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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2013-07-04 18:54:49 UTC

Update Date

2019-07-23 07:14:55 UTC

HMDB ID

HMDB0060718

Secondary Accession Numbers

HMDB60718

Metabolite Identification

Common Name

2-Hydroxyclomipramine

Description

2-Hydroxyclomipramine 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. In humans, 2-hydroxyclomipramine is involved in the clomipramine metabolism pathway. 2-Hydroxyclomipramine is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. Based on a literature review a significant number of articles have been published on 2-Hydroxyclomipramine.

Structure

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

HMDB0060718
     RDKit          3D
2-Hydroxyclomipramine
 46 48  0  0  0  0  0  0  0  0999 V2000
   -5.1110   -0.3960    1.3090 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6663   -0.5871    0.9711 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7031   -1.3402   -0.2581 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0225    0.6772    0.9225 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5418    0.7219    0.8108 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9356    0.1040   -0.4409 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5016    0.2120   -0.4284 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.0511    1.5416   -0.2979 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2087    2.4802   -0.8165 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6019    3.7945   -0.7637 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8116    4.1273   -0.2001 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6397    3.1513    0.3155 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2695    1.8006    0.2777 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3275    1.0147    0.8801 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2719   -0.4337    0.9608 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4487   -1.2334    0.0843 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0157   -2.4691   -0.1483 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3911   -3.4110   -0.9683 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9462   -4.6480   -1.2085 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1737   -3.1147   -1.5707 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3474   -4.2654   -2.6107 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    0.5901   -1.9068   -1.3620 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2394   -1.0060   -0.5453 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4455    0.5120    0.7801 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6765   -1.2635    0.9475 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1678   -0.2759    2.4272 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1051   -2.2676   -0.1146 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4220   -0.7892   -1.1556 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7389   -1.7461   -0.4770 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2545    1.1783    1.9181 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5282    1.3452    0.1688 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1058    1.7093    1.0434 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1871    0.1291    1.7317 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4232    0.3389   -1.3666 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1849   -0.9734   -0.2394 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7224    2.1475   -1.2429 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0771    4.5475   -1.1810 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0930    5.1814   -0.1742 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5685    3.4674    0.7409 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4509    1.4259    1.9332 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2879    1.3694    0.3920 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3390   -0.8160    0.8660 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0229   -0.7750    2.0187 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9587   -2.7182    0.3083 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8241   -4.9701   -0.8263 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3615   -1.5709   -1.8011 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  1  0
  8  9  2  0
  9 10  1  0
 10 11  2  0
 11 12  1  0
 12 13  2  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  2  0
 17 18  1  0
 18 19  1  0
 18 20  2  0
 20 21  1  0
 20 22  1  0
 22 23  2  0
 23  7  1  0
 13  8  1  0
 23 16  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
  4 30  1  0
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  5 32  1  0
  5 33  1  0
  6 34  1  0
  6 35  1  0
  9 36  1  0
 10 37  1  0
 11 38  1  0
 12 39  1  0
 14 40  1  0
 14 41  1  0
 15 42  1  0
 15 43  1  0
 17 44  1  0
 19 45  1  0
 22 46  1  0
M  END


  Mrv0541 07041311542D          

 23 25  0  0  0  0            999 V2000
   -1.9394   -2.3662    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2250   -1.9537    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2250   -1.1287    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5105   -2.3662    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2040   -1.9537    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9184   -2.3662    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6329   -1.9537    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.5713   -1.1310    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7829   -0.8878    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5993   -0.0835    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2041    0.4776    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9925    0.2345    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1760   -0.5698    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9918   -0.6928    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4043   -1.4073    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1029   -2.1752    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7077   -2.7364    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5241   -3.5407    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1289   -4.1018    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7358   -3.7839    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5522   -4.5882    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    2.1310   -3.2227    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3146   -2.4184    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
  8 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  2  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 18 20  2  0  0  0  0
 20 21  1  0  0  0  0
 20 22  1  0  0  0  0
 22 23  2  0  0  0  0
  7 23  1  0  0  0  0
 16 23  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0060718

> <DATABASE_NAME>
hmdb

> <SMILES>
CN(C)CCCN1C2=CC=CC=C2CCC2=CC(O)=C(Cl)C=C12

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

> <INCHI_KEY>
QXZNSJJZRXNDJQ-UHFFFAOYSA-N

> <FORMULA>
C19H23ClN2O

> <MOLECULAR_WEIGHT>
330.852

> <EXACT_MASS>
330.149891075

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
36.948207597421884

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
5-chloro-2-[3-(dimethylamino)propyl]-2-azatricyclo[9.4.0.0³,⁸]pentadeca-1(15),3,5,7,11,13-hexaen-6-ol

> <ALOGPS_LOGP>
4.51

> <JCHEM_LOGP>
3.866329630829245

> <ALOGPS_LOGS>
-3.46

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.747355457137191

> <JCHEM_PKA_STRONGEST_BASIC>
9.387500150493228

> <JCHEM_POLAR_SURFACE_AREA>
26.71

> <JCHEM_REFRACTIVITY>
97.3913

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.14e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5-chloro-2-[3-(dimethylamino)propyl]-2-azatricyclo[9.4.0.0³,⁸]pentadeca-1(15),3,5,7,11,13-hexaen-6-ol

> <JCHEM_VEBER_RULE>
1

$$$$

HMDB0060718
     RDKit          3D
2-Hydroxyclomipramine
 46 48  0  0  0  0  0  0  0  0999 V2000
   -5.1110   -0.3960    1.3090 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6663   -0.5871    0.9711 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7031   -1.3402   -0.2581 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0225    0.6772    0.9225 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5418    0.7219    0.8108 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9356    0.1040   -0.4409 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5016    0.2120   -0.4284 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.0511    1.5416   -0.2979 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2087    2.4802   -0.8165 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6019    3.7945   -0.7637 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8116    4.1273   -0.2001 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6397    3.1513    0.3155 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2695    1.8006    0.2777 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3275    1.0147    0.8801 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2719   -0.4337    0.9608 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4487   -1.2334    0.0843 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0157   -2.4691   -0.1483 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3911   -3.4110   -0.9683 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9462   -4.6480   -1.2085 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1737   -3.1147   -1.5707 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3474   -4.2654   -2.6107 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    0.5901   -1.9068   -1.3620 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2394   -1.0060   -0.5453 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4455    0.5120    0.7801 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6765   -1.2635    0.9475 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1678   -0.2759    2.4272 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1051   -2.2676   -0.1146 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4220   -0.7892   -1.1556 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7389   -1.7461   -0.4770 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2545    1.1783    1.9181 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5282    1.3452    0.1688 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1058    1.7093    1.0434 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1871    0.1291    1.7317 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4232    0.3389   -1.3666 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1849   -0.9734   -0.2394 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7224    2.1475   -1.2429 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0771    4.5475   -1.1810 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0930    5.1814   -0.1742 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5685    3.4674    0.7409 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4509    1.4259    1.9332 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2879    1.3694    0.3920 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3390   -0.8160    0.8660 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0229   -0.7750    2.0187 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9587   -2.7182    0.3083 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8241   -4.9701   -0.8263 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3615   -1.5709   -1.8011 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  1  0
  8  9  2  0
  9 10  1  0
 10 11  2  0
 11 12  1  0
 12 13  2  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  2  0
 17 18  1  0
 18 19  1  0
 18 20  2  0
 20 21  1  0
 20 22  1  0
 22 23  2  0
 23  7  1  0
 13  8  1  0
 23 16  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
  4 30  1  0
  4 31  1  0
  5 32  1  0
  5 33  1  0
  6 34  1  0
  6 35  1  0
  9 36  1  0
 10 37  1  0
 11 38  1  0
 12 39  1  0
 14 40  1  0
 14 41  1  0
 15 42  1  0
 15 43  1  0
 17 44  1  0
 19 45  1  0
 22 46  1  0
M  END

HEADER    PROTEIN                                 04-JUL-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-JUL-13         0                                  
HETATM    1  C   UNK     0      -3.620  -4.417   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0      -2.287  -3.647   0.000  0.00  0.00           N+0
HETATM    3  C   UNK     0      -2.287  -2.107   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.953  -4.417   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.381  -3.647   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.714  -4.417   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0       3.048  -3.647   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0       2.933  -2.111   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.461  -1.657   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.119  -0.156   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       2.248   0.892   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       3.719   0.438   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       4.062  -1.064   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       5.585  -1.293   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       6.355  -2.627   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       5.792  -4.060   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       6.921  -5.108   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       6.578  -6.609   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       7.707  -7.657   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0       5.107  -7.063   0.000  0.00  0.00           C+0
HETATM   21 Cl   UNK     0       4.764  -8.565   0.000  0.00  0.00          Cl+0
HETATM   22  C   UNK     0       3.978  -6.016   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       4.321  -4.514   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8   23                                                  
CONECT    8    7    9   13                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12    8   14                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17   23                                                  
CONECT   17   16   18                                                       
CONECT   18   17   19   20                                                  
CONECT   19   18                                                            
CONECT   20   18   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20   23                                                       
CONECT   23   22    7   16                                                  
MASTER        0    0    0    0    0    0    0    0   23    0   50    0
END

COMPND    HMDB0060718
HETATM    1  C1  UNL     1      -5.111  -0.396   1.309  1.00  0.00           C  
HETATM    2  N1  UNL     1      -3.666  -0.587   0.971  1.00  0.00           N  
HETATM    3  C2  UNL     1      -3.703  -1.340  -0.258  1.00  0.00           C  
HETATM    4  C3  UNL     1      -3.023   0.677   0.923  1.00  0.00           C  
HETATM    5  C4  UNL     1      -1.542   0.722   0.811  1.00  0.00           C  
HETATM    6  C5  UNL     1      -0.936   0.104  -0.441  1.00  0.00           C  
HETATM    7  N2  UNL     1       0.502   0.212  -0.428  1.00  0.00           N  
HETATM    8  C6  UNL     1       1.051   1.542  -0.298  1.00  0.00           C  
HETATM    9  C7  UNL     1       0.209   2.480  -0.817  1.00  0.00           C  
HETATM   10  C8  UNL     1       0.602   3.795  -0.764  1.00  0.00           C  
HETATM   11  C9  UNL     1       1.812   4.127  -0.200  1.00  0.00           C  
HETATM   12  C10 UNL     1       2.640   3.151   0.315  1.00  0.00           C  
HETATM   13  C11 UNL     1       2.270   1.801   0.278  1.00  0.00           C  
HETATM   14  C12 UNL     1       3.328   1.015   0.880  1.00  0.00           C  
HETATM   15  C13 UNL     1       3.272  -0.434   0.961  1.00  0.00           C  
HETATM   16  C14 UNL     1       2.449  -1.233   0.084  1.00  0.00           C  
HETATM   17  C15 UNL     1       3.016  -2.469  -0.148  1.00  0.00           C  
HETATM   18  C16 UNL     1       2.391  -3.411  -0.968  1.00  0.00           C  
HETATM   19  O1  UNL     1       2.946  -4.648  -1.208  1.00  0.00           O  
HETATM   20  C17 UNL     1       1.174  -3.115  -1.571  1.00  0.00           C  
HETATM   21 CL1  UNL     1       0.347  -4.265  -2.611  1.00  0.00          CL  
HETATM   22  C18 UNL     1       0.590  -1.907  -1.362  1.00  0.00           C  
HETATM   23  C19 UNL     1       1.239  -1.006  -0.545  1.00  0.00           C  
HETATM   24  H1  UNL     1      -5.445   0.512   0.780  1.00  0.00           H  
HETATM   25  H2  UNL     1      -5.677  -1.264   0.947  1.00  0.00           H  
HETATM   26  H3  UNL     1      -5.168  -0.276   2.427  1.00  0.00           H  
HETATM   27  H4  UNL     1      -3.105  -2.268  -0.115  1.00  0.00           H  
HETATM   28  H5  UNL     1      -3.422  -0.789  -1.156  1.00  0.00           H  
HETATM   29  H6  UNL     1      -4.739  -1.746  -0.477  1.00  0.00           H  
HETATM   30  H7  UNL     1      -3.254   1.178   1.918  1.00  0.00           H  
HETATM   31  H8  UNL     1      -3.528   1.345   0.169  1.00  0.00           H  
HETATM   32  H9  UNL     1      -1.106   1.709   1.043  1.00  0.00           H  
HETATM   33  H10 UNL     1      -1.187   0.129   1.732  1.00  0.00           H  
HETATM   34  H11 UNL     1      -1.423   0.339  -1.367  1.00  0.00           H  
HETATM   35  H12 UNL     1      -1.185  -0.973  -0.239  1.00  0.00           H  
HETATM   36  H13 UNL     1      -0.722   2.147  -1.243  1.00  0.00           H  
HETATM   37  H14 UNL     1      -0.077   4.547  -1.181  1.00  0.00           H  
HETATM   38  H15 UNL     1       2.093   5.181  -0.174  1.00  0.00           H  
HETATM   39  H16 UNL     1       3.568   3.467   0.741  1.00  0.00           H  
HETATM   40  H17 UNL     1       3.451   1.426   1.933  1.00  0.00           H  
HETATM   41  H18 UNL     1       4.288   1.369   0.392  1.00  0.00           H  
HETATM   42  H19 UNL     1       4.339  -0.816   0.866  1.00  0.00           H  
HETATM   43  H20 UNL     1       3.023  -0.775   2.019  1.00  0.00           H  
HETATM   44  H21 UNL     1       3.959  -2.718   0.308  1.00  0.00           H  
HETATM   45  H22 UNL     1       3.824  -4.970  -0.826  1.00  0.00           H  
HETATM   46  H23 UNL     1      -0.361  -1.571  -1.801  1.00  0.00           H  
CONECT    1    2   24   25   26
CONECT    2    3    4
CONECT    3   27   28   29
CONECT    4    5   30   31
CONECT    5    6   32   33
CONECT    6    7   34   35
CONECT    7    8   23
CONECT    8    9    9   13
CONECT    9   10   36
CONECT   10   11   11   37
CONECT   11   12   38
CONECT   12   13   13   39
CONECT   13   14
CONECT   14   15   40   41
CONECT   15   16   42   43
CONECT   16   17   17   23
CONECT   17   18   44
CONECT   18   19   20   20
CONECT   19   45
CONECT   20   21   22
CONECT   22   23   23   46
END

HMDB0060718
     RDKit          3D
2-Hydroxyclomipramine
 46 48  0  0  0  0  0  0  0  0999 V2000
   -5.1110   -0.3960    1.3090 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6663   -0.5871    0.9711 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7031   -1.3402   -0.2581 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0225    0.6772    0.9225 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5418    0.7219    0.8108 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9356    0.1040   -0.4409 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5016    0.2120   -0.4284 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.0511    1.5416   -0.2979 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2087    2.4802   -0.8165 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6019    3.7945   -0.7637 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8116    4.1273   -0.2001 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6397    3.1513    0.3155 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2695    1.8006    0.2777 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3275    1.0147    0.8801 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2719   -0.4337    0.9608 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4487   -1.2334    0.0843 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0157   -2.4691   -0.1483 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3911   -3.4110   -0.9683 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9462   -4.6480   -1.2085 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1737   -3.1147   -1.5707 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3474   -4.2654   -2.6107 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    0.5901   -1.9068   -1.3620 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2394   -1.0060   -0.5453 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4455    0.5120    0.7801 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6765   -1.2635    0.9475 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1678   -0.2759    2.4272 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1051   -2.2676   -0.1146 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4220   -0.7892   -1.1556 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7389   -1.7461   -0.4770 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2545    1.1783    1.9181 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5282    1.3452    0.1688 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1058    1.7093    1.0434 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1871    0.1291    1.7317 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4232    0.3389   -1.3666 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1849   -0.9734   -0.2394 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7224    2.1475   -1.2429 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0771    4.5475   -1.1810 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0930    5.1814   -0.1742 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5685    3.4674    0.7409 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4509    1.4259    1.9332 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2879    1.3694    0.3920 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3390   -0.8160    0.8660 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0229   -0.7750    2.0187 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9587   -2.7182    0.3083 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8241   -4.9701   -0.8263 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3615   -1.5709   -1.8011 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  1  0
  8  9  2  0
  9 10  1  0
 10 11  2  0
 11 12  1  0
 12 13  2  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  2  0
 17 18  1  0
 18 19  1  0
 18 20  2  0
 20 21  1  0
 20 22  1  0
 22 23  2  0
 23  7  1  0
 13  8  1  0
 23 16  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
  4 30  1  0
  4 31  1  0
  5 32  1  0
  5 33  1  0
  6 34  1  0
  6 35  1  0
  9 36  1  0
 10 37  1  0
 11 38  1  0
 12 39  1  0
 14 40  1  0
 14 41  1  0
 15 42  1  0
 15 43  1  0
 17 44  1  0
 19 45  1  0
 22 46  1  0
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

5-chloro-2-[3-(dimethylamino)propyl]-2-azatricyclo[9.4.0.0³,⁸]pentadeca-1(15),3,5,7,11,13-hexaen-6-ol

Traditional Name

5-chloro-2-[3-(dimethylamino)propyl]-2-azatricyclo[9.4.0.0³,⁸]pentadeca-1(15),3,5,7,11,13-hexaen-6-ol

CAS Registry Number

Not Available

SMILES

CN(C)CCCN1C2=CC=CC=C2CCC2=CC(O)=C(Cl)C=C12

InChI Identifier

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

InChI Key

QXZNSJJZRXNDJQ-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
1-hydroxy-2-unsubstituted benzenoid
Aryl chloride
Aryl halide
Benzenoid
Tertiary aliphatic amine
Tertiary amine
Azacycle
Amine
Organooxygen compound
Organonitrogen compound
Organochloride
Organohalogen compound
Organic nitrogen compound
Organopnictogen compound
Organic oxygen compound
Hydrocarbon derivative
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: HMDB0060718)

Organ

Kidney (HMDB: HMDB0060718)
Liver (HMDB: HMDB0060718)

Excreta

Biofluid or Excreta

Urine (HMDB: HMDB0060718)

Cellular substructure

Cytoplasm (HMDB: HMDB0060718)
Membrane (HMDB: HMDB0060718)

Source

Endogenous

Endogenous (HMDB: HMDB0060718)

Process

Naturally occurring process

Biological process

Biochemical pathway

Metabolic pathway

Clomipramine Metabolism Pathway (PathBank: SMP0000639)

Role

Not Available

Physical Properties

State

Not Available

Experimental Molecular Properties

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

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	0.11 g/L	ALOGPS
logP	4.51	ALOGPS
logP	3.87	ChemAxon
logS	-3.5	ALOGPS
pKa (Strongest Acidic)	8.75	ChemAxon
pKa (Strongest Basic)	9.39	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	26.71 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	97.39 m³·mol⁻¹	ChemAxon
Polarizability	36.95 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-2H]-	205.031	30932474
DeepCCS	[M+Na]+	180.596	30932474
AllCCS	[M+H]+	177.6	32859911
AllCCS	[M+H-H2O]+	174.4	32859911
AllCCS	[M+NH4]+	180.6	32859911
AllCCS	[M+Na]+	181.4	32859911
AllCCS	[M-H]-	183.5	32859911
AllCCS	[M+Na-2H]-	183.3	32859911
AllCCS	[M+HCOO]-	183.2	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.	6.68 minutes	32390414
Predicted by Siyang on May 30, 2022	11.3772 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	2.37 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	1109.1 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	223.3 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	168.4 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	176.5 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	95.9 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	383.9 seconds	40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid	377.2 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	681.4 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	981.6 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	366.8 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	1205.1 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	240.2 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	326.3 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	415.2 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	378.0 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	8.0 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
2-Hydroxyclomipramine	CN(C)CCCN1C2=CC=CC=C2CCC2=CC(O)=C(Cl)C=C12	3892.0	Standard polar	33892256
2-Hydroxyclomipramine	CN(C)CCCN1C2=CC=CC=C2CCC2=CC(O)=C(Cl)C=C12	2650.9	Standard non polar	33892256
2-Hydroxyclomipramine	CN(C)CCCN1C2=CC=CC=C2CCC2=CC(O)=C(Cl)C=C12	2632.8	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
2-Hydroxyclomipramine,1TMS,isomer #1	CN(C)CCCN1C2=CC=CC=C2CCC2=CC(O[Si](C)(C)C)=C(Cl)C=C21	2698.7	Semi standard non polar	33892256
2-Hydroxyclomipramine,1TBDMS,isomer #1	CN(C)CCCN1C2=CC=CC=C2CCC2=CC(O[Si](C)(C)C(C)(C)C)=C(Cl)C=C21	2912.8	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 - 2-Hydroxyclomipramine GC-MS (Non-derivatized) - 70eV, Positive	splash10-0a4i-9041000000-89861a69f1102bb6f449	2017-09-20	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-Hydroxyclomipramine GC-MS (1 TMS) - 70eV, Positive	splash10-0a4i-9006000000-f09d1e3b6dca54ade028	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-Hydroxyclomipramine GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-Hydroxyclomipramine 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 - 2-Hydroxyclomipramine 10V, Positive-QTOF	splash10-001i-1019000000-82357c1a7453ad59b151	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Hydroxyclomipramine 20V, Positive-QTOF	splash10-0019-9076000000-c7407a8ce26aaa45e00c	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Hydroxyclomipramine 40V, Positive-QTOF	splash10-007c-9030000000-8e6f62fef4f37af5fc41	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Hydroxyclomipramine 10V, Negative-QTOF	splash10-004i-0009000000-082fcd6ec05ad0106a0f	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Hydroxyclomipramine 20V, Negative-QTOF	splash10-004l-0069000000-f14886d10f483d4f2d11	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Hydroxyclomipramine 40V, Negative-QTOF	splash10-052f-2090000000-761a5dbed1a3bf13bcf2	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Hydroxyclomipramine 10V, Positive-QTOF	splash10-001i-4009000000-b8e4530355474fd1a79e	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Hydroxyclomipramine 20V, Positive-QTOF	splash10-000i-9001000000-9ef27e0c1b14c5e97051	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Hydroxyclomipramine 40V, Positive-QTOF	splash10-0a4r-9010000000-b4833d997f93ffd7515c	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Hydroxyclomipramine 10V, Negative-QTOF	splash10-004i-0009000000-a3d27897664f6e55b7f5	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Hydroxyclomipramine 20V, Negative-QTOF	splash10-0006-0094000000-6c9ca7982e37fb84dcf1	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Hydroxyclomipramine 40V, Negative-QTOF	splash10-000x-5291000000-e7dbe91b99fe5f098163	2021-10-12	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Cytoplasm
Membrane (predicted from logP)

Biospecimen Locations

Blood
Urine

Tissue Locations

Kidney
Liver

Pathways

Name	SMPDB/PathBank	KEGG
Clomipramine Metabolism Pathway		Not Available

Normal Concentrations

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

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

8421597

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

10246110

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 2-Hydroxyclomipramine (HMDB0060718)

MOL for HMDB0060718 (2-Hydroxyclomipramine)

3D MOL for HMDB0060718 (2-Hydroxyclomipramine)

3D SDF for HMDB0060718 (2-Hydroxyclomipramine)

3D-SDF for HMDB0060718 (2-Hydroxyclomipramine)

PDB for HMDB0060718 (2-Hydroxyclomipramine)

3D PDB for HMDB0060718 (2-Hydroxyclomipramine)

SMILES for HMDB0060718 (2-Hydroxyclomipramine)

INCHI for HMDB0060718 (2-Hydroxyclomipramine)

Structure for HMDB0060718 (2-Hydroxyclomipramine)

3D Structure for HMDB0060718 (2-Hydroxyclomipramine)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra