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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-06 15:00:49 UTC

Update Date

2020-02-26 21:39:20 UTC

HMDB ID

HMDB0014012

Secondary Accession Numbers

HMDB14012

Metabolite Identification

Common Name

Omeprazole sulfone

Description

Omeprazole sulfone is only found in individuals that have used or taken Omeprazole. Omeprazole sulfone is a metabolite of Omeprazole. Omeprazole sulfone belongs to the family of Sulfinylbenzimidazoles. These are polycyclic aromatic compounds containing a sulfinyl group attached at the position 2 of a benzimidazole moiety.

Structure

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

HMDB0014012
     RDKit          3D
Omeprazole sulfone
 44 46  0  0  0  0  0  0  0  0999 V2000
    7.2256    1.7269   -1.1863 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.3076    0.4929   -0.5289 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.1895   -0.2174   -0.1205 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3826   -1.4205    0.5176 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3090   -2.1918    0.9575 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0229   -1.7359    0.7470 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8083   -2.2221    1.0381 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.8380   -1.3926    0.6198 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0985   -1.6076    0.7795 S   0  0  0  0  0  6  0  0  0  0  0  0
   -0.2718   -1.8394    2.1998 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2606   -2.8199   -0.0308 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7514   -0.2251    0.0625 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2089   -0.4100    0.1988 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7283   -1.4906    0.7897 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0621   -1.6336    0.9005 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9640   -0.7031    0.4263 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4456   -0.8852    0.5618 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4446    0.4185   -0.1865 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3095    1.3760   -0.6759 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7579    2.4594    0.0982 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0617    0.5371   -0.2855 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5396    1.7453   -0.9446 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4659   -0.3438    0.0430 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.7987   -0.5235    0.1047 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9015    0.2241   -0.3232 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1210    1.5608   -2.2594 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.2080    2.2454   -1.0189 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4001    2.3240   -0.7413 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.3952   -1.7954    0.6919 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4531   -3.1394    1.4602 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4601   -0.2043   -1.0188 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3982    0.7387    0.4806 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4960   -2.5203    1.3855 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8537   -0.3130    1.4203 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9742   -0.5381   -0.3517 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7148   -1.9380    0.7043 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8033    2.3466    0.4475 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6975    3.4216   -0.4832 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0867    2.6081    0.9720 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1677    2.6063   -0.5979 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5051    1.9962   -0.6840 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7017    1.6389   -2.0388 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0171    0.4779   -0.3845 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7223    1.1659   -0.8220 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  2  0
  9 11  2  0
  9 12  1  0
 12 13  1  0
 13 14  2  0
 14 15  1  0
 15 16  2  0
 16 17  1  0
 16 18  1  0
 18 19  1  0
 19 20  1  0
 18 21  2  0
 21 22  1  0
  8 23  1  0
 23 24  1  0
 24 25  2  0
 25  3  1  0
 24  6  1  0
 21 13  1  0
  1 26  1  0
  1 27  1  0
  1 28  1  0
  4 29  1  0
  5 30  1  0
 12 31  1  0
 12 32  1  0
 15 33  1  0
 17 34  1  0
 17 35  1  0
 17 36  1  0
 20 37  1  0
 20 38  1  0
 20 39  1  0
 22 40  1  0
 22 41  1  0
 22 42  1  0
 23 43  1  0
 25 44  1  0
M  END

338
  Mrv0541 02271201052D          

 25 27  0  0  1  0            999 V2000
    6.5951    0.4967    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    9.4827   -1.6468    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.0076    1.2111    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3645    1.3217    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.2886    1.1606    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.2886   -0.1672    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    8.2451    0.4967    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    7.0076   -0.2178    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.8326   -0.2178    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.2451   -0.9323    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7701    0.4967    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5080    0.9092    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.0702   -0.9323    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5080    0.0842    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.4827   -0.2178    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.8326   -1.6468    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7935    1.3217    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.0702    0.4967    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7935   -0.3284    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0791    0.9092    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0791    0.0842    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.3077   -0.2178    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.3077   -1.6468    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500    0.9092    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1826   -0.2178    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  3  2  0  0  0  0
  1  8  1  0  0  0  0
  1 11  1  0  0  0  0
  2 13  1  0  0  0  0
  2 23  1  0  0  0  0
  4 20  1  0  0  0  0
  4 24  1  0  0  0  0
  5 11  1  0  0  0  0
  5 12  1  0  0  0  0
  6 11  2  0  0  0  0
  6 14  1  0  0  0  0
  7  9  2  0  0  0  0
  7 18  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 13  2  0  0  0  0
 10 16  1  0  0  0  0
 12 14  2  0  0  0  0
 12 17  1  0  0  0  0
 13 15  1  0  0  0  0
 14 19  1  0  0  0  0
 15 18  2  0  0  0  0
 15 22  1  0  0  0  0
 17 20  2  0  0  0  0
 19 21  2  0  0  0  0
 20 21  1  0  0  0  0
  1 25  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0014012

> <DATABASE_NAME>
hmdb

> <SMILES>
COC1=CC2=C(C=C1)N=C(N2)S(=O)(=O)CC1=NC=C(C)C(OC)=C1C

> <INCHI_IDENTIFIER>
InChI=1S/C17H19N3O4S/c1-10-8-18-15(11(2)16(10)24-4)9-25(21,22)17-19-13-6-5-12(23-3)7-14(13)20-17/h5-8H,9H2,1-4H3,(H,19,20)

> <INCHI_KEY>
IXEQEYRTSRFZEO-UHFFFAOYSA-N

> <FORMULA>
C17H19N3O4S

> <MOLECULAR_WEIGHT>
361.415

> <EXACT_MASS>
361.109626801

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_AVERAGE_POLARIZABILITY>
36.57722154958929

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
6-methoxy-2-[(4-methoxy-3,5-dimethylpyridin-2-yl)methanesulfonyl]-1H-1,3-benzodiazole

> <ALOGPS_LOGP>
1.80

> <JCHEM_LOGP>
2.4113618189266885

> <ALOGPS_LOGS>
-3.66

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
16.44436327876104

> <JCHEM_PKA_STRONGEST_ACIDIC>
6.289574370476986

> <JCHEM_PKA_STRONGEST_BASIC>
4.4720554343539725

> <JCHEM_POLAR_SURFACE_AREA>
94.17000000000002

> <JCHEM_REFRACTIVITY>
93.13869999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.98e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5-methoxy-2-[(4-methoxy-3,5-dimethylpyridin-2-yl)methanesulfonyl]-3H-1,3-benzodiazole

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0014012
     RDKit          3D
Omeprazole sulfone
 44 46  0  0  0  0  0  0  0  0999 V2000
    7.2256    1.7269   -1.1863 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.3076    0.4929   -0.5289 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.1895   -0.2174   -0.1205 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3826   -1.4205    0.5176 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3090   -2.1918    0.9575 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0229   -1.7359    0.7470 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8083   -2.2221    1.0381 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.8380   -1.3926    0.6198 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0985   -1.6076    0.7795 S   0  0  0  0  0  6  0  0  0  0  0  0
   -0.2718   -1.8394    2.1998 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2606   -2.8199   -0.0308 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7514   -0.2251    0.0625 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2089   -0.4100    0.1988 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7283   -1.4906    0.7897 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0621   -1.6336    0.9005 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9640   -0.7031    0.4263 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4456   -0.8852    0.5618 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4446    0.4185   -0.1865 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3095    1.3760   -0.6759 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7579    2.4594    0.0982 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0617    0.5371   -0.2855 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5396    1.7453   -0.9446 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4659   -0.3438    0.0430 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.7987   -0.5235    0.1047 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9015    0.2241   -0.3232 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1210    1.5608   -2.2594 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.2080    2.2454   -1.0189 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4001    2.3240   -0.7413 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.3952   -1.7954    0.6919 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4531   -3.1394    1.4602 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4601   -0.2043   -1.0188 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3982    0.7387    0.4806 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4960   -2.5203    1.3855 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8537   -0.3130    1.4203 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9742   -0.5381   -0.3517 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7148   -1.9380    0.7043 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8033    2.3466    0.4475 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6975    3.4216   -0.4832 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0867    2.6081    0.9720 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1677    2.6063   -0.5979 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5051    1.9962   -0.6840 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7017    1.6389   -2.0388 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0171    0.4779   -0.3845 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7223    1.1659   -0.8220 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  2  0
  9 11  2  0
  9 12  1  0
 12 13  1  0
 13 14  2  0
 14 15  1  0
 15 16  2  0
 16 17  1  0
 16 18  1  0
 18 19  1  0
 19 20  1  0
 18 21  2  0
 21 22  1  0
  8 23  1  0
 23 24  1  0
 24 25  2  0
 25  3  1  0
 24  6  1  0
 21 13  1  0
  1 26  1  0
  1 27  1  0
  1 28  1  0
  4 29  1  0
  5 30  1  0
 12 31  1  0
 12 32  1  0
 15 33  1  0
 17 34  1  0
 17 35  1  0
 17 36  1  0
 20 37  1  0
 20 38  1  0
 20 39  1  0
 22 40  1  0
 22 41  1  0
 22 42  1  0
 23 43  1  0
 25 44  1  0
M  END

HEADER    PROTEIN                                 27-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: 338                                               
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-FEB-12         0                                  
HETATM    1  S   UNK     0      12.311   0.927   0.000  0.00  0.00           S+0
HETATM    2  O   UNK     0      17.701  -3.074   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      13.081   2.261   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0       4.414   2.467   0.000  0.00  0.00           O+0
HETATM    5  N   UNK     0       9.872   2.166   0.000  0.00  0.00           N+0
HETATM    6  N   UNK     0       9.872  -0.312   0.000  0.00  0.00           N+0
HETATM    7  N   UNK     0      15.391   0.927   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0      13.081  -0.407   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      14.621  -0.407   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      15.391  -1.740   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      10.771   0.927   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       8.415   1.697   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      16.931  -1.740   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       8.415   0.157   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      17.701  -0.407   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      14.621  -3.074   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       7.081   2.467   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      16.931   0.927   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       7.081  -0.613   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       5.748   1.697   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       5.748   0.157   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      19.241  -0.407   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      19.241  -3.074   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       3.080   1.697   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0      11.541  -0.407   0.000  0.00  0.00           O+0
CONECT    1    3    8   11   25                                             
CONECT    2   13   23                                                       
CONECT    3    1                                                            
CONECT    4   20   24                                                       
CONECT    5   11   12                                                       
CONECT    6   11   14                                                       
CONECT    7    9   18                                                       
CONECT    8    1    9                                                       
CONECT    9    7    8   10                                                  
CONECT   10    9   13   16                                                  
CONECT   11    1    5    6                                                  
CONECT   12    5   14   17                                                  
CONECT   13    2   10   15                                                  
CONECT   14    6   12   19                                                  
CONECT   15   13   18   22                                                  
CONECT   16   10                                                            
CONECT   17   12   20                                                       
CONECT   18    7   15                                                       
CONECT   19   14   21                                                       
CONECT   20    4   17   21                                                  
CONECT   21   19   20                                                       
CONECT   22   15                                                            
CONECT   23    2                                                            
CONECT   24    4                                                            
CONECT   25    1                                                            
MASTER        0    0    0    0    0    0    0    0   25    0   54    0
END

COMPND    HMDB0014012
HETATM    1  C1  UNL     1       7.226   1.727  -1.186  1.00  0.00           C  
HETATM    2  O1  UNL     1       7.308   0.493  -0.529  1.00  0.00           O  
HETATM    3  C2  UNL     1       6.189  -0.217  -0.120  1.00  0.00           C  
HETATM    4  C3  UNL     1       6.383  -1.420   0.518  1.00  0.00           C  
HETATM    5  C4  UNL     1       5.309  -2.192   0.957  1.00  0.00           C  
HETATM    6  C5  UNL     1       4.023  -1.736   0.747  1.00  0.00           C  
HETATM    7  N1  UNL     1       2.808  -2.222   1.038  1.00  0.00           N  
HETATM    8  C6  UNL     1       1.838  -1.393   0.620  1.00  0.00           C  
HETATM    9  S1  UNL     1       0.099  -1.608   0.779  1.00  0.00           S  
HETATM   10  O2  UNL     1      -0.272  -1.839   2.200  1.00  0.00           O  
HETATM   11  O3  UNL     1      -0.261  -2.820  -0.031  1.00  0.00           O  
HETATM   12  C7  UNL     1      -0.751  -0.225   0.062  1.00  0.00           C  
HETATM   13  C8  UNL     1      -2.209  -0.410   0.199  1.00  0.00           C  
HETATM   14  N2  UNL     1      -2.728  -1.491   0.790  1.00  0.00           N  
HETATM   15  C9  UNL     1      -4.062  -1.634   0.900  1.00  0.00           C  
HETATM   16  C10 UNL     1      -4.964  -0.703   0.426  1.00  0.00           C  
HETATM   17  C11 UNL     1      -6.446  -0.885   0.562  1.00  0.00           C  
HETATM   18  C12 UNL     1      -4.445   0.418  -0.186  1.00  0.00           C  
HETATM   19  O4  UNL     1      -5.309   1.376  -0.676  1.00  0.00           O  
HETATM   20  C13 UNL     1      -5.758   2.459   0.098  1.00  0.00           C  
HETATM   21  C14 UNL     1      -3.062   0.537  -0.285  1.00  0.00           C  
HETATM   22  C15 UNL     1      -2.540   1.745  -0.945  1.00  0.00           C  
HETATM   23  N3  UNL     1       2.466  -0.344   0.043  1.00  0.00           N  
HETATM   24  C16 UNL     1       3.799  -0.523   0.105  1.00  0.00           C  
HETATM   25  C17 UNL     1       4.901   0.224  -0.323  1.00  0.00           C  
HETATM   26  H1  UNL     1       7.121   1.561  -2.259  1.00  0.00           H  
HETATM   27  H2  UNL     1       8.208   2.245  -1.019  1.00  0.00           H  
HETATM   28  H3  UNL     1       6.400   2.324  -0.741  1.00  0.00           H  
HETATM   29  H4  UNL     1       7.395  -1.795   0.692  1.00  0.00           H  
HETATM   30  H5  UNL     1       5.453  -3.139   1.460  1.00  0.00           H  
HETATM   31  H6  UNL     1      -0.460  -0.204  -1.019  1.00  0.00           H  
HETATM   32  H7  UNL     1      -0.398   0.739   0.481  1.00  0.00           H  
HETATM   33  H8  UNL     1      -4.496  -2.520   1.386  1.00  0.00           H  
HETATM   34  H9  UNL     1      -6.854  -0.313   1.420  1.00  0.00           H  
HETATM   35  H10 UNL     1      -6.974  -0.538  -0.352  1.00  0.00           H  
HETATM   36  H11 UNL     1      -6.715  -1.938   0.704  1.00  0.00           H  
HETATM   37  H12 UNL     1      -6.803   2.347   0.447  1.00  0.00           H  
HETATM   38  H13 UNL     1      -5.698   3.422  -0.483  1.00  0.00           H  
HETATM   39  H14 UNL     1      -5.087   2.608   0.972  1.00  0.00           H  
HETATM   40  H15 UNL     1      -3.168   2.606  -0.598  1.00  0.00           H  
HETATM   41  H16 UNL     1      -1.505   1.996  -0.684  1.00  0.00           H  
HETATM   42  H17 UNL     1      -2.702   1.639  -2.039  1.00  0.00           H  
HETATM   43  H18 UNL     1       2.017   0.478  -0.385  1.00  0.00           H  
HETATM   44  H19 UNL     1       4.722   1.166  -0.822  1.00  0.00           H  
CONECT    1    2   26   27   28
CONECT    2    3
CONECT    3    4    4   25
CONECT    4    5   29
CONECT    5    6    6   30
CONECT    6    7   24
CONECT    7    8    8
CONECT    8    9   23
CONECT    9   10   10   11   11
CONECT    9   12
CONECT   12   13   31   32
CONECT   13   14   14   21
CONECT   14   15
CONECT   15   16   16   33
CONECT   16   17   18
CONECT   17   34   35   36
CONECT   18   19   21   21
CONECT   19   20
CONECT   20   37   38   39
CONECT   21   22
CONECT   22   40   41   42
CONECT   23   24   43
CONECT   24   25   25
CONECT   25   44
END

HMDB0014012
     RDKit          3D
Omeprazole sulfone
 44 46  0  0  0  0  0  0  0  0999 V2000
    7.2256    1.7269   -1.1863 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.3076    0.4929   -0.5289 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.1895   -0.2174   -0.1205 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3826   -1.4205    0.5176 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3090   -2.1918    0.9575 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0229   -1.7359    0.7470 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8083   -2.2221    1.0381 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.8380   -1.3926    0.6198 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0985   -1.6076    0.7795 S   0  0  0  0  0  6  0  0  0  0  0  0
   -0.2718   -1.8394    2.1998 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2606   -2.8199   -0.0308 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7514   -0.2251    0.0625 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2089   -0.4100    0.1988 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7283   -1.4906    0.7897 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0621   -1.6336    0.9005 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9640   -0.7031    0.4263 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4456   -0.8852    0.5618 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4446    0.4185   -0.1865 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3095    1.3760   -0.6759 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7579    2.4594    0.0982 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0617    0.5371   -0.2855 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5396    1.7453   -0.9446 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4659   -0.3438    0.0430 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.7987   -0.5235    0.1047 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9015    0.2241   -0.3232 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1210    1.5608   -2.2594 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.2080    2.2454   -1.0189 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4001    2.3240   -0.7413 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.3952   -1.7954    0.6919 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4531   -3.1394    1.4602 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4601   -0.2043   -1.0188 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3982    0.7387    0.4806 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4960   -2.5203    1.3855 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8537   -0.3130    1.4203 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9742   -0.5381   -0.3517 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7148   -1.9380    0.7043 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8033    2.3466    0.4475 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6975    3.4216   -0.4832 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0867    2.6081    0.9720 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1677    2.6063   -0.5979 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5051    1.9962   -0.6840 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7017    1.6389   -2.0388 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0171    0.4779   -0.3845 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7223    1.1659   -0.8220 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  2  0
  9 11  2  0
  9 12  1  0
 12 13  1  0
 13 14  2  0
 14 15  1  0
 15 16  2  0
 16 17  1  0
 16 18  1  0
 18 19  1  0
 19 20  1  0
 18 21  2  0
 21 22  1  0
  8 23  1  0
 23 24  1  0
 24 25  2  0
 25  3  1  0
 24  6  1  0
 21 13  1  0
  1 26  1  0
  1 27  1  0
  1 28  1  0
  4 29  1  0
  5 30  1  0
 12 31  1  0
 12 32  1  0
 15 33  1  0
 17 34  1  0
 17 35  1  0
 17 36  1  0
 20 37  1  0
 20 38  1  0
 20 39  1  0
 22 40  1  0
 22 41  1  0
 22 42  1  0
 23 43  1  0
 25 44  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
Omeprazole sulphone	Generator
6-Methoxy-2-[(4-methoxy-3,5-dimethylpyridin-2-yl)methanesulphonyl]-1H-1,3-benzodiazole	HMDB
Omeprazole sulfone	MeSH

Chemical Formula

C₁₇H₁₉N₃O₄S

Average Molecular Weight

361.415

Monoisotopic Molecular Weight

361.109626801

IUPAC Name

6-methoxy-2-[(4-methoxy-3,5-dimethylpyridin-2-yl)methanesulfonyl]-1H-1,3-benzodiazole

Traditional Name

5-methoxy-2-[(4-methoxy-3,5-dimethylpyridin-2-yl)methanesulfonyl]-3H-1,3-benzodiazole

CAS Registry Number

88546-55-8

SMILES

COC1=CC2=C(C=C1)N=C(N2)S(=O)(=O)CC1=NC=C(C)C(OC)=C1C

InChI Identifier

InChI=1S/C17H19N3O4S/c1-10-8-18-15(11(2)16(10)24-4)9-25(21,22)17-19-13-6-5-12(23-3)7-14(13)20-17/h5-8H,9H2,1-4H3,(H,19,20)

InChI Key

IXEQEYRTSRFZEO-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as sulfinylbenzimidazoles. These are polycyclic aromatic compounds containing a sulfinyl group attached at the position 2 of a benzimidazole moiety.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Benzimidazoles

Sub Class

Sulfinylbenzimidazoles

Direct Parent

Sulfinylbenzimidazoles

Alternative Parents

Substituents

Sulfinylbenzimidazole
Anisole
Alkyl aryl ether
Methylpyridine
Pyridine
Benzenoid
Azole
Imidazole
Sulfone
Sulfonyl
Heteroaromatic compound
Azacycle
Ether
Organic oxide
Organopnictogen compound
Organosulfur compound
Organooxygen compound
Organonitrogen compound
Organic oxygen compound
Organic nitrogen compound
Hydrocarbon derivative
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: 21059682)

Organ

Liver (HMDB: HMDB0014012)
Kidney (HMDB: HMDB0014012)

Excreta

Biofluid or Excreta

Urine (PMID: 21059682)

Cellular substructure

Extracellular (HMDB: HMDB0014012)

Source

Endogenous

Endogenous (HMDB: HMDB0014012)

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
Water Solubility	0.08 g/L	ALOGPS
logP	1.8	ALOGPS
logP	2.41	ChemAxon
logS	-3.7	ALOGPS
pKa (Strongest Acidic)	6.29	ChemAxon
pKa (Strongest Basic)	4.47	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	94.17 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	93.14 m³·mol⁻¹	ChemAxon
Polarizability	36.58 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	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DarkChem	[M+H]+	184.484	31661259
DarkChem	[M-H]-	183.765	31661259
DeepCCS	[M+H]+	184.446	30932474
DeepCCS	[M-H]-	182.088	30932474
DeepCCS	[M-2H]-	215.937	30932474
DeepCCS	[M+Na]+	191.165	30932474
AllCCS	[M+H]+	184.0	32859911
AllCCS	[M+H-H2O]+	181.0	32859911
AllCCS	[M+NH4]+	186.7	32859911
AllCCS	[M+Na]+	187.4	32859911
AllCCS	[M-H]-	184.8	32859911
AllCCS	[M+Na-2H]-	184.6	32859911
AllCCS	[M+HCOO]-	184.6	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.	5.95 minutes	32390414
Predicted by Siyang on May 30, 2022	10.9979 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	1.23 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	1801.4 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	213.0 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	164.0 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	167.3 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	115.6 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	558.5 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	415.2 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	219.6 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	911.0 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	356.1 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	1272.7 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	305.9 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	374.4 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	318.4 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	193.9 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	41.6 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Omeprazole sulfone	COC1=CC2=C(C=C1)N=C(N2)S(=O)(=O)CC1=NC=C(C)C(OC)=C1C	3998.3	Standard polar	33892256
Omeprazole sulfone	COC1=CC2=C(C=C1)N=C(N2)S(=O)(=O)CC1=NC=C(C)C(OC)=C1C	3179.1	Standard non polar	33892256
Omeprazole sulfone	COC1=CC2=C(C=C1)N=C(N2)S(=O)(=O)CC1=NC=C(C)C(OC)=C1C	3311.5	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Omeprazole sulfone,1TMS,isomer #1	COC1=CC=C2N=C(S(=O)(=O)CC3=NC=C(C)C(OC)=C3C)N([Si](C)(C)C)C2=C1	3178.1	Semi standard non polar	33892256
Omeprazole sulfone,1TMS,isomer #1	COC1=CC=C2N=C(S(=O)(=O)CC3=NC=C(C)C(OC)=C3C)N([Si](C)(C)C)C2=C1	3087.6	Standard non polar	33892256
Omeprazole sulfone,1TMS,isomer #1	COC1=CC=C2N=C(S(=O)(=O)CC3=NC=C(C)C(OC)=C3C)N([Si](C)(C)C)C2=C1	4300.0	Standard polar	33892256
Omeprazole sulfone,1TBDMS,isomer #1	COC1=CC=C2N=C(S(=O)(=O)CC3=NC=C(C)C(OC)=C3C)N([Si](C)(C)C(C)(C)C)C2=C1	3298.8	Semi standard non polar	33892256
Omeprazole sulfone,1TBDMS,isomer #1	COC1=CC=C2N=C(S(=O)(=O)CC3=NC=C(C)C(OC)=C3C)N([Si](C)(C)C(C)(C)C)C2=C1	3341.4	Standard non polar	33892256
Omeprazole sulfone,1TBDMS,isomer #1	COC1=CC=C2N=C(S(=O)(=O)CC3=NC=C(C)C(OC)=C3C)N([Si](C)(C)C(C)(C)C)C2=C1	4228.6	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - Omeprazole sulfone GC-MS (Non-derivatized) - 70eV, Positive	splash10-0udi-0910000000-e860e146ba017ec91053	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Omeprazole sulfone 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 - Omeprazole sulfone 10V, Positive-QTOF	splash10-03di-0159000000-b02c183d8a1dbcf387e6	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Omeprazole sulfone 20V, Positive-QTOF	splash10-0udi-0910000000-1e7467ee2e824f541632	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Omeprazole sulfone 40V, Positive-QTOF	splash10-0ul0-3900000000-8665b359f427b435f125	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Omeprazole sulfone 10V, Negative-QTOF	splash10-03di-0179000000-1c8644bf907b10e0178a	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Omeprazole sulfone 20V, Negative-QTOF	splash10-03dl-0970000000-ef738afa79c0a38da140	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Omeprazole sulfone 40V, Negative-QTOF	splash10-0006-0910000000-f2247eddd0ac67182456	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Omeprazole sulfone 10V, Negative-QTOF	splash10-03di-0009000000-59312493d06515651662	2021-09-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Omeprazole sulfone 20V, Negative-QTOF	splash10-03di-3759000000-640d59056a55d1b4c053	2021-09-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Omeprazole sulfone 40V, Negative-QTOF	splash10-001s-2921000000-d623e92bd236b9087451	2021-09-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Omeprazole sulfone 10V, Positive-QTOF	splash10-03di-0019000000-47df4911f5475121b28e	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Omeprazole sulfone 20V, Positive-QTOF	splash10-0ik9-2914000000-1b8ce92c5592281973a6	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Omeprazole sulfone 40V, Positive-QTOF	splash10-05g0-2930000000-e2908558759e21344c53	2021-09-25	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Extracellular

Biospecimen Locations

Blood
Urine

Tissue Locations

Kidney
Liver

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Expected but not Quantified	Not Quantified	Not Available	Not Available	Taking drug identified by DrugBank entry	21059682	details
Urine	Expected but not Quantified	Not Quantified	Not Available	Not Available	Taking drug identified by DrugBank entry	21059682	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

128709

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

145900

PDB ID

Not Available

ChEBI ID

388428

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

Not Available

Showing metabocard for Omeprazole sulfone (HMDB0014012)

MOL for HMDB0014012 (Omeprazole sulfone)

3D MOL for HMDB0014012 (Omeprazole sulfone)

3D SDF for HMDB0014012 (Omeprazole sulfone)

3D-SDF for HMDB0014012 (Omeprazole sulfone)

PDB for HMDB0014012 (Omeprazole sulfone)

3D PDB for HMDB0014012 (Omeprazole sulfone)

SMILES for HMDB0014012 (Omeprazole sulfone)

INCHI for HMDB0014012 (Omeprazole sulfone)

Structure for HMDB0014012 (Omeprazole sulfone)

3D Structure for HMDB0014012 (Omeprazole sulfone)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra