Jump To Section:

Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References XML

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

HMDB0014011

Secondary Accession Numbers

HMDB14011

Metabolite Identification

Common Name

5'-O-Desmethyl omeprazole

Description

5'-O-Desmethyl omeprazole is only found in individuals that have used or taken Omeprazole. 5'-O-Desmethyl omeprazole is a metabolite of Omeprazole. 5'-o-desmethyl omeprazole 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

HMDB0014011
     RDKit          3D
5'-O-Desmethyl omeprazole
 40 42  0  0  0  0  0  0  0  0999 V2000
   -4.3637    1.5404   -0.6394 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3241    0.2244   -0.0833 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0784   -0.3068    0.2013 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5234   -0.1021    1.4432 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3019    0.6899    2.4276 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2803   -0.6384    1.7111 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6389   -1.3495    0.7523 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1692   -1.5551   -0.4595 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4119   -2.3394   -1.4522 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1303   -2.8556   -0.7424 S   0  0  0  0  0  4  0  0  0  0  0  0
    1.9580   -3.6938   -1.7045 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1147   -1.4647   -0.2529 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1039   -0.8556    0.9458 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.9702    0.1502    0.9555 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3651    1.0987    1.9051 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3178    2.0560    1.6290 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8998    2.0812    0.3813 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8584    3.0622    0.1379 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5316    1.1594   -0.5760 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5703    0.1990   -0.2870 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0295   -0.7974   -1.0038 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4082   -1.0409   -0.7781 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0338   -1.2378   -2.0925 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1450    2.1455   -0.1280 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3810    2.0540   -0.5161 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6192    1.5020   -1.7162 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9331   -0.0037    3.0516 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9162    1.4114    1.8896 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5936    1.1728    3.1433 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8330   -0.4841    2.6850 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9861   -3.2311   -1.8042 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2010   -1.6925   -2.3490 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8740    1.0300    2.8667 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5623    2.7468    2.4165 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2964    3.0840   -0.7957 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9819    1.1736   -1.5519 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2619   -1.0326   -1.9748 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1259   -1.3744   -1.9740 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6608   -2.1420   -2.6187 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8975   -0.3837   -2.7814 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
  4  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  2  0
 10 12  1  0
 12 13  2  0
 13 14  1  0
 14 15  2  0
 15 16  1  0
 16 17  2  0
 17 18  1  0
 17 19  1  0
 19 20  2  0
 20 21  1  0
  8 22  2  0
 22 23  1  0
 22  3  1  0
 21 12  1  0
 20 14  1  0
  1 24  1  0
  1 25  1  0
  1 26  1  0
  5 27  1  0
  5 28  1  0
  5 29  1  0
  6 30  1  0
  9 31  1  0
  9 32  1  0
 15 33  1  0
 16 34  1  0
 18 35  1  0
 19 36  1  0
 21 37  1  0
 23 38  1  0
 23 39  1  0
 23 40  1  0
M  END

  Mrv0541 06191310392D          

 23 25  0  0  0  0            999 V2000
    8.9765   -3.1632    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
   11.8641   -5.3068    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.3890   -2.4489    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.7459   -2.3382    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.6700   -2.4993    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    7.6700   -3.8272    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   10.6265   -3.1632    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    9.3890   -3.8778    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.2140   -3.8778    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.6265   -4.5922    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.1515   -3.1632    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8894   -2.7507    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.4516   -4.5922    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8894   -3.5757    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.8641   -3.8778    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.2140   -5.3068    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1749   -2.3382    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.4516   -3.1632    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1749   -3.9883    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4605   -2.7507    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4605   -3.5757    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.6891   -3.8778    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.6891   -5.3068    0.0000 C   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
  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
M  END
> <DATABASE_ID>
HMDB0014011

> <DATABASE_NAME>
hmdb

> <SMILES>
COC1=C(C)C(CS(=O)C2=NC3=C(N2)C=C(O)C=C3)=NC=C1C

> <INCHI_IDENTIFIER>
InChI=1S/C16H17N3O3S/c1-9-7-17-14(10(2)15(9)22-3)8-23(21)16-18-12-5-4-11(20)6-13(12)19-16/h4-7,20H,8H2,1-3H3,(H,18,19)

> <INCHI_KEY>
TWXDTVZNDQKCOS-UHFFFAOYSA-N

> <FORMULA>
C16H17N3O3S

> <MOLECULAR_WEIGHT>
331.389

> <EXACT_MASS>
331.099062115

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_AVERAGE_POLARIZABILITY>
35.339751686536175

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
2-[(4-methoxy-3,5-dimethylpyridin-2-yl)methanesulfinyl]-1H-1,3-benzodiazol-6-ol

> <ALOGPS_LOGP>
1.96

> <JCHEM_LOGP>
2.287615067333333

> <ALOGPS_LOGS>
-2.73

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
10.64504567202295

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.026308551475472

> <JCHEM_PKA_STRONGEST_BASIC>
4.7727580095166475

> <JCHEM_POLAR_SURFACE_AREA>
88.10000000000001

> <JCHEM_REFRACTIVITY>
89.18

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.15e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-[(4-methoxy-3,5-dimethylpyridin-2-yl)methanesulfinyl]-3H-1,3-benzodiazol-5-ol

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0014011
     RDKit          3D
5'-O-Desmethyl omeprazole
 40 42  0  0  0  0  0  0  0  0999 V2000
   -4.3637    1.5404   -0.6394 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3241    0.2244   -0.0833 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0784   -0.3068    0.2013 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5234   -0.1021    1.4432 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3019    0.6899    2.4276 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2803   -0.6384    1.7111 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6389   -1.3495    0.7523 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1692   -1.5551   -0.4595 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4119   -2.3394   -1.4522 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1303   -2.8556   -0.7424 S   0  0  0  0  0  4  0  0  0  0  0  0
    1.9580   -3.6938   -1.7045 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1147   -1.4647   -0.2529 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1039   -0.8556    0.9458 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.9702    0.1502    0.9555 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3651    1.0987    1.9051 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3178    2.0560    1.6290 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8998    2.0812    0.3813 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8584    3.0622    0.1379 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5316    1.1594   -0.5760 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5703    0.1990   -0.2870 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0295   -0.7974   -1.0038 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4082   -1.0409   -0.7781 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0338   -1.2378   -2.0925 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1450    2.1455   -0.1280 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3810    2.0540   -0.5161 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6192    1.5020   -1.7162 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9331   -0.0037    3.0516 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9162    1.4114    1.8896 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5936    1.1728    3.1433 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8330   -0.4841    2.6850 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9861   -3.2311   -1.8042 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2010   -1.6925   -2.3490 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8740    1.0300    2.8667 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5623    2.7468    2.4165 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2964    3.0840   -0.7957 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9819    1.1736   -1.5519 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2619   -1.0326   -1.9748 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1259   -1.3744   -1.9740 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6608   -2.1420   -2.6187 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8975   -0.3837   -2.7814 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
  4  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  2  0
 10 12  1  0
 12 13  2  0
 13 14  1  0
 14 15  2  0
 15 16  1  0
 16 17  2  0
 17 18  1  0
 17 19  1  0
 19 20  2  0
 20 21  1  0
  8 22  2  0
 22 23  1  0
 22  3  1  0
 21 12  1  0
 20 14  1  0
  1 24  1  0
  1 25  1  0
  1 26  1  0
  5 27  1  0
  5 28  1  0
  5 29  1  0
  6 30  1  0
  9 31  1  0
  9 32  1  0
 15 33  1  0
 16 34  1  0
 18 35  1  0
 19 36  1  0
 21 37  1  0
 23 38  1  0
 23 39  1  0
 23 40  1  0
M  END

HEADER    PROTEIN                                 19-JUN-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   19-JUN-13         0                                  
HETATM    1  S   UNK     0      16.756  -5.905   0.000  0.00  0.00           S+0
HETATM    2  O   UNK     0      22.146  -9.906   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      17.526  -4.571   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0       8.859  -4.365   0.000  0.00  0.00           O+0
HETATM    5  N   UNK     0      14.317  -4.665   0.000  0.00  0.00           N+0
HETATM    6  N   UNK     0      14.317  -7.144   0.000  0.00  0.00           N+0
HETATM    7  N   UNK     0      19.836  -5.905   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0      17.526  -7.238   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      19.066  -7.238   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      19.836  -8.572   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      15.216  -5.905   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      12.860  -5.135   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      21.376  -8.572   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      12.860  -6.675   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      22.146  -7.238   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      19.066  -9.906   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      11.527  -4.365   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      21.376  -5.905   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      11.527  -7.445   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      10.193  -5.135   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      10.193  -6.675   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      23.686  -7.238   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      23.686  -9.906   0.000  0.00  0.00           C+0
CONECT    1    3    8   11                                                  
CONECT    2   13   23                                                       
CONECT    3    1                                                            
CONECT    4   20                                                            
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                                                            
MASTER        0    0    0    0    0    0    0    0   23    0   50    0
END

COMPND    HMDB0014011
HETATM    1  C1  UNL     1      -4.364   1.540  -0.639  1.00  0.00           C  
HETATM    2  O1  UNL     1      -4.324   0.224  -0.083  1.00  0.00           O  
HETATM    3  C2  UNL     1      -3.078  -0.307   0.201  1.00  0.00           C  
HETATM    4  C3  UNL     1      -2.523  -0.102   1.443  1.00  0.00           C  
HETATM    5  C4  UNL     1      -3.302   0.690   2.428  1.00  0.00           C  
HETATM    6  C5  UNL     1      -1.280  -0.638   1.711  1.00  0.00           C  
HETATM    7  N1  UNL     1      -0.639  -1.349   0.752  1.00  0.00           N  
HETATM    8  C6  UNL     1      -1.169  -1.555  -0.460  1.00  0.00           C  
HETATM    9  C7  UNL     1      -0.412  -2.339  -1.452  1.00  0.00           C  
HETATM   10  S1  UNL     1       1.130  -2.856  -0.742  1.00  0.00           S  
HETATM   11  O2  UNL     1       1.958  -3.694  -1.705  1.00  0.00           O  
HETATM   12  C8  UNL     1       2.115  -1.465  -0.253  1.00  0.00           C  
HETATM   13  N2  UNL     1       2.104  -0.856   0.946  1.00  0.00           N  
HETATM   14  C9  UNL     1       2.970   0.150   0.956  1.00  0.00           C  
HETATM   15  C10 UNL     1       3.365   1.099   1.905  1.00  0.00           C  
HETATM   16  C11 UNL     1       4.318   2.056   1.629  1.00  0.00           C  
HETATM   17  C12 UNL     1       4.900   2.081   0.381  1.00  0.00           C  
HETATM   18  O3  UNL     1       5.858   3.062   0.138  1.00  0.00           O  
HETATM   19  C13 UNL     1       4.532   1.159  -0.576  1.00  0.00           C  
HETATM   20  C14 UNL     1       3.570   0.199  -0.287  1.00  0.00           C  
HETATM   21  N3  UNL     1       3.030  -0.797  -1.004  1.00  0.00           N  
HETATM   22  C15 UNL     1      -2.408  -1.041  -0.778  1.00  0.00           C  
HETATM   23  C16 UNL     1      -3.034  -1.238  -2.093  1.00  0.00           C  
HETATM   24  H1  UNL     1      -5.145   2.145  -0.128  1.00  0.00           H  
HETATM   25  H2  UNL     1      -3.381   2.054  -0.516  1.00  0.00           H  
HETATM   26  H3  UNL     1      -4.619   1.502  -1.716  1.00  0.00           H  
HETATM   27  H4  UNL     1      -3.933  -0.004   3.052  1.00  0.00           H  
HETATM   28  H5  UNL     1      -3.916   1.411   1.890  1.00  0.00           H  
HETATM   29  H6  UNL     1      -2.594   1.173   3.143  1.00  0.00           H  
HETATM   30  H7  UNL     1      -0.833  -0.484   2.685  1.00  0.00           H  
HETATM   31  H8  UNL     1      -0.986  -3.231  -1.804  1.00  0.00           H  
HETATM   32  H9  UNL     1      -0.201  -1.693  -2.349  1.00  0.00           H  
HETATM   33  H10 UNL     1       2.874   1.030   2.867  1.00  0.00           H  
HETATM   34  H11 UNL     1       4.562   2.747   2.417  1.00  0.00           H  
HETATM   35  H12 UNL     1       6.296   3.084  -0.796  1.00  0.00           H  
HETATM   36  H13 UNL     1       4.982   1.174  -1.552  1.00  0.00           H  
HETATM   37  H14 UNL     1       3.262  -1.033  -1.975  1.00  0.00           H  
HETATM   38  H15 UNL     1      -4.126  -1.374  -1.974  1.00  0.00           H  
HETATM   39  H16 UNL     1      -2.661  -2.142  -2.619  1.00  0.00           H  
HETATM   40  H17 UNL     1      -2.897  -0.384  -2.781  1.00  0.00           H  
CONECT    1    2   24   25   26
CONECT    2    3
CONECT    3    4    4   22
CONECT    4    5    6
CONECT    5   27   28   29
CONECT    6    7    7   30
CONECT    7    8
CONECT    8    9   22   22
CONECT    9   10   31   32
CONECT   10   11   11   12
CONECT   12   13   13   21
CONECT   13   14
CONECT   14   15   15   20
CONECT   15   16   33
CONECT   16   17   17   34
CONECT   17   18   19
CONECT   18   35
CONECT   19   20   20   36
CONECT   20   21
CONECT   21   37
CONECT   22   23
CONECT   23   38   39   40
END

HMDB0014011
     RDKit          3D
5'-O-Desmethyl omeprazole
 40 42  0  0  0  0  0  0  0  0999 V2000
   -4.3637    1.5404   -0.6394 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3241    0.2244   -0.0833 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0784   -0.3068    0.2013 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5234   -0.1021    1.4432 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3019    0.6899    2.4276 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2803   -0.6384    1.7111 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6389   -1.3495    0.7523 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1692   -1.5551   -0.4595 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4119   -2.3394   -1.4522 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1303   -2.8556   -0.7424 S   0  0  0  0  0  4  0  0  0  0  0  0
    1.9580   -3.6938   -1.7045 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1147   -1.4647   -0.2529 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1039   -0.8556    0.9458 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.9702    0.1502    0.9555 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3651    1.0987    1.9051 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3178    2.0560    1.6290 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8998    2.0812    0.3813 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8584    3.0622    0.1379 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5316    1.1594   -0.5760 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5703    0.1990   -0.2870 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0295   -0.7974   -1.0038 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4082   -1.0409   -0.7781 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0338   -1.2378   -2.0925 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1450    2.1455   -0.1280 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3810    2.0540   -0.5161 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6192    1.5020   -1.7162 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9331   -0.0037    3.0516 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9162    1.4114    1.8896 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5936    1.1728    3.1433 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8330   -0.4841    2.6850 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9861   -3.2311   -1.8042 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2010   -1.6925   -2.3490 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8740    1.0300    2.8667 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5623    2.7468    2.4165 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2964    3.0840   -0.7957 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9819    1.1736   -1.5519 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2619   -1.0326   -1.9748 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1259   -1.3744   -1.9740 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6608   -2.1420   -2.6187 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8975   -0.3837   -2.7814 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
  4  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  2  0
 10 12  1  0
 12 13  2  0
 13 14  1  0
 14 15  2  0
 15 16  1  0
 16 17  2  0
 17 18  1  0
 17 19  1  0
 19 20  2  0
 20 21  1  0
  8 22  2  0
 22 23  1  0
 22  3  1  0
 21 12  1  0
 20 14  1  0
  1 24  1  0
  1 25  1  0
  1 26  1  0
  5 27  1  0
  5 28  1  0
  5 29  1  0
  6 30  1  0
  9 31  1  0
  9 32  1  0
 15 33  1  0
 16 34  1  0
 18 35  1  0
 19 36  1  0
 21 37  1  0
 23 38  1  0
 23 39  1  0
 23 40  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
2-[(4-Methoxy-3,5-dimethylpyridin-2-yl)methanesulphinyl]-1H-1,3-benzodiazol-6-ol	HMDB

Chemical Formula

C₁₆H₁₇N₃O₃S

Average Molecular Weight

331.389

Monoisotopic Molecular Weight

331.099062115

IUPAC Name

2-[(4-methoxy-3,5-dimethylpyridin-2-yl)methanesulfinyl]-1H-1,3-benzodiazol-6-ol

Traditional Name

2-[(4-methoxy-3,5-dimethylpyridin-2-yl)methanesulfinyl]-3H-1,3-benzodiazol-5-ol

CAS Registry Number

Not Available

SMILES

COC1=C(C)C(CS(=O)C2=NC3=C(N2)C=C(O)C=C3)=NC=C1C

InChI Identifier

InChI=1S/C16H17N3O3S/c1-9-7-17-14(10(2)15(9)22-3)8-23(21)16-18-12-5-4-11(20)6-13(12)19-16/h4-7,20H,8H2,1-3H3,(H,18,19)

InChI Key

TWXDTVZNDQKCOS-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
Alkyl aryl ether
1-hydroxy-2-unsubstituted benzenoid
Methylpyridine
Pyridine
Benzenoid
Azole
Imidazole
Heteroaromatic compound
Sulfoxide
Ether
Azacycle
Sulfinyl compound
Organic oxide
Organosulfur compound
Organooxygen compound
Organonitrogen compound
Organopnictogen compound
Organic nitrogen compound
Hydrocarbon derivative
Organic oxygen 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: 21059682)

Organ

Liver (HMDB: HMDB0014011)
Kidney (HMDB: HMDB0014011)

Excreta

Biofluid or Excreta

Urine (PMID: 21059682)

Cellular substructure

Extracellular (HMDB: HMDB0014011)

Source

Endogenous

Endogenous (HMDB: HMDB0014011)

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	0.62 g/L	ALOGPS
logP	1.96	ALOGPS
logP	2.29	ChemAxon
logS	-2.7	ALOGPS
pKa (Strongest Acidic)	9.03	ChemAxon
pKa (Strongest Basic)	4.77	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	88.1 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	89.18 m³·mol⁻¹	ChemAxon
Polarizability	35.34 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]+	180.175	31661259
DarkChem	[M-H]-	177.453	31661259
DeepCCS	[M+H]+	183.809	30932474
DeepCCS	[M-H]-	181.451	30932474
DeepCCS	[M-2H]-	215.664	30932474
DeepCCS	[M+Na]+	191.189	30932474
AllCCS	[M+H]+	176.5	32859911
AllCCS	[M+H-H2O]+	173.4	32859911
AllCCS	[M+NH4]+	179.5	32859911
AllCCS	[M+Na]+	180.3	32859911
AllCCS	[M-H]-	177.7	32859911
AllCCS	[M+Na-2H]-	177.3	32859911
AllCCS	[M+HCOO]-	177.0	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
5'-O-Desmethyl omeprazole	COC1=C(C)C(CS(=O)C2=NC3=C(N2)C=C(O)C=C3)=NC=C1C	4066.1	Standard polar	33892256
5'-O-Desmethyl omeprazole	COC1=C(C)C(CS(=O)C2=NC3=C(N2)C=C(O)C=C3)=NC=C1C	3224.3	Standard non polar	33892256
5'-O-Desmethyl omeprazole	COC1=C(C)C(CS(=O)C2=NC3=C(N2)C=C(O)C=C3)=NC=C1C	3345.0	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
5'-O-Desmethyl omeprazole,1TMS,isomer #1	COC1=C(C)C=NC(CS(=O)C2=NC3=CC=C(O[Si](C)(C)C)C=C3[NH]2)=C1C	3068.8	Semi standard non polar	33892256
5'-O-Desmethyl omeprazole,1TMS,isomer #2	COC1=C(C)C=NC(CS(=O)C2=NC3=CC=C(O)C=C3N2[Si](C)(C)C)=C1C	3064.0	Semi standard non polar	33892256
5'-O-Desmethyl omeprazole,2TMS,isomer #1	COC1=C(C)C=NC(CS(=O)C2=NC3=CC=C(O[Si](C)(C)C)C=C3N2[Si](C)(C)C)=C1C	3122.8	Semi standard non polar	33892256
5'-O-Desmethyl omeprazole,2TMS,isomer #1	COC1=C(C)C=NC(CS(=O)C2=NC3=CC=C(O[Si](C)(C)C)C=C3N2[Si](C)(C)C)=C1C	3008.3	Standard non polar	33892256
5'-O-Desmethyl omeprazole,2TMS,isomer #1	COC1=C(C)C=NC(CS(=O)C2=NC3=CC=C(O[Si](C)(C)C)C=C3N2[Si](C)(C)C)=C1C	3645.0	Standard polar	33892256
5'-O-Desmethyl omeprazole,1TBDMS,isomer #1	COC1=C(C)C=NC(CS(=O)C2=NC3=CC=C(O[Si](C)(C)C(C)(C)C)C=C3[NH]2)=C1C	3298.7	Semi standard non polar	33892256
5'-O-Desmethyl omeprazole,1TBDMS,isomer #2	COC1=C(C)C=NC(CS(=O)C2=NC3=CC=C(O)C=C3N2[Si](C)(C)C(C)(C)C)=C1C	3259.9	Semi standard non polar	33892256
5'-O-Desmethyl omeprazole,2TBDMS,isomer #1	COC1=C(C)C=NC(CS(=O)C2=NC3=CC=C(O[Si](C)(C)C(C)(C)C)C=C3N2[Si](C)(C)C(C)(C)C)=C1C	3440.5	Semi standard non polar	33892256
5'-O-Desmethyl omeprazole,2TBDMS,isomer #1	COC1=C(C)C=NC(CS(=O)C2=NC3=CC=C(O[Si](C)(C)C(C)(C)C)C=C3N2[Si](C)(C)C(C)(C)C)=C1C	3447.3	Standard non polar	33892256
5'-O-Desmethyl omeprazole,2TBDMS,isomer #1	COC1=C(C)C=NC(CS(=O)C2=NC3=CC=C(O[Si](C)(C)C(C)(C)C)C=C3N2[Si](C)(C)C(C)(C)C)=C1C	3748.8	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - 5'-O-Desmethyl omeprazole GC-MS (Non-derivatized) - 70eV, Positive	splash10-0a4j-0902000000-75102c97171b715592f9	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5'-O-Desmethyl omeprazole GC-MS (1 TMS) - 70eV, Positive	splash10-0wbi-2903000000-acea1516dc9a54576618	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5'-O-Desmethyl omeprazole GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5'-O-Desmethyl omeprazole 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 - 5'-O-Desmethyl omeprazole 10V, Positive-QTOF	splash10-001j-0619000000-55f0d5556bd6a6d667c4	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5'-O-Desmethyl omeprazole 20V, Positive-QTOF	splash10-0f7k-0911000000-8fb8729eea3cc95ebd09	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5'-O-Desmethyl omeprazole 40V, Positive-QTOF	splash10-0ul9-3900000000-c85d5c4c944eead559dc	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5'-O-Desmethyl omeprazole 10V, Negative-QTOF	splash10-001i-0809000000-e91eeecfc55d32563d9c	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5'-O-Desmethyl omeprazole 20V, Negative-QTOF	splash10-001i-0900000000-a60d7182017c341c1819	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5'-O-Desmethyl omeprazole 40V, Negative-QTOF	splash10-001i-2900000000-26711dd8beb356db99df	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5'-O-Desmethyl omeprazole 10V, Positive-QTOF	splash10-0f6t-0920000000-360c211c9e8308c6f66c	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5'-O-Desmethyl omeprazole 20V, Positive-QTOF	splash10-0uyj-0911000000-e25c3d14b222c35bbcce	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5'-O-Desmethyl omeprazole 40V, Positive-QTOF	splash10-001i-1901000000-7610b9ad74473bbdfaed	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5'-O-Desmethyl omeprazole 10V, Negative-QTOF	splash10-001i-0907000000-057851ff363646336626	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5'-O-Desmethyl omeprazole 20V, Negative-QTOF	splash10-001i-0900000000-3681f62a33acbc5287c2	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5'-O-Desmethyl omeprazole 40V, Negative-QTOF	splash10-001i-0900000000-e5cd4f87d7ba1534b04f	2021-09-24	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

8579886

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

10404448

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

Not Available

Showing metabocard for 5'-O-Desmethyl omeprazole (HMDB0014011)

MOL for HMDB0014011 (5'-O-Desmethyl omeprazole)

3D MOL for HMDB0014011 (5'-O-Desmethyl omeprazole)

3D SDF for HMDB0014011 (5'-O-Desmethyl omeprazole)

3D-SDF for HMDB0014011 (5'-O-Desmethyl omeprazole)

PDB for HMDB0014011 (5'-O-Desmethyl omeprazole)

3D PDB for HMDB0014011 (5'-O-Desmethyl omeprazole)

SMILES for HMDB0014011 (5'-O-Desmethyl omeprazole)

INCHI for HMDB0014011 (5'-O-Desmethyl omeprazole)

Structure for HMDB0014011 (5'-O-Desmethyl omeprazole)

3D Structure for HMDB0014011 (5'-O-Desmethyl omeprazole)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra