Showing metabocard for Esomeprazole (HMDB0005009) (original) (raw)

Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2006-10-16 12:36:47 UTC

Update Date

2022-03-07 02:49:25 UTC

HMDB ID

HMDB0005009

Secondary Accession Numbers

HMDB0014874
HMDB05009
HMDB14874

Metabolite Identification

Common Name

Esomeprazole

Description

Esomeprazole (brand names Nexium; Lucen; Esopral and Axagon in Italy) is a proton pump inhibitor which reduces gastric acid secretion through the inhibition of H+/K+-ATPase in gastric parietal cells. By inhibiting the functioning of this enzyme, the drug prevents the formation of gastric acid. Esomeprazole is used in the treatment of dyspepsia, peptic ulcer disease (PUD), gastroesophageal reflux disease (GORD/GERD), and Zollinger-Ellison syndrome. Esomeprazole is the S-enantiomer of omeprazole (marketed as Losec/Prilosec), and AstraZeneca claims improved efficacy of this single enantiomer product over the racemic mixture of omeprazole.

Structure

Data?1582752339

COC1=CC2=C(NC(=N2)S@@CC2=NC=C(C)C(OC)=C2C)C=C1

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)/t24-/m0/s1

Synonyms

Value	Source
(-)-Omeprazole	ChEBI
(S)-(-)-Omeprazole	ChEBI
(S)-Omeprazole	ChEBI
Alenia	ChEBI
Escz	ChEBI
Esofag	ChEBI
Esomeprazol	ChEBI
Esomeprazolum	ChEBI
Inexium paranova	ChEBI
(S)-5-Methoxy-2-[[(4-methoxy-3,5-dimethyl-2-pyridinyl)methyl]sulfinyl]-1H-benzimidazole	HMDB
(S)-5-Methoxy-2-[[(4-methoxy-3,5-dimethyl-2-pyridyl)methyl]sulfinyl]-1H-benzimidazole	HMDB
Esomeprazole strontium anhydrous	HMDB
Strontium, esomeprazole	HMDB
Esomeprazole sodium	HMDB
Esomeprazole strontium	HMDB
Nexium	HMDB
AstraZeneca brand OF esomeprazole magnesium	HMDB
Esomeprazole magnesium	HMDB
Esomeprazole potassium	HMDB

Chemical Formula

C17H19N3O3S

Average Molecular Weight

345.416

Monoisotopic Molecular Weight

345.114712179

IUPAC Name

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

Traditional Name

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

CAS Registry Number

119141-88-7

SMILES

COC1=CC2=C(NC(=N2)[S@@](=O)CC2=NC=C(C)C(OC)=C2C)C=C1

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)/t24-/m0/s1

InChI Key

SUBDBMMJDZJVOS-DEOSSOPVSA-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
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 Framework

Aromatic heteropolycyclic compounds

External Descriptors

5-methoxy-2-\{[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl]sulfinyl\}-1H-benzimidazole (CHEBI:50275 )

Ontology

Physiological effect

Health effect

Nervous system disorder

Headache (HMDB: HMDB0014874) Central nervous system disorder Psychiatric disorder * Confusion (HMDB: HMDB0014874)

Peripheral nervous system disorder Sympathetic nervous system disorder Visual system disorder * Blurred vision (HMDB: HMDB0014874) Digestive system disorder Gastrointestinal disorder * Nausea (HMDB: HMDB0014874)

Dry mouth (HMDB: HMDB0014874)
Drowsiness (HMDB: HMDB0014874)

Disposition

Biological location

Cell membrane (HMDB: HMDB0014874) Biofluid or Excreta
- Blood (HMDB: HMDB0014874)
- Urine (HMDB: HMDB0014874) Excreta Biofluid or Excreta
  - Urine (PMID: 21059682)

Non-excretory biofluid Biofluid or Excreta * Blood (PMID: 21059682) Cellular substructure

Membrane (HMDB: HMDB0014874)

Route of exposure

Enteral

Ingestion (HMDB: HMDB0014874)

Process

Naturally occurring process

Biological process Biochemical pathway * Esomeprazole Action Pathway (HMDB: HMDB0014874) Drug action pathway * Esomeprazole Action Pathway (PathBank: SMP0000225) Metabolic pathway * Esomeprazole Metabolism Pathway (PathBank: SMP0000612)

Role

Industrial application

Pharmaceutical industry

Anti-histamine (HMDB: HMDB0014874)

Biological role

Modulator Inhibitor Enzyme inhibitor * Enzyme inhibitor (HMDB: HMDB0014874)

Physical Properties

State

Solid

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	0.35 g/L	ALOGPS
logP	1.66	ALOGPS
logP	2.43	ChemAxon
logS	-3	ALOGPS
pKa (Strongest Acidic)	9.68	ChemAxon
pKa (Strongest Basic)	4.77	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	5	ChemAxon
Refractivity	93.66 m³·mol⁻¹	ChemAxon
Polarizability	35.81 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]+	180.345	31661259
DarkChem	[M-H]-	181.743	31661259
DeepCCS	[M+H]+	183.793	30932474
DeepCCS	[M-H]-	181.435	30932474
DeepCCS	[M-2H]-	215.418	30932474
DeepCCS	[M+Na]+	190.646	30932474
AllCCS	[M+H]+	181.1	32859911
AllCCS	[M+H-H2O]+	178.1	32859911
AllCCS	[M+NH4]+	183.9	32859911
AllCCS	[M+Na]+	184.8	32859911
AllCCS	[M-H]-	182.6	32859911
AllCCS	[M+Na-2H]-	182.4	32859911
AllCCS	[M+HCOO]-	182.4	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Esomeprazole	COC1=CC2=C(NC(=N2)S@@CC2=NC=C(C)C(OC)=C2C)C=C1	3958.2	Standard polar	33892256
Esomeprazole	COC1=CC2=C(NC(=N2)S@@CC2=NC=C(C)C(OC)=C2C)C=C1	3152.4	Standard non polar	33892256
Esomeprazole	COC1=CC2=C(NC(=N2)S@@CC2=NC=C(C)C(OC)=C2C)C=C1	3254.3	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Esomeprazole,1TMS,isomer #1	COC1=CC=C2C(=C1)N=C(S@@CC1=NC=C(C)C(OC)=C1C)N2Si(C)C	3141.4	Semi standard non polar	33892256
Esomeprazole,1TMS,isomer #1	COC1=CC=C2C(=C1)N=C(S@@CC1=NC=C(C)C(OC)=C1C)N2Si(C)C	2957.0	Standard non polar	33892256
Esomeprazole,1TMS,isomer #1	COC1=CC=C2C(=C1)N=C(S@@CC1=NC=C(C)C(OC)=C1C)N2Si(C)C	4039.9	Standard polar	33892256
Esomeprazole,1TBDMS,isomer #1	COC1=CC=C2C(=C1)N=C(S@@CC1=NC=C(C)C(OC)=C1C)N2Si(C)C(C)(C)C	3269.7	Semi standard non polar	33892256
Esomeprazole,1TBDMS,isomer #1	COC1=CC=C2C(=C1)N=C(S@@CC1=NC=C(C)C(OC)=C1C)N2Si(C)C(C)(C)C	3183.5	Standard non polar	33892256
Esomeprazole,1TBDMS,isomer #1	COC1=CC=C2C(=C1)N=C(S@@CC1=NC=C(C)C(OC)=C1C)N2Si(C)C(C)(C)C	4010.9	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - Esomeprazole GC-MS (Non-derivatized) - 70eV, Positive	splash10-0udj-0902000000-d7c360235f936b712320	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Esomeprazole 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
Experimental LC-MS/MS	LC-MS/MS Spectrum - Esomeprazole 35V, Positive-QTOF	splash10-0f7t-0900000000-f43785dbdafca5df5996	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Esomeprazole 35V, Negative-QTOF	splash10-0006-0900000000-e0837329e37e32c98da2	2021-09-20	HMDB team, MONA	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Esomeprazole 10V, Positive-QTOF	splash10-0002-0509000000-a35086072388d122723e	2016-08-02	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Esomeprazole 20V, Positive-QTOF	splash10-0002-0902000000-cf6c80499c6b8e76c5d5	2016-08-02	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Esomeprazole 40V, Positive-QTOF	splash10-0ul9-3900000000-2356754b2ae17bd3bc19	2016-08-02	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Esomeprazole 10V, Negative-QTOF	splash10-0007-0709000000-1b29375937cfcb406414	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Esomeprazole 20V, Negative-QTOF	splash10-002b-0900000000-3383df9e4bfd7979d5e5	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Esomeprazole 40V, Negative-QTOF	splash10-004i-0900000000-4fb7ec8321857498646d	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Esomeprazole 10V, Negative-QTOF	splash10-0007-0809000000-40107975e9855389175a	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Esomeprazole 20V, Negative-QTOF	splash10-004i-0900000000-ce24ac86003c1fd0c915	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Esomeprazole 40V, Negative-QTOF	splash10-004i-0900000000-7094bcd15e524be40740	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Esomeprazole 10V, Positive-QTOF	splash10-0002-0907000000-7d804584599dc64c2e69	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Esomeprazole 20V, Positive-QTOF	splash10-0f6t-0900000000-cd37c0cf17dabe7285d1	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Esomeprazole 40V, Positive-QTOF	splash10-00m0-0900000000-c05d93e4947b35f8cede	2021-09-24	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Membrane (predicted from logP)

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Pathways

Normal Concentrations

Not Available

Abnormal Concentrations

Not Available

Predicted Concentrations

Biospecimen	Value	Original age	Original sex	Original condition	Comments
Blood	0.000 uM	Adult (>18 years old)	Both	Normal	Predicted based on drug qualities
Blood	0.000 umol/mmol creatinine	Adult (>18 years old)	Both	Normal	Predicted based on drug qualities

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

DB00736

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB023582

KNApSAcK ID

Not Available

Chemspider ID

7843323

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Esomeprazole

METLIN ID

Not Available

PubChem Compound

9568614

PDB ID

Not Available

ChEBI ID

50275

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Kohl, Bernhard; Senn-Bilfinger, Joerg. Enantiomerically pure (pyridylmethylsulfinyl)benzimidazoles useful as drugs, and their preparation from racemates. Ger. Offen. (1992), 8 pp. CODEN: GWXXBX DE 4035455 A1 19920514 CAN 117:90285 AN 1992:490285

Material Safety Data Sheet (MSDS)

Not Available

General References

Lind T, Rydberg L, Kyleback A, Jonsson A, Andersson T, Hasselgren G, Holmberg J, Rohss K: Esomeprazole provides improved acid control vs. omeprazole In patients with symptoms of gastro-oesophageal reflux disease. Aliment Pharmacol Ther. 2000 Jul;14(7):861-7. [PubMed:10886041 ]