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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2017-11-21 17:43:52 UTC

Update Date

2022-03-07 03:18:14 UTC

HMDB ID

HMDB0240247

Secondary Accession Numbers

None

Metabolite Identification

Common Name

Pimethixene

Description

Pimethixene, also known as calmixene, belongs to the class of organic compounds known as thioxanthenes. These are organic polycyclic compounds containing a thioxanthene moiety, which is an aromatic tricycle derived from xanthene by replacing the oxygen atom with a sulfur atom. In humans, pimethixene is involved in the pimethixene h1-antihistamine action pathway. Pimethixene 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 very few articles have been published on Pimethixene.

Structure

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

HMDB0240247
     RDKit          3D
Pimethixene
 40 43  0  0  0  0  0  0  0  0999 V2000
    4.1342   -0.2557   -1.4372 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5456    0.2074   -0.1988 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.5518    1.2266   -0.5458 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4327    1.0767    0.4137 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6089   -0.1093    0.0925 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6941   -0.0328   -0.1138 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3356    1.3113   -0.0449 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6876    2.4131   -0.5834 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3379    3.6117   -0.7591 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6558    3.8036   -0.4264 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2856    2.6999    0.1007 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6386    1.5264    0.2731 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6304    0.2222    0.9847 S   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8384   -1.2798    0.4559 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6540   -2.3906    0.4893 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1029   -3.6096    0.1736 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7715   -3.6634   -0.1606 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9781   -2.5157   -0.1864 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5026   -1.2763    0.1280 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5502   -1.2462    0.0978 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9835   -0.8376    0.5696 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4563   -0.8535   -2.0556 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1084   -0.7524   -1.2493 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3769    0.6610   -2.0285 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0016    2.2257   -0.5933 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1770    0.9696   -1.5805 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9617    1.9328    0.8612 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0372    0.7791    1.4209 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3103    2.3175   -0.9907 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7790    4.4584   -1.1859 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1614    4.7489   -0.5674 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3390    2.8507    0.3647 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7010   -2.3506    0.7498 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6965   -4.5100    0.1855 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2889   -4.5870   -0.4143 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0158   -2.6094   -0.5230 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3441   -1.9872    0.8731 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8044   -1.5967   -0.9223 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6031   -1.7625    0.2956 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0752   -0.8161    1.6489 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  2  3
  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  2  0
 15 16  1  0
 16 17  2  0
 17 18  1  0
 18 19  2  0
  5 20  1  0
 20 21  1  0
 21  2  1  0
 19  6  1  0
 12  7  1  0
 19 14  1  0
  1 22  1  0
  1 23  1  0
  1 24  1  0
  3 25  1  0
  3 26  1  0
  4 27  1  0
  4 28  1  0
  8 29  1  0
  9 30  1  0
 10 31  1  0
 11 32  1  0
 15 33  1  0
 16 34  1  0
 17 35  1  0
 18 36  1  0
 20 37  1  0
 20 38  1  0
 21 39  1  0
 21 40  1  0
M  END

4822
  Mrv1652309251707242D          

 21 24  0  0  0  0            999 V2000
    3.8493   -2.4606    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    3.8493    1.6642    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.8493    0.0142    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1348    0.4267    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5638    0.4267    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1348    1.2517    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5638    1.2517    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8493   -0.8107    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5638   -1.2231    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1348   -1.2231    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8493    2.4891    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5638   -2.0481    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1348   -2.0481    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3012   -0.7820    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3974   -0.7820    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3012   -2.4891    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3974   -2.4891    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6499   -1.2060    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0487   -1.2060    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0487   -2.0653    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6499   -2.0653    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1 12  1  0  0  0  0
  1 13  1  0  0  0  0
  2  6  1  0  0  0  0
  2  7  1  0  0  0  0
  2 11  1  0  0  0  0
  3  4  1  0  0  0  0
  3  5  1  0  0  0  0
  3  8  2  0  0  0  0
  4  6  1  0  0  0  0
  5  7  1  0  0  0  0
  8  9  1  0  0  0  0
  8 10  1  0  0  0  0
  9 12  1  0  0  0  0
  9 14  2  0  0  0  0
 10 13  1  0  0  0  0
 10 15  2  0  0  0  0
 12 16  2  0  0  0  0
 13 17  2  0  0  0  0
 14 19  1  0  0  0  0
 15 18  1  0  0  0  0
 16 20  1  0  0  0  0
 17 21  1  0  0  0  0
 18 21  2  0  0  0  0
 19 20  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0240247

> <DATABASE_NAME>
hmdb

> <SMILES>
CN1CCC(CC1)=C1C2=CC=CC=C2SC2=CC=CC=C12

> <INCHI_IDENTIFIER>
InChI=1S/C19H19NS/c1-20-12-10-14(11-13-20)19-15-6-2-4-8-17(15)21-18-9-5-3-7-16(18)19/h2-9H,10-13H2,1H3

> <INCHI_KEY>
NZLVRVYNQYGMAB-UHFFFAOYSA-N

> <FORMULA>
C19H19NS

> <MOLECULAR_WEIGHT>
293.43

> <EXACT_MASS>
293.12382079

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
40

> <JCHEM_AVERAGE_POLARIZABILITY>
33.782694151887725

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
1-methyl-4-(9H-thioxanthen-9-ylidene)piperidine

> <ALOGPS_LOGP>
4.88

> <JCHEM_LOGP>
4.231750075333333

> <ALOGPS_LOGS>
-4.83

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_BASIC>
7.959094211956229

> <JCHEM_POLAR_SURFACE_AREA>
3.24

> <JCHEM_REFRACTIVITY>
102.40350000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.33e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
pimethixene

> <JCHEM_VEBER_RULE>
1

$$$$

HMDB0240247
     RDKit          3D
Pimethixene
 40 43  0  0  0  0  0  0  0  0999 V2000
    4.1342   -0.2557   -1.4372 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5456    0.2074   -0.1988 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.5518    1.2266   -0.5458 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4327    1.0767    0.4137 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6089   -0.1093    0.0925 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6941   -0.0328   -0.1138 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3356    1.3113   -0.0449 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6876    2.4131   -0.5834 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3379    3.6117   -0.7591 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6558    3.8036   -0.4264 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2856    2.6999    0.1007 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6386    1.5264    0.2731 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6304    0.2222    0.9847 S   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8384   -1.2798    0.4559 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6540   -2.3906    0.4893 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1029   -3.6096    0.1736 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7715   -3.6634   -0.1606 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9781   -2.5157   -0.1864 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5026   -1.2763    0.1280 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5502   -1.2462    0.0978 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9835   -0.8376    0.5696 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4563   -0.8535   -2.0556 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1084   -0.7524   -1.2493 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3769    0.6610   -2.0285 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0016    2.2257   -0.5933 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1770    0.9696   -1.5805 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9617    1.9328    0.8612 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0372    0.7791    1.4209 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3103    2.3175   -0.9907 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7790    4.4584   -1.1859 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1614    4.7489   -0.5674 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3390    2.8507    0.3647 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7010   -2.3506    0.7498 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6965   -4.5100    0.1855 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2889   -4.5870   -0.4143 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0158   -2.6094   -0.5230 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3441   -1.9872    0.8731 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8044   -1.5967   -0.9223 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6031   -1.7625    0.2956 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0752   -0.8161    1.6489 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  2  3
  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  2  0
 15 16  1  0
 16 17  2  0
 17 18  1  0
 18 19  2  0
  5 20  1  0
 20 21  1  0
 21  2  1  0
 19  6  1  0
 12  7  1  0
 19 14  1  0
  1 22  1  0
  1 23  1  0
  1 24  1  0
  3 25  1  0
  3 26  1  0
  4 27  1  0
  4 28  1  0
  8 29  1  0
  9 30  1  0
 10 31  1  0
 11 32  1  0
 15 33  1  0
 16 34  1  0
 17 35  1  0
 18 36  1  0
 20 37  1  0
 20 38  1  0
 21 39  1  0
 21 40  1  0
M  END

HEADER    PROTEIN                                 25-SEP-17   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: 4822                                              
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   25-SEP-17         0                                  
HETATM    1  S   UNK     0       7.185  -4.593   0.000  0.00  0.00           S+0
HETATM    2  N   UNK     0       7.185   3.107   0.000  0.00  0.00           N+0
HETATM    3  C   UNK     0       7.185   0.027   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.852   0.797   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       8.519   0.797   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       5.852   2.337   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       8.519   2.337   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       7.185  -1.513   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       8.519  -2.283   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       5.852  -2.283   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       7.185   4.646   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       8.519  -3.823   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       5.852  -3.823   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       9.896  -1.460   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       4.475  -1.460   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       9.896  -4.646   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       4.475  -4.646   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       3.080  -2.251   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      11.291  -2.251   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      11.291  -3.855   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       3.080  -3.855   0.000  0.00  0.00           C+0
CONECT    1   12   13                                                       
CONECT    2    6    7   11                                                  
CONECT    3    4    5    8                                                  
CONECT    4    3    6                                                       
CONECT    5    3    7                                                       
CONECT    6    2    4                                                       
CONECT    7    2    5                                                       
CONECT    8    3    9   10                                                  
CONECT    9    8   12   14                                                  
CONECT   10    8   13   15                                                  
CONECT   11    2                                                            
CONECT   12    1    9   16                                                  
CONECT   13    1   10   17                                                  
CONECT   14    9   19                                                       
CONECT   15   10   18                                                       
CONECT   16   12   20                                                       
CONECT   17   13   21                                                       
CONECT   18   15   21                                                       
CONECT   19   14   20                                                       
CONECT   20   16   19                                                       
CONECT   21   17   18                                                       
MASTER        0    0    0    0    0    0    0    0   21    0   48    0
END

COMPND    HMDB0240247
HETATM    1  C1  UNL     1       4.134  -0.256  -1.437  1.00  0.00           C  
HETATM    2  N1  UNL     1       3.546   0.207  -0.199  1.00  0.00           N  
HETATM    3  C2  UNL     1       2.552   1.227  -0.546  1.00  0.00           C  
HETATM    4  C3  UNL     1       1.433   1.077   0.414  1.00  0.00           C  
HETATM    5  C4  UNL     1       0.609  -0.109   0.093  1.00  0.00           C  
HETATM    6  C5  UNL     1      -0.694  -0.033  -0.114  1.00  0.00           C  
HETATM    7  C6  UNL     1      -1.336   1.311  -0.045  1.00  0.00           C  
HETATM    8  C7  UNL     1      -0.688   2.413  -0.583  1.00  0.00           C  
HETATM    9  C8  UNL     1      -1.338   3.612  -0.759  1.00  0.00           C  
HETATM   10  C9  UNL     1      -2.656   3.804  -0.426  1.00  0.00           C  
HETATM   11  C10 UNL     1      -3.286   2.700   0.101  1.00  0.00           C  
HETATM   12  C11 UNL     1      -2.639   1.526   0.273  1.00  0.00           C  
HETATM   13  S1  UNL     1      -3.630   0.222   0.985  1.00  0.00           S  
HETATM   14  C12 UNL     1      -2.838  -1.280   0.456  1.00  0.00           C  
HETATM   15  C13 UNL     1      -3.654  -2.391   0.489  1.00  0.00           C  
HETATM   16  C14 UNL     1      -3.103  -3.610   0.174  1.00  0.00           C  
HETATM   17  C15 UNL     1      -1.772  -3.663  -0.161  1.00  0.00           C  
HETATM   18  C16 UNL     1      -0.978  -2.516  -0.186  1.00  0.00           C  
HETATM   19  C17 UNL     1      -1.503  -1.276   0.128  1.00  0.00           C  
HETATM   20  C18 UNL     1       1.550  -1.246   0.098  1.00  0.00           C  
HETATM   21  C19 UNL     1       2.984  -0.838   0.570  1.00  0.00           C  
HETATM   22  H1  UNL     1       3.456  -0.854  -2.056  1.00  0.00           H  
HETATM   23  H2  UNL     1       5.108  -0.752  -1.249  1.00  0.00           H  
HETATM   24  H3  UNL     1       4.377   0.661  -2.029  1.00  0.00           H  
HETATM   25  H4  UNL     1       3.002   2.226  -0.593  1.00  0.00           H  
HETATM   26  H5  UNL     1       2.177   0.970  -1.580  1.00  0.00           H  
HETATM   27  H6  UNL     1       0.962   1.933   0.861  1.00  0.00           H  
HETATM   28  H7  UNL     1       2.037   0.779   1.421  1.00  0.00           H  
HETATM   29  H8  UNL     1       0.310   2.317  -0.991  1.00  0.00           H  
HETATM   30  H9  UNL     1      -0.779   4.458  -1.186  1.00  0.00           H  
HETATM   31  H10 UNL     1      -3.161   4.749  -0.567  1.00  0.00           H  
HETATM   32  H11 UNL     1      -4.339   2.851   0.365  1.00  0.00           H  
HETATM   33  H12 UNL     1      -4.701  -2.351   0.750  1.00  0.00           H  
HETATM   34  H13 UNL     1      -3.696  -4.510   0.185  1.00  0.00           H  
HETATM   35  H14 UNL     1      -1.289  -4.587  -0.414  1.00  0.00           H  
HETATM   36  H15 UNL     1       0.016  -2.609  -0.523  1.00  0.00           H  
HETATM   37  H16 UNL     1       1.344  -1.987   0.873  1.00  0.00           H  
HETATM   38  H17 UNL     1       1.804  -1.597  -0.922  1.00  0.00           H  
HETATM   39  H18 UNL     1       3.603  -1.763   0.296  1.00  0.00           H  
HETATM   40  H19 UNL     1       3.075  -0.816   1.649  1.00  0.00           H  
CONECT    1    2   22   23   24
CONECT    2    3   21
CONECT    3    4   25   26
CONECT    4    5   27   28
CONECT    5    6    6   20
CONECT    6    7   19
CONECT    7    8    8   12
CONECT    8    9   29
CONECT    9   10   10   30
CONECT   10   11   31
CONECT   11   12   12   32
CONECT   12   13
CONECT   13   14
CONECT   14   15   15   19
CONECT   15   16   33
CONECT   16   17   17   34
CONECT   17   18   35
CONECT   18   19   19   36
CONECT   20   21   37   38
CONECT   21   39   40
END

HMDB0240247
     RDKit          3D
Pimethixene
 40 43  0  0  0  0  0  0  0  0999 V2000
    4.1342   -0.2557   -1.4372 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5456    0.2074   -0.1988 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.5518    1.2266   -0.5458 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4327    1.0767    0.4137 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6089   -0.1093    0.0925 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6941   -0.0328   -0.1138 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3356    1.3113   -0.0449 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6876    2.4131   -0.5834 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3379    3.6117   -0.7591 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6558    3.8036   -0.4264 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2856    2.6999    0.1007 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6386    1.5264    0.2731 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6304    0.2222    0.9847 S   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8384   -1.2798    0.4559 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6540   -2.3906    0.4893 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1029   -3.6096    0.1736 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7715   -3.6634   -0.1606 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9781   -2.5157   -0.1864 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5026   -1.2763    0.1280 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5502   -1.2462    0.0978 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9835   -0.8376    0.5696 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4563   -0.8535   -2.0556 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1084   -0.7524   -1.2493 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3769    0.6610   -2.0285 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0016    2.2257   -0.5933 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1770    0.9696   -1.5805 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9617    1.9328    0.8612 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0372    0.7791    1.4209 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3103    2.3175   -0.9907 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7790    4.4584   -1.1859 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1614    4.7489   -0.5674 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3390    2.8507    0.3647 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7010   -2.3506    0.7498 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6965   -4.5100    0.1855 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2889   -4.5870   -0.4143 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0158   -2.6094   -0.5230 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3441   -1.9872    0.8731 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8044   -1.5967   -0.9223 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6031   -1.7625    0.2956 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0752   -0.8161    1.6489 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  2  3
  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  2  0
 15 16  1  0
 16 17  2  0
 17 18  1  0
 18 19  2  0
  5 20  1  0
 20 21  1  0
 21  2  1  0
 19  6  1  0
 12  7  1  0
 19 14  1  0
  1 22  1  0
  1 23  1  0
  1 24  1  0
  3 25  1  0
  3 26  1  0
  4 27  1  0
  4 28  1  0
  8 29  1  0
  9 30  1  0
 10 31  1  0
 11 32  1  0
 15 33  1  0
 16 34  1  0
 17 35  1  0
 18 36  1  0
 20 37  1  0
 20 38  1  0
 21 39  1  0
 21 40  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
Calmixene	Kegg
BP 400	HMDB
BP 400S	HMDB
CGA 123427	HMDB
Calmixen	HMDB
Mepithiathene	HMDB
Pimetixene	HMDB
Pimethixene	HMDB
1-Methyl-4-thioxanthen-9-ylidenepiperidine	MeSH, HMDB

Chemical Formula

C₁₉H₁₉NS

Average Molecular Weight

293.43

Monoisotopic Molecular Weight

293.12382079

IUPAC Name

1-methyl-4-(9H-thioxanthen-9-ylidene)piperidine

Traditional Name

pimethixene

CAS Registry Number

314-03-4

SMILES

CN1CCC(CC1)=C1C2=CC=CC=C2SC2=CC=CC=C12

InChI Identifier

InChI=1S/C19H19NS/c1-20-12-10-14(11-13-20)19-15-6-2-4-8-17(15)21-18-9-5-3-7-16(18)19/h2-9H,10-13H2,1H3

InChI Key

NZLVRVYNQYGMAB-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as thioxanthenes. These are organic polycyclic compounds containing a thioxanthene moiety, which is an aromatic tricycle derived from xanthene by replacing the oxygen atom with a sulfur atom.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Benzothiopyrans

Sub Class

1-benzothiopyrans

Direct Parent

Thioxanthenes

Alternative Parents

Substituents

Thioxanthene
Diarylthioether
Aryl thioether
Benzenoid
Piperidine
Tertiary aliphatic amine
Tertiary amine
Azacycle
Thioether
Organic nitrogen compound
Organopnictogen compound
Hydrocarbon derivative
Organonitrogen compound
Amine
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Ontology

Not Available

Exogenous (HMDB: HMDB0240247)

Process

Naturally occurring process

Biological process

Biochemical pathway

Drug action pathway

Pimethixene H1-Antihistamine Action (PathBank: SMP0062886)

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

Experimental Collision Cross Sections

Adduct Type	Data Source	CCS Value (Å²)	Reference
[M+H]+	Not Available	169.07	http://allccs.zhulab.cn/database/detail?ID=AllCCS00001074

Predicted Molecular Properties

Property	Value	Source
logP	4.88	ALOGPS
logP	4.23	ChemAxon
logS	-4.8	ALOGPS
pKa (Strongest Basic)	7.96	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	1	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	3.24 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	102.4 m³·mol⁻¹	ChemAxon
Polarizability	33.78 Å³	ChemAxon
Number of Rings	4	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
DarkChem	[M+H]+	170.307	31661259
DarkChem	[M-H]-	168.295	31661259
DeepCCS	[M-2H]-	195.347	30932474
DeepCCS	[M+Na]+	170.913	30932474
AllCCS	[M+H]+	169.1	32859911
AllCCS	[M+H-H2O]+	165.5	32859911
AllCCS	[M+NH4]+	172.3	32859911
AllCCS	[M+Na]+	173.3	32859911
AllCCS	[M-H]-	175.0	32859911
AllCCS	[M+Na-2H]-	174.1	32859911
AllCCS	[M+HCOO]-	173.2	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.	6.92 minutes	32390414
Predicted by Siyang on May 30, 2022	10.7676 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	2.66 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	1214.4 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	261.4 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	165.9 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	112.7 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	363.3 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	410.1 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	597.6 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	864.3 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	282.5 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	957.7 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	236.4 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	331.5 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	434.1 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	416.3 seconds	40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water	77.3 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Pimethixene	CN1CCC(CC1)=C1C2=CC=CC=C2SC2=CC=CC=C12	3634.1	Standard polar	33892256
Pimethixene	CN1CCC(CC1)=C1C2=CC=CC=C2SC2=CC=CC=C12	2458.4	Standard non polar	33892256
Pimethixene	CN1CCC(CC1)=C1C2=CC=CC=C2SC2=CC=CC=C12	2414.1	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 - Pimethixene GC-MS (Non-derivatized) - 70eV, Positive	splash10-0fvu-0090000000-669233b3d4017cf5ae6d	2017-08-28	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Pimethixene 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 - Pimethixene 10V, Positive-QTOF	splash10-0006-0090000000-961e3d483425f281edea	2017-07-26	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Pimethixene 20V, Positive-QTOF	splash10-0006-2290000000-582d1975ecd2ae8340bc	2017-07-26	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Pimethixene 40V, Positive-QTOF	splash10-0570-9360000000-5940717536a594fe752b	2017-07-26	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Pimethixene 10V, Negative-QTOF	splash10-0006-0090000000-22f5dd3814fa15438ad3	2017-07-26	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Pimethixene 20V, Negative-QTOF	splash10-0006-0090000000-3fb864ec42379977b864	2017-07-26	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Pimethixene 40V, Negative-QTOF	splash10-00fu-5090000000-ab276ee3bf3790a8f1b8	2017-07-26	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Pimethixene 10V, Positive-QTOF	splash10-0006-0090000000-b51412c963a6f2ebbd01	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Pimethixene 20V, Positive-QTOF	splash10-0006-0090000000-b51412c963a6f2ebbd01	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Pimethixene 40V, Positive-QTOF	splash10-02ac-1290000000-252a235950675b6d0f63	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Pimethixene 10V, Negative-QTOF	splash10-0006-0090000000-b01c5a3dad8ef5bed833	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Pimethixene 20V, Negative-QTOF	splash10-0006-0090000000-e3ee3f3242211dc7bb2c	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Pimethixene 40V, Negative-QTOF	splash10-00di-0190000000-d5f3cf217c7817ffa1f5	2021-09-22	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Pathways

Name	SMPDB/PathBank	KEGG
Pimethixene H1-Antihistamine Action		Not Available

Normal Concentrations

Not Available

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

DB13292

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

4656

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Pimethixene

METLIN ID

Not Available

PubChem Compound

4822

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

Schmitz B, Ullmer C, Segelcke D, Gwarek M, Zhu XR, Lubbert H: BF-1--a novel selective 5-HT2B receptor antagonist blocking neurogenic dural plasma protein extravasation in guinea pigs. Eur J Pharmacol. 2015 Mar 15;751:73-80. doi: 10.1016/j.ejphar.2015.01.043. Epub 2015 Feb 7. [PubMed:25666387 ]

Showing metabocard for Pimethixene (HMDB0240247)

MOL for HMDB0240247 (Pimethixene)

3D MOL for HMDB0240247 (Pimethixene)

3D SDF for HMDB0240247 (Pimethixene)

3D-SDF for HMDB0240247 (Pimethixene)

PDB for HMDB0240247 (Pimethixene)

3D PDB for HMDB0240247 (Pimethixene)

SMILES for HMDB0240247 (Pimethixene)

INCHI for HMDB0240247 (Pimethixene)

Structure for HMDB0240247 (Pimethixene)

3D Structure for HMDB0240247 (Pimethixene)

Experimental Collision Cross Sections

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

GC-MS Spectra

MS/MS Spectra