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Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References enzymes (5) Show 5 proteins XML

Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-06 15:16:52 UTC

Update Date

2022-03-07 02:52:03 UTC

HMDB ID

HMDB0015636

Secondary Accession Numbers

HMDB15636

Metabolite Identification

Common Name

Agomelatine

Description

Agomelatine is structurally closely related to melatonin. Agomelatine is a potent agonist at melatonin receptors and an antagonist at serotonin-2C (5-HT2C) receptors, tested in an animal model of depression. Agomelatine was discovered and developed by the European pharmaceutical company Servier Laboratories Ltd. Servier continue to develop the drug and conduct phase III trials in the European Union. In 2005 Servier submitted Agomelatine to the European Medicines Agency (EMEA). On 27 July 2006 the Committee for Medical Products for Human Use (CHMP) of the EMEA recommended a refusal of the marketing authorisation of Valdoxan/Thymanax. The major concern was that efficacy had not been sufficiently shown. In 2006 Servier sold the rights to develop Agomelatine in the US to Novartis. The development for the US market was discontinued in October 2011. It is currently sold in Australia under the Valdoxan trade name.

Structure

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

HMDB0015636
     RDKit          3D
Agomelatine
 35 36  0  0  0  0  0  0  0  0999 V2000
   -3.8571    3.1368   -0.6693 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6081    2.5613   -0.4073 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5148    1.1856   -0.3015 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5862    0.3526   -0.4409 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4190   -0.9955   -0.3231 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1870   -1.5425   -0.0654 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0690   -2.8924    0.0524 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8623   -3.4892    0.3173 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2285   -2.6680    0.4595 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1599   -1.2753    0.3475 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3748   -0.4477    0.4853 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9620   -0.0175   -0.8469 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1288    0.7905   -0.5706 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.2786    0.3655    0.1197 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4245    1.2654    0.3579 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3664   -0.8022    0.5578 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0823   -0.7400    0.0814 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2653    0.6240   -0.0396 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1409    3.0622   -1.7460 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6668    2.6914   -0.0845 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8031    4.2198   -0.3523 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5729    0.7418   -0.6443 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3090   -1.6338   -0.4428 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9582   -3.5001   -0.0669 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8171   -4.5629    0.4017 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1921   -3.1201    0.6697 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1078    0.4742    1.0335 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1380   -1.0410    1.0504 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2089    0.5453   -1.3931 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2260   -0.9145   -1.4657 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1134    1.7765   -0.9157 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4471    2.0867   -0.4011 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4006    1.7581    1.3505 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.3780    0.7058    0.2354 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4165    1.2994    0.0785 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
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 14 16  2  0
 10 17  1  0
 17 18  2  0
 18  3  1  0
 17  6  1  0
  1 19  1  0
  1 20  1  0
  1 21  1  0
  4 22  1  0
  5 23  1  0
  7 24  1  0
  8 25  1  0
  9 26  1  0
 11 27  1  0
 11 28  1  0
 12 29  1  0
 12 30  1  0
 13 31  1  0
 15 32  1  0
 15 33  1  0
 15 34  1  0
 18 35  1  0
M  END


  Mrv0541 02231218172D          

 18 19  0  0  0  0            999 V2000
    2.3645    0.8332    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.3649   -1.2827    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.9361   -1.2661    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.2455    0.8046    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2360   -0.0204    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5080    1.2457    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5080    2.0707    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9457   -0.4411    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9930    1.2285    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7935    0.8332    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2455    2.5118    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7935    2.4832    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9930    2.0879    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0791    1.2457    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0791    2.0707    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.6458   -1.6868    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.6362   -2.5118    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500    1.2457    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1 14  1  0  0  0  0
  1 18  1  0  0  0  0
  2 16  2  0  0  0  0
  3  8  1  0  0  0  0
  3 16  1  0  0  0  0
  4  5  1  0  0  0  0
  4  6  1  0  0  0  0
  4  9  2  0  0  0  0
  5  8  1  0  0  0  0
  6  7  2  0  0  0  0
  6 10  1  0  0  0  0
  7 11  1  0  0  0  0
  7 12  1  0  0  0  0
  9 13  1  0  0  0  0
 10 14  2  0  0  0  0
 11 13  2  0  0  0  0
 12 15  2  0  0  0  0
 14 15  1  0  0  0  0
 16 17  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0015636

> <DATABASE_NAME>
hmdb

> <SMILES>
COC1=CC2=C(C=CC=C2CCNC(C)=O)C=C1

> <INCHI_IDENTIFIER>
InChI=1S/C15H17NO2/c1-11(17)16-9-8-13-5-3-4-12-6-7-14(18-2)10-15(12)13/h3-7,10H,8-9H2,1-2H3,(H,16,17)

> <INCHI_KEY>
YJYPHIXNFHFHND-UHFFFAOYSA-N

> <FORMULA>
C15H17NO2

> <MOLECULAR_WEIGHT>
243.301

> <EXACT_MASS>
243.125928793

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_AVERAGE_POLARIZABILITY>
27.17506315193257

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
N-[2-(7-methoxynaphthalen-1-yl)ethyl]acetamide

> <ALOGPS_LOGP>
2.83

> <JCHEM_LOGP>
2.038327551

> <ALOGPS_LOGS>
-4.50

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
15.96453318039661

> <JCHEM_PKA_STRONGEST_BASIC>
-0.9409155616357626

> <JCHEM_POLAR_SURFACE_AREA>
38.33

> <JCHEM_REFRACTIVITY>
71.64360000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.76e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
agomelatine

> <JCHEM_VEBER_RULE>
1

$$$$

HMDB0015636
     RDKit          3D
Agomelatine
 35 36  0  0  0  0  0  0  0  0999 V2000
   -3.8571    3.1368   -0.6693 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6081    2.5613   -0.4073 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5148    1.1856   -0.3015 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5862    0.3526   -0.4409 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4190   -0.9955   -0.3231 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1870   -1.5425   -0.0654 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0690   -2.8924    0.0524 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8623   -3.4892    0.3173 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2285   -2.6680    0.4595 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1599   -1.2753    0.3475 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3748   -0.4477    0.4853 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9620   -0.0175   -0.8469 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1288    0.7905   -0.5706 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.2786    0.3655    0.1197 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4245    1.2654    0.3579 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3664   -0.8022    0.5578 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0823   -0.7400    0.0814 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2653    0.6240   -0.0396 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1409    3.0622   -1.7460 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6668    2.6914   -0.0845 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8031    4.2198   -0.3523 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5729    0.7418   -0.6443 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3090   -1.6338   -0.4428 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9582   -3.5001   -0.0669 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8171   -4.5629    0.4017 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1921   -3.1201    0.6697 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1078    0.4742    1.0335 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1380   -1.0410    1.0504 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2089    0.5453   -1.3931 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2260   -0.9145   -1.4657 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1134    1.7765   -0.9157 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4471    2.0867   -0.4011 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4006    1.7581    1.3505 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.3780    0.7058    0.2354 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4165    1.2994    0.0785 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
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 14 16  2  0
 10 17  1  0
 17 18  2  0
 18  3  1  0
 17  6  1  0
  1 19  1  0
  1 20  1  0
  1 21  1  0
  4 22  1  0
  5 23  1  0
  7 24  1  0
  8 25  1  0
  9 26  1  0
 11 27  1  0
 11 28  1  0
 12 29  1  0
 12 30  1  0
 13 31  1  0
 15 32  1  0
 15 33  1  0
 15 34  1  0
 18 35  1  0
M  END

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  O   UNK     0       4.414   1.555   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0      13.748  -2.394   0.000  0.00  0.00           O+0
HETATM    3  N   UNK     0      11.081  -2.363   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0       9.792   1.502   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       9.774  -0.038   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       8.415   2.325   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       8.415   3.865   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      11.099  -0.823   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      11.187   2.293   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       7.081   1.555   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       9.792   4.689   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       7.081   4.635   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      11.187   3.897   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       5.748   2.325   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       5.748   3.865   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      12.405  -3.149   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      12.388  -4.689   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       3.080   2.325   0.000  0.00  0.00           C+0
CONECT    1   14   18                                                       
CONECT    2   16                                                            
CONECT    3    8   16                                                       
CONECT    4    5    6    9                                                  
CONECT    5    4    8                                                       
CONECT    6    4    7   10                                                  
CONECT    7    6   11   12                                                  
CONECT    8    3    5                                                       
CONECT    9    4   13                                                       
CONECT   10    6   14                                                       
CONECT   11    7   13                                                       
CONECT   12    7   15                                                       
CONECT   13    9   11                                                       
CONECT   14    1   10   15                                                  
CONECT   15   12   14                                                       
CONECT   16    2    3   17                                                  
CONECT   17   16                                                            
CONECT   18    1                                                            
MASTER        0    0    0    0    0    0    0    0   18    0   38    0
END

COMPND    HMDB0015636
HETATM    1  C1  UNL     1      -3.857   3.137  -0.669  1.00  0.00           C  
HETATM    2  O1  UNL     1      -2.608   2.561  -0.407  1.00  0.00           O  
HETATM    3  C2  UNL     1      -2.515   1.186  -0.301  1.00  0.00           C  
HETATM    4  C3  UNL     1      -3.586   0.353  -0.441  1.00  0.00           C  
HETATM    5  C4  UNL     1      -3.419  -0.995  -0.323  1.00  0.00           C  
HETATM    6  C5  UNL     1      -2.187  -1.543  -0.065  1.00  0.00           C  
HETATM    7  C6  UNL     1      -2.069  -2.892   0.052  1.00  0.00           C  
HETATM    8  C7  UNL     1      -0.862  -3.489   0.317  1.00  0.00           C  
HETATM    9  C8  UNL     1       0.228  -2.668   0.460  1.00  0.00           C  
HETATM   10  C9  UNL     1       0.160  -1.275   0.347  1.00  0.00           C  
HETATM   11  C10 UNL     1       1.375  -0.448   0.485  1.00  0.00           C  
HETATM   12  C11 UNL     1       1.962  -0.017  -0.847  1.00  0.00           C  
HETATM   13  N1  UNL     1       3.129   0.791  -0.571  1.00  0.00           N  
HETATM   14  C12 UNL     1       4.279   0.365   0.120  1.00  0.00           C  
HETATM   15  C13 UNL     1       5.424   1.265   0.358  1.00  0.00           C  
HETATM   16  O2  UNL     1       4.366  -0.802   0.558  1.00  0.00           O  
HETATM   17  C14 UNL     1      -1.082  -0.740   0.081  1.00  0.00           C  
HETATM   18  C15 UNL     1      -1.265   0.624  -0.040  1.00  0.00           C  
HETATM   19  H1  UNL     1      -4.141   3.062  -1.746  1.00  0.00           H  
HETATM   20  H2  UNL     1      -4.667   2.691  -0.084  1.00  0.00           H  
HETATM   21  H3  UNL     1      -3.803   4.220  -0.352  1.00  0.00           H  
HETATM   22  H4  UNL     1      -4.573   0.742  -0.644  1.00  0.00           H  
HETATM   23  H5  UNL     1      -4.309  -1.634  -0.443  1.00  0.00           H  
HETATM   24  H6  UNL     1      -2.958  -3.500  -0.067  1.00  0.00           H  
HETATM   25  H7  UNL     1      -0.817  -4.563   0.402  1.00  0.00           H  
HETATM   26  H8  UNL     1       1.192  -3.120   0.670  1.00  0.00           H  
HETATM   27  H9  UNL     1       1.108   0.474   1.034  1.00  0.00           H  
HETATM   28  H10 UNL     1       2.138  -1.041   1.050  1.00  0.00           H  
HETATM   29  H11 UNL     1       1.209   0.545  -1.393  1.00  0.00           H  
HETATM   30  H12 UNL     1       2.226  -0.914  -1.466  1.00  0.00           H  
HETATM   31  H13 UNL     1       3.113   1.777  -0.916  1.00  0.00           H  
HETATM   32  H14 UNL     1       5.447   2.087  -0.401  1.00  0.00           H  
HETATM   33  H15 UNL     1       5.401   1.758   1.350  1.00  0.00           H  
HETATM   34  H16 UNL     1       6.378   0.706   0.235  1.00  0.00           H  
HETATM   35  H17 UNL     1      -0.416   1.299   0.078  1.00  0.00           H  
CONECT    1    2   19   20   21
CONECT    2    3
CONECT    3    4    4   18
CONECT    4    5   22
CONECT    5    6    6   23
CONECT    6    7   17
CONECT    7    8    8   24
CONECT    8    9   25
CONECT    9   10   10   26
CONECT   10   11   17
CONECT   11   12   27   28
CONECT   12   13   29   30
CONECT   13   14   31
CONECT   14   15   16   16
CONECT   15   32   33   34
CONECT   17   18   18
CONECT   18   35
END

HMDB0015636
     RDKit          3D
Agomelatine
 35 36  0  0  0  0  0  0  0  0999 V2000
   -3.8571    3.1368   -0.6693 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6081    2.5613   -0.4073 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5148    1.1856   -0.3015 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5862    0.3526   -0.4409 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4190   -0.9955   -0.3231 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1870   -1.5425   -0.0654 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0690   -2.8924    0.0524 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8623   -3.4892    0.3173 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2285   -2.6680    0.4595 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1599   -1.2753    0.3475 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3748   -0.4477    0.4853 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9620   -0.0175   -0.8469 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1288    0.7905   -0.5706 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.2786    0.3655    0.1197 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4245    1.2654    0.3579 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3664   -0.8022    0.5578 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0823   -0.7400    0.0814 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2653    0.6240   -0.0396 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1409    3.0622   -1.7460 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6668    2.6914   -0.0845 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8031    4.2198   -0.3523 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5729    0.7418   -0.6443 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3090   -1.6338   -0.4428 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9582   -3.5001   -0.0669 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8171   -4.5629    0.4017 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1921   -3.1201    0.6697 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1078    0.4742    1.0335 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1380   -1.0410    1.0504 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2089    0.5453   -1.3931 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2260   -0.9145   -1.4657 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1134    1.7765   -0.9157 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4471    2.0867   -0.4011 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4006    1.7581    1.3505 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.3780    0.7058    0.2354 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4165    1.2994    0.0785 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
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 14 16  2  0
 10 17  1  0
 17 18  2  0
 18  3  1  0
 17  6  1  0
  1 19  1  0
  1 20  1  0
  1 21  1  0
  4 22  1  0
  5 23  1  0
  7 24  1  0
  8 25  1  0
  9 26  1  0
 11 27  1  0
 11 28  1  0
 12 29  1  0
 12 30  1  0
 13 31  1  0
 15 32  1  0
 15 33  1  0
 15 34  1  0
 18 35  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
Valdoxan	Kegg
S-20098	HMDB
S20098	HMDB
N-(2-(7-Methoxy-1-naphthyl)ethyl)acetamide	HMDB
Thymanax	HMDB
Ago 178	HMDB
Ago-178	HMDB

Chemical Formula

C₁₅H₁₇NO₂

Average Molecular Weight

243.301

Monoisotopic Molecular Weight

243.125928793

IUPAC Name

N-[2-(7-methoxynaphthalen-1-yl)ethyl]acetamide

Traditional Name

agomelatine

CAS Registry Number

138112-76-2

SMILES

COC1=CC2=C(C=CC=C2CCNC(C)=O)C=C1

InChI Identifier

InChI=1S/C15H17NO2/c1-11(17)16-9-8-13-5-3-4-12-6-7-14(18-2)10-15(12)13/h3-7,10H,8-9H2,1-2H3,(H,16,17)

InChI Key

YJYPHIXNFHFHND-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as n-acetyl-2-arylethylamines. N-acetyl-2-arylethylamines are compounds containing an acetamide group that is N-linked to an arylethylamine.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Carboxylic acid derivatives

Direct Parent

N-acetyl-2-arylethylamines

Alternative Parents

Substituents

N-acetyl-2-arylethylamine
Naphthalene
Anisole
Alkyl aryl ether
Benzenoid
Secondary carboxylic acid amide
Ether
Organic oxide
Organooxygen compound
Organonitrogen compound
Organopnictogen compound
Organic nitrogen compound
Carbonyl group
Organic oxygen compound
Hydrocarbon derivative
Aromatic homopolycyclic compound

Molecular Framework

Aromatic homopolycyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 21059682)

Excreta

Biofluid or Excreta

Urine (PMID: 21059682)

Cellular substructure

Membrane (HMDB: HMDB0015636)

Source

Exogenous

Exogenous (HMDB: HMDB0015636)

Process

Not Available

Role

Not Available

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	0.0078 g/L	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Experimental Collision Cross Sections

Adduct Type	Data Source	CCS Value (Å²)	Reference
[M+H]+	CBM	156.3	30932474

Predicted Molecular Properties

Property	Value	Source
Water Solubility	0.0078 g/L	ALOGPS
logP	2.83	ALOGPS
logP	2.04	ChemAxon
logS	-4.5	ALOGPS
pKa (Strongest Acidic)	15.96	ChemAxon
pKa (Strongest Basic)	-0.94	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	38.33 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	71.64 m³·mol⁻¹	ChemAxon
Polarizability	27.18 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DarkChem	[M+H]+	156.622	31661259
DarkChem	[M-H]-	155.562	31661259
DeepCCS	[M+H]+	160.301	30932474
DeepCCS	[M-H]-	157.943	30932474
DeepCCS	[M-2H]-	190.83	30932474
DeepCCS	[M+Na]+	166.394	30932474
AllCCS	[M+H]+	156.2	32859911
AllCCS	[M+H-H2O]+	152.4	32859911
AllCCS	[M+NH4]+	159.8	32859911
AllCCS	[M+Na]+	160.8	32859911
AllCCS	[M-H]-	161.7	32859911
AllCCS	[M+Na-2H]-	161.7	32859911
AllCCS	[M+HCOO]-	161.8	32859911

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022. Predicted by Afia on May 17, 2022.	6.71 minutes	32390414
Predicted by Siyang on May 30, 2022	13.308 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	1.73 minutes	32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid	25.5 seconds	40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	1770.6 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	364.9 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	176.8 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	202.2 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	113.6 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	553.5 seconds	40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid	595.1 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	86.0 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	972.3 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	519.2 seconds	40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid	1453.5 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	320.4 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	378.9 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	317.5 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	194.8 seconds	40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water	8.0 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Agomelatine	COC1=CC2=C(C=CC=C2CCNC(C)=O)C=C1	3342.0	Standard polar	33892256
Agomelatine	COC1=CC2=C(C=CC=C2CCNC(C)=O)C=C1	2233.0	Standard non polar	33892256
Agomelatine	COC1=CC2=C(C=CC=C2CCNC(C)=O)C=C1	2332.7	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Agomelatine,1TMS,isomer #1	COC1=CC=C2C=CC=C(CCN(C(C)=O)[Si](C)(C)C)C2=C1	2210.6	Semi standard non polar	33892256
Agomelatine,1TMS,isomer #1	COC1=CC=C2C=CC=C(CCN(C(C)=O)[Si](C)(C)C)C2=C1	2477.3	Standard non polar	33892256
Agomelatine,1TMS,isomer #1	COC1=CC=C2C=CC=C(CCN(C(C)=O)[Si](C)(C)C)C2=C1	2924.4	Standard polar	33892256
Agomelatine,1TBDMS,isomer #1	COC1=CC=C2C=CC=C(CCN(C(C)=O)[Si](C)(C)C(C)(C)C)C2=C1	2417.0	Semi standard non polar	33892256
Agomelatine,1TBDMS,isomer #1	COC1=CC=C2C=CC=C(CCN(C(C)=O)[Si](C)(C)C(C)(C)C)C2=C1	2670.0	Standard non polar	33892256
Agomelatine,1TBDMS,isomer #1	COC1=CC=C2C=CC=C(CCN(C(C)=O)[Si](C)(C)C(C)(C)C)C2=C1	2987.6	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - Agomelatine GC-MS (Non-derivatized) - 70eV, Positive	splash10-0096-9870000000-12644f5c2eef8ac161ff	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Agomelatine 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 - Agomelatine , positive-QTOF	splash10-000i-1910000000-17cebfbe6b9845617b5d	2017-09-14	HMDB team, MONA	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Agomelatine 10V, Positive-QTOF	splash10-0udl-0290000000-2f32e7333df35f0d31e0	2016-06-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Agomelatine 20V, Positive-QTOF	splash10-0udi-1890000000-f8670d6acc856a2aef34	2016-06-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Agomelatine 40V, Positive-QTOF	splash10-103c-1900000000-44f5e0bbe33a080e259b	2016-06-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Agomelatine 10V, Negative-QTOF	splash10-0006-1190000000-60e7560fd8d53fc46465	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Agomelatine 20V, Negative-QTOF	splash10-0zfu-3590000000-b1f2b056df1b588a9894	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Agomelatine 40V, Negative-QTOF	splash10-052f-9200000000-7d7eb2751fc51b48fda4	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Agomelatine 10V, Positive-QTOF	splash10-000l-0960000000-1b1a339607ebe3d5742f	2021-10-11	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Agomelatine 20V, Positive-QTOF	splash10-000i-0900000000-84ce72fe2cc1bb7fae00	2021-10-11	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Agomelatine 40V, Positive-QTOF	splash10-0a4i-1900000000-0471137531ade7533965	2021-10-11	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Agomelatine 10V, Negative-QTOF	splash10-00di-0910000000-64f66595ca495c9bd240	2021-10-11	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Agomelatine 20V, Negative-QTOF	splash10-0a4i-1900000000-5cf1d78282a06e7b1962	2021-10-11	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Agomelatine 40V, Negative-QTOF	splash10-0a4l-5900000000-9ed4ac12ad0427b40af3	2021-10-11	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Membrane

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 DB06594	21059682	details
Urine	Expected but not Quantified	Not Quantified	Not Available	Not Available	Taking drug identified by DrugBank entry DB06594	21059682	details

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

DB06594

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

74141

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Agomelatine

METLIN ID

Not Available

PubChem Compound

82148

PDB ID

Not Available

ChEBI ID

108209

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

Millan MJ, Brocco M, Gobert A, Dekeyne A: Anxiolytic properties of agomelatine, an antidepressant with melatoninergic and serotonergic properties: role of 5-HT2C receptor blockade. Psychopharmacology (Berl). 2005 Feb;177(4):448-58. Epub 2004 Jul 31. [PubMed:15289999 ]
Racagni G, Riva MA, Popoli M: The interaction between the internal clock and antidepressant efficacy. Int Clin Psychopharmacol. 2007 Oct;22 Suppl 2:S9-S14. [PubMed:17917564 ]
Hardeland R, Poeggeler B, Srinivasan V, Trakht I, Pandi-Perumal SR, Cardinali DP: Melatonergic drugs in clinical practice. Arzneimittelforschung. 2008;58(1):1-10. doi: 10.1055/s-0031-1296459. [PubMed:18368944 ]

Enzymes

Enzyme Details

1. Cytochrome P450 2C9

General function:: Involved in monooxygenase activity
Specific function:: Cytochromes P450 are a group of heme-thiolate monooxygenases. In liver microsomes, this enzyme is involved in an NADPH-dependent electron transport pathway. It oxidizes a variety of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics. This enzyme contributes to the wide pharmacokinetics variability of the metabolism of drugs such as S-warfarin, diclofenac, phenytoin, tolbutamide and losartan.
Gene Name:: CYP2C9
Uniprot ID:: P11712
Molecular weight:: 55627.365

References

Dolder CR, Nelson M, Snider M: Agomelatine treatment of major depressive disorder. Ann Pharmacother. 2008 Dec;42(12):1822-31. doi: 10.1345/aph.1L296. Epub 2008 Nov 25. [PubMed:19033480 ]

Enzyme Details

2. Cytochrome P450 1A2

General function:: Involved in monooxygenase activity
Specific function:: Cytochromes P450 are a group of heme-thiolate monooxygenases. In liver microsomes, this enzyme is involved in an NADPH-dependent electron transport pathway. It oxidizes a variety of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics. Most active in catalyzing 2-hydroxylation. Caffeine is metabolized primarily by cytochrome CYP1A2 in the liver through an initial N3-demethylation. Also acts in the metabolism of aflatoxin B1 and acetaminophen. Participates in the bioactivation of carcinogenic aromatic and heterocyclic amines. Catalizes the N-hydroxylation of heterocyclic amines and the O-deethylation of phenacetin.
Gene Name:: CYP1A2
Uniprot ID:: P05177
Molecular weight:: 58406.915

References

Carney RM, Shelton RC: Agomelatine for the treatment of major depressive disorder. Expert Opin Pharmacother. 2011 Oct;12(15):2411-9. doi: 10.1517/14656566.2011.607812. [PubMed:21916789 ]

Enzyme Details

3. 5-hydroxytryptamine receptor 2C

General function:: Involved in G-protein coupled receptor protein signaling pathway
Specific function:: This is one of the several different receptors for 5- hydroxytryptamine (serotonin), a biogenic hormone that functions as a neurotransmitter, a hormone, and a mitogen. This receptor mediates its action by association with G proteins that activate a phosphatidylinositol-calcium second messenger system
Gene Name:: HTR2C
Uniprot ID:: P28335
Molecular weight:: 51820.7

References

Millan MJ, Brocco M, Gobert A, Dekeyne A: Anxiolytic properties of agomelatine, an antidepressant with melatoninergic and serotonergic properties: role of 5-HT2C receptor blockade. Psychopharmacology (Berl). 2005 Feb;177(4):448-58. Epub 2004 Jul 31. [PubMed:15289999 ]

Enzyme Details

4. Melatonin receptor type 1A

General function:: Involved in G-protein coupled receptor protein signaling pathway
Specific function:: High affinity receptor for melatonin. Likely to mediates the reproductive and circadian actions of melatonin. The activity of this receptor is mediated by pertussis toxin sensitive G proteins that inhibit adenylate cyclase activity
Gene Name:: MTNR1A
Uniprot ID:: P48039
Molecular weight:: 39374.3

References

Millan MJ, Brocco M, Gobert A, Dekeyne A: Anxiolytic properties of agomelatine, an antidepressant with melatoninergic and serotonergic properties: role of 5-HT2C receptor blockade. Psychopharmacology (Berl). 2005 Feb;177(4):448-58. Epub 2004 Jul 31. [PubMed:15289999 ]

Enzyme Details

5. Melatonin receptor type 1B

General function:: Involved in G-protein coupled receptor protein signaling pathway
Specific function:: High affinity receptor for melatonin. Likely to mediates the reproductive and circadian actions of melatonin. The activity of this receptor is mediated by pertussis toxin sensitive G proteins that inhibit adenylate cyclase activity
Gene Name:: MTNR1B
Uniprot ID:: P49286
Molecular weight:: 40187.9

References

Millan MJ, Brocco M, Gobert A, Dekeyne A: Anxiolytic properties of agomelatine, an antidepressant with melatoninergic and serotonergic properties: role of 5-HT2C receptor blockade. Psychopharmacology (Berl). 2005 Feb;177(4):448-58. Epub 2004 Jul 31. [PubMed:15289999 ]

Showing metabocard for Agomelatine (HMDB0015636)

MOL for HMDB0015636 (Agomelatine)

3D MOL for HMDB0015636 (Agomelatine)

3D SDF for HMDB0015636 (Agomelatine)

3D-SDF for HMDB0015636 (Agomelatine)

PDB for HMDB0015636 (Agomelatine)

3D PDB for HMDB0015636 (Agomelatine)

SMILES for HMDB0015636 (Agomelatine)

INCHI for HMDB0015636 (Agomelatine)

Structure for HMDB0015636 (Agomelatine)

3D Structure for HMDB0015636 (Agomelatine)

Experimental Collision Cross Sections

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

Enzymes

References

References

References

References

References