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Pantoprazole

Athanor · official

C16H15F2N3O4S · 383.4 g/mol

IUPAC name: 6-(difluoromethoxy)-2-[(3,4-dimethoxy-2-pyridinyl)methylsulfinyl]-1H-benzimidazole

Also called Protonix, proton pump inhibitor

DrugsRings
Open in Athanor
The structure of Pantoprazole
Drawn from its SMILES with RDKit
Harmful or irritantHealth hazardEnvironmental hazardWarningHarmful if swallowed, in contact with skin or if inhaled · Harmful if swallowed · Harmful in contact with skin · Causes skin irritation · Causes serious eye irritation · Harmful if inhaled · May cause respiratory irritation · May cause drowsiness or dizziness · Suspected of causing genetic defects · Suspected of causing cancer · Very toxic to aquatic life · Very toxic to aquatic life with long lasting effects · Harmful to aquatic life with long lasting effects

Names and identifiers

IUPAC name
6-(difluoromethoxy)-2-[(3,4-dimethoxy-2-pyridinyl)methylsulfinyl]-1H-benzimidazole
Synonyms
Protonix, proton pump inhibitor, Pantozol
+ 36 more

Pantoprazol, Pantoprazolum, Pantoloc, BY-1023, SK&F-96022, Altopan, Zovanta, SK&F 96022, SKF-96022, DTXSID4023416, SK-96022, NSC-759257, 6-(difluoromethoxy)-2-[(3,4-dimethoxypyridin-2-yl)methylsulfinyl]-1H-benzimidazole, D8TST4O562, 1H-Benzimidazole, 5-(difluoromethoxy)-2-(((3,4-dimethoxy-2-pyridinyl)methyl)sulfinyl)-, BY1023, CHEBI:7915, DTXCID803416, 2-(((3,4-Dimethoxy-2-pyridinyl)methyl)-sulfinyl)-5-methyl-1H-1,3-benzimidazole, 6-(difluoromethoxy)-2-[(3,4-dimethoxypyridin-2-yl)methanesulfinyl]-1H-1,3-benzodiazole, 6-(difluoromethoxy)-2-(((3,4-dimethoxypyridin-2-yl)methane)sulfinyl)-1H-1,3-benzodiazole, 6-(difluoromethoxy)-2-((3,4-dimethoxypyridin-2-yl)methanesulfinyl)-1H-1,3-benzodiazole, 6-(difluoromethoxy)-2-((3,4-dimethoxypyridin-2-yl)methylsulfinyl)-1H-benzimidazole, 6-(difluoromethoxy)-2-{[(3,4-dimethoxypyridin-2-yl)methane]sulfinyl}-1H-1,3-benzodiazole, Protium i.v., RefChem:6100, A02BC02, SKF96022, SK&F96022, SKF 96022, C16H15F2N3O4S, BY 1023, (S)-Pantoprazole, MFCD00870182, Pantoloc Control, CHEMBL1502

Molecular formula
C16H15F2N3O4S
Empirical formula
C16H15F2N3O4S
Molecular weight
383.4 g/mol
Exact mass
383.07513
CAS number
102625-70-7
PubChem CID
4679
Canonical SMILES
COC1=C(C(=NC=C1)CS(=O)C2=NC3=C(N2)C=C(C=C3)OC(F)F)OC
Isomeric SMILES
COC1=C(C(=NC=C1)CS(=O)C2=NC3=C(N2)C=C(C=C3)OC(F)F)OC
InChI
InChI=1S/C16H15F2N3O4S/c1-23-13-5-6-19-12(14(13)24-2)8-26(22)16-20-10-4-3-9(25-15(17)18)7-11(10)21-16/h3-7,15H,8H2,1-2H3,(H,20,21)
InChIKey
IQPSEEYGBUAQFF-UHFFFAOYSA-N
Molfile

Names, InChI and the identifiers from PubChem, retrieved 2026-10-14.

Physical properties

TemperaturePressureDensity
Solubility in water
In water, 48 mg/L at 25 °C (estimated)[1]
log P
log Kow = 2.2 (estimated)[1]
Vapor pressure
1.25 × 10⁻¹² mmHg at 25 °C (estimated)[1]

Each value as its source reports it, with the source's number after it (listed under References). Where several sources report a property, the row shows the value most of them agree on, the rule the app uses; open the values to see every one.

Calculated

Heavy atoms
26
Rings
3
Aromatic rings
3
Fraction sp³ carbons (Fsp3)
0.25
H-bond donors
1
H-bond acceptors
6 computed here · PubChem 9
Rotatable bonds
7
TPSA (Ų)
86.3 computed here · PubChem 106
Formal charge
0
XLogP3
2.4 PubChem
Complexity
490 PubChem
Stereocenters
0 defined, 1 undefinedCIP: S9: undefined
Double-bond geometry
None specified
Point group
C1 of one 3D conformer with its hydrogens, by Athanor’s engine (as in the app)

Elemental analysis

  • C50.13%
  • H3.94%
  • F9.91%
  • N10.96%
  • O16.69%
  • S8.36%

Isotope pattern

100%383.07520%384.0787.2%385.0741.1%386.076387.077

Each peak is a nominal mass with its abundance-weighted exact mass, as a percentage of the tallest, from IUPAC natural isotope abundances.

Computed from the structure with RDKit 2026.09 when this page was built, beside PubChem's own computed values from its record; where the two differ, both are shown.

Predicted

log P
2.88 Crippen (Wildman and Crippen 1999)
log S (water solubility)
-4 ESOL (Delaney 2004), log mol/L
Synthetic accessibility
3.17 SA score, 1 easy to 10 hard (Ertl and Schuffenhauer 2009)

Drug-likeness: Lipinski’s rule of five

  • Molecular weight ≤ 500: 383.38
  • log P ≤ 5 (Crippen): 2.88
  • H-bond donors ≤ 5: 1
  • H-bond acceptors ≤ 10: 6

Passes all four rules.

¹³C NMR shifts, predicted

Predictions, not measurements; each names its method. A measured log P, where a source reports one, is under Physical properties.

Safety

Warning

Most widely reported: 10 company reports to ECHA. Source [2].

  • Harmful or irritant
  • Health hazard
  • Environmental hazard
  • H302+H312+H332Harmful if swallowed, in contact with skin or if inhaled (20% of reports)
  • H302Harmful if swallowed
  • H312Harmful in contact with skin (20% of reports)
  • H315Causes skin irritation (50% of reports)
  • H319Causes serious eye irritation (40% of reports)
  • H332Harmful if inhaled (20% of reports)
  • H335May cause respiratory irritation (40% of reports)
  • H336May cause drowsiness or dizziness (10% of reports)
  • H341Suspected of causing genetic defects (10% of reports)
  • H351Suspected of causing cancer (10% of reports)
  • H400Very toxic to aquatic life (10% of reports)
  • H410Very toxic to aquatic life with long lasting effects (10% of reports)
  • H412Harmful to aquatic life with long lasting effects (10% of reports)

Precautionary statements: P203, P261, P264, P264+P265, P270, P271, P273, P280, P301+P317, P302+P352, P304+P340, P305+P351+P338, P317, P318, P319, P321, P330, P332+P317, P337+P317, P362+P364, P391, P403+P233, P405, P501

Safety data sheets on the supplier’s page: Angene Chemical, Biosynth, Clearsynth.

Always read the supplier’s safety data sheet before working with it.

Spectra

Experimental spectra held by these sources; each link opens the source's own record.

Literature

Reading PubChem, OpenAlex and GSRS…

Bioactivity

Reading ChEMBL…

References

  1. [1]Hazardous Substances Data Bank (HSDB) · Public domain (US NLM) · via PubChem · retrieved 2026-10-14
  2. [2]European Chemicals Agency (ECHA) · ECHA legal notice: reuse with acknowledgement · via PubChem · retrieved 2026-10-14
  3. [3]SpectraBase · Linked only · via PubChem · retrieved 2026-10-14
  4. [4]Human Metabolome Database (HMDB) · Linked only · via PubChem · retrieved 2026-10-14
  5. [5]MassBank Europe · Linked only · via PubChem · retrieved 2026-10-14
  6. [6]MassBank of North America (MoNA) · CC BY 4.0 · via PubChem · retrieved 2026-10-14
  7. ·Calculated values: computed by Athanor with RDKit 2026.09 from the structure.
  8. ·Literature on PubChem

Data last updated 2026-10-14.