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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-11 22:49:33 UTC

Update Date

2022-11-23 22:29:21 UTC

HMDB ID

HMDB0259875

Secondary Accession Numbers

None

Metabolite Identification

Common Name

Vortioxetine

Description

Vortioxetine, also known as brintellix, belongs to the class of organic compounds known as phenylpiperazines. Phenylpiperazines are compounds containing a phenylpiperazine skeleton, which consists of a piperazine bound to a phenyl group. Based on a literature review very few articles have been published on Vortioxetine. This compound has been identified in human blood as reported by (PMID: 31557052 ). Vortioxetine is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Vortioxetine is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.

Structure

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

HMDB0259875
     RDKit          3D
VORTIOXETINE
 43 45  0  0  0  0  0  0  0  0999 V2000
    6.1537    0.2035   -0.7212 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6837    0.3180   -0.5576 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8880   -0.0039   -1.6341 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5237    0.0840   -1.5383 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9380    0.4980   -0.3551 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1724    0.5903   -0.2964 S   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5032   -0.9697    0.2484 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3481   -2.0143    0.5476 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1399   -3.2458    0.9754 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4990   -3.4380    1.1067 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3205   -2.3759    0.8003 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8765   -1.1420    0.3739 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7451   -0.0709    0.0669 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7434    1.2169    0.7229 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0506    2.2688   -0.3021 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3889    2.0787   -0.7929 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8542    0.7275   -0.7020 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7213   -0.2655   -0.9884 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7429    0.8185    0.7180 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1282    1.2646    1.9950 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1090    0.7260    0.6084 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4972    0.6081   -1.6901 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.6440    0.7758    0.0880 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4860   -0.8680   -0.6248 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3508   -0.3281   -2.5599 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9227   -0.1790   -2.4116 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4144   -1.8734    0.4479 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5215   -4.0707    1.2123 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9077   -4.4019    1.4429 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3822   -2.5282    0.9036 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5864    1.2101    1.4579 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8240    1.4140    1.2977 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8883    3.3035    0.0933 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3601    2.1871   -1.1872 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0851    2.7072   -0.3784 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3154    0.4663    0.2576 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6484    0.5973   -1.4815 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1151   -1.2939   -0.8689 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3061   -0.1164   -1.9932 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8997    1.2564    2.7896 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3341    0.5669    2.3278 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7527    2.3233    1.9156 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7504    0.9748    1.4438 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  2  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
 17 18  1  0
  5 19  1  0
 19 20  1  0
 19 21  2  0
 21  2  1  0
 12  7  1  0
 18 13  1  0
  1 22  1  0
  1 23  1  0
  1 24  1  0
  3 25  1  0
  4 26  1  0
  8 27  1  0
  9 28  1  0
 10 29  1  0
 11 30  1  0
 14 31  1  0
 14 32  1  0
 15 33  1  0
 15 34  1  0
 16 35  1  0
 17 36  1  0
 17 37  1  0
 18 38  1  0
 18 39  1  0
 20 40  1  0
 20 41  1  0
 20 42  1  0
 21 43  1  0
M  END


  Mrv1652309122100492D          

 21 23  0  0  0  0            999 V2000
    3.5724   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -3.7125    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -5.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -5.3625    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -6.1875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -6.6000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -6.1875    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -5.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  2  7  1  0  0  0  0
  5  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
  9 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 15 20  1  0  0  0  0
  4 21  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0259875

> <DATABASE_NAME>
hmdb

> <SMILES>
CC1=CC(C)=C(SC2=CC=CC=C2N2CCNCC2)C=C1

> <INCHI_IDENTIFIER>
InChI=1S/C18H22N2S/c1-14-7-8-17(15(2)13-14)21-18-6-4-3-5-16(18)20-11-9-19-10-12-20/h3-8,13,19H,9-12H2,1-2H3

> <INCHI_KEY>
YQNWZWMKLDQSAC-UHFFFAOYSA-N

> <FORMULA>
C18H22N2S

> <MOLECULAR_WEIGHT>
298.45

> <EXACT_MASS>
298.15036989

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
43

> <JCHEM_AVERAGE_POLARIZABILITY>
34.58061575418328

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
1-{2-[(2,4-dimethylphenyl)sulfanyl]phenyl}piperazine

> <ALOGPS_LOGP>
4.51

> <JCHEM_LOGP>
4.7609535586666665

> <ALOGPS_LOGS>
-4.92

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_BASIC>
8.84631496768157

> <JCHEM_POLAR_SURFACE_AREA>
15.27

> <JCHEM_REFRACTIVITY>
94.0085

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.62e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
vortioxetine

> <JCHEM_VEBER_RULE>
1

$$$$

HMDB0259875
     RDKit          3D
VORTIOXETINE
 43 45  0  0  0  0  0  0  0  0999 V2000
    6.1537    0.2035   -0.7212 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6837    0.3180   -0.5576 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8880   -0.0039   -1.6341 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5237    0.0840   -1.5383 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9380    0.4980   -0.3551 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1724    0.5903   -0.2964 S   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5032   -0.9697    0.2484 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3481   -2.0143    0.5476 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1399   -3.2458    0.9754 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4990   -3.4380    1.1067 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3205   -2.3759    0.8003 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8765   -1.1420    0.3739 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7451   -0.0709    0.0669 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7434    1.2169    0.7229 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0506    2.2688   -0.3021 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3889    2.0787   -0.7929 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8542    0.7275   -0.7020 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7213   -0.2655   -0.9884 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7429    0.8185    0.7180 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1282    1.2646    1.9950 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1090    0.7260    0.6084 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4972    0.6081   -1.6901 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.6440    0.7758    0.0880 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4860   -0.8680   -0.6248 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3508   -0.3281   -2.5599 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9227   -0.1790   -2.4116 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4144   -1.8734    0.4479 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5215   -4.0707    1.2123 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9077   -4.4019    1.4429 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3822   -2.5282    0.9036 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5864    1.2101    1.4579 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8240    1.4140    1.2977 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8883    3.3035    0.0933 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3601    2.1871   -1.1872 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0851    2.7072   -0.3784 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3154    0.4663    0.2576 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6484    0.5973   -1.4815 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1151   -1.2939   -0.8689 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3061   -0.1164   -1.9932 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8997    1.2564    2.7896 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3341    0.5669    2.3278 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7527    2.3233    1.9156 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7504    0.9748    1.4438 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  2  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
 17 18  1  0
  5 19  1  0
 19 20  1  0
 19 21  2  0
 21  2  1  0
 12  7  1  0
 18 13  1  0
  1 22  1  0
  1 23  1  0
  1 24  1  0
  3 25  1  0
  4 26  1  0
  8 27  1  0
  9 28  1  0
 10 29  1  0
 11 30  1  0
 14 31  1  0
 14 32  1  0
 15 33  1  0
 15 34  1  0
 16 35  1  0
 17 36  1  0
 17 37  1  0
 18 38  1  0
 18 39  1  0
 20 40  1  0
 20 41  1  0
 20 42  1  0
 21 43  1  0
M  END

HEADER    PROTEIN                                 12-SEP-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   12-SEP-21         0                                  
HETATM    1  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       6.668  -2.310   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       8.002  -3.080   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       8.002  -4.620   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       6.668  -5.390   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       5.335  -4.620   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM    8  S   UNK     0       6.668  -6.930   0.000  0.00  0.00           S+0
HETATM    9  C   UNK     0       8.002  -7.700   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       9.336  -6.930   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      10.669  -7.700   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      10.669  -9.240   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       9.336 -10.010   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       8.002  -9.240   0.000  0.00  0.00           C+0
HETATM   15  N   UNK     0       6.668 -10.010   0.000  0.00  0.00           N+0
HETATM   16  C   UNK     0       6.668 -11.550   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       5.335 -12.320   0.000  0.00  0.00           C+0
HETATM   18  N   UNK     0       4.001 -11.550   0.000  0.00  0.00           N+0
HETATM   19  C   UNK     0       4.001 -10.010   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       5.335  -9.240   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       9.336  -5.390   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    7                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   21                                                  
CONECT    5    4    6    8                                                  
CONECT    6    5    7                                                       
CONECT    7    6    2                                                       
CONECT    8    5    9                                                       
CONECT    9    8   10   14                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13    9   15                                                  
CONECT   15   14   16   20                                                  
CONECT   16   15   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   15                                                       
CONECT   21    4                                                            
MASTER        0    0    0    0    0    0    0    0   21    0   46    0
END

COMPND    HMDB0259875
HETATM    1  C1  UNL     1       6.154   0.203  -0.721  1.00  0.00           C  
HETATM    2  C2  UNL     1       4.684   0.318  -0.558  1.00  0.00           C  
HETATM    3  C3  UNL     1       3.888  -0.004  -1.634  1.00  0.00           C  
HETATM    4  C4  UNL     1       2.524   0.084  -1.538  1.00  0.00           C  
HETATM    5  C5  UNL     1       1.938   0.498  -0.355  1.00  0.00           C  
HETATM    6  S1  UNL     1       0.172   0.590  -0.296  1.00  0.00           S  
HETATM    7  C6  UNL     1      -0.503  -0.970   0.248  1.00  0.00           C  
HETATM    8  C7  UNL     1       0.348  -2.014   0.548  1.00  0.00           C  
HETATM    9  C8  UNL     1      -0.140  -3.246   0.975  1.00  0.00           C  
HETATM   10  C9  UNL     1      -1.499  -3.438   1.107  1.00  0.00           C  
HETATM   11  C10 UNL     1      -2.321  -2.376   0.800  1.00  0.00           C  
HETATM   12  C11 UNL     1      -1.876  -1.142   0.374  1.00  0.00           C  
HETATM   13  N1  UNL     1      -2.745  -0.071   0.067  1.00  0.00           N  
HETATM   14  C12 UNL     1      -2.743   1.217   0.723  1.00  0.00           C  
HETATM   15  C13 UNL     1      -3.051   2.269  -0.302  1.00  0.00           C  
HETATM   16  N2  UNL     1      -4.389   2.079  -0.793  1.00  0.00           N  
HETATM   17  C14 UNL     1      -4.854   0.728  -0.702  1.00  0.00           C  
HETATM   18  C15 UNL     1      -3.721  -0.265  -0.988  1.00  0.00           C  
HETATM   19  C16 UNL     1       2.743   0.818   0.718  1.00  0.00           C  
HETATM   20  C17 UNL     1       2.128   1.265   1.995  1.00  0.00           C  
HETATM   21  C18 UNL     1       4.109   0.726   0.608  1.00  0.00           C  
HETATM   22  H1  UNL     1       6.497   0.608  -1.690  1.00  0.00           H  
HETATM   23  H2  UNL     1       6.644   0.776   0.088  1.00  0.00           H  
HETATM   24  H3  UNL     1       6.486  -0.868  -0.625  1.00  0.00           H  
HETATM   25  H4  UNL     1       4.351  -0.328  -2.560  1.00  0.00           H  
HETATM   26  H5  UNL     1       1.923  -0.179  -2.412  1.00  0.00           H  
HETATM   27  H6  UNL     1       1.414  -1.873   0.448  1.00  0.00           H  
HETATM   28  H7  UNL     1       0.522  -4.071   1.212  1.00  0.00           H  
HETATM   29  H8  UNL     1      -1.908  -4.402   1.443  1.00  0.00           H  
HETATM   30  H9  UNL     1      -3.382  -2.528   0.904  1.00  0.00           H  
HETATM   31  H10 UNL     1      -3.586   1.210   1.458  1.00  0.00           H  
HETATM   32  H11 UNL     1      -1.824   1.414   1.298  1.00  0.00           H  
HETATM   33  H12 UNL     1      -2.888   3.303   0.093  1.00  0.00           H  
HETATM   34  H13 UNL     1      -2.360   2.187  -1.187  1.00  0.00           H  
HETATM   35  H14 UNL     1      -5.085   2.707  -0.378  1.00  0.00           H  
HETATM   36  H15 UNL     1      -5.315   0.466   0.258  1.00  0.00           H  
HETATM   37  H16 UNL     1      -5.648   0.597  -1.481  1.00  0.00           H  
HETATM   38  H17 UNL     1      -4.115  -1.294  -0.869  1.00  0.00           H  
HETATM   39  H18 UNL     1      -3.306  -0.116  -1.993  1.00  0.00           H  
HETATM   40  H19 UNL     1       2.900   1.256   2.790  1.00  0.00           H  
HETATM   41  H20 UNL     1       1.334   0.567   2.328  1.00  0.00           H  
HETATM   42  H21 UNL     1       1.753   2.323   1.916  1.00  0.00           H  
HETATM   43  H22 UNL     1       4.750   0.975   1.444  1.00  0.00           H  
CONECT    1    2   22   23   24
CONECT    2    3    3   21
CONECT    3    4   25
CONECT    4    5    5   26
CONECT    5    6   19
CONECT    6    7
CONECT    7    8    8   12
CONECT    8    9   27
CONECT    9   10   10   28
CONECT   10   11   29
CONECT   11   12   12   30
CONECT   12   13
CONECT   13   14   18
CONECT   14   15   31   32
CONECT   15   16   33   34
CONECT   16   17   35
CONECT   17   18   36   37
CONECT   18   38   39
CONECT   19   20   21   21
CONECT   20   40   41   42
CONECT   21   43
END

HMDB0259875
     RDKit          3D
VORTIOXETINE
 43 45  0  0  0  0  0  0  0  0999 V2000
    6.1537    0.2035   -0.7212 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6837    0.3180   -0.5576 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8880   -0.0039   -1.6341 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5237    0.0840   -1.5383 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9380    0.4980   -0.3551 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1724    0.5903   -0.2964 S   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5032   -0.9697    0.2484 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3481   -2.0143    0.5476 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1399   -3.2458    0.9754 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4990   -3.4380    1.1067 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3205   -2.3759    0.8003 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8765   -1.1420    0.3739 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7451   -0.0709    0.0669 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7434    1.2169    0.7229 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0506    2.2688   -0.3021 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3889    2.0787   -0.7929 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8542    0.7275   -0.7020 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7213   -0.2655   -0.9884 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7429    0.8185    0.7180 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1282    1.2646    1.9950 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1090    0.7260    0.6084 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4972    0.6081   -1.6901 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.6440    0.7758    0.0880 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4860   -0.8680   -0.6248 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3508   -0.3281   -2.5599 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9227   -0.1790   -2.4116 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4144   -1.8734    0.4479 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5215   -4.0707    1.2123 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9077   -4.4019    1.4429 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3822   -2.5282    0.9036 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5864    1.2101    1.4579 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8240    1.4140    1.2977 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8883    3.3035    0.0933 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3601    2.1871   -1.1872 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0851    2.7072   -0.3784 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3154    0.4663    0.2576 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6484    0.5973   -1.4815 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1151   -1.2939   -0.8689 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3061   -0.1164   -1.9932 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8997    1.2564    2.7896 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3341    0.5669    2.3278 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7527    2.3233    1.9156 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7504    0.9748    1.4438 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  2  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
 17 18  1  0
  5 19  1  0
 19 20  1  0
 19 21  2  0
 21  2  1  0
 12  7  1  0
 18 13  1  0
  1 22  1  0
  1 23  1  0
  1 24  1  0
  3 25  1  0
  4 26  1  0
  8 27  1  0
  9 28  1  0
 10 29  1  0
 11 30  1  0
 14 31  1  0
 14 32  1  0
 15 33  1  0
 15 34  1  0
 16 35  1  0
 17 36  1  0
 17 37  1  0
 18 38  1  0
 18 39  1  0
 20 40  1  0
 20 41  1  0
 20 42  1  0
 21 43  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
Brintellix	Kegg
1-{2-[(2,4-dimethylphenyl)sulphanyl]phenyl}piperazine	HMDB
1-(2-(2,4-Dimethylphenylsulfanyl)phenyl)piperazine	HMDB
Vortioxetine hydrobromide	HMDB

Chemical Formula

C₁₈H₂₂N₂S

Average Molecular Weight

298.45

Monoisotopic Molecular Weight

298.15036989

IUPAC Name

1-{2-[(2,4-dimethylphenyl)sulfanyl]phenyl}piperazine

Traditional Name

vortioxetine

CAS Registry Number

Not Available

SMILES

CC1=CC(C)=C(SC2=CC=CC=C2N2CCNCC2)C=C1

InChI Identifier

InChI=1S/C18H22N2S/c1-14-7-8-17(15(2)13-14)21-18-6-4-3-5-16(18)20-11-9-19-10-12-20/h3-8,13,19H,9-12H2,1-2H3

InChI Key

YQNWZWMKLDQSAC-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as phenylpiperazines. Phenylpiperazines are compounds containing a phenylpiperazine skeleton, which consists of a piperazine bound to a phenyl group.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Diazinanes

Sub Class

Piperazines

Direct Parent

Phenylpiperazines

Alternative Parents

Substituents

Phenylpiperazine
N-arylpiperazine
Diarylthioether
Aryl thioether
M-xylene
Xylene
Tertiary aliphatic/aromatic amine
Aniline or substituted anilines
Dialkylarylamine
Thiophenol ether
Monocyclic benzene moiety
Benzenoid
Tertiary amine
Secondary aliphatic amine
Secondary amine
Azacycle
Thioether
Sulfenyl compound
Organopnictogen compound
Organosulfur compound
Hydrocarbon derivative
Organic nitrogen compound
Amine
Organonitrogen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

N-arylpiperazine (CHEBI:76016 )
aryl sulfide (CHEBI:76016 )

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 31557052)

Source

Exogenous

Exogenous (PMID: 31557052)

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
logP	4.51	ALOGPS
logP	4.76	ChemAxon
logS	-4.9	ALOGPS
pKa (Strongest Basic)	8.85	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	15.27 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	94.01 m³·mol⁻¹	ChemAxon
Polarizability	34.58 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
AllCCS	[M+H]+	170.367	32859911
AllCCS	[M+H-H2O]+	166.985	32859911
AllCCS	[M+Na]+	174.404	32859911
AllCCS	[M+NH4]+	173.503	32859911
AllCCS	[M-H]-	174.306	32859911
AllCCS	[M+Na-2H]-	173.692	32859911
AllCCS	[M+HCOO]-	173.145	32859911
DeepCCS	[M+H]+	168.883	30932474
DeepCCS	[M-H]-	166.525	30932474
DeepCCS	[M-2H]-	199.411	30932474
DeepCCS	[M+Na]+	174.977	30932474

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.	4.41 minutes	32390414
Predicted by Siyang on May 30, 2022	13.0345 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	2.56 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	1315.3 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	300.9 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	187.7 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	189.5 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	132.3 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	518.8 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	524.9 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	138.3 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	1133.2 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	471.8 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	1378.2 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	342.6 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	379.0 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	282.4 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	152.0 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	8.9 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
VORTIOXETINE	CC1=CC(C)=C(SC2=CC=CC=C2N2CCNCC2)C=C1	3212.6	Standard polar	33892256
VORTIOXETINE	CC1=CC(C)=C(SC2=CC=CC=C2N2CCNCC2)C=C1	2403.1	Standard non polar	33892256
VORTIOXETINE	CC1=CC(C)=C(SC2=CC=CC=C2N2CCNCC2)C=C1	2555.9	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
VORTIOXETINE,1TMS,isomer #1	CC1=CC=C(SC2=CC=CC=C2N2CCN([Si](C)(C)C)CC2)C(C)=C1	2726.1	Semi standard non polar	33892256
VORTIOXETINE,1TMS,isomer #1	CC1=CC=C(SC2=CC=CC=C2N2CCN([Si](C)(C)C)CC2)C(C)=C1	2573.2	Standard non polar	33892256
VORTIOXETINE,1TMS,isomer #1	CC1=CC=C(SC2=CC=CC=C2N2CCN([Si](C)(C)C)CC2)C(C)=C1	3262.6	Standard polar	33892256
VORTIOXETINE,1TBDMS,isomer #1	CC1=CC=C(SC2=CC=CC=C2N2CCN([Si](C)(C)C(C)(C)C)CC2)C(C)=C1	2946.1	Semi standard non polar	33892256
VORTIOXETINE,1TBDMS,isomer #1	CC1=CC=C(SC2=CC=CC=C2N2CCN([Si](C)(C)C(C)(C)C)CC2)C(C)=C1	2763.4	Standard non polar	33892256
VORTIOXETINE,1TBDMS,isomer #1	CC1=CC=C(SC2=CC=CC=C2N2CCN([Si](C)(C)C(C)(C)C)CC2)C(C)=C1	3398.2	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - Vortioxetine GC-MS (Non-derivatized) - 70eV, Positive	splash10-052o-1980000000-f946530f9325fe92b2f1	2021-09-23	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Vortioxetine GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	31557052	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

8141643

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Vortioxetine

METLIN ID

Not Available

PubChem Compound

9966051

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

Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]

Showing metabocard for Vortioxetine (HMDB0259875)

MOL for HMDB0259875 (Vortioxetine)

3D MOL for HMDB0259875 (Vortioxetine)

3D SDF for HMDB0259875 (Vortioxetine)

3D-SDF for HMDB0259875 (Vortioxetine)

PDB for HMDB0259875 (Vortioxetine)

3D PDB for HMDB0259875 (Vortioxetine)

SMILES for HMDB0259875 (Vortioxetine)

INCHI for HMDB0259875 (Vortioxetine)

Structure for HMDB0259875 (Vortioxetine)

3D Structure for HMDB0259875 (Vortioxetine)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra