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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2006-10-17 09:25:06 UTC
Update Date2020-02-26 21:25:41 UTC
HMDB IDHMDB0005026
Secondary Accession Numbers
  • HMDB05026
Metabolite Identification
Common NameRabeprazole
DescriptionRabeprazole, 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. In humans, rabeprazole is involved in the rabeprazole metabolism pathway. Rabeprazole is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. Based on a literature review a significant number of articles have been published on Rabeprazole.
Structure
Data?1582752341
Synonyms
ValueSource
ClofezoneChEBI
EralocKegg
AciphexHMDB, MeSH
HabeprazoleHMDB
ParietHMDB, MeSH
ParietsHMDB
Rabeprazole sodiumHMDB, MeSH
Sodium rabeprazoleHMDB
DexrabeprazoleMeSH, HMDB
1H-Benzimidazole, 2-(((4-(3-methoxypropoxy)-3-methyl-2-pyridinyl)methyl)sulfinyl)-, sodium saltMeSH, HMDB
2-((4-(3-Methoxypropoxy)-3-methylpyridin-2-yl)methylsulfinyl)-1H-benzimidazoleMeSH, HMDB
Sodium, rabeprazoleMeSH, HMDB
Chemical FormulaC18H21N3O3S
Average Molecular Weight359.443
Monoisotopic Molecular Weight359.130362243
IUPAC Name2-{[4-(3-methoxypropoxy)-3-methylpyridin-2-yl]methanesulfinyl}-1H-1,3-benzodiazole
Traditional Namerabeprazole
CAS Registry Number117976-89-3
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 KeyYREYEVIYCVEVJK-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.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassBenzimidazoles
Sub ClassSulfinylbenzimidazoles
Direct ParentSulfinylbenzimidazoles
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 FrameworkAromatic heteropolycyclic compounds
External Descriptors
Ontology
Disposition

Source

Route of exposure

Process

Naturally occurring process

Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point101.7 - 103.9 °CNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility0.34 g/LALOGPS
logP10(2.04) g/LALOGPS
logP10(2.09) g/LChemAxon
logS10(-3) g/LALOGPS
pKa (Strongest Acidic)9.35ChemAxon
pKa (Strongest Basic)4.24ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area77.1 ŲChemAxon
Rotatable Bond Count8ChemAxon
Refractivity98.07 m³·mol⁻¹ChemAxon
Polarizability39.64 ųChemAxon
Number of Rings3ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+182.04531661259
DarkChem[M-H]-183.3731661259

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
RabeprazoleCOCCCOC1=C(C)C(CS(=O)C2=NC3=CC=CC=C3N2)=NC=C14061.7Standard polar33892256
RabeprazoleCOCCCOC1=C(C)C(CS(=O)C2=NC3=CC=CC=C3N2)=NC=C13018.8Standard non polar33892256
RabeprazoleCOCCCOC1=C(C)C(CS(=O)C2=NC3=CC=CC=C3N2)=NC=C13268.7Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Rabeprazole,1TMS,isomer #1COCCCOC1=CC=NC(CS(=O)C2=NC3=CC=CC=C3N2[Si](C)(C)C)=C1C3079.2Semi standard non polar33892256
Rabeprazole,1TMS,isomer #1COCCCOC1=CC=NC(CS(=O)C2=NC3=CC=CC=C3N2[Si](C)(C)C)=C1C2996.9Standard non polar33892256
Rabeprazole,1TMS,isomer #1COCCCOC1=CC=NC(CS(=O)C2=NC3=CC=CC=C3N2[Si](C)(C)C)=C1C3880.2Standard polar33892256
Rabeprazole,1TBDMS,isomer #1COCCCOC1=CC=NC(CS(=O)C2=NC3=CC=CC=C3N2[Si](C)(C)C(C)(C)C)=C1C3219.6Semi standard non polar33892256
Rabeprazole,1TBDMS,isomer #1COCCCOC1=CC=NC(CS(=O)C2=NC3=CC=CC=C3N2[Si](C)(C)C(C)(C)C)=C1C3206.9Standard non polar33892256
Rabeprazole,1TBDMS,isomer #1COCCCOC1=CC=NC(CS(=O)C2=NC3=CC=CC=C3N2[Si](C)(C)C(C)(C)C)=C1C3908.5Standard polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Rabeprazole GC-MS (Non-derivatized) - 70eV, Positivesplash10-009e-9843000000-7b2764dc90023b55c85c2017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Rabeprazole GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Rabeprazole GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Rabeprazole 10V, Positive-QTOFsplash10-03dl-2159000000-f97510bdc8045ab08ca62017-07-26Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Rabeprazole 20V, Positive-QTOFsplash10-006x-5792000000-af268bb77b35247f0f412017-07-26Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Rabeprazole 40V, Positive-QTOFsplash10-00dl-9800000000-6bea6647768de1869c4d2017-07-26Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Rabeprazole 10V, Negative-QTOFsplash10-066r-1938000000-25678fb8a17be5befc292017-07-26Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Rabeprazole 20V, Negative-QTOFsplash10-014i-0900000000-c503bc067607aca1451e2017-07-26Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Rabeprazole 40V, Negative-QTOFsplash10-014i-2910000000-aa7552fe843abc4a67e62017-07-26Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Rabeprazole 10V, Negative-QTOFsplash10-0a4i-0119000000-c5f221b3ffcf7b5cc55c2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Rabeprazole 20V, Negative-QTOFsplash10-014i-0900000000-3214248b0f4d9b60f1532021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Rabeprazole 40V, Negative-QTOFsplash10-014i-0900000000-9c4b8759dd61ba0972162021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Rabeprazole 10V, Positive-QTOFsplash10-03di-0093000000-14b0419adbad3c76149e2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Rabeprazole 20V, Positive-QTOFsplash10-0229-1950000000-ce8b99f657880db6f1d02021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Rabeprazole 40V, Positive-QTOFsplash10-08ml-2910000000-2fbee5190b8417e0ac8a2021-09-22Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Membrane (predicted from logP)
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDDB01129
Phenol Explorer Compound IDNot Available
FooDB IDFDB023595
KNApSAcK IDNot Available
Chemspider ID4853
KEGG Compound IDC07864
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkRabeprazole
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI ID8768
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceSouda, Shigeru; Ueda, Norihiro; Miyazawa, Shuhei; Tagami, Katsuya; Nomoto, Seiichiro; Okita, Makoto; Shimomura, Naoyuki; Kaneko, Toshihiko; Fujimoto, Masatoshi; et al. Preparation of 2-[(4-alkoxypyrid-2-yl)methylthio]benzimidazoles, -benzothiazoles, and -benzoxazoles as ulcer inhibitors. Eur. Pat. Appl. (1988), 96 pp. CODEN: EPXXDW EP 268956 A2 19880601 CAN 110:23889 AN 1989:23889
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available

Enzymes

General function:
Involved in monooxygenase activity
Specific function:
Cytochromes P450 are a group of heme-thiolate monooxygenases. In liver microsomes, this enzyme is involved in an NADPH-dependent electron transport pathway. It performs a variety of oxidation reactions (e.g. caffeine 8-oxidation, omeprazole sulphoxidation, midazolam 1'-hydroxylation and midazolam 4-hydroxylation) of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics. Acts as a 1,8-cineole 2-exo-monooxygenase. The enzyme also hydroxylates etoposide.
Gene Name:
CYP3A4
Uniprot ID:
P08684
Molecular weight:
57255.585
General function:
Involved in monooxygenase activity
Specific function:
Responsible for the metabolism of a number of therapeutic agents such as the anticonvulsant drug S-mephenytoin, omeprazole, proguanil, certain barbiturates, diazepam, propranolol, citalopram and imipramine.
Gene Name:
CYP2C19
Uniprot ID:
P33261
Molecular weight:
55944.565
General function:
Involved in sodium:potassium-exchanging ATPase activity
Specific function:
Not Available
Gene Name:
ATP4B
Uniprot ID:
P51164
Molecular weight:
33367.0
General function:
Involved in ATP binding
Specific function:
Catalyzes the hydrolysis of ATP coupled with the exchange of H(+) and K(+) ions across the plasma membrane. Responsible for acid production in the stomach.
Gene Name:
ATP4A
Uniprot ID:
P20648
Molecular weight:
114117.74