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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-10 21:35:13 UTC

Update Date

2021-09-26 22:52:09 UTC

HMDB ID

HMDB0244427

Secondary Accession Numbers

None

Metabolite Identification

Common Name

Rabeprazole thioether

Description

Rabeprazole thioether 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 a significant number of articles have been published on Rabeprazole thioether. This compound has been identified in human blood as reported by (PMID: 31557052 ). Rabeprazole thioether is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Rabeprazole thioether 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

HMDB0244427
     RDKit          3D
Rabeprazole thioether
 45 47  0  0  0  0  0  0  0  0999 V2000
    6.8128   -0.9818    0.9304 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0521   -2.0782    1.0054 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9539   -2.3144    0.3030 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7556   -1.4522    0.3561 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8800   -0.0477   -0.0998 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7533    0.7333   -0.0659 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5487    0.7123   -0.6637 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0778   -0.1808   -1.5738 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2095   -0.0627   -2.1075 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0098    0.9430   -1.7282 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5940    1.8523   -0.8332 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4554    2.9879   -0.3959 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0457    2.8739   -1.2361 S   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9366    1.4503   -0.6589 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7287    1.4705    0.4345 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2742    0.2669    0.6528 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1323   -0.1954    1.6251 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5147   -1.5333    1.5612 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0739   -2.3889    0.5815 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2145   -1.8664   -0.3661 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8052   -0.5521   -0.3494 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9914    0.2000   -1.1337 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.6678    1.7478   -0.3011 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1040    2.7859    0.7022 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2145   -0.7102   -0.0725 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4989   -0.1633    1.5676 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.8173   -1.2989    1.4518 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6142   -3.3801    0.5871 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1902   -2.4296   -0.8243 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9526   -1.9771   -0.2396 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3744   -1.5035    1.4207 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2686   -0.0561   -1.1490 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6492    0.5000    0.5210 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7098   -0.9865   -1.8988 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5694   -0.7820   -2.8304 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9458    3.9519   -0.5883 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5652    2.8773    0.7066 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4841    0.4656    2.3975 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1872   -1.8748    2.3325 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4011   -3.4177    0.5775 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8691   -2.5440   -1.1370 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5055   -0.1749   -1.9738 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3676    2.7990    1.5423 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1405    3.7906    0.2289 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1096    2.5442    1.0409 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  1  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  1  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
 19 20  1  0
 20 21  2  0
 21 22  1  0
 11 23  2  0
 23 24  1  0
 23  7  1  0
 22 14  1  0
 21 16  1  0
  1 25  1  0
  1 26  1  0
  1 27  1  0
  3 28  1  0
  3 29  1  0
  4 30  1  0
  4 31  1  0
  5 32  1  0
  5 33  1  0
  8 34  1  0
  9 35  1  0
 12 36  1  0
 12 37  1  0
 17 38  1  0
 18 39  1  0
 19 40  1  0
 20 41  1  0
 22 42  1  0
 24 43  1  0
 24 44  1  0
 24 45  1  0
M  END

  Mrv1652309102123352D          

 24 26  0  0  0  0            999 V2000
    5.4190   -1.7991    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7045   -2.2116    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7045   -3.0366    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9900   -3.4491    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2756   -3.0366    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2756   -2.2116    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.9900   -1.7991    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9900   -0.9741    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2756   -0.5616    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    3.2756    0.2634    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6081    0.7483    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.8631    1.5329    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4506    2.2474    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8631    2.9619    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6881    2.9619    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1006    2.2474    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6881    1.5329    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9430    0.7483    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.4190   -3.4491    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.1334   -3.0366    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8479   -3.4491    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.5624   -3.0366    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.2769   -3.4491    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.9913   -3.0366    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  1  0  0  0  0
 10 11  2  0  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
 13 14  1  0  0  0  0
 14 15  2  0  0  0  0
 15 16  1  0  0  0  0
 16 17  2  0  0  0  0
 12 17  1  0  0  0  0
 17 18  1  0  0  0  0
 10 18  1  0  0  0  0
  3 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0244427

> <DATABASE_NAME>
hmdb

> <SMILES>
COCCCOC1=C(C)C(CSC2=NC3=CC=CC=C3N2)=NC=C1

> <INCHI_IDENTIFIER>
InChI=1S/C18H21N3O2S/c1-13-16(19-9-8-17(13)23-11-5-10-22-2)12-24-18-20-14-6-3-4-7-15(14)21-18/h3-4,6-9H,5,10-12H2,1-2H3,(H,20,21)

> <INCHI_KEY>
BSXAHDOWMOSVAP-UHFFFAOYSA-N

> <FORMULA>
C18H21N3O2S

> <MOLECULAR_WEIGHT>
343.45

> <EXACT_MASS>
343.135448102

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
45

> <JCHEM_AVERAGE_POLARIZABILITY>
38.9786820678754

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
2-({[4-(3-methoxypropoxy)-3-methylpyridin-2-yl]methyl}sulfanyl)-1H-1,3-benzodiazole

> <ALOGPS_LOGP>
3.37

> <JCHEM_LOGP>
3.2176441843333325

> <ALOGPS_LOGS>
-5.09

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
10.421230858072027

> <JCHEM_PKA_STRONGEST_BASIC>
6.161633322417007

> <JCHEM_POLAR_SURFACE_AREA>
60.03

> <JCHEM_REFRACTIVITY>
96.69510000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.79e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-({[4-(3-methoxypropoxy)-3-methylpyridin-2-yl]methyl}sulfanyl)-1H-1,3-benzodiazole

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0244427
     RDKit          3D
Rabeprazole thioether
 45 47  0  0  0  0  0  0  0  0999 V2000
    6.8128   -0.9818    0.9304 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0521   -2.0782    1.0054 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9539   -2.3144    0.3030 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7556   -1.4522    0.3561 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8800   -0.0477   -0.0998 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7533    0.7333   -0.0659 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5487    0.7123   -0.6637 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0778   -0.1808   -1.5738 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2095   -0.0627   -2.1075 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0098    0.9430   -1.7282 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5940    1.8523   -0.8332 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4554    2.9879   -0.3959 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0457    2.8739   -1.2361 S   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9366    1.4503   -0.6589 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7287    1.4705    0.4345 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2742    0.2669    0.6528 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1323   -0.1954    1.6251 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5147   -1.5333    1.5612 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0739   -2.3889    0.5815 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2145   -1.8664   -0.3661 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8052   -0.5521   -0.3494 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9914    0.2000   -1.1337 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.6678    1.7478   -0.3011 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1040    2.7859    0.7022 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2145   -0.7102   -0.0725 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4989   -0.1633    1.5676 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.8173   -1.2989    1.4518 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6142   -3.3801    0.5871 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1902   -2.4296   -0.8243 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9526   -1.9771   -0.2396 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3744   -1.5035    1.4207 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2686   -0.0561   -1.1490 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6492    0.5000    0.5210 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7098   -0.9865   -1.8988 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5694   -0.7820   -2.8304 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9458    3.9519   -0.5883 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5652    2.8773    0.7066 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4841    0.4656    2.3975 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1872   -1.8748    2.3325 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4011   -3.4177    0.5775 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8691   -2.5440   -1.1370 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5055   -0.1749   -1.9738 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3676    2.7990    1.5423 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1405    3.7906    0.2289 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1096    2.5442    1.0409 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  1  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  1  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
 19 20  1  0
 20 21  2  0
 21 22  1  0
 11 23  2  0
 23 24  1  0
 23  7  1  0
 22 14  1  0
 21 16  1  0
  1 25  1  0
  1 26  1  0
  1 27  1  0
  3 28  1  0
  3 29  1  0
  4 30  1  0
  4 31  1  0
  5 32  1  0
  5 33  1  0
  8 34  1  0
  9 35  1  0
 12 36  1  0
 12 37  1  0
 17 38  1  0
 18 39  1  0
 19 40  1  0
 20 41  1  0
 22 42  1  0
 24 43  1  0
 24 44  1  0
 24 45  1  0
M  END

HEADER    PROTEIN                                 10-SEP-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   10-SEP-21         0                                  
HETATM    1  C   UNK     0      10.115  -3.358   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       8.782  -4.128   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       8.782  -5.668   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       7.448  -6.438   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       6.114  -5.668   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0       6.114  -4.128   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0       7.448  -3.358   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       7.448  -1.818   0.000  0.00  0.00           C+0
HETATM    9  S   UNK     0       6.114  -1.048   0.000  0.00  0.00           S+0
HETATM   10  C   UNK     0       6.114   0.492   0.000  0.00  0.00           C+0
HETATM   11  N   UNK     0       4.869   1.397   0.000  0.00  0.00           N+0
HETATM   12  C   UNK     0       5.344   2.861   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       4.574   4.195   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       5.344   5.529   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       6.884   5.529   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       7.654   4.195   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       6.884   2.861   0.000  0.00  0.00           C+0
HETATM   18  N   UNK     0       7.360   1.397   0.000  0.00  0.00           N+0
HETATM   19  O   UNK     0      10.115  -6.438   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0      11.449  -5.668   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      12.783  -6.438   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      14.116  -5.668   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0      15.450  -6.438   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0      16.784  -5.668   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    7                                                  
CONECT    3    2    4   19                                                  
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                                                       
CONECT   10    9   11   18                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13   17                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   12   18                                                  
CONECT   18   17   10                                                       
CONECT   19    3   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   23                                                       
CONECT   23   22   24                                                       
CONECT   24   23                                                            
MASTER        0    0    0    0    0    0    0    0   24    0   52    0
END

COMPND    HMDB0244427
HETATM    1  C1  UNL     1       6.813  -0.982   0.930  1.00  0.00           C  
HETATM    2  O1  UNL     1       6.052  -2.078   1.005  1.00  0.00           O  
HETATM    3  C2  UNL     1       4.954  -2.314   0.303  1.00  0.00           C  
HETATM    4  C3  UNL     1       3.756  -1.452   0.356  1.00  0.00           C  
HETATM    5  C4  UNL     1       3.880  -0.048  -0.100  1.00  0.00           C  
HETATM    6  O2  UNL     1       2.753   0.733  -0.066  1.00  0.00           O  
HETATM    7  C5  UNL     1       1.549   0.712  -0.664  1.00  0.00           C  
HETATM    8  C6  UNL     1       1.078  -0.181  -1.574  1.00  0.00           C  
HETATM    9  C7  UNL     1      -0.209  -0.063  -2.108  1.00  0.00           C  
HETATM   10  N1  UNL     1      -1.010   0.943  -1.728  1.00  0.00           N  
HETATM   11  C8  UNL     1      -0.594   1.852  -0.833  1.00  0.00           C  
HETATM   12  C9  UNL     1      -1.455   2.988  -0.396  1.00  0.00           C  
HETATM   13  S1  UNL     1      -3.046   2.874  -1.236  1.00  0.00           S  
HETATM   14  C10 UNL     1      -3.937   1.450  -0.659  1.00  0.00           C  
HETATM   15  N2  UNL     1      -4.729   1.470   0.435  1.00  0.00           N  
HETATM   16  C11 UNL     1      -5.274   0.267   0.653  1.00  0.00           C  
HETATM   17  C12 UNL     1      -6.132  -0.195   1.625  1.00  0.00           C  
HETATM   18  C13 UNL     1      -6.515  -1.533   1.561  1.00  0.00           C  
HETATM   19  C14 UNL     1      -6.074  -2.389   0.582  1.00  0.00           C  
HETATM   20  C15 UNL     1      -5.215  -1.866  -0.366  1.00  0.00           C  
HETATM   21  C16 UNL     1      -4.805  -0.552  -0.349  1.00  0.00           C  
HETATM   22  N3  UNL     1      -3.991   0.200  -1.134  1.00  0.00           N  
HETATM   23  C17 UNL     1       0.668   1.748  -0.301  1.00  0.00           C  
HETATM   24  C18 UNL     1       1.104   2.786   0.702  1.00  0.00           C  
HETATM   25  H1  UNL     1       7.214  -0.710  -0.073  1.00  0.00           H  
HETATM   26  H2  UNL     1       6.499  -0.163   1.568  1.00  0.00           H  
HETATM   27  H3  UNL     1       7.817  -1.299   1.452  1.00  0.00           H  
HETATM   28  H4  UNL     1       4.614  -3.380   0.587  1.00  0.00           H  
HETATM   29  H5  UNL     1       5.190  -2.430  -0.824  1.00  0.00           H  
HETATM   30  H6  UNL     1       2.953  -1.977  -0.240  1.00  0.00           H  
HETATM   31  H7  UNL     1       3.374  -1.504   1.421  1.00  0.00           H  
HETATM   32  H8  UNL     1       4.269  -0.056  -1.149  1.00  0.00           H  
HETATM   33  H9  UNL     1       4.649   0.500   0.521  1.00  0.00           H  
HETATM   34  H10 UNL     1       1.710  -0.986  -1.899  1.00  0.00           H  
HETATM   35  H11 UNL     1      -0.569  -0.782  -2.830  1.00  0.00           H  
HETATM   36  H12 UNL     1      -0.946   3.952  -0.588  1.00  0.00           H  
HETATM   37  H13 UNL     1      -1.565   2.877   0.707  1.00  0.00           H  
HETATM   38  H14 UNL     1      -6.484   0.466   2.397  1.00  0.00           H  
HETATM   39  H15 UNL     1      -7.187  -1.875   2.333  1.00  0.00           H  
HETATM   40  H16 UNL     1      -6.401  -3.418   0.578  1.00  0.00           H  
HETATM   41  H17 UNL     1      -4.869  -2.544  -1.137  1.00  0.00           H  
HETATM   42  H18 UNL     1      -3.506  -0.175  -1.974  1.00  0.00           H  
HETATM   43  H19 UNL     1       0.368   2.799   1.542  1.00  0.00           H  
HETATM   44  H20 UNL     1       1.140   3.791   0.229  1.00  0.00           H  
HETATM   45  H21 UNL     1       2.110   2.544   1.041  1.00  0.00           H  
CONECT    1    2   25   26   27
CONECT    2    3
CONECT    3    4   28   29
CONECT    4    5   30   31
CONECT    5    6   32   33
CONECT    6    7
CONECT    7    8    8   23
CONECT    8    9   34
CONECT    9   10   10   35
CONECT   10   11
CONECT   11   12   23   23
CONECT   12   13   36   37
CONECT   13   14
CONECT   14   15   15   22
CONECT   15   16
CONECT   16   17   17   21
CONECT   17   18   38
CONECT   18   19   19   39
CONECT   19   20   40
CONECT   20   21   21   41
CONECT   21   22
CONECT   22   42
CONECT   23   24
CONECT   24   43   44   45
END

HMDB0244427
     RDKit          3D
Rabeprazole thioether
 45 47  0  0  0  0  0  0  0  0999 V2000
    6.8128   -0.9818    0.9304 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0521   -2.0782    1.0054 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9539   -2.3144    0.3030 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7556   -1.4522    0.3561 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8800   -0.0477   -0.0998 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7533    0.7333   -0.0659 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5487    0.7123   -0.6637 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0778   -0.1808   -1.5738 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2095   -0.0627   -2.1075 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0098    0.9430   -1.7282 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5940    1.8523   -0.8332 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4554    2.9879   -0.3959 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0457    2.8739   -1.2361 S   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9366    1.4503   -0.6589 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7287    1.4705    0.4345 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2742    0.2669    0.6528 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1323   -0.1954    1.6251 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5147   -1.5333    1.5612 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0739   -2.3889    0.5815 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2145   -1.8664   -0.3661 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8052   -0.5521   -0.3494 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9914    0.2000   -1.1337 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.6678    1.7478   -0.3011 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1040    2.7859    0.7022 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2145   -0.7102   -0.0725 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4989   -0.1633    1.5676 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.8173   -1.2989    1.4518 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6142   -3.3801    0.5871 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1902   -2.4296   -0.8243 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9526   -1.9771   -0.2396 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3744   -1.5035    1.4207 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2686   -0.0561   -1.1490 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6492    0.5000    0.5210 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7098   -0.9865   -1.8988 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5694   -0.7820   -2.8304 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9458    3.9519   -0.5883 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5652    2.8773    0.7066 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4841    0.4656    2.3975 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1872   -1.8748    2.3325 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4011   -3.4177    0.5775 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8691   -2.5440   -1.1370 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5055   -0.1749   -1.9738 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3676    2.7990    1.5423 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1405    3.7906    0.2289 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1096    2.5442    1.0409 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  1  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  1  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
 19 20  1  0
 20 21  2  0
 21 22  1  0
 11 23  2  0
 23 24  1  0
 23  7  1  0
 22 14  1  0
 21 16  1  0
  1 25  1  0
  1 26  1  0
  1 27  1  0
  3 28  1  0
  3 29  1  0
  4 30  1  0
  4 31  1  0
  5 32  1  0
  5 33  1  0
  8 34  1  0
  9 35  1  0
 12 36  1  0
 12 37  1  0
 17 38  1  0
 18 39  1  0
 19 40  1  0
 20 41  1  0
 22 42  1  0
 24 43  1  0
 24 44  1  0
 24 45  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
Rabeprazole-thioether	HMDB

Chemical Formula

C₁₈H₂₁N₃O₂S

Average Molecular Weight

343.45

Monoisotopic Molecular Weight

343.135448102

IUPAC Name

2-({[4-(3-methoxypropoxy)-3-methylpyridin-2-yl]methyl}sulfanyl)-1H-1,3-benzodiazole

Traditional Name

2-({[4-(3-methoxypropoxy)-3-methylpyridin-2-yl]methyl}sulfanyl)-1H-1,3-benzodiazole

CAS Registry Number

Not Available

SMILES

COCCCOC1=C(C)C(CSC2=NC3=CC=CC=C3N2)=NC=C1

InChI Identifier

InChI=1S/C18H21N3O2S/c1-13-16(19-9-8-17(13)23-11-5-10-22-2)12-24-18-20-14-6-3-4-7-15(14)21-18/h3-4,6-9H,5,10-12H2,1-2H3,(H,20,21)

InChI Key

BSXAHDOWMOSVAP-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).

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Benzimidazoles

Sub Class

Not Available

Direct Parent

Benzimidazoles

Alternative Parents

Substituents

Benzimidazole
Aryl thioether
Alkyl aryl ether
Methylpyridine
Alkylarylthioether
Benzenoid
Pyridine
Azole
Heteroaromatic compound
Imidazole
Dialkyl ether
Ether
Azacycle
Sulfenyl compound
Thioether
Organic oxygen compound
Organonitrogen compound
Organooxygen compound
Organosulfur compound
Hydrocarbon derivative
Organic nitrogen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (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	3.37	ALOGPS
logP	3.22	ChemAxon
logS	-5.1	ALOGPS
pKa (Strongest Acidic)	10.42	ChemAxon
pKa (Strongest Basic)	6.16	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	60.03 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	96.7 m³·mol⁻¹	ChemAxon
Polarizability	38.98 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DeepCCS	[M+H]+	186.422	30932474
DeepCCS	[M-H]-	184.064	30932474
DeepCCS	[M-2H]-	216.975	30932474
DeepCCS	[M+Na]+	192.665	30932474
AllCCS	[M+H]+	181.8	32859911
AllCCS	[M+H-H2O]+	178.8	32859911
AllCCS	[M+NH4]+	184.5	32859911
AllCCS	[M+Na]+	185.3	32859911
AllCCS	[M-H]-	183.0	32859911
AllCCS	[M+Na-2H]-	182.9	32859911
AllCCS	[M+HCOO]-	182.9	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Rabeprazole thioether	COCCCOC1=C(C)C(CSC2=NC3=CC=CC=C3N2)=NC=C1	3705.4	Standard polar	33892256
Rabeprazole thioether	COCCCOC1=C(C)C(CSC2=NC3=CC=CC=C3N2)=NC=C1	2803.5	Standard non polar	33892256
Rabeprazole thioether	COCCCOC1=C(C)C(CSC2=NC3=CC=CC=C3N2)=NC=C1	3237.1	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Rabeprazole thioether,1TMS,isomer #1	COCCCOC1=CC=NC(CSC2=NC3=CC=CC=C3N2[Si](C)(C)C)=C1C	2996.4	Semi standard non polar	33892256
Rabeprazole thioether,1TMS,isomer #1	COCCCOC1=CC=NC(CSC2=NC3=CC=CC=C3N2[Si](C)(C)C)=C1C	2701.3	Standard non polar	33892256
Rabeprazole thioether,1TMS,isomer #1	COCCCOC1=CC=NC(CSC2=NC3=CC=CC=C3N2[Si](C)(C)C)=C1C	3713.8	Standard polar	33892256
Rabeprazole thioether,1TBDMS,isomer #1	COCCCOC1=CC=NC(CSC2=NC3=CC=CC=C3N2[Si](C)(C)C(C)(C)C)=C1C	3169.8	Semi standard non polar	33892256
Rabeprazole thioether,1TBDMS,isomer #1	COCCCOC1=CC=NC(CSC2=NC3=CC=CC=C3N2[Si](C)(C)C(C)(C)C)=C1C	2892.0	Standard non polar	33892256
Rabeprazole thioether,1TBDMS,isomer #1	COCCCOC1=CC=NC(CSC2=NC3=CC=CC=C3N2[Si](C)(C)C(C)(C)C)=C1C	3762.7	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - Rabeprazole thioether GC-MS (Non-derivatized) - 70eV, Positive	splash10-006t-9663000000-0f1eb0527f1641f5d332	2021-09-24	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Rabeprazole thioether 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 - Rabeprazole thioether 10V, Positive-QTOF	splash10-03dl-0209000000-5751f1b545b9d76aa9d4	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Rabeprazole thioether 20V, Positive-QTOF	splash10-0fk9-1962000000-0db71f41880328b0d2c8	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Rabeprazole thioether 40V, Positive-QTOF	splash10-0f6y-2910000000-a2fd6a0c41d13283ba7d	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Rabeprazole thioether 10V, Negative-QTOF	splash10-006y-0369000000-8037e73a312fb481c749	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Rabeprazole thioether 20V, Negative-QTOF	splash10-0002-0940000000-2df81bc229504c430980	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Rabeprazole thioether 40V, Negative-QTOF	splash10-0uk9-0910000000-9f2fcda0e9c40a730ff1	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

8125607

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

9949996

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 Rabeprazole thioether (HMDB0244427)

MOL for HMDB0244427 (Rabeprazole thioether)

3D MOL for HMDB0244427 (Rabeprazole thioether)

3D SDF for HMDB0244427 (Rabeprazole thioether)

3D-SDF for HMDB0244427 (Rabeprazole thioether)

PDB for HMDB0244427 (Rabeprazole thioether)

3D PDB for HMDB0244427 (Rabeprazole thioether)

SMILES for HMDB0244427 (Rabeprazole thioether)

INCHI for HMDB0244427 (Rabeprazole thioether)

Structure for HMDB0244427 (Rabeprazole thioether)

3D Structure for HMDB0244427 (Rabeprazole thioether)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra