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Showing metabocard for (+)-Nicotine (HMDB0243542)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-10 20:47:32 UTC
Update Date2021-09-26 22:50:39 UTC
HMDB IDHMDB0243542
Secondary Accession NumbersNone
Metabolite Identification
Common Name(+)-Nicotine
Description(+)-Nicotine, also known as nikotin or L-nicotine, 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 (+)-Nicotine 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 significant number of articles have been published on (+)-Nicotine. This compound has been identified in human blood as reported by (PMID: 31557052 ). (+)-nicotine is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically (+)-Nicotine is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0243542 ((+)-Nicotine)

184
  Mrv0541 02231214302D          

 12 13  0  0  1  0            999 V2000
    2.4347    1.0877    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.3876   -1.4598    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.1022    0.6028    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7696    1.0877    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5147    1.8723    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6896    1.8723    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1022   -0.2223    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500    0.8327    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8166   -0.6348    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3876   -0.6348    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8166   -1.4598    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1022   -1.8723    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  3  1  0  0  0  0
  1  6  1  0  0  0  0
  1  8  1  0  0  0  0
  2 10  1  0  0  0  0
  2 12  2  0  0  0  0
  3  4  1  0  0  0  0
  3  7  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  7  9  1  0  0  0  0
  7 10  2  0  0  0  0
  9 11  2  0  0  0  0
 11 12  1  0  0  0  0
M  END
Download

3D MOL for HMDB0243542 ((+)-Nicotine)

HMDB0243542
     RDKit          3D
(+)-Nicotine
 26 27  0  0  0  0  0  0  0  0999 V2000
   -1.1196    0.3865    1.5708 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2082    0.8703    0.2057 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5084    0.5441   -0.3412 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3806   -0.6933   -1.1510 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9539   -1.1646   -0.8227 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3054    0.1923   -0.6760 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0780    0.1332   -0.2611 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7758    1.2082    0.2335 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1097    1.0985    0.6216 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7331   -0.1261    0.5009 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0343   -1.1635    0.0158 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.7414   -1.0669   -0.3629 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1214   -0.0344    1.7814 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3111    1.2299    2.2573 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9114   -0.3686    1.7784 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8511    1.4074   -0.9843 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2674    0.3856    0.4707 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3689   -0.4909   -2.2429 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1106   -1.4855   -0.8898 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9944   -1.7319    0.1132 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5460   -1.7490   -1.6746 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3921    0.6831   -1.6691 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2433    2.1612    0.3126 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6151    1.9740    1.0047 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7859   -0.2300    0.8028 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2340   -1.9696   -0.7526 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  2  0
  6  2  1  0
 12  7  1  0
  1 13  1  0
  1 14  1  0
  1 15  1  0
  3 16  1  0
  3 17  1  0
  4 18  1  0
  4 19  1  0
  5 20  1  0
  5 21  1  0
  6 22  1  0
  8 23  1  0
  9 24  1  0
 10 25  1  0
 12 26  1  0
M  END
Download

3D SDF for HMDB0243542 ((+)-Nicotine)

184
  Mrv0541 02231214302D          

 12 13  0  0  1  0            999 V2000
    2.4347    1.0877    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.3876   -1.4598    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.1022    0.6028    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7696    1.0877    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5147    1.8723    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6896    1.8723    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1022   -0.2223    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500    0.8327    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8166   -0.6348    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3876   -0.6348    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8166   -1.4598    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1022   -1.8723    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  3  1  0  0  0  0
  1  6  1  0  0  0  0
  1  8  1  0  0  0  0
  2 10  1  0  0  0  0
  2 12  2  0  0  0  0
  3  4  1  0  0  0  0
  3  7  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  7  9  1  0  0  0  0
  7 10  2  0  0  0  0
  9 11  2  0  0  0  0
 11 12  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0243542

> <DATABASE_NAME>
hmdb

> <SMILES>
CN1CCCC1C1=CN=CC=C1

> <INCHI_IDENTIFIER>
InChI=1S/C10H14N2/c1-12-7-3-5-10(12)9-4-2-6-11-8-9/h2,4,6,8,10H,3,5,7H2,1H3

> <INCHI_KEY>
SNICXCGAKADSCV-UHFFFAOYSA-N

> <FORMULA>
C10H14N2

> <MOLECULAR_WEIGHT>
162.2316

> <EXACT_MASS>
162.115698458

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_AVERAGE_POLARIZABILITY>
18.6152877327242

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
3-(1-methylpyrrolidin-2-yl)pyridine

> <ALOGPS_LOGP>
0.87

> <JCHEM_LOGP>
1.1625346926666664

> <ALOGPS_LOGS>
-0.24

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_BASIC>
8.861872125269352

> <JCHEM_POLAR_SURFACE_AREA>
16.130000000000003

> <JCHEM_REFRACTIVITY>
49.65500000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
9.33e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
nicotine

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0243542 ((+)-Nicotine)

HMDB0243542
     RDKit          3D
(+)-Nicotine
 26 27  0  0  0  0  0  0  0  0999 V2000
   -1.1196    0.3865    1.5708 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2082    0.8703    0.2057 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5084    0.5441   -0.3412 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3806   -0.6933   -1.1510 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9539   -1.1646   -0.8227 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3054    0.1923   -0.6760 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0780    0.1332   -0.2611 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7758    1.2082    0.2335 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1097    1.0985    0.6216 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7331   -0.1261    0.5009 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0343   -1.1635    0.0158 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.7414   -1.0669   -0.3629 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1214   -0.0344    1.7814 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3111    1.2299    2.2573 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9114   -0.3686    1.7784 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8511    1.4074   -0.9843 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2674    0.3856    0.4707 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3689   -0.4909   -2.2429 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1106   -1.4855   -0.8898 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9944   -1.7319    0.1132 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5460   -1.7490   -1.6746 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3921    0.6831   -1.6691 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2433    2.1612    0.3126 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6151    1.9740    1.0047 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7859   -0.2300    0.8028 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2340   -1.9696   -0.7526 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  2  0
  6  2  1  0
 12  7  1  0
  1 13  1  0
  1 14  1  0
  1 15  1  0
  3 16  1  0
  3 17  1  0
  4 18  1  0
  4 19  1  0
  5 20  1  0
  5 21  1  0
  6 22  1  0
  8 23  1  0
  9 24  1  0
 10 25  1  0
 12 26  1  0
M  END
Download

PDB for HMDB0243542 ((+)-Nicotine)

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: 184                                               
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  N   UNK     0       4.545   2.030   0.000  0.00  0.00           N+0
HETATM    2  N   UNK     0       4.457  -2.725   0.000  0.00  0.00           N+0
HETATM    3  C   UNK     0       5.791   1.125   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       7.037   2.030   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       6.561   3.495   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       5.021   3.495   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       5.791  -0.415   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       3.080   1.554   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       7.124  -1.185   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       4.457  -1.185   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       7.124  -2.725   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       5.791  -3.495   0.000  0.00  0.00           C+0
CONECT    1    3    6    8                                                  
CONECT    2   10   12                                                       
CONECT    3    1    4    7                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    1    5                                                       
CONECT    7    3    9   10                                                  
CONECT    8    1                                                            
CONECT    9    7   11                                                       
CONECT   10    2    7                                                       
CONECT   11    9   12                                                       
CONECT   12    2   11                                                       
MASTER        0    0    0    0    0    0    0    0   12    0   26    0
END
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3D PDB for HMDB0243542 ((+)-Nicotine)

COMPND    HMDB0243542
HETATM    1  C1  UNL     1      -1.120   0.386   1.571  1.00  0.00           C  
HETATM    2  N1  UNL     1      -1.208   0.870   0.206  1.00  0.00           N  
HETATM    3  C2  UNL     1      -2.508   0.544  -0.341  1.00  0.00           C  
HETATM    4  C3  UNL     1      -2.381  -0.693  -1.151  1.00  0.00           C  
HETATM    5  C4  UNL     1      -0.954  -1.165  -0.823  1.00  0.00           C  
HETATM    6  C5  UNL     1      -0.305   0.192  -0.676  1.00  0.00           C  
HETATM    7  C6  UNL     1       1.078   0.133  -0.261  1.00  0.00           C  
HETATM    8  C7  UNL     1       1.776   1.208   0.233  1.00  0.00           C  
HETATM    9  C8  UNL     1       3.110   1.099   0.622  1.00  0.00           C  
HETATM   10  C9  UNL     1       3.733  -0.126   0.501  1.00  0.00           C  
HETATM   11  N2  UNL     1       3.034  -1.164   0.016  1.00  0.00           N  
HETATM   12  C10 UNL     1       1.741  -1.067  -0.363  1.00  0.00           C  
HETATM   13  H1  UNL     1      -0.121  -0.034   1.781  1.00  0.00           H  
HETATM   14  H2  UNL     1      -1.311   1.230   2.257  1.00  0.00           H  
HETATM   15  H3  UNL     1      -1.911  -0.369   1.778  1.00  0.00           H  
HETATM   16  H4  UNL     1      -2.851   1.407  -0.984  1.00  0.00           H  
HETATM   17  H5  UNL     1      -3.267   0.386   0.471  1.00  0.00           H  
HETATM   18  H6  UNL     1      -2.369  -0.491  -2.243  1.00  0.00           H  
HETATM   19  H7  UNL     1      -3.111  -1.486  -0.890  1.00  0.00           H  
HETATM   20  H8  UNL     1      -0.994  -1.732   0.113  1.00  0.00           H  
HETATM   21  H9  UNL     1      -0.546  -1.749  -1.675  1.00  0.00           H  
HETATM   22  H10 UNL     1      -0.392   0.683  -1.669  1.00  0.00           H  
HETATM   23  H11 UNL     1       1.243   2.161   0.313  1.00  0.00           H  
HETATM   24  H12 UNL     1       3.615   1.974   1.005  1.00  0.00           H  
HETATM   25  H13 UNL     1       4.786  -0.230   0.803  1.00  0.00           H  
HETATM   26  H14 UNL     1       1.234  -1.970  -0.753  1.00  0.00           H  
CONECT    1    2   13   14   15
CONECT    2    3    6
CONECT    3    4   16   17
CONECT    4    5   18   19
CONECT    5    6   20   21
CONECT    6    7   22
CONECT    7    8    8   12
CONECT    8    9   23
CONECT    9   10   10   24
CONECT   10   11   25
CONECT   11   12   12
CONECT   12   26
END
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SMILES for HMDB0243542 ((+)-Nicotine)

CN1CCCC1C1=CN=CC=C1
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INCHI for HMDB0243542 ((+)-Nicotine)

InChI=1S/C10H14N2/c1-12-7-3-5-10(12)9-4-2-6-11-8-9/h2,4,6,8,10H,3,5,7H2,1H3
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
(+-)-3-(1-Methyl-2-pyrrolidinyl)pyridineKegg
(+-)-NicotineHMDB
(R,S)-NicotineHMDB
(RS)-NicotineHMDB
NicotinHMDB
NikotinHMDB
L-NicotineHMDB
Nicotine alkaloidHMDB
Chemical FormulaC10H14N2
Average Molecular Weight162.2316
Monoisotopic Molecular Weight162.115698458
IUPAC Name3-(1-methylpyrrolidin-2-yl)pyridine
Traditional Namenicotine
CAS Registry NumberNot Available
SMILES
CN1CCCC1C1=CN=CC=C1
InChI Identifier
InChI=1S/C10H14N2/c1-12-7-3-5-10(12)9-4-2-6-11-8-9/h2,4,6,8,10H,3,5,7H2,1H3
InChI KeySNICXCGAKADSCV-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
  • Alkaloid or derivatives
  • Aralkylamine
  • N-alkylpyrrolidine
  • Heteroaromatic compound
  • Pyrrolidine
  • Tertiary aliphatic amine
  • Tertiary amine
  • Azacycle
  • Organic nitrogen compound
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Organonitrogen compound
  • Amine
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Ontology
Physiological effect
Health effectOrganoleptic effect
Disposition
Biological locationRoute of exposureSource
Process
Naturally occurring process
Role
Industrial applicationEnvironmental roleBiological roleIndirect biological role
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
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID917
KEGG Compound IDC16150
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNicotine
METLIN IDNot Available
PubChem Compound942
PDB IDNot Available
ChEBI ID138000
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. Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]