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Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References enzymes (3) Show 3 proteins XML

Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-06 15:16:49 UTC

Update Date

2022-03-07 02:51:41 UTC

HMDB ID

HMDB0014623

Secondary Accession Numbers

HMDB14623

Metabolite Identification

Common Name

Lenalidomide

Description

Lenalidomide (initially known as CC-5013 and marketed as Revlimid by Celgene) is a derivative of thalidomide introduced in 2004. It was initially intended as a treatment for multiple myeloma, for which thalidomide is an accepted therapeutic modality, but has also shown efficacy in the hematological disorders known as the myelodysplastic syndromes. [Wikipedia ]

Structure

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

HMDB0259413
     RDKit          3D
(3R)-3-(7-Amino-3-oxo-1H-isoindol-2-yl)piperidine-2,6-dione
 32 34  0  0  0  0  0  0  0  0999 V2000
   -2.7161   -0.5495   -2.2748 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8725   -0.3368   -0.8801 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1538   -0.3175   -0.3299 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3297   -0.1126    1.0219 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2043    0.0702    1.7989 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9211    0.0503    1.2440 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7434   -0.1528   -0.0973 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3050   -0.1319   -0.4469 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3999    0.1017    0.7921 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.8276    0.2127    1.0158 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4335    1.3541    0.2691 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9727    1.0025   -1.0790 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8503   -0.1721   -1.0852 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8007   -0.2114   -1.9077 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5923   -1.2183   -0.1626 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.5123   -1.0915    0.7234 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0756   -2.1074    1.3166 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5850    0.2089    1.7978 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4059    0.4168    3.0498 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2263    0.1267   -2.8964 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0960   -1.4081   -2.7253 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0096   -0.4641   -0.9680 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3215   -0.0934    1.4746 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2873    0.2327    2.8518 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0078   -1.0592   -0.9522 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1453    0.6937   -1.1891 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9807    0.3918    2.0952 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6777    2.1547    0.1376 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2779    1.7957    0.8576 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1641    0.8132   -1.8306 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5316    1.8788   -1.4648 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2179   -2.0780   -0.1564 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  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  2  0
 13 15  1  0
 15 16  1  0
 16 17  2  0
  9 18  1  0
 18 19  2  0
  7  2  1  0
 16 10  1  0
 18  6  1  0
  1 20  1  0
  1 21  1  0
  3 22  1  0
  4 23  1  0
  5 24  1  0
  8 25  1  0
  8 26  1  0
 10 27  1  0
 11 28  1  0
 11 29  1  0
 12 30  1  0
 12 31  1  0
 15 32  1  0
M  END

480
  Mrv0541 02231214422D          

 19 21  0  0  1  0            999 V2000
    4.1159   -1.6769    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.1662    1.2002    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.6412   -0.2289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3412   -0.2289    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.4037    0.4857    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.3645    1.4212    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.1662   -0.2289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5787   -0.9433    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8597    0.4351    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0791    0.1836    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8597   -0.8928    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4037   -0.9433    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0791   -0.6414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5787    0.4857    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8162   -0.2289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3645    0.5962    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3645   -1.0539    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500    0.1836    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500   -0.6414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1 11  2  0  0  0  0
  2 14  2  0  0  0  0
  3 15  2  0  0  0  0
  4  7  1  0  0  0  0
  4  9  1  0  0  0  0
  4 11  1  0  0  0  0
  5 14  1  0  0  0  0
  5 15  1  0  0  0  0
  6 16  1  0  0  0  0
  7  8  1  0  0  0  0
  7 14  1  0  0  0  0
  8 12  1  0  0  0  0
  9 10  1  0  0  0  0
 10 13  2  0  0  0  0
 10 16  1  0  0  0  0
 11 13  1  0  0  0  0
 12 15  1  0  0  0  0
 13 17  1  0  0  0  0
 16 18  2  0  0  0  0
 17 19  2  0  0  0  0
 18 19  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0014623

> <DATABASE_NAME>
hmdb

> <SMILES>
NC1=CC=CC2=C1CN(C1CCC(=O)NC1=O)C2=O

> <INCHI_IDENTIFIER>
InChI=1S/C13H13N3O3/c14-9-3-1-2-7-8(9)6-16(13(7)19)10-4-5-11(17)15-12(10)18/h1-3,10H,4-6,14H2,(H,15,17,18)

> <INCHI_KEY>
GOTYRUGSSMKFNF-UHFFFAOYSA-N

> <FORMULA>
C13H13N3O3

> <MOLECULAR_WEIGHT>
259.2606

> <EXACT_MASS>
259.095691297

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
25.54588111496085

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-(4-amino-1-oxo-2,3-dihydro-1H-isoindol-2-yl)piperidine-2,6-dione

> <ALOGPS_LOGP>
-0.43

> <JCHEM_LOGP>
-0.707852159

> <ALOGPS_LOGS>
-2.05

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
15.21184443222047

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.613173643508485

> <JCHEM_PKA_STRONGEST_BASIC>
2.3135467380676977

> <JCHEM_POLAR_SURFACE_AREA>
92.5

> <JCHEM_REFRACTIVITY>
68.29810000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.33e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
lenalidomide

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0259413
     RDKit          3D
(3R)-3-(7-Amino-3-oxo-1H-isoindol-2-yl)piperidine-2,6-dione
 32 34  0  0  0  0  0  0  0  0999 V2000
   -2.7161   -0.5495   -2.2748 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8725   -0.3368   -0.8801 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1538   -0.3175   -0.3299 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3297   -0.1126    1.0219 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2043    0.0702    1.7989 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9211    0.0503    1.2440 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7434   -0.1528   -0.0973 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3050   -0.1319   -0.4469 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3999    0.1017    0.7921 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.8276    0.2127    1.0158 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4335    1.3541    0.2691 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9727    1.0025   -1.0790 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8503   -0.1721   -1.0852 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8007   -0.2114   -1.9077 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5923   -1.2183   -0.1626 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.5123   -1.0915    0.7234 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0756   -2.1074    1.3166 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5850    0.2089    1.7978 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4059    0.4168    3.0498 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2263    0.1267   -2.8964 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0960   -1.4081   -2.7253 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0096   -0.4641   -0.9680 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3215   -0.0934    1.4746 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2873    0.2327    2.8518 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0078   -1.0592   -0.9522 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1453    0.6937   -1.1891 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9807    0.3918    2.0952 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6777    2.1547    0.1376 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2779    1.7957    0.8576 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1641    0.8132   -1.8306 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5316    1.8788   -1.4648 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2179   -2.0780   -0.1564 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  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  2  0
 13 15  1  0
 15 16  1  0
 16 17  2  0
  9 18  1  0
 18 19  2  0
  7  2  1  0
 16 10  1  0
 18  6  1  0
  1 20  1  0
  1 21  1  0
  3 22  1  0
  4 23  1  0
  5 24  1  0
  8 25  1  0
  8 26  1  0
 10 27  1  0
 11 28  1  0
 11 29  1  0
 12 30  1  0
 12 31  1  0
 15 32  1  0
M  END

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: 480                                               
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  O   UNK     0       7.683  -3.130   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0       9.644   2.240   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      14.264  -0.427   0.000  0.00  0.00           O+0
HETATM    4  N   UNK     0       8.104  -0.427   0.000  0.00  0.00           N+0
HETATM    5  N   UNK     0      11.954   0.907   0.000  0.00  0.00           N+0
HETATM    6  N   UNK     0       4.414   2.653   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0       9.644  -0.427   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      10.414  -1.761   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       7.205   0.812   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       5.748   0.343   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       7.205  -1.667   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      11.954  -1.761   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       5.748  -1.197   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      10.414   0.907   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      12.724  -0.427   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       4.414   1.113   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       4.414  -1.967   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       3.080   0.343   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       3.080  -1.197   0.000  0.00  0.00           C+0
CONECT    1   11                                                            
CONECT    2   14                                                            
CONECT    3   15                                                            
CONECT    4    7    9   11                                                  
CONECT    5   14   15                                                       
CONECT    6   16                                                            
CONECT    7    4    8   14                                                  
CONECT    8    7   12                                                       
CONECT    9    4   10                                                       
CONECT   10    9   13   16                                                  
CONECT   11    1    4   13                                                  
CONECT   12    8   15                                                       
CONECT   13   10   11   17                                                  
CONECT   14    2    5    7                                                  
CONECT   15    3    5   12                                                  
CONECT   16    6   10   18                                                  
CONECT   17   13   19                                                       
CONECT   18   16   19                                                       
CONECT   19   17   18                                                       
MASTER        0    0    0    0    0    0    0    0   19    0   42    0
END

COMPND    HMDB0259413
HETATM    1  N1  UNL     1      -2.716  -0.550  -2.275  1.00  0.00           N  
HETATM    2  C1  UNL     1      -2.873  -0.337  -0.880  1.00  0.00           C  
HETATM    3  C2  UNL     1      -4.154  -0.318  -0.330  1.00  0.00           C  
HETATM    4  C3  UNL     1      -4.330  -0.113   1.022  1.00  0.00           C  
HETATM    5  C4  UNL     1      -3.204   0.070   1.799  1.00  0.00           C  
HETATM    6  C5  UNL     1      -1.921   0.050   1.244  1.00  0.00           C  
HETATM    7  C6  UNL     1      -1.743  -0.153  -0.097  1.00  0.00           C  
HETATM    8  C7  UNL     1      -0.305  -0.132  -0.447  1.00  0.00           C  
HETATM    9  N2  UNL     1       0.400   0.102   0.792  1.00  0.00           N  
HETATM   10  C8  UNL     1       1.828   0.213   1.016  1.00  0.00           C  
HETATM   11  C9  UNL     1       2.433   1.354   0.269  1.00  0.00           C  
HETATM   12  C10 UNL     1       2.973   1.003  -1.079  1.00  0.00           C  
HETATM   13  C11 UNL     1       3.850  -0.172  -1.085  1.00  0.00           C  
HETATM   14  O1  UNL     1       4.801  -0.211  -1.908  1.00  0.00           O  
HETATM   15  N3  UNL     1       3.592  -1.218  -0.163  1.00  0.00           N  
HETATM   16  C12 UNL     1       2.512  -1.092   0.723  1.00  0.00           C  
HETATM   17  O2  UNL     1       2.076  -2.107   1.317  1.00  0.00           O  
HETATM   18  C13 UNL     1      -0.585   0.209   1.798  1.00  0.00           C  
HETATM   19  O3  UNL     1      -0.406   0.417   3.050  1.00  0.00           O  
HETATM   20  H1  UNL     1      -2.226   0.127  -2.896  1.00  0.00           H  
HETATM   21  H2  UNL     1      -3.096  -1.408  -2.725  1.00  0.00           H  
HETATM   22  H3  UNL     1      -5.010  -0.464  -0.968  1.00  0.00           H  
HETATM   23  H4  UNL     1      -5.321  -0.093   1.475  1.00  0.00           H  
HETATM   24  H5  UNL     1      -3.287   0.233   2.852  1.00  0.00           H  
HETATM   25  H6  UNL     1       0.008  -1.059  -0.952  1.00  0.00           H  
HETATM   26  H7  UNL     1      -0.145   0.694  -1.189  1.00  0.00           H  
HETATM   27  H8  UNL     1       1.981   0.392   2.095  1.00  0.00           H  
HETATM   28  H9  UNL     1       1.678   2.155   0.138  1.00  0.00           H  
HETATM   29  H10 UNL     1       3.278   1.796   0.858  1.00  0.00           H  
HETATM   30  H11 UNL     1       2.164   0.813  -1.831  1.00  0.00           H  
HETATM   31  H12 UNL     1       3.532   1.879  -1.465  1.00  0.00           H  
HETATM   32  H13 UNL     1       4.218  -2.078  -0.156  1.00  0.00           H  
CONECT    1    2   20   21
CONECT    2    3    3    7
CONECT    3    4   22
CONECT    4    5    5   23
CONECT    5    6   24
CONECT    6    7    7   18
CONECT    7    8
CONECT    8    9   25   26
CONECT    9   10   18
CONECT   10   11   16   27
CONECT   11   12   28   29
CONECT   12   13   30   31
CONECT   13   14   14   15
CONECT   15   16   32
CONECT   16   17   17
CONECT   18   19   19
END

HMDB0259413
     RDKit          3D
(3R)-3-(7-Amino-3-oxo-1H-isoindol-2-yl)piperidine-2,6-dione
 32 34  0  0  0  0  0  0  0  0999 V2000
   -2.7161   -0.5495   -2.2748 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8725   -0.3368   -0.8801 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1538   -0.3175   -0.3299 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3297   -0.1126    1.0219 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2043    0.0702    1.7989 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9211    0.0503    1.2440 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7434   -0.1528   -0.0973 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3050   -0.1319   -0.4469 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3999    0.1017    0.7921 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.8276    0.2127    1.0158 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4335    1.3541    0.2691 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9727    1.0025   -1.0790 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8503   -0.1721   -1.0852 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8007   -0.2114   -1.9077 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5923   -1.2183   -0.1626 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.5123   -1.0915    0.7234 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0756   -2.1074    1.3166 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5850    0.2089    1.7978 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4059    0.4168    3.0498 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2263    0.1267   -2.8964 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0960   -1.4081   -2.7253 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0096   -0.4641   -0.9680 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3215   -0.0934    1.4746 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2873    0.2327    2.8518 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0078   -1.0592   -0.9522 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1453    0.6937   -1.1891 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9807    0.3918    2.0952 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6777    2.1547    0.1376 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2779    1.7957    0.8576 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1641    0.8132   -1.8306 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5316    1.8788   -1.4648 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2179   -2.0780   -0.1564 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  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  2  0
 13 15  1  0
 15 16  1  0
 16 17  2  0
  9 18  1  0
 18 19  2  0
  7  2  1  0
 16 10  1  0
 18  6  1  0
  1 20  1  0
  1 21  1  0
  3 22  1  0
  4 23  1  0
  5 24  1  0
  8 25  1  0
  8 26  1  0
 10 27  1  0
 11 28  1  0
 11 29  1  0
 12 30  1  0
 12 31  1  0
 15 32  1  0
M  END

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
1-oxo-2-(2,6-Dioxopiperidin-3-yl)-4-aminoisoindoline	ChEBI
3-(4-Amino-1-oxoisoindolin-2-yl)piperidine-2,6-dione	ChEBI
Revlimid	ChEBI
CC-5013	HMDB
CDC 501	HMDB
IMiD3	HMDB
Revimid	MeSH, HMDB
Celgene brand OF lenalidomide	MeSH, HMDB
IMiD3 CPD	MeSH, HMDB

Chemical Formula

C₁₃H₁₃N₃O₃

Average Molecular Weight

259.2606

Monoisotopic Molecular Weight

259.095691297

IUPAC Name

3-(4-amino-1-oxo-2,3-dihydro-1H-isoindol-2-yl)piperidine-2,6-dione

Traditional Name

lenalidomide

CAS Registry Number

191732-72-6

SMILES

NC1=CC=CC2=C1CN(C1CCC(=O)NC1=O)C2=O

InChI Identifier

InChI=1S/C13H13N3O3/c14-9-3-1-2-7-8(9)6-16(13(7)19)10-4-5-11(17)15-12(10)18/h1-3,10H,4-6,14H2,(H,15,17,18)

InChI Key

GOTYRUGSSMKFNF-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as isoindolones. These are aromatic polycyclic compounds that an isoindole bearing a ketone.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Isoindoles and derivatives

Sub Class

Isoindolines

Direct Parent

Isoindolones

Alternative Parents

Substituents

Isoindolone
Alpha-amino acid or derivatives
Isoindole
Piperidinedione
Piperidinone
Delta-lactam
Benzenoid
Piperidine
Tertiary carboxylic acid amide
Carboxylic acid imide, n-unsubstituted
Dicarboximide
Carboxylic acid imide
Lactam
Carboxamide group
Amino acid or derivatives
Azacycle
Carboxylic acid derivative
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Primary amine
Organooxygen compound
Organonitrogen compound
Carbonyl group
Amine
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

dicarboximide (CHEBI:63791 )
aromatic amine (CHEBI:63791 )
piperidones (CHEBI:63791 )
isoindoles (CHEBI:63791 )

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

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	2.33 g/L	Not Available
LogP	-0.4	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	2.33 g/L	ALOGPS
logP	-0.43	ALOGPS
logP	-0.71	ChemAxon
logS	-2	ALOGPS
pKa (Strongest Acidic)	11.61	ChemAxon
pKa (Strongest Basic)	2.31	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	92.5 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	68.3 m³·mol⁻¹	ChemAxon
Polarizability	25.55 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	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]+	160.347	31661259
DarkChem	[M-H]-	157.537	31661259
DeepCCS	[M+H]+	161.09	30932474
DeepCCS	[M-H]-	158.732	30932474
DeepCCS	[M-2H]-	191.659	30932474
DeepCCS	[M+Na]+	167.184	30932474
AllCCS	[M+H]+	159.0	32859911
AllCCS	[M+H-H2O]+	155.4	32859911
AllCCS	[M+NH4]+	162.3	32859911
AllCCS	[M+Na]+	163.3	32859911
AllCCS	[M-H]-	160.3	32859911
AllCCS	[M+Na-2H]-	159.9	32859911
AllCCS	[M+HCOO]-	159.5	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.	2.82 minutes	32390414
Predicted by Siyang on May 30, 2022	10.0042 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	3.37 minutes	32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid	46.2 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Lenalidomide	NC1=CC=CC2=C1CN(C1CCC(=O)NC1=O)C2=O	4149.2	Standard polar	33892256
Lenalidomide	NC1=CC=CC2=C1CN(C1CCC(=O)NC1=O)C2=O	2572.0	Standard non polar	33892256
Lenalidomide	NC1=CC=CC2=C1CN(C1CCC(=O)NC1=O)C2=O	2817.3	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Lenalidomide,1TMS,isomer #1	C[Si](C)(C)NC1=CC=CC2=C1CN(C1CCC(=O)NC1=O)C2=O	2796.3	Semi standard non polar	33892256
Lenalidomide,1TMS,isomer #1	C[Si](C)(C)NC1=CC=CC2=C1CN(C1CCC(=O)NC1=O)C2=O	2726.2	Standard non polar	33892256
Lenalidomide,1TMS,isomer #1	C[Si](C)(C)NC1=CC=CC2=C1CN(C1CCC(=O)NC1=O)C2=O	4146.3	Standard polar	33892256
Lenalidomide,1TMS,isomer #2	C[Si](C)(C)N1C(=O)CCC(N2CC3=C(N)C=CC=C3C2=O)C1=O	2618.4	Semi standard non polar	33892256
Lenalidomide,1TMS,isomer #2	C[Si](C)(C)N1C(=O)CCC(N2CC3=C(N)C=CC=C3C2=O)C1=O	2639.2	Standard non polar	33892256
Lenalidomide,1TMS,isomer #2	C[Si](C)(C)N1C(=O)CCC(N2CC3=C(N)C=CC=C3C2=O)C1=O	4008.2	Standard polar	33892256
Lenalidomide,2TMS,isomer #1	C[Si](C)(C)N(C1=CC=CC2=C1CN(C1CCC(=O)NC1=O)C2=O)[Si](C)(C)C	2721.8	Semi standard non polar	33892256
Lenalidomide,2TMS,isomer #1	C[Si](C)(C)N(C1=CC=CC2=C1CN(C1CCC(=O)NC1=O)C2=O)[Si](C)(C)C	2793.7	Standard non polar	33892256
Lenalidomide,2TMS,isomer #1	C[Si](C)(C)N(C1=CC=CC2=C1CN(C1CCC(=O)NC1=O)C2=O)[Si](C)(C)C	3902.1	Standard polar	33892256
Lenalidomide,2TMS,isomer #2	C[Si](C)(C)NC1=CC=CC2=C1CN(C1CCC(=O)N([Si](C)(C)C)C1=O)C2=O	2686.8	Semi standard non polar	33892256
Lenalidomide,2TMS,isomer #2	C[Si](C)(C)NC1=CC=CC2=C1CN(C1CCC(=O)N([Si](C)(C)C)C1=O)C2=O	2741.1	Standard non polar	33892256
Lenalidomide,2TMS,isomer #2	C[Si](C)(C)NC1=CC=CC2=C1CN(C1CCC(=O)N([Si](C)(C)C)C1=O)C2=O	3583.7	Standard polar	33892256
Lenalidomide,3TMS,isomer #1	C[Si](C)(C)N1C(=O)CCC(N2CC3=C(C=CC=C3N([Si](C)(C)C)[Si](C)(C)C)C2=O)C1=O	2571.5	Semi standard non polar	33892256
Lenalidomide,3TMS,isomer #1	C[Si](C)(C)N1C(=O)CCC(N2CC3=C(C=CC=C3N([Si](C)(C)C)[Si](C)(C)C)C2=O)C1=O	2837.6	Standard non polar	33892256
Lenalidomide,3TMS,isomer #1	C[Si](C)(C)N1C(=O)CCC(N2CC3=C(C=CC=C3N([Si](C)(C)C)[Si](C)(C)C)C2=O)C1=O	3315.5	Standard polar	33892256
Lenalidomide,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)NC1=CC=CC2=C1CN(C1CCC(=O)NC1=O)C2=O	3050.7	Semi standard non polar	33892256
Lenalidomide,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)NC1=CC=CC2=C1CN(C1CCC(=O)NC1=O)C2=O	2961.8	Standard non polar	33892256
Lenalidomide,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)NC1=CC=CC2=C1CN(C1CCC(=O)NC1=O)C2=O	4137.0	Standard polar	33892256
Lenalidomide,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)N1C(=O)CCC(N2CC3=C(N)C=CC=C3C2=O)C1=O	2869.2	Semi standard non polar	33892256
Lenalidomide,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)N1C(=O)CCC(N2CC3=C(N)C=CC=C3C2=O)C1=O	2871.9	Standard non polar	33892256
Lenalidomide,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)N1C(=O)CCC(N2CC3=C(N)C=CC=C3C2=O)C1=O	4002.8	Standard polar	33892256
Lenalidomide,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N(C1=CC=CC2=C1CN(C1CCC(=O)NC1=O)C2=O)[Si](C)(C)C(C)(C)C	3181.7	Semi standard non polar	33892256
Lenalidomide,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N(C1=CC=CC2=C1CN(C1CCC(=O)NC1=O)C2=O)[Si](C)(C)C(C)(C)C	3247.6	Standard non polar	33892256
Lenalidomide,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N(C1=CC=CC2=C1CN(C1CCC(=O)NC1=O)C2=O)[Si](C)(C)C(C)(C)C	3874.6	Standard polar	33892256
Lenalidomide,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)NC1=CC=CC2=C1CN(C1CCC(=O)N([Si](C)(C)C(C)(C)C)C1=O)C2=O	3131.6	Semi standard non polar	33892256
Lenalidomide,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)NC1=CC=CC2=C1CN(C1CCC(=O)N([Si](C)(C)C(C)(C)C)C1=O)C2=O	3194.0	Standard non polar	33892256
Lenalidomide,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)NC1=CC=CC2=C1CN(C1CCC(=O)N([Si](C)(C)C(C)(C)C)C1=O)C2=O	3589.3	Standard polar	33892256
Lenalidomide,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N1C(=O)CCC(N2CC3=C(C=CC=C3N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)C2=O)C1=O	3262.2	Semi standard non polar	33892256
Lenalidomide,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N1C(=O)CCC(N2CC3=C(C=CC=C3N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)C2=O)C1=O	3481.9	Standard non polar	33892256
Lenalidomide,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N1C(=O)CCC(N2CC3=C(C=CC=C3N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)C2=O)C1=O	3449.2	Standard polar	33892256

Spectra

Biological Properties

Cellular Locations

Cytoplasm
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 DB00480	21059682	details
Urine	Expected but not Quantified	Not Quantified	Not Available	Not Available	Taking drug identified by DrugBank entry DB00480	21059682	details

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

DB00480

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

187515

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Lenalidomide

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

63791

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

List A, Kurtin S, Roe DJ, Buresh A, Mahadevan D, Fuchs D, Rimsza L, Heaton R, Knight R, Zeldis JB: Efficacy of lenalidomide in myelodysplastic syndromes. N Engl J Med. 2005 Feb 10;352(6):549-57. [PubMed:15703420 ]
Anderson KC: Lenalidomide and thalidomide: mechanisms of action--similarities and differences. Semin Hematol. 2005 Oct;42(4 Suppl 4):S3-8. [PubMed:16344099 ]
Chang DH, Liu N, Klimek V, Hassoun H, Mazumder A, Nimer SD, Jagannath S, Dhodapkar MV: Enhancement of ligand-dependent activation of human natural killer T cells by lenalidomide: therapeutic implications. Blood. 2006 Jul 15;108(2):618-21. Epub 2006 Mar 28. [PubMed:16569772 ]

Enzymes

Enzyme Details

1. Prostaglandin G/H synthase 2

General function:: Involved in peroxidase activity
Specific function:: Mediates the formation of prostaglandins from arachidonate. May have a role as a major mediator of inflammation and/or a role for prostanoid signaling in activity-dependent plasticity.
Gene Name:: PTGS2
Uniprot ID:: P35354
Molecular weight:: 68995.625

References

Payvandi F, Wu L, Haley M, Schafer PH, Zhang LH, Chen RS, Muller GW, Stirling DI: Immunomodulatory drugs inhibit expression of cyclooxygenase-2 from TNF-alpha, IL-1beta, and LPS-stimulated human PBMC in a partially IL-10-dependent manner. Cell Immunol. 2004 Aug;230(2):81-8. [PubMed:15598423 ]
Zeldis JB, Schafer PH, Bennett BL, Mercurio F, Stirling DI: Potential new therapeutics for Waldenstrom's macroglobulinemia. Semin Oncol. 2003 Apr;30(2):275-81. [PubMed:12720152 ]

Enzyme Details

2. Tumor necrosis factor ligand superfamily member 11

General function:: Involved in tumor necrosis factor receptor binding
Specific function:: Cytokine that binds to TNFRSF11B/OPG and to TNFRSF11A/RANK. Osteoclast differentiation and activation factor. Augments the ability of dendritic cells to stimulate naive T-cell proliferation. May be an important regulator of interactions between T-cells and dendritic cells and may play a role in the regulation of the T-cell-dependent immune response. May also play an important role in enhanced bone-resorption in humoral hypercalcemia of malignancy
Gene Name:: TNFSF11
Uniprot ID:: O14788
Molecular weight:: 35477.8

References

Akobeng AK, Stokkers PC: Thalidomide and thalidomide analogues for maintenance of remission in Crohn's disease. Cochrane Database Syst Rev. 2009 Apr 15;(2):CD007351. doi: 10.1002/14651858.CD007351.pub2. [PubMed:19370685 ]
Melchert M, List A: The thalidomide saga. Int J Biochem Cell Biol. 2007;39(7-8):1489-99. Epub 2007 Jan 30. [PubMed:17369076 ]

Enzyme Details

3. Cadherin-5

General function:: Involved in calcium ion binding
Specific function:: Cadherins are calcium dependent cell adhesion proteins. They preferentially interact with themselves in a homophilic manner in connecting cells; cadherins may thus contribute to the sorting of heterogeneous cell types. This cadherin may play a important role in endothelial cell biology through control of the cohesion and organization of the intercellular junctions. It associates with alpha-catenin forming a link to the cytoskeleton
Gene Name:: CDH5
Uniprot ID:: P33151
Molecular weight:: 87515.7

References

Lu L, Payvandi F, Wu L, Zhang LH, Hariri RJ, Man HW, Chen RS, Muller GW, Hughes CC, Stirling DI, Schafer PH, Bartlett JB: The anti-cancer drug lenalidomide inhibits angiogenesis and metastasis via multiple inhibitory effects on endothelial cell function in normoxic and hypoxic conditions. Microvasc Res. 2009 Mar;77(2):78-86. doi: 10.1016/j.mvr.2008.08.003. Epub 2008 Sep 4. [PubMed:18805433 ]

Showing metabocard for Lenalidomide (HMDB0014623)

MOL for HMDB0014623 (Lenalidomide)

3D MOL for HMDB0014623 (Lenalidomide)

3D SDF for HMDB0014623 (Lenalidomide)

3D-SDF for HMDB0014623 (Lenalidomide)

PDB for HMDB0014623 (Lenalidomide)

3D PDB for HMDB0014623 (Lenalidomide)

SMILES for HMDB0014623 (Lenalidomide)

INCHI for HMDB0014623 (Lenalidomide)

Structure for HMDB0014623 (Lenalidomide)

3D Structure for HMDB0014623 (Lenalidomide)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

Enzymes

References

References

References