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Showing metabocard for Nornicotine (HMDB0001126)

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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2023-02-21 17:15:28 UTC
HMDB IDHMDB0001126
Secondary Accession Numbers
  • HMDB01126
Metabolite Identification
Common NameNornicotine
DescriptionNornicotine, also known as (+-)-nornicotine or DL-norcitine, 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. In humans, nornicotine is involved in the nicotine metabolism pathway. Nornicotine has been detected, but not quantified in, a few different foods, such as anatidaes (Anatidae), chickens (Gallus gallus), and domestic pigs (Sus scrofa domestica). This could make nornicotine a potential biomarker for the consumption of these foods. Nornicotine is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. Based on a literature review a small amount of articles have been published on Nornicotine.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0001126 (Nornicotine)

  Mrv0541 02231218562D          

 11 12  0  0  0  0            999 V2000
    0.5004    0.2899    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2105   -0.1208    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5866    1.1111    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2561   -0.0483    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9214    0.2933    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2105   -0.9455    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3941    1.2802    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8082    0.5659    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6391   -0.1208    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9214   -1.3596    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6391   -0.9455    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  0  0  0  0
  2  5  2  0  0  0  0
  2  6  1  0  0  0  0
  3  7  1  0  0  0  0
  4  8  1  0  0  0  0
  5  9  1  0  0  0  0
  6 10  2  0  0  0  0
  9 11  2  0  0  0  0
  7  8  1  0  0  0  0
 10 11  1  0  0  0  0
M  END
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3D MOL for HMDB0001126 (Nornicotine)

HMDB0246695
     RDKit          3D
l-Nor-nicotine
 23 24  0  0  0  0  0  0  0  0999 V2000
    2.9814    0.8590   -0.8314 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4447    0.8961    0.4697 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6649    0.4546    1.4617 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4291   -0.0373    1.2887 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9439   -0.0845   -0.0036 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4001   -0.6007   -0.3497 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2988   -0.7146    0.8602 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6458   -0.8667    0.1423 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5041    0.2206   -0.9146 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1004    0.2330   -1.2782 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.7205    0.3627   -1.0546 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6025    1.2133   -1.6434 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4510    1.2913    0.6561 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8049   -0.3939    2.1088 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3267   -1.6279   -0.7889 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3578    0.2044    1.4438 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0847   -1.6225    1.4576 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6207   -1.8546   -0.3617 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4910   -0.7130    0.8024 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7148    1.1981   -0.4374 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1414    0.0556   -1.7855 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7039    1.1959   -1.3429 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3476    0.3309   -2.0860 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
  5 11  2  0
 11  1  1  0
 10  6  1  0
  1 12  1  0
  2 13  1  0
  4 14  1  0
  6 15  1  0
  7 16  1  0
  7 17  1  0
  8 18  1  0
  8 19  1  0
  9 20  1  0
  9 21  1  0
 10 22  1  0
 11 23  1  0
M  END
Download

3D SDF for HMDB0001126 (Nornicotine)

  Mrv0541 02231218562D          

 11 12  0  0  0  0            999 V2000
    0.5004    0.2899    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2105   -0.1208    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5866    1.1111    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2561   -0.0483    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9214    0.2933    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2105   -0.9455    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3941    1.2802    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8082    0.5659    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6391   -0.1208    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9214   -1.3596    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6391   -0.9455    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  0  0  0  0
  2  5  2  0  0  0  0
  2  6  1  0  0  0  0
  3  7  1  0  0  0  0
  4  8  1  0  0  0  0
  5  9  1  0  0  0  0
  6 10  2  0  0  0  0
  9 11  2  0  0  0  0
  7  8  1  0  0  0  0
 10 11  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0001126

> <DATABASE_NAME>
hmdb

> <SMILES>
C1CNC(C1)C1=CC=CN=C1

> <INCHI_IDENTIFIER>
InChI=1S/C9H12N2/c1-3-8(7-10-5-1)9-4-2-6-11-9/h1,3,5,7,9,11H,2,4,6H2

> <INCHI_KEY>
MYKUKUCHPMASKF-UHFFFAOYSA-N

> <FORMULA>
C9H12N2

> <MOLECULAR_WEIGHT>
148.205

> <EXACT_MASS>
148.100048394

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_AVERAGE_POLARIZABILITY>
16.664988841293663

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-(pyrrolidin-2-yl)pyridine

> <ALOGPS_LOGP>
0.66

> <JCHEM_LOGP>
0.7794867553333333

> <ALOGPS_LOGS>
-0.76

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_BASIC>
10.211523847236988

> <JCHEM_POLAR_SURFACE_AREA>
24.92

> <JCHEM_REFRACTIVITY>
44.3603

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.60e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(+-)-nornicotine

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0001126 (Nornicotine)

HMDB0246695
     RDKit          3D
l-Nor-nicotine
 23 24  0  0  0  0  0  0  0  0999 V2000
    2.9814    0.8590   -0.8314 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4447    0.8961    0.4697 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6649    0.4546    1.4617 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4291   -0.0373    1.2887 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9439   -0.0845   -0.0036 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4001   -0.6007   -0.3497 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2988   -0.7146    0.8602 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6458   -0.8667    0.1423 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5041    0.2206   -0.9146 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1004    0.2330   -1.2782 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.7205    0.3627   -1.0546 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6025    1.2133   -1.6434 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4510    1.2913    0.6561 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8049   -0.3939    2.1088 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3267   -1.6279   -0.7889 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3578    0.2044    1.4438 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0847   -1.6225    1.4576 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6207   -1.8546   -0.3617 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4910   -0.7130    0.8024 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7148    1.1981   -0.4374 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1414    0.0556   -1.7855 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7039    1.1959   -1.3429 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3476    0.3309   -2.0860 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
  5 11  2  0
 11  1  1  0
 10  6  1  0
  1 12  1  0
  2 13  1  0
  4 14  1  0
  6 15  1  0
  7 16  1  0
  7 17  1  0
  8 18  1  0
  8 19  1  0
  9 20  1  0
  9 21  1  0
 10 22  1  0
 11 23  1  0
M  END
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PDB for HMDB0001126 (Nornicotine)

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  C   UNK     0       0.934   0.541   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -0.393  -0.225   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.095   2.074   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0       2.345  -0.090   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0      -1.720   0.547   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -0.393  -1.765   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.602   2.390   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       3.375   1.056   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -3.060  -0.225   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0      -1.720  -2.538   0.000  0.00  0.00           N+0
HETATM   11  C   UNK     0      -3.060  -1.765   0.000  0.00  0.00           C+0
CONECT    1    2    3    4                                                  
CONECT    2    1    5    6                                                  
CONECT    3    1    7                                                       
CONECT    4    1    8                                                       
CONECT    5    2    9                                                       
CONECT    6    2   10                                                       
CONECT    7    3    8                                                       
CONECT    8    4    7                                                       
CONECT    9    5   11                                                       
CONECT   10    6   11                                                       
CONECT   11    9   10                                                       
MASTER        0    0    0    0    0    0    0    0   11    0   24    0
END
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3D PDB for HMDB0001126 (Nornicotine)

COMPND    HMDB0001126
HETATM    1  C1  UNL     1       3.035   0.888  -0.518  1.00  0.00           C  
HETATM    2  C2  UNL     1       3.604  -0.339  -0.583  1.00  0.00           C  
HETATM    3  N1  UNL     1       2.839  -1.407  -0.308  1.00  0.00           N  
HETATM    4  C3  UNL     1       1.548  -1.346   0.027  1.00  0.00           C  
HETATM    5  C4  UNL     1       0.943  -0.117   0.101  1.00  0.00           C  
HETATM    6  C5  UNL     1      -0.472   0.083   0.461  1.00  0.00           C  
HETATM    7  C6  UNL     1      -1.320  -1.134   0.334  1.00  0.00           C  
HETATM    8  C7  UNL     1      -2.678  -0.569  -0.018  1.00  0.00           C  
HETATM    9  C8  UNL     1      -2.490   0.876  -0.328  1.00  0.00           C  
HETATM   10  N2  UNL     1      -1.053   1.028  -0.464  1.00  0.00           N  
HETATM   11  C9  UNL     1       1.691   1.008  -0.173  1.00  0.00           C  
HETATM   12  H1  UNL     1       3.579   1.795  -0.723  1.00  0.00           H  
HETATM   13  H2  UNL     1       4.666  -0.442  -0.855  1.00  0.00           H  
HETATM   14  H3  UNL     1       0.941  -2.210   0.246  1.00  0.00           H  
HETATM   15  H4  UNL     1      -0.504   0.430   1.509  1.00  0.00           H  
HETATM   16  H5  UNL     1      -1.003  -1.847  -0.439  1.00  0.00           H  
HETATM   17  H6  UNL     1      -1.416  -1.643   1.323  1.00  0.00           H  
HETATM   18  H7  UNL     1      -3.147  -1.130  -0.854  1.00  0.00           H  
HETATM   19  H8  UNL     1      -3.390  -0.648   0.834  1.00  0.00           H  
HETATM   20  H9  UNL     1      -2.948   1.128  -1.328  1.00  0.00           H  
HETATM   21  H10 UNL     1      -2.928   1.567   0.411  1.00  0.00           H  
HETATM   22  H11 UNL     1      -0.761   2.023  -0.274  1.00  0.00           H  
HETATM   23  H12 UNL     1       1.263   2.006  -0.129  1.00  0.00           H  
CONECT    1    2    2   11   12
CONECT    2    3   13
CONECT    3    4    4
CONECT    4    5   14
CONECT    5    6   11   11
CONECT    6    7   10   15
CONECT    7    8   16   17
CONECT    8    9   18   19
CONECT    9   10   20   21
CONECT   10   22
CONECT   11   23
END
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SMILES for HMDB0001126 (Nornicotine)

C1CNC(C1)C1=CC=CN=C1
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INCHI for HMDB0001126 (Nornicotine)

InChI=1S/C9H12N2/c1-3-8(7-10-5-1)9-4-2-6-11-9/h1,3,5,7,9,11H,2,4,6H2
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
(+-)-1'-Demethyl-nicotineHMDB
(+-)-1'-DemethylnicotineHMDB
(+-)-3-(2-Pyrrolidinyl)pyridineHMDB
(+-)-NornicotineHMDB
(R)-3-(Pyrrolidin-2-yl)pyridineHMDB
(R,S)-NornicotineHMDB
(S)-2-(3-Pyridyl)pyrrolidineHMDB
2-(3-Pyridyl)pyrrolidineHMDB
3-(2-Pyrrolidinyl)pyridineHMDB
DL-NorcitineHMDB
L-Nor-nicotineHMDB
NornicotinHMDB
S-(-)-NornicotineHMDB
Nornicotine tartrate, (S)-(R-(r*,r*))-isomerHMDB
Nornicotine, (R)-isomerHMDB
Nornicotine, (S)-isomerHMDB
Chemical FormulaC9H12N2
Average Molecular Weight148.205
Monoisotopic Molecular Weight148.100048394
IUPAC Name3-(pyrrolidin-2-yl)pyridine
Traditional Name(+-)-nornicotine
CAS Registry Number494-97-3
SMILES
C1CNC(C1)C1=CC=CN=C1
InChI Identifier
InChI=1S/C9H12N2/c1-3-8(7-10-5-1)9-4-2-6-11-9/h1,3,5,7,9,11H,2,4,6H2
InChI KeyMYKUKUCHPMASKF-UHFFFAOYSA-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
  • Aralkylamine
  • Heteroaromatic compound
  • Pyrrolidine
  • Azacycle
  • Secondary amine
  • Secondary aliphatic amine
  • Organic nitrogen compound
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Organonitrogen compound
  • Amine
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Ontology
Not AvailableNot Available
Physical Properties
StateLiquid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling Point270 °CNot Available
Water SolubilityNot AvailableNot Available
LogP0.17HANSCH,C ET AL. (1995)
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm
Biospecimen Locations
  • Blood
  • Urine
Tissue Locations
  • Kidney
  • Liver
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot QuantifiedNot AvailableNot AvailableNormal
      Not Available
 details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
UrineDetected and Quantified0.20 (0.01-0.40) umol/mmol creatinineAdult (>18 years old)BothActive tobacco user details
Associated Disorders and Diseases
Disease References
Smoking
  1. Moyer TP, Charlson JR, Enger RJ, Dale LC, Ebbert JO, Schroeder DR, Hurt RD: Simultaneous analysis of nicotine, nicotine metabolites, and tobacco alkaloids in serum or urine by tandem mass spectrometry, with clinically relevant metabolic profiles. Clin Chem. 2002 Sep;48(9):1460-71. [PubMed:12194923 ]
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB022439
KNApSAcK IDC00042792
Chemspider ID21108497
KEGG Compound IDC06524
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNornicotine
METLIN ID1534
PubChem Compound412
PDB IDNot Available
ChEBI ID28313
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferencePapadopoulos, Nick M. Formation of nornicotine and other metabolites from nicotine in vitro and in vivo. Canadian Journal of Biochemistry and Physiology (1964), 42(4), 435-42.
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Moyer TP, Charlson JR, Enger RJ, Dale LC, Ebbert JO, Schroeder DR, Hurt RD: Simultaneous analysis of nicotine, nicotine metabolites, and tobacco alkaloids in serum or urine by tandem mass spectrometry, with clinically relevant metabolic profiles. Clin Chem. 2002 Sep;48(9):1460-71. [PubMed:12194923 ]
  2. Idris AM, Prokopczyk B, Hoffmann D: Toombak: a major risk factor for cancer of the oral cavity in Sudan. Prev Med. 1994 Nov;23(6):832-9. [PubMed:7855117 ]
  3. Schweinsberg F, Sander J, Schweinsberg E, Kollat P: [Examinations of the possibilities to nitrosate nicotine and nornicotine and of the formation of N-nitrosonornicotine in the stomach of smokers (author's transl)]. Z Krebsforsch Klin Onkol Cancer Res Clin Oncol. 1975 Sep 22;84(1):81-7. [PubMed:127438 ]
  4. Jacob P 3rd, Yu L, Liang G, Shulgin AT, Benowitz NL: Gas chromatographic-mass spectrometric method for determination of anabasine, anatabine and other tobacco alkaloids in urine of smokers and smokeless tobacco users. J Chromatogr. 1993 Sep 8;619(1):49-61. [PubMed:8245163 ]
  5. Xu X, Iba MM, Weisel CP: Simultaneous and sensitive measurement of anabasine, nicotine, and nicotine metabolites in human urine by liquid chromatography-tandem mass spectrometry. Clin Chem. 2004 Dec;50(12):2323-30. Epub 2004 Oct 7. [PubMed:15472033 ]