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Showing metabocard for Thioxanthene (HMDB0259038)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 20:56:59 UTC
Update Date2021-09-26 23:16:19 UTC
HMDB IDHMDB0259038
Secondary Accession NumbersNone
Metabolite Identification
Common NameThioxanthene
Description9H-thioxanthene 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. Based on a literature review very few articles have been published on 9H-thioxanthene. This compound has been identified in human blood as reported by (PMID: 31557052 ). Thioxanthene is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Thioxanthene 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
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0259038 (Thioxanthene)


  Mrv1652309112122572D          

 14 16  0  0  0  0            999 V2000
    2.1434    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.8250    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    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    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
  7  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
  1 14  1  0  0  0  0
M  END
Download

3D MOL for HMDB0259038 (Thioxanthene)

HMDB0259038
     RDKit          3D
Thioxanthene
 24 26  0  0  0  0  0  0  0  0999 V2000
   -3.4831    0.3386   -0.6827 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5383    1.0842    0.4520 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4270    1.0479    1.3134 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3378    0.2902    1.0144 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2524   -0.4732   -0.1221 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3723   -0.4287   -0.9785 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1196   -1.3314   -0.4983 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1666   -0.6512   -0.1844 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2352   -0.7680   -1.0910 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4537   -0.1874   -0.8617 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6726    0.5441    0.2893 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6102    0.6613    1.1916 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4229    0.0774    0.9353 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0771    0.2729    2.0976 S   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3486    0.3656   -1.3563 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4071    1.6796    0.6764 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5183    1.6570    2.2022 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3981   -0.9961   -1.8982 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1440   -1.5379   -1.5840 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1073   -2.2715    0.0972 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0730   -1.3337   -1.9858 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2769   -0.2867   -1.5766 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6395    0.9943    0.4533 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8261    1.2528    2.0968 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  5  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
  6  1  1  0
 13  8  1  0
 14  4  1  0
  1 15  1  0
  2 16  1  0
  3 17  1  0
  6 18  1  0
  7 19  1  0
  7 20  1  0
  9 21  1  0
 10 22  1  0
 11 23  1  0
 12 24  1  0
M  END
Download

3D SDF for HMDB0259038 (Thioxanthene)


  Mrv1652309112122572D          

 14 16  0  0  0  0            999 V2000
    2.1434    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.8250    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    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    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
  7  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
  1 14  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0259038

> <DATABASE_NAME>
hmdb

> <SMILES>
C1C2=CC=CC=C2SC2=CC=CC=C12

> <INCHI_IDENTIFIER>
InChI=1S/C13H10S/c1-3-7-12-10(5-1)9-11-6-2-4-8-13(11)14-12/h1-8H,9H2

> <INCHI_KEY>
PQJUJGAVDBINPI-UHFFFAOYSA-N

> <FORMULA>
C13H10S

> <MOLECULAR_WEIGHT>
198.28

> <EXACT_MASS>
198.050321496

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_ATOM_COUNT>
24

> <JCHEM_AVERAGE_POLARIZABILITY>
22.235025854690036

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
9H-thioxanthene

> <ALOGPS_LOGP>
4.61

> <JCHEM_LOGP>
4.280543490666666

> <ALOGPS_LOGS>
-4.83

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_POLAR_SURFACE_AREA>
0.0

> <JCHEM_REFRACTIVITY>
62.42130000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.96e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
thioxanthene

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0259038 (Thioxanthene)

HMDB0259038
     RDKit          3D
Thioxanthene
 24 26  0  0  0  0  0  0  0  0999 V2000
   -3.4831    0.3386   -0.6827 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5383    1.0842    0.4520 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4270    1.0479    1.3134 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3378    0.2902    1.0144 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2524   -0.4732   -0.1221 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3723   -0.4287   -0.9785 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1196   -1.3314   -0.4983 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1666   -0.6512   -0.1844 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2352   -0.7680   -1.0910 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4537   -0.1874   -0.8617 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6726    0.5441    0.2893 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6102    0.6613    1.1916 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4229    0.0774    0.9353 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0771    0.2729    2.0976 S   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3486    0.3656   -1.3563 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4071    1.6796    0.6764 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5183    1.6570    2.2022 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3981   -0.9961   -1.8982 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1440   -1.5379   -1.5840 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1073   -2.2715    0.0972 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0730   -1.3337   -1.9858 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2769   -0.2867   -1.5766 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6395    0.9943    0.4533 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8261    1.2528    2.0968 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  5  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
  6  1  1  0
 13  8  1  0
 14  4  1  0
  1 15  1  0
  2 16  1  0
  3 17  1  0
  6 18  1  0
  7 19  1  0
  7 20  1  0
  9 21  1  0
 10 22  1  0
 11 23  1  0
 12 24  1  0
M  END
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PDB for HMDB0259038 (Thioxanthene)

HEADER    PROTEIN                                 11-SEP-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-SEP-21         0                                  
HETATM    1  C   UNK     0       4.001   2.310   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       5.335   1.540   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       6.668   2.310   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       8.002   1.540   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       8.002  -0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM    8  S   UNK     0       4.001  -0.770   0.000  0.00  0.00           S+0
HETATM    9  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
CONECT    1    2   14                                                       
CONECT    2    1    3    7                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    2    8                                                  
CONECT    8    7    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    1                                                  
MASTER        0    0    0    0    0    0    0    0   14    0   32    0
END
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3D PDB for HMDB0259038 (Thioxanthene)

COMPND    HMDB0259038
HETATM    1  C1  UNL     1      -3.483   0.339  -0.683  1.00  0.00           C  
HETATM    2  C2  UNL     1      -3.538   1.084   0.452  1.00  0.00           C  
HETATM    3  C3  UNL     1      -2.427   1.048   1.313  1.00  0.00           C  
HETATM    4  C4  UNL     1      -1.338   0.290   1.014  1.00  0.00           C  
HETATM    5  C5  UNL     1      -1.252  -0.473  -0.122  1.00  0.00           C  
HETATM    6  C6  UNL     1      -2.372  -0.429  -0.978  1.00  0.00           C  
HETATM    7  C7  UNL     1      -0.120  -1.331  -0.498  1.00  0.00           C  
HETATM    8  C8  UNL     1       1.167  -0.651  -0.184  1.00  0.00           C  
HETATM    9  C9  UNL     1       2.235  -0.768  -1.091  1.00  0.00           C  
HETATM   10  C10 UNL     1       3.454  -0.187  -0.862  1.00  0.00           C  
HETATM   11  C11 UNL     1       3.673   0.544   0.289  1.00  0.00           C  
HETATM   12  C12 UNL     1       2.610   0.661   1.192  1.00  0.00           C  
HETATM   13  C13 UNL     1       1.423   0.077   0.935  1.00  0.00           C  
HETATM   14  S1  UNL     1       0.077   0.273   2.098  1.00  0.00           S  
HETATM   15  H1  UNL     1      -4.349   0.366  -1.356  1.00  0.00           H  
HETATM   16  H2  UNL     1      -4.407   1.680   0.676  1.00  0.00           H  
HETATM   17  H3  UNL     1      -2.518   1.657   2.202  1.00  0.00           H  
HETATM   18  H4  UNL     1      -2.398  -0.996  -1.898  1.00  0.00           H  
HETATM   19  H5  UNL     1      -0.144  -1.538  -1.584  1.00  0.00           H  
HETATM   20  H6  UNL     1      -0.107  -2.272   0.097  1.00  0.00           H  
HETATM   21  H7  UNL     1       2.073  -1.334  -1.986  1.00  0.00           H  
HETATM   22  H8  UNL     1       4.277  -0.287  -1.577  1.00  0.00           H  
HETATM   23  H9  UNL     1       4.640   0.994   0.453  1.00  0.00           H  
HETATM   24  H10 UNL     1       2.826   1.253   2.097  1.00  0.00           H  
CONECT    1    2    2    6   15
CONECT    2    3   16
CONECT    3    4    4   17
CONECT    4    5   14
CONECT    5    6    6    7
CONECT    6   18
CONECT    7    8   19   20
CONECT    8    9    9   13
CONECT    9   10   21
CONECT   10   11   11   22
CONECT   11   12   23
CONECT   12   13   13   24
CONECT   13   14
END
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SMILES for HMDB0259038 (Thioxanthene)

C1C2=CC=CC=C2SC2=CC=CC=C12
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INCHI for HMDB0259038 (Thioxanthene)

InChI=1S/C13H10S/c1-3-7-12-10(5-1)9-11-6-2-4-8-13(11)14-12/h1-8H,9H2
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View in JSmolView Stereo Labels
Synonyms
ValueSource
ThioxantheneChEBI
ThioxanthineChEBI
6-ThioxanthineMeSH
Chemical FormulaC13H10S
Average Molecular Weight198.28
Monoisotopic Molecular Weight198.050321496
IUPAC Name9H-thioxanthene
Traditional Namethioxanthene
CAS Registry NumberNot Available
SMILES
C1C2=CC=CC=C2SC2=CC=CC=C12
InChI Identifier
InChI=1S/C13H10S/c1-3-7-12-10(5-1)9-11-6-2-4-8-13(11)14-12/h1-8H,9H2
InChI KeyPQJUJGAVDBINPI-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.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassBenzothiopyrans
Sub Class1-benzothiopyrans
Direct ParentThioxanthenes
Alternative Parents
Substituents
  • Thioxanthene
  • Diarylthioether
  • Aryl thioether
  • Benzenoid
  • Thioether
  • Hydrocarbon derivative
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological location
ProcessNot Available
RoleNot Available
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
logP4.61ALOGPS
logP4.28ChemAxon
logS-4.8ALOGPS
Physiological Charge0ChemAxon
Hydrogen Acceptor Count0ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area0 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity62.42 m³·mol⁻¹ChemAxon
Polarizability22.24 ųChemAxon
Number of Rings3ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M-2H]-170.34830932474
DeepCCS[M+Na]+145.88730932474
AllCCS[M+H]+140.532859911
AllCCS[M+H-H2O]+136.132859911
AllCCS[M+NH4]+144.632859911
AllCCS[M+Na]+145.832859911
AllCCS[M-H]-141.032859911
AllCCS[M+Na-2H]-140.532859911
AllCCS[M+HCOO]-140.032859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
ThioxantheneC1C2=CC=CC=C2SC2=CC=CC=C122529.2Standard polar33892256
ThioxantheneC1C2=CC=CC=C2SC2=CC=CC=C121808.4Standard non polar33892256
ThioxantheneC1C2=CC=CC=C2SC2=CC=CC=C121966.3Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Thioxanthene GC-MS (Non-derivatized) - 70eV, Positivesplash10-006t-0900000000-c3658abe1eb0b707f2872021-09-24Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Thioxanthene GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID60819
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkThioxanthene
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI ID51055
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1372771
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. 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 ]