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Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References enzymes (2) Show 2 proteins XML

Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2013-05-17 01:23:18 UTC

Update Date

2021-09-14 15:45:49 UTC

HMDB ID

HMDB0060472

Secondary Accession Numbers

HMDB60472

Metabolite Identification

Common Name

Didemethylcitalopram

Description

Didemethylcitalopram belongs to the class of organic compounds known as phenylbutylamines. Phenylbutylamines are compounds containing a phenylbutylamine moiety, which consists of a phenyl group substituted at the fourth carbon by an butan-1-amine. Didemethylcitalopram is a very strong basic compound (based on its pKa). Didemethylcitalopram exists in all living organisms, ranging from bacteria to humans. Within humans, didemethylcitalopram participates in a number of enzymatic reactions. In particular, didemethylcitalopram can be converted into citalopram aldehyde through the action of the enzymes amine oxidase [flavin-containing] a and amine oxidase [flavin-containing] b. In addition, didemethylcitalopram and formaldehyde can be biosynthesized from N-desmethylcitalopram; which is mediated by the enzyme cytochrome P450 2D6. In humans, didemethylcitalopram is involved in citalopram metabolism pathway.

Structure

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

HMDB0060472
     RDKit          3D
Didemethylcitalopram
 39 41  0  0  0  0  0  0  0  0999 V2000
    6.1405   -1.3552   -0.9414 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.0144   -1.0658   -0.7826 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6505   -0.6914   -0.5942 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8424   -0.3712   -1.6603 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5351   -0.0192   -1.3978 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9916    0.0317   -0.1466 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8133   -0.2918    0.9104 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1233   -0.6488    0.6997 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0389   -0.1737    2.1467 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2179    0.3013    1.8028 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3195    0.3575    0.4373 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3927   -0.6245    0.0188 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0831   -2.0283    0.4354 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2423   -2.9006   -0.0496 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0657   -4.2780    0.2890 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8185    1.7101    0.0796 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2344    2.0181   -1.2132 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6958    3.2713   -1.5487 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7686    4.2829   -0.6192 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2252    5.5129   -0.9626 F   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3585    3.9904    0.6690 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8964    2.7334    1.0024 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2342   -0.3984   -2.6757 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9305    0.2262   -2.2683 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7399   -0.8965    1.5525 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8705   -1.1526    2.6645 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4622    0.5198    2.8921 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3425   -0.2776    0.4726 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4797   -0.5979   -1.0721 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9958   -2.1530    1.5339 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1361   -2.3326   -0.0670 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2449   -2.7863   -1.1637 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1586   -2.4484    0.3778 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3771   -4.9304   -0.4544 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1584   -4.5095    0.7222 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1986    1.2685   -1.9671 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0072    3.4669   -2.5591 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3954    4.7363    1.4218 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5744    2.5043    2.0149 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  3  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
  7  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 11 16  1  0
 16 17  2  0
 17 18  1  0
 18 19  2  0
 19 20  1  0
 19 21  1  0
 21 22  2  0
  8  3  1  0
 22 16  1  0
 11  6  1  0
  4 23  1  0
  5 24  1  0
  8 25  1  0
  9 26  1  0
  9 27  1  0
 12 28  1  0
 12 29  1  0
 13 30  1  0
 13 31  1  0
 14 32  1  0
 14 33  1  0
 15 34  1  0
 15 35  1  0
 17 36  1  0
 18 37  1  0
 21 38  1  0
 22 39  1  0
M  END


  Mrv0541 05161318232D          

 22 24  0  0  0  0            999 V2000
    2.9359    1.9199    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9934    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0654    2.3174    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3509    1.0799    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3509    2.7299    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3636    1.4924    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2789    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1154    1.8336    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2714    2.6735    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2789   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7079   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7798   -0.2549    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9934    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5645    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0654    1.4924    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3636    2.3174    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5645    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7798    1.0799    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0780    2.7299    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
    4.0919    2.7598    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.4223   -0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2949    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  5  3  1  0  0  0  0
  6  4  2  0  0  0  0
  7  2  2  0  0  0  0
  8  1  1  0  0  0  0
  9  1  1  0  0  0  0
 13  2  1  0  0  0  0
 13 10  2  0  0  0  0
 13 11  1  0  0  0  0
 14 10  1  0  0  0  0
 14 12  1  0  0  0  0
 15  3  2  0  0  0  0
 15  4  1  0  0  0  0
 16  5  2  0  0  0  0
 16  6  1  0  0  0  0
 17  7  1  0  0  0  0
 17 14  2  0  0  0  0
 18  8  1  0  0  0  0
 18 15  1  0  0  0  0
 18 17  1  0  0  0  0
 19 16  1  0  0  0  0
 20  9  1  0  0  0  0
 21 11  3  0  0  0  0
 22 12  1  0  0  0  0
 22 18  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0060472

> <DATABASE_NAME>
hmdb

> <SMILES>
NCCCC1(OCC2=C1C=CC(=C2)C#N)C1=CC=C(F)C=C1

> <INCHI_IDENTIFIER>
InChI=1S/C18H17FN2O/c19-16-5-3-15(4-6-16)18(8-1-9-20)17-7-2-13(11-21)10-14(17)12-22-18/h2-7,10H,1,8-9,12,20H2

> <INCHI_KEY>
RKUKMUWCRLRPEJ-UHFFFAOYSA-N

> <FORMULA>
C18H17FN2O

> <MOLECULAR_WEIGHT>
296.3388

> <EXACT_MASS>
296.132491381

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
31.16272621020575

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
1-(3-aminopropyl)-1-(4-fluorophenyl)-1,3-dihydro-2-benzofuran-5-carbonitrile

> <ALOGPS_LOGP>
2.69

> <JCHEM_LOGP>
2.948675875333333

> <ALOGPS_LOGS>
-4.75

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_BASIC>
10.201573413246082

> <JCHEM_POLAR_SURFACE_AREA>
59.040000000000006

> <JCHEM_REFRACTIVITY>
83.9509

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.25e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
didemethylcitalopram

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0060472
     RDKit          3D
Didemethylcitalopram
 39 41  0  0  0  0  0  0  0  0999 V2000
    6.1405   -1.3552   -0.9414 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.0144   -1.0658   -0.7826 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6505   -0.6914   -0.5942 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8424   -0.3712   -1.6603 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5351   -0.0192   -1.3978 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9916    0.0317   -0.1466 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8133   -0.2918    0.9104 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1233   -0.6488    0.6997 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0389   -0.1737    2.1467 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2179    0.3013    1.8028 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3195    0.3575    0.4373 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3927   -0.6245    0.0188 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0831   -2.0283    0.4354 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2423   -2.9006   -0.0496 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0657   -4.2780    0.2890 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8185    1.7101    0.0796 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2344    2.0181   -1.2132 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6958    3.2713   -1.5487 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7686    4.2829   -0.6192 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2252    5.5129   -0.9626 F   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3585    3.9904    0.6690 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8964    2.7334    1.0024 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2342   -0.3984   -2.6757 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9305    0.2262   -2.2683 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7399   -0.8965    1.5525 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8705   -1.1526    2.6645 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4622    0.5198    2.8921 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3425   -0.2776    0.4726 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4797   -0.5979   -1.0721 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9958   -2.1530    1.5339 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1361   -2.3326   -0.0670 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2449   -2.7863   -1.1637 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1586   -2.4484    0.3778 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3771   -4.9304   -0.4544 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1584   -4.5095    0.7222 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1986    1.2685   -1.9671 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0072    3.4669   -2.5591 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3954    4.7363    1.4218 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5744    2.5043    2.0149 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  3  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
  7  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 11 16  1  0
 16 17  2  0
 17 18  1  0
 18 19  2  0
 19 20  1  0
 19 21  1  0
 21 22  2  0
  8  3  1  0
 22 16  1  0
 11  6  1  0
  4 23  1  0
  5 24  1  0
  8 25  1  0
  9 26  1  0
  9 27  1  0
 12 28  1  0
 12 29  1  0
 13 30  1  0
 13 31  1  0
 14 32  1  0
 14 33  1  0
 15 34  1  0
 15 35  1  0
 17 36  1  0
 18 37  1  0
 21 38  1  0
 22 39  1  0
M  END

HEADER    PROTEIN                                 16-MAY-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   16-MAY-13         0                                  
HETATM    1  C   UNK     0       5.480   3.584   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       7.454   1.540   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.989   4.326   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.655   2.016   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.655   5.096   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -0.679   2.786   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       6.121   2.310   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       3.949   3.423   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       6.107   4.991   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       6.121  -0.770   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       8.788  -0.770   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       3.322  -0.476   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       7.454   0.000   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       4.787   0.000   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       1.989   2.786   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -0.679   4.326   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       4.787   1.540   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       3.322   2.016   0.000  0.00  0.00           C+0
HETATM   19  F   UNK     0      -2.012   5.096   0.000  0.00  0.00           F+0
HETATM   20  N   UNK     0       7.638   5.152   0.000  0.00  0.00           N+0
HETATM   21  N   UNK     0      10.122  -1.540   0.000  0.00  0.00           N+0
HETATM   22  O   UNK     0       2.417   0.770   0.000  0.00  0.00           O+0
CONECT    1    8    9                                                       
CONECT    2    7   13                                                       
CONECT    3    5   15                                                       
CONECT    4    6   15                                                       
CONECT    5    3   16                                                       
CONECT    6    4   16                                                       
CONECT    7    2   17                                                       
CONECT    8    1   18                                                       
CONECT    9    1   20                                                       
CONECT   10   13   14                                                       
CONECT   11   13   21                                                       
CONECT   12   14   22                                                       
CONECT   13    2   10   11                                                  
CONECT   14   10   12   17                                                  
CONECT   15    3    4   18                                                  
CONECT   16    5    6   19                                                  
CONECT   17    7   14   18                                                  
CONECT   18    8   15   17   22                                             
CONECT   19   16                                                            
CONECT   20    9                                                            
CONECT   21   11                                                            
CONECT   22   12   18                                                       
MASTER        0    0    0    0    0    0    0    0   22    0   48    0
END

COMPND    HMDB0251225
HETATM    1  N1  UNL     1       6.502  -0.608   1.722  1.00  0.00           N  
HETATM    2  C1  UNL     1       5.399  -0.472   1.421  1.00  0.00           C  
HETATM    3  C2  UNL     1       4.013  -0.300   1.057  1.00  0.00           C  
HETATM    4  C3  UNL     1       3.204   0.520   1.812  1.00  0.00           C  
HETATM    5  C4  UNL     1       1.870   0.652   1.417  1.00  0.00           C  
HETATM    6  C5  UNL     1       1.389  -0.014   0.315  1.00  0.00           C  
HETATM    7  C6  UNL     1       2.204  -0.841  -0.447  1.00  0.00           C  
HETATM    8  C7  UNL     1       3.512  -0.970  -0.059  1.00  0.00           C  
HETATM    9  C8  UNL     1       1.346  -1.376  -1.537  1.00  0.00           C  
HETATM   10  O1  UNL     1       0.320  -0.453  -1.620  1.00  0.00           O  
HETATM   11  C9  UNL     1       0.068  -0.057  -0.310  1.00  0.00           C  
HETATM   12  C10 UNL     1      -0.847  -1.102   0.302  1.00  0.00           C  
HETATM   13  C11 UNL     1      -2.157  -1.026  -0.448  1.00  0.00           C  
HETATM   14  C12 UNL     1      -3.187  -2.010   0.052  1.00  0.00           C  
HETATM   15  N2  UNL     1      -2.654  -3.335  -0.107  1.00  0.00           N  
HETATM   16  C13 UNL     1      -0.628   1.250  -0.289  1.00  0.00           C  
HETATM   17  C14 UNL     1      -0.614   2.011  -1.434  1.00  0.00           C  
HETATM   18  C15 UNL     1      -1.233   3.231  -1.481  1.00  0.00           C  
HETATM   19  C16 UNL     1      -1.868   3.665  -0.343  1.00  0.00           C  
HETATM   20  F1  UNL     1      -2.499   4.878  -0.347  1.00  0.00           F  
HETATM   21  C17 UNL     1      -1.905   2.932   0.822  1.00  0.00           C  
HETATM   22  C18 UNL     1      -1.272   1.707   0.841  1.00  0.00           C  
HETATM   23  H1  UNL     1       3.627   1.019   2.665  1.00  0.00           H  
HETATM   24  H2  UNL     1       1.256   1.306   2.032  1.00  0.00           H  
HETATM   25  H3  UNL     1       4.171  -1.609  -0.634  1.00  0.00           H  
HETATM   26  H4  UNL     1       1.008  -2.400  -1.355  1.00  0.00           H  
HETATM   27  H5  UNL     1       1.900  -1.371  -2.501  1.00  0.00           H  
HETATM   28  H6  UNL     1      -0.993  -0.937   1.399  1.00  0.00           H  
HETATM   29  H7  UNL     1      -0.381  -2.109   0.212  1.00  0.00           H  
HETATM   30  H8  UNL     1      -2.514   0.011  -0.425  1.00  0.00           H  
HETATM   31  H9  UNL     1      -1.897  -1.230  -1.524  1.00  0.00           H  
HETATM   32  H10 UNL     1      -3.514  -1.774   1.071  1.00  0.00           H  
HETATM   33  H11 UNL     1      -4.061  -1.930  -0.645  1.00  0.00           H  
HETATM   34  H12 UNL     1      -2.691  -3.634  -1.083  1.00  0.00           H  
HETATM   35  H13 UNL     1      -1.814  -3.528   0.436  1.00  0.00           H  
HETATM   36  H14 UNL     1      -0.101   1.642  -2.325  1.00  0.00           H  
HETATM   37  H15 UNL     1      -1.249   3.857  -2.348  1.00  0.00           H  
HETATM   38  H16 UNL     1      -2.413   3.283   1.727  1.00  0.00           H  
HETATM   39  H17 UNL     1      -1.297   1.121   1.761  1.00  0.00           H  
CONECT    1    2    2    2
CONECT    2    3
CONECT    3    4    4    8
CONECT    4    5   23
CONECT    5    6    6   24
CONECT    6    7   11
CONECT    7    8    8    9
CONECT    8   25
CONECT    9   10   26   27
CONECT   10   11
CONECT   11   12   16
CONECT   12   13   28   29
CONECT   13   14   30   31
CONECT   14   15   32   33
CONECT   15   34   35
CONECT   16   17   17   22
CONECT   17   18   36
CONECT   18   19   19   37
CONECT   19   20   21
CONECT   21   22   22   38
CONECT   22   39
END

HMDB0060472
     RDKit          3D
Didemethylcitalopram
 39 41  0  0  0  0  0  0  0  0999 V2000
    6.1405   -1.3552   -0.9414 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.0144   -1.0658   -0.7826 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6505   -0.6914   -0.5942 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8424   -0.3712   -1.6603 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5351   -0.0192   -1.3978 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9916    0.0317   -0.1466 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8133   -0.2918    0.9104 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1233   -0.6488    0.6997 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0389   -0.1737    2.1467 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2179    0.3013    1.8028 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3195    0.3575    0.4373 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3927   -0.6245    0.0188 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0831   -2.0283    0.4354 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2423   -2.9006   -0.0496 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0657   -4.2780    0.2890 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8185    1.7101    0.0796 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2344    2.0181   -1.2132 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6958    3.2713   -1.5487 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7686    4.2829   -0.6192 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2252    5.5129   -0.9626 F   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3585    3.9904    0.6690 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8964    2.7334    1.0024 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2342   -0.3984   -2.6757 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9305    0.2262   -2.2683 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7399   -0.8965    1.5525 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8705   -1.1526    2.6645 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4622    0.5198    2.8921 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3425   -0.2776    0.4726 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4797   -0.5979   -1.0721 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9958   -2.1530    1.5339 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1361   -2.3326   -0.0670 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2449   -2.7863   -1.1637 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1586   -2.4484    0.3778 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3771   -4.9304   -0.4544 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1584   -4.5095    0.7222 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1986    1.2685   -1.9671 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0072    3.4669   -2.5591 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3954    4.7363    1.4218 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5744    2.5043    2.0149 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  3  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
  7  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 11 16  1  0
 16 17  2  0
 17 18  1  0
 18 19  2  0
 19 20  1  0
 19 21  1  0
 21 22  2  0
  8  3  1  0
 22 16  1  0
 11  6  1  0
  4 23  1  0
  5 24  1  0
  8 25  1  0
  9 26  1  0
  9 27  1  0
 12 28  1  0
 12 29  1  0
 13 30  1  0
 13 31  1  0
 14 32  1  0
 14 33  1  0
 15 34  1  0
 15 35  1  0
 17 36  1  0
 18 37  1  0
 21 38  1  0
 22 39  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
Didesmethylcitalopram oxalate	HMDB
Didesmethylcitalopram	MeSH

Chemical Formula

C₁₈H₁₇FN₂O

Average Molecular Weight

296.3388

Monoisotopic Molecular Weight

296.132491381

IUPAC Name

1-(3-aminopropyl)-1-(4-fluorophenyl)-1,3-dihydro-2-benzofuran-5-carbonitrile

Traditional Name

didemethylcitalopram

CAS Registry Number

Not Available

SMILES

NCCCC1(OCC2=C1C=CC(=C2)C#N)C1=CC=C(F)C=C1

InChI Identifier

InChI=1S/C18H17FN2O/c19-16-5-3-15(4-6-16)18(8-1-9-20)17-7-2-13(11-21)10-14(17)12-22-18/h2-7,10H,1,8-9,12,20H2

InChI Key

RKUKMUWCRLRPEJ-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as phenylbutylamines. Phenylbutylamines are compounds containing a phenylbutylamine moiety, which consists of a phenyl group substituted at the fourth carbon by an butan-1-amine.

Kingdom

Organic compounds

Super Class

Benzenoids

Class

Benzene and substituted derivatives

Sub Class

Phenylbutylamines

Direct Parent

Phenylbutylamines

Alternative Parents

Substituents

Phenylbutylamine
Isocoumaran
Fluorobenzene
Halobenzene
Aralkylamine
Aryl halide
Aryl fluoride
Oxacycle
Dialkyl ether
Ether
Carbonitrile
Nitrile
Organoheterocyclic compound
Organohalogen compound
Organic oxygen compound
Organopnictogen compound
Primary aliphatic amine
Amine
Organofluoride
Organonitrogen compound
Organooxygen compound
Organic nitrogen compound
Primary amine
Hydrocarbon derivative
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

organic amino compound (CHEBI:80604 )
benzenes (CHEBI:80604 )

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 31557052)

Source

Exogenous

Exogenous (PMID: 31557052)

Process

Not Available

Role

Not Available

Physical Properties

State

Not Available

Experimental Molecular Properties

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

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	0.0052 g/L	ALOGPS
logP	2.69	ALOGPS
logP	2.95	ChemAxon
logS	-4.8	ALOGPS
pKa (Strongest Basic)	10.2	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	59.04 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	83.95 m³·mol⁻¹	ChemAxon
Polarizability	31.16 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
DeepCCS	[M+H]+	177.269	30932474
DeepCCS	[M-H]-	174.911	30932474
DeepCCS	[M-2H]-	207.797	30932474
DeepCCS	[M+Na]+	183.362	30932474
AllCCS	[M+H]+	169.3	32859911
AllCCS	[M+H-H2O]+	165.9	32859911
AllCCS	[M+NH4]+	172.5	32859911
AllCCS	[M+Na]+	173.4	32859911
AllCCS	[M-H]-	174.4	32859911
AllCCS	[M+Na-2H]-	174.1	32859911
AllCCS	[M+HCOO]-	173.8	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.	4.09 minutes	32390414
Predicted by Siyang on May 30, 2022	11.2061 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	3.57 minutes	32390414

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Didemethylcitalopram	NCCCC1(OCC2=C1C=CC(=C2)C#N)C1=CC=C(F)C=C1	3567.9	Standard polar	33892256
Didemethylcitalopram	NCCCC1(OCC2=C1C=CC(=C2)C#N)C1=CC=C(F)C=C1	2575.4	Standard non polar	33892256
Didemethylcitalopram	NCCCC1(OCC2=C1C=CC(=C2)C#N)C1=CC=C(F)C=C1	2467.9	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Didemethylcitalopram,1TMS,isomer #1	C[Si](C)(C)NCCCC1(C2=CC=C(F)C=C2)OCC2=CC(C#N)=CC=C21	2563.5	Semi standard non polar	33892256
Didemethylcitalopram,1TMS,isomer #1	C[Si](C)(C)NCCCC1(C2=CC=C(F)C=C2)OCC2=CC(C#N)=CC=C21	2577.2	Standard non polar	33892256
Didemethylcitalopram,1TMS,isomer #1	C[Si](C)(C)NCCCC1(C2=CC=C(F)C=C2)OCC2=CC(C#N)=CC=C21	3232.3	Standard polar	33892256
Didemethylcitalopram,2TMS,isomer #1	C[Si](C)(C)N(CCCC1(C2=CC=C(F)C=C2)OCC2=CC(C#N)=CC=C21)[Si](C)(C)C	2741.9	Semi standard non polar	33892256
Didemethylcitalopram,2TMS,isomer #1	C[Si](C)(C)N(CCCC1(C2=CC=C(F)C=C2)OCC2=CC(C#N)=CC=C21)[Si](C)(C)C	2729.4	Standard non polar	33892256
Didemethylcitalopram,2TMS,isomer #1	C[Si](C)(C)N(CCCC1(C2=CC=C(F)C=C2)OCC2=CC(C#N)=CC=C21)[Si](C)(C)C	3178.6	Standard polar	33892256
Didemethylcitalopram,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)NCCCC1(C2=CC=C(F)C=C2)OCC2=CC(C#N)=CC=C21	2832.2	Semi standard non polar	33892256
Didemethylcitalopram,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)NCCCC1(C2=CC=C(F)C=C2)OCC2=CC(C#N)=CC=C21	2781.5	Standard non polar	33892256
Didemethylcitalopram,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)NCCCC1(C2=CC=C(F)C=C2)OCC2=CC(C#N)=CC=C21	3313.7	Standard polar	33892256
Didemethylcitalopram,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N(CCCC1(C2=CC=C(F)C=C2)OCC2=CC(C#N)=CC=C21)[Si](C)(C)C(C)(C)C	3246.4	Semi standard non polar	33892256
Didemethylcitalopram,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N(CCCC1(C2=CC=C(F)C=C2)OCC2=CC(C#N)=CC=C21)[Si](C)(C)C(C)(C)C	3083.0	Standard non polar	33892256
Didemethylcitalopram,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N(CCCC1(C2=CC=C(F)C=C2)OCC2=CC(C#N)=CC=C21)[Si](C)(C)C(C)(C)C	3303.7	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - Didemethylcitalopram GC-MS (Non-derivatized) - 70eV, Positive	splash10-0019-5190000000-27267b21fbfd2667ad0a	2017-09-20	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Didemethylcitalopram GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Didemethylcitalopram 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 - Didemethylcitalopram 10V, Positive-QTOF	splash10-001j-0090000000-6d8ae8086154e9386c59	2016-06-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Didemethylcitalopram 20V, Positive-QTOF	splash10-001i-1190000000-a3bd6197e10242280d3e	2016-06-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Didemethylcitalopram 40V, Positive-QTOF	splash10-0f6x-9850000000-29310282b6b9fbd8e49f	2016-06-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Didemethylcitalopram 10V, Negative-QTOF	splash10-0002-0090000000-b966c93238a3cd3d8dbe	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Didemethylcitalopram 20V, Negative-QTOF	splash10-0002-1090000000-6f09b8194f9dc7f22ae0	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Didemethylcitalopram 40V, Negative-QTOF	splash10-0002-5290000000-4ebf655263c971b6b6fc	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Didemethylcitalopram 10V, Positive-QTOF	splash10-0002-0090000000-1839b3c3aa4333bd08f6	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Didemethylcitalopram 20V, Positive-QTOF	splash10-0f6t-0290000000-ee8bb8dcc6c4bee4016a	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Didemethylcitalopram 40V, Positive-QTOF	splash10-0a4i-0930000000-59d6738739988f333915	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Didemethylcitalopram 10V, Negative-QTOF	splash10-0002-0090000000-009c4b2c3fd1dd912a1c	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Didemethylcitalopram 20V, Negative-QTOF	splash10-000i-0090000000-e2f03fdefbdbf6669449	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Didemethylcitalopram 40V, Negative-QTOF	splash10-000i-1590000000-373645739048c7d4b1c2	2021-10-12	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Cytoplasm
Membrane (predicted from logP)

Biospecimen Locations

Blood
Feces
Urine

Tissue Locations

Kidney
Liver

Pathways

Name	SMPDB/PathBank	KEGG
Citalopram Action Pathway		Not Available
Citalopram Metabolism Pathway		Not Available

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Expected but not Quantified	Not Quantified	Not Available	Not Available	Normal	Not Available	details
Feces	Detected but not Quantified	Not Quantified	Infant (0-1 year old)	Both	Normal	28701177	details
Urine	Expected but not Quantified	Not Quantified	Not Available	Not Available	Normal	Not Available	details

Abnormal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Feces	Detected but not Quantified	Not Quantified	Newborn (0-30 days old)	Both	Sepsis	28701177	details

Associated Disorders and Diseases

Disease References

Sepsis
Stewart CJ, Embleton ND, Marrs ECL, Smith DP, Fofanova T, Nelson A, Skeath T, Perry JD, Petrosino JF, Berrington JE, Cummings SP: Longitudinal development of the gut microbiome and metabolome in preterm neonates with late onset sepsis and healthy controls. Microbiome. 2017 Jul 12;5(1):75. doi: 10.1186/s40168-017-0295-1. [PubMed:28701177 ]

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

C16609

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

162976

PDB ID

Not Available

ChEBI ID

80604

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

Magrane M: UniProt Knowledgebase: a hub of integrated protein data. Database (Oxford). 2011 Mar 29;2011:bar009. doi: 10.1093/database/bar009. Print 2011. [PubMed:21447597 ]
Howland RH: A critical evaluation of the cardiac toxicity of citalopram: part 2. J Psychosoc Nurs Ment Health Serv. 2011 Dec;49(12):13-6. doi: 10.3928/02793695-20111102-04. Epub 2011 Nov 16. [PubMed:22085614 ]
Rocha A, Coelho EB, Lanchote VL: Influence of quinidine, fluvoxamine, and ketoconazole on the enantioselective pharmacokinetics of citalopram in rats. Can J Physiol Pharmacol. 2008 Nov;86(11):770-6. doi: 10.1139/Y08-088. [PubMed:19011672 ]

Enzymes

Enzyme Details

1. Amine oxidase [flavin-containing] B

General function:: Involved in oxidoreductase activity
Specific function:: Catalyzes the oxidative deamination of biogenic and xenobiotic amines and has important functions in the metabolism of neuroactive and vasoactive amines in the central nervous system and peripheral tissues. MAOB preferentially degrades benzylamine and phenylethylamine.
Gene Name:: MAOB
Uniprot ID:: P27338
Molecular weight:: 58762.475

Reactions

Didemethylcitalopram + Water + Oxygen → Citalopram aldehyde + Ammonia + Hydrogen peroxide	details

Enzyme Details

2. Amine oxidase [flavin-containing] A

General function:: Involved in oxidoreductase activity
Specific function:: Catalyzes the oxidative deamination of biogenic and xenobiotic amines and has important functions in the metabolism of neuroactive and vasoactive amines in the central nervous system and peripheral tissues. MAOA preferentially oxidizes biogenic amines such as 5-hydroxytryptamine (5-HT), norepinephrine and epinephrine.
Gene Name:: MAOA
Uniprot ID:: P21397
Molecular weight:: 59681.27

Reactions

Didemethylcitalopram + Water + Oxygen → Citalopram aldehyde + Ammonia + Hydrogen peroxide	details

Showing metabocard for Didemethylcitalopram (HMDB0060472)

MOL for HMDB0060472 (Didemethylcitalopram)

3D MOL for HMDB0060472 (Didemethylcitalopram)

3D SDF for HMDB0060472 (Didemethylcitalopram)

3D-SDF for HMDB0060472 (Didemethylcitalopram)

PDB for HMDB0060472 (Didemethylcitalopram)

3D PDB for HMDB0060472 (Didemethylcitalopram)

SMILES for HMDB0060472 (Didemethylcitalopram)

INCHI for HMDB0060472 (Didemethylcitalopram)

Structure for HMDB0060472 (Didemethylcitalopram)

3D Structure for HMDB0060472 (Didemethylcitalopram)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

Enzymes

Reactions

Reactions