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Showing NP-Card for Pantoprazole (NP0334563)

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Record Information
Version2.0
Created at2024-09-10 18:55:12 UTC
Updated at2024-09-10 18:55:12 UTC
NP-MRD IDNP0334563
Secondary Accession NumbersNone
Natural Product Identification
Common NamePantoprazole
DescriptionPantoprazole, also known as SK and F 96022 or protonix, 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. Pantoprazole is a strong basic compound (based on its pKa). In humans, pantoprazole is involved in pantoprazole action pathway. Pantoprazole is a bitter tasting compound. Pantoprazole was first documented in 2000 (PMID: 11110229). Outside of the human body, (PMID: 11240974).
Structure
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MOLSDFPDBSMILESInChI

MOL for NP0334563 (Pantoprazole)

213
  Mrv0541 02231214312D          

 26 28  0  0  1  0            999 V2000
    7.3097    0.0000    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    2.3645   -0.4125    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500    0.8250    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
    8.5472    0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0791    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.7222    0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.1972    0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0031    0.6639    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.0031   -0.6639    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    8.9597   -1.4290    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.2224    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4846    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2224   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.7222   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.5472   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5080    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5080   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.9597    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7935    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7935   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.7847    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.1972   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.7847   -1.4290    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.9597    1.4290    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3645    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.0222    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  6  2  0  0  0  0
  1 12  1  0  0  0  0
  1 14  1  0  0  0  0
  2 25  1  0  0  0  0
  3 25  1  0  0  0  0
  4 18  1  0  0  0  0
  4 24  1  0  0  0  0
  5 19  1  0  0  0  0
  5 25  1  0  0  0  0
  7 21  1  0  0  0  0
  7 26  1  0  0  0  0
  8 11  1  0  0  0  0
  8 12  1  0  0  0  0
  9 12  2  0  0  0  0
  9 13  1  0  0  0  0
 10 15  2  0  0  0  0
 10 23  1  0  0  0  0
 11 13  2  0  0  0  0
 11 16  1  0  0  0  0
 13 17  1  0  0  0  0
 14 15  1  0  0  0  0
 15 18  1  0  0  0  0
 16 19  2  0  0  0  0
 17 20  2  0  0  0  0
 18 21  2  0  0  0  0
 19 20  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  2  0  0  0  0
M  END
Download

3D MOL for NP0334563 (Pantoprazole)

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3D SDF for NP0334563 (Pantoprazole)
213
  Mrv0541 02231214312D          

 26 28  0  0  1  0            999 V2000
    7.3097    0.0000    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    2.3645   -0.4125    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500    0.8250    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
    8.5472    0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0791    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.7222    0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.1972    0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0031    0.6639    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.0031   -0.6639    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    8.9597   -1.4290    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.2224    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4846    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2224   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.7222   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.5472   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5080    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5080   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.9597    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7935    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7935   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.7847    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.1972   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.7847   -1.4290    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.9597    1.4290    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3645    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.0222    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  6  2  0  0  0  0
  1 12  1  0  0  0  0
  1 14  1  0  0  0  0
  2 25  1  0  0  0  0
  3 25  1  0  0  0  0
  4 18  1  0  0  0  0
  4 24  1  0  0  0  0
  5 19  1  0  0  0  0
  5 25  1  0  0  0  0
  7 21  1  0  0  0  0
  7 26  1  0  0  0  0
  8 11  1  0  0  0  0
  8 12  1  0  0  0  0
  9 12  2  0  0  0  0
  9 13  1  0  0  0  0
 10 15  2  0  0  0  0
 10 23  1  0  0  0  0
 11 13  2  0  0  0  0
 11 16  1  0  0  0  0
 13 17  1  0  0  0  0
 14 15  1  0  0  0  0
 15 18  1  0  0  0  0
 16 19  2  0  0  0  0
 17 20  2  0  0  0  0
 18 21  2  0  0  0  0
 19 20  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0334563

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC1=C(OC)C(CS(=O)C2=NC3=C(N2)C=C(OC(F)F)C=C3)=NC=C1

> <INCHI_IDENTIFIER>
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)

> <INCHI_KEY>
IQPSEEYGBUAQFF-UHFFFAOYSA-N

> <FORMULA>
C16H15F2N3O4S

> <MOLECULAR_WEIGHT>
383.37

> <EXACT_MASS>
383.075133083

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_AVERAGE_POLARIZABILITY>
35.16844686637351

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
6-(difluoromethoxy)-2-[(3,4-dimethoxypyridin-2-yl)methanesulfinyl]-1H-1,3-benzodiazole

> <ALOGPS_LOGP>
2.11

> <JCHEM_LOGP>
2.1757533226666665

> <ALOGPS_LOGS>
-2.89

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
15.75737352285693

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.152252771451785

> <JCHEM_PKA_STRONGEST_BASIC>
3.554451857291244

> <JCHEM_POLAR_SURFACE_AREA>
86.33

> <JCHEM_REFRACTIVITY>
90.05200000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.95e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
pantoprazole

> <JCHEM_VEBER_RULE>
0

$$$$

Download
3D-SDF for NP0334563 (Pantoprazole)
Download
PDB for NP0334563 (Pantoprazole)
HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: 213                                               
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  S   UNK     0      13.645   0.000   0.000  0.00  0.00           S+0
HETATM    2  F   UNK     0       4.414  -0.770   0.000  0.00  0.00           F+0
HETATM    3  F   UNK     0       3.080   1.540   0.000  0.00  0.00           F+0
HETATM    4  O   UNK     0      15.955   1.334   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0       5.748   1.540   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0      14.415   1.334   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0      19.035   1.334   0.000  0.00  0.00           O+0
HETATM    8  N   UNK     0      11.206   1.239   0.000  0.00  0.00           N+0
HETATM    9  N   UNK     0      11.206  -1.239   0.000  0.00  0.00           N+0
HETATM   10  N   UNK     0      16.725  -2.667   0.000  0.00  0.00           N+0
HETATM   11  C   UNK     0       9.748   0.770   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      12.105   0.000   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       9.748  -0.770   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      14.415  -1.334   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      15.955  -1.334   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       8.415   1.540   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       8.415  -1.540   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      16.725   0.000   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       7.081   0.770   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       7.081  -0.770   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      18.265   0.000   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      19.035  -1.334   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      18.265  -2.667   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      16.725   2.667   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       4.414   0.770   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      20.575   1.334   0.000  0.00  0.00           C+0
CONECT    1    6   12   14                                                  
CONECT    2   25                                                            
CONECT    3   25                                                            
CONECT    4   18   24                                                       
CONECT    5   19   25                                                       
CONECT    6    1                                                            
CONECT    7   21   26                                                       
CONECT    8   11   12                                                       
CONECT    9   12   13                                                       
CONECT   10   15   23                                                       
CONECT   11    8   13   16                                                  
CONECT   12    1    8    9                                                  
CONECT   13    9   11   17                                                  
CONECT   14    1   15                                                       
CONECT   15   10   14   18                                                  
CONECT   16   11   19                                                       
CONECT   17   13   20                                                       
CONECT   18    4   15   21                                                  
CONECT   19    5   16   20                                                  
CONECT   20   17   19                                                       
CONECT   21    7   18   22                                                  
CONECT   22   21   23                                                       
CONECT   23   10   22                                                       
CONECT   24    4                                                            
CONECT   25    2    3    5                                                  
CONECT   26    7                                                            
MASTER        0    0    0    0    0    0    0    0   26    0   56    0
END

Download
3D PDB for NP0334563 (Pantoprazole)
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SMILES for NP0334563 (Pantoprazole)
COC1=C(OC)C(CS(=O)C2=NC3=C(N2)C=C(OC(F)F)C=C3)=NC=C1
Download
INCHI for NP0334563 (Pantoprazole)
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)
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View in JSmol
Synonyms
ValueSource
PantoprazolChEBI
PantoprazolumChEBI
PantolocHMDB
Pantoprazole sodiumHMDB
Pantoprazole sodium hydrateHMDB
PantozolHMDB
ProtonixHMDB
Protonix i.v.HMDB
SK And F 96022HMDB
SK And F-96022HMDB
SK And F96022HMDB
Chemical FormulaC16H15F2N3O4S
Average Mass383.3700 Da
Monoisotopic Mass383.07513 Da
IUPAC Name6-(difluoromethoxy)-2-[(3,4-dimethoxypyridin-2-yl)methanesulfinyl]-1H-1,3-benzodiazole
Traditional Namepantoprazole
CAS Registry NumberNot Available
SMILES
COC1=C(OC)C(CS(=O)C2=NC3=C(N2)C=C(OC(F)F)C=C3)=NC=C1
InChI Identifier
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)
InChI KeyIQPSEEYGBUAQFF-UHFFFAOYSA-N
Experimental Spectra
Not Available
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of OriginNot 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.
KingdomOrganic compounds  
Super ClassOrganoheterocyclic compounds  
ClassBenzimidazoles  
Sub ClassSulfinylbenzimidazoles  
Direct ParentSulfinylbenzimidazoles  
Alternative Parents
Substituents
  • Sulfinylbenzimidazole
    • 

  • Alkyl aryl ether
    • 

  • Pyridine
    • 

  • Benzenoid
    • 

  • Azole
    • 

  • Imidazole
    • 

  • Heteroaromatic compound
    • 

  • Sulfoxide
    • 

  • Azacycle
    • 

  • Sulfinyl compound
    • 

  • Ether
    • 

  • Hydrocarbon derivative
    • 

  • Organic oxygen compound
    • 

  • Organosulfur compound
    • 

  • Organooxygen compound
    • 

  • Organonitrogen compound
    • 

  • Organofluoride
    • 

  • Organohalogen compound
    • 

  • Alkyl fluoride
    • 

  • Organopnictogen compound
    • 

  • Organic nitrogen compound
    • 

  • Organic oxide
    • 

  • Alkyl halide
    • 

  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External Descriptors
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP2.11ALOGPS
logP2.18ChemAxon
logS-2.9ALOGPS
pKa (Strongest Acidic)9.15ChemAxon
pKa (Strongest Basic)3.55ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count6ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area86.33 ŲChemAxon
Rotatable Bond Count7ChemAxon
Refractivity90.05 m³·mol⁻¹ChemAxon
Polarizability35.17 ųChemAxon
Number of Rings3ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
HMDB IDHMDB0005017  
DrugBank IDDB00213  
Phenol Explorer Compound IDNot Available
FoodDB IDFDB023589  
KNApSAcK IDNot Available
Chemspider ID4517  
KEGG Compound IDC11806  
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkPantoprazole  
METLIN ID1697  
PubChem Compound4679  
PDB IDNot Available
ChEBI ID7915  
Good Scents IDNot Available
References
General References
  1. Avner DL: Clinical experience with pantoprazole in gastroesophageal reflux disease. Clin Ther. 2000 Oct;22(10):1169-85; discussion 1149-50. doi:  10.1016/s0149-2918(00)83061-1. [PubMed:11110229  ] 
  2. Tanaka M, Ohkubo T, Otani K, Suzuki A, Kaneko S, Sugawara K, Ryokawa Y, Ishizaki T: Stereoselective pharmacokinetics of pantoprazole, a proton pump inhibitor, in extensive and poor metabolizers of S-mephenytoin. Clin Pharmacol Ther. 2001 Mar;69(3):108-13. doi: 10.1067/mcp.2001.113723. [PubMed:11240974  ]