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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-06 15:00:50 UTC

Update Date

2020-02-26 21:39:20 UTC

HMDB ID

HMDB0014013

Secondary Accession Numbers

HMDB14013

Metabolite Identification

Common Name

3-Hydroxyomeprazole

Description

3-Hydroxyomeprazole is only found in individuals that have used or taken Omeprazole. 3-Hydroxyomeprazole is a metabolite of Omeprazole. 3-hydroxyomeprazole 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

HMDB0014013
     RDKit          3D
3-Hydroxyomeprazole
 44 46  0  0  0  0  0  0  0  0999 V2000
    7.6556    0.4506    1.7135 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.5334   -0.5707    0.7393 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.3240   -0.6738    0.0765 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1834   -1.6610   -0.8758 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9972   -1.8245   -1.5819 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9471   -0.9721   -1.3121 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6943   -0.8766   -1.8172 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0368    0.1500   -1.2058 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3802    0.7067   -1.4874 S   0  0  0  0  0  4  0  0  0  0  0  0
    0.2654    2.2176   -1.2776 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7636   -0.1578   -0.4042 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1519    0.2720   -0.6025 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4741    1.2101   -1.5063 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7415    1.6280   -1.7135 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7885    1.0984   -0.9896 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1924    1.5372   -1.1945 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4552    0.1248   -0.0513 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4865   -0.4282    0.6944 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7990    0.2503    1.9200 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1607   -0.3001    0.1580 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8246   -1.3587    1.1778 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9774   -1.7956    1.8202 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8805    0.6991   -0.3152 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.0449    0.0425   -0.3553 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2557    0.1453    0.3079 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8928    0.3491    2.5133 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.4134    1.4284    1.2073 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.6404    0.4687    2.2027 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.9961   -2.3350   -1.0975 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8979   -2.5948   -2.3200 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6739   -1.2447   -0.6453 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4341   -0.0057    0.6281 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9383    2.3781   -2.4469 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8880    0.8083   -0.7517 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3629    2.5723   -0.8371 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3647    1.5455   -2.2918 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5777    1.0251    1.7470 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2100   -0.4379    2.6765 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9080    0.7356    2.3570 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0689   -1.0025    1.8934 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3861   -2.2503    0.6686 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4150   -2.4706    1.2242 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6624    1.5046    0.3049 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3415    0.9274    1.0502 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  1  0
 11 12  1  0
 12 13  2  0
 13 14  1  0
 14 15  2  0
 15 16  1  0
 15 17  1  0
 17 18  1  0
 18 19  1  0
 17 20  2  0
 20 21  1  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
 20 12  1  0
  1 26  1  0
  1 27  1  0
  1 28  1  0
  4 29  1  0
  5 30  1  0
 11 31  1  0
 11 32  1  0
 14 33  1  0
 16 34  1  0
 16 35  1  0
 16 36  1  0
 19 37  1  0
 19 38  1  0
 19 39  1  0
 21 40  1  0
 21 41  1  0
 22 42  1  0
 23 43  1  0
 25 44  1  0
M  END


  Mrv0541 06191310392D          

 25 27  0  0  0  0            999 V2000
    9.3338   -3.1632    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
   12.2214   -5.3068    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.7463   -2.4489    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.1032   -2.3382    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.0272   -2.4993    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    8.0272   -3.8272    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   10.9838   -3.1632    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    9.7463   -3.8778    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.5713   -3.8778    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.9838   -4.5922    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.5088   -3.1632    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2467   -2.7507    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.8089   -4.5922    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2467   -3.5757    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.2214   -3.8778    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.5713   -5.3068    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5321   -2.3382    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.8089   -3.1632    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5321   -3.9883    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8177   -2.7507    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8177   -3.5757    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.0464   -3.8778    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.0464   -5.3068    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3886   -2.7507    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.7463   -5.3068    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
 16 25  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0014013

> <DATABASE_NAME>
hmdb

> <SMILES>
COC1=CC2=C(C=C1)N=C(N2)S(=O)CC1=NC=C(C)C(OC)=C1CO

> <INCHI_IDENTIFIER>
InChI=1S/C17H19N3O4S/c1-10-7-18-15(12(8-21)16(10)24-3)9-25(22)17-19-13-5-4-11(23-2)6-14(13)20-17/h4-7,21H,8-9H2,1-3H3,(H,19,20)

> <INCHI_KEY>
IGVYIWUGJPECAJ-UHFFFAOYSA-N

> <FORMULA>
C17H19N3O4S

> <MOLECULAR_WEIGHT>
361.415

> <EXACT_MASS>
361.109626801

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_AVERAGE_POLARIZABILITY>
38.297686608454605

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(4-methoxy-2-{[(6-methoxy-1H-1,3-benzodiazol-2-yl)sulfinyl]methyl}-5-methylpyridin-3-yl)methanol

> <ALOGPS_LOGP>
1.07

> <JCHEM_LOGP>
1.1527379666666664

> <ALOGPS_LOGS>
-2.65

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.362930041202372

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.294130001887263

> <JCHEM_PKA_STRONGEST_BASIC>
3.9164735974234484

> <JCHEM_POLAR_SURFACE_AREA>
97.33000000000001

> <JCHEM_REFRACTIVITY>
95.437

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.07e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
{4-methoxy-2-[(5-methoxy-3H-1,3-benzodiazol-2-ylsulfinyl)methyl]-5-methylpyridin-3-yl}methanol

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0014013
     RDKit          3D
3-Hydroxyomeprazole
 44 46  0  0  0  0  0  0  0  0999 V2000
    7.6556    0.4506    1.7135 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.5334   -0.5707    0.7393 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.3240   -0.6738    0.0765 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1834   -1.6610   -0.8758 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9972   -1.8245   -1.5819 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9471   -0.9721   -1.3121 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6943   -0.8766   -1.8172 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0368    0.1500   -1.2058 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3802    0.7067   -1.4874 S   0  0  0  0  0  4  0  0  0  0  0  0
    0.2654    2.2176   -1.2776 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7636   -0.1578   -0.4042 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1519    0.2720   -0.6025 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4741    1.2101   -1.5063 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7415    1.6280   -1.7135 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7885    1.0984   -0.9896 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1924    1.5372   -1.1945 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4552    0.1248   -0.0513 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4865   -0.4282    0.6944 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7990    0.2503    1.9200 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1607   -0.3001    0.1580 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8246   -1.3587    1.1778 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9774   -1.7956    1.8202 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8805    0.6991   -0.3152 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.0449    0.0425   -0.3553 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2557    0.1453    0.3079 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8928    0.3491    2.5133 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.4134    1.4284    1.2073 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.6404    0.4687    2.2027 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.9961   -2.3350   -1.0975 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8979   -2.5948   -2.3200 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6739   -1.2447   -0.6453 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4341   -0.0057    0.6281 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9383    2.3781   -2.4469 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8880    0.8083   -0.7517 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3629    2.5723   -0.8371 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3647    1.5455   -2.2918 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5777    1.0251    1.7470 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2100   -0.4379    2.6765 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9080    0.7356    2.3570 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0689   -1.0025    1.8934 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3861   -2.2503    0.6686 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4150   -2.4706    1.2242 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6624    1.5046    0.3049 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3415    0.9274    1.0502 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  1  0
 11 12  1  0
 12 13  2  0
 13 14  1  0
 14 15  2  0
 15 16  1  0
 15 17  1  0
 17 18  1  0
 18 19  1  0
 17 20  2  0
 20 21  1  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
 20 12  1  0
  1 26  1  0
  1 27  1  0
  1 28  1  0
  4 29  1  0
  5 30  1  0
 11 31  1  0
 11 32  1  0
 14 33  1  0
 16 34  1  0
 16 35  1  0
 16 36  1  0
 19 37  1  0
 19 38  1  0
 19 39  1  0
 21 40  1  0
 21 41  1  0
 22 42  1  0
 23 43  1  0
 25 44  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      17.423  -5.905   0.000  0.00  0.00           S+0
HETATM    2  O   UNK     0      22.813  -9.906   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      18.193  -4.571   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0       9.526  -4.365   0.000  0.00  0.00           O+0
HETATM    5  N   UNK     0      14.984  -4.665   0.000  0.00  0.00           N+0
HETATM    6  N   UNK     0      14.984  -7.144   0.000  0.00  0.00           N+0
HETATM    7  N   UNK     0      20.503  -5.905   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0      18.193  -7.238   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      19.733  -7.238   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      20.503  -8.572   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      15.883  -5.905   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      13.527  -5.135   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      22.043  -8.572   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      13.527  -6.675   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      22.813  -7.238   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      19.733  -9.906   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      12.193  -4.365   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      22.043  -5.905   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      12.193  -7.445   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      10.860  -5.135   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      10.860  -6.675   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      24.353  -7.238   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      24.353  -9.906   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       8.192  -5.135   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0      18.193  -9.906   0.000  0.00  0.00           O+0
CONECT    1    3    8   11                                                  
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   25                                                       
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   16                                                            
MASTER        0    0    0    0    0    0    0    0   25    0   54    0
END

COMPND    HMDB0014013
HETATM    1  C1  UNL     1       7.656   0.451   1.714  1.00  0.00           C  
HETATM    2  O1  UNL     1       7.533  -0.571   0.739  1.00  0.00           O  
HETATM    3  C2  UNL     1       6.324  -0.674   0.076  1.00  0.00           C  
HETATM    4  C3  UNL     1       6.183  -1.661  -0.876  1.00  0.00           C  
HETATM    5  C4  UNL     1       4.997  -1.825  -1.582  1.00  0.00           C  
HETATM    6  C5  UNL     1       3.947  -0.972  -1.312  1.00  0.00           C  
HETATM    7  N1  UNL     1       2.694  -0.877  -1.817  1.00  0.00           N  
HETATM    8  C6  UNL     1       2.037   0.150  -1.206  1.00  0.00           C  
HETATM    9  S1  UNL     1       0.380   0.707  -1.487  1.00  0.00           S  
HETATM   10  O2  UNL     1       0.265   2.218  -1.278  1.00  0.00           O  
HETATM   11  C7  UNL     1      -0.764  -0.158  -0.404  1.00  0.00           C  
HETATM   12  C8  UNL     1      -2.152   0.272  -0.603  1.00  0.00           C  
HETATM   13  N2  UNL     1      -2.474   1.210  -1.506  1.00  0.00           N  
HETATM   14  C9  UNL     1      -3.741   1.628  -1.714  1.00  0.00           C  
HETATM   15  C10 UNL     1      -4.789   1.098  -0.990  1.00  0.00           C  
HETATM   16  C11 UNL     1      -6.192   1.537  -1.194  1.00  0.00           C  
HETATM   17  C12 UNL     1      -4.455   0.125  -0.051  1.00  0.00           C  
HETATM   18  O3  UNL     1      -5.486  -0.428   0.694  1.00  0.00           O  
HETATM   19  C13 UNL     1      -5.799   0.250   1.920  1.00  0.00           C  
HETATM   20  C14 UNL     1      -3.161  -0.300   0.158  1.00  0.00           C  
HETATM   21  C15 UNL     1      -2.825  -1.359   1.178  1.00  0.00           C  
HETATM   22  O4  UNL     1      -3.977  -1.796   1.820  1.00  0.00           O  
HETATM   23  N3  UNL     1       2.880   0.699  -0.315  1.00  0.00           N  
HETATM   24  C16 UNL     1       4.045   0.042  -0.355  1.00  0.00           C  
HETATM   25  C17 UNL     1       5.256   0.145   0.308  1.00  0.00           C  
HETATM   26  H1  UNL     1       6.893   0.349   2.513  1.00  0.00           H  
HETATM   27  H2  UNL     1       7.413   1.428   1.207  1.00  0.00           H  
HETATM   28  H3  UNL     1       8.640   0.469   2.203  1.00  0.00           H  
HETATM   29  H4  UNL     1       6.996  -2.335  -1.097  1.00  0.00           H  
HETATM   30  H5  UNL     1       4.898  -2.595  -2.320  1.00  0.00           H  
HETATM   31  H6  UNL     1      -0.674  -1.245  -0.645  1.00  0.00           H  
HETATM   32  H7  UNL     1      -0.434  -0.006   0.628  1.00  0.00           H  
HETATM   33  H8  UNL     1      -3.938   2.378  -2.447  1.00  0.00           H  
HETATM   34  H9  UNL     1      -6.888   0.808  -0.752  1.00  0.00           H  
HETATM   35  H10 UNL     1      -6.363   2.572  -0.837  1.00  0.00           H  
HETATM   36  H11 UNL     1      -6.365   1.546  -2.292  1.00  0.00           H  
HETATM   37  H12 UNL     1      -6.578   1.025   1.747  1.00  0.00           H  
HETATM   38  H13 UNL     1      -6.210  -0.438   2.676  1.00  0.00           H  
HETATM   39  H14 UNL     1      -4.908   0.736   2.357  1.00  0.00           H  
HETATM   40  H15 UNL     1      -2.069  -1.002   1.893  1.00  0.00           H  
HETATM   41  H16 UNL     1      -2.386  -2.250   0.669  1.00  0.00           H  
HETATM   42  H17 UNL     1      -4.415  -2.471   1.224  1.00  0.00           H  
HETATM   43  H18 UNL     1       2.662   1.505   0.305  1.00  0.00           H  
HETATM   44  H19 UNL     1       5.342   0.927   1.050  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
CONECT   11   12   31   32
CONECT   12   13   13   20
CONECT   13   14
CONECT   14   15   15   33
CONECT   15   16   17
CONECT   16   34   35   36
CONECT   17   18   20   20
CONECT   18   19
CONECT   19   37   38   39
CONECT   20   21
CONECT   21   22   40   41
CONECT   22   42
CONECT   23   24   43
CONECT   24   25   25
CONECT   25   44
END

HMDB0014013
     RDKit          3D
3-Hydroxyomeprazole
 44 46  0  0  0  0  0  0  0  0999 V2000
    7.6556    0.4506    1.7135 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.5334   -0.5707    0.7393 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.3240   -0.6738    0.0765 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1834   -1.6610   -0.8758 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9972   -1.8245   -1.5819 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9471   -0.9721   -1.3121 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6943   -0.8766   -1.8172 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0368    0.1500   -1.2058 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3802    0.7067   -1.4874 S   0  0  0  0  0  4  0  0  0  0  0  0
    0.2654    2.2176   -1.2776 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7636   -0.1578   -0.4042 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1519    0.2720   -0.6025 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4741    1.2101   -1.5063 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7415    1.6280   -1.7135 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7885    1.0984   -0.9896 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1924    1.5372   -1.1945 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4552    0.1248   -0.0513 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4865   -0.4282    0.6944 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7990    0.2503    1.9200 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1607   -0.3001    0.1580 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8246   -1.3587    1.1778 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9774   -1.7956    1.8202 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8805    0.6991   -0.3152 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.0449    0.0425   -0.3553 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2557    0.1453    0.3079 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8928    0.3491    2.5133 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.4134    1.4284    1.2073 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.6404    0.4687    2.2027 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.9961   -2.3350   -1.0975 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8979   -2.5948   -2.3200 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6739   -1.2447   -0.6453 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4341   -0.0057    0.6281 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9383    2.3781   -2.4469 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8880    0.8083   -0.7517 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3629    2.5723   -0.8371 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3647    1.5455   -2.2918 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5777    1.0251    1.7470 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2100   -0.4379    2.6765 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9080    0.7356    2.3570 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0689   -1.0025    1.8934 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3861   -2.2503    0.6686 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4150   -2.4706    1.2242 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6624    1.5046    0.3049 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3415    0.9274    1.0502 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  1  0
 11 12  1  0
 12 13  2  0
 13 14  1  0
 14 15  2  0
 15 16  1  0
 15 17  1  0
 17 18  1  0
 18 19  1  0
 17 20  2  0
 20 21  1  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
 20 12  1  0
  1 26  1  0
  1 27  1  0
  1 28  1  0
  4 29  1  0
  5 30  1  0
 11 31  1  0
 11 32  1  0
 14 33  1  0
 16 34  1  0
 16 35  1  0
 16 36  1  0
 19 37  1  0
 19 38  1  0
 19 39  1  0
 21 40  1  0
 21 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
(4-Methoxy-2-{[(6-methoxy-1H-1,3-benzodiazol-2-yl)sulphinyl]methyl}-5-methylpyridin-3-yl)methanol	HMDB

Chemical Formula

C₁₇H₁₉N₃O₄S

Average Molecular Weight

361.415

Monoisotopic Molecular Weight

361.109626801

IUPAC Name

(4-methoxy-2-{[(6-methoxy-1H-1,3-benzodiazol-2-yl)sulfinyl]methyl}-5-methylpyridin-3-yl)methanol

Traditional Name

{4-methoxy-2-[(5-methoxy-3H-1,3-benzodiazol-2-ylsulfinyl)methyl]-5-methylpyridin-3-yl}methanol

CAS Registry Number

Not Available

SMILES

COC1=CC2=C(C=C1)N=C(N2)S(=O)CC1=NC=C(C)C(OC)=C1CO

InChI Identifier

InChI=1S/C17H19N3O4S/c1-10-7-18-15(12(8-21)16(10)24-3)9-25(22)17-19-13-5-4-11(23-2)6-14(13)20-17/h4-7,21H,8-9H2,1-3H3,(H,19,20)

InChI Key

IGVYIWUGJPECAJ-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
Heteroaromatic compound
Sulfoxide
Sulfinyl compound
Ether
Azacycle
Aromatic alcohol
Organic oxide
Organopnictogen compound
Primary alcohol
Organosulfur compound
Organooxygen compound
Organonitrogen compound
Organic nitrogen compound
Alcohol
Hydrocarbon derivative
Organic oxygen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Ontology

Not Available

Liver (HMDB: HMDB0014013)
Kidney (HMDB: HMDB0014013)

Excreta

Biofluid or Excreta

Urine (PMID: 21059682)

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 21059682)

Cellular substructure

Extracellular (HMDB: HMDB0014013)

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	0.81 g/L	ALOGPS
logP	1.07	ALOGPS
logP	1.15	ChemAxon
logS	-2.6	ALOGPS
pKa (Strongest Acidic)	9.29	ChemAxon
pKa (Strongest Basic)	3.92	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	97.33 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	95.44 m³·mol⁻¹	ChemAxon
Polarizability	38.3 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
DarkChem	[M+H]+	183.722	31661259
DarkChem	[M-H]-	182.741	31661259
DeepCCS	[M+H]+	186.074	30932474
DeepCCS	[M-H]-	183.716	30932474
DeepCCS	[M-2H]-	217.753	30932474
DeepCCS	[M+Na]+	192.98	30932474
AllCCS	[M+H]+	184.2	32859911
AllCCS	[M+H-H2O]+	181.3	32859911
AllCCS	[M+NH4]+	186.9	32859911
AllCCS	[M+Na]+	187.6	32859911
AllCCS	[M-H]-	183.5	32859911
AllCCS	[M+Na-2H]-	183.5	32859911
AllCCS	[M+HCOO]-	183.6	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
3-Hydroxyomeprazole	COC1=CC2=C(C=C1)N=C(N2)S(=O)CC1=NC=C(C)C(OC)=C1CO	4269.8	Standard polar	33892256
3-Hydroxyomeprazole	COC1=CC2=C(C=C1)N=C(N2)S(=O)CC1=NC=C(C)C(OC)=C1CO	3348.9	Standard non polar	33892256
3-Hydroxyomeprazole	COC1=CC2=C(C=C1)N=C(N2)S(=O)CC1=NC=C(C)C(OC)=C1CO	3492.4	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
3-Hydroxyomeprazole,1TMS,isomer #1	COC1=CC=C2N=C(S(=O)CC3=NC=C(C)C(OC)=C3CO[Si](C)(C)C)[NH]C2=C1	3240.8	Semi standard non polar	33892256
3-Hydroxyomeprazole,1TMS,isomer #2	COC1=CC=C2N=C(S(=O)CC3=NC=C(C)C(OC)=C3CO)N([Si](C)(C)C)C2=C1	3187.5	Semi standard non polar	33892256
3-Hydroxyomeprazole,2TMS,isomer #1	COC1=CC=C2N=C(S(=O)CC3=NC=C(C)C(OC)=C3CO[Si](C)(C)C)N([Si](C)(C)C)C2=C1	3252.9	Semi standard non polar	33892256
3-Hydroxyomeprazole,2TMS,isomer #1	COC1=CC=C2N=C(S(=O)CC3=NC=C(C)C(OC)=C3CO[Si](C)(C)C)N([Si](C)(C)C)C2=C1	3172.5	Standard non polar	33892256
3-Hydroxyomeprazole,2TMS,isomer #1	COC1=CC=C2N=C(S(=O)CC3=NC=C(C)C(OC)=C3CO[Si](C)(C)C)N([Si](C)(C)C)C2=C1	4026.7	Standard polar	33892256
3-Hydroxyomeprazole,1TBDMS,isomer #1	COC1=CC=C2N=C(S(=O)CC3=NC=C(C)C(OC)=C3CO[Si](C)(C)C(C)(C)C)[NH]C2=C1	3452.4	Semi standard non polar	33892256
3-Hydroxyomeprazole,1TBDMS,isomer #2	COC1=CC=C2N=C(S(=O)CC3=NC=C(C)C(OC)=C3CO)N([Si](C)(C)C(C)(C)C)C2=C1	3377.7	Semi standard non polar	33892256
3-Hydroxyomeprazole,2TBDMS,isomer #1	COC1=CC=C2N=C(S(=O)CC3=NC=C(C)C(OC)=C3CO[Si](C)(C)C(C)(C)C)N([Si](C)(C)C(C)(C)C)C2=C1	3552.4	Semi standard non polar	33892256
3-Hydroxyomeprazole,2TBDMS,isomer #1	COC1=CC=C2N=C(S(=O)CC3=NC=C(C)C(OC)=C3CO[Si](C)(C)C(C)(C)C)N([Si](C)(C)C(C)(C)C)C2=C1	3585.2	Standard non polar	33892256
3-Hydroxyomeprazole,2TBDMS,isomer #1	COC1=CC=C2N=C(S(=O)CC3=NC=C(C)C(OC)=C3CO[Si](C)(C)C(C)(C)C)N([Si](C)(C)C(C)(C)C)C2=C1	4083.8	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - 3-Hydroxyomeprazole GC-MS (Non-derivatized) - 70eV, Positive	splash10-01b9-0903000000-c4dbf67c7dea8078156e	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3-Hydroxyomeprazole GC-MS (1 TMS) - 70eV, Positive	splash10-00di-5951200000-12db1dc829e95b8b2bbc	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3-Hydroxyomeprazole 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 - 3-Hydroxyomeprazole 10V, Positive-QTOF	splash10-03dl-0129000000-3eec8fe34eaf293be27a	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Hydroxyomeprazole 20V, Positive-QTOF	splash10-01oy-0839000000-b77107d8bc8e5ab88322	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Hydroxyomeprazole 40V, Positive-QTOF	splash10-0udi-0900000000-2236fd41c8f2c61bb43f	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Hydroxyomeprazole 10V, Negative-QTOF	splash10-03dj-0609000000-c06ffda295e4fd7e8175	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Hydroxyomeprazole 20V, Negative-QTOF	splash10-002b-0901000000-787f675efc6f4137f676	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Hydroxyomeprazole 40V, Negative-QTOF	splash10-004j-0901000000-5bf399bf19c0308b9c0e	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Hydroxyomeprazole 10V, Negative-QTOF	splash10-03dj-0709000000-433d264defa30b358ce9	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Hydroxyomeprazole 20V, Negative-QTOF	splash10-0002-0902000000-b2dd7a1fd85beabdf263	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Hydroxyomeprazole 40V, Negative-QTOF	splash10-001j-0900000000-95a48f2a477f606ef038	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Hydroxyomeprazole 10V, Positive-QTOF	splash10-03di-0297000000-890679b2c77982c1e7b4	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Hydroxyomeprazole 20V, Positive-QTOF	splash10-03dj-0951000000-0c37f999b16bf7a58e50	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Hydroxyomeprazole 40V, Positive-QTOF	splash10-0002-0910000000-d235fe9996fd16e169b8	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

32697733

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

71587579

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 3-Hydroxyomeprazole (HMDB0014013)

MOL for HMDB0014013 (3-Hydroxyomeprazole)

3D MOL for HMDB0014013 (3-Hydroxyomeprazole)

3D SDF for HMDB0014013 (3-Hydroxyomeprazole)

3D-SDF for HMDB0014013 (3-Hydroxyomeprazole)

PDB for HMDB0014013 (3-Hydroxyomeprazole)

3D PDB for HMDB0014013 (3-Hydroxyomeprazole)

SMILES for HMDB0014013 (3-Hydroxyomeprazole)

INCHI for HMDB0014013 (3-Hydroxyomeprazole)

Structure for HMDB0014013 (3-Hydroxyomeprazole)

3D Structure for HMDB0014013 (3-Hydroxyomeprazole)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra