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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-06 15:00:17 UTC

Update Date

2021-09-14 15:38:57 UTC

HMDB ID

HMDB0013870

Secondary Accession Numbers

HMDB13870

Metabolite Identification

Common Name

cis,trans-5'-Hydroxythalidomide

Description

cis,trans-5'-Hydroxythalidomide, also known as 5'-OH-thalidomide, 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. cis,trans-5'-Hydroxythalidomide is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

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

HMDB0013870
     RDKit          3D
cis,trans-5'-Hydroxythalidomide
 30 32  0  0  0  0  0  0  0  0999 V2000
   -4.5099   -1.9445   -0.7296 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6771   -1.0127   -0.5907 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7662   -0.6890   -1.6357 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7904    0.3027   -1.3539 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2797    0.9772   -2.2762 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3436    0.5736    0.0342 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0748    0.4208    0.1098 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.9797    1.4733    0.3986 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6987    2.6979    0.6335 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3490    0.9630    0.3956 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5913    1.5514    0.6128 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7619    0.8363    0.5519 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6962   -0.5115    0.2650 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4790   -1.1263    0.0441 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3045   -0.3853    0.1101 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8891   -0.7324   -0.0698 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4173   -1.8598   -0.3414 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0888   -0.2597    1.0450 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5680   -0.1859    0.6403 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3957   -0.6355    1.6556 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8237   -1.1687   -2.5697 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6202    1.6289    0.2341 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5723    2.6242    0.8358 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7050    1.3561    0.7321 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6242   -1.0968    0.2128 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4019   -2.1750   -0.1812 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0319    0.1878    2.0469 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8184   -1.3132    1.0508 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8581    0.8455    0.3628 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9735   -1.3424    1.2771 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  2  0
  4  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  2  0
  8 10  1  0
 10 11  2  0
 11 12  1  0
 12 13  2  0
 13 14  1  0
 14 15  2  0
 15 16  1  0
 16 17  2  0
  6 18  1  0
 18 19  1  0
 19 20  1  0
 19  2  1  0
 16  7  1  0
 15 10  1  0
  3 21  1  0
  6 22  1  0
 11 23  1  0
 12 24  1  0
 13 25  1  0
 14 26  1  0
 18 27  1  0
 18 28  1  0
 19 29  1  0
 20 30  1  0
M  END


  Mrv0541 06191311472D          

 20 22  0  0  0  0            999 V2000
    9.2381   -5.2514    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.1878   -5.2706    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.1878   -2.3744    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.7130   -3.8225    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.4131   -3.8225    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   10.4755   -4.5370    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    9.2381   -3.8225    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.6506   -3.1080    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.4755   -3.1080    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.6506   -4.5370    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.9316   -4.4864    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.9316   -3.1586    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1511   -4.2350    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1511   -3.4100    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.8880   -3.8225    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4365   -4.6475    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4365   -2.9975    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7220   -4.2350    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7220   -3.4100    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.8880   -2.3936    0.0000 O   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
  9 20  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0013870

> <DATABASE_NAME>
hmdb

> <SMILES>
OC1CC(N2C(=O)C3=CC=CC=C3C2=O)C(=O)NC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C13H10N2O5/c16-9-5-8(10(17)14-11(9)18)15-12(19)6-3-1-2-4-7(6)13(15)20/h1-4,8-9,16H,5H2,(H,14,17,18)

> <INCHI_KEY>
HHTOWVWIVBSOKC-UHFFFAOYSA-N

> <FORMULA>
C13H10N2O5

> <MOLECULAR_WEIGHT>
274.2289

> <EXACT_MASS>
274.05897144

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_AVERAGE_POLARIZABILITY>
25.193599445012104

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-(5-hydroxy-2,6-dioxopiperidin-3-yl)-2,3-dihydro-1H-isoindole-1,3-dione

> <ALOGPS_LOGP>
-0.18

> <JCHEM_LOGP>
-0.9281525706666667

> <ALOGPS_LOGS>
-1.62

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.388887505916735

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.212959648754811

> <JCHEM_PKA_STRONGEST_BASIC>
-3.648991385556452

> <JCHEM_POLAR_SURFACE_AREA>
103.78

> <JCHEM_REFRACTIVITY>
65.77340000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.51e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-(5-hydroxy-2,6-dioxopiperidin-3-yl)isoindole-1,3-dione

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0013870
     RDKit          3D
cis,trans-5'-Hydroxythalidomide
 30 32  0  0  0  0  0  0  0  0999 V2000
   -4.5099   -1.9445   -0.7296 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6771   -1.0127   -0.5907 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7662   -0.6890   -1.6357 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7904    0.3027   -1.3539 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2797    0.9772   -2.2762 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3436    0.5736    0.0342 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0748    0.4208    0.1098 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.9797    1.4733    0.3986 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6987    2.6979    0.6335 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3490    0.9630    0.3956 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5913    1.5514    0.6128 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7619    0.8363    0.5519 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6962   -0.5115    0.2650 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4790   -1.1263    0.0441 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3045   -0.3853    0.1101 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8891   -0.7324   -0.0698 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4173   -1.8598   -0.3414 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0888   -0.2597    1.0450 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5680   -0.1859    0.6403 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3957   -0.6355    1.6556 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8237   -1.1687   -2.5697 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6202    1.6289    0.2341 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5723    2.6242    0.8358 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7050    1.3561    0.7321 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6242   -1.0968    0.2128 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4019   -2.1750   -0.1812 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0319    0.1878    2.0469 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8184   -1.3132    1.0508 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8581    0.8455    0.3628 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9735   -1.3424    1.2771 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  2  0
  4  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  2  0
  8 10  1  0
 10 11  2  0
 11 12  1  0
 12 13  2  0
 13 14  1  0
 14 15  2  0
 15 16  1  0
 16 17  2  0
  6 18  1  0
 18 19  1  0
 19 20  1  0
 19  2  1  0
 16  7  1  0
 15 10  1  0
  3 21  1  0
  6 22  1  0
 11 23  1  0
 12 24  1  0
 13 25  1  0
 14 26  1  0
 18 27  1  0
 18 28  1  0
 19 29  1  0
 20 30  1  0
M  END

HEADER    PROTEIN                                 19-JUN-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   19-JUN-13         0                                  
HETATM    1  O   UNK     0      17.244  -9.803   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0      15.284  -9.839   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      15.284  -4.432   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0      21.864  -7.135   0.000  0.00  0.00           O+0
HETATM    5  N   UNK     0      15.704  -7.135   0.000  0.00  0.00           N+0
HETATM    6  N   UNK     0      19.554  -8.469   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0      17.244  -7.135   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      18.014  -5.802   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      19.554  -5.802   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      18.014  -8.469   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      14.806  -8.375   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      14.806  -5.896   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      13.349  -7.905   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      13.349  -6.365   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      20.324  -7.135   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      12.015  -8.675   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      12.015  -5.595   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      10.681  -7.905   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      10.681  -6.365   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0      20.324  -4.468   0.000  0.00  0.00           O+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   20                                                  
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                                                       
CONECT   20    9                                                            
MASTER        0    0    0    0    0    0    0    0   20    0   44    0
END

COMPND    HMDB0013870
HETATM    1  O1  UNL     1      -4.510  -1.945  -0.730  1.00  0.00           O  
HETATM    2  C1  UNL     1      -3.677  -1.013  -0.591  1.00  0.00           C  
HETATM    3  N1  UNL     1      -2.766  -0.689  -1.636  1.00  0.00           N  
HETATM    4  C2  UNL     1      -1.790   0.303  -1.354  1.00  0.00           C  
HETATM    5  O2  UNL     1      -1.280   0.977  -2.276  1.00  0.00           O  
HETATM    6  C3  UNL     1      -1.344   0.574   0.034  1.00  0.00           C  
HETATM    7  N2  UNL     1       0.075   0.421   0.110  1.00  0.00           N  
HETATM    8  C4  UNL     1       0.980   1.473   0.399  1.00  0.00           C  
HETATM    9  O3  UNL     1       0.699   2.698   0.633  1.00  0.00           O  
HETATM   10  C5  UNL     1       2.349   0.963   0.396  1.00  0.00           C  
HETATM   11  C6  UNL     1       3.591   1.551   0.613  1.00  0.00           C  
HETATM   12  C7  UNL     1       4.762   0.836   0.552  1.00  0.00           C  
HETATM   13  C8  UNL     1       4.696  -0.512   0.265  1.00  0.00           C  
HETATM   14  C9  UNL     1       3.479  -1.126   0.044  1.00  0.00           C  
HETATM   15  C10 UNL     1       2.305  -0.385   0.110  1.00  0.00           C  
HETATM   16  C11 UNL     1       0.889  -0.732  -0.070  1.00  0.00           C  
HETATM   17  O4  UNL     1       0.417  -1.860  -0.341  1.00  0.00           O  
HETATM   18  C12 UNL     1      -2.089  -0.260   1.045  1.00  0.00           C  
HETATM   19  C13 UNL     1      -3.568  -0.186   0.640  1.00  0.00           C  
HETATM   20  O5  UNL     1      -4.396  -0.635   1.656  1.00  0.00           O  
HETATM   21  H1  UNL     1      -2.824  -1.169  -2.570  1.00  0.00           H  
HETATM   22  H2  UNL     1      -1.620   1.629   0.234  1.00  0.00           H  
HETATM   23  H3  UNL     1       3.572   2.624   0.836  1.00  0.00           H  
HETATM   24  H4  UNL     1       5.705   1.356   0.732  1.00  0.00           H  
HETATM   25  H5  UNL     1       5.624  -1.097   0.213  1.00  0.00           H  
HETATM   26  H6  UNL     1       3.402  -2.175  -0.181  1.00  0.00           H  
HETATM   27  H7  UNL     1      -2.032   0.188   2.047  1.00  0.00           H  
HETATM   28  H8  UNL     1      -1.818  -1.313   1.051  1.00  0.00           H  
HETATM   29  H9  UNL     1      -3.858   0.846   0.363  1.00  0.00           H  
HETATM   30  H10 UNL     1      -4.973  -1.342   1.277  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3   19
CONECT    3    4   21
CONECT    4    5    5    6
CONECT    6    7   18   22
CONECT    7    8   16
CONECT    8    9    9   10
CONECT   10   11   11   15
CONECT   11   12   23
CONECT   12   13   13   24
CONECT   13   14   25
CONECT   14   15   15   26
CONECT   15   16
CONECT   16   17   17
CONECT   18   19   27   28
CONECT   19   20   29
CONECT   20   30
END

HMDB0013870
     RDKit          3D
cis,trans-5'-Hydroxythalidomide
 30 32  0  0  0  0  0  0  0  0999 V2000
   -4.5099   -1.9445   -0.7296 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6771   -1.0127   -0.5907 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7662   -0.6890   -1.6357 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7904    0.3027   -1.3539 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2797    0.9772   -2.2762 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3436    0.5736    0.0342 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0748    0.4208    0.1098 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.9797    1.4733    0.3986 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6987    2.6979    0.6335 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3490    0.9630    0.3956 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5913    1.5514    0.6128 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7619    0.8363    0.5519 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6962   -0.5115    0.2650 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4790   -1.1263    0.0441 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3045   -0.3853    0.1101 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8891   -0.7324   -0.0698 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4173   -1.8598   -0.3414 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0888   -0.2597    1.0450 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5680   -0.1859    0.6403 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3957   -0.6355    1.6556 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8237   -1.1687   -2.5697 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6202    1.6289    0.2341 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5723    2.6242    0.8358 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7050    1.3561    0.7321 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6242   -1.0968    0.2128 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4019   -2.1750   -0.1812 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0319    0.1878    2.0469 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8184   -1.3132    1.0508 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8581    0.8455    0.3628 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9735   -1.3424    1.2771 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  2  0
  4  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  2  0
  8 10  1  0
 10 11  2  0
 11 12  1  0
 12 13  2  0
 13 14  1  0
 14 15  2  0
 15 16  1  0
 16 17  2  0
  6 18  1  0
 18 19  1  0
 19 20  1  0
 19  2  1  0
 16  7  1  0
 15 10  1  0
  3 21  1  0
  6 22  1  0
 11 23  1  0
 12 24  1  0
 13 25  1  0
 14 26  1  0
 18 27  1  0
 18 28  1  0
 19 29  1  0
 20 30  1  0
M  END

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
5'-OH-Thalidomide	HMDB
5'-Hydroxythalidomide	MeSH

Chemical Formula

C₁₃H₁₀N₂O₅

Average Molecular Weight

274.2289

Monoisotopic Molecular Weight

274.05897144

IUPAC Name

2-(5-hydroxy-2,6-dioxopiperidin-3-yl)-2,3-dihydro-1H-isoindole-1,3-dione

Traditional Name

2-(5-hydroxy-2,6-dioxopiperidin-3-yl)isoindole-1,3-dione

CAS Registry Number

Not Available

SMILES

OC1CC(N2C(=O)C3=CC=CC=C3C2=O)C(=O)NC1=O

InChI Identifier

InChI=1S/C13H10N2O5/c16-9-5-8(10(17)14-11(9)18)15-12(19)6-3-1-2-4-7(6)13(15)20/h1-4,8-9,16H,5H2,(H,14,17,18)

InChI Key

HHTOWVWIVBSOKC-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
Secondary alcohol
Carboxylic acid derivative
Azacycle
Organic nitrogen compound
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Organic oxygen compound
Alcohol
Carbonyl group
Organooxygen compound
Organonitrogen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Ontology

Not Available

Liver (HMDB: HMDB0013870)
Kidney (HMDB: HMDB0013870)

Excreta

Biofluid or Excreta

Urine (PMID: 21059682)

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 21059682)

Cellular substructure

Extracellular (HMDB: HMDB0013870)

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	Not Available	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	6.51 g/L	ALOGPS
logP	-0.18	ALOGPS
logP	-0.93	ChemAxon
logS	-1.6	ALOGPS
pKa (Strongest Acidic)	11.21	ChemAxon
pKa (Strongest Basic)	-3.6	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	103.78 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	65.77 m³·mol⁻¹	ChemAxon
Polarizability	25.19 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]+	164.127	31661259
DarkChem	[M-H]-	159.741	31661259
DeepCCS	[M+H]+	166.464	30932474
DeepCCS	[M-H]-	164.106	30932474
DeepCCS	[M-2H]-	196.993	30932474
DeepCCS	[M+Na]+	172.558	30932474
AllCCS	[M+H]+	161.1	32859911
AllCCS	[M+H-H2O]+	157.5	32859911
AllCCS	[M+NH4]+	164.4	32859911
AllCCS	[M+Na]+	165.3	32859911
AllCCS	[M-H]-	160.5	32859911
AllCCS	[M+Na-2H]-	159.9	32859911
AllCCS	[M+HCOO]-	159.3	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
cis,trans-5'-Hydroxythalidomide	OC1CC(N2C(=O)C3=CC=CC=C3C2=O)C(=O)NC1=O	4255.1	Standard polar	33892256
cis,trans-5'-Hydroxythalidomide	OC1CC(N2C(=O)C3=CC=CC=C3C2=O)C(=O)NC1=O	2334.6	Standard non polar	33892256
cis,trans-5'-Hydroxythalidomide	OC1CC(N2C(=O)C3=CC=CC=C3C2=O)C(=O)NC1=O	2609.2	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
cis,trans-5'-Hydroxythalidomide,1TMS,isomer #1	C[Si](C)(C)OC1CC(N2C(=O)C3=CC=CC=C3C2=O)C(=O)NC1=O	2632.8	Semi standard non polar	33892256
cis,trans-5'-Hydroxythalidomide,1TMS,isomer #2	C[Si](C)(C)N1C(=O)C(O)CC(N2C(=O)C3=CC=CC=C3C2=O)C1=O	2473.2	Semi standard non polar	33892256
cis,trans-5'-Hydroxythalidomide,2TMS,isomer #1	C[Si](C)(C)OC1CC(N2C(=O)C3=CC=CC=C3C2=O)C(=O)N([Si](C)(C)C)C1=O	2501.8	Semi standard non polar	33892256
cis,trans-5'-Hydroxythalidomide,2TMS,isomer #1	C[Si](C)(C)OC1CC(N2C(=O)C3=CC=CC=C3C2=O)C(=O)N([Si](C)(C)C)C1=O	2613.0	Standard non polar	33892256
cis,trans-5'-Hydroxythalidomide,2TMS,isomer #1	C[Si](C)(C)OC1CC(N2C(=O)C3=CC=CC=C3C2=O)C(=O)N([Si](C)(C)C)C1=O	3362.2	Standard polar	33892256
cis,trans-5'-Hydroxythalidomide,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC1CC(N2C(=O)C3=CC=CC=C3C2=O)C(=O)NC1=O	2868.1	Semi standard non polar	33892256
cis,trans-5'-Hydroxythalidomide,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)N1C(=O)C(O)CC(N2C(=O)C3=CC=CC=C3C2=O)C1=O	2736.5	Semi standard non polar	33892256
cis,trans-5'-Hydroxythalidomide,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC1CC(N2C(=O)C3=CC=CC=C3C2=O)C(=O)N([Si](C)(C)C(C)(C)C)C1=O	2964.2	Semi standard non polar	33892256
cis,trans-5'-Hydroxythalidomide,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC1CC(N2C(=O)C3=CC=CC=C3C2=O)C(=O)N([Si](C)(C)C(C)(C)C)C1=O	3034.9	Standard non polar	33892256
cis,trans-5'-Hydroxythalidomide,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC1CC(N2C(=O)C3=CC=CC=C3C2=O)C(=O)N([Si](C)(C)C(C)(C)C)C1=O	3447.2	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - cis,trans-5'-Hydroxythalidomide GC-MS (Non-derivatized) - 70eV, Positive	splash10-05fr-3960000000-0d3d37ff76fdfb87791e	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - cis,trans-5'-Hydroxythalidomide GC-MS (1 TMS) - 70eV, Positive	splash10-00di-4963000000-5c3650820ae538f05811	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - cis,trans-5'-Hydroxythalidomide GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - cis,trans-5'-Hydroxythalidomide 10V, Positive-QTOF	splash10-004i-0090000000-079837f6d6cfe874a480	2016-08-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - cis,trans-5'-Hydroxythalidomide 20V, Positive-QTOF	splash10-0kdi-0390000000-b2931b26f95e0d654ba2	2016-08-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - cis,trans-5'-Hydroxythalidomide 40V, Positive-QTOF	splash10-05g1-7910000000-127e1af15d9ce6980642	2016-08-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - cis,trans-5'-Hydroxythalidomide 10V, Negative-QTOF	splash10-00ec-3190000000-252159f1998f82fd39dc	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - cis,trans-5'-Hydroxythalidomide 20V, Negative-QTOF	splash10-05fu-3590000000-daefbb2dfdeb1a8bc739	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - cis,trans-5'-Hydroxythalidomide 40V, Negative-QTOF	splash10-0007-9200000000-4897f0c5d2567b205009	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - cis,trans-5'-Hydroxythalidomide 10V, Negative-QTOF	splash10-00dj-0790000000-cf25d8d92906fb5756db	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - cis,trans-5'-Hydroxythalidomide 20V, Negative-QTOF	splash10-00dj-2980000000-2cd101c0bcf2b3350bb5	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - cis,trans-5'-Hydroxythalidomide 40V, Negative-QTOF	splash10-0002-3900000000-fb7da6edc3222a7defa5	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - cis,trans-5'-Hydroxythalidomide 10V, Positive-QTOF	splash10-004i-0190000000-60d396dd0f7677a62d71	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - cis,trans-5'-Hydroxythalidomide 20V, Positive-QTOF	splash10-004i-0690000000-76bf4597a518ab5a1539	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - cis,trans-5'-Hydroxythalidomide 40V, Positive-QTOF	splash10-0a4i-2900000000-fdf792b17831511bef06	2021-09-24	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Extracellular

Biospecimen Locations

Blood
Urine

Tissue Locations

Kidney
Liver

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

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

8054323

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

9878646

PDB ID

Not Available

ChEBI ID

212535

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

Not Available

Only showing the first 10 proteins. There are 11 proteins in total.

Show all enzymes and transporters

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

Enzyme Details

2. Prostaglandin G/H synthase 1

General function:: Involved in peroxidase activity
Specific function:: May play an important role in regulating or promoting cell proliferation in some normal and neoplastically transformed cells.
Gene Name:: PTGS1
Uniprot ID:: P23219
Molecular weight:: 68685.82

References

Enzyme Details

3. Cytochrome P450 2C9

General function:: Involved in monooxygenase activity
Specific function:: Cytochromes P450 are a group of heme-thiolate monooxygenases. In liver microsomes, this enzyme is involved in an NADPH-dependent electron transport pathway. It oxidizes a variety of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics. This enzyme contributes to the wide pharmacokinetics variability of the metabolism of drugs such as S-warfarin, diclofenac, phenytoin, tolbutamide and losartan.
Gene Name:: CYP2C9
Uniprot ID:: P11712
Molecular weight:: 55627.365

References

Enzyme Details

4. Cytochrome P450 2C19

General function:: Involved in monooxygenase activity
Specific function:: Responsible for the metabolism of a number of therapeutic agents such as the anticonvulsant drug S-mephenytoin, omeprazole, proguanil, certain barbiturates, diazepam, propranolol, citalopram and imipramine.
Gene Name:: CYP2C19
Uniprot ID:: P33261
Molecular weight:: 55944.565

References

Enzyme Details

5. Fibroblast growth factor receptor 2

General function:: Involved in protein kinase activity
Specific function:: Receptor for acidic and basic fibroblast growth factors
Gene Name:: FGFR2
Uniprot ID:: P21802
Molecular weight:: 92024.3

References

Enzyme Details

6. Cytochrome P450 2E1

General function:: Involved in monooxygenase activity
Specific function:: Metabolizes several precarcinogens, drugs, and solvents to reactive metabolites. Inactivates a number of drugs and xenobiotics and also bioactivates many xenobiotic substrates to their hepatotoxic or carcinogenic forms.
Gene Name:: CYP2E1
Uniprot ID:: P05181
Molecular weight:: 56848.42

References

Enzyme Details

7. Cytochrome P450 3A5

General function:: Involved in monooxygenase activity
Specific function:: Cytochromes P450 are a group of heme-thiolate monooxygenases. In liver microsomes, this enzyme is involved in an NADPH-dependent electron transport pathway. It oxidizes a variety of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics.
Gene Name:: CYP3A5
Uniprot ID:: P20815
Molecular weight:: 57108.065

References

Enzyme Details

8. Cytochrome P450 1A1

General function:: Involved in monooxygenase activity
Specific function:: Cytochromes P450 are a group of heme-thiolate monooxygenases. In liver microsomes, this enzyme is involved in an NADPH-dependent electron transport pathway. It oxidizes a variety of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics.
Gene Name:: CYP1A1
Uniprot ID:: P04798
Molecular weight:: 58164.815

References

Enzyme Details

9. Cytochrome P450 1A2

General function:: Involved in monooxygenase activity
Specific function:: Cytochromes P450 are a group of heme-thiolate monooxygenases. In liver microsomes, this enzyme is involved in an NADPH-dependent electron transport pathway. It oxidizes a variety of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics. Most active in catalyzing 2-hydroxylation. Caffeine is metabolized primarily by cytochrome CYP1A2 in the liver through an initial N3-demethylation. Also acts in the metabolism of aflatoxin B1 and acetaminophen. Participates in the bioactivation of carcinogenic aromatic and heterocyclic amines. Catalizes the N-hydroxylation of heterocyclic amines and the O-deethylation of phenacetin.
Gene Name:: CYP1A2
Uniprot ID:: P05177
Molecular weight:: 58406.915

References

Enzyme Details

10. Tumor necrosis factor

General function:: Involved in tumor necrosis factor receptor binding
Specific function:: Cytokine that binds to TNFRSF1A/TNFR1 and TNFRSF1B/TNFBR. It is mainly secreted by macrophages and can induce cell death of certain tumor cell lines. It is potent pyrogen causing fever by direct action or by stimulation of interleukin-1 secretion and is implicated in the induction of cachexia, Under certain conditions it can stimulate cell proliferation and induce cell differentiation
Gene Name:: TNF
Uniprot ID:: P01375
Molecular weight:: 25644.1

References

Only showing the first 10 proteins. There are 11 proteins in total.

Show all enzymes and transporters

Showing metabocard for cis,trans-5'-Hydroxythalidomide (HMDB0013870)

MOL for HMDB0013870 (cis,trans-5'-Hydroxythalidomide)

3D MOL for HMDB0013870 (cis,trans-5'-Hydroxythalidomide)

3D SDF for HMDB0013870 (cis,trans-5'-Hydroxythalidomide)

3D-SDF for HMDB0013870 (cis,trans-5'-Hydroxythalidomide)

PDB for HMDB0013870 (cis,trans-5'-Hydroxythalidomide)

3D PDB for HMDB0013870 (cis,trans-5'-Hydroxythalidomide)

SMILES for HMDB0013870 (cis,trans-5'-Hydroxythalidomide)

INCHI for HMDB0013870 (cis,trans-5'-Hydroxythalidomide)

Structure for HMDB0013870 (cis,trans-5'-Hydroxythalidomide)

3D Structure for HMDB0013870 (cis,trans-5'-Hydroxythalidomide)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

Enzymes

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