaleptin, Leponex, Fazaclo, Froidir; Denzapine, Zaponex in the UK; Klozapol in Poland, Clopine in Australia and New Zealand) is an atypical antipsychotic medication used in the treatment of schizophrenia, and is also used off-label in the treatment of bipolar disorder. Wyatt. R and Chew. (Wikipedia )

Structure

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

HMDB0060900
     RDKit          3D
Clozapine N-oxide
 43 46  0  0  0  0  0  0  0  0999 V2000
    4.9962   -1.1984   -0.0301 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7754   -0.4553   -0.0859 N   0  0  0  0  0  4  0  0  0  0  0  0
    4.0130    0.8302   -0.4954 O   0  0  0  0  0  1  0  0  0  0  0  0
    3.1225   -0.3380    1.2174 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0312    0.7305    1.0365 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1640    0.3447   -0.0584 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2409    0.1946    0.0345 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7168   -0.8555    0.6088 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0539   -1.3028    0.8624 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0880   -2.3297    1.7833 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3238   -2.8463    2.1078 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5024   -4.1557    3.2668 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   -4.4955   -2.3545    1.5312 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4133   -1.3306    0.6184 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2039   -0.7879    0.2676 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3417    0.2596   -0.6904 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3792    1.3202   -0.8741 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9792    2.4190   -1.4247 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2018    3.5315   -1.6665 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8603    3.5207   -1.3567 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2745    2.4074   -0.8041 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0281    1.2875   -0.5542 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8160    0.0912   -1.3301 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8319   -1.0208   -1.0199 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3209   -1.3163    1.0282 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8761   -2.1775   -0.5431 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8211   -0.6145   -0.5308 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8522    0.0591    1.9335 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6772   -1.2913    1.5484 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4663    0.8049    1.9652 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5995    1.6602    0.8271 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1871   -2.7200    2.2376 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4615   -2.7803    1.8047 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2971   -0.9057    0.1350 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1774    0.2576   -1.2821 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0508    2.3857   -1.6564 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6442    4.4229   -2.1030 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2468    4.3995   -1.5479 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7964    2.3882   -0.5512 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3731    0.9893   -1.6674 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1070   -0.2777   -2.0970 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2835   -1.4269   -1.9249 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2447   -1.8189   -0.5200 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
  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  1  0
 11 13  2  0
 13 14  1  0
 14 15  2  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
 21 22  2  0
  6 23  1  0
 23 24  1  0
 24  2  1  0
 22  7  1  0
 15  9  1  0
 22 17  1  0
  1 25  1  0
  1 26  1  0
  1 27  1  0
  4 28  1  0
  4 29  1  0
  5 30  1  0
  5 31  1  0
 10 32  1  0
 13 33  1  0
 14 34  1  0
 16 35  1  0
 18 36  1  0
 19 37  1  0
 20 38  1  0
 21 39  1  0
 23 40  1  0
 23 41  1  0
 24 42  1  0
 24 43  1  0
M  CHG  2   2   1   3  -1
M  END


  Mrv0541 09041313182D          

 24 27  0  0  0  0            999 V2000
    6.0420   -2.6812    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1237    0.8510    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9401    1.6553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5189    0.2898    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1517    1.8985    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6673    1.6553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4556    1.8985    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1094   -1.5370    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3968   -0.9170    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4673   -2.2803    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7548   -1.6603    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0884    0.2898    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4837    0.8510    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7305    0.5330    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5470    1.3373    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0604    1.3373    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8768    0.5330    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2162   -0.1120    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6953    0.6078    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    3.8037    1.6953    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.3912   -0.1120    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.5741   -0.8553    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.2900   -2.3419    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    5.0865   -3.1414    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
  3  2  2  0  0  0  0
  4  2  1  0  0  0  0
  5  3  1  0  0  0  0
  7  6  2  0  0  0  0
 10  8  1  0  0  0  0
 11  9  1  0  0  0  0
 13  6  1  0  0  0  0
 13 12  2  0  0  0  0
 14  4  2  0  0  0  0
 15  5  2  0  0  0  0
 15 14  1  0  0  0  0
 16  7  1  0  0  0  0
 17 12  1  0  0  0  0
 17 16  2  0  0  0  0
 18 14  1  0  0  0  0
 19 13  1  0  0  0  0
 20 15  1  0  0  0  0
 20 16  1  0  0  0  0
 21 17  1  0  0  0  0
 21 18  2  0  0  0  0
 22  8  1  0  0  0  0
 22  9  1  0  0  0  0
 22 18  1  0  0  0  0
 23  1  1  0  0  0  0
 23 10  1  0  0  0  0
 23 11  1  0  0  0  0
 24 23  1  0  0  0  0
M  CHG  2  23   1  24  -1
M  END
> <DATABASE_ID>
HMDB0060900

> <DATABASE_NAME>
hmdb

> <SMILES>
C[N+]1([O-])CCN(CC1)C1=NC2=C(NC3=CC=CC=C13)C=CC(Cl)=C2

> <INCHI_IDENTIFIER>
InChI=1S/C18H19ClN4O/c1-23(24)10-8-22(9-11-23)18-14-4-2-3-5-15(14)20-16-7-6-13(19)12-17(16)21-18/h2-7,12,20H,8-11H2,1H3

> <INCHI_KEY>
OGUCZBIQSYYWEF-UHFFFAOYSA-N

> <FORMULA>
C18H19ClN4O

> <MOLECULAR_WEIGHT>
342.823

> <EXACT_MASS>
342.124738957

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
36.27018356986723

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
4-{6-chloro-2,9-diazatricyclo[9.4.0.0³,⁸]pentadeca-1(15),3(8),4,6,9,11,13-heptaen-10-yl}-1-methylpiperazin-1-ium-1-olate

> <ALOGPS_LOGP>
1.50

> <JCHEM_LOGP>
2.275865841

> <ALOGPS_LOGS>
-3.77

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
19.425435702750494

> <JCHEM_PKA_STRONGEST_ACIDIC>
15.899332049004347

> <JCHEM_PKA_STRONGEST_BASIC>
3.7384170892362714

> <JCHEM_POLAR_SURFACE_AREA>
54.510000000000005

> <JCHEM_REFRACTIVITY>
99.4014

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.78e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
4-{6-chloro-2,9-diazatricyclo[9.4.0.0³,⁸]pentadeca-1(15),3(8),4,6,9,11,13-heptaen-10-yl}-1-methylpiperazin-1-ium-1-olate

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0060900
     RDKit          3D
Clozapine N-oxide
 43 46  0  0  0  0  0  0  0  0999 V2000
    4.9962   -1.1984   -0.0301 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7754   -0.4553   -0.0859 N   0  0  0  0  0  4  0  0  0  0  0  0
    4.0130    0.8302   -0.4954 O   0  0  0  0  0  1  0  0  0  0  0  0
    3.1225   -0.3380    1.2174 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0312    0.7305    1.0365 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1640    0.3447   -0.0584 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2409    0.1946    0.0345 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7168   -0.8555    0.6088 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0539   -1.3028    0.8624 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0880   -2.3297    1.7833 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3238   -2.8463    2.1078 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5024   -4.1557    3.2668 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   -4.4955   -2.3545    1.5312 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4133   -1.3306    0.6184 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2039   -0.7879    0.2676 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3417    0.2596   -0.6904 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3792    1.3202   -0.8741 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9792    2.4190   -1.4247 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2018    3.5315   -1.6665 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8603    3.5207   -1.3567 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2745    2.4074   -0.8041 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0281    1.2875   -0.5542 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8160    0.0912   -1.3301 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8319   -1.0208   -1.0199 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3209   -1.3163    1.0282 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8761   -2.1775   -0.5431 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8211   -0.6145   -0.5308 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8522    0.0591    1.9335 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6772   -1.2913    1.5484 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4663    0.8049    1.9652 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5995    1.6602    0.8271 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1871   -2.7200    2.2376 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4615   -2.7803    1.8047 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2971   -0.9057    0.1350 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1774    0.2576   -1.2821 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0508    2.3857   -1.6564 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6442    4.4229   -2.1030 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2468    4.3995   -1.5479 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7964    2.3882   -0.5512 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3731    0.9893   -1.6674 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1070   -0.2777   -2.0970 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2835   -1.4269   -1.9249 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2447   -1.8189   -0.5200 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
  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  1  0
 11 13  2  0
 13 14  1  0
 14 15  2  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
 21 22  2  0
  6 23  1  0
 23 24  1  0
 24  2  1  0
 22  7  1  0
 15  9  1  0
 22 17  1  0
  1 25  1  0
  1 26  1  0
  1 27  1  0
  4 28  1  0
  4 29  1  0
  5 30  1  0
  5 31  1  0
 10 32  1  0
 13 33  1  0
 14 34  1  0
 16 35  1  0
 18 36  1  0
 19 37  1  0
 20 38  1  0
 21 39  1  0
 23 40  1  0
 23 41  1  0
 24 42  1  0
 24 43  1  0
M  CHG  2   2   1   3  -1
M  END

HEADER    PROTEIN                                 04-SEP-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-13         0                                  
HETATM    1  C   UNK     0      11.278  -5.005   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      11.431   1.589   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      11.088   3.090   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      10.302   0.541   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       9.617   3.544   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       3.112   3.090   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       4.584   3.544   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       7.671  -2.869   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      10.074  -1.712   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       8.339  -4.257   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      10.742  -3.099   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       3.898   0.541   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       2.770   1.589   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       8.830   0.995   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       8.488   2.496   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       5.713   2.496   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       5.370   0.995   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       7.870  -0.209   0.000  0.00  0.00           C+0
HETATM   19 Cl   UNK     0       1.298   1.135   0.000  0.00  0.00          Cl+0
HETATM   20  N   UNK     0       7.100   3.165   0.000  0.00  0.00           N+0
HETATM   21  N   UNK     0       6.330  -0.209   0.000  0.00  0.00           N+0
HETATM   22  N   UNK     0       8.538  -1.597   0.000  0.00  0.00           N+0
HETATM   23  N   UNK     0       9.875  -4.372   0.000  0.00  0.00           N+1
HETATM   24  O   UNK     0       9.495  -5.864   0.000  0.00  0.00           O-1
CONECT    1   23                                                            
CONECT    2    3    4                                                       
CONECT    3    2    5                                                       
CONECT    4    2   14                                                       
CONECT    5    3   15                                                       
CONECT    6    7   13                                                       
CONECT    7    6   16                                                       
CONECT    8   10   22                                                       
CONECT    9   11   22                                                       
CONECT   10    8   23                                                       
CONECT   11    9   23                                                       
CONECT   12   13   17                                                       
CONECT   13    6   12   19                                                  
CONECT   14    4   15   18                                                  
CONECT   15    5   14   20                                                  
CONECT   16    7   17   20                                                  
CONECT   17   12   16   21                                                  
CONECT   18   14   21   22                                                  
CONECT   19   13                                                            
CONECT   20   15   16                                                       
CONECT   21   17   18                                                       
CONECT   22    8    9   18                                                  
CONECT   23    1   10   11   24                                             
CONECT   24   23                                                            
MASTER        0    0    0    0    0    0    0    0   24    0   54    0
END

COMPND    HMDB0060900
HETATM    1  C1  UNL     1       4.996  -1.198  -0.030  1.00  0.00           C  
HETATM    2  N1  UNL     1       3.775  -0.455  -0.086  1.00  0.00           N1+
HETATM    3  O1  UNL     1       4.013   0.830  -0.495  1.00  0.00           O1-
HETATM    4  C2  UNL     1       3.123  -0.338   1.217  1.00  0.00           C  
HETATM    5  C3  UNL     1       2.031   0.731   1.037  1.00  0.00           C  
HETATM    6  N2  UNL     1       1.164   0.345  -0.058  1.00  0.00           N  
HETATM    7  C4  UNL     1      -0.241   0.195   0.035  1.00  0.00           C  
HETATM    8  N3  UNL     1      -0.717  -0.855   0.609  1.00  0.00           N  
HETATM    9  C5  UNL     1      -2.054  -1.303   0.862  1.00  0.00           C  
HETATM   10  C6  UNL     1      -2.088  -2.330   1.783  1.00  0.00           C  
HETATM   11  C7  UNL     1      -3.324  -2.846   2.108  1.00  0.00           C  
HETATM   12 CL1  UNL     1      -3.502  -4.156   3.267  1.00  0.00          CL  
HETATM   13  C8  UNL     1      -4.495  -2.354   1.531  1.00  0.00           C  
HETATM   14  C9  UNL     1      -4.413  -1.331   0.618  1.00  0.00           C  
HETATM   15  C10 UNL     1      -3.204  -0.788   0.268  1.00  0.00           C  
HETATM   16  N4  UNL     1      -3.342   0.260  -0.690  1.00  0.00           N  
HETATM   17  C11 UNL     1      -2.379   1.320  -0.874  1.00  0.00           C  
HETATM   18  C12 UNL     1      -2.979   2.419  -1.425  1.00  0.00           C  
HETATM   19  C13 UNL     1      -2.202   3.532  -1.666  1.00  0.00           C  
HETATM   20  C14 UNL     1      -0.860   3.521  -1.357  1.00  0.00           C  
HETATM   21  C15 UNL     1      -0.274   2.407  -0.804  1.00  0.00           C  
HETATM   22  C16 UNL     1      -1.028   1.287  -0.554  1.00  0.00           C  
HETATM   23  C17 UNL     1       1.816   0.091  -1.330  1.00  0.00           C  
HETATM   24  C18 UNL     1       2.832  -1.021  -1.020  1.00  0.00           C  
HETATM   25  H1  UNL     1       5.321  -1.316   1.028  1.00  0.00           H  
HETATM   26  H2  UNL     1       4.876  -2.178  -0.543  1.00  0.00           H  
HETATM   27  H3  UNL     1       5.821  -0.615  -0.531  1.00  0.00           H  
HETATM   28  H4  UNL     1       3.852   0.059   1.933  1.00  0.00           H  
HETATM   29  H5  UNL     1       2.677  -1.291   1.548  1.00  0.00           H  
HETATM   30  H6  UNL     1       1.466   0.805   1.965  1.00  0.00           H  
HETATM   31  H7  UNL     1       2.600   1.660   0.827  1.00  0.00           H  
HETATM   32  H8  UNL     1      -1.187  -2.720   2.238  1.00  0.00           H  
HETATM   33  H9  UNL     1      -5.461  -2.780   1.805  1.00  0.00           H  
HETATM   34  H10 UNL     1      -5.297  -0.906   0.135  1.00  0.00           H  
HETATM   35  H11 UNL     1      -4.177   0.258  -1.282  1.00  0.00           H  
HETATM   36  H12 UNL     1      -4.051   2.386  -1.656  1.00  0.00           H  
HETATM   37  H13 UNL     1      -2.644   4.423  -2.103  1.00  0.00           H  
HETATM   38  H14 UNL     1      -0.247   4.400  -1.548  1.00  0.00           H  
HETATM   39  H15 UNL     1       0.796   2.388  -0.551  1.00  0.00           H  
HETATM   40  H16 UNL     1       2.373   0.989  -1.667  1.00  0.00           H  
HETATM   41  H17 UNL     1       1.107  -0.278  -2.097  1.00  0.00           H  
HETATM   42  H18 UNL     1       3.284  -1.427  -1.925  1.00  0.00           H  
HETATM   43  H19 UNL     1       2.245  -1.819  -0.520  1.00  0.00           H  
CONECT    1    2   25   26   27
CONECT    2    3    4   24
CONECT    4    5   28   29
CONECT    5    6   30   31
CONECT    6    7   23
CONECT    7    8    8   22
CONECT    8    9
CONECT    9   10   10   15
CONECT   10   11   32
CONECT   11   12   13   13
CONECT   13   14   33
CONECT   14   15   15   34
CONECT   15   16
CONECT   16   17   35
CONECT   17   18   18   22
CONECT   18   19   36
CONECT   19   20   20   37
CONECT   20   21   38
CONECT   21   22   22   39
CONECT   23   24   40   41
CONECT   24   42   43
END

HMDB0060900
     RDKit          3D
Clozapine N-oxide
 43 46  0  0  0  0  0  0  0  0999 V2000
    4.9962   -1.1984   -0.0301 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7754   -0.4553   -0.0859 N   0  0  0  0  0  4  0  0  0  0  0  0
    4.0130    0.8302   -0.4954 O   0  0  0  0  0  1  0  0  0  0  0  0
    3.1225   -0.3380    1.2174 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0312    0.7305    1.0365 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1640    0.3447   -0.0584 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2409    0.1946    0.0345 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7168   -0.8555    0.6088 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0539   -1.3028    0.8624 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0880   -2.3297    1.7833 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3238   -2.8463    2.1078 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5024   -4.1557    3.2668 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   -4.4955   -2.3545    1.5312 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4133   -1.3306    0.6184 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2039   -0.7879    0.2676 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3417    0.2596   -0.6904 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3792    1.3202   -0.8741 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9792    2.4190   -1.4247 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2018    3.5315   -1.6665 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8603    3.5207   -1.3567 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2745    2.4074   -0.8041 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0281    1.2875   -0.5542 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8160    0.0912   -1.3301 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8319   -1.0208   -1.0199 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3209   -1.3163    1.0282 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8761   -2.1775   -0.5431 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8211   -0.6145   -0.5308 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8522    0.0591    1.9335 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6772   -1.2913    1.5484 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4663    0.8049    1.9652 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5995    1.6602    0.8271 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1871   -2.7200    2.2376 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4615   -2.7803    1.8047 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2971   -0.9057    0.1350 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1774    0.2576   -1.2821 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0508    2.3857   -1.6564 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6442    4.4229   -2.1030 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2468    4.3995   -1.5479 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7964    2.3882   -0.5512 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3731    0.9893   -1.6674 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1070   -0.2777   -2.0970 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2835   -1.4269   -1.9249 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2447   -1.8189   -0.5200 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
  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  1  0
 11 13  2  0
 13 14  1  0
 14 15  2  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
 21 22  2  0
  6 23  1  0
 23 24  1  0
 24  2  1  0
 22  7  1  0
 15  9  1  0
 22 17  1  0
  1 25  1  0
  1 26  1  0
  1 27  1  0
  4 28  1  0
  4 29  1  0
  5 30  1  0
  5 31  1  0
 10 32  1  0
 13 33  1  0
 14 34  1  0
 16 35  1  0
 18 36  1  0
 19 37  1  0
 20 38  1  0
 21 39  1  0
 23 40  1  0
 23 41  1  0
 24 42  1  0
 24 43  1  0
M  CHG  2   2   1   3  -1
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
Clozapine-N-oxide	HMDB
8-Chloro-11-(4-methyl-1-piperazinyl)-5H-dibenzo(b,e)(1,4)diazepine N-oxide	MeSH

Chemical Formula

C₁₈H₁₉ClN₄O

Average Molecular Weight

342.823

Monoisotopic Molecular Weight

342.124738957

IUPAC Name

4-{6-chloro-2,9-diazatricyclo[9.4.0.0³,⁸]pentadeca-1(15),3(8),4,6,9,11,13-heptaen-10-yl}-1-methylpiperazin-1-ium-1-olate

Traditional Name

4-{6-chloro-2,9-diazatricyclo[9.4.0.0³,⁸]pentadeca-1(15),3(8),4,6,9,11,13-heptaen-10-yl}-1-methylpiperazin-1-ium-1-olate

CAS Registry Number

Not Available

SMILES

C[N+]1([O-])CCN(CC1)C1=NC2=C(NC3=CC=CC=C13)C=CC(Cl)=C2

InChI Identifier

InChI=1S/C18H19ClN4O/c1-23(24)10-8-22(9-11-23)18-14-4-2-3-5-15(14)20-16-7-6-13(19)12-17(16)21-18/h2-7,12,20H,8-11H2,1H3

InChI Key

OGUCZBIQSYYWEF-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as dibenzodiazepines. Dibenzodiazepines are compounds containing a dibenzodiazepine moiety, which consists of two benzene connected by diazepine ring.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Benzodiazepines

Sub Class

Dibenzodiazepines

Direct Parent

Dibenzodiazepines

Alternative Parents

Substituents

Dibenzodiazepine
1,4-benzodiazepine
N-methylpiperazine
N-alkylpiperazine
Aryl chloride
Aryl halide
1,4-diazinane
Imidolactam
Piperazine
Benzenoid
Trialkyl amine oxide
Azacycle
Carboxylic acid amidine
Organic 1,3-dipolar compound
Secondary amine
Trisubstituted n-oxide
Amidine
N-oxide
Propargyl-type 1,3-dipolar organic compound
Organochloride
Organohalogen compound
Organic nitrogen compound
Organonitrogen compound
Amine
Hydrocarbon derivative
Organopnictogen compound
Organic oxide
Organic zwitterion
Organic oxygen compound
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: HMDB0060900)

Organ

Kidney (HMDB: HMDB0060900)
Liver (HMDB: HMDB0060900)

Excreta

Biofluid or Excreta

Urine (HMDB: HMDB0060900)

Cellular substructure

Cytoplasm (HMDB: HMDB0060900)
Membrane (HMDB: HMDB0060900)

Source

Endogenous

Endogenous (HMDB: HMDB0060900)

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	0.058 g/L	ALOGPS
logP	1.5	ALOGPS
logP	2.28	ChemAxon
logS	-3.8	ALOGPS
pKa (Strongest Acidic)	15.9	ChemAxon
pKa (Strongest Basic)	3.74	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	54.51 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	99.4 m³·mol⁻¹	ChemAxon
Polarizability	36.27 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DeepCCS	[M-2H]-	206.469	30932474
DeepCCS	[M+Na]+	181.696	30932474
AllCCS	[M+H]+	178.5	32859911
AllCCS	[M+H-H2O]+	175.4	32859911
AllCCS	[M+NH4]+	181.3	32859911
AllCCS	[M+Na]+	182.1	32859911
AllCCS	[M-H]-	184.1	32859911
AllCCS	[M+Na-2H]-	184.1	32859911
AllCCS	[M+HCOO]-	184.2	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.	2.66 minutes	32390414
Predicted by Siyang on May 30, 2022	10.3706 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	2.78 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	665.7 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	206.5 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	129.2 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	172.3 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	56.4 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	316.7 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	362.2 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	678.0 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	747.1 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	86.1 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	802.6 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	182.3 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	260.2 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	419.6 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	389.3 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	31.3 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Clozapine N-oxide	C[N+]1([O-])CCN(CC1)C1=NC2=C(NC3=CC=CC=C13)C=CC(Cl)=C2	4475.7	Standard polar	33892256
Clozapine N-oxide	C[N+]1([O-])CCN(CC1)C1=NC2=C(NC3=CC=CC=C13)C=CC(Cl)=C2	2155.6	Standard non polar	33892256
Clozapine N-oxide	C[N+]1([O-])CCN(CC1)C1=NC2=C(NC3=CC=CC=C13)C=CC(Cl)=C2	3050.5	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Clozapine N-oxide,1TMS,isomer #1	C[N+]1([O-])CCN(C2=NC3=CC(Cl)=CC=C3N([Si](C)(C)C)C3=CC=CC=C23)CC1	2909.3	Semi standard non polar	33892256
Clozapine N-oxide,1TMS,isomer #1	C[N+]1([O-])CCN(C2=NC3=CC(Cl)=CC=C3N([Si](C)(C)C)C3=CC=CC=C23)CC1	2881.9	Standard non polar	33892256
Clozapine N-oxide,1TMS,isomer #1	C[N+]1([O-])CCN(C2=NC3=CC(Cl)=CC=C3N([Si](C)(C)C)C3=CC=CC=C23)CC1	4087.1	Standard polar	33892256
Clozapine N-oxide,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N1C2=CC=C(Cl)C=C2N=C(N2CC[N+](C)([O-])CC2)C2=CC=CC=C21	3071.1	Semi standard non polar	33892256
Clozapine N-oxide,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N1C2=CC=C(Cl)C=C2N=C(N2CC[N+](C)([O-])CC2)C2=CC=CC=C21	3113.9	Standard non polar	33892256
Clozapine N-oxide,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N1C2=CC=C(Cl)C=C2N=C(N2CC[N+](C)([O-])CC2)C2=CC=CC=C21	4145.3	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - Clozapine N-oxide GC-MS (Non-derivatized) - 70eV, Positive	splash10-00or-6259000000-662cd23aab72b789b171	2017-09-20	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Clozapine 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 - Clozapine N-oxide 10V, Positive-QTOF	splash10-0006-0009000000-720c1bf442a1969fee50	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Clozapine N-oxide 20V, Positive-QTOF	splash10-006x-0069000000-8ecd0b8a4838120f9e1e	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Clozapine N-oxide 40V, Positive-QTOF	splash10-00rf-3190000000-9265041433db0f713b56	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Clozapine N-oxide 10V, Negative-QTOF	splash10-0006-0009000000-57d5c44d79a2def1bb1d	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Clozapine N-oxide 20V, Negative-QTOF	splash10-0006-0009000000-a1724631e17f5f48858a	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Clozapine N-oxide 40V, Negative-QTOF	splash10-00kf-0190000000-857722fe42b044f35122	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

21169512

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Clozapine N-oxide

METLIN ID

Not Available

PubChem Compound

135445691

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 Clozapine N-oxide (HMDB0060900)

MOL for HMDB0060900 (Clozapine N-oxide)

3D MOL for HMDB0060900 (Clozapine N-oxide)

3D SDF for HMDB0060900 (Clozapine N-oxide)

3D-SDF for HMDB0060900 (Clozapine N-oxide)

PDB for HMDB0060900 (Clozapine N-oxide)

3D PDB for HMDB0060900 (Clozapine N-oxide)

SMILES for HMDB0060900 (Clozapine N-oxide)

INCHI for HMDB0060900 (Clozapine N-oxide)

Structure for HMDB0060900 (Clozapine N-oxide)

3D Structure for HMDB0060900 (Clozapine N-oxide)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra