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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-06 15:16:51 UTC

Update Date

2022-03-07 02:51:52 UTC

HMDB ID

HMDB0015116

Secondary Accession Numbers

HMDB15116

Metabolite Identification

Common Name

Physostigmine

Description

Physostigmine, also known as eserine or antilirium, belongs to the class of organic compounds known as pyrroloindoles. Pyrroloindoles are compounds containing a pyrroloindole moiety, which is a tricyclic heterocycle which consists of a pyrrole ring fused to an indole. Pyrrole is 5-membered ring consisting of four carbon atoms and one nitrogen atom. Indole is a bicyclic compound consisting of a six-membered benzene ring fused to a five-membered nitrogen-containing pyrrole ring. Physostigmine is a drug which is used for the treatment of glaucoma, and in the treatment of severe anticholinergic toxicity. Physostigmine is a very strong basic compound (based on its pKa).

Structure

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

HMDB0015116
     RDKit          3D
Physostigmine
 41 43  0  0  0  0  0  0  0  0999 V2000
    6.3943    1.7165   -0.8352 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5737    1.2909    0.2695 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.3127    0.6844    0.0095 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9075    0.5161   -1.1696 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4807    0.2553    1.0283 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2415   -0.3399    0.7389 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1827   -1.7101    0.5752 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9338   -2.2255    0.2927 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1829   -1.4137    0.1824 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0856   -0.0567    0.3518 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1535    0.4864    0.6355 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4440    0.5390    0.1812 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.3568    1.8927   -0.4729 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2161    0.5500    1.4587 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5745    0.0641    1.0774 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5339   -0.3597   -0.2891 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2239    0.5185   -1.1987 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1386   -0.4859   -0.6569 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.5680   -1.7159   -0.1081 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1708   -2.9966    0.1296 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4317    0.8879   -1.5940 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.4286    1.9554   -0.5119 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9094    2.5711   -1.3319 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8687    1.4105    1.2493 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0644   -2.3512    0.6623 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8219   -3.3106    0.1513 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2096    1.5666    0.7663 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4675    2.4106   -0.0315 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2261    2.5425   -0.2073 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1773    1.8249   -1.5478 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7251   -0.1568    2.1804 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2496    1.5571    1.9300 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8930   -0.7997    1.7184 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3027    0.9079    1.1743 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5857    1.2366   -1.7123 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0508    1.0605   -0.6664 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7245   -0.1125   -1.9843 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9683   -0.3822   -1.7316 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5191   -3.8181   -0.2477 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1219   -3.0768   -0.4615 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4080   -3.1335    1.2059 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  3  5  1  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  2  0
 10 12  1  0
 12 13  1  6
 12 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
 16 18  1  0
 18 19  1  0
 19 20  1  0
 11  6  1  0
 18 12  1  0
 19  9  1  0
  1 21  1  0
  1 22  1  0
  1 23  1  0
  2 24  1  0
  7 25  1  0
  8 26  1  0
 11 27  1  0
 13 28  1  0
 13 29  1  0
 13 30  1  0
 14 31  1  0
 14 32  1  0
 15 33  1  0
 15 34  1  0
 17 35  1  0
 17 36  1  0
 17 37  1  0
 18 38  1  6
 20 39  1  0
 20 40  1  0
 20 41  1  0
M  END

981
  Mrv0541 02231215092D          

 21 23  0  0  1  0            999 V2000
    3.5651    0.0678    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2627    1.4644    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.7863   -0.6839    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.8691    0.5845    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.2044    0.5042    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.4566   -0.6851    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    7.1240   -0.2001    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    6.7121   -1.4644    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7891   -0.2001    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.5322   -1.4637    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0441    0.5845    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7891   -1.1700    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.5714   -0.4303    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9514   -0.3917    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.3540    1.2520    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4789    1.2319    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3715    0.2425    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6370    1.0597    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0107    0.6787    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500    1.1151    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6586    0.1871    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  1 17  1  0  0  0  0
  1 19  1  0  0  0  0
  2 19  2  0  0  0  0
  3  7  1  0  0  0  0
  3 10  1  0  0  0  0
  3 13  1  0  0  0  0
  4  7  1  0  0  0  0
  4 11  1  0  0  0  0
  4 15  1  0  0  0  0
  5 19  1  0  0  0  0
  5 20  1  0  0  0  0
  6  7  1  0  0  0  0
  6  8  1  0  0  0  0
  6  9  1  0  0  0  0
  6 12  1  6  0  0  0
  7 21  1  6  0  0  0
  8 10  1  0  0  0  0
  9 11  2  0  0  0  0
  9 14  1  0  0  0  0
 11 16  1  0  0  0  0
 14 17  2  0  0  0  0
 16 18  2  0  0  0  0
 17 18  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0015116

> <DATABASE_NAME>
hmdb

> <SMILES>
[H][C@]12N(C)CC[C@@]1(C)C1=C(C=CC(OC(=O)NC)=C1)N2C

> <INCHI_IDENTIFIER>
InChI=1S/C15H21N3O2/c1-15-7-8-17(3)13(15)18(4)12-6-5-10(9-11(12)15)20-14(19)16-2/h5-6,9,13H,7-8H2,1-4H3,(H,16,19)/t13-,15+/m1/s1

> <INCHI_KEY>
PIJVFDBKTWXHHD-HIFRSBDPSA-N

> <FORMULA>
C15H21N3O2

> <MOLECULAR_WEIGHT>
275.3461

> <EXACT_MASS>
275.163376931

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
30.618093581107985

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(3aS,8aR)-1,3a,8-trimethyl-1H,2H,3H,3aH,8H,8aH-pyrrolo[2,3-b]indol-5-yl N-methylcarbamate

> <ALOGPS_LOGP>
1.80

> <JCHEM_LOGP>
2.2325330733333337

> <ALOGPS_LOGS>
-2.44

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.772488335318307

> <JCHEM_PKA_STRONGEST_BASIC>
6.585999039777742

> <JCHEM_POLAR_SURFACE_AREA>
44.81

> <JCHEM_REFRACTIVITY>
78.39679999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
9.92e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
physostigmine

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0015116
     RDKit          3D
Physostigmine
 41 43  0  0  0  0  0  0  0  0999 V2000
    6.3943    1.7165   -0.8352 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5737    1.2909    0.2695 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.3127    0.6844    0.0095 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9075    0.5161   -1.1696 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4807    0.2553    1.0283 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2415   -0.3399    0.7389 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1827   -1.7101    0.5752 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9338   -2.2255    0.2927 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1829   -1.4137    0.1824 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0856   -0.0567    0.3518 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1535    0.4864    0.6355 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4440    0.5390    0.1812 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.3568    1.8927   -0.4729 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2161    0.5500    1.4587 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5745    0.0641    1.0774 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5339   -0.3597   -0.2891 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2239    0.5185   -1.1987 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1386   -0.4859   -0.6569 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.5680   -1.7159   -0.1081 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1708   -2.9966    0.1296 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4317    0.8879   -1.5940 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.4286    1.9554   -0.5119 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9094    2.5711   -1.3319 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8687    1.4105    1.2493 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0644   -2.3512    0.6623 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8219   -3.3106    0.1513 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2096    1.5666    0.7663 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4675    2.4106   -0.0315 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2261    2.5425   -0.2073 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1773    1.8249   -1.5478 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7251   -0.1568    2.1804 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2496    1.5571    1.9300 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8930   -0.7997    1.7184 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3027    0.9079    1.1743 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5857    1.2366   -1.7123 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0508    1.0605   -0.6664 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7245   -0.1125   -1.9843 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9683   -0.3822   -1.7316 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5191   -3.8181   -0.2477 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1219   -3.0768   -0.4615 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4080   -3.1335    1.2059 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  3  5  1  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  2  0
 10 12  1  0
 12 13  1  6
 12 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
 16 18  1  0
 18 19  1  0
 19 20  1  0
 11  6  1  0
 18 12  1  0
 19  9  1  0
  1 21  1  0
  1 22  1  0
  1 23  1  0
  2 24  1  0
  7 25  1  0
  8 26  1  0
 11 27  1  0
 13 28  1  0
 13 29  1  0
 13 30  1  0
 14 31  1  0
 14 32  1  0
 15 33  1  0
 15 34  1  0
 17 35  1  0
 17 36  1  0
 17 37  1  0
 18 38  1  6
 20 39  1  0
 20 40  1  0
 20 41  1  0
M  END

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: 981                                               
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  O   UNK     0       6.655   0.127   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0       6.090   2.734   0.000  0.00  0.00           O+0
HETATM    3  N   UNK     0      14.534  -1.277   0.000  0.00  0.00           N+0
HETATM    4  N   UNK     0      12.822   1.091   0.000  0.00  0.00           N+0
HETATM    5  N   UNK     0       4.115   0.941   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0      12.052  -1.279   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      13.298  -0.374   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      12.529  -2.734   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      10.806  -0.374   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      14.060  -2.732   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      11.282   1.091   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      10.806  -2.184   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      16.000  -0.803   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       9.243  -0.731   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      13.727   2.337   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      10.227   2.300   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       8.160   0.453   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       8.656   1.978   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       5.620   1.267   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       3.080   2.082   0.000  0.00  0.00           C+0
HETATM   21  H   UNK     0      14.296   0.349   0.000  0.00  0.00           H+0
CONECT    1   17   19                                                       
CONECT    2   19                                                            
CONECT    3    7   10   13                                                  
CONECT    4    7   11   15                                                  
CONECT    5   19   20                                                       
CONECT    6    7    8    9   12                                             
CONECT    7    3    4    6   21                                             
CONECT    8    6   10                                                       
CONECT    9    6   11   14                                                  
CONECT   10    3    8                                                       
CONECT   11    4    9   16                                                  
CONECT   12    6                                                            
CONECT   13    3                                                            
CONECT   14    9   17                                                       
CONECT   15    4                                                            
CONECT   16   11   18                                                       
CONECT   17    1   14   18                                                  
CONECT   18   16   17                                                       
CONECT   19    1    2    5                                                  
CONECT   20    5                                                            
CONECT   21    7                                                            
MASTER        0    0    0    0    0    0    0    0   21    0   46    0
END

COMPND    HMDB0015116
HETATM    1  C1  UNL     1       6.394   1.716  -0.835  1.00  0.00           C  
HETATM    2  N1  UNL     1       5.574   1.291   0.270  1.00  0.00           N  
HETATM    3  C2  UNL     1       4.313   0.684   0.009  1.00  0.00           C  
HETATM    4  O1  UNL     1       3.908   0.516  -1.170  1.00  0.00           O  
HETATM    5  O2  UNL     1       3.481   0.255   1.028  1.00  0.00           O  
HETATM    6  C3  UNL     1       2.241  -0.340   0.739  1.00  0.00           C  
HETATM    7  C4  UNL     1       2.183  -1.710   0.575  1.00  0.00           C  
HETATM    8  C5  UNL     1       0.934  -2.225   0.293  1.00  0.00           C  
HETATM    9  C6  UNL     1      -0.183  -1.414   0.182  1.00  0.00           C  
HETATM   10  C7  UNL     1      -0.086  -0.057   0.352  1.00  0.00           C  
HETATM   11  C8  UNL     1       1.154   0.486   0.635  1.00  0.00           C  
HETATM   12  C9  UNL     1      -1.444   0.539   0.181  1.00  0.00           C  
HETATM   13  C10 UNL     1      -1.357   1.893  -0.473  1.00  0.00           C  
HETATM   14  C11 UNL     1      -2.216   0.550   1.459  1.00  0.00           C  
HETATM   15  C12 UNL     1      -3.575   0.064   1.077  1.00  0.00           C  
HETATM   16  N2  UNL     1      -3.534  -0.360  -0.289  1.00  0.00           N  
HETATM   17  C13 UNL     1      -4.224   0.519  -1.199  1.00  0.00           C  
HETATM   18  C14 UNL     1      -2.139  -0.486  -0.657  1.00  0.00           C  
HETATM   19  N3  UNL     1      -1.568  -1.716  -0.108  1.00  0.00           N  
HETATM   20  C15 UNL     1      -2.171  -2.997   0.130  1.00  0.00           C  
HETATM   21  H1  UNL     1       6.432   0.888  -1.594  1.00  0.00           H  
HETATM   22  H2  UNL     1       7.429   1.955  -0.512  1.00  0.00           H  
HETATM   23  H3  UNL     1       5.909   2.571  -1.332  1.00  0.00           H  
HETATM   24  H4  UNL     1       5.869   1.410   1.249  1.00  0.00           H  
HETATM   25  H5  UNL     1       3.064  -2.351   0.662  1.00  0.00           H  
HETATM   26  H6  UNL     1       0.822  -3.311   0.151  1.00  0.00           H  
HETATM   27  H7  UNL     1       1.210   1.567   0.766  1.00  0.00           H  
HETATM   28  H8  UNL     1      -0.468   2.411  -0.031  1.00  0.00           H  
HETATM   29  H9  UNL     1      -2.226   2.543  -0.207  1.00  0.00           H  
HETATM   30  H10 UNL     1      -1.177   1.825  -1.548  1.00  0.00           H  
HETATM   31  H11 UNL     1      -1.725  -0.157   2.180  1.00  0.00           H  
HETATM   32  H12 UNL     1      -2.250   1.557   1.930  1.00  0.00           H  
HETATM   33  H13 UNL     1      -3.893  -0.800   1.718  1.00  0.00           H  
HETATM   34  H14 UNL     1      -4.303   0.908   1.174  1.00  0.00           H  
HETATM   35  H15 UNL     1      -3.586   1.237  -1.712  1.00  0.00           H  
HETATM   36  H16 UNL     1      -5.051   1.060  -0.666  1.00  0.00           H  
HETATM   37  H17 UNL     1      -4.724  -0.113  -1.984  1.00  0.00           H  
HETATM   38  H18 UNL     1      -1.968  -0.382  -1.732  1.00  0.00           H  
HETATM   39  H19 UNL     1      -1.519  -3.818  -0.248  1.00  0.00           H  
HETATM   40  H20 UNL     1      -3.122  -3.077  -0.461  1.00  0.00           H  
HETATM   41  H21 UNL     1      -2.408  -3.133   1.206  1.00  0.00           H  
CONECT    1    2   21   22   23
CONECT    2    3   24
CONECT    3    4    4    5
CONECT    5    6
CONECT    6    7    7   11
CONECT    7    8   25
CONECT    8    9    9   26
CONECT    9   10   19
CONECT   10   11   11   12
CONECT   11   27
CONECT   12   13   14   18
CONECT   13   28   29   30
CONECT   14   15   31   32
CONECT   15   16   33   34
CONECT   16   17   18
CONECT   17   35   36   37
CONECT   18   19   38
CONECT   19   20
CONECT   20   39   40   41
END

HMDB0015116
     RDKit          3D
Physostigmine
 41 43  0  0  0  0  0  0  0  0999 V2000
    6.3943    1.7165   -0.8352 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5737    1.2909    0.2695 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.3127    0.6844    0.0095 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9075    0.5161   -1.1696 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4807    0.2553    1.0283 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2415   -0.3399    0.7389 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1827   -1.7101    0.5752 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9338   -2.2255    0.2927 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1829   -1.4137    0.1824 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0856   -0.0567    0.3518 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1535    0.4864    0.6355 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4440    0.5390    0.1812 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.3568    1.8927   -0.4729 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2161    0.5500    1.4587 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5745    0.0641    1.0774 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5339   -0.3597   -0.2891 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2239    0.5185   -1.1987 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1386   -0.4859   -0.6569 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.5680   -1.7159   -0.1081 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1708   -2.9966    0.1296 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4317    0.8879   -1.5940 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.4286    1.9554   -0.5119 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9094    2.5711   -1.3319 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8687    1.4105    1.2493 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0644   -2.3512    0.6623 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8219   -3.3106    0.1513 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2096    1.5666    0.7663 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4675    2.4106   -0.0315 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2261    2.5425   -0.2073 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1773    1.8249   -1.5478 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7251   -0.1568    2.1804 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2496    1.5571    1.9300 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8930   -0.7997    1.7184 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3027    0.9079    1.1743 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5857    1.2366   -1.7123 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0508    1.0605   -0.6664 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7245   -0.1125   -1.9843 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9683   -0.3822   -1.7316 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5191   -3.8181   -0.2477 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1219   -3.0768   -0.4615 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4080   -3.1335    1.2059 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  3  5  1  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  2  0
 10 12  1  0
 12 13  1  6
 12 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
 16 18  1  0
 18 19  1  0
 19 20  1  0
 11  6  1  0
 18 12  1  0
 19  9  1  0
  1 21  1  0
  1 22  1  0
  1 23  1  0
  2 24  1  0
  7 25  1  0
  8 26  1  0
 11 27  1  0
 13 28  1  0
 13 29  1  0
 13 30  1  0
 14 31  1  0
 14 32  1  0
 15 33  1  0
 15 34  1  0
 17 35  1  0
 17 36  1  0
 17 37  1  0
 18 38  1  6
 20 39  1  0
 20 40  1  0
 20 41  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
Antilirium	ChEBI
Eserine	ChEBI
Physostol	ChEBI
Erserine	HMDB
Eserine sulfate	HMDB
Eserolein, methylcarbamate	HMDB

Chemical Formula

C₁₅H₂₁N₃O₂

Average Molecular Weight

275.3461

Monoisotopic Molecular Weight

275.163376931

IUPAC Name

(3aS,8aR)-1,3a,8-trimethyl-1H,2H,3H,3aH,8H,8aH-pyrrolo[2,3-b]indol-5-yl N-methylcarbamate

Traditional Name

physostigmine

CAS Registry Number

57-47-6

SMILES

[H][C@]12N(C)CC[C@@]1(C)C1=C(C=CC(OC(=O)NC)=C1)N2C

InChI Identifier

InChI=1S/C15H21N3O2/c1-15-7-8-17(3)13(15)18(4)12-6-5-10(9-11(12)15)20-14(19)16-2/h5-6,9,13H,7-8H2,1-4H3,(H,16,19)/t13-,15+/m1/s1

InChI Key

PIJVFDBKTWXHHD-HIFRSBDPSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyrroloindoles. Pyrroloindoles are compounds containing a pyrroloindole moiety, which is a tricyclic heterocycle which consists of a pyrrole ring fused to an indole. Pyrrole is 5-membered ring consisting of four carbon atoms and one nitrogen atom. Indole is a bicyclic compound consisting of a six-membered benzene ring fused to a five-membered nitrogen-containing pyrrole ring.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Indoles and derivatives

Sub Class

Pyrroloindoles

Direct Parent

Pyrroloindoles

Alternative Parents

Substituents

Pyrroloindole
Indole
Dialkylarylamine
Benzenoid
N-alkylpyrrolidine
Pyrrole
Pyrrolidine
Carbamic acid ester
Carbonic acid derivative
Azacycle
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Organooxygen compound
Organonitrogen compound
Organic oxygen compound
Organic nitrogen compound
Carbonyl group
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

carbamate ester (CHEBI:27953 )
indole alkaloid (CHEBI:27953 )
Alkaloids (C06535 )
Pyrroloindole alkaloids (C06535 )

Ontology

Not Available

Urine (PMID: 21059682)

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 21059682)

Cellular substructure

Cytoplasm (HMDB: HMDB0015116)

Process

Not Available

Role

Not Available

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	105.5 °C	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	0.99 g/L	Not Available
LogP	1.7	Not Available

Experimental Chromatographic Properties

Experimental Collision Cross Sections

Adduct Type	Data Source	CCS Value (Å²)	Reference
[M+H]+	Not Available	167.899	http://allccs.zhulab.cn/database/detail?ID=AllCCS00000978

Predicted Molecular Properties

Property	Value	Source
Water Solubility	0.99 g/L	ALOGPS
logP	1.8	ALOGPS
logP	2.23	ChemAxon
logS	-2.4	ALOGPS
pKa (Strongest Acidic)	14.77	ChemAxon
pKa (Strongest Basic)	6.59	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	44.81 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	78.4 m³·mol⁻¹	ChemAxon
Polarizability	30.62 Å³	ChemAxon
Number of Rings	3	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
DarkChem	[M+H]+	164.4	31661259
DarkChem	[M-H]-	164.075	31661259
DeepCCS	[M-2H]-	194.848	30932474
DeepCCS	[M+Na]+	169.891	30932474
AllCCS	[M+H]+	164.3	32859911
AllCCS	[M+H-H2O]+	160.8	32859911
AllCCS	[M+NH4]+	167.5	32859911
AllCCS	[M+Na]+	168.5	32859911
AllCCS	[M-H]-	172.3	32859911
AllCCS	[M+Na-2H]-	172.2	32859911
AllCCS	[M+HCOO]-	172.2	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Physostigmine	[H][C@]12N(C)CC[C@@]1(C)C1=C(C=CC(OC(=O)NC)=C1)N2C	3403.6	Standard polar	33892256
Physostigmine	[H][C@]12N(C)CC[C@@]1(C)C1=C(C=CC(OC(=O)NC)=C1)N2C	2214.4	Standard non polar	33892256
Physostigmine	[H][C@]12N(C)CC[C@@]1(C)C1=C(C=CC(OC(=O)NC)=C1)N2C	2299.8	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Physostigmine,1TMS,isomer #1	CN1CC[C@@]2(C)C3=CC(OC(=O)N(C)[Si](C)(C)C)=CC=C3N(C)[C@@H]12	2241.0	Semi standard non polar	33892256
Physostigmine,1TMS,isomer #1	CN1CC[C@@]2(C)C3=CC(OC(=O)N(C)[Si](C)(C)C)=CC=C3N(C)[C@@H]12	2316.9	Standard non polar	33892256
Physostigmine,1TMS,isomer #1	CN1CC[C@@]2(C)C3=CC(OC(=O)N(C)[Si](C)(C)C)=CC=C3N(C)[C@@H]12	2676.5	Standard polar	33892256
Physostigmine,1TBDMS,isomer #1	CN1CC[C@@]2(C)C3=CC(OC(=O)N(C)[Si](C)(C)C(C)(C)C)=CC=C3N(C)[C@@H]12	2461.1	Semi standard non polar	33892256
Physostigmine,1TBDMS,isomer #1	CN1CC[C@@]2(C)C3=CC(OC(=O)N(C)[Si](C)(C)C(C)(C)C)=CC=C3N(C)[C@@H]12	2536.4	Standard non polar	33892256
Physostigmine,1TBDMS,isomer #1	CN1CC[C@@]2(C)C3=CC(OC(=O)N(C)[Si](C)(C)C(C)(C)C)=CC=C3N(C)[C@@H]12	2816.5	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Experimental GC-MS	GC-MS Spectrum - Physostigmine GC-EI-TOF (Non-derivatized)	splash10-001j-1590000000-508da23acfe2c8a2f568	2017-09-12	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - Physostigmine GC-EI-TOF (Non-derivatized)	splash10-00ea-6790000000-c7dad12610a8d73fb915	2017-09-12	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - Physostigmine GC-EI-TOF (Non-derivatized)	splash10-001j-1590000000-508da23acfe2c8a2f568	2018-05-18	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - Physostigmine GC-EI-TOF (Non-derivatized)	splash10-00ea-6790000000-c7dad12610a8d73fb915	2018-05-18	HMDB team, MONA, MassBank	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Physostigmine GC-MS (Non-derivatized) - 70eV, Positive	splash10-03ea-3290000000-ff0ad85b80701aa56609	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Physostigmine GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Physostigmine 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 - Physostigmine LC-ESI-qTof , Positive-QTOF	splash10-03dj-2900000000-b9d164a9a3afaf8a17cf	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Physostigmine LC-ESI-QQ , positive-QTOF	splash10-00or-0090000000-1f322550abc600bd72a9	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Physostigmine LC-ESI-QQ , positive-QTOF	splash10-014i-0490000000-e4a06a93b3b18d738157	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Physostigmine LC-ESI-QQ , positive-QTOF	splash10-03di-0900000000-d9ddac609ada184032ac	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Physostigmine LC-ESI-QQ , positive-QTOF	splash10-03di-0900000000-ef8f7c2ddbdba70fe1d3	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Physostigmine LC-ESI-QQ , positive-QTOF	splash10-01ot-0900000000-daf3030c2c85de1db72e	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Physostigmine LC-ESI-IT , positive-QTOF	splash10-014i-0090000000-8a9155530ad88f483e2e	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Physostigmine , positive-QTOF	splash10-03dj-2900000000-b9d164a9a3afaf8a17cf	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Physostigmine 6V, Positive-QTOF	splash10-03di-0900000000-d3eb59c5c9b1e38fcb05	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Physostigmine 6V, Positive-QTOF	splash10-03xr-0960000000-5c126e885fa694d4eeac	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Physostigmine 30V, Positive-QTOF	splash10-03di-0900000000-a1155e879f5d35d96bb7	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Physostigmine 10V, Positive-QTOF	splash10-016r-0090000000-5864a0721423095f52ac	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Physostigmine 6V, Positive-QTOF	splash10-016r-0090000000-5fdb9bd8096eedcd6a56	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Physostigmine 50V, Positive-QTOF	splash10-0002-0900000000-d4927334d1d827874b42	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Physostigmine 10V, Positive-QTOF	splash10-03xr-0960000000-11d52cd0d5583d0e2c27	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Physostigmine 10V, Positive-QTOF	splash10-03xr-0950000000-e238974d00c6c1a74ff8	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Physostigmine 35V, Positive-QTOF	splash10-03di-0910000000-f5b98a709049c6a598e0	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Physostigmine 15V, Positive-QTOF	splash10-014i-0190000000-5bee8bebe8f73ca69075	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Physostigmine 10V, Positive-QTOF	splash10-016r-0090000000-77bf45d5232f86cce363	2021-09-20	HMDB team, MONA	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Physostigmine 10V, Positive-QTOF	splash10-00or-3090000000-4d4b520473a9f2047c89	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Physostigmine 20V, Positive-QTOF	splash10-0uxr-3090000000-a96a130ca2964214aa50	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Physostigmine 40V, Positive-QTOF	splash10-0pdi-9440000000-97f447b7b63d60cd222b	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Physostigmine 10V, Negative-QTOF	splash10-0ab9-8090000000-c4df4baeb1b2ed495e64	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Physostigmine 20V, Negative-QTOF	splash10-0a4i-6090000000-03d5fd62a0bf34c26c01	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Physostigmine 40V, Negative-QTOF	splash10-0pb9-9380000000-7df539c4225faf494471	2016-08-03	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Cytoplasm

Biospecimen Locations

Blood
Urine

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Expected but not Quantified	Not Quantified	Not Available	Not Available	Taking drug identified by DrugBank entry DB00981	21059682	details
Urine	Expected but not Quantified	Not Quantified	Not Available	Not Available	Taking drug identified by DrugBank entry DB00981	21059682	details

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

DB00981

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

C00001757

Chemspider ID

5763

KEGG Compound ID

C06535

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Physostigmine

METLIN ID

Not Available

PubChem Compound

5983

PDB ID

Not Available

ChEBI ID

27953

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)

Download (PDF)

General References

Not Available

Enzymes

Enzyme Details

1. Acetylcholinesterase

General function:: Involved in carboxylesterase activity
Specific function:: Terminates signal transduction at the neuromuscular junction by rapid hydrolysis of the acetylcholine released into the synaptic cleft. Role in neuronal apoptosis.
Gene Name:: ACHE
Uniprot ID:: P22303
Molecular weight:: 67795.525

References

Nguyen PV, Aniksztejn L, Catarsi S, Drapeau P: Maturation of neuromuscular transmission during early development in zebrafish. J Neurophysiol. 1999 Jun;81(6):2852-61. [PubMed:10368402 ]
Tuovinen K, Kaliste-Korhonen E, Raushel FM, Hanninen O: Success of pyridostigmine, physostigmine, eptastigmine and phosphotriesterase treatments in acute sarin intoxication. Toxicology. 1999 Jun 15;134(2-3):169-78. [PubMed:10403635 ]
Blasina MF, Faria AC, Gardino PF, Hokoc JN, Almeida OM, de Mello FG, Arruti C, Dajas F: Evidence for a noncholinergic function of acetylcholinesterase during development of chicken retina as shown by fasciculin. Cell Tissue Res. 2000 Feb;299(2):173-84. [PubMed:10741458 ]
Monnet-Tschudi F, Zurich MG, Schilter B, Costa LG, Honegger P: Maturation-dependent effects of chlorpyrifos and parathion and their oxygen analogs on acetylcholinesterase and neuronal and glial markers in aggregating brain cell cultures. Toxicol Appl Pharmacol. 2000 Jun 15;165(3):175-83. [PubMed:10873710 ]
Bolognesi ML, Andrisano V, Bartolini M, Minarini A, Rosini M, Tumiatti V, Melchiorre C: Hexahydrochromeno[4,3-b]pyrrole derivatives as acetylcholinesterase inhibitors. J Med Chem. 2001 Jan 4;44(1):105-9. [PubMed:11141093 ]
Chen X, Ji ZL, Chen YZ: TTD: Therapeutic Target Database. Nucleic Acids Res. 2002 Jan 1;30(1):412-5. [PubMed:11752352 ]

Showing metabocard for Physostigmine (HMDB0015116)

MOL for HMDB0015116 (Physostigmine)

3D MOL for HMDB0015116 (Physostigmine)

3D SDF for HMDB0015116 (Physostigmine)

3D-SDF for HMDB0015116 (Physostigmine)

PDB for HMDB0015116 (Physostigmine)

3D PDB for HMDB0015116 (Physostigmine)

SMILES for HMDB0015116 (Physostigmine)

INCHI for HMDB0015116 (Physostigmine)

Structure for HMDB0015116 (Physostigmine)

3D Structure for HMDB0015116 (Physostigmine)

Experimental Collision Cross Sections

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

Enzymes

References