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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-06 15:16:52 UTC

Update Date

2022-03-07 02:52:02 UTC

HMDB ID

HMDB0015568

Secondary Accession Numbers

HMDB15568

Metabolite Identification

Common Name

Vorinostat

Description

Vorinostat (rINN) or suberoylanilide hydroxamic acid (SAHA), is a drug currently under investigation for the treatment of cutaneous T cell lymphoma (CTCL), a type of skin cancer, to be used when the disease persists, gets worse, or comes back during or after treatment with other medicines. It is the first in a new class of agents known as histone deacetylase inhibitors. A recent study suggested that vorinostat also possesses some activity against recurrent glioblastoma multiforme, resulting in a median overall survival of 5.7 months (compared to 4 - 4.4 months in earlier studies). Further brain tumor trials are planned in which vorinostat will be combined with other drugs. [Wikipedia ]

Structure

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

HMDB0015568
     RDKit          3D
Vorinostat
 39 39  0  0  0  0  0  0  0  0999 V2000
    4.9624    0.7459   -2.3174 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.8223   -0.1667   -1.4609 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8973    0.1259   -0.3249 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2967    1.4857   -0.4238 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3881    1.7165    0.7566 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2543    0.7282    0.8395 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4056    1.0539    2.0405 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7553    0.1642    2.2604 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7373    0.2230    1.1137 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5577    1.0183    0.1871 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8363   -0.6541    1.1593 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8555   -0.7328    0.1738 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7851   -1.7718    0.2448 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8070   -1.9267   -0.6474 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9339   -1.0199   -1.6683 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0479    0.0262   -1.7905 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0237    0.1456   -0.8608 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5045   -1.3979   -1.5723 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.3256   -1.6168   -2.6100 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0925   -0.6381   -0.4117 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4147   -0.0116    0.6341 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0307    2.2943   -0.5540 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6194    1.4706   -1.3228 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0166    2.7518    0.7889 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9892    1.5944    1.7059 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6621   -0.3217    0.9513 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6571    0.7239   -0.0615 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0636    1.0821    2.9350 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0055    2.0910    1.8477 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4201   -0.8865    2.3906 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3127    0.5244    3.1487 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9006   -1.3089    2.0127 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6473   -2.4707    1.0711 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4938   -2.7394   -0.5506 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7320   -1.1142   -2.3915 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1398    0.7558   -2.6014 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3570    0.9805   -0.9872 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3692   -2.1271   -0.8540 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.5656   -0.7975   -3.0981 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  2  0
  9 11  1  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
  2 18  1  0
 18 19  1  0
 17 12  1  0
  3 20  1  0
  3 21  1  0
  4 22  1  0
  4 23  1  0
  5 24  1  0
  5 25  1  0
  6 26  1  0
  6 27  1  0
  7 28  1  0
  7 29  1  0
  8 30  1  0
  8 31  1  0
 11 32  1  0
 13 33  1  0
 14 34  1  0
 15 35  1  0
 16 36  1  0
 17 37  1  0
 18 38  1  0
 19 39  1  0
M  END


  Mrv0541 02231216162D          

 19 19  0  0  0  0            999 V2000
    3.7935   -1.9842    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5080    3.3784    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.9370    4.2035    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3645   -1.9842    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.9370    3.3784    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.7935    0.4909    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5080    0.9034    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7935   -0.3341    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5080    1.7284    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0791   -0.7466    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2224    2.1409    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0791   -1.5717    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2224    2.9659    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3645   -2.8092    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0791   -3.2217    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500   -3.2217    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0791   -4.0467    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500   -4.0467    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3645   -4.4592    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1 12  2  0  0  0  0
  2 13  2  0  0  0  0
  3  5  1  0  0  0  0
  4 12  1  0  0  0  0
  4 14  1  0  0  0  0
  5 13  1  0  0  0  0
  6  7  1  0  0  0  0
  6  8  1  0  0  0  0
  7  9  1  0  0  0  0
  8 10  1  0  0  0  0
  9 11  1  0  0  0  0
 10 12  1  0  0  0  0
 11 13  1  0  0  0  0
 14 15  2  0  0  0  0
 14 16  1  0  0  0  0
 15 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>
HMDB0015568

> <DATABASE_NAME>
hmdb

> <SMILES>
ONC(=O)CCCCCCC(=O)NC1=CC=CC=C1

> <INCHI_IDENTIFIER>
InChI=1S/C14H20N2O3/c17-13(15-12-8-4-3-5-9-12)10-6-1-2-7-11-14(18)16-19/h3-5,8-9,19H,1-2,6-7,10-11H2,(H,15,17)(H,16,18)

> <INCHI_KEY>
WAEXFXRVDQXREF-UHFFFAOYSA-N

> <FORMULA>
C14H20N2O3

> <MOLECULAR_WEIGHT>
264.3202

> <EXACT_MASS>
264.147392516

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
28.386758455309753

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
N-hydroxy-N'-phenyloctanediamide

> <ALOGPS_LOGP>
1.88

> <JCHEM_LOGP>
2.003969249333333

> <ALOGPS_LOGS>
-3.57

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.203978435931308

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.90753598024551

> <JCHEM_PKA_STRONGEST_BASIC>
-3.521337304210903

> <JCHEM_POLAR_SURFACE_AREA>
78.43

> <JCHEM_REFRACTIVITY>
73.80510000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.16e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
SAHA

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0015568
     RDKit          3D
Vorinostat
 39 39  0  0  0  0  0  0  0  0999 V2000
    4.9624    0.7459   -2.3174 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.8223   -0.1667   -1.4609 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8973    0.1259   -0.3249 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2967    1.4857   -0.4238 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3881    1.7165    0.7566 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2543    0.7282    0.8395 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4056    1.0539    2.0405 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7553    0.1642    2.2604 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7373    0.2230    1.1137 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5577    1.0183    0.1871 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8363   -0.6541    1.1593 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8555   -0.7328    0.1738 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7851   -1.7718    0.2448 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8070   -1.9267   -0.6474 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9339   -1.0199   -1.6683 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0479    0.0262   -1.7905 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0237    0.1456   -0.8608 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5045   -1.3979   -1.5723 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.3256   -1.6168   -2.6100 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0925   -0.6381   -0.4117 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4147   -0.0116    0.6341 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0307    2.2943   -0.5540 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6194    1.4706   -1.3228 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0166    2.7518    0.7889 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9892    1.5944    1.7059 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6621   -0.3217    0.9513 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6571    0.7239   -0.0615 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0636    1.0821    2.9350 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0055    2.0910    1.8477 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4201   -0.8865    2.3906 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3127    0.5244    3.1487 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9006   -1.3089    2.0127 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6473   -2.4707    1.0711 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4938   -2.7394   -0.5506 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7320   -1.1142   -2.3915 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1398    0.7558   -2.6014 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3570    0.9805   -0.9872 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3692   -2.1271   -0.8540 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.5656   -0.7975   -3.0981 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  2  0
  9 11  1  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
  2 18  1  0
 18 19  1  0
 17 12  1  0
  3 20  1  0
  3 21  1  0
  4 22  1  0
  4 23  1  0
  5 24  1  0
  5 25  1  0
  6 26  1  0
  6 27  1  0
  7 28  1  0
  7 29  1  0
  8 30  1  0
  8 31  1  0
 11 32  1  0
 13 33  1  0
 14 34  1  0
 15 35  1  0
 16 36  1  0
 17 37  1  0
 18 38  1  0
 19 39  1  0
M  END

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  O   UNK     0       7.081  -3.704   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0       8.415   6.306   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      11.082   7.847   0.000  0.00  0.00           O+0
HETATM    4  N   UNK     0       4.414  -3.704   0.000  0.00  0.00           N+0
HETATM    5  N   UNK     0      11.082   6.306   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0       7.081   0.916   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       8.415   1.686   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       7.081  -0.624   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       8.415   3.226   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       5.748  -1.394   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       9.748   3.996   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       5.748  -2.934   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       9.748   5.536   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       4.414  -5.244   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       5.748  -6.014   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       3.080  -6.014   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       5.748  -7.554   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       3.080  -7.554   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       4.414  -8.324   0.000  0.00  0.00           C+0
CONECT    1   12                                                            
CONECT    2   13                                                            
CONECT    3    5                                                            
CONECT    4   12   14                                                       
CONECT    5    3   13                                                       
CONECT    6    7    8                                                       
CONECT    7    6    9                                                       
CONECT    8    6   10                                                       
CONECT    9    7   11                                                       
CONECT   10    8   12                                                       
CONECT   11    9   13                                                       
CONECT   12    1    4   10                                                  
CONECT   13    2    5   11                                                  
CONECT   14    4   15   16                                                  
CONECT   15   14   17                                                       
CONECT   16   14   18                                                       
CONECT   17   15   19                                                       
CONECT   18   16   19                                                       
CONECT   19   17   18                                                       
MASTER        0    0    0    0    0    0    0    0   19    0   38    0
END

COMPND    HMDB0015568
HETATM    1  O1  UNL     1       4.962   0.746  -2.317  1.00  0.00           O  
HETATM    2  C1  UNL     1       4.822  -0.167  -1.461  1.00  0.00           C  
HETATM    3  C2  UNL     1       3.897   0.126  -0.325  1.00  0.00           C  
HETATM    4  C3  UNL     1       3.297   1.486  -0.424  1.00  0.00           C  
HETATM    5  C4  UNL     1       2.388   1.717   0.757  1.00  0.00           C  
HETATM    6  C5  UNL     1       1.254   0.728   0.840  1.00  0.00           C  
HETATM    7  C6  UNL     1       0.406   1.054   2.041  1.00  0.00           C  
HETATM    8  C7  UNL     1      -0.755   0.164   2.260  1.00  0.00           C  
HETATM    9  C8  UNL     1      -1.737   0.223   1.114  1.00  0.00           C  
HETATM   10  O2  UNL     1      -1.558   1.018   0.187  1.00  0.00           O  
HETATM   11  N1  UNL     1      -2.836  -0.654   1.159  1.00  0.00           N  
HETATM   12  C9  UNL     1      -3.855  -0.733   0.174  1.00  0.00           C  
HETATM   13  C10 UNL     1      -4.785  -1.772   0.245  1.00  0.00           C  
HETATM   14  C11 UNL     1      -5.807  -1.927  -0.647  1.00  0.00           C  
HETATM   15  C12 UNL     1      -5.934  -1.020  -1.668  1.00  0.00           C  
HETATM   16  C13 UNL     1      -5.048   0.026  -1.790  1.00  0.00           C  
HETATM   17  C14 UNL     1      -4.024   0.146  -0.861  1.00  0.00           C  
HETATM   18  N2  UNL     1       5.504  -1.398  -1.572  1.00  0.00           N  
HETATM   19  O3  UNL     1       6.326  -1.617  -2.610  1.00  0.00           O  
HETATM   20  H1  UNL     1       3.093  -0.638  -0.412  1.00  0.00           H  
HETATM   21  H2  UNL     1       4.415  -0.012   0.634  1.00  0.00           H  
HETATM   22  H3  UNL     1       4.031   2.294  -0.554  1.00  0.00           H  
HETATM   23  H4  UNL     1       2.619   1.471  -1.323  1.00  0.00           H  
HETATM   24  H5  UNL     1       2.017   2.752   0.789  1.00  0.00           H  
HETATM   25  H6  UNL     1       2.989   1.594   1.706  1.00  0.00           H  
HETATM   26  H7  UNL     1       1.662  -0.322   0.951  1.00  0.00           H  
HETATM   27  H8  UNL     1       0.657   0.724  -0.061  1.00  0.00           H  
HETATM   28  H9  UNL     1       1.064   1.082   2.935  1.00  0.00           H  
HETATM   29  H10 UNL     1       0.005   2.091   1.848  1.00  0.00           H  
HETATM   30  H11 UNL     1      -0.420  -0.886   2.391  1.00  0.00           H  
HETATM   31  H12 UNL     1      -1.313   0.524   3.149  1.00  0.00           H  
HETATM   32  H13 UNL     1      -2.901  -1.309   2.013  1.00  0.00           H  
HETATM   33  H14 UNL     1      -4.647  -2.471   1.071  1.00  0.00           H  
HETATM   34  H15 UNL     1      -6.494  -2.739  -0.551  1.00  0.00           H  
HETATM   35  H16 UNL     1      -6.732  -1.114  -2.391  1.00  0.00           H  
HETATM   36  H17 UNL     1      -5.140   0.756  -2.601  1.00  0.00           H  
HETATM   37  H18 UNL     1      -3.357   0.981  -0.987  1.00  0.00           H  
HETATM   38  H19 UNL     1       5.369  -2.127  -0.854  1.00  0.00           H  
HETATM   39  H20 UNL     1       6.566  -0.798  -3.098  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3   18
CONECT    3    4   20   21
CONECT    4    5   22   23
CONECT    5    6   24   25
CONECT    6    7   26   27
CONECT    7    8   28   29
CONECT    8    9   30   31
CONECT    9   10   10   11
CONECT   11   12   32
CONECT   12   13   13   17
CONECT   13   14   33
CONECT   14   15   15   34
CONECT   15   16   35
CONECT   16   17   17   36
CONECT   17   37
CONECT   18   19   38
CONECT   19   39
END

HMDB0015568
     RDKit          3D
Vorinostat
 39 39  0  0  0  0  0  0  0  0999 V2000
    4.9624    0.7459   -2.3174 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.8223   -0.1667   -1.4609 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8973    0.1259   -0.3249 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2967    1.4857   -0.4238 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3881    1.7165    0.7566 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2543    0.7282    0.8395 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4056    1.0539    2.0405 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7553    0.1642    2.2604 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7373    0.2230    1.1137 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5577    1.0183    0.1871 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8363   -0.6541    1.1593 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8555   -0.7328    0.1738 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7851   -1.7718    0.2448 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8070   -1.9267   -0.6474 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9339   -1.0199   -1.6683 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0479    0.0262   -1.7905 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0237    0.1456   -0.8608 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5045   -1.3979   -1.5723 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.3256   -1.6168   -2.6100 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0925   -0.6381   -0.4117 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4147   -0.0116    0.6341 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0307    2.2943   -0.5540 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6194    1.4706   -1.3228 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0166    2.7518    0.7889 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9892    1.5944    1.7059 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6621   -0.3217    0.9513 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6571    0.7239   -0.0615 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0636    1.0821    2.9350 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0055    2.0910    1.8477 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4201   -0.8865    2.3906 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3127    0.5244    3.1487 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9006   -1.3089    2.0127 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6473   -2.4707    1.0711 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4938   -2.7394   -0.5506 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7320   -1.1142   -2.3915 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1398    0.7558   -2.6014 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3570    0.9805   -0.9872 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3692   -2.1271   -0.8540 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.5656   -0.7975   -3.0981 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  2  0
  9 11  1  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
  2 18  1  0
 18 19  1  0
 17 12  1  0
  3 20  1  0
  3 21  1  0
  4 22  1  0
  4 23  1  0
  5 24  1  0
  5 25  1  0
  6 26  1  0
  6 27  1  0
  7 28  1  0
  7 29  1  0
  8 30  1  0
  8 31  1  0
 11 32  1  0
 13 33  1  0
 14 34  1  0
 15 35  1  0
 16 36  1  0
 17 37  1  0
 18 38  1  0
 19 39  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
Octanedioic acid hydroxyamide phenylamide	ChEBI
SAHA	ChEBI
SHH	ChEBI
Suberanilohydroxamic acid	ChEBI
Suberoylanilide hydroxamic acid	ChEBI
Vorinostatum	ChEBI
Zolinza	ChEBI
Octanedioate hydroxyamide phenylamide	Generator
Suberanilohydroxamate	Generator
Suberoylanilide hydroxamate	Generator
MK0683	HMDB
N-Hydroxy-n'-phenyloctanediamide	HMDB
N-Hyrdroxy-n'-phenyloctanediamide	HMDB
18F-SAHA	HMDB
18F-Suberoylanilide hydroxamic acid	HMDB
Merck brand OF vorinostat	HMDB
N1-Hydroxy-N8-phenyloctanediamide	HMDB
NHNPODA	HMDB
Suberoyl anilide hydroxamic acid	HMDB
18F Suberoylanilide hydroxamic acid	HMDB
N Hydroxy n' phenyloctanediamide	HMDB
N1 Hydroxy N8 phenyloctanediamide	HMDB

Chemical Formula

C₁₄H₂₀N₂O₃

Average Molecular Weight

264.3202

Monoisotopic Molecular Weight

264.147392516

IUPAC Name

N-hydroxy-N'-phenyloctanediamide

Traditional Name

SAHA

CAS Registry Number

149647-78-9

SMILES

ONC(=O)CCCCCCC(=O)NC1=CC=CC=C1

InChI Identifier

InChI=1S/C14H20N2O3/c17-13(15-12-8-4-3-5-9-12)10-6-1-2-7-11-14(18)16-19/h3-5,8-9,19H,1-2,6-7,10-11H2,(H,15,17)(H,16,18)

InChI Key

WAEXFXRVDQXREF-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as benzene and substituted derivatives. These are aromatic compounds containing one monocyclic ring system consisting of benzene.

Kingdom

Organic compounds

Super Class

Benzenoids

Class

Benzene and substituted derivatives

Sub Class

Not Available

Direct Parent

Benzene and substituted derivatives

Alternative Parents

Substituents

Monocyclic benzene moiety
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Carboximidic acid derivative
Carboximidic acid
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Aromatic homomonocyclic compound

Molecular Framework

Aromatic homomonocyclic compounds

External Descriptors

dicarboxylic acid diamide (CHEBI:45716 )
hydroxamic acid (CHEBI:45716 )

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 21059682)

Excreta

Biofluid or Excreta

Urine (PMID: 21059682)

Cellular substructure

Source

Exogenous

Exogenous (HMDB: HMDB0015568)

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	0.072 g/L	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	0.072 g/L	ALOGPS
logP	1.88	ALOGPS
logP	2	ChemAxon
logS	-3.6	ALOGPS
pKa (Strongest Acidic)	8.91	ChemAxon
pKa (Strongest Basic)	-3.5	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	78.43 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	73.81 m³·mol⁻¹	ChemAxon
Polarizability	28.39 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DarkChem	[M+H]+	164.097	31661259
DarkChem	[M-H]-	164.249	31661259
DeepCCS	[M+H]+	164.475	30932474
DeepCCS	[M-H]-	162.117	30932474
DeepCCS	[M-2H]-	195.211	30932474
DeepCCS	[M+Na]+	170.568	30932474
AllCCS	[M+H]+	160.7	32859911
AllCCS	[M+H-H2O]+	157.4	32859911
AllCCS	[M+NH4]+	163.7	32859911
AllCCS	[M+Na]+	164.5	32859911
AllCCS	[M-H]-	165.5	32859911
AllCCS	[M+Na-2H]-	165.9	32859911
AllCCS	[M+HCOO]-	166.5	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.	5.5 minutes	32390414
Predicted by Siyang on May 30, 2022	12.0278 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	1.98 minutes	32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid	29.4 seconds	40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	2146.7 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	268.4 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	155.0 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	163.9 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	188.1 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	406.0 seconds	40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid	527.8 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	67.3 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	1053.7 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	379.6 seconds	40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid	1182.4 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	305.3 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	323.2 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	282.1 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	135.1 seconds	40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water	57.0 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Vorinostat	ONC(=O)CCCCCCC(=O)NC1=CC=CC=C1	3464.6	Standard polar	33892256
Vorinostat	ONC(=O)CCCCCCC(=O)NC1=CC=CC=C1	2514.8	Standard non polar	33892256
Vorinostat	ONC(=O)CCCCCCC(=O)NC1=CC=CC=C1	2618.1	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Vorinostat,1TMS,isomer #1	C[Si](C)(C)N(O)C(=O)CCCCCCC(=O)NC1=CC=CC=C1	2634.4	Semi standard non polar	33892256
Vorinostat,1TMS,isomer #1	C[Si](C)(C)N(O)C(=O)CCCCCCC(=O)NC1=CC=CC=C1	2452.2	Standard non polar	33892256
Vorinostat,1TMS,isomer #1	C[Si](C)(C)N(O)C(=O)CCCCCCC(=O)NC1=CC=CC=C1	3411.3	Standard polar	33892256
Vorinostat,1TMS,isomer #2	C[Si](C)(C)N(C(=O)CCCCCCC(=O)NO)C1=CC=CC=C1	2467.5	Semi standard non polar	33892256
Vorinostat,1TMS,isomer #2	C[Si](C)(C)N(C(=O)CCCCCCC(=O)NO)C1=CC=CC=C1	2397.1	Standard non polar	33892256
Vorinostat,1TMS,isomer #2	C[Si](C)(C)N(C(=O)CCCCCCC(=O)NO)C1=CC=CC=C1	3215.8	Standard polar	33892256
Vorinostat,2TMS,isomer #1	C[Si](C)(C)N(O)C(=O)CCCCCCC(=O)N(C1=CC=CC=C1)[Si](C)(C)C	2399.6	Semi standard non polar	33892256
Vorinostat,2TMS,isomer #1	C[Si](C)(C)N(O)C(=O)CCCCCCC(=O)N(C1=CC=CC=C1)[Si](C)(C)C	2396.7	Standard non polar	33892256
Vorinostat,2TMS,isomer #1	C[Si](C)(C)N(O)C(=O)CCCCCCC(=O)N(C1=CC=CC=C1)[Si](C)(C)C	3073.7	Standard polar	33892256
Vorinostat,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N(O)C(=O)CCCCCCC(=O)NC1=CC=CC=C1	2841.9	Semi standard non polar	33892256
Vorinostat,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N(O)C(=O)CCCCCCC(=O)NC1=CC=CC=C1	2641.3	Standard non polar	33892256
Vorinostat,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N(O)C(=O)CCCCCCC(=O)NC1=CC=CC=C1	3412.8	Standard polar	33892256
Vorinostat,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)N(C(=O)CCCCCCC(=O)NO)C1=CC=CC=C1	2710.0	Semi standard non polar	33892256
Vorinostat,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)N(C(=O)CCCCCCC(=O)NO)C1=CC=CC=C1	2615.2	Standard non polar	33892256
Vorinostat,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)N(C(=O)CCCCCCC(=O)NO)C1=CC=CC=C1	3247.8	Standard polar	33892256
Vorinostat,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N(O)C(=O)CCCCCCC(=O)N(C1=CC=CC=C1)[Si](C)(C)C(C)(C)C	2886.2	Semi standard non polar	33892256
Vorinostat,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N(O)C(=O)CCCCCCC(=O)N(C1=CC=CC=C1)[Si](C)(C)C(C)(C)C	2767.8	Standard non polar	33892256
Vorinostat,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N(O)C(=O)CCCCCCC(=O)N(C1=CC=CC=C1)[Si](C)(C)C(C)(C)C	3193.0	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - Vorinostat GC-MS (Non-derivatized) - 70eV, Positive	splash10-006x-4920000000-0b60d0a81534425ab7be	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Vorinostat 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 - Vorinostat LC-ESI-Hybrid FT , Positive-QTOF	splash10-0udi-0859000000-0a83404097a3e01eb158	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Vorinostat , positive-QTOF	splash10-001l-9750000000-d26ffebbce9b1bc73b92	2017-09-14	HMDB team, MONA	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Vorinostat 10V, Positive-QTOF	splash10-00kf-7190000000-877b56b4601e9fa6d5b1	2016-06-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Vorinostat 20V, Positive-QTOF	splash10-0006-9220000000-99ea61440739c3064b34	2016-06-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Vorinostat 40V, Positive-QTOF	splash10-0006-9100000000-6506e221f51e0d54cbd7	2016-06-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Vorinostat 10V, Negative-QTOF	splash10-03di-2190000000-9403e0edb1371ac82130	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Vorinostat 20V, Negative-QTOF	splash10-06ry-9360000000-2ac5220873ae653bb80d	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Vorinostat 40V, Negative-QTOF	splash10-0006-9100000000-81d3844e3cacdfb678fa	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Vorinostat 10V, Positive-QTOF	splash10-0159-0490000000-8855a77bf8f5c1e58821	2021-10-11	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Vorinostat 20V, Positive-QTOF	splash10-0f6y-9740000000-3649f9eb7bb51fe7dcaa	2021-10-11	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Vorinostat 40V, Positive-QTOF	splash10-0006-9100000000-bbb1690ce5a4b45dd169	2021-10-11	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Vorinostat 10V, Negative-QTOF	splash10-03di-0090000000-7aa1ceac7690e76ffdbe	2021-10-11	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Vorinostat 20V, Negative-QTOF	splash10-01ox-6190000000-ac3a50ce21bd2b6f7ef2	2021-10-11	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Vorinostat 40V, Negative-QTOF	splash10-0006-9000000000-32187e1065af5e96be36	2021-10-11	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Cytoplasm
Extracellular
Membrane

Biospecimen Locations

Blood
Urine

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Expected but not Quantified	Not Quantified	Not Available	Not Available	Taking drug identified by DrugBank entry DB02546	21059682	details
Urine	Expected but not Quantified	Not Quantified	Not Available	Not Available	Taking drug identified by DrugBank entry DB02546	21059682	details

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

DB02546

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

5120

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Vorinostat

METLIN ID

Not Available

PubChem Compound

5311

PDB ID

SHH

ChEBI ID

45716

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

Munshi A, Tanaka T, Hobbs ML, Tucker SL, Richon VM, Meyn RE: Vorinostat, a histone deacetylase inhibitor, enhances the response of human tumor cells to ionizing radiation through prolongation of gamma-H2AX foci. Mol Cancer Ther. 2006 Aug;5(8):1967-74. [PubMed:16928817 ]

Enzymes

Enzyme Details

1. Histone deacetylase 2

General function:: Involved in histone deacetylase activity
Specific function:: Forms transcriptional repressor complexes by associating with MAD, SIN3, YY1 and N-COR. Interacts in the late S-phase of DNA-replication with DNMT1 in the other transcriptional repressor complex composed of DNMT1, DMAP1, PCNA, CAF1. Deacetylates TSHZ3 and regulates its transcriptional repressor activity
Gene Name:: HDAC2
Uniprot ID:: Q92769
Molecular weight:: 55363.9

References

Xu WS, Parmigiani RB, Marks PA: Histone deacetylase inhibitors: molecular mechanisms of action. Oncogene. 2007 Aug 13;26(37):5541-52. [PubMed:17694093 ]

Enzyme Details

2. Histone deacetylase 3

General function:: Involved in histone deacetylase activity
Specific function:: Responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events. Histone deacetylases act via the formation of large multiprotein complexes. Probably participates in the regulation of transcription through its binding to the zinc-finger transcription factor YY1; increases YY1 repression activity. Required to repress transcription of the POU1F1 transcription factor
Gene Name:: HDAC3
Uniprot ID:: O15379
Molecular weight:: 48847.4

References

Xu WS, Parmigiani RB, Marks PA: Histone deacetylase inhibitors: molecular mechanisms of action. Oncogene. 2007 Aug 13;26(37):5541-52. [PubMed:17694093 ]

Showing metabocard for Vorinostat (HMDB0015568)

MOL for HMDB0015568 (Vorinostat)

3D MOL for HMDB0015568 (Vorinostat)

3D SDF for HMDB0015568 (Vorinostat)

3D-SDF for HMDB0015568 (Vorinostat)

PDB for HMDB0015568 (Vorinostat)

3D PDB for HMDB0015568 (Vorinostat)

SMILES for HMDB0015568 (Vorinostat)

INCHI for HMDB0015568 (Vorinostat)

Structure for HMDB0015568 (Vorinostat)

3D Structure for HMDB0015568 (Vorinostat)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

Enzymes

References

References