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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2006-05-17 14:44:52 UTC
Update Date2022-03-07 02:49:11 UTC
HMDB IDHMDB0001913
Secondary Accession Numbers
  • HMDB01913
Metabolite Identification
Common NameOmeprazole
DescriptionOmeprazole is a highly effective inhibitor of gastric acid secretion used in the therapy of stomach ulcers, dyspepsia, peptic ulcer disease , gastroesophageal reflux disease and Zollinger-Ellison syndrome. The drug inhibits the H(+)-K(+)-ATPase (H(+)-K(+)-exchanging ATPase) in the proton pump of Gastric Parietal Cells.--Pubchem. Omeprazole is one of the most widely prescribed drugs internationally and is available over the counter in some countries.
Structure
Data?1582752216
Synonyms
ValueSource
PrilosecKegg
( -)-OmeprazoleHMDB
(-)-OmeprazoleHMDB
(S)-(-)-OmeprazoleHMDB
(S)-OmeprazoleHMDB
2,3,5-Trimethylpyridine/OmeprazoleHMDB
AntraHMDB
Antra mupsHMDB
AudazolHMDB
AulcerHMDB
BelmazolHMDB
CeprandalHMDB
DanloxHMDB
DemeprazolHMDB
DesecHMDB
DizprazolHMDB
DudencerHMDB
ElgamHMDB
EmeprotonHMDB
EpirazoleHMDB
ErbolinHMDB
EsomeprazoleHMDB
EsomperazoleHMDB
ExterHMDB
GasecHMDB
GastrimutHMDB
GastrolocHMDB
GibancerHMDB
IndurganHMDB
InhibitronHMDB
InhipumpHMDB
LensorHMDB
LogastricHMDB
LomacHMDB
LosecHMDB
MepralHMDB
MiolHMDB
MiracidHMDB
MopralHMDB
MoreconHMDB
NexiamHMDB
NexiumHMDB
Nexium IVHMDB
NilsecHMDB
NopraminHMDB
NuclosinaHMDB
OcidHMDB
OlexinHMDB
OmaprenHMDB
Omebeta 20HMDB
OmedHMDB
OmegastHMDB
OMEPHMDB
OmepradexHMDB
OmepralHMDB
OmeprazolHMDB
Omeprazole pelletsHMDB
OmeprazolumHMDB
OmeprazonHMDB
OmeprolHMDB
OmesekHMDB
OmezHMDB
OmezolHMDB
OmezolanHMDB
OmidHMDB
OmisecHMDB
OmizacHMDB
OmpanytHMDB
OMZHMDB
OrtanolHMDB
OsirenHMDB
OzokenHMDB
PaprazolHMDB
ParizacHMDB
PepticumHMDB
PepticusHMDB
PeptilcerHMDB
PrazentolHMDB
PrazidecHMDB
PrazolitHMDB
Prestwick_808HMDB
Prilosec otcHMDB
ProcelacHMDB
ProclorHMDB
PrysmaHMDB
RamezolHMDB
RegulacidHMDB
ResultHMDB
SanamidolHMDB
SecrepinaHMDB
Tedec ulceralHMDB
UlceralHMDB
UlcesepHMDB
UlcometionHMDB
UlcozolHMDB
UlcsepHMDB
UlsenHMDB
UltopHMDB
UlzolHMDB
VictrixHMDB
ZefxonHMDB
ZegeridHMDB
ZepralHMDB
ZimorHMDB
ZoltumHMDB
Magnesium, omeprazoleMeSH, HMDB
Omeprazole magnesiumMeSH, HMDB
Omeprazole sodiumMeSH, HMDB
Sodium, omeprazoleMeSH, HMDB
Chemical FormulaC17H19N3O3S
Average Molecular Weight345.416
Monoisotopic Molecular Weight345.114712179
IUPAC Name6-methoxy-2-[(4-methoxy-3,5-dimethylpyridin-2-yl)methanesulfinyl]-1H-1,3-benzodiazole
Traditional Nameomeprazole
CAS Registry Number73590-58-6
SMILES
COC1=CC2=C(C=C1)N=C(N2)S(=O)CC1=NC=C(C)C(OC)=C1C
InChI Identifier
InChI=1S/C17H19N3O3S/c1-10-8-18-15(11(2)16(10)23-4)9-24(21)17-19-13-6-5-12(22-3)7-14(13)20-17/h5-8H,9H2,1-4H3,(H,19,20)
InChI KeySUBDBMMJDZJVOS-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
  • Anisole
  • Alkyl aryl ether
  • Methylpyridine
  • Pyridine
  • Benzenoid
  • Azole
  • Imidazole
  • Heteroaromatic compound
  • Sulfoxide
  • Azacycle
  • Ether
  • Sulfinyl compound
  • Organic nitrogen compound
  • Hydrocarbon derivative
  • Organosulfur compound
  • Organooxygen compound
  • Organonitrogen compound
  • Organic oxide
  • Organopnictogen compound
  • Organic oxygen compound
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External Descriptors
Ontology
Disposition

Biological location

Process

Naturally occurring process

Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point156 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility0.5 mg/mLNot Available
LogP2.23SANGSTER (1994)
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility0.36 g/LALOGPS
logP1.66ALOGPS
logP2.43ChemAxon
logS-3ALOGPS
pKa (Strongest Acidic)9.29ChemAxon
pKa (Strongest Basic)4.77ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area77.1 ŲChemAxon
Rotatable Bond Count5ChemAxon
Refractivity93.66 m³·mol⁻¹ChemAxon
Polarizability37.45 ųChemAxon
Number of Rings3ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+180.89831661259
DarkChem[M-H]-181.49231661259
AllCCS[M+H]+180.74132859911
AllCCS[M-H]-182.64532859911
DeepCCS[M+H]+182.22630932474
DeepCCS[M-H]-179.86830932474
DeepCCS[M-2H]-213.9930932474
DeepCCS[M+Na]+189.21730932474

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
OmeprazoleCOC1=CC2=C(C=C1)N=C(N2)S(=O)CC1=NC=C(C)C(OC)=C1C3958.2Standard polar33892256
OmeprazoleCOC1=CC2=C(C=C1)N=C(N2)S(=O)CC1=NC=C(C)C(OC)=C1C3152.4Standard non polar33892256
OmeprazoleCOC1=CC2=C(C=C1)N=C(N2)S(=O)CC1=NC=C(C)C(OC)=C1C3254.3Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Omeprazole,1TMS,isomer #1COC1=CC=C2N=C(S(=O)CC3=NC=C(C)C(OC)=C3C)N([Si](C)(C)C)C2=C13109.7Semi standard non polar33892256
Omeprazole,1TMS,isomer #1COC1=CC=C2N=C(S(=O)CC3=NC=C(C)C(OC)=C3C)N([Si](C)(C)C)C2=C12949.4Standard non polar33892256
Omeprazole,1TMS,isomer #1COC1=CC=C2N=C(S(=O)CC3=NC=C(C)C(OC)=C3C)N([Si](C)(C)C)C2=C14035.5Standard polar33892256
Omeprazole,1TBDMS,isomer #1COC1=CC=C2N=C(S(=O)CC3=NC=C(C)C(OC)=C3C)N([Si](C)(C)C(C)(C)C)C2=C13236.5Semi standard non polar33892256
Omeprazole,1TBDMS,isomer #1COC1=CC=C2N=C(S(=O)CC3=NC=C(C)C(OC)=C3C)N([Si](C)(C)C(C)(C)C)C2=C13179.0Standard non polar33892256
Omeprazole,1TBDMS,isomer #1COC1=CC=C2N=C(S(=O)CC3=NC=C(C)C(OC)=C3C)N([Si](C)(C)C(C)(C)C)C2=C14006.4Standard polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Omeprazole GC-MS (Non-derivatized) - 70eV, Positivesplash10-0udj-0902000000-cfa5184c794ea62ab9952017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Omeprazole GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Experimental LC-MS/MSLC-MS/MS Spectrum - Omeprazole LC-ESI-qTof , Positive-QTOFsplash10-014i-1669000000-51f9342d7e4bbd0356b22017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Omeprazole LC-ESI-QFT , negative-QTOFsplash10-002f-0900000000-412912cbbcdbd1b346992017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Omeprazole LC-ESI-QTOF , positive-QTOFsplash10-0002-0901000000-189e81fb724041d504982017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Omeprazole LC-ESI-QTOF , positive-QTOFsplash10-0f6t-0900000000-db101d248a4e861d4c3b2017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Omeprazole LC-ESI-QTOF , positive-QTOFsplash10-0uds-0900000000-f579fb74ac97c56dd3eb2017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Omeprazole LC-ESI-QTOF , positive-QTOFsplash10-000i-0900000000-eefbf9686f0313da581e2017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Omeprazole LC-ESI-QTOF , positive-QTOFsplash10-000i-0900000000-363d6954875894f433ba2017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Omeprazole , positive-QTOFsplash10-0f6t-1900000000-d8c64d496f1d9b3ed4652017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Omeprazole , positive-QTOFsplash10-014i-1669000000-51f9342d7e4bbd0356b22017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Omeprazole , positive-QTOFsplash10-0f6t-0900000000-d21755acc44ff2d29cfa2017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Omeprazole , positive-QTOFsplash10-0f80-2900000000-9989d19c171c612ea3dc2017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Omeprazole LC-ESI-QFT , positive-QTOFsplash10-0002-0900000000-f74adb7f41e2d390b6022017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Omeprazole 0V, Positive-QTOFsplash10-0002-0409000000-2b0fcbe3df799f1ec2412021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Omeprazole 30V, Positive-QTOFsplash10-0uei-0900000000-58302b1ea18e3edd3c3a2021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Omeprazole 40V, Positive-QTOFsplash10-000i-0900000000-402a71bf70e5c334e30e2021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Omeprazole 35V, Positive-QTOFsplash10-0002-0900000000-47fc966796e8dcf3bab02021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Omeprazole 35V, Negative-QTOFsplash10-002f-0900000000-412912cbbcdbd1b346992021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Omeprazole 35V, Negative-QTOFsplash10-0006-0900000000-a0fafeeed7c16763d7852021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Omeprazole 10V, Positive-QTOFsplash10-0002-0900000000-f37aa5029ed7b67f1ca02021-09-20HMDB team, MONAView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Omeprazole 10V, Positive-QTOFsplash10-0002-0509000000-a35086072388d122723e2016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Omeprazole 20V, Positive-QTOFsplash10-0002-0902000000-cf6c80499c6b8e76c5d52016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Omeprazole 40V, Positive-QTOFsplash10-0ul9-3900000000-2356754b2ae17bd3bc192016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Omeprazole 10V, Negative-QTOFsplash10-0007-0709000000-1b29375937cfcb4064142016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Omeprazole 20V, Negative-QTOFsplash10-002b-0900000000-3383df9e4bfd7979d5e52016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Omeprazole 40V, Negative-QTOFsplash10-004i-0900000000-4fb7ec8321857498646d2016-08-03Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Experimental 2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, CD3OD, experimental)2012-12-05Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
Biospecimen Locations
  • Blood
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified0.34 (0.014-7.24) uMAdult (>18 years old)BothNormal details
Abnormal Concentrations
Not Available
Predicted Concentrations
BiospecimenValueOriginal ageOriginal sexOriginal conditionComments
Blood0.000 umol/mmol creatinineAdult (>18 years old)BothNormalPredicted based on drug qualities
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDDB00338
Phenol Explorer Compound IDNot Available
FooDB IDFDB021863
KNApSAcK IDNot Available
Chemspider ID4433
KEGG Compound IDC07324
BioCyc IDNot Available
BiGG ID2299956
Wikipedia LinkOmeprazole
METLIN ID1632
PubChem Compound4594
PDB IDNot Available
ChEBI ID77260
Food Biomarker OntologyNot Available
VMH IDOMEPRAZOLE
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Download (PDF)
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 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
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 oxidizes a variety of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics. Most active in catalyzing 2-hydroxylation. Caffeine is metabolized primarily by cytochrome CYP1A2 in the liver through an initial N3-demethylation. Also acts in the metabolism of aflatoxin B1 and acetaminophen. Participates in the bioactivation of carcinogenic aromatic and heterocyclic amines. Catalizes the N-hydroxylation of heterocyclic amines and the O-deethylation of phenacetin.
Gene Name:
CYP1A2
Uniprot ID:
P05177
Molecular weight:
58406.915