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Showing metabocard for 5-Hydroxythiabendazole (HMDB0247680)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 00:44:14 UTC
Update Date2021-09-26 22:57:31 UTC
HMDB IDHMDB0247680
Secondary Accession NumbersNone
Metabolite Identification
Common Name5-Hydroxythiabendazole
Description5-Hydroxythiabendazole belongs to the class of organic compounds known as benzimidazoles. These are organic compounds containing a benzene ring fused to an imidazole ring (five member ring containing a nitrogen atom, 4 carbon atoms, and two double bonds). Based on a literature review very few articles have been published on 5-Hydroxythiabendazole. This compound has been identified in human blood as reported by (PMID: 31557052 ). 5-hydroxythiabendazole is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 5-Hydroxythiabendazole 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 HMDB0247680 (5-Hydroxythiabendazole)

  Mrv1652306031607152D          

 15 17  0  0  0  0            999 V2000
    3.9934    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2789    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2789   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0150   -0.2549    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7996    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9934    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5645    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5645    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4699    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2949    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0150    1.0799    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.7798    1.0799    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.7798   -0.2549    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.7079   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7996    0.0000    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  2  0  0  0  0
  6  1  1  0  0  0  0
  6  3  2  0  0  0  0
  7  2  1  0  0  0  0
  8  3  1  0  0  0  0
  8  7  2  0  0  0  0
  9  4  2  0  0  0  0
 10  9  1  0  0  0  0
 11  5  2  0  0  0  0
 11  9  1  0  0  0  0
 12  7  1  0  0  0  0
 12 10  2  0  0  0  0
 13  8  1  0  0  0  0
 13 10  1  0  0  0  0
 14  6  1  0  0  0  0
 15  4  1  0  0  0  0
 15  5  1  0  0  0  0
M  END
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3D MOL for HMDB0247680 (5-Hydroxythiabendazole)

HMDB0247680
     RDKit          3D
5-Hydroxythiabendazole
 22 24  0  0  0  0  0  0  0  0999 V2000
    4.6344   -0.1850    0.5716 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2902   -0.3712    0.2047 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0598   -1.3218   -0.7698 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7483   -1.5171   -1.1413 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7096   -0.7990   -0.5695 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6196   -0.7731   -0.7240 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1993    0.1249    0.0885 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6560    0.4348    0.1985 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1156    1.3858    1.0799 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7973    1.3309    0.7975 S   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8170    0.1206   -0.4061 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5353   -0.1778   -0.5285 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2045    0.6882    0.7823 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.9771    0.1416    0.4000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2796    0.3548    0.7881 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8608    0.4867    1.2688 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8772   -1.8764   -1.2093 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5092   -2.2403   -1.8914 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5136    2.0021    1.7730 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6629   -0.3257   -0.9637 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3206    1.4332    1.5058 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4955    1.0837    1.5407 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  2  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  1  0
 11 12  2  0
  7 13  1  0
 13 14  1  0
 14 15  2  0
 15  2  1  0
 14  5  1  0
 12  8  1  0
  1 16  1  0
  3 17  1  0
  4 18  1  0
  9 19  1  0
 11 20  1  0
 13 21  1  0
 15 22  1  0
M  END
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3D SDF for HMDB0247680 (5-Hydroxythiabendazole)

  Mrv1652306031607152D          

 15 17  0  0  0  0            999 V2000
    3.9934    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2789    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2789   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0150   -0.2549    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7996    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9934    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5645    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5645    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4699    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2949    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0150    1.0799    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.7798    1.0799    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.7798   -0.2549    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.7079   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7996    0.0000    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  2  0  0  0  0
  6  1  1  0  0  0  0
  6  3  2  0  0  0  0
  7  2  1  0  0  0  0
  8  3  1  0  0  0  0
  8  7  2  0  0  0  0
  9  4  2  0  0  0  0
 10  9  1  0  0  0  0
 11  5  2  0  0  0  0
 11  9  1  0  0  0  0
 12  7  1  0  0  0  0
 12 10  2  0  0  0  0
 13  8  1  0  0  0  0
 13 10  1  0  0  0  0
 14  6  1  0  0  0  0
 15  4  1  0  0  0  0
 15  5  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0247680

> <DATABASE_NAME>
hmdb

> <SMILES>
OC1=CC2=C(C=C1)N=C(N2)C1=CSC=N1

> <INCHI_IDENTIFIER>
InChI=1S/C10H7N3OS/c14-6-1-2-7-8(3-6)13-10(12-7)9-4-15-5-11-9/h1-5,14H,(H,12,13)

> <INCHI_KEY>
VNENJHUOPQAPAT-UHFFFAOYSA-N

> <FORMULA>
C10H7N3OS

> <MOLECULAR_WEIGHT>
217.25

> <EXACT_MASS>
217.030983031

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
22

> <JCHEM_AVERAGE_POLARIZABILITY>
22.061363315936653

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
2-(1,3-thiazol-4-yl)-1H-1,3-benzodiazol-6-ol

> <ALOGPS_LOGP>
2.25

> <JCHEM_LOGP>
2.0253520326666665

> <ALOGPS_LOGS>
-3.17

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
11.312273377623963

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.286748722959025

> <JCHEM_PKA_STRONGEST_BASIC>
4.378788951196795

> <JCHEM_POLAR_SURFACE_AREA>
61.8

> <JCHEM_REFRACTIVITY>
66.88739999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.47e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-(1,3-thiazol-4-yl)-3H-1,3-benzodiazol-5-ol

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0247680 (5-Hydroxythiabendazole)

HMDB0247680
     RDKit          3D
5-Hydroxythiabendazole
 22 24  0  0  0  0  0  0  0  0999 V2000
    4.6344   -0.1850    0.5716 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2902   -0.3712    0.2047 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0598   -1.3218   -0.7698 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7483   -1.5171   -1.1413 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7096   -0.7990   -0.5695 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6196   -0.7731   -0.7240 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1993    0.1249    0.0885 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6560    0.4348    0.1985 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1156    1.3858    1.0799 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7973    1.3309    0.7975 S   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8170    0.1206   -0.4061 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5353   -0.1778   -0.5285 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2045    0.6882    0.7823 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.9771    0.1416    0.4000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2796    0.3548    0.7881 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8608    0.4867    1.2688 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8772   -1.8764   -1.2093 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5092   -2.2403   -1.8914 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5136    2.0021    1.7730 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6629   -0.3257   -0.9637 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3206    1.4332    1.5058 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4955    1.0837    1.5407 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  2  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  1  0
 11 12  2  0
  7 13  1  0
 13 14  1  0
 14 15  2  0
 15  2  1  0
 14  5  1  0
 12  8  1  0
  1 16  1  0
  3 17  1  0
  4 18  1  0
  9 19  1  0
 11 20  1  0
 13 21  1  0
 15 22  1  0
M  END
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PDB for HMDB0247680 (5-Hydroxythiabendazole)

HEADER    PROTEIN                                 03-JUN-16   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   03-JUN-16         0                                  
HETATM    1  C   UNK     0       7.454   1.540   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       6.121   2.310   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       6.121  -0.770   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.028  -0.476   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -1.493   1.540   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       7.454   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       4.787   1.540   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.787   0.000   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.877   0.770   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.417   0.770   0.000  0.00  0.00           C+0
HETATM   11  N   UNK     0      -0.028   2.016   0.000  0.00  0.00           N+0
HETATM   12  N   UNK     0       3.322   2.016   0.000  0.00  0.00           N+0
HETATM   13  N   UNK     0       3.322  -0.476   0.000  0.00  0.00           N+0
HETATM   14  O   UNK     0       8.788  -0.770   0.000  0.00  0.00           O+0
HETATM   15  S   UNK     0      -1.493   0.000   0.000  0.00  0.00           S+0
CONECT    1    2    6                                                       
CONECT    2    1    7                                                       
CONECT    3    6    8                                                       
CONECT    4    9   15                                                       
CONECT    5   11   15                                                       
CONECT    6    1    3   14                                                  
CONECT    7    2    8   12                                                  
CONECT    8    3    7   13                                                  
CONECT    9    4   10   11                                                  
CONECT   10    9   12   13                                                  
CONECT   11    5    9                                                       
CONECT   12    7   10                                                       
CONECT   13    8   10                                                       
CONECT   14    6                                                            
CONECT   15    4    5                                                       
MASTER        0    0    0    0    0    0    0    0   15    0   34    0
END
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3D PDB for HMDB0247680 (5-Hydroxythiabendazole)

COMPND    HMDB0247680
HETATM    1  O1  UNL     1       4.634  -0.185   0.572  1.00  0.00           O  
HETATM    2  C1  UNL     1       3.290  -0.371   0.205  1.00  0.00           C  
HETATM    3  C2  UNL     1       3.060  -1.322  -0.770  1.00  0.00           C  
HETATM    4  C3  UNL     1       1.748  -1.517  -1.141  1.00  0.00           C  
HETATM    5  C4  UNL     1       0.710  -0.799  -0.570  1.00  0.00           C  
HETATM    6  N1  UNL     1      -0.620  -0.773  -0.724  1.00  0.00           N  
HETATM    7  C5  UNL     1      -1.199   0.125   0.088  1.00  0.00           C  
HETATM    8  C6  UNL     1      -2.656   0.435   0.199  1.00  0.00           C  
HETATM    9  C7  UNL     1      -3.116   1.386   1.080  1.00  0.00           C  
HETATM   10  S1  UNL     1      -4.797   1.331   0.797  1.00  0.00           S  
HETATM   11  C8  UNL     1      -4.817   0.121  -0.406  1.00  0.00           C  
HETATM   12  N2  UNL     1      -3.535  -0.178  -0.529  1.00  0.00           N  
HETATM   13  N3  UNL     1      -0.205   0.688   0.782  1.00  0.00           N  
HETATM   14  C9  UNL     1       0.977   0.142   0.400  1.00  0.00           C  
HETATM   15  C10 UNL     1       2.280   0.355   0.788  1.00  0.00           C  
HETATM   16  H1  UNL     1       4.861   0.487   1.269  1.00  0.00           H  
HETATM   17  H2  UNL     1       3.877  -1.876  -1.209  1.00  0.00           H  
HETATM   18  H3  UNL     1       1.509  -2.240  -1.891  1.00  0.00           H  
HETATM   19  H4  UNL     1      -2.514   2.002   1.773  1.00  0.00           H  
HETATM   20  H5  UNL     1      -5.663  -0.326  -0.964  1.00  0.00           H  
HETATM   21  H6  UNL     1      -0.321   1.433   1.506  1.00  0.00           H  
HETATM   22  H7  UNL     1       2.495   1.084   1.541  1.00  0.00           H  
CONECT    1    2   16
CONECT    2    3    3   15
CONECT    3    4   17
CONECT    4    5    5   18
CONECT    5    6   14
CONECT    6    7    7
CONECT    7    8   13
CONECT    8    9    9   12
CONECT    9   10   19
CONECT   10   11
CONECT   11   12   12   20
CONECT   13   14   21
CONECT   14   15   15
CONECT   15   22
END
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SMILES for HMDB0247680 (5-Hydroxythiabendazole)

OC1=CC2=C(C=C1)N=C(N2)C1=CSC=N1
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INCHI for HMDB0247680 (5-Hydroxythiabendazole)

InChI=1S/C10H7N3OS/c14-6-1-2-7-8(3-6)13-10(12-7)9-4-15-5-11-9/h1-5,14H,(H,12,13)
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View in JSmolView Stereo Labels
Synonyms
ValueSource
5-HydroxythiabendazoleMeSH
Chemical FormulaC10H7N3OS
Average Molecular Weight217.25
Monoisotopic Molecular Weight217.030983031
IUPAC Name2-(1,3-thiazol-4-yl)-1H-1,3-benzodiazol-6-ol
Traditional Name2-(1,3-thiazol-4-yl)-3H-1,3-benzodiazol-5-ol
CAS Registry NumberNot Available
SMILES
OC1=CC2=C(C=C1)N=C(N2)C1=CSC=N1
InChI Identifier
InChI=1S/C10H7N3OS/c14-6-1-2-7-8(3-6)13-10(12-7)9-4-15-5-11-9/h1-5,14H,(H,12,13)
InChI KeyVNENJHUOPQAPAT-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as benzimidazoles. These are organic compounds containing a benzene ring fused to an imidazole ring (five member ring containing a nitrogen atom, 4 carbon atoms, and two double bonds).
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassBenzimidazoles
Sub ClassNot Available
Direct ParentBenzimidazoles
Alternative Parents
Substituents
  • Benzimidazole
  • 1-hydroxy-2-unsubstituted benzenoid
  • Benzenoid
  • Heteroaromatic compound
  • Thiazole
  • Imidazole
  • Azole
  • Azacycle
  • Organic nitrogen compound
  • Organic oxygen compound
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organonitrogen compound
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
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
Predicted Chromatographic Properties
Spectra
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 ID97293
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound108227
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
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 ]