NP-MRD: Showing NP-Card for Rabeprazole (NP0334586)

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Record Information

Version

2.0

Created at

2024-09-10 19:01:38 UTC

Updated at

2024-09-10 19:01:39 UTC

NP-MRD ID

NP0334586

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Rabeprazole

Description

Rabeprazole, also known as clofezone or eraloc, 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. Rabeprazole is a drug which is used for the treatment of acid-reflux disorders (gerd), peptic ulcer disease, h. Pylori eradication, and prevention of gastroinetestinal bleeds with nsaid use. Rabeprazole is a strong basic compound (based on its pKa). In humans, rabeprazole is involved in rabeprazole action pathway. Therefore, it is not expected to react with CYP2C19 substrates like theophylline, warfarin, diazepam, and phenytoin.

Structure

MOL SDF PDB SMILES InChI

1129
  Mrv0541 02231215162D          

 25 27  0  0  1  0            999 V2000
    5.1662    1.2111    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    8.0537   -0.9323    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.5288   -2.3613    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.5787    1.9257    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8597    1.8751    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.8597    0.5472    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.8162    1.2111    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.5787    0.4967    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4037    0.4967    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8162   -0.2178    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6412   -0.2178    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3412    1.2111    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0791    1.6236    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.8788   -0.9323    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.2913   -1.6468    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0791    0.7986    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4037   -0.9323    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.0537    0.4967    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.1163   -1.6468    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3645    2.0361    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6412    1.2111    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3645    0.3861    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500    1.6236    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500    0.7986    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.3538   -2.3613    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  4  2  0  0  0  0
  1  8  1  0  0  0  0
  1 12  1  0  0  0  0
  2 11  1  0  0  0  0
  2 14  1  0  0  0  0
  3 19  1  0  0  0  0
  3 25  1  0  0  0  0
  5 12  1  0  0  0  0
  5 13  1  0  0  0  0
  6 12  2  0  0  0  0
  6 16  1  0  0  0  0
  7  9  2  0  0  0  0
  7 21  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
 10 17  1  0  0  0  0
 11 18  1  0  0  0  0
 13 16  1  0  0  0  0
 13 20  2  0  0  0  0
 14 15  1  0  0  0  0
 15 19  1  0  0  0  0
 16 22  2  0  0  0  0
 18 21  2  0  0  0  0
 20 23  1  0  0  0  0
 22 24  1  0  0  0  0
 23 24  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0334586

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COCCCOC1=C(C)C(CS(=O)C2=NC3=CC=CC=C3N2)=NC=C1

> <INCHI_IDENTIFIER>
InChI=1S/C18H21N3O3S/c1-13-16(19-9-8-17(13)24-11-5-10-23-2)12-25(22)18-20-14-6-3-4-7-15(14)21-18/h3-4,6-9H,5,10-12H2,1-2H3,(H,20,21)

> <INCHI_KEY>
YREYEVIYCVEVJK-UHFFFAOYSA-N

> <FORMULA>
C18H21N3O3S

> <MOLECULAR_WEIGHT>
359.443

> <EXACT_MASS>
359.130362243

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_AVERAGE_POLARIZABILITY>
39.63690033611189

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

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

> <ALOGPS_LOGP>
2.04

> <JCHEM_LOGP>
2.0907432303333326

> <ALOGPS_LOGS>
-3.03

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
17.329381007589777

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.346710821346507

> <JCHEM_PKA_STRONGEST_BASIC>
4.23997374588058

> <JCHEM_POLAR_SURFACE_AREA>
77.10000000000001

> <JCHEM_REFRACTIVITY>
98.0668

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.36e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
rabeprazole

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: 1129                                              
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  S   UNK     0       9.644   2.261   0.000  0.00  0.00           S+0
HETATM    2  O   UNK     0      15.034  -1.740   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      19.654  -4.408   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0      10.414   3.595   0.000  0.00  0.00           O+0
HETATM    5  N   UNK     0       7.205   3.500   0.000  0.00  0.00           N+0
HETATM    6  N   UNK     0       7.205   1.021   0.000  0.00  0.00           N+0
HETATM    7  N   UNK     0      12.724   2.261   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0      10.414   0.927   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      11.954   0.927   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      12.724  -0.407   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      14.264  -0.407   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       8.104   2.261   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       5.748   3.031   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      16.574  -1.740   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      17.344  -3.074   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       5.748   1.491   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      11.954  -1.740   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      15.034   0.927   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      18.884  -3.074   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       4.414   3.801   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      14.264   2.261   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       4.414   0.721   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       3.080   3.031   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       3.080   1.491   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      21.194  -4.408   0.000  0.00  0.00           C+0
CONECT    1    4    8   12                                                  
CONECT    2   11   14                                                       
CONECT    3   19   25                                                       
CONECT    4    1                                                            
CONECT    5   12   13                                                       
CONECT    6   12   16                                                       
CONECT    7    9   21                                                       
CONECT    8    1    9                                                       
CONECT    9    7    8   10                                                  
CONECT   10    9   11   17                                                  
CONECT   11    2   10   18                                                  
CONECT   12    1    5    6                                                  
CONECT   13    5   16   20                                                  
CONECT   14    2   15                                                       
CONECT   15   14   19                                                       
CONECT   16    6   13   22                                                  
CONECT   17   10                                                            
CONECT   18   11   21                                                       
CONECT   19    3   15                                                       
CONECT   20   13   23                                                       
CONECT   21    7   18                                                       
CONECT   22   16   24                                                       
CONECT   23   20   24                                                       
CONECT   24   22   23                                                       
CONECT   25    3                                                            
MASTER        0    0    0    0    0    0    0    0   25    0   54    0
END

View in JSmol

Synonyms

Value	Source
Clofezone	ChEBI
Eraloc	Kegg
Aciphex	HMDB
Habeprazole	HMDB
Pariet	HMDB
Pariets	HMDB
Rabeprazole sodium	HMDB
Sodium rabeprazole	HMDB
Dexrabeprazole	HMDB
1H-Benzimidazole, 2-(((4-(3-methoxypropoxy)-3-methyl-2-pyridinyl)methyl)sulfinyl)-, sodium salt	HMDB
2-((4-(3-Methoxypropoxy)-3-methylpyridin-2-yl)methylsulfinyl)-1H-benzimidazole	HMDB
Sodium, rabeprazole	HMDB

Chemical Formula

C₁₈H₂₁N₃O₃S

Average Mass

359.4430 Da

Monoisotopic Mass

359.13036 Da

IUPAC Name

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

Traditional Name

rabeprazole

CAS Registry Number

Not Available

SMILES

COCCCOC1=C(C)C(CS(=O)C2=NC3=CC=CC=C3N2)=NC=C1

InChI Identifier

InChI=1S/C18H21N3O3S/c1-13-16(19-9-8-17(13)24-11-5-10-23-2)12-25(22)18-20-14-6-3-4-7-15(14)21-18/h3-4,6-9H,5,10-12H2,1-2H3,(H,20,21)

InChI Key

YREYEVIYCVEVJK-UHFFFAOYSA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Not Available

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
Methylpyridine
Pyridine
Benzenoid
Azole
Imidazole
Heteroaromatic compound
Sulfoxide
Sulfinyl compound
Ether
Dialkyl ether
Azacycle
Organic nitrogen compound
Hydrocarbon derivative
Organic oxide
Organosulfur compound
Organooxygen compound
Organonitrogen compound
Organopnictogen compound
Organic oxygen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

sulfoxide (CHEBI:8768 )
pyridines (CHEBI:8768 )
benzimidazoles (CHEBI:8768 )

Physical Properties

State

Not Available

Experimental 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

Predicted Properties

Property	Value	Source
logP	2.04	ALOGPS
logP	2.09	ChemAxon
logS	-3	ALOGPS
pKa (Strongest Acidic)	9.35	ChemAxon
pKa (Strongest Basic)	4.24	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	77.1 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	98.07 m³·mol⁻¹	ChemAxon
Polarizability	39.64 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