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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-06 15:00:36 UTC

Update Date

2021-09-14 14:57:58 UTC

HMDB ID

HMDB0013960

Secondary Accession Numbers

HMDB13960

Metabolite Identification

Common Name

Donepezil metabolite M4

Description

Donepezil metabolite M4 is a metabolite of Donepezil. Donepezil, marketed under the trade name Aricept by its developer Eisai and partner Pfizer, and also marketed under the brand name DONEP by Alkem Pentacare, is a centrally acting reversible acetylcholinesterase inhibitor. Its main therapeutic use is in the palliative treatment of Alzheimer's disease. Common side effects include gastrointestinal upset. It has an oral bioavailability of 100% and easily crosses the blood–brain barrier. Because it has a biological half-life of about 70 hours, it can be taken once a day. (Wikipedia)

Structure

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

HMDB0013960
     RDKit          3D
Donepezil metabolite M4
 44 46  0  0  0  0  0  0  0  0999 V2000
    5.3203   -0.3283    1.8315 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8993    0.3023    0.6468 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6579   -0.0128    0.1188 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8029   -0.9239    0.7019 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5696   -1.2332    0.1723 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1918   -0.5970   -0.9868 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0602    0.3295   -1.5804 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2935    0.6334   -1.0434 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1064    1.5497   -1.6659 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8321    2.2459   -2.8260 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1324   -1.0925   -1.3348 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6285   -1.0523   -2.4881 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7602   -1.6362   -0.1013 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2822   -0.4786    0.6916 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3166    0.3257   -0.0769 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8275    1.4787    0.7307 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9423    0.9712    1.6293 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1328    0.6339    0.9027 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7502    0.1879   -0.4264 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4862   -0.6200   -0.3331 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4793   -2.1739    0.6165 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2787    0.0856    2.1969 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5946   -0.2001    2.6678 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4596   -1.4052    1.6936 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1101   -1.4291    1.6278 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7179    0.8119   -2.5029 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7420    2.5448   -2.8120 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3757    3.2070   -2.9273 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9593    1.5844   -3.6964 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4921   -2.4173   -0.2995 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6757   -0.8272    1.6642 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4417    0.2107    0.9146 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8804    0.6503   -1.0224 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2488    2.2699    0.0806 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0467    1.9086    1.3996 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1928    1.7416    2.3994 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5778    0.0713    2.1921 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6665   -0.0951    1.4164 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5559   -0.4343   -0.8856 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5818    1.0431   -1.0864 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2692   -1.1916   -1.2391 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5815   -1.3588    0.5022 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2967   -2.0904    1.7080 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7218   -3.1896    0.2992 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  1  0
  6 11  1  0
 11 12  2  0
 11 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
 17 18  1  0
 18 19  1  0
 19 20  1  0
 13 21  1  0
  8  3  1  0
 20 15  1  0
 21  5  1  0
  1 22  1  0
  1 23  1  0
  1 24  1  0
  4 25  1  0
  7 26  1  0
 10 27  1  0
 10 28  1  0
 10 29  1  0
 13 30  1  0
 14 31  1  0
 14 32  1  0
 15 33  1  0
 16 34  1  0
 16 35  1  0
 17 36  1  0
 17 37  1  0
 18 38  1  0
 19 39  1  0
 19 40  1  0
 20 41  1  0
 20 42  1  0
 21 43  1  0
 21 44  1  0
M  END


  Mrv0541 09051309132D          

 21 23  0  0  0  0            999 V2000
    8.9576   -2.1277    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7771   -4.4008    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7771   -2.7508    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.2453   -5.7193    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   10.4203   -4.2903    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.0077   -3.5758    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.1827   -3.5758    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.2453   -4.2903    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.0077   -5.0048    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.6578   -5.0048    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.4203   -5.7193    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.7013   -4.2397    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.7013   -2.9119    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.9206   -3.9883    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.9206   -3.1632    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2063   -4.4008    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2063   -2.7508    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4916   -3.9883    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4916   -3.1632    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7771   -5.2258    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7771   -1.9257    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1 13  2  0  0  0  0
  2 18  1  0  0  0  0
  2 20  1  0  0  0  0
  3 19  1  0  0  0  0
  3 21  1  0  0  0  0
  4 10  1  0  0  0  0
  4 11  1  0  0  0  0
  5  6  1  0  0  0  0
  5  8  1  0  0  0  0
  5  9  1  0  0  0  0
  6  7  1  0  0  0  0
  7 12  1  0  0  0  0
  7 13  1  0  0  0  0
  8 10  1  0  0  0  0
  9 11  1  0  0  0  0
 12 14  1  0  0  0  0
 13 15  1  0  0  0  0
 14 15  1  0  0  0  0
 14 16  2  0  0  0  0
 15 17  2  0  0  0  0
 16 18  1  0  0  0  0
 17 19  1  0  0  0  0
 18 19  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0013960

> <DATABASE_NAME>
hmdb

> <SMILES>
COC1=C(OC)C=C2C(=O)C(CC3CCNCC3)CC2=C1

> <INCHI_IDENTIFIER>
InChI=1S/C17H23NO3/c1-20-15-9-12-8-13(7-11-3-5-18-6-4-11)17(19)14(12)10-16(15)21-2/h9-11,13,18H,3-8H2,1-2H3

> <INCHI_KEY>
PGBZORAISITZTF-UHFFFAOYSA-N

> <FORMULA>
C17H23NO3

> <MOLECULAR_WEIGHT>
289.3694

> <EXACT_MASS>
289.167793607

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
33.038626809250125

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
5,6-dimethoxy-2-(piperidin-4-ylmethyl)-2,3-dihydro-1H-inden-1-one

> <ALOGPS_LOGP>
2.49

> <JCHEM_LOGP>
2.1004119390000002

> <ALOGPS_LOGS>
-3.94

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_ACIDIC>
17.022167987203105

> <JCHEM_PKA_STRONGEST_BASIC>
10.255884327075243

> <JCHEM_POLAR_SURFACE_AREA>
47.56

> <JCHEM_REFRACTIVITY>
82.2074

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.32e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5,6-dimethoxy-2-(piperidin-4-ylmethyl)-2,3-dihydroinden-1-one

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0013960
     RDKit          3D
Donepezil metabolite M4
 44 46  0  0  0  0  0  0  0  0999 V2000
    5.3203   -0.3283    1.8315 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8993    0.3023    0.6468 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6579   -0.0128    0.1188 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8029   -0.9239    0.7019 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5696   -1.2332    0.1723 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1918   -0.5970   -0.9868 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0602    0.3295   -1.5804 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2935    0.6334   -1.0434 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1064    1.5497   -1.6659 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8321    2.2459   -2.8260 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1324   -1.0925   -1.3348 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6285   -1.0523   -2.4881 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7602   -1.6362   -0.1013 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2822   -0.4786    0.6916 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3166    0.3257   -0.0769 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8275    1.4787    0.7307 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9423    0.9712    1.6293 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1328    0.6339    0.9027 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7502    0.1879   -0.4264 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4862   -0.6200   -0.3331 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4793   -2.1739    0.6165 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2787    0.0856    2.1969 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5946   -0.2001    2.6678 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4596   -1.4052    1.6936 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1101   -1.4291    1.6278 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7179    0.8119   -2.5029 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7420    2.5448   -2.8120 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3757    3.2070   -2.9273 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9593    1.5844   -3.6964 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4921   -2.4173   -0.2995 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6757   -0.8272    1.6642 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4417    0.2107    0.9146 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8804    0.6503   -1.0224 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2488    2.2699    0.0806 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0467    1.9086    1.3996 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1928    1.7416    2.3994 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5778    0.0713    2.1921 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6665   -0.0951    1.4164 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5559   -0.4343   -0.8856 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5818    1.0431   -1.0864 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2692   -1.1916   -1.2391 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5815   -1.3588    0.5022 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2967   -2.0904    1.7080 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7218   -3.1896    0.2992 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  1  0
  6 11  1  0
 11 12  2  0
 11 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
 17 18  1  0
 18 19  1  0
 19 20  1  0
 13 21  1  0
  8  3  1  0
 20 15  1  0
 21  5  1  0
  1 22  1  0
  1 23  1  0
  1 24  1  0
  4 25  1  0
  7 26  1  0
 10 27  1  0
 10 28  1  0
 10 29  1  0
 13 30  1  0
 14 31  1  0
 14 32  1  0
 15 33  1  0
 16 34  1  0
 16 35  1  0
 17 36  1  0
 17 37  1  0
 18 38  1  0
 19 39  1  0
 19 40  1  0
 20 41  1  0
 20 42  1  0
 21 43  1  0
 21 44  1  0
M  END

HEADER    PROTEIN                                 05-SEP-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   05-SEP-13         0                                  
HETATM    1  O   UNK     0      16.721  -3.972   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0      10.784  -8.215   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      10.784  -5.135   0.000  0.00  0.00           O+0
HETATM    4  N   UNK     0      20.991 -10.676   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0      19.451  -8.009   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      18.681  -6.675   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      17.141  -6.675   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      20.991  -8.009   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      18.681  -9.342   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      21.761  -9.342   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      19.451 -10.676   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      16.242  -7.914   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      16.242  -5.436   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      14.785  -7.445   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      14.785  -5.905   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      13.452  -8.215   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      13.452  -5.135   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      12.118  -7.445   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      12.118  -5.905   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      10.784  -9.755   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      10.784  -3.595   0.000  0.00  0.00           C+0
CONECT    1   13                                                            
CONECT    2   18   20                                                       
CONECT    3   19   21                                                       
CONECT    4   10   11                                                       
CONECT    5    6    8    9                                                  
CONECT    6    5    7                                                       
CONECT    7    6   12   13                                                  
CONECT    8    5   10                                                       
CONECT    9    5   11                                                       
CONECT   10    4    8                                                       
CONECT   11    4    9                                                       
CONECT   12    7   14                                                       
CONECT   13    1    7   15                                                  
CONECT   14   12   15   16                                                  
CONECT   15   13   14   17                                                  
CONECT   16   14   18                                                       
CONECT   17   15   19                                                       
CONECT   18    2   16   19                                                  
CONECT   19    3   17   18                                                  
CONECT   20    2                                                            
CONECT   21    3                                                            
MASTER        0    0    0    0    0    0    0    0   21    0   46    0
END

COMPND    HMDB0013960
HETATM    1  C1  UNL     1       5.320  -0.328   1.831  1.00  0.00           C  
HETATM    2  O1  UNL     1       4.899   0.302   0.647  1.00  0.00           O  
HETATM    3  C2  UNL     1       3.658  -0.013   0.119  1.00  0.00           C  
HETATM    4  C3  UNL     1       2.803  -0.924   0.702  1.00  0.00           C  
HETATM    5  C4  UNL     1       1.570  -1.233   0.172  1.00  0.00           C  
HETATM    6  C5  UNL     1       1.192  -0.597  -0.987  1.00  0.00           C  
HETATM    7  C6  UNL     1       2.060   0.330  -1.580  1.00  0.00           C  
HETATM    8  C7  UNL     1       3.293   0.633  -1.043  1.00  0.00           C  
HETATM    9  O2  UNL     1       4.106   1.550  -1.666  1.00  0.00           O  
HETATM   10  C8  UNL     1       3.832   2.246  -2.826  1.00  0.00           C  
HETATM   11  C9  UNL     1      -0.132  -1.093  -1.335  1.00  0.00           C  
HETATM   12  O3  UNL     1      -0.628  -1.052  -2.488  1.00  0.00           O  
HETATM   13  C10 UNL     1      -0.760  -1.636  -0.101  1.00  0.00           C  
HETATM   14  C11 UNL     1      -1.282  -0.479   0.692  1.00  0.00           C  
HETATM   15  C12 UNL     1      -2.317   0.326  -0.077  1.00  0.00           C  
HETATM   16  C13 UNL     1      -2.828   1.479   0.731  1.00  0.00           C  
HETATM   17  C14 UNL     1      -3.942   0.971   1.629  1.00  0.00           C  
HETATM   18  N1  UNL     1      -5.133   0.634   0.903  1.00  0.00           N  
HETATM   19  C15 UNL     1      -4.750   0.188  -0.426  1.00  0.00           C  
HETATM   20  C16 UNL     1      -3.486  -0.620  -0.333  1.00  0.00           C  
HETATM   21  C17 UNL     1       0.479  -2.174   0.617  1.00  0.00           C  
HETATM   22  H1  UNL     1       6.279   0.086   2.197  1.00  0.00           H  
HETATM   23  H2  UNL     1       4.595  -0.200   2.668  1.00  0.00           H  
HETATM   24  H3  UNL     1       5.460  -1.405   1.694  1.00  0.00           H  
HETATM   25  H4  UNL     1       3.110  -1.429   1.628  1.00  0.00           H  
HETATM   26  H5  UNL     1       1.718   0.812  -2.503  1.00  0.00           H  
HETATM   27  H6  UNL     1       2.742   2.545  -2.812  1.00  0.00           H  
HETATM   28  H7  UNL     1       4.376   3.207  -2.927  1.00  0.00           H  
HETATM   29  H8  UNL     1       3.959   1.584  -3.696  1.00  0.00           H  
HETATM   30  H9  UNL     1      -1.492  -2.417  -0.300  1.00  0.00           H  
HETATM   31  H10 UNL     1      -1.676  -0.827   1.664  1.00  0.00           H  
HETATM   32  H11 UNL     1      -0.442   0.211   0.915  1.00  0.00           H  
HETATM   33  H12 UNL     1      -1.880   0.650  -1.022  1.00  0.00           H  
HETATM   34  H13 UNL     1      -3.249   2.270   0.081  1.00  0.00           H  
HETATM   35  H14 UNL     1      -2.047   1.909   1.400  1.00  0.00           H  
HETATM   36  H15 UNL     1      -4.193   1.742   2.399  1.00  0.00           H  
HETATM   37  H16 UNL     1      -3.578   0.071   2.192  1.00  0.00           H  
HETATM   38  H17 UNL     1      -5.667  -0.095   1.416  1.00  0.00           H  
HETATM   39  H18 UNL     1      -5.556  -0.434  -0.886  1.00  0.00           H  
HETATM   40  H19 UNL     1      -4.582   1.043  -1.086  1.00  0.00           H  
HETATM   41  H20 UNL     1      -3.269  -1.192  -1.239  1.00  0.00           H  
HETATM   42  H21 UNL     1      -3.581  -1.359   0.502  1.00  0.00           H  
HETATM   43  H22 UNL     1       0.297  -2.090   1.708  1.00  0.00           H  
HETATM   44  H23 UNL     1       0.722  -3.190   0.299  1.00  0.00           H  
CONECT    1    2   22   23   24
CONECT    2    3
CONECT    3    4    4    8
CONECT    4    5   25
CONECT    5    6    6   21
CONECT    6    7   11
CONECT    7    8    8   26
CONECT    8    9
CONECT    9   10
CONECT   10   27   28   29
CONECT   11   12   12   13
CONECT   13   14   21   30
CONECT   14   15   31   32
CONECT   15   16   20   33
CONECT   16   17   34   35
CONECT   17   18   36   37
CONECT   18   19   38
CONECT   19   20   39   40
CONECT   20   41   42
CONECT   21   43   44
END

HMDB0013960
     RDKit          3D
Donepezil metabolite M4
 44 46  0  0  0  0  0  0  0  0999 V2000
    5.3203   -0.3283    1.8315 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8993    0.3023    0.6468 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6579   -0.0128    0.1188 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8029   -0.9239    0.7019 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5696   -1.2332    0.1723 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1918   -0.5970   -0.9868 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0602    0.3295   -1.5804 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2935    0.6334   -1.0434 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1064    1.5497   -1.6659 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8321    2.2459   -2.8260 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1324   -1.0925   -1.3348 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6285   -1.0523   -2.4881 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7602   -1.6362   -0.1013 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2822   -0.4786    0.6916 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3166    0.3257   -0.0769 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8275    1.4787    0.7307 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9423    0.9712    1.6293 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1328    0.6339    0.9027 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7502    0.1879   -0.4264 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4862   -0.6200   -0.3331 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4793   -2.1739    0.6165 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2787    0.0856    2.1969 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5946   -0.2001    2.6678 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4596   -1.4052    1.6936 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1101   -1.4291    1.6278 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7179    0.8119   -2.5029 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7420    2.5448   -2.8120 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3757    3.2070   -2.9273 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9593    1.5844   -3.6964 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4921   -2.4173   -0.2995 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6757   -0.8272    1.6642 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4417    0.2107    0.9146 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8804    0.6503   -1.0224 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2488    2.2699    0.0806 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0467    1.9086    1.3996 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1928    1.7416    2.3994 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5778    0.0713    2.1921 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6665   -0.0951    1.4164 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5559   -0.4343   -0.8856 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5818    1.0431   -1.0864 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2692   -1.1916   -1.2391 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5815   -1.3588    0.5022 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2967   -2.0904    1.7080 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7218   -3.1896    0.2992 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  1  0
  6 11  1  0
 11 12  2  0
 11 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
 17 18  1  0
 18 19  1  0
 19 20  1  0
 13 21  1  0
  8  3  1  0
 20 15  1  0
 21  5  1  0
  1 22  1  0
  1 23  1  0
  1 24  1  0
  4 25  1  0
  7 26  1  0
 10 27  1  0
 10 28  1  0
 10 29  1  0
 13 30  1  0
 14 31  1  0
 14 32  1  0
 15 33  1  0
 16 34  1  0
 16 35  1  0
 17 36  1  0
 17 37  1  0
 18 38  1  0
 19 39  1  0
 19 40  1  0
 20 41  1  0
 20 42  1  0
 21 43  1  0
 21 44  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
(2S,3R,4E)-2-Alkanamido-3-hydroxyoctadec-4-en-1-yl 3-O-(5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranonosyl)-beta-D-galactopyranoside	HMDB
(2S,3R,4E)-2-Alkanamido-3-hydroxyoctadec-4-en-1-yl 5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranonosyl-(2Right3)-beta-D-galactopyranoside	HMDB
(Acetyloxy)(tributyl)stannane (acd/name 4.0)	HMDB
(Acetyloxy)tributyl-stannane	HMDB
(Gal)1 (neu5ac)1 (cer)1	HMDB
Acetoxytributyl-stannane	HMDB
Acetoxytributyl-tin	HMDB
Acetoxytributylstannane	HMDB
Acetoxytributyltin	HMDB
alpha-Neu5ac-(2Right3)-beta-D-gal-(1leftright1')-cer	HMDB
alpha-Neup5ac-(2Right3)-beta-D-galp-(1leftright1')-cer	HMDB
Ganglioside GM4	HMDB
GM4	HMDB
N-Acetyl-alpha-neuraminosyl-(2Right3)-beta-D-galactosylceramides	HMDB
N-Acetylneuraminyl-galactosylceramide	HMDB
Neu5ac-alpha2->3gal-beta1->1'cer	HMDB
Neu5ac-gal-beta1->1'cer	HMDB
NeuAcalpha2-3galbeta-cer	HMDB
TBTA	HMDB
Tin, tributyl-, acetate	HMDB
Tri-N-butyltin acetate	HMDB
Tributylacetoxystannane	HMDB
Tributylstannyl acetate	HMDB
Tributyltin acetate	HMDB
Tribuyltin acetate	HMDB

Chemical Formula

C₁₇H₂₃NO₃

Average Molecular Weight

289.3694

Monoisotopic Molecular Weight

289.167793607

IUPAC Name

5,6-dimethoxy-2-(piperidin-4-ylmethyl)-2,3-dihydro-1H-inden-1-one

Traditional Name

5,6-dimethoxy-2-(piperidin-4-ylmethyl)-2,3-dihydroinden-1-one

CAS Registry Number

56-36-0

SMILES

COC1=C(OC)C=C2C(=O)C(CC3CCNCC3)CC2=C1

InChI Identifier

InChI=1S/C17H23NO3/c1-20-15-9-12-8-13(7-11-3-5-18-6-4-11)17(19)14(12)10-16(15)21-2/h9-11,13,18H,3-8H2,1-2H3

InChI Key

PGBZORAISITZTF-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as indanones. Indanones are compounds containing an indane ring bearing a ketone group.

Kingdom

Super Class

Class

Sub Class

Direct Parent

Alternative Parents

Substituents

Indanone
Anisole
Aryl ketone
Aryl alkyl ketone
Alkyl aryl ether
Aralkylamine
Piperidine
Ketone
Secondary aliphatic amine
Ether
Secondary amine
Azacycle
Organoheterocyclic compound
Organonitrogen compound
Organic oxide
Organopnictogen compound
Amine
Organooxygen compound
Hydrocarbon derivative
Organic oxygen compound
Organic nitrogen compound
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: 21059682)

Organ

Liver (HMDB: HMDB0013960)
Kidney (HMDB: HMDB0013960)

Excreta

Biofluid or Excreta

Urine (PMID: 21059682)

Cellular substructure

Extracellular (HMDB: HMDB0013960)

Source

Endogenous

Endogenous (HMDB: HMDB0013960)

Process

Not Available

Role

Not Available

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	84.7 °C	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	0.065 mg/mL	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	0.033 g/L	ALOGPS
logP	2.49	ALOGPS
logP	2.1	ChemAxon
logS	-3.9	ALOGPS
pKa (Strongest Acidic)	17.02	ChemAxon
pKa (Strongest Basic)	10.26	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	47.56 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	82.21 m³·mol⁻¹	ChemAxon
Polarizability	33.04 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]+	167.596	31661259
DarkChem	[M-H]-	169.355	31661259
DeepCCS	[M+H]+	170.167	30932474
DeepCCS	[M-H]-	167.809	30932474
DeepCCS	[M-2H]-	200.696	30932474
DeepCCS	[M+Na]+	176.261	30932474
AllCCS	[M+H]+	169.5	32859911
AllCCS	[M+H-H2O]+	166.1	32859911
AllCCS	[M+NH4]+	172.7	32859911
AllCCS	[M+Na]+	173.6	32859911
AllCCS	[M-H]-	175.4	32859911
AllCCS	[M+Na-2H]-	175.5	32859911
AllCCS	[M+HCOO]-	175.8	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.	3.71 minutes	32390414
Predicted by Siyang on May 30, 2022	10.1128 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	3.31 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	1202.7 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	201.9 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	151.0 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	171.6 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	92.0 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	279.2 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	340.2 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	561.6 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	772.2 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	313.1 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	1006.7 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	223.8 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	264.4 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	577.0 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	428.9 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	119.7 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Donepezil metabolite M4	COC1=C(OC)C=C2C(=O)C(CC3CCNCC3)CC2=C1	3082.9	Standard polar	33892256
Donepezil metabolite M4	COC1=C(OC)C=C2C(=O)C(CC3CCNCC3)CC2=C1	2483.5	Standard non polar	33892256
Donepezil metabolite M4	COC1=C(OC)C=C2C(=O)C(CC3CCNCC3)CC2=C1	2600.9	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Donepezil metabolite M4,1TMS,isomer #1	COC1=CC2=C(C=C1OC)C(=O)C(CC1CCN([Si](C)(C)C)CC1)C2	2609.1	Semi standard non polar	33892256
Donepezil metabolite M4,1TMS,isomer #1	COC1=CC2=C(C=C1OC)C(=O)C(CC1CCN([Si](C)(C)C)CC1)C2	2702.8	Standard non polar	33892256
Donepezil metabolite M4,1TMS,isomer #1	COC1=CC2=C(C=C1OC)C(=O)C(CC1CCN([Si](C)(C)C)CC1)C2	3343.1	Standard polar	33892256
Donepezil metabolite M4,1TBDMS,isomer #1	COC1=CC2=C(C=C1OC)C(=O)C(CC1CCN([Si](C)(C)C(C)(C)C)CC1)C2	2855.3	Semi standard non polar	33892256
Donepezil metabolite M4,1TBDMS,isomer #1	COC1=CC2=C(C=C1OC)C(=O)C(CC1CCN([Si](C)(C)C(C)(C)C)CC1)C2	2924.6	Standard non polar	33892256
Donepezil metabolite M4,1TBDMS,isomer #1	COC1=CC2=C(C=C1OC)C(=O)C(CC1CCN([Si](C)(C)C(C)(C)C)CC1)C2	3499.1	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - Donepezil metabolite M4 GC-MS (Non-derivatized) - 70eV, Positive	splash10-008a-7390000000-30b373dbaf089a113774	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Donepezil metabolite M4 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
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Donepezil metabolite M4 10V, Positive-QTOF	splash10-0006-0090000000-da28a41bd1b829d71a8e	2016-06-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Donepezil metabolite M4 20V, Positive-QTOF	splash10-0bu3-4970000000-801d3c0b32c93fd11165	2016-06-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Donepezil metabolite M4 40V, Positive-QTOF	splash10-0a59-9510000000-6d1d9c2e6a3d68e3dff0	2016-06-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Donepezil metabolite M4 10V, Negative-QTOF	splash10-000i-0090000000-e07661d76997ea63c579	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Donepezil metabolite M4 20V, Negative-QTOF	splash10-000i-1190000000-7f3cb62ab8e739b13f28	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Donepezil metabolite M4 40V, Negative-QTOF	splash10-005l-2960000000-4aff8e96600a8dcc0cd7	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Donepezil metabolite M4 10V, Negative-QTOF	splash10-000i-0090000000-1f5244541851cecc3419	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Donepezil metabolite M4 20V, Negative-QTOF	splash10-000i-0090000000-ea661d63d95f0276ff50	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Donepezil metabolite M4 40V, Negative-QTOF	splash10-017i-0190000000-bbc4b50b5f9509e31d35	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Donepezil metabolite M4 10V, Positive-QTOF	splash10-0006-0090000000-33b322e33c44f750998f	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Donepezil metabolite M4 20V, Positive-QTOF	splash10-0006-0090000000-a157f4737fa76857bd9f	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Donepezil metabolite M4 40V, Positive-QTOF	splash10-08g4-2960000000-aa5279093d72dcc7f374	2021-09-22	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Extracellular

Biospecimen Locations

Blood
Urine

Tissue Locations

Kidney
Liver

Pathways

Name	SMPDB/PathBank	KEGG
Starch and sucrose metabolism	Not Available
Gaucher Disease		Not Available
Globoid Cell Leukodystrophy		Not Available
Metachromatic Leukodystrophy (MLD)		Not Available
Fabry disease		Not Available

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

8622316

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

10446897

PDB ID

Not Available

ChEBI ID

308602

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

rw1291941

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Not Available

Showing metabocard for Donepezil metabolite M4 (HMDB0013960)

MOL for HMDB0013960 (Donepezil metabolite M4)

3D MOL for HMDB0013960 (Donepezil metabolite M4)

3D SDF for HMDB0013960 (Donepezil metabolite M4)

3D-SDF for HMDB0013960 (Donepezil metabolite M4)

PDB for HMDB0013960 (Donepezil metabolite M4)

3D PDB for HMDB0013960 (Donepezil metabolite M4)

SMILES for HMDB0013960 (Donepezil metabolite M4)

INCHI for HMDB0013960 (Donepezil metabolite M4)

Structure for HMDB0013960 (Donepezil metabolite M4)

3D Structure for HMDB0013960 (Donepezil metabolite M4)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra