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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-06 15:16:51 UTC

Update Date

2022-03-07 02:51:54 UTC

HMDB ID

HMDB0015201

Secondary Accession Numbers

HMDB15201

Metabolite Identification

Common Name

Clonazepam

Description

Clonazepam, also known as klonopin or rivotril, belongs to the class of organic compounds known as 1,4-benzodiazepines. These are organic compounds containing a benzene ring fused to a 1,4-azepine. It is used in the treatment of all types of epilepsy and seizures, as well as myoclonus and associated abnormal movements, and panic disorders. Clonazepam is a moderately basic compound (based on its pKa). Clonazepam is a potentially toxic compound. 1,3-Dihydro-2H-1,4-benzodiazepin-2-one in which the hydrogens at positions 5 and 7 are substituted by 2-chlorophenyl and nitro groups, respectively. However, its use can be limited by the development of tolerance and by sedation.

Structure

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

HMDB0015201
     RDKit          3D
Clonazepam
 32 34  0  0  0  0  0  0  0  0999 V2000
    1.1331   -4.5235   -0.5848 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0456   -3.3619   -0.1219 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0172   -3.0806    0.9264 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8573   -1.9803    0.5385 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5463   -0.7813    0.1124 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6086    0.1210   -0.2156 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5621    1.3439   -0.8031 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6695    2.1766   -0.9882 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8962    1.7345   -0.5513 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0073    0.5078    0.0465 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8927   -0.2744    0.2082 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0805   -1.8550    0.9868 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    0.8034   -0.2902    0.0444 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9195    1.0304    0.4069 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1534    1.6819    0.3566 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2553    3.0474    0.7269 N   0  0  0  0  0  4  0  0  0  0  0  0
    3.3669    3.6067    0.6687 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1188    3.7222    1.1424 O   0  0  0  0  0  1  0  0  0  0  0  0
    3.2499    0.9752   -0.0594 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1289   -0.3588   -0.4190 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9179   -1.0087   -0.3720 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9682   -2.4125   -0.6671 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5386   -3.9907    1.1231 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5597   -2.7628    1.8316 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6149    1.6843   -1.2222 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5964    3.1335   -1.4520 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7656    2.3949   -0.6997 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9706    0.1495    0.3934 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0531    1.5412    0.7908 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2228    1.4519   -0.1115 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9695   -0.9310   -0.7469 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7233   -2.6912   -1.2888 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  2  0
 11 12  1  0
  5 13  1  0
 13 14  2  0
 14 15  1  0
 15 16  1  0
 16 17  2  0
 16 18  1  0
 15 19  2  0
 19 20  1  0
 20 21  2  0
 21 22  1  0
 22  2  1  0
 11  6  1  0
 21 13  1  0
  3 23  1  0
  3 24  1  0
  7 25  1  0
  8 26  1  0
  9 27  1  0
 10 28  1  0
 14 29  1  0
 19 30  1  0
 20 31  1  0
 22 32  1  0
M  CHG  2  16   1  18  -1
M  END

1068
  Mrv0541 02231215132D          

 22 24  0  0  0  0            999 V2000
    3.6081   -1.2313    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    2.3403    2.5929    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8668   -2.5929    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    3.2913   -2.4806    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1839    1.2046    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.0375    1.2046    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.5467   -2.1255    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    3.1107    0.0423    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3674    0.4003    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8540    0.4003    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4990   -0.1141    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1881   -0.8135    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500   -0.0728    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5232    1.8496    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4818   -1.3031    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6982    1.8496    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7076   -0.9302    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3760   -0.9299    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2670    0.1873    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0210   -1.4442    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9120   -0.3271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7890   -1.1429    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1 18  1  0  0  0  0
  2 16  2  0  0  0  0
  3  7  1  0  0  0  0
  4  7  2  0  0  0  0
  5  9  1  0  0  0  0
  5 16  1  0  0  0  0
  6 10  2  0  0  0  0
  6 14  1  0  0  0  0
  7 15  1  0  0  0  0
  8  9  2  0  0  0  0
  8 10  1  0  0  0  0
  8 12  1  0  0  0  0
  9 13  1  0  0  0  0
 10 11  1  0  0  0  0
 11 18  1  0  0  0  0
 11 19  2  0  0  0  0
 12 15  2  0  0  0  0
 13 17  2  0  0  0  0
 14 16  1  0  0  0  0
 15 17  1  0  0  0  0
 18 20  2  0  0  0  0
 19 21  1  0  0  0  0
 20 22  1  0  0  0  0
 21 22  2  0  0  0  0
M  CHG  2   3  -1   7   1
M  END
> <DATABASE_ID>
HMDB0015201

> <DATABASE_NAME>
hmdb

> <SMILES>
[O-][N+](=O)C1=CC2=C(NC(=O)CN=C2C2=CC=CC=C2Cl)C=C1

> <INCHI_IDENTIFIER>
InChI=1S/C15H10ClN3O3/c16-12-4-2-1-3-10(12)15-11-7-9(19(21)22)5-6-13(11)18-14(20)8-17-15/h1-7H,8H2,(H,18,20)

> <INCHI_KEY>
DGBIGWXXNGSACT-UHFFFAOYSA-N

> <FORMULA>
C15H10ClN3O3

> <MOLECULAR_WEIGHT>
315.711

> <EXACT_MASS>
315.041068908

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
29.585434367361763

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
5-(2-chlorophenyl)-7-nitro-2,3-dihydro-1H-1,4-benzodiazepin-2-one

> <ALOGPS_LOGP>
2.76

> <JCHEM_LOGP>
3.152004688

> <ALOGPS_LOGS>
-4.47

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.894771930436995

> <JCHEM_PKA_STRONGEST_BASIC>
1.8562715274495132

> <JCHEM_POLAR_SURFACE_AREA>
87.28

> <JCHEM_REFRACTIVITY>
84.02070000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.06e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
clonazepam

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0015201
     RDKit          3D
Clonazepam
 32 34  0  0  0  0  0  0  0  0999 V2000
    1.1331   -4.5235   -0.5848 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0456   -3.3619   -0.1219 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0172   -3.0806    0.9264 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8573   -1.9803    0.5385 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5463   -0.7813    0.1124 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6086    0.1210   -0.2156 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5621    1.3439   -0.8031 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6695    2.1766   -0.9882 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8962    1.7345   -0.5513 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0073    0.5078    0.0465 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8927   -0.2744    0.2082 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0805   -1.8550    0.9868 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    0.8034   -0.2902    0.0444 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9195    1.0304    0.4069 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1534    1.6819    0.3566 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2553    3.0474    0.7269 N   0  0  0  0  0  4  0  0  0  0  0  0
    3.3669    3.6067    0.6687 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1188    3.7222    1.1424 O   0  0  0  0  0  1  0  0  0  0  0  0
    3.2499    0.9752   -0.0594 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1289   -0.3588   -0.4190 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9179   -1.0087   -0.3720 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9682   -2.4125   -0.6671 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5386   -3.9907    1.1231 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5597   -2.7628    1.8316 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6149    1.6843   -1.2222 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5964    3.1335   -1.4520 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7656    2.3949   -0.6997 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9706    0.1495    0.3934 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0531    1.5412    0.7908 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2228    1.4519   -0.1115 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9695   -0.9310   -0.7469 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7233   -2.6912   -1.2888 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  2  0
 11 12  1  0
  5 13  1  0
 13 14  2  0
 14 15  1  0
 15 16  1  0
 16 17  2  0
 16 18  1  0
 15 19  2  0
 19 20  1  0
 20 21  2  0
 21 22  1  0
 22  2  1  0
 11  6  1  0
 21 13  1  0
  3 23  1  0
  3 24  1  0
  7 25  1  0
  8 26  1  0
  9 27  1  0
 10 28  1  0
 14 29  1  0
 19 30  1  0
 20 31  1  0
 22 32  1  0
M  CHG  2  16   1  18  -1
M  END

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: 1068                                              
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1 Cl   UNK     0       6.735  -2.298   0.000  0.00  0.00          Cl+0
HETATM    2  O   UNK     0       4.369   4.840   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0       3.485  -4.840   0.000  0.00  0.00           O-1
HETATM    4  O   UNK     0       6.144  -4.630   0.000  0.00  0.00           O+0
HETATM    5  N   UNK     0       4.077   2.249   0.000  0.00  0.00           N+0
HETATM    6  N   UNK     0       7.537   2.249   0.000  0.00  0.00           N+0
HETATM    7  N   UNK     0       4.754  -3.968   0.000  0.00  0.00           N+1
HETATM    8  C   UNK     0       5.807   0.079   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       4.419   0.747   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       7.194   0.747   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       8.398  -0.213   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       5.951  -1.519   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       3.080  -0.136   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       6.577   3.453   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       4.633  -2.432   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       5.037   3.453   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       3.188  -1.736   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       8.169  -1.736   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       9.832   0.350   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       9.373  -2.696   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      11.036  -0.611   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      10.806  -2.133   0.000  0.00  0.00           C+0
CONECT    1   18                                                            
CONECT    2   16                                                            
CONECT    3    7                                                            
CONECT    4    7                                                            
CONECT    5    9   16                                                       
CONECT    6   10   14                                                       
CONECT    7    3    4   15                                                  
CONECT    8    9   10   12                                                  
CONECT    9    5    8   13                                                  
CONECT   10    6    8   11                                                  
CONECT   11   10   18   19                                                  
CONECT   12    8   15                                                       
CONECT   13    9   17                                                       
CONECT   14    6   16                                                       
CONECT   15    7   12   17                                                  
CONECT   16    2    5   14                                                  
CONECT   17   13   15                                                       
CONECT   18    1   11   20                                                  
CONECT   19   11   21                                                       
CONECT   20   18   22                                                       
CONECT   21   19   22                                                       
CONECT   22   20   21                                                       
MASTER        0    0    0    0    0    0    0    0   22    0   48    0
END

COMPND    HMDB0015201
HETATM    1  O1  UNL     1       1.133  -4.523  -0.585  1.00  0.00           O  
HETATM    2  C1  UNL     1       1.046  -3.362  -0.122  1.00  0.00           C  
HETATM    3  C2  UNL     1       0.017  -3.081   0.926  1.00  0.00           C  
HETATM    4  N1  UNL     1      -0.857  -1.980   0.538  1.00  0.00           N  
HETATM    5  C3  UNL     1      -0.546  -0.781   0.112  1.00  0.00           C  
HETATM    6  C4  UNL     1      -1.609   0.121  -0.216  1.00  0.00           C  
HETATM    7  C5  UNL     1      -1.562   1.344  -0.803  1.00  0.00           C  
HETATM    8  C6  UNL     1      -2.669   2.177  -0.988  1.00  0.00           C  
HETATM    9  C7  UNL     1      -3.896   1.735  -0.551  1.00  0.00           C  
HETATM   10  C8  UNL     1      -4.007   0.508   0.046  1.00  0.00           C  
HETATM   11  C9  UNL     1      -2.893  -0.274   0.208  1.00  0.00           C  
HETATM   12 CL1  UNL     1      -3.080  -1.855   0.987  1.00  0.00          CL  
HETATM   13  C10 UNL     1       0.803  -0.290   0.044  1.00  0.00           C  
HETATM   14  C11 UNL     1       0.920   1.030   0.407  1.00  0.00           C  
HETATM   15  C12 UNL     1       2.153   1.682   0.357  1.00  0.00           C  
HETATM   16  N2  UNL     1       2.255   3.047   0.727  1.00  0.00           N1+
HETATM   17  O2  UNL     1       3.367   3.607   0.669  1.00  0.00           O  
HETATM   18  O3  UNL     1       1.119   3.722   1.142  1.00  0.00           O1-
HETATM   19  C13 UNL     1       3.250   0.975  -0.059  1.00  0.00           C  
HETATM   20  C14 UNL     1       3.129  -0.359  -0.419  1.00  0.00           C  
HETATM   21  C15 UNL     1       1.918  -1.009  -0.372  1.00  0.00           C  
HETATM   22  N3  UNL     1       1.968  -2.413  -0.667  1.00  0.00           N  
HETATM   23  H1  UNL     1      -0.539  -3.991   1.123  1.00  0.00           H  
HETATM   24  H2  UNL     1       0.560  -2.763   1.832  1.00  0.00           H  
HETATM   25  H3  UNL     1      -0.615   1.684  -1.222  1.00  0.00           H  
HETATM   26  H4  UNL     1      -2.596   3.134  -1.452  1.00  0.00           H  
HETATM   27  H5  UNL     1      -4.766   2.395  -0.700  1.00  0.00           H  
HETATM   28  H6  UNL     1      -4.971   0.150   0.393  1.00  0.00           H  
HETATM   29  H7  UNL     1       0.053   1.541   0.791  1.00  0.00           H  
HETATM   30  H8  UNL     1       4.223   1.452  -0.112  1.00  0.00           H  
HETATM   31  H9  UNL     1       3.970  -0.931  -0.747  1.00  0.00           H  
HETATM   32  H10 UNL     1       2.723  -2.691  -1.289  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3   22
CONECT    3    4   23   24
CONECT    4    5    5
CONECT    5    6   13
CONECT    6    7    7   11
CONECT    7    8   25
CONECT    8    9    9   26
CONECT    9   10   27
CONECT   10   11   11   28
CONECT   11   12
CONECT   13   14   14   21
CONECT   14   15   29
CONECT   15   16   19   19
CONECT   16   17   17   18
CONECT   19   20   30
CONECT   20   21   21   31
CONECT   21   22
CONECT   22   32
END

HMDB0015201
     RDKit          3D
Clonazepam
 32 34  0  0  0  0  0  0  0  0999 V2000
    1.1331   -4.5235   -0.5848 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0456   -3.3619   -0.1219 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0172   -3.0806    0.9264 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8573   -1.9803    0.5385 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5463   -0.7813    0.1124 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6086    0.1210   -0.2156 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5621    1.3439   -0.8031 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6695    2.1766   -0.9882 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8962    1.7345   -0.5513 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0073    0.5078    0.0465 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8927   -0.2744    0.2082 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0805   -1.8550    0.9868 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    0.8034   -0.2902    0.0444 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9195    1.0304    0.4069 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1534    1.6819    0.3566 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2553    3.0474    0.7269 N   0  0  0  0  0  4  0  0  0  0  0  0
    3.3669    3.6067    0.6687 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1188    3.7222    1.1424 O   0  0  0  0  0  1  0  0  0  0  0  0
    3.2499    0.9752   -0.0594 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1289   -0.3588   -0.4190 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9179   -1.0087   -0.3720 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9682   -2.4125   -0.6671 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5386   -3.9907    1.1231 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5597   -2.7628    1.8316 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6149    1.6843   -1.2222 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5964    3.1335   -1.4520 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7656    2.3949   -0.6997 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9706    0.1495    0.3934 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0531    1.5412    0.7908 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2228    1.4519   -0.1115 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9695   -0.9310   -0.7469 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7233   -2.6912   -1.2888 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  2  0
 11 12  1  0
  5 13  1  0
 13 14  2  0
 14 15  1  0
 15 16  1  0
 16 17  2  0
 16 18  1  0
 15 19  2  0
 19 20  1  0
 20 21  2  0
 21 22  1  0
 22  2  1  0
 11  6  1  0
 21 13  1  0
  3 23  1  0
  3 24  1  0
  7 25  1  0
  8 26  1  0
  9 27  1  0
 10 28  1  0
 14 29  1  0
 19 30  1  0
 20 31  1  0
 22 32  1  0
M  CHG  2  16   1  18  -1
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
1,3-Dihydro-7-nitro-5-(2-chlorophenyl)-2H-1,4.benzodiazepin-2-one	ChEBI
5-(2-Chloro-phenyl)-7-nitro-1,3-dihydro-benzo[e][1,4]diazepin-2-one	ChEBI
5-(2-Chlorophenyl)-7-nitro-1H-benzo[e][1,4]diazepin-2(3H)-one	ChEBI
5-(O-Chlorophenyl)-7-nitro-1,3-dihydro-2H-1,4-benzodiazepin-2-one	ChEBI
Clonazepamum	ChEBI
Klonopin	Kegg
Clonazepam fine granules	HMDB
Clonazepam tablets	HMDB
Chlonazepam	HMDB
Rivotril	HMDB
Antelepsin	HMDB

Chemical Formula

C₁₅H₁₀ClN₃O₃

Average Molecular Weight

315.711

Monoisotopic Molecular Weight

315.041068908

IUPAC Name

5-(2-chlorophenyl)-7-nitro-2,3-dihydro-1H-1,4-benzodiazepin-2-one

Traditional Name

clonazepam

CAS Registry Number

1622-61-3

SMILES

[O-][N+](=O)C1=CC2=C(NC(=O)CN=C2C2=CC=CC=C2Cl)C=C1

InChI Identifier

InChI=1S/C15H10ClN3O3/c16-12-4-2-1-3-10(12)15-11-7-9(19(21)22)5-6-13(11)18-14(20)8-17-15/h1-7H,8H2,(H,18,20)

InChI Key

DGBIGWXXNGSACT-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as 1,4-benzodiazepines. These are organic compounds containing a benzene ring fused to a 1,4-azepine.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Benzodiazepines

Sub Class

1,4-benzodiazepines

Direct Parent

1,4-benzodiazepines

Alternative Parents

Substituents

1,4-benzodiazepine
Nitroaromatic compound
Chlorobenzene
Halobenzene
Aryl chloride
Aryl halide
Monocyclic benzene moiety
Benzenoid
Cyclic carboximidic acid
Ketimine
C-nitro compound
Organic nitro compound
Allyl-type 1,3-dipolar organic compound
Azacycle
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Organic oxoazanium
Organic oxygen compound
Organochloride
Organonitrogen compound
Organohalogen compound
Organic nitrogen compound
Imine
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Organooxygen compound
Organic zwitterion
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

monochlorobenzenes (CHEBI:3756 )
1,4-benzodiazepinone (CHEBI:3756 )

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 21059682)

Excreta

Biofluid or Excreta

Urine (PMID: 21059682)

Cellular substructure

Source

Exogenous

Exogenous (HMDB: HMDB0015201)

Process

Not Available

Role

Industrial application

Manufacturing industry

Material processing agent

Coloring agent

Fluorescent agent

Anticonvulsant (HMDB: HMDB0015201)

Pharmaceutical industry

Anxiolytic drug (HMDB: HMDB0015201)

Biological role

Modulator

GABA modulator (HMDB: HMDB0015201)

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	236.5 - 238.5 °C	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	0.011 g/L	Not Available
LogP	2.7	Not Available

Experimental Chromatographic Properties

Experimental Collision Cross Sections

Adduct Type	Data Source	CCS Value (Å²)	Reference
[M+H]+	CBM	168.2	30932474

Predicted Molecular Properties

Property	Value	Source
Water Solubility	0.011 g/L	ALOGPS
logP	2.76	ALOGPS
logP	3.15	ChemAxon
logS	-4.5	ALOGPS
pKa (Strongest Acidic)	11.89	ChemAxon
pKa (Strongest Basic)	1.86	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	87.28 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	84.02 m³·mol⁻¹	ChemAxon
Polarizability	29.59 Å³	ChemAxon
Number of Rings	3	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+H]+	165.048	30932474
DeepCCS	[M-H]-	162.69	30932474
DeepCCS	[M-2H]-	196.369	30932474
DeepCCS	[M+Na]+	171.596	30932474
AllCCS	[M+H]+	168.0	32859911
AllCCS	[M+H-H2O]+	164.5	32859911
AllCCS	[M+NH4]+	171.3	32859911
AllCCS	[M+Na]+	172.3	32859911
AllCCS	[M-H]-	166.5	32859911
AllCCS	[M+Na-2H]-	165.6	32859911
AllCCS	[M+HCOO]-	164.7	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.	4.7 minutes	32390414
Predicted by Siyang on May 30, 2022	12.9988 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	0.95 minutes	32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid	28.3 seconds	40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	1967.3 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	372.0 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	153.7 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	207.3 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	123.4 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	462.7 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	664.6 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	73.2 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	1179.7 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	456.5 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	1254.5 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	387.9 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	385.6 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	320.0 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	176.2 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	26.6 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Clonazepam	[O-][N+](=O)C1=CC2=C(NC(=O)CN=C2C2=CC=CC=C2Cl)C=C1	4299.0	Standard polar	33892256
Clonazepam	[O-][N+](=O)C1=CC2=C(NC(=O)CN=C2C2=CC=CC=C2Cl)C=C1	2867.9	Standard non polar	33892256
Clonazepam	[O-][N+](=O)C1=CC2=C(NC(=O)CN=C2C2=CC=CC=C2Cl)C=C1	2851.2	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Clonazepam,1TMS,isomer #1	C[Si](C)(C)N1C(=O)CN=C(C2=CC=CC=C2Cl)C2=CC([N+](=O)[O-])=CC=C21	2692.9	Semi standard non polar	33892256
Clonazepam,1TMS,isomer #1	C[Si](C)(C)N1C(=O)CN=C(C2=CC=CC=C2Cl)C2=CC([N+](=O)[O-])=CC=C21	2717.8	Standard non polar	33892256
Clonazepam,1TMS,isomer #1	C[Si](C)(C)N1C(=O)CN=C(C2=CC=CC=C2Cl)C2=CC([N+](=O)[O-])=CC=C21	3980.3	Standard polar	33892256
Clonazepam,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N1C(=O)CN=C(C2=CC=CC=C2Cl)C2=CC([N+](=O)[O-])=CC=C21	2926.8	Semi standard non polar	33892256
Clonazepam,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N1C(=O)CN=C(C2=CC=CC=C2Cl)C2=CC([N+](=O)[O-])=CC=C21	2901.6	Standard non polar	33892256
Clonazepam,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N1C(=O)CN=C(C2=CC=CC=C2Cl)C2=CC([N+](=O)[O-])=CC=C21	3999.5	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - Clonazepam GC-MS (Non-derivatized) - 70eV, Positive	splash10-02br-1190000000-1354614c337562e212cc	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Clonazepam GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Clonazepam GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
MS	Mass Spectrum (Electron Ionization)	splash10-02a9-2492000000-109e2626e8a128b9e433	2014-09-20	Not Available	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Clonazepam 10V, Positive-QTOF	splash10-014i-0009000000-f625038036279ea1ad02	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Clonazepam 20V, Positive-QTOF	splash10-014i-0049000000-4dfcaef6e6f274ea9b0a	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Clonazepam 40V, Positive-QTOF	splash10-0a59-8911000000-fe9a4a8a76c224b6cb90	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Clonazepam 10V, Negative-QTOF	splash10-03di-0009000000-cd9167e21ef0d5b8f888	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Clonazepam 20V, Negative-QTOF	splash10-03di-0009000000-f28067a73f446175adef	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Clonazepam 40V, Negative-QTOF	splash10-0006-9000000000-ab88c27eceb0f144d9c2	2016-08-03	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Cytoplasm
Extracellular
Membrane

Biospecimen Locations

Blood
Urine

Tissue Locations

Not Available

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	Taking drug identified by DrugBank entry DB01068	21059682	details
Urine	Expected but not Quantified	Not Quantified	Not Available	Not Available	Taking drug identified by DrugBank entry DB01068	21059682	details

Abnormal Concentrations

Not Available

Predicted Concentrations

Biospecimen	Value	Original age	Original sex	Original condition	Comments
Blood	0.000 uM	Adult (>18 years old)	Both	Normal	Predicted based on drug qualities
Blood	0.000 umol/mmol creatinine	Adult (>18 years old)	Both	Normal	Predicted based on drug qualities

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

DB01068

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

2700

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Clonazepam

METLIN ID

Not Available

PubChem Compound

2802

PDB ID

Not Available

ChEBI ID

3756

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

Earley JV, Fryer RI, Ning RY: Quinazolines and 1,4-benzodiazepines. LXXXIX: Haptens useful in benzodiazepine immunoassay development. J Pharm Sci. 1979 Jul;68(7):845-50. [PubMed:458601 ]
Dreifuss FE, Penry JK, Rose SW, Kupferberg HJ, Dyken P, Sato S: Serum clonazepam concentrations in children with absence seizures. Neurology. 1975 Mar;25(3):255-8. [PubMed:1089913 ]
Rosen GM, Turner MJ 3rd: Synthesis of spin traps specific for hydroxyl radical. J Med Chem. 1988 Feb;31(2):428-32. [PubMed:2828624 ]
Rosen GM, Demos HA, Rauckman EJ: Not all aromatic nitro compounds form free radicals. Toxicol Lett. 1984 Aug;22(2):145-52. [PubMed:6089382 ]
Robertson MD, Drummer OH: Postmortem drug metabolism by bacteria. J Forensic Sci. 1995 May;40(3):382-6. [PubMed:7782744 ]

Only showing the first 10 proteins. There are 20 proteins in total.

Show all enzymes and transporters

Enzymes

Enzyme Details

1. Cytochrome P450 3A4

General function:: Involved in monooxygenase activity
Specific function:: Cytochromes P450 are a group of heme-thiolate monooxygenases. In liver microsomes, this enzyme is involved in an NADPH-dependent electron transport pathway. It performs a variety of oxidation reactions (e.g. caffeine 8-oxidation, omeprazole sulphoxidation, midazolam 1'-hydroxylation and midazolam 4-hydroxylation) of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics. Acts as a 1,8-cineole 2-exo-monooxygenase. The enzyme also hydroxylates etoposide.
Gene Name:: CYP3A4
Uniprot ID:: P08684
Molecular weight:: 57255.585

References

Enzyme Details

2. Gamma-aminobutyric acid receptor subunit gamma-2

General function:: Involved in ion transport
Specific function:: GABA, the major inhibitory neurotransmitter in the vertebrate brain, mediates neuronal inhibition by binding to the GABA/benzodiazepine receptor and opening an integral chloride channel
Gene Name:: GABRG2
Uniprot ID:: P18507
Molecular weight:: 54161.8

References

Enzyme Details

3. Translocator protein

General function:: Signal transduction mechanisms
Specific function:: Responsible for the manifestation of peripheral-type benzodiazepine recognition sites and is most likely to comprise binding domains for benzodiazepines and isoquinoline carboxamides. May play a role in the transport of porphyrins and heme. Plays a role in the transport of cholesterol across mitochondrial membranes in steroidogenic cells
Gene Name:: TSPO
Uniprot ID:: P30536
Molecular weight:: 18778.7

References

Enzyme Details

4. Gamma-aminobutyric acid receptor subunit alpha-1

General function:: Involved in ion transport
Specific function:: GABA, the major inhibitory neurotransmitter in the vertebrate brain, mediates neuronal inhibition by binding to the GABA/benzodiazepine receptor and opening an integral chloride channel
Gene Name:: GABRA1
Uniprot ID:: P14867
Molecular weight:: 51801.4

References

Enzyme Details

5. Gamma-aminobutyric acid receptor subunit alpha-2

General function:: Involved in ion transport
Specific function:: GABA, the major inhibitory neurotransmitter in the vertebrate brain, mediates neuronal inhibition by binding to the GABA/benzodiazepine receptor and opening an integral chloride channel
Gene Name:: GABRA2
Uniprot ID:: P47869
Molecular weight:: 51325.9

References

Enzyme Details

6. Gamma-aminobutyric acid receptor subunit alpha-3

General function:: Involved in ion transport
Specific function:: GABA, the major inhibitory neurotransmitter in the vertebrate brain, mediates neuronal inhibition by binding to the GABA/benzodiazepine receptor and opening an integral chloride channel
Gene Name:: GABRA3
Uniprot ID:: P34903
Molecular weight:: 55164.1

References

Enzyme Details

7. Gamma-aminobutyric acid receptor subunit alpha-4

General function:: Involved in ion transport
Specific function:: GABA, the major inhibitory neurotransmitter in the vertebrate brain, mediates neuronal inhibition by binding to the GABA/benzodiazepine receptor and opening an integral chloride channel
Gene Name:: GABRA4
Uniprot ID:: P48169
Molecular weight:: 61622.6

References

Enzyme Details

8. Gamma-aminobutyric acid receptor subunit alpha-5

General function:: Involved in ion transport
Specific function:: GABA, the major inhibitory neurotransmitter in the vertebrate brain, mediates neuronal inhibition by binding to the GABA/benzodiazepine receptor and opening an integral chloride channel
Gene Name:: GABRA5
Uniprot ID:: P31644
Molecular weight:: 52145.6

References

Enzyme Details

9. Gamma-aminobutyric acid receptor subunit beta-1

General function:: Involved in ion transport
Specific function:: GABA, the major inhibitory neurotransmitter in the vertebrate brain, mediates neuronal inhibition by binding to the GABA/benzodiazepine receptor and opening an integral chloride channel
Gene Name:: GABRB1
Uniprot ID:: P18505
Molecular weight:: 54234.1

References

Enzyme Details

10. Gamma-aminobutyric acid receptor subunit beta-2

General function:: Involved in ion transport
Specific function:: GABA, the major inhibitory neurotransmitter in the vertebrate brain, mediates neuronal inhibition by binding to the GABA/benzodiazepine receptor and opening an integral chloride channel
Gene Name:: GABRB2
Uniprot ID:: P47870
Molecular weight:: 59149.9

References

Only showing the first 10 proteins. There are 20 proteins in total.

Show all enzymes and transporters

Showing metabocard for Clonazepam (HMDB0015201)

MOL for HMDB0015201 (Clonazepam)

3D MOL for HMDB0015201 (Clonazepam)

3D SDF for HMDB0015201 (Clonazepam)

3D-SDF for HMDB0015201 (Clonazepam)

PDB for HMDB0015201 (Clonazepam)

3D PDB for HMDB0015201 (Clonazepam)

SMILES for HMDB0015201 (Clonazepam)

INCHI for HMDB0015201 (Clonazepam)

Structure for HMDB0015201 (Clonazepam)

3D Structure for HMDB0015201 (Clonazepam)

Experimental Collision Cross Sections

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

Enzymes

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