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Showing metabocard for (2S)-Nicotine 1-oxide (HMDB0341208)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2022-09-09 19:42:27 UTC
Update Date2022-09-22 18:34:39 UTC
HMDB IDHMDB0341208
Secondary Accession NumbersNone
Metabolite Identification
Common Name(2S)-Nicotine 1-oxide
Description(S)-nicotine 1-N-oxide belongs to the class of organic compounds known as pyrrolidinylpyridines. Pyrrolidinylpyridines are compounds containing a pyrrolidinylpyridine ring system, which consists of a pyrrolidine ring linked to a pyridine ring (S)-nicotine 1-N-oxide is a very strong basic compound (based on its pKa).
Structure
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MOLSDFPDBSMILESInChI

MOL for HMDB0341208 ((2S)-Nicotine 1-oxide)


  Mrv1652305311613062D          

 14 15  0  0  1  0            999 V2000
    1.2991   -0.2916    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0367    2.0009    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1637   -1.3312    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0367    1.1759    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4186   -0.5465    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3387   -1.3312    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7512    2.4134    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4656    1.1759    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7512    0.7634    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7512   -0.0616    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.0837   -0.5465    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.4656    2.0009    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.1801    2.4134    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4863    0.3129    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  4  2  2  0  0  0  0
  5  3  1  0  0  0  0
  6  3  1  0  0  0  0
  7  2  1  0  0  0  0
  9  4  1  0  0  0  0
  9  8  2  0  0  0  0
 10  5  1  0  0  0  0
 10  9  1  6  0  0  0
 11  1  1  0  0  0  0
 11  6  1  0  0  0  0
 11 10  1  0  0  0  0
 12  7  2  0  0  0  0
 12  8  1  0  0  0  0
 13 12  2  0  0  0  0
 10 14  1  1  0  0  0
M  END
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3D MOL for HMDB0341208 ((2S)-Nicotine 1-oxide)

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3D SDF for HMDB0341208 ((2S)-Nicotine 1-oxide)

  Mrv1652305311613062D          

 14 15  0  0  1  0            999 V2000
    1.2991   -0.2916    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0367    2.0009    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1637   -1.3312    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0367    1.1759    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4186   -0.5465    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3387   -1.3312    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7512    2.4134    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4656    1.1759    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7512    0.7634    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7512   -0.0616    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.0837   -0.5465    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.4656    2.0009    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.1801    2.4134    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4863    0.3129    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  4  2  2  0  0  0  0
  5  3  1  0  0  0  0
  6  3  1  0  0  0  0
  7  2  1  0  0  0  0
  9  4  1  0  0  0  0
  9  8  2  0  0  0  0
 10  5  1  0  0  0  0
 10  9  1  6  0  0  0
 11  1  1  0  0  0  0
 11  6  1  0  0  0  0
 11 10  1  0  0  0  0
 12  7  2  0  0  0  0
 12  8  1  0  0  0  0
 13 12  2  0  0  0  0
 10 14  1  1  0  0  0
M  END
> <DATABASE_ID>
HMDB0341208

> <DATABASE_NAME>
hmdb

> <SMILES>
[H][C@]1(CCCN1C)C1=CN(=O)=CC=C1

> <INCHI_IDENTIFIER>
InChI=1S/C10H14N2O/c1-11-6-3-5-10(11)9-4-2-7-12(13)8-9/h2,4,7-8,10H,3,5-6H2,1H3/t10-/m0/s1

> <INCHI_KEY>
YHXKVHQFWVYXIC-JTQLQIEISA-N

> <FORMULA>
C10H14N2O

> <MOLECULAR_WEIGHT>
178.235

> <EXACT_MASS>
178.110613079

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
27

> <JCHEM_AVERAGE_POLARIZABILITY>
19.59580116721456

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
3-[(2S)-1-methylpyrrolidin-2-yl]-1lambda5-pyridin-1-one

> <ALOGPS_LOGP>
-0.51

> <JCHEM_LOGP>
-0.09762223500000022

> <ALOGPS_LOGS>
-1.48

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_BASIC>
7.959287587104336

> <JCHEM_POLAR_SURFACE_AREA>
28.700000000000003

> <JCHEM_REFRACTIVITY>
53.344500000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.89e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-[(2S)-1-methylpyrrolidin-2-yl]-1lambda5-pyridin-1-one

> <JCHEM_VEBER_RULE>
1

$$$$

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3D-SDF for HMDB0341208 ((2S)-Nicotine 1-oxide)
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PDB for HMDB0341208 ((2S)-Nicotine 1-oxide)
HEADER    PROTEIN                                 31-MAY-16   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   31-MAY-16         0                                  
HETATM    1  C   UNK     0       2.425  -0.544   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       3.802   3.735   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.906  -2.485   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       3.802   2.195   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       6.381  -1.020   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       4.366  -2.485   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       5.136   4.505   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       6.469   2.195   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       5.136   1.425   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       5.136  -0.115   0.000  0.00  0.00           C+0
HETATM   11  N   UNK     0       3.890  -1.020   0.000  0.00  0.00           N+0
HETATM   12  N   UNK     0       6.469   3.735   0.000  0.00  0.00           N+0
HETATM   13  O   UNK     0       7.803   4.505   0.000  0.00  0.00           O+0
HETATM   14  H   UNK     0       6.508   0.584   0.000  0.00  0.00           H+0
CONECT    1   11                                                            
CONECT    2    4    7                                                       
CONECT    3    5    6                                                       
CONECT    4    2    9                                                       
CONECT    5    3   10                                                       
CONECT    6    3   11                                                       
CONECT    7    2   12                                                       
CONECT    8    9   12                                                       
CONECT    9    4    8   10                                                  
CONECT   10    5    9   11   14                                             
CONECT   11    1    6   10                                                  
CONECT   12    7    8   13                                                  
CONECT   13   12                                                            
CONECT   14   10                                                            
MASTER        0    0    0    0    0    0    0    0   14    0   30    0
END

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3D PDB for HMDB0341208 ((2S)-Nicotine 1-oxide)
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SMILES for HMDB0341208 ((2S)-Nicotine 1-oxide)
[H][C@]1(CCCN1C)C1=CN(=O)=CC=C1
Download
INCHI for HMDB0341208 ((2S)-Nicotine 1-oxide)
InChI=1S/C10H14N2O/c1-11-6-3-5-10(11)9-4-2-7-12(13)8-9/h2,4,7-8,10H,3,5-6H2,1H3/t10-/m0/s1
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View in JSmolView Stereo Labels
Synonyms
ValueSource
(S)-3-(1-Methyl-2-pyrrolidinyl)pyridine 1-oxideChEBI
(S)-Nicotine N-oxideChEBI
Nicotine 1-N-oxideChEBI
Nicotine N-oxideChEBI
Nicotine, 1-oxideChEBI
Chemical FormulaC10H14N2O
Average Molecular Weight178.235
Monoisotopic Molecular Weight178.110613079
IUPAC Name3-[(2S)-1-methylpyrrolidin-2-yl]-1lambda5-pyridin-1-one
Traditional Name3-[(2S)-1-methylpyrrolidin-2-yl]-1lambda5-pyridin-1-one
CAS Registry NumberNot Available
SMILES
[H][C@]1(CCCN1C)C1=CN(=O)=CC=C1
InChI Identifier
InChI=1S/C10H14N2O/c1-11-6-3-5-10(11)9-4-2-7-12(13)8-9/h2,4,7-8,10H,3,5-6H2,1H3/t10-/m0/s1
InChI KeyYHXKVHQFWVYXIC-JTQLQIEISA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as pyrrolidinylpyridines. Pyrrolidinylpyridines are compounds containing a pyrrolidinylpyridine ring system, which consists of a pyrrolidine ring linked to a pyridine ring.
KingdomOrganic compounds  
Super ClassOrganoheterocyclic compounds  
ClassPyridines and derivatives  
Sub ClassPyrrolidinylpyridines  
Direct ParentPyrrolidinylpyridines  
Alternative Parents
Substituents
  • Pyrrolidinylpyridine
    • 

  • Alkaloid or derivatives
    • 

  • Aralkylamine
    • 

  • Pyridinium
    • 

  • N-alkylpyrrolidine
    • 

  • Pyrrolidine
    • 

  • Heteroaromatic compound
    • 

  • Tertiary aliphatic amine
    • 

  • Tertiary amine
    • 

  • Azacycle
    • 

  • Hydrocarbon derivative
    • 

  • Organic oxide
    • 

  • Organopnictogen compound
    • 

  • Organic oxygen compound
    • 

  • Amine
    • 

  • Organic nitrogen compound
    • 

  • Organonitrogen compound
    • 

  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
Not AvailableNot Available
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
logP-0.51ALOGPS
logP-0.098ChemAxon
logS-1.5ALOGPS
pKa (Strongest Basic)7.96ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area28.7 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity53.34 m³·mol⁻¹ChemAxon
Polarizability19.6 ųChemAxon
Number of Rings2ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties
Predicted Retention Times 
Not Available
Predicted Kovats Retention Indices
Not Available
Spectra
MS/MS Spectra
Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (2S)-Nicotine 1-oxide  10V, Positive-QTOFsplash10-004i-0900000000-606af7bde34ae15674102019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (2S)-Nicotine 1-oxide  20V, Positive-QTOFsplash10-00bi-0900000000-d0367a8d158c7a7fd6c42019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (2S)-Nicotine 1-oxide  40V, Positive-QTOFsplash10-066r-6900000000-0fa5277111e10b4801b82019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (2S)-Nicotine 1-oxide  10V, Negative-QTOFsplash10-004i-0900000000-da10a73bc057634c265f2019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (2S)-Nicotine 1-oxide  20V, Negative-QTOFsplash10-004i-1900000000-a5714405de9b2e0024412019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (2S)-Nicotine 1-oxide  40V, Negative-QTOFsplash10-0006-9800000000-02becb08785189d966372019-02-23Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
    • 

  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedCancer patients undergoing total body irradiation  details
UrineDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedCancer patients undergoing total body irradiation  details
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound211457  
PDB IDNot Available
ChEBI ID132572  
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Simon-Manso Y, Marupaka R, Yan X, Liang Y, Telu KH, Mirokhin Y, Stein SE: Mass Spectrometry Fingerprints of Small-Molecule Metabolites in Biofluids: Building a Spectral Library of Recurrent Spectra for Urine Analysis. Anal Chem. 2019 Sep 17;91(18):12021-12029. doi: 10.1021/acs.analchem.9b02977. Epub 2019 Aug 30. [PubMed:31424920  ]