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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-11 17:14:42 UTC

Update Date

2021-09-26 23:12:33 UTC

HMDB ID

HMDB0256694

Secondary Accession Numbers

None

Metabolite Identification

Common Name

Pomalidomide

Description

Pomalidomide, also known as pomalyst or CC 4047, 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. Based on a literature review a significant number of articles have been published on Pomalidomide. This compound has been identified in human blood as reported by (PMID: 31557052 ). Pomalidomide is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Pomalidomide is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.

Structure

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

HMDB0259687
     RDKit          3D
(R)-Pomalidomide
 31 33  0  0  0  0  0  0  0  0999 V2000
   -3.0983    0.1569   -2.5260 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1498    0.2804   -1.1113 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3353    0.4519   -0.4338 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3511    0.5685    0.9396 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1861    0.5162    1.6611 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9834    0.3449    1.0060 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9727    0.2286   -0.3696 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5801    0.0614   -0.7557 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1153   -0.0803   -1.9097 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2631    0.0769    0.4034 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.6780   -0.0547    0.4665 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1862   -1.3507   -0.1060 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6574   -1.4756    0.0069 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3895   -0.2061    0.1878 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5352   -0.2232    0.6702 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8010    1.0209   -0.1812 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.3771    1.0410   -0.2923 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7617    1.8927   -0.9603 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6059    0.2541    1.5144 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2647    0.3241    2.7430 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3359   -0.3215   -3.0304 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8656    0.5671   -3.0961 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2461    0.4932   -0.9937 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2833    0.7046    1.4862 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1563    0.6033    2.7354 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0268   -0.0007    1.5139 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8005   -1.4858   -1.1353 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7210   -2.1717    0.5143 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0356   -1.9151   -0.9630 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9617   -2.1981    0.8101 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3352    1.8963   -0.3737 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  8 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  2  0
 14 16  1  0
 16 17  1  0
 17 18  2  0
 10 19  1  0
 19 20  2  0
  7  2  1  0
 17 11  1  0
 19  6  1  0
  1 21  1  0
  1 22  1  0
  3 23  1  0
  4 24  1  0
  5 25  1  0
 11 26  1  0
 12 27  1  0
 12 28  1  0
 13 29  1  0
 13 30  1  0
 16 31  1  0
M  END

 
  Mrv0541 06201316152D          
 
 20 22  0  0  0  0            999 V2000
   15.4857   -9.4819    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   16.3138   -9.4819    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.9888  -10.1444    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.9888   -8.8194    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.7278   -8.7366    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.7278  -10.1858    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.2021   -9.8959    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.2787  -10.9311    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.2021   -9.0678    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.2372   -8.0327    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.5560   -8.7366    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   16.3138   -8.0327    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.5974  -10.1858    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.4982  -10.3100    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.4982   -8.6538    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.9700   -9.4405    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.7943   -9.8959    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.7943   -9.0678    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.7981   -9.4405    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.4982   -7.8257    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  0  0  0  0
  2  5  1  0  0  0  0
  2  6  1  0  0  0  0
  3  7  1  0  0  0  0
  3  8  2  0  0  0  0
  4  9  1  0  0  0  0
  4 10  2  0  0  0  0
  5 11  1  0  0  0  0
  5 12  2  0  0  0  0
  6 13  1  0  0  0  0
  7 14  1  0  0  0  0
  9 15  1  0  0  0  0
 11 16  1  0  0  0  0
 14 17  2  0  0  0  0
 15 18  2  0  0  0  0
 16 19  2  0  0  0  0
  7  9  2  0  0  0  0
 13 16  1  0  0  0  0
 17 18  1  0  0  0  0
 15 20  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0256694

> <DATABASE_NAME>
hmdb

> <SMILES>
NC1=CC=CC2=C1C(=O)N(C1CCC(=O)NC1=O)C2=O

> <INCHI_IDENTIFIER>
InChI=1S/C13H11N3O4/c14-7-3-1-2-6-10(7)13(20)16(12(6)19)8-4-5-9(17)15-11(8)18/h1-3,8H,4-5,14H2,(H,15,17,18)

> <INCHI_KEY>
UVSMNLNDYGZFPF-UHFFFAOYSA-N

> <FORMULA>
C13H11N3O4

> <MOLECULAR_WEIGHT>
273.2441

> <EXACT_MASS>
273.074955855

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_AVERAGE_POLARIZABILITY>
25.812774920377443

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

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

> <ALOGPS_LOGP>
0.02

> <JCHEM_LOGP>
-0.16321859799999983

> <ALOGPS_LOGS>
-2.03

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
16.74266805587048

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.593277713635468

> <JCHEM_PKA_STRONGEST_BASIC>
1.5569195735712902

> <JCHEM_POLAR_SURFACE_AREA>
109.57000000000001

> <JCHEM_REFRACTIVITY>
69.02520000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.57e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
pomalidomide

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0259687
     RDKit          3D
(R)-Pomalidomide
 31 33  0  0  0  0  0  0  0  0999 V2000
   -3.0983    0.1569   -2.5260 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1498    0.2804   -1.1113 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3353    0.4519   -0.4338 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3511    0.5685    0.9396 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1861    0.5162    1.6611 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9834    0.3449    1.0060 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9727    0.2286   -0.3696 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5801    0.0614   -0.7557 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1153   -0.0803   -1.9097 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2631    0.0769    0.4034 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.6780   -0.0547    0.4665 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1862   -1.3507   -0.1060 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6574   -1.4756    0.0069 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3895   -0.2061    0.1878 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5352   -0.2232    0.6702 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8010    1.0209   -0.1812 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.3771    1.0410   -0.2923 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7617    1.8927   -0.9603 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6059    0.2541    1.5144 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2647    0.3241    2.7430 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3359   -0.3215   -3.0304 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8656    0.5671   -3.0961 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2461    0.4932   -0.9937 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2833    0.7046    1.4862 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1563    0.6033    2.7354 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0268   -0.0007    1.5139 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8005   -1.4858   -1.1353 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7210   -2.1717    0.5143 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0356   -1.9151   -0.9630 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9617   -2.1981    0.8101 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3352    1.8963   -0.3737 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  8 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  2  0
 14 16  1  0
 16 17  1  0
 17 18  2  0
 10 19  1  0
 19 20  2  0
  7  2  1  0
 17 11  1  0
 19  6  1  0
  1 21  1  0
  1 22  1  0
  3 23  1  0
  4 24  1  0
  5 25  1  0
 11 26  1  0
 12 27  1  0
 12 28  1  0
 13 29  1  0
 13 30  1  0
 16 31  1  0
M  END

HEADER    PROTEIN                                 20-JUN-13   NONE
TITLE     NULL                                                        
COMPND    MOLECULE:                                                   
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   20-JUN-13         0                                  
HETATM    1  N   UNK     0      28.907 -17.700   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0      30.452 -17.700   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      27.979 -18.936   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      27.979 -16.463   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      31.225 -16.308   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      31.225 -19.013   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      26.511 -18.472   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      28.520 -20.405   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      26.511 -16.927   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      28.443 -14.994   0.000  0.00  0.00           O+0
HETATM   11  N   UNK     0      32.771 -16.308   0.000  0.00  0.00           N+0
HETATM   12  O   UNK     0      30.452 -14.994   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0      32.848 -19.013   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      25.197 -19.245   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      25.197 -16.154   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      33.544 -17.622   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      23.883 -18.472   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      23.883 -16.927   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      35.090 -17.622   0.000  0.00  0.00           O+0
HETATM   20  N   UNK     0      25.197 -14.608   0.000  0.00  0.00           N+0
CONECT    1    2    3    4                                                  
CONECT    2    1    5    6                                                  
CONECT    3    1    7    8                                                  
CONECT    4    1    9   10                                                  
CONECT    5    2   11   12                                                  
CONECT    6    2   13                                                       
CONECT    7    3   14    9                                                  
CONECT    8    3                                                            
CONECT    9    4   15    7                                                  
CONECT   10    4                                                            
CONECT   11    5   16                                                       
CONECT   12    5                                                            
CONECT   13    6   16                                                       
CONECT   14    7   17                                                       
CONECT   15    9   18   20                                                  
CONECT   16   11   19   13                                                  
CONECT   17   14   18                                                       
CONECT   18   15   17                                                       
CONECT   19   16                                                            
CONECT   20   15                                                            
MASTER        0    0    0    0    0    0    0    0   20    0   44    0
END

COMPND    HMDB0256694
HETATM    1  N1  UNL     1       3.789  -1.784   0.861  1.00  0.00           N  
HETATM    2  C1  UNL     1       3.433  -0.594   0.148  1.00  0.00           C  
HETATM    3  C2  UNL     1       4.379   0.249  -0.404  1.00  0.00           C  
HETATM    4  C3  UNL     1       3.983   1.387  -1.082  1.00  0.00           C  
HETATM    5  C4  UNL     1       2.673   1.732  -1.241  1.00  0.00           C  
HETATM    6  C5  UNL     1       1.725   0.872  -0.679  1.00  0.00           C  
HETATM    7  C6  UNL     1       2.095  -0.271   0.004  1.00  0.00           C  
HETATM    8  C7  UNL     1       0.865  -0.942   0.462  1.00  0.00           C  
HETATM    9  O1  UNL     1       0.866  -2.014   1.117  1.00  0.00           O  
HETATM   10  N2  UNL     1      -0.258  -0.177   0.040  1.00  0.00           N  
HETATM   11  C8  UNL     1      -1.647  -0.457   0.266  1.00  0.00           C  
HETATM   12  C9  UNL     1      -2.346   0.568   1.101  1.00  0.00           C  
HETATM   13  C10 UNL     1      -3.814   0.680   0.897  1.00  0.00           C  
HETATM   14  C11 UNL     1      -4.426  -0.376   0.066  1.00  0.00           C  
HETATM   15  O2  UNL     1      -5.559  -0.819   0.329  1.00  0.00           O  
HETATM   16  N3  UNL     1      -3.701  -0.883  -1.046  1.00  0.00           N  
HETATM   17  C12 UNL     1      -2.299  -0.763  -1.011  1.00  0.00           C  
HETATM   18  O3  UNL     1      -1.635  -0.915  -2.038  1.00  0.00           O  
HETATM   19  C13 UNL     1       0.283   0.936  -0.661  1.00  0.00           C  
HETATM   20  O4  UNL     1      -0.409   1.844  -1.187  1.00  0.00           O  
HETATM   21  H1  UNL     1       4.062  -2.622   0.268  1.00  0.00           H  
HETATM   22  H2  UNL     1       3.779  -1.823   1.905  1.00  0.00           H  
HETATM   23  H3  UNL     1       5.429  -0.005  -0.291  1.00  0.00           H  
HETATM   24  H4  UNL     1       4.733   2.023  -1.500  1.00  0.00           H  
HETATM   25  H5  UNL     1       2.321   2.608  -1.761  1.00  0.00           H  
HETATM   26  H6  UNL     1      -1.696  -1.422   0.857  1.00  0.00           H  
HETATM   27  H7  UNL     1      -1.907   1.593   0.982  1.00  0.00           H  
HETATM   28  H8  UNL     1      -2.132   0.331   2.187  1.00  0.00           H  
HETATM   29  H9  UNL     1      -4.323   0.719   1.897  1.00  0.00           H  
HETATM   30  H10 UNL     1      -4.069   1.659   0.390  1.00  0.00           H  
HETATM   31  H11 UNL     1      -4.191  -1.334  -1.873  1.00  0.00           H  
CONECT    1    2   21   22
CONECT    2    3    3    7
CONECT    3    4   23
CONECT    4    5    5   24
CONECT    5    6   25
CONECT    6    7    7   19
CONECT    7    8
CONECT    8    9    9   10
CONECT   10   11   19
CONECT   11   12   17   26
CONECT   12   13   27   28
CONECT   13   14   29   30
CONECT   14   15   15   16
CONECT   16   17   31
CONECT   17   18   18
CONECT   19   20   20
END

HMDB0259687
     RDKit          3D
(R)-Pomalidomide
 31 33  0  0  0  0  0  0  0  0999 V2000
   -3.0983    0.1569   -2.5260 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1498    0.2804   -1.1113 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3353    0.4519   -0.4338 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3511    0.5685    0.9396 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1861    0.5162    1.6611 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9834    0.3449    1.0060 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9727    0.2286   -0.3696 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5801    0.0614   -0.7557 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1153   -0.0803   -1.9097 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2631    0.0769    0.4034 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.6780   -0.0547    0.4665 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1862   -1.3507   -0.1060 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6574   -1.4756    0.0069 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3895   -0.2061    0.1878 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5352   -0.2232    0.6702 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8010    1.0209   -0.1812 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.3771    1.0410   -0.2923 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7617    1.8927   -0.9603 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6059    0.2541    1.5144 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2647    0.3241    2.7430 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3359   -0.3215   -3.0304 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8656    0.5671   -3.0961 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2461    0.4932   -0.9937 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2833    0.7046    1.4862 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1563    0.6033    2.7354 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0268   -0.0007    1.5139 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8005   -1.4858   -1.1353 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7210   -2.1717    0.5143 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0356   -1.9151   -0.9630 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9617   -2.1981    0.8101 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3352    1.8963   -0.3737 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  8 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  2  0
 14 16  1  0
 16 17  1  0
 17 18  2  0
 10 19  1  0
 19 20  2  0
  7  2  1  0
 17 11  1  0
 19  6  1  0
  1 21  1  0
  1 22  1  0
  3 23  1  0
  4 24  1  0
  5 25  1  0
 11 26  1  0
 12 27  1  0
 12 28  1  0
 13 29  1  0
 13 30  1  0
 16 31  1  0
M  END

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
3-Amino-N-(2,6-dioxo-3-piperidyl)phthalimide	ChEBI
4-Amino-2-(2,6-dioxo-3-piperidyl)isoindoline-1,3-dione	ChEBI
4-Aminothalidomide	ChEBI
CC 4047	ChEBI
CC-4047	ChEBI
Pomalyst	ChEBI
S-3-amino-phthalimido-Glutarimide	MeSH
3-Aminophthalimidoglutarimide	MeSH
S-3APG	MeSH
3-aminio-phthalimido-Glutarimide	MeSH

Chemical Formula

C₁₃H₁₁N₃O₄

Average Molecular Weight

273.2441

Monoisotopic Molecular Weight

273.074955855

IUPAC Name

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

Traditional Name

pomalidomide

CAS Registry Number

Not Available

SMILES

NC1=CC=CC2=C1C(=O)N(C1CCC(=O)NC1=O)C2=O

InChI Identifier

InChI=1S/C13H11N3O4/c14-7-3-1-2-6-10(7)13(20)16(12(6)19)8-4-5-9(17)15-11(8)18/h1-3,8H,4-5,14H2,(H,15,17,18)

InChI Key

UVSMNLNDYGZFPF-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
Vinylogous amide
Carboxylic acid imide, n-unsubstituted
Amino acid or derivatives
Lactam
Carboxylic acid derivative
Azacycle
Primary amine
Amine
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Organic nitrogen compound
Carbonyl group
Organic oxygen compound
Organooxygen compound
Organonitrogen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

dicarboximide (CHEBI:72690 )
aromatic amine (CHEBI:72690 )
piperidones (CHEBI:72690 )
isoindoles (CHEBI:72690 )

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (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
logP	0.02	ALOGPS
logP	-0.16	ChemAxon
logS	-2	ALOGPS
pKa (Strongest Acidic)	11.59	ChemAxon
pKa (Strongest Basic)	1.56	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	109.57 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	69.03 m³·mol⁻¹	ChemAxon
Polarizability	25.81 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]+	165.084	30932474
DeepCCS	[M-H]-	162.726	30932474
DeepCCS	[M-2H]-	195.612	30932474
DeepCCS	[M+Na]+	171.177	30932474
AllCCS	[M+H]+	161.2	32859911
AllCCS	[M+H-H2O]+	157.6	32859911
AllCCS	[M+NH4]+	164.4	32859911
AllCCS	[M+Na]+	165.4	32859911
AllCCS	[M-H]-	161.4	32859911
AllCCS	[M+Na-2H]-	160.9	32859911
AllCCS	[M+HCOO]-	160.3	32859911

Predicted Kovats Retention Indices

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Pomalidomide,1TMS,isomer #1	C[Si](C)(C)NC1=CC=CC2=C1C(=O)N(C1CCC(=O)NC1=O)C2=O	2841.2	Semi standard non polar	33892256
Pomalidomide,1TMS,isomer #1	C[Si](C)(C)NC1=CC=CC2=C1C(=O)N(C1CCC(=O)NC1=O)C2=O	2838.0	Standard non polar	33892256
Pomalidomide,1TMS,isomer #1	C[Si](C)(C)NC1=CC=CC2=C1C(=O)N(C1CCC(=O)NC1=O)C2=O	4437.5	Standard polar	33892256
Pomalidomide,1TMS,isomer #2	C[Si](C)(C)N1C(=O)CCC(N2C(=O)C3=CC=CC(N)=C3C2=O)C1=O	2684.2	Semi standard non polar	33892256
Pomalidomide,1TMS,isomer #2	C[Si](C)(C)N1C(=O)CCC(N2C(=O)C3=CC=CC(N)=C3C2=O)C1=O	2624.6	Standard non polar	33892256
Pomalidomide,1TMS,isomer #2	C[Si](C)(C)N1C(=O)CCC(N2C(=O)C3=CC=CC(N)=C3C2=O)C1=O	4136.4	Standard polar	33892256
Pomalidomide,2TMS,isomer #1	C[Si](C)(C)N(C1=CC=CC2=C1C(=O)N(C1CCC(=O)NC1=O)C2=O)[Si](C)(C)C	2682.7	Semi standard non polar	33892256
Pomalidomide,2TMS,isomer #1	C[Si](C)(C)N(C1=CC=CC2=C1C(=O)N(C1CCC(=O)NC1=O)C2=O)[Si](C)(C)C	2882.1	Standard non polar	33892256
Pomalidomide,2TMS,isomer #1	C[Si](C)(C)N(C1=CC=CC2=C1C(=O)N(C1CCC(=O)NC1=O)C2=O)[Si](C)(C)C	4084.8	Standard polar	33892256
Pomalidomide,2TMS,isomer #2	C[Si](C)(C)NC1=CC=CC2=C1C(=O)N(C1CCC(=O)N([Si](C)(C)C)C1=O)C2=O	2715.4	Semi standard non polar	33892256
Pomalidomide,2TMS,isomer #2	C[Si](C)(C)NC1=CC=CC2=C1C(=O)N(C1CCC(=O)N([Si](C)(C)C)C1=O)C2=O	2831.7	Standard non polar	33892256
Pomalidomide,2TMS,isomer #2	C[Si](C)(C)NC1=CC=CC2=C1C(=O)N(C1CCC(=O)N([Si](C)(C)C)C1=O)C2=O	3716.4	Standard polar	33892256
Pomalidomide,3TMS,isomer #1	C[Si](C)(C)N1C(=O)CCC(N2C(=O)C3=CC=CC(N([Si](C)(C)C)[Si](C)(C)C)=C3C2=O)C1=O	2583.7	Semi standard non polar	33892256
Pomalidomide,3TMS,isomer #1	C[Si](C)(C)N1C(=O)CCC(N2C(=O)C3=CC=CC(N([Si](C)(C)C)[Si](C)(C)C)=C3C2=O)C1=O	2907.0	Standard non polar	33892256
Pomalidomide,3TMS,isomer #1	C[Si](C)(C)N1C(=O)CCC(N2C(=O)C3=CC=CC(N([Si](C)(C)C)[Si](C)(C)C)=C3C2=O)C1=O	3417.6	Standard polar	33892256
Pomalidomide,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)NC1=CC=CC2=C1C(=O)N(C1CCC(=O)NC1=O)C2=O	3077.1	Semi standard non polar	33892256
Pomalidomide,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)NC1=CC=CC2=C1C(=O)N(C1CCC(=O)NC1=O)C2=O	3057.5	Standard non polar	33892256
Pomalidomide,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)NC1=CC=CC2=C1C(=O)N(C1CCC(=O)NC1=O)C2=O	4349.4	Standard polar	33892256
Pomalidomide,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)N1C(=O)CCC(N2C(=O)C3=CC=CC(N)=C3C2=O)C1=O	2921.4	Semi standard non polar	33892256
Pomalidomide,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)N1C(=O)CCC(N2C(=O)C3=CC=CC(N)=C3C2=O)C1=O	2819.9	Standard non polar	33892256
Pomalidomide,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)N1C(=O)CCC(N2C(=O)C3=CC=CC(N)=C3C2=O)C1=O	4088.5	Standard polar	33892256
Pomalidomide,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N(C1=CC=CC2=C1C(=O)N(C1CCC(=O)NC1=O)C2=O)[Si](C)(C)C(C)(C)C	3145.1	Semi standard non polar	33892256
Pomalidomide,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N(C1=CC=CC2=C1C(=O)N(C1CCC(=O)NC1=O)C2=O)[Si](C)(C)C(C)(C)C	3275.3	Standard non polar	33892256
Pomalidomide,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N(C1=CC=CC2=C1C(=O)N(C1CCC(=O)NC1=O)C2=O)[Si](C)(C)C(C)(C)C	3999.2	Standard polar	33892256
Pomalidomide,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)NC1=CC=CC2=C1C(=O)N(C1CCC(=O)N([Si](C)(C)C(C)(C)C)C1=O)C2=O	3125.0	Semi standard non polar	33892256
Pomalidomide,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)NC1=CC=CC2=C1C(=O)N(C1CCC(=O)N([Si](C)(C)C(C)(C)C)C1=O)C2=O	3229.6	Standard non polar	33892256
Pomalidomide,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)NC1=CC=CC2=C1C(=O)N(C1CCC(=O)N([Si](C)(C)C(C)(C)C)C1=O)C2=O	3678.2	Standard polar	33892256
Pomalidomide,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N1C(=O)CCC(N2C(=O)C3=CC=CC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=C3C2=O)C1=O	3244.5	Semi standard non polar	33892256
Pomalidomide,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N1C(=O)CCC(N2C(=O)C3=CC=CC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=C3C2=O)C1=O	3475.1	Standard non polar	33892256
Pomalidomide,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N1C(=O)CCC(N2C(=O)C3=CC=CC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=C3C2=O)C1=O	3533.6	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - Pomalidomide GC-MS (Non-derivatized) - 70eV, Positive	splash10-0gej-4980000000-d041e1fb3b612b5f8e22	2017-08-28	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Pomalidomide GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Pomalidomide GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Experimental LC-MS/MS	LC-MS/MS Spectrum - Pomalidomide LC-ESI-qTof , Positive-QTOF	splash10-0udi-1590000000-a511655f5e07f3ab2179	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Pomalidomide , positive-QTOF	splash10-0udi-1590000000-a511655f5e07f3ab2179	2017-09-14	HMDB team, MONA	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Pomalidomide 10V, Positive-QTOF	splash10-05fr-0090000000-7d14af32a1640f645afc	2017-07-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Pomalidomide 20V, Positive-QTOF	splash10-0ab9-0190000000-734f84ec8cd642684084	2017-07-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Pomalidomide 40V, Positive-QTOF	splash10-0f76-8940000000-362915b4187ee23f2fcf	2017-07-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Pomalidomide 10V, Negative-QTOF	splash10-00di-0190000000-c438caf9103271bcb665	2017-07-26	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Pomalidomide 20V, Negative-QTOF	splash10-0h90-1390000000-eb3387d4568613b0761f	2017-07-26	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Pomalidomide 40V, Negative-QTOF	splash10-03dl-9700000000-b666e9e333f7bcb1b3c5	2017-07-26	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-10-27	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-10-27	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-10-27	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-10-27	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-10-27	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-10-27	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-10-27	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-10-27	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-10-27	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-10-27	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-10-27	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-10-27	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-10-27	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-10-27	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-10-27	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-10-27	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-10-27	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-10-27	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-10-27	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-10-27	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	31557052	details

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

DB08910

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

118785

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Pomalidomide

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

72690

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

Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]

Showing metabocard for Pomalidomide (HMDB0256694)

MOL for HMDB0256694 (Pomalidomide)

3D MOL for HMDB0256694 (Pomalidomide)

3D SDF for HMDB0256694 (Pomalidomide)

3D-SDF for HMDB0256694 (Pomalidomide)

PDB for HMDB0256694 (Pomalidomide)

3D PDB for HMDB0256694 (Pomalidomide)

SMILES for HMDB0256694 (Pomalidomide)

INCHI for HMDB0256694 (Pomalidomide)

Structure for HMDB0256694 (Pomalidomide)

3D Structure for HMDB0256694 (Pomalidomide)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra