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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-06 15:16:51 UTC

Update Date

2022-03-07 02:51:53 UTC

HMDB ID

HMDB0015175

Secondary Accession Numbers

HMDB15175

Metabolite Identification

Common Name

Thalidomide

Description

A piperidinyl isoindole originally introduced as a non-barbiturate hypnotic, but withdrawn from the market due to teratogenic effects. It has been reintroduced and used for a number of immunological and inflammatory disorders. Thalidomide displays immunosuppresive and anti-angiogenic activity. It inhibits release of tumor necrosis factor-alpha from monocytes, and modulates other cytokine action. [PubChem]

Structure

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

HMDB0015175
     RDKit          3D
Thalidomide
 29 31  0  0  0  0  0  0  0  0999 V2000
   -5.3362    0.2458   -0.5360 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1578   -0.1542   -0.3760 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4077   -0.6628   -1.5337 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9503   -0.8534   -1.2666 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4538    0.2009   -0.3073 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0378    0.2083   -0.1604 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.8099   -0.8601    0.3103 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4025   -1.9982    0.6733 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1703   -0.3441    0.2698 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3438   -0.9738    0.6183 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5075   -0.2478    0.4821 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5259    1.0494    0.0213 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3507    1.6794   -0.3276 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1669    0.9531   -0.1934 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8011    1.3099   -0.4649 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4498    2.4539   -0.9101 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1536   -0.0671    0.9998 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5500   -0.2458    2.0686 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5754   -0.1039    0.9335 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5326    0.0593   -2.3866 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8593   -1.6608   -1.7971 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7796   -1.8473   -0.8143 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3706   -0.8340   -2.2129 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7925    1.1800   -0.6923 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3259   -1.9929    0.9800 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4664   -0.6984    0.7441 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4515    1.6007   -0.0777 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3330    2.6978   -0.6928 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1479   -0.0941    1.7965 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  7  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  2  0
 12 13  1  0
 13 14  2  0
 14 15  1  0
 15 16  2  0
  5 17  1  0
 17 18  2  0
 17 19  1  0
 19  2  1  0
 15  6  1  0
 14  9  1  0
  3 20  1  0
  3 21  1  0
  4 22  1  0
  4 23  1  0
  5 24  1  0
 10 25  1  0
 11 26  1  0
 12 27  1  0
 13 28  1  0
 19 29  1  0
M  END

1041
  Mrv0541 02231215122D          

 19 21  0  0  1  0            999 V2000
    5.1662   -1.4290    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1159   -1.4482    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1159    1.4482    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.6412    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3412    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.4037   -0.7145    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.1662    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5787    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4037    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5787   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8597   -0.6639    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8597    0.6639    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0791   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0791    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8162    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3645   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3645    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1 10  2  0  0  0  0
  2 11  2  0  0  0  0
  3 12  2  0  0  0  0
  4 15  2  0  0  0  0
  5  7  1  0  0  0  0
  5 11  1  0  0  0  0
  5 12  1  0  0  0  0
  6 10  1  0  0  0  0
  6 15  1  0  0  0  0
  7  8  1  0  0  0  0
  7 10  1  0  0  0  0
  8  9  1  0  0  0  0
  9 15  1  0  0  0  0
 11 13  1  0  0  0  0
 12 14  1  0  0  0  0
 13 14  1  0  0  0  0
 13 16  2  0  0  0  0
 14 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>
HMDB0015175

> <DATABASE_NAME>
hmdb

> <SMILES>
O=C1N(C2CCC(=O)NC2=O)C(=O)C2=CC=CC=C12

> <INCHI_IDENTIFIER>
InChI=1S/C13H10N2O4/c16-10-6-5-9(11(17)14-10)15-12(18)7-3-1-2-4-8(7)13(15)19/h1-4,9H,5-6H2,(H,14,16,17)

> <INCHI_KEY>
UEJJHQNACJXSKW-UHFFFAOYSA-N

> <FORMULA>
C13H10N2O4

> <MOLECULAR_WEIGHT>
258.2295

> <EXACT_MASS>
258.064056818

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
24.42456996837572

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
2-(2,6-dioxopiperidin-3-yl)-2,3-dihydro-1H-isoindole-1,3-dione

> <ALOGPS_LOGP>
0.42

> <JCHEM_LOGP>
0.01570735600000027

> <ALOGPS_LOGS>
-2.00

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
16.74270753163753

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.593278965606643

> <JCHEM_PKA_STRONGEST_BASIC>
-6.448342644269868

> <JCHEM_POLAR_SURFACE_AREA>
83.55

> <JCHEM_REFRACTIVITY>
64.32480000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.55e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
thalidomide

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0015175
     RDKit          3D
Thalidomide
 29 31  0  0  0  0  0  0  0  0999 V2000
   -5.3362    0.2458   -0.5360 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1578   -0.1542   -0.3760 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4077   -0.6628   -1.5337 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9503   -0.8534   -1.2666 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4538    0.2009   -0.3073 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0378    0.2083   -0.1604 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.8099   -0.8601    0.3103 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4025   -1.9982    0.6733 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1703   -0.3441    0.2698 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3438   -0.9738    0.6183 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5075   -0.2478    0.4821 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5259    1.0494    0.0213 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3507    1.6794   -0.3276 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1669    0.9531   -0.1934 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8011    1.3099   -0.4649 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4498    2.4539   -0.9101 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1536   -0.0671    0.9998 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5500   -0.2458    2.0686 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5754   -0.1039    0.9335 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5326    0.0593   -2.3866 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8593   -1.6608   -1.7971 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7796   -1.8473   -0.8143 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3706   -0.8340   -2.2129 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7925    1.1800   -0.6923 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3259   -1.9929    0.9800 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4664   -0.6984    0.7441 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4515    1.6007   -0.0777 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3330    2.6978   -0.6928 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1479   -0.0941    1.7965 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  7  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  2  0
 12 13  1  0
 13 14  2  0
 14 15  1  0
 15 16  2  0
  5 17  1  0
 17 18  2  0
 17 19  1  0
 19  2  1  0
 15  6  1  0
 14  9  1  0
  3 20  1  0
  3 21  1  0
  4 22  1  0
  4 23  1  0
  5 24  1  0
 10 25  1  0
 11 26  1  0
 12 27  1  0
 13 28  1  0
 19 29  1  0
M  END

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: 1041                                              
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  O   UNK     0       9.644  -2.667   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0       7.683  -2.703   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0       7.683   2.703   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0      14.264   0.000   0.000  0.00  0.00           O+0
HETATM    5  N   UNK     0       8.104   0.000   0.000  0.00  0.00           N+0
HETATM    6  N   UNK     0      11.954  -1.334   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0       9.644   0.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      10.414   1.334   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      11.954   1.334   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      10.414  -1.334   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       7.205  -1.239   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       7.205   1.239   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       5.748  -0.770   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       5.748   0.770   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      12.724   0.000   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       4.414  -1.540   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       4.414   1.540   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       3.080  -0.770   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       3.080   0.770   0.000  0.00  0.00           C+0
CONECT    1   10                                                            
CONECT    2   11                                                            
CONECT    3   12                                                            
CONECT    4   15                                                            
CONECT    5    7   11   12                                                  
CONECT    6   10   15                                                       
CONECT    7    5    8   10                                                  
CONECT    8    7    9                                                       
CONECT    9    8   15                                                       
CONECT   10    1    6    7                                                  
CONECT   11    2    5   13                                                  
CONECT   12    3    5   14                                                  
CONECT   13   11   14   16                                                  
CONECT   14   12   13   17                                                  
CONECT   15    4    6    9                                                  
CONECT   16   13   18                                                       
CONECT   17   14   19                                                       
CONECT   18   16   19                                                       
CONECT   19   17   18                                                       
MASTER        0    0    0    0    0    0    0    0   19    0   42    0
END

COMPND    HMDB0015175
HETATM    1  O1  UNL     1      -5.336   0.246  -0.536  1.00  0.00           O  
HETATM    2  C1  UNL     1      -4.158  -0.154  -0.376  1.00  0.00           C  
HETATM    3  C2  UNL     1      -3.408  -0.663  -1.534  1.00  0.00           C  
HETATM    4  C3  UNL     1      -1.950  -0.853  -1.267  1.00  0.00           C  
HETATM    5  C4  UNL     1      -1.454   0.201  -0.307  1.00  0.00           C  
HETATM    6  N1  UNL     1      -0.038   0.208  -0.160  1.00  0.00           N  
HETATM    7  C5  UNL     1       0.810  -0.860   0.310  1.00  0.00           C  
HETATM    8  O2  UNL     1       0.402  -1.998   0.673  1.00  0.00           O  
HETATM    9  C6  UNL     1       2.170  -0.344   0.270  1.00  0.00           C  
HETATM   10  C7  UNL     1       3.344  -0.974   0.618  1.00  0.00           C  
HETATM   11  C8  UNL     1       4.507  -0.248   0.482  1.00  0.00           C  
HETATM   12  C9  UNL     1       4.526   1.049   0.021  1.00  0.00           C  
HETATM   13  C10 UNL     1       3.351   1.679  -0.328  1.00  0.00           C  
HETATM   14  C11 UNL     1       2.167   0.953  -0.193  1.00  0.00           C  
HETATM   15  C12 UNL     1       0.801   1.310  -0.465  1.00  0.00           C  
HETATM   16  O3  UNL     1       0.450   2.454  -0.910  1.00  0.00           O  
HETATM   17  C13 UNL     1      -2.154  -0.067   1.000  1.00  0.00           C  
HETATM   18  O4  UNL     1      -1.550  -0.246   2.069  1.00  0.00           O  
HETATM   19  N2  UNL     1      -3.575  -0.104   0.934  1.00  0.00           N  
HETATM   20  H1  UNL     1      -3.533   0.059  -2.387  1.00  0.00           H  
HETATM   21  H2  UNL     1      -3.859  -1.661  -1.797  1.00  0.00           H  
HETATM   22  H3  UNL     1      -1.780  -1.847  -0.814  1.00  0.00           H  
HETATM   23  H4  UNL     1      -1.371  -0.834  -2.213  1.00  0.00           H  
HETATM   24  H5  UNL     1      -1.792   1.180  -0.692  1.00  0.00           H  
HETATM   25  H6  UNL     1       3.326  -1.993   0.980  1.00  0.00           H  
HETATM   26  H7  UNL     1       5.466  -0.698   0.744  1.00  0.00           H  
HETATM   27  H8  UNL     1       5.452   1.601  -0.078  1.00  0.00           H  
HETATM   28  H9  UNL     1       3.333   2.698  -0.693  1.00  0.00           H  
HETATM   29  H10 UNL     1      -4.148  -0.094   1.796  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3   19
CONECT    3    4   20   21
CONECT    4    5   22   23
CONECT    5    6   17   24
CONECT    6    7   15
CONECT    7    8    8    9
CONECT    9   10   10   14
CONECT   10   11   25
CONECT   11   12   12   26
CONECT   12   13   27
CONECT   13   14   14   28
CONECT   14   15
CONECT   15   16   16
CONECT   17   18   18   19
CONECT   19   29
END

HMDB0015175
     RDKit          3D
Thalidomide
 29 31  0  0  0  0  0  0  0  0999 V2000
   -5.3362    0.2458   -0.5360 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1578   -0.1542   -0.3760 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4077   -0.6628   -1.5337 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9503   -0.8534   -1.2666 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4538    0.2009   -0.3073 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0378    0.2083   -0.1604 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.8099   -0.8601    0.3103 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4025   -1.9982    0.6733 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1703   -0.3441    0.2698 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3438   -0.9738    0.6183 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5075   -0.2478    0.4821 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5259    1.0494    0.0213 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3507    1.6794   -0.3276 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1669    0.9531   -0.1934 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8011    1.3099   -0.4649 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4498    2.4539   -0.9101 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1536   -0.0671    0.9998 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5500   -0.2458    2.0686 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5754   -0.1039    0.9335 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5326    0.0593   -2.3866 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8593   -1.6608   -1.7971 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7796   -1.8473   -0.8143 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3706   -0.8340   -2.2129 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7925    1.1800   -0.6923 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3259   -1.9929    0.9800 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4664   -0.6984    0.7441 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4515    1.6007   -0.0777 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3330    2.6978   -0.6928 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1479   -0.0941    1.7965 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  7  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  2  0
 12 13  1  0
 13 14  2  0
 14 15  1  0
 15 16  2  0
  5 17  1  0
 17 18  2  0
 17 19  1  0
 19  2  1  0
 15  6  1  0
 14  9  1  0
  3 20  1  0
  3 21  1  0
  4 22  1  0
  4 23  1  0
  5 24  1  0
 10 25  1  0
 11 26  1  0
 12 27  1  0
 13 28  1  0
 19 29  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
Thalomid	Kegg
Thaled	Kegg
alpha-Phthalimidoglutarimide	HMDB
N-Phthalimidoglutamic acid imide	HMDB
N-Phthaloylglutamimide	HMDB
N-Phthalylglutamic acid imide	HMDB
Thalidomine usp26	HMDB
Sedoval	HMDB
Celgene brand OF thalidomide	HMDB
Thalidomide	MeSH

Chemical Formula

C₁₃H₁₀N₂O₄

Average Molecular Weight

258.2295

Monoisotopic Molecular Weight

258.064056818

IUPAC Name

2-(2,6-dioxopiperidin-3-yl)-2,3-dihydro-1H-isoindole-1,3-dione

Traditional Name

thalidomide

CAS Registry Number

50-35-1

SMILES

O=C1N(C2CCC(=O)NC2=O)C(=O)C2=CC=CC=C12

InChI Identifier

InChI=1S/C13H10N2O4/c16-10-6-5-9(11(17)14-10)15-12(18)7-3-1-2-4-8(7)13(15)19/h1-4,9H,5-6H2,(H,14,16,17)

InChI Key

UEJJHQNACJXSKW-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as phthalimides. These are aromatic heterocyclic compounds containing a 1,3-dioxoisoindoline moiety. They are imide derivatives of phthalic anhydrides.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Isoindoles and derivatives

Sub Class

Isoindolines

Direct Parent

Phthalimides

Alternative Parents

Substituents

Phthalimide
Alpha-amino acid or derivatives
Isoindole
Piperidinedione
Delta-lactam
Piperidinone
Benzenoid
Piperidine
Carboxylic acid imide, n-substituted
Carboxylic acid imide
Dicarboximide
Carboxylic acid imide, n-unsubstituted
Lactam
Carboxylic acid derivative
Azacycle
Organic nitrogen compound
Organonitrogen compound
Organooxygen compound
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Organic oxygen compound
Carbonyl group
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

piperidones (CHEBI:74947 )
phthalimides (CHEBI:74947 )

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

Source

Exogenous

Exogenous (HMDB: HMDB0015175)

Process

Not Available

Role

Industrial application

Manufacturing industry

Material processing agent

Coloring agent

Fluorescent agent

Anticonvulsant (HMDB: HMDB0015175)
Sedative (HMDB: HMDB0015175)
Immunosuppressive Agent (HMDB: HMDB0015175)

Antineoplastic agent (HMDB: HMDB0015175)
Antiemetic (HMDB: HMDB0015175)

Pharmaceutical industry

Leprostatic drug (HMDB: HMDB0015175)
Anti-inflammatory drug (HMDB: HMDB0015175)

Biological role

Teratogenic agent (HMDB: HMDB0015175)
Antiangiogenic (HMDB: HMDB0015175)

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	270 °C	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	2.55 g/L	Not Available
LogP	0.3	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	2.55 g/L	ALOGPS
logP	0.42	ALOGPS
logP	0.016	ChemAxon
logS	-2	ALOGPS
pKa (Strongest Acidic)	11.59	ChemAxon
pKa (Strongest Basic)	-6.4	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	83.55 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	64.32 m³·mol⁻¹	ChemAxon
Polarizability	24.42 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]+	160.001	31661259
DarkChem	[M-H]-	158.386	31661259
DeepCCS	[M-2H]-	186.103	30932474
DeepCCS	[M+Na]+	161.531	30932474
AllCCS	[M+H]+	157.7	32859911
AllCCS	[M+H-H2O]+	154.0	32859911
AllCCS	[M+NH4]+	161.1	32859911
AllCCS	[M+Na]+	162.1	32859911
AllCCS	[M-H]-	158.5	32859911
AllCCS	[M+Na-2H]-	158.0	32859911
AllCCS	[M+HCOO]-	157.5	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Thalidomide	O=C1N(C2CCC(=O)NC2=O)C(=O)C2=CC=CC=C12	3936.1	Standard polar	33892256
Thalidomide	O=C1N(C2CCC(=O)NC2=O)C(=O)C2=CC=CC=C12	2473.6	Standard non polar	33892256
Thalidomide	O=C1N(C2CCC(=O)NC2=O)C(=O)C2=CC=CC=C12	2445.2	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Thalidomide,1TMS,isomer #1	C[Si](C)(C)N1C(=O)CCC(N2C(=O)C3=CC=CC=C3C2=O)C1=O	2394.3	Semi standard non polar	33892256
Thalidomide,1TMS,isomer #1	C[Si](C)(C)N1C(=O)CCC(N2C(=O)C3=CC=CC=C3C2=O)C1=O	2476.5	Standard non polar	33892256
Thalidomide,1TMS,isomer #1	C[Si](C)(C)N1C(=O)CCC(N2C(=O)C3=CC=CC=C3C2=O)C1=O	3369.5	Standard polar	33892256
Thalidomide,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N1C(=O)CCC(N2C(=O)C3=CC=CC=C3C2=O)C1=O	2642.9	Semi standard non polar	33892256
Thalidomide,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N1C(=O)CCC(N2C(=O)C3=CC=CC=C3C2=O)C1=O	2674.5	Standard non polar	33892256
Thalidomide,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N1C(=O)CCC(N2C(=O)C3=CC=CC=C3C2=O)C1=O	3418.0	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - Thalidomide GC-MS (Non-derivatized) - 70eV, Positive	splash10-05d0-4950000000-f29254c7cc48a749c100	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Thalidomide GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Thalidomide GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Thalidomide GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
MS	Mass Spectrum (Electron Ionization)	splash10-0wba-4900000000-77362eaf27267f59650d	2014-09-20	Not Available	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Experimental LC-MS/MS	LC-MS/MS Spectrum - Thalidomide LC-ESI-qTof , Positive-QTOF	splash10-000i-1940000000-f6d6997d1eaa7a83ec1b	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Thalidomide LC-ESI-qTof , Positive-QTOF	splash10-000i-0930000000-e92e8e23d5db87f50f53	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Thalidomide LC-ESI-qTof , Positive-QTOF	splash10-0019-2900000000-ecfd1b7ec17b857ea977	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Thalidomide , positive-QTOF	splash10-000i-0930000000-e92e8e23d5db87f50f53	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Thalidomide , positive-QTOF	splash10-000i-1940000000-f6d6997d1eaa7a83ec1b	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Thalidomide , positive-QTOF	splash10-0019-2900000000-ecfd1b7ec17b857ea977	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Thalidomide 60V, Positive-QTOF	splash10-0aou-3910000000-91636cf8948ff2a1ec8c	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Thalidomide 75V, Negative-QTOF	splash10-0aou-4900000000-0354536dffa9acdee12d	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Thalidomide 90V, Negative-QTOF	splash10-066u-6900000000-ea3e7b4b381e65a7c9a4	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Thalidomide 75V, Positive-QTOF	splash10-0aou-4900000000-c5062441ebfb6523331b	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Thalidomide 45V, Negative-QTOF	splash10-0bvl-2970000000-1e251d07e623c9fbe2a2	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Thalidomide 60V, Negative-QTOF	splash10-0aou-3910000000-19940b0b041ba51e96e0	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Thalidomide 30V, Negative-QTOF	splash10-0a6r-0190000000-a818a5ae6100d0f996ba	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Thalidomide 15V, Negative-QTOF	splash10-0a4i-0090000000-42e8be928c8508c213f2	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Thalidomide 45V, Positive-QTOF	splash10-0bvl-2970000000-fcf57e68d7f7156f09d4	2021-09-20	HMDB team, MONA	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Thalidomide 10V, Positive-QTOF	splash10-0a4i-0090000000-094c39302b7589d69293	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Thalidomide 20V, Positive-QTOF	splash10-0a4r-0590000000-a8eb9abb005e68bb1fdf	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Thalidomide 40V, Positive-QTOF	splash10-000f-9800000000-e219527727ba0e4f62dd	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Thalidomide 10V, Negative-QTOF	splash10-0a4i-0190000000-88a6f8cb2bfe0f1b603f	2016-08-04	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Thalidomide 20V, Negative-QTOF	splash10-0bti-1790000000-bdf020cb11e65e0077f7	2016-08-04	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Thalidomide 40V, Negative-QTOF	splash10-01oy-9700000000-ce19845489ffe3fdb389	2016-08-04	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Thalidomide 10V, Negative-QTOF	splash10-0bta-0960000000-38a7ecf36472375bfe14	2021-10-11	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Thalidomide 20V, Negative-QTOF	splash10-0a4j-1590000000-40230dba1a083dee9f10	2021-10-11	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Thalidomide 40V, Negative-QTOF	splash10-0005-4900000000-b49c37804603e0525f05	2021-10-11	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Thalidomide 10V, Positive-QTOF	splash10-052b-0960000000-d36ac6ec3b1b89dff27d	2021-10-12	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Cytoplasm
Extracellular
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 DB01041	21059682	details
Urine	Expected but not Quantified	Not Quantified	Not Available	Not Available	Taking drug identified by DrugBank entry DB01041	21059682	details

Abnormal Concentrations

Not Available

Predicted Concentrations

Biospecimen	Value	Original age	Original sex	Original condition	Comments
Blood	0.000 uM	Adult (>18 years old)	Both	Normal	Predicted based on drug qualities
Blood	0.000 umol/mmol creatinine	Adult (>18 years old)	Both	Normal	Predicted based on drug qualities

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

DB01041

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

5233

KEGG Compound ID

C07910

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Thalidomide

METLIN ID

Not Available

PubChem Compound

5426

PDB ID

Not Available

ChEBI ID

74947

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

rw1215651

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Not Available

Showing metabocard for Thalidomide (HMDB0015175)

MOL for HMDB0015175 (Thalidomide)

3D MOL for HMDB0015175 (Thalidomide)

3D SDF for HMDB0015175 (Thalidomide)

3D-SDF for HMDB0015175 (Thalidomide)

PDB for HMDB0015175 (Thalidomide)

3D PDB for HMDB0015175 (Thalidomide)

SMILES for HMDB0015175 (Thalidomide)

INCHI for HMDB0015175 (Thalidomide)

Structure for HMDB0015175 (Thalidomide)

3D Structure for HMDB0015175 (Thalidomide)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra