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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-11 10:36:31 UTC

Update Date

2021-09-26 23:05:23 UTC

HMDB ID

HMDB0252666

Secondary Accession Numbers

None

Metabolite Identification

Common Name

Gelsemin

Description

2'-ethenyl-4'-methyl-9'-oxa-4'-azaspiro[indole-3,7'-tetracyclo[6.3.1.0²,⁶.0⁵,¹¹]dodecane]-2-ol belongs to the class of organic compounds known as gelsemium alkaloids. These are alkaloids with a structure that is based on the tetracyclic gelsemium skeleton. These alkaloids contain an oxindole function and a cage-like, hydroaromatic residue which is believed to arise from an intermediate related to anhydrovobasinediol by formation of a 6,20 bond and rearrangement to an oxindole. The major alkaloids in this group are related to Gelsemine; however, a smaller group, characterized by Gelsedine, lack the 6,20 bond, and have also lost C-21. 2'-ethenyl-4'-methyl-9'-oxa-4'-azaspiro[indole-3,7'-tetracyclo[6.3.1.0²,⁶.0⁵,¹¹]dodecane]-2-ol is a very strong basic compound (based on its pKa). This compound has been identified in human blood as reported by (PMID: 31557052 ). Gelsemin is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Gelsemin 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

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI

HMDB0252666
     RDKit          3D
Gelsemin
 46 51  0  0  0  0  0  0  0  0999 V2000
   -0.0206    2.7982    1.3444 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3842    1.5790    1.6868 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9758    0.5808    0.8536 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3784    1.0489    0.4511 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6274    0.4805   -0.8492 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9424   -0.0994   -0.9771 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5775   -0.5240   -0.9654 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7738   -1.4878    0.1789 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2347   -2.8510   -0.0433 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1063   -2.8246   -0.3146 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7854   -1.7709    0.3536 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1320   -1.5082    1.6613 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1678   -0.7838    1.4037 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8366   -0.5612   -0.5236 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9784   -0.9704   -1.9450 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3355   -1.9174   -2.5323 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9382   -0.1550   -2.5519 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.5897    0.5679   -1.5025 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7026    1.4180   -1.6012 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2885    1.9372   -0.4689 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7440    1.5919    0.7489 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6539    0.7623    0.8489 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0671    0.2453   -0.2900 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3965    0.3015   -0.4978 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4136    3.4821    2.0249 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1709    3.1320    0.3034 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1958    1.3318    2.7499 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3677    2.1473    0.3559 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0980    0.6821    1.2016 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5471    0.5431   -1.6698 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8252   -1.0844   -1.4712 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4324   -0.2339    0.0051 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5203   -0.9640   -1.9373 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8779   -1.5309    0.4166 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5074   -3.4598    0.8566 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8121   -3.3067   -0.8759 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8289   -2.1257    0.4956 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7362   -0.9801    2.3793 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1729   -2.5224    2.0611 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8037   -0.8618    2.2826 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1547   -0.0755   -3.5910 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0944    1.6604   -2.5799 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1529    2.5966   -0.5629 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2293    2.0168    1.6453 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2759    0.5298    1.8507 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2335    1.1658   -1.1281 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  3
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  5  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 11 14  1  0
 14 15  1  0
 15 16  2  0
 15 17  1  0
 17 18  1  0
 18 19  2  0
 19 20  1  0
 20 21  2  0
 21 22  1  0
 22 23  2  0
 14 24  1  0
 13  3  1  0
 23 14  1  0
 24  3  1  0
 24  7  1  0
 13  8  1  0
 23 18  1  0
  1 25  1  0
  1 26  1  0
  2 27  1  0
  4 28  1  0
  4 29  1  0
  6 30  1  0
  6 31  1  0
  6 32  1  0
  7 33  1  0
  8 34  1  0
  9 35  1  0
  9 36  1  0
 11 37  1  0
 12 38  1  0
 12 39  1  0
 13 40  1  0
 17 41  1  0
 19 42  1  0
 20 43  1  0
 21 44  1  0
 22 45  1  0
 24 46  1  0
M  END

  Mrv1533004241523182D          

 24 29  0  0  0  0            999 V2000
    1.2263    2.6623    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9699    1.8176    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4868    1.1676    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6368    0.7679    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1152    0.3463    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3342   -0.5509    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1369   -0.8408    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9723   -0.4958    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9959    0.4002    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3327    1.1811    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5317    0.8792    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1695    0.2299    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8965   -0.6832    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7484   -0.2158    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0596    0.5483    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8769    0.6608    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3830    0.0093    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0718   -0.7548    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2545   -0.8673    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7912   -1.5500    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.9988   -1.3203    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6013   -2.0938    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0155    1.6331    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8445    1.9812    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  4  9  1  0  0  0  0
  9 10  1  0  0  0  0
  2 10  1  0  0  0  0
 10 11  1  0  0  0  0
  5 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
  7 13  1  0  0  0  0
  8 14  1  0  0  0  0
 14 15  2  0  0  0  0
 15 16  1  0  0  0  0
 16 17  2  0  0  0  0
 17 18  1  0  0  0  0
 18 19  2  0  0  0  0
 14 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
  8 21  1  0  0  0  0
 21 22  2  0  0  0  0
  4 23  1  0  0  0  0
 23 24  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0252666

> <DATABASE_NAME>
hmdb

> <SMILES>
CN1CC2(C=C)C3CC4OCC3C1C2C41C(=O)NC2=CC=CC=C12

> <INCHI_IDENTIFIER>
InChI=1S/C20H22N2O2/c1-3-19-10-22(2)16-11-9-24-15(8-13(11)19)20(17(16)19)12-6-4-5-7-14(12)21-18(20)23/h3-7,11,13,15-17H,1,8-10H2,2H3,(H,21,23)

> <INCHI_KEY>
NFYYATWFXNPTRM-UHFFFAOYSA-N

> <FORMULA>
C20H22N2O2

> <MOLECULAR_WEIGHT>
322.408

> <EXACT_MASS>
322.168127956

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
46

> <JCHEM_AVERAGE_POLARIZABILITY>
34.49761994211255

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
2'-ethenyl-4'-methyl-1,2-dihydro-9'-oxa-4'-azaspiro[indole-3,7'-tetracyclo[6.3.1.0²,⁶.0⁵,¹¹]dodecane]-2-one

> <ALOGPS_LOGP>
1.79

> <JCHEM_LOGP>
1.4175211360000004

> <ALOGPS_LOGS>
-2.65

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.101784215977787

> <JCHEM_PKA_STRONGEST_BASIC>
9.79303913673213

> <JCHEM_POLAR_SURFACE_AREA>
41.57

> <JCHEM_REFRACTIVITY>
92.7646

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.18e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
gelsemine

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0252666
     RDKit          3D
Gelsemin
 46 51  0  0  0  0  0  0  0  0999 V2000
   -0.0206    2.7982    1.3444 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3842    1.5790    1.6868 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9758    0.5808    0.8536 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3784    1.0489    0.4511 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6274    0.4805   -0.8492 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9424   -0.0994   -0.9771 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5775   -0.5240   -0.9654 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7738   -1.4878    0.1789 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2347   -2.8510   -0.0433 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1063   -2.8246   -0.3146 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7854   -1.7709    0.3536 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1320   -1.5082    1.6613 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1678   -0.7838    1.4037 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8366   -0.5612   -0.5236 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9784   -0.9704   -1.9450 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3355   -1.9174   -2.5323 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9382   -0.1550   -2.5519 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.5897    0.5679   -1.5025 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7026    1.4180   -1.6012 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2885    1.9372   -0.4689 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7440    1.5919    0.7489 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6539    0.7623    0.8489 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0671    0.2453   -0.2900 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3965    0.3015   -0.4978 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4136    3.4821    2.0249 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1709    3.1320    0.3034 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1958    1.3318    2.7499 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3677    2.1473    0.3559 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0980    0.6821    1.2016 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5471    0.5431   -1.6698 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8252   -1.0844   -1.4712 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4324   -0.2339    0.0051 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5203   -0.9640   -1.9373 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8779   -1.5309    0.4166 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5074   -3.4598    0.8566 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8121   -3.3067   -0.8759 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8289   -2.1257    0.4956 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7362   -0.9801    2.3793 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1729   -2.5224    2.0611 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8037   -0.8618    2.2826 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1547   -0.0755   -3.5910 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0944    1.6604   -2.5799 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1529    2.5966   -0.5629 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2293    2.0168    1.6453 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2759    0.5298    1.8507 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2335    1.1658   -1.1281 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  3
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  5  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 11 14  1  0
 14 15  1  0
 15 16  2  0
 15 17  1  0
 17 18  1  0
 18 19  2  0
 19 20  1  0
 20 21  2  0
 21 22  1  0
 22 23  2  0
 14 24  1  0
 13  3  1  0
 23 14  1  0
 24  3  1  0
 24  7  1  0
 13  8  1  0
 23 18  1  0
  1 25  1  0
  1 26  1  0
  2 27  1  0
  4 28  1  0
  4 29  1  0
  6 30  1  0
  6 31  1  0
  6 32  1  0
  7 33  1  0
  8 34  1  0
  9 35  1  0
  9 36  1  0
 11 37  1  0
 12 38  1  0
 12 39  1  0
 13 40  1  0
 17 41  1  0
 19 42  1  0
 20 43  1  0
 21 44  1  0
 22 45  1  0
 24 46  1  0
M  END

HEADER    PROTEIN                                 24-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-APR-15         0                                  
HETATM    1  C   UNK     0       2.289   4.970   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0       1.811   3.393   0.000  0.00  0.00           N+0
HETATM    3  C   UNK     0       2.775   2.180   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.189   1.433   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -0.215   0.646   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -0.624  -1.028   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.256  -1.570   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.815  -0.925   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.859   0.747   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.621   2.205   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -0.993   1.641   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -2.183   0.429   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0      -1.673  -1.275   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       3.264  -0.403   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       3.845   1.023   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       5.370   1.234   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       6.315   0.017   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       5.734  -1.409   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       4.208  -1.619   0.000  0.00  0.00           C+0
HETATM   20  N   UNK     0       3.344  -2.893   0.000  0.00  0.00           N+0
HETATM   21  C   UNK     0       1.864  -2.465   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0       1.123  -3.908   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0      -0.029   3.049   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      -1.576   3.698   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   10                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    9   23                                             
CONECT    5    4    6   11                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8   13                                                  
CONECT    8    7    9   14   21                                             
CONECT    9    8    4   10                                                  
CONECT   10    9    2   11                                                  
CONECT   11   10    5   12                                                  
CONECT   12   11   13                                                       
CONECT   13   12    7                                                       
CONECT   14    8   15   19                                                  
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   14   20                                                  
CONECT   20   19   21                                                       
CONECT   21   20    8   22                                                  
CONECT   22   21                                                            
CONECT   23    4   24                                                       
CONECT   24   23                                                            
MASTER        0    0    0    0    0    0    0    0   24    0   58    0
END

COMPND    HMDB0252666
HETATM    1  C1  UNL     1      -0.021   2.798   1.344  1.00  0.00           C  
HETATM    2  C2  UNL     1      -0.384   1.579   1.687  1.00  0.00           C  
HETATM    3  C3  UNL     1      -0.976   0.581   0.854  1.00  0.00           C  
HETATM    4  C4  UNL     1      -2.378   1.049   0.451  1.00  0.00           C  
HETATM    5  N1  UNL     1      -2.627   0.480  -0.849  1.00  0.00           N  
HETATM    6  C5  UNL     1      -3.942  -0.099  -0.977  1.00  0.00           C  
HETATM    7  C6  UNL     1      -1.578  -0.524  -0.965  1.00  0.00           C  
HETATM    8  C7  UNL     1      -1.774  -1.488   0.179  1.00  0.00           C  
HETATM    9  C8  UNL     1      -1.235  -2.851  -0.043  1.00  0.00           C  
HETATM   10  O1  UNL     1       0.106  -2.825  -0.315  1.00  0.00           O  
HETATM   11  C9  UNL     1       0.785  -1.771   0.354  1.00  0.00           C  
HETATM   12  C10 UNL     1       0.132  -1.508   1.661  1.00  0.00           C  
HETATM   13  C11 UNL     1      -1.168  -0.784   1.404  1.00  0.00           C  
HETATM   14  C12 UNL     1       0.837  -0.561  -0.524  1.00  0.00           C  
HETATM   15  C13 UNL     1       0.978  -0.970  -1.945  1.00  0.00           C  
HETATM   16  O2  UNL     1       0.336  -1.917  -2.532  1.00  0.00           O  
HETATM   17  N2  UNL     1       1.938  -0.155  -2.552  1.00  0.00           N  
HETATM   18  C14 UNL     1       2.590   0.568  -1.502  1.00  0.00           C  
HETATM   19  C15 UNL     1       3.703   1.418  -1.601  1.00  0.00           C  
HETATM   20  C16 UNL     1       4.288   1.937  -0.469  1.00  0.00           C  
HETATM   21  C17 UNL     1       3.744   1.592   0.749  1.00  0.00           C  
HETATM   22  C18 UNL     1       2.654   0.762   0.849  1.00  0.00           C  
HETATM   23  C19 UNL     1       2.067   0.245  -0.290  1.00  0.00           C  
HETATM   24  C20 UNL     1      -0.397   0.302  -0.498  1.00  0.00           C  
HETATM   25  H1  UNL     1       0.414   3.482   2.025  1.00  0.00           H  
HETATM   26  H2  UNL     1      -0.171   3.132   0.303  1.00  0.00           H  
HETATM   27  H3  UNL     1      -0.196   1.332   2.750  1.00  0.00           H  
HETATM   28  H4  UNL     1      -2.368   2.147   0.356  1.00  0.00           H  
HETATM   29  H5  UNL     1      -3.098   0.682   1.202  1.00  0.00           H  
HETATM   30  H6  UNL     1      -4.547   0.543  -1.670  1.00  0.00           H  
HETATM   31  H7  UNL     1      -3.825  -1.084  -1.471  1.00  0.00           H  
HETATM   32  H8  UNL     1      -4.432  -0.234   0.005  1.00  0.00           H  
HETATM   33  H9  UNL     1      -1.520  -0.964  -1.937  1.00  0.00           H  
HETATM   34  H10 UNL     1      -2.878  -1.531   0.417  1.00  0.00           H  
HETATM   35  H11 UNL     1      -1.507  -3.460   0.857  1.00  0.00           H  
HETATM   36  H12 UNL     1      -1.812  -3.307  -0.876  1.00  0.00           H  
HETATM   37  H13 UNL     1       1.829  -2.126   0.496  1.00  0.00           H  
HETATM   38  H14 UNL     1       0.736  -0.980   2.379  1.00  0.00           H  
HETATM   39  H15 UNL     1      -0.173  -2.522   2.061  1.00  0.00           H  
HETATM   40  H16 UNL     1      -1.804  -0.862   2.283  1.00  0.00           H  
HETATM   41  H17 UNL     1       2.155  -0.076  -3.591  1.00  0.00           H  
HETATM   42  H18 UNL     1       4.094   1.660  -2.580  1.00  0.00           H  
HETATM   43  H19 UNL     1       5.153   2.597  -0.563  1.00  0.00           H  
HETATM   44  H20 UNL     1       4.229   2.017   1.645  1.00  0.00           H  
HETATM   45  H21 UNL     1       2.276   0.530   1.851  1.00  0.00           H  
HETATM   46  H22 UNL     1      -0.233   1.166  -1.128  1.00  0.00           H  
CONECT    1    2    2   25   26
CONECT    2    3   27
CONECT    3    4   13   24
CONECT    4    5   28   29
CONECT    5    6    7
CONECT    6   30   31   32
CONECT    7    8   24   33
CONECT    8    9   13   34
CONECT    9   10   35   36
CONECT   10   11
CONECT   11   12   14   37
CONECT   12   13   38   39
CONECT   13   40
CONECT   14   15   23   24
CONECT   15   16   16   17
CONECT   17   18   41
CONECT   18   19   19   23
CONECT   19   20   42
CONECT   20   21   21   43
CONECT   21   22   44
CONECT   22   23   23   45
CONECT   24   46
END

HMDB0252666
     RDKit          3D
Gelsemin
 46 51  0  0  0  0  0  0  0  0999 V2000
   -0.0206    2.7982    1.3444 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3842    1.5790    1.6868 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9758    0.5808    0.8536 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3784    1.0489    0.4511 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6274    0.4805   -0.8492 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9424   -0.0994   -0.9771 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5775   -0.5240   -0.9654 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7738   -1.4878    0.1789 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2347   -2.8510   -0.0433 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1063   -2.8246   -0.3146 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7854   -1.7709    0.3536 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1320   -1.5082    1.6613 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1678   -0.7838    1.4037 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8366   -0.5612   -0.5236 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9784   -0.9704   -1.9450 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3355   -1.9174   -2.5323 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9382   -0.1550   -2.5519 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.5897    0.5679   -1.5025 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7026    1.4180   -1.6012 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2885    1.9372   -0.4689 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7440    1.5919    0.7489 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6539    0.7623    0.8489 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0671    0.2453   -0.2900 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3965    0.3015   -0.4978 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4136    3.4821    2.0249 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1709    3.1320    0.3034 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1958    1.3318    2.7499 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3677    2.1473    0.3559 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0980    0.6821    1.2016 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5471    0.5431   -1.6698 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8252   -1.0844   -1.4712 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4324   -0.2339    0.0051 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5203   -0.9640   -1.9373 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8779   -1.5309    0.4166 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5074   -3.4598    0.8566 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8121   -3.3067   -0.8759 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8289   -2.1257    0.4956 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7362   -0.9801    2.3793 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1729   -2.5224    2.0611 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8037   -0.8618    2.2826 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1547   -0.0755   -3.5910 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0944    1.6604   -2.5799 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1529    2.5966   -0.5629 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2293    2.0168    1.6453 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2759    0.5298    1.8507 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2335    1.1658   -1.1281 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  3
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  5  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 11 14  1  0
 14 15  1  0
 15 16  2  0
 15 17  1  0
 17 18  1  0
 18 19  2  0
 19 20  1  0
 20 21  2  0
 21 22  1  0
 22 23  2  0
 14 24  1  0
 13  3  1  0
 23 14  1  0
 24  3  1  0
 24  7  1  0
 13  8  1  0
 23 18  1  0
  1 25  1  0
  1 26  1  0
  2 27  1  0
  4 28  1  0
  4 29  1  0
  6 30  1  0
  6 31  1  0
  6 32  1  0
  7 33  1  0
  8 34  1  0
  9 35  1  0
  9 36  1  0
 11 37  1  0
 12 38  1  0
 12 39  1  0
 13 40  1  0
 17 41  1  0
 19 42  1  0
 20 43  1  0
 21 44  1  0
 22 45  1  0
 24 46  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
Gelsemin	MeSH

Chemical Formula

C₂₀H₂₂N₂O₂

Average Molecular Weight

322.408

Monoisotopic Molecular Weight

322.168127956

IUPAC Name

2'-ethenyl-4'-methyl-1,2-dihydro-9'-oxa-4'-azaspiro[indole-3,7'-tetracyclo[6.3.1.0²,⁶.0⁵,¹¹]dodecane]-2-one

Traditional Name

gelsemine

CAS Registry Number

Not Available

SMILES

CN1CC2(C=C)C3CC4OCC3C1C2C41C(=O)NC2=CC=CC=C12

InChI Identifier

InChI=1S/C20H22N2O2/c1-3-19-10-22(2)16-11-9-24-15(8-13(11)19)20(17(16)19)12-6-4-5-7-14(12)21-18(20)23/h3-7,11,13,15-17H,1,8-10H2,2H3,(H,21,23)

InChI Key

NFYYATWFXNPTRM-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as gelsemium alkaloids. These are alkaloids with a structure that is based on the tetracyclic gelsemium skeleton. These alkaloids contain an oxindole function and a cage-like, hydroaromatic residue which is believed to arise from an intermediate related to anhydrovobasinediol by formation of a 6,20 bond and rearrangement to an oxindole. The major alkaloids in this group are related to Gelsemine; however, a smaller group, characterized by Gelsedine, lack the 6,20 bond, and have also lost C-21.

Kingdom

Organic compounds

Super Class

Alkaloids and derivatives

Class

Gelsemium alkaloids

Sub Class

Not Available

Direct Parent

Gelsemium alkaloids

Alternative Parents

Substituents

Gelsemium skeleton
Indole or derivatives
Dihydroindole
Isoindoline
Isoindole or derivatives
Oxepane
Aralkylamine
Oxane
Piperidine
N-alkylpyrrolidine
Benzenoid
Pyrrolidine
Tertiary aliphatic amine
Tertiary amine
Secondary carboxylic acid amide
Amino acid or derivatives
Carboxamide group
Lactam
Azacycle
Organoheterocyclic compound
Oxacycle
Carboxylic acid derivative
Dialkyl ether
Ether
Hydrocarbon derivative
Organic oxygen compound
Organic nitrogen compound
Organopnictogen compound
Organic oxide
Organonitrogen compound
Organooxygen compound
Carbonyl group
Amine
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 31557052)

Source

Exogenous

Exogenous (PMID: 31557052)

Process

Not Available

Role

Not Available

Physical Properties

State

Not Available

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
logP	1.79	ALOGPS
logP	1.42	ChemAxon
logS	-2.6	ALOGPS
pKa (Strongest Acidic)	13.1	ChemAxon
pKa (Strongest Basic)	9.79	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	41.57 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	92.76 m³·mol⁻¹	ChemAxon
Polarizability	34.5 Å³	ChemAxon
Number of Rings	6	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DeepCCS	[M-2H]-	203.818	30932474
DeepCCS	[M+Na]+	179.3	30932474
AllCCS	[M+H]+	177.1	32859911
AllCCS	[M+H-H2O]+	174.1	32859911
AllCCS	[M+NH4]+	179.9	32859911
AllCCS	[M+Na]+	180.7	32859911
AllCCS	[M-H]-	180.8	32859911
AllCCS	[M+Na-2H]-	180.2	32859911
AllCCS	[M+HCOO]-	179.6	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Gelsemin	CN1CC2(C=C)C3CC4OCC3C1C2C41C(=O)NC2=CC=CC=C12	3891.8	Standard polar	33892256
Gelsemin	CN1CC2(C=C)C3CC4OCC3C1C2C41C(=O)NC2=CC=CC=C12	2696.8	Standard non polar	33892256
Gelsemin	CN1CC2(C=C)C3CC4OCC3C1C2C41C(=O)NC2=CC=CC=C12	2690.5	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Gelsemin,1TMS,isomer #1	C=CC12CN(C)C3C4COC(CC41)C1(C(=O)N([Si](C)(C)C)C4=CC=CC=C41)C32	2599.5	Semi standard non polar	33892256
Gelsemin,1TMS,isomer #1	C=CC12CN(C)C3C4COC(CC41)C1(C(=O)N([Si](C)(C)C)C4=CC=CC=C41)C32	2619.2	Standard non polar	33892256
Gelsemin,1TMS,isomer #1	C=CC12CN(C)C3C4COC(CC41)C1(C(=O)N([Si](C)(C)C)C4=CC=CC=C41)C32	3224.3	Standard polar	33892256
Gelsemin,1TBDMS,isomer #1	C=CC12CN(C)C3C4COC(CC41)C1(C(=O)N([Si](C)(C)C(C)(C)C)C4=CC=CC=C41)C32	2826.1	Semi standard non polar	33892256
Gelsemin,1TBDMS,isomer #1	C=CC12CN(C)C3C4COC(CC41)C1(C(=O)N([Si](C)(C)C(C)(C)C)C4=CC=CC=C41)C32	2882.9	Standard non polar	33892256
Gelsemin,1TBDMS,isomer #1	C=CC12CN(C)C3C4COC(CC41)C1(C(=O)N([Si](C)(C)C(C)(C)C)C4=CC=CC=C41)C32	3331.0	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - Gelsemin GC-MS (Non-derivatized) - 70eV, Positive	splash10-000x-1794000000-4d5567d7590f257fa21b	2021-09-24	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Gelsemin GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Experimental LC-MS/MS	LC-MS/MS Spectrum - Gelsemin 6V, Positive-QTOF	splash10-052f-0940000000-8790389f37e43aaadc7b	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Gelsemin 6V, Positive-QTOF	splash10-0006-0900000000-274fe61788b79e7d063b	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Gelsemin 6V, Positive-QTOF	splash10-0002-0900000000-717d6661afa5943d671c	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Gelsemin 6V, Positive-QTOF	splash10-007o-1932000000-ac5cd9e81d23ad5f4795	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Gelsemin 6V, Positive-QTOF	splash10-00xr-0960000000-a7c095fb30537ceeff94	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Gelsemin 6V, Positive-QTOF	splash10-00di-0009000000-b8de92e04289f41c2715	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Gelsemin 6V, Positive-QTOF	splash10-00di-0109000000-8cb93d3808ab11727d52	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Gelsemin 6V, Positive-QTOF	splash10-00di-0009000000-3074bd7f71f8ed577284	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Gelsemin 6V, Positive-QTOF	splash10-00di-0319000000-5ca7a28dfaa338d50b85	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Gelsemin 6V, Positive-QTOF	splash10-00di-0009000000-62f18e64477f059adb7f	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Gelsemin 6V, Positive-QTOF	splash10-001m-0910000000-9c16ab8dac36da0013f3	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Gelsemin 6V, Negative-QTOF	splash10-00di-0009000000-bca59c378d3a16de3fec	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Gelsemin 6V, Positive-QTOF	splash10-00di-0009000000-e557d85935e58cd47675	2021-09-20	HMDB team, MONA	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Gelsemin 10V, Positive-QTOF	splash10-00di-0009000000-4311325ab2bb597c4814	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Gelsemin 20V, Positive-QTOF	splash10-00di-0019000000-298017ff85ce10f4eb16	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Gelsemin 40V, Positive-QTOF	splash10-00dl-1697000000-8352331895f2f94b593c	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Gelsemin 10V, Negative-QTOF	splash10-00di-0009000000-ef145f7b42b2cd0c897b	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Gelsemin 20V, Negative-QTOF	splash10-00di-0019000000-56a2daf50392df96f384	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Gelsemin 40V, Negative-QTOF	splash10-00sl-0915000000-e9f7d1877c24fa69f39a	2021-10-12	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	31557052	details

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

279057

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

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 ]

Showing metabocard for Gelsemin (HMDB0252666)

MOL for HMDB0252666 (Gelsemin)

3D MOL for HMDB0252666 (Gelsemin)

3D SDF for HMDB0252666 (Gelsemin)

3D-SDF for HMDB0252666 (Gelsemin)

PDB for HMDB0252666 (Gelsemin)

3D PDB for HMDB0252666 (Gelsemin)

SMILES for HMDB0252666 (Gelsemin)

INCHI for HMDB0252666 (Gelsemin)

Structure for HMDB0252666 (Gelsemin)

3D Structure for HMDB0252666 (Gelsemin)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra