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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-06 15:16:49 UTC

Update Date

2022-03-07 02:51:38 UTC

HMDB ID

HMDB0014457

Secondary Accession Numbers

HMDB14457

Metabolite Identification

Common Name

Pentobarbital

Description

Pentobarbital, also known as nembutal or pentobarbitone, belongs to the class of organic compounds known as pyrimidones. Pyrimidones are compounds that contain a pyrimidine ring, which bears a ketone. Pyrimidine is a 6-membered ring consisting of four carbon atoms and two nitrogen centers at the 1- and 3- ring positions. Pentobarbital is a drug which is used for the short-term treatment of insomnia. Based on a literature review a significant number of articles have been published on Pentobarbital.

Structure

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

HMDB0243544
     RDKit          3D
(+)-Pentobarbital
 34 34  0  0  0  0  0  0  0  0999 V2000
    3.5185    0.8951   -0.2995 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2438    1.4351   -0.8418 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9941    1.0807   -0.1487 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6210   -0.3648   -0.1723 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6103   -1.2273    0.4855 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8218   -0.5499    0.2829 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1894   -1.9859    0.2540 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6394   -2.2166    0.6793 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9034   -0.0715    1.7031 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4821   -0.8054    2.6466 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4361    1.1860    2.0798 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1082    1.9710    1.1350 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5835    3.0862    1.4590 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2597    1.5177   -0.1951 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7271    0.2562   -0.5796 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0717   -0.1591   -1.7257 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0186    0.1395   -0.9728 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4956    0.5872    0.7501 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3171    1.7427   -0.3138 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2140    1.1285   -1.9411 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3529    2.5725   -0.9466 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0668    1.4201    0.9436 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1846    1.7195   -0.6122 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5982   -0.7044   -1.2703 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9282   -0.9206    1.5022 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5195   -1.3321   -0.1353 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2597   -2.3223    0.5376 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0697   -2.3911   -0.7592 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5755   -2.5497    1.0027 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6707   -2.2670    1.7857 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2870   -1.3672    0.3795 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0067   -3.1936    0.3012 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3356    1.5432    3.0619 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7752    2.1472   -0.8714 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  4  6  1  0
  6  7  1  0
  7  8  1  0
  6  9  1  0
  9 10  2  0
  9 11  1  0
 11 12  1  0
 12 13  2  0
 12 14  1  0
 14 15  1  0
 15 16  2  0
 15  6  1  0
  1 17  1  0
  1 18  1  0
  1 19  1  0
  2 20  1  0
  2 21  1  0
  3 22  1  0
  3 23  1  0
  4 24  1  0
  5 25  1  0
  5 26  1  0
  5 27  1  0
  7 28  1  0
  7 29  1  0
  8 30  1  0
  8 31  1  0
  8 32  1  0
 11 33  1  0
 14 34  1  0
M  END

312
  Mrv0541 02231214352D          

 16 16  0  0  1  0            999 V2000
    4.5080   -0.1915    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500   -0.1915    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0791   -2.6665    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7935   -1.4290    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.3645   -1.4290    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.0791   -0.1915    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4916    0.5231    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0791    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6665    0.5231    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7935   -0.6040    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3645   -0.6040    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3166    0.5231    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4916    1.9520    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8415    0.5231    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0791   -1.8415    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0791    2.6665    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1 10  2  0  0  0  0
  2 11  2  0  0  0  0
  3 15  2  0  0  0  0
  4 10  1  0  0  0  0
  4 15  1  0  0  0  0
  5 11  1  0  0  0  0
  5 15  1  0  0  0  0
  6  7  1  0  0  0  0
  6  9  1  0  0  0  0
  6 10  1  0  0  0  0
  6 11  1  0  0  0  0
  7  8  1  0  0  0  0
  7 12  1  0  0  0  0
  8 13  1  0  0  0  0
  9 14  1  0  0  0  0
 13 16  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0014457

> <DATABASE_NAME>
hmdb

> <SMILES>
CCCC(C)C1(CC)C(=O)NC(=O)NC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C11H18N2O3/c1-4-6-7(3)11(5-2)8(14)12-10(16)13-9(11)15/h7H,4-6H2,1-3H3,(H2,12,13,14,15,16)

> <INCHI_KEY>
WEXRUCMBJFQVBZ-UHFFFAOYSA-N

> <FORMULA>
C11H18N2O3

> <MOLECULAR_WEIGHT>
226.2722

> <EXACT_MASS>
226.131742452

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
23.407281054349912

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
5-ethyl-5-(pentan-2-yl)-1,3-diazinane-2,4,6-trione

> <ALOGPS_LOGP>
2.16

> <JCHEM_LOGP>
1.8932512466666667

> <ALOGPS_LOGS>
-2.42

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.15188824310562

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.482022727708522

> <JCHEM_POLAR_SURFACE_AREA>
75.27

> <JCHEM_REFRACTIVITY>
58.00289999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.64e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
pentobarbital

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0243544
     RDKit          3D
(+)-Pentobarbital
 34 34  0  0  0  0  0  0  0  0999 V2000
    3.5185    0.8951   -0.2995 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2438    1.4351   -0.8418 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9941    1.0807   -0.1487 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6210   -0.3648   -0.1723 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6103   -1.2273    0.4855 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8218   -0.5499    0.2829 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1894   -1.9859    0.2540 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6394   -2.2166    0.6793 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9034   -0.0715    1.7031 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4821   -0.8054    2.6466 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4361    1.1860    2.0798 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1082    1.9710    1.1350 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5835    3.0862    1.4590 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2597    1.5177   -0.1951 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7271    0.2562   -0.5796 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0717   -0.1591   -1.7257 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0186    0.1395   -0.9728 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4956    0.5872    0.7501 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3171    1.7427   -0.3138 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2140    1.1285   -1.9411 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3529    2.5725   -0.9466 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0668    1.4201    0.9436 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1846    1.7195   -0.6122 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5982   -0.7044   -1.2703 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9282   -0.9206    1.5022 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5195   -1.3321   -0.1353 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2597   -2.3223    0.5376 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0697   -2.3911   -0.7592 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5755   -2.5497    1.0027 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6707   -2.2670    1.7857 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2870   -1.3672    0.3795 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0067   -3.1936    0.3012 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3356    1.5432    3.0619 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7752    2.1472   -0.8714 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  4  6  1  0
  6  7  1  0
  7  8  1  0
  6  9  1  0
  9 10  2  0
  9 11  1  0
 11 12  1  0
 12 13  2  0
 12 14  1  0
 14 15  1  0
 15 16  2  0
 15  6  1  0
  1 17  1  0
  1 18  1  0
  1 19  1  0
  2 20  1  0
  2 21  1  0
  3 22  1  0
  3 23  1  0
  4 24  1  0
  5 25  1  0
  5 26  1  0
  5 27  1  0
  7 28  1  0
  7 29  1  0
  8 30  1  0
  8 31  1  0
  8 32  1  0
 11 33  1  0
 14 34  1  0
M  END

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: 312                                               
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  O   UNK     0       8.415  -0.357   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0       3.080  -0.357   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0       5.748  -4.977   0.000  0.00  0.00           O+0
HETATM    4  N   UNK     0       7.081  -2.667   0.000  0.00  0.00           N+0
HETATM    5  N   UNK     0       4.414  -2.667   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0       5.748  -0.357   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       6.518   0.976   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       5.748   2.310   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       4.977   0.976   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       7.081  -1.127   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.414  -1.127   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       8.058   0.976   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       6.518   3.644   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       3.437   0.976   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       5.748  -3.437   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       5.748   4.977   0.000  0.00  0.00           C+0
CONECT    1   10                                                            
CONECT    2   11                                                            
CONECT    3   15                                                            
CONECT    4   10   15                                                       
CONECT    5   11   15                                                       
CONECT    6    7    9   10   11                                             
CONECT    7    6    8   12                                                  
CONECT    8    7   13                                                       
CONECT    9    6   14                                                       
CONECT   10    1    4    6                                                  
CONECT   11    2    5    6                                                  
CONECT   12    7                                                            
CONECT   13    8   16                                                       
CONECT   14    9                                                            
CONECT   15    3    4    5                                                  
CONECT   16   13                                                            
MASTER        0    0    0    0    0    0    0    0   16    0   32    0
END

COMPND    HMDB0014457
HETATM    1  C1  UNL     1       3.466  -0.973   0.718  1.00  0.00           C  
HETATM    2  C2  UNL     1       2.190  -0.121   0.882  1.00  0.00           C  
HETATM    3  C3  UNL     1       1.595   0.002  -0.468  1.00  0.00           C  
HETATM    4  C4  UNL     1       0.351   0.776  -0.624  1.00  0.00           C  
HETATM    5  C5  UNL     1       0.577   2.205  -0.176  1.00  0.00           C  
HETATM    6  C6  UNL     1      -0.897   0.157  -0.098  1.00  0.00           C  
HETATM    7  C7  UNL     1      -2.090   1.040  -0.317  1.00  0.00           C  
HETATM    8  C8  UNL     1      -2.421   1.388  -1.712  1.00  0.00           C  
HETATM    9  C9  UNL     1      -1.137  -1.080  -0.910  1.00  0.00           C  
HETATM   10  O1  UNL     1      -1.152  -0.958  -2.160  1.00  0.00           O  
HETATM   11  N1  UNL     1      -1.344  -2.356  -0.356  1.00  0.00           N  
HETATM   12  C10 UNL     1      -1.318  -2.542   1.047  1.00  0.00           C  
HETATM   13  O2  UNL     1      -1.504  -3.687   1.534  1.00  0.00           O  
HETATM   14  N2  UNL     1      -1.079  -1.417   1.917  1.00  0.00           N  
HETATM   15  C11 UNL     1      -0.872  -0.136   1.350  1.00  0.00           C  
HETATM   16  O3  UNL     1      -0.651   0.817   2.131  1.00  0.00           O  
HETATM   17  H1  UNL     1       4.249  -0.320   0.310  1.00  0.00           H  
HETATM   18  H2  UNL     1       3.247  -1.862   0.096  1.00  0.00           H  
HETATM   19  H3  UNL     1       3.827  -1.317   1.723  1.00  0.00           H  
HETATM   20  H4  UNL     1       2.587   0.849   1.287  1.00  0.00           H  
HETATM   21  H5  UNL     1       1.595  -0.669   1.621  1.00  0.00           H  
HETATM   22  H6  UNL     1       2.382   0.448  -1.140  1.00  0.00           H  
HETATM   23  H7  UNL     1       1.488  -1.051  -0.869  1.00  0.00           H  
HETATM   24  H8  UNL     1       0.190   0.850  -1.745  1.00  0.00           H  
HETATM   25  H9  UNL     1       0.528   2.941  -1.000  1.00  0.00           H  
HETATM   26  H10 UNL     1      -0.088   2.522   0.639  1.00  0.00           H  
HETATM   27  H11 UNL     1       1.623   2.312   0.239  1.00  0.00           H  
HETATM   28  H12 UNL     1      -2.967   0.498   0.147  1.00  0.00           H  
HETATM   29  H13 UNL     1      -2.020   1.986   0.277  1.00  0.00           H  
HETATM   30  H14 UNL     1      -3.276   0.743  -2.072  1.00  0.00           H  
HETATM   31  H15 UNL     1      -1.644   1.305  -2.464  1.00  0.00           H  
HETATM   32  H16 UNL     1      -2.847   2.433  -1.771  1.00  0.00           H  
HETATM   33  H17 UNL     1      -1.515  -3.161  -0.974  1.00  0.00           H  
HETATM   34  H18 UNL     1      -1.073  -1.622   2.937  1.00  0.00           H  
CONECT    1    2   17   18   19
CONECT    2    3   20   21
CONECT    3    4   22   23
CONECT    4    5    6   24
CONECT    5   25   26   27
CONECT    6    7    9   15
CONECT    7    8   28   29
CONECT    8   30   31   32
CONECT    9   10   10   11
CONECT   11   12   33
CONECT   12   13   13   14
CONECT   14   15   34
CONECT   15   16   16
END

HMDB0243544
     RDKit          3D
(+)-Pentobarbital
 34 34  0  0  0  0  0  0  0  0999 V2000
    3.5185    0.8951   -0.2995 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2438    1.4351   -0.8418 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9941    1.0807   -0.1487 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6210   -0.3648   -0.1723 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6103   -1.2273    0.4855 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8218   -0.5499    0.2829 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1894   -1.9859    0.2540 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6394   -2.2166    0.6793 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9034   -0.0715    1.7031 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4821   -0.8054    2.6466 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4361    1.1860    2.0798 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1082    1.9710    1.1350 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5835    3.0862    1.4590 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2597    1.5177   -0.1951 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7271    0.2562   -0.5796 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0717   -0.1591   -1.7257 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0186    0.1395   -0.9728 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4956    0.5872    0.7501 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3171    1.7427   -0.3138 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2140    1.1285   -1.9411 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3529    2.5725   -0.9466 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0668    1.4201    0.9436 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1846    1.7195   -0.6122 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5982   -0.7044   -1.2703 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9282   -0.9206    1.5022 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5195   -1.3321   -0.1353 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2597   -2.3223    0.5376 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0697   -2.3911   -0.7592 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5755   -2.5497    1.0027 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6707   -2.2670    1.7857 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2870   -1.3672    0.3795 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0067   -3.1936    0.3012 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3356    1.5432    3.0619 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7752    2.1472   -0.8714 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  4  6  1  0
  6  7  1  0
  7  8  1  0
  6  9  1  0
  9 10  2  0
  9 11  1  0
 11 12  1  0
 12 13  2  0
 12 14  1  0
 14 15  1  0
 15 16  2  0
 15  6  1  0
  1 17  1  0
  1 18  1  0
  1 19  1  0
  2 20  1  0
  2 21  1  0
  3 22  1  0
  3 23  1  0
  4 24  1  0
  5 25  1  0
  5 26  1  0
  5 27  1  0
  7 28  1  0
  7 29  1  0
  8 30  1  0
  8 31  1  0
  8 32  1  0
 11 33  1  0
 14 34  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
5-Ethyl-5-(1-methyl-butyl)-pyrimidine-2,4,6-trione	ChEBI
5-Ethyl-5-(1-methylbutyl)-2,4,6(1H,3H,5H)-pyrimidinetrione	ChEBI
5-Ethyl-5-(1-methylbutyl)barbituric acid	ChEBI
5-Ethyl-5-(sec-pentyl)barbituric acid	ChEBI
Nembutal	ChEBI
Pentobarbitone	ChEBI
5-Ethyl-5-(1-methylbutyl)barbitate	Generator
5-Ethyl-5-(1-methylbutyl)barbitic acid	Generator
5-Ethyl-5-(sec-pentyl)barbitate	Generator
5-Ethyl-5-(sec-pentyl)barbitic acid	Generator
Pentabarbital	HMDB
Pentabarbitone	HMDB
Pentobarbiturate	HMDB
Pentobarbituric acid	HMDB
Sodium pentobarbital	HMDB
Etaminal	MeSH, HMDB
Ethaminal	MeSH, HMDB
Pentobarbital sodium	MeSH, HMDB
Sagatal	MeSH, HMDB
Diabutal	MeSH, HMDB
Pentobarbital, monosodium salt	MeSH, HMDB
Mebubarbital	MeSH, HMDB
Mebumal	MeSH, HMDB
Monosodium salt pentobarbital	MeSH, HMDB

Chemical Formula

C₁₁H₁₈N₂O₃

Average Molecular Weight

226.2722

Monoisotopic Molecular Weight

226.131742452

IUPAC Name

5-ethyl-5-(pentan-2-yl)-1,3-diazinane-2,4,6-trione

Traditional Name

pentobarbital

CAS Registry Number

76-74-4

SMILES

CCCC(C)C1(CC)C(=O)NC(=O)NC1=O

InChI Identifier

InChI=1S/C11H18N2O3/c1-4-6-7(3)11(5-2)8(14)12-10(16)13-9(11)15/h7H,4-6H2,1-3H3,(H2,12,13,14,15,16)

InChI Key

WEXRUCMBJFQVBZ-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyrimidones. Pyrimidones are compounds that contain a pyrimidine ring, which bears a ketone. Pyrimidine is a 6-membered ring consisting of four carbon atoms and two nitrogen centers at the 1- and 3- ring positions.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Diazines

Sub Class

Pyrimidines and pyrimidine derivatives

Direct Parent

Pyrimidones

Alternative Parents

Substituents

Pyrimidone
Hydropyrimidine
2,5-dihydropyrimidine
Carbonic acid derivative
Propargyl-type 1,3-dipolar organic compound
Organic 1,3-dipolar compound
Azacycle
Organic oxide
Organooxygen compound
Organonitrogen compound
Organopnictogen compound
Organic oxygen compound
Carbonyl group
Organic nitrogen compound
Hydrocarbon derivative
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

barbiturates (CHEBI:7983 )

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 31557052)

Cellular substructure

Membrane (HMDB: HMDB0243544)

Source

Exogenous

Exogenous (PMID: 31557052)

Process

Not Available

Role

Not Available

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	129.5 °C	Not Available
Boiling Point	226.50 °C. @ 760.00 mm Hg (est)	The Good Scents Company Information System
Water Solubility	0.86 g/L	Not Available
LogP	2.1	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	0.86 g/L	ALOGPS
logP	2.16	ALOGPS
logP	1.89	ChemAxon
logS	-2.4	ALOGPS
pKa (Strongest Acidic)	8.48	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	75.27 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	58 m³·mol⁻¹	ChemAxon
Polarizability	23.41 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]+	153.597	31661259
DarkChem	[M-H]-	149.231	31661259
DeepCCS	[M+H]+	153.62	30932474
DeepCCS	[M-H]-	149.793	30932474
DeepCCS	[M-2H]-	186.675	30932474
DeepCCS	[M+Na]+	162.259	30932474
AllCCS	[M+H]+	152.1	32859911
AllCCS	[M+H-H2O]+	148.3	32859911
AllCCS	[M+NH4]+	155.6	32859911
AllCCS	[M+Na]+	156.6	32859911
AllCCS	[M-H]-	154.8	32859911
AllCCS	[M+Na-2H]-	155.5	32859911
AllCCS	[M+HCOO]-	156.3	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.	5.39 minutes	32390414
Predicted by Siyang on May 30, 2022	16.5653 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	1.74 minutes	32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid	25.1 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Pentobarbital	CCCC(C)C1(CC)C(=O)NC(=O)NC1=O	2987.8	Standard polar	33892256
Pentobarbital	CCCC(C)C1(CC)C(=O)NC(=O)NC1=O	1697.5	Standard non polar	33892256
Pentobarbital	CCCC(C)C1(CC)C(=O)NC(=O)NC1=O	1726.6	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Pentobarbital,1TMS,isomer #1	CCCC(C)C1(CC)C(=O)NC(=O)N([Si](C)(C)C)C1=O	1699.4	Semi standard non polar	33892256
Pentobarbital,1TMS,isomer #1	CCCC(C)C1(CC)C(=O)NC(=O)N([Si](C)(C)C)C1=O	1879.2	Standard non polar	33892256
Pentobarbital,1TMS,isomer #1	CCCC(C)C1(CC)C(=O)NC(=O)N([Si](C)(C)C)C1=O	2756.0	Standard polar	33892256
Pentobarbital,2TMS,isomer #1	CCCC(C)C1(CC)C(=O)N([Si](C)(C)C)C(=O)N([Si](C)(C)C)C1=O	1686.4	Semi standard non polar	33892256
Pentobarbital,2TMS,isomer #1	CCCC(C)C1(CC)C(=O)N([Si](C)(C)C)C(=O)N([Si](C)(C)C)C1=O	1921.9	Standard non polar	33892256
Pentobarbital,2TMS,isomer #1	CCCC(C)C1(CC)C(=O)N([Si](C)(C)C)C(=O)N([Si](C)(C)C)C1=O	2286.6	Standard polar	33892256
Pentobarbital,1TBDMS,isomer #1	CCCC(C)C1(CC)C(=O)NC(=O)N([Si](C)(C)C(C)(C)C)C1=O	1908.7	Semi standard non polar	33892256
Pentobarbital,1TBDMS,isomer #1	CCCC(C)C1(CC)C(=O)NC(=O)N([Si](C)(C)C(C)(C)C)C1=O	2107.2	Standard non polar	33892256
Pentobarbital,1TBDMS,isomer #1	CCCC(C)C1(CC)C(=O)NC(=O)N([Si](C)(C)C(C)(C)C)C1=O	2785.1	Standard polar	33892256
Pentobarbital,2TBDMS,isomer #1	CCCC(C)C1(CC)C(=O)N([Si](C)(C)C(C)(C)C)C(=O)N([Si](C)(C)C(C)(C)C)C1=O	2115.0	Semi standard non polar	33892256
Pentobarbital,2TBDMS,isomer #1	CCCC(C)C1(CC)C(=O)N([Si](C)(C)C(C)(C)C)C(=O)N([Si](C)(C)C(C)(C)C)C1=O	2357.2	Standard non polar	33892256
Pentobarbital,2TBDMS,isomer #1	CCCC(C)C1(CC)C(=O)N([Si](C)(C)C(C)(C)C)C(=O)N([Si](C)(C)C(C)(C)C)C1=O	2435.5	Standard polar	33892256

Spectra

Biological Properties

Cellular Locations

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 DB00312	21059682	details
Urine	Expected but not Quantified	Not Quantified	Not Available	Not Available	Taking drug identified by DrugBank entry DB00312	21059682	details

Abnormal Concentrations

Not Available

Predicted Concentrations

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

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

DB00312

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

4575

KEGG Compound ID

C07422

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Pentobarbital

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

7983

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

rw1621031

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Knodell RG, Spector MH, Brooks DA, Keller FX, Kyner WT: Alterations in pentobarbital pharmacokinetics in response to parenteral and enteral alimentation in the rat. Gastroenterology. 1980 Dec;79(6):1211-6. [PubMed:6777235 ]

Enzymes

Enzyme Details

1. Cytochrome P450 3A4

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 performs a variety of oxidation reactions (e.g. caffeine 8-oxidation, omeprazole sulphoxidation, midazolam 1'-hydroxylation and midazolam 4-hydroxylation) of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics. Acts as a 1,8-cineole 2-exo-monooxygenase. The enzyme also hydroxylates etoposide.
Gene Name:: CYP3A4
Uniprot ID:: P08684
Molecular weight:: 57255.585

Enzyme Details

2. 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

Preissner S, Kroll K, Dunkel M, Senger C, Goldsobel G, Kuzman D, Guenther S, Winnenburg R, Schroeder M, Preissner R: SuperCYP: a comprehensive database on Cytochrome P450 enzymes including a tool for analysis of CYP-drug interactions. Nucleic Acids Res. 2010 Jan;38(Database issue):D237-43. doi: 10.1093/nar/gkp970. Epub 2009 Nov 24. [PubMed:19934256 ]

Enzyme Details

3. Glutamate receptor, ionotropic kainate 2

General function:: Involved in ionotropic glutamate receptor activity
Specific function:: Ionotropic glutamate receptor. L-glutamate acts as an excitatory neurotransmitter at many synapses in the central nervous system. Binding of the excitatory neurotransmitter L- glutamate induces a conformation change, leading to the opening of the cation channel, and thereby converts the chemical signal to an electrical impulse. The receptor then desensitizes rapidly and enters a transient inactive state, characterized by the presence of bound agonist. May be involved in the transmission of light information from the retina to the hypothalamus. Modulates cell surface expression of NETO2
Gene Name:: GRIK2
Uniprot ID:: Q13002
Molecular weight:: 102582.5

References

Yamakura T, Bertaccini E, Trudell JR, Harris RA: Anesthetics and ion channels: molecular models and sites of action. Annu Rev Pharmacol Toxicol. 2001;41:23-51. [PubMed:11264449 ]
Krasowski MD, Harrison NL: General anaesthetic actions on ligand-gated ion channels. Cell Mol Life Sci. 1999 Aug 15;55(10):1278-303. [PubMed:10487207 ]

Enzyme Details

4. Glutamate receptor 2

General function:: Involved in ionotropic glutamate receptor activity
Specific function:: Ionotropic glutamate receptor. L-glutamate acts as an excitatory neurotransmitter at many synapses in the central nervous system. Binding of the excitatory neurotransmitter L- glutamate induces a conformation change, leading to the opening of the cation channel, and thereby converts the chemical signal to an electrical impulse. The receptor then desensitizes rapidly and enters a transient inactive state, characterized by the presence of bound agonist
Gene Name:: GRIA2
Uniprot ID:: P42262
Molecular weight:: 98820.3

References

Yamakura T, Bertaccini E, Trudell JR, Harris RA: Anesthetics and ion channels: molecular models and sites of action. Annu Rev Pharmacol Toxicol. 2001;41:23-51. [PubMed:11264449 ]
Krasowski MD, Harrison NL: General anaesthetic actions on ligand-gated ion channels. Cell Mol Life Sci. 1999 Aug 15;55(10):1278-303. [PubMed:10487207 ]

Enzyme Details

5. Gamma-aminobutyric acid receptor subunit alpha-1

General function:: Involved in ion transport
Specific function:: GABA, the major inhibitory neurotransmitter in the vertebrate brain, mediates neuronal inhibition by binding to the GABA/benzodiazepine receptor and opening an integral chloride channel
Gene Name:: GABRA1
Uniprot ID:: P14867
Molecular weight:: 51801.4

References

Steinbach JH, Akk G: Modulation of GABA(A) receptor channel gating by pentobarbital. J Physiol. 2001 Dec 15;537(Pt 3):715-33. [PubMed:11744750 ]
Whiting PJ: The GABAA receptor gene family: new opportunities for drug development. Curr Opin Drug Discov Devel. 2003 Sep;6(5):648-57. [PubMed:14579514 ]
Mehta AK, Ticku MK: An update on GABAA receptors. Brain Res Brain Res Rev. 1999 Apr;29(2-3):196-217. [PubMed:10209232 ]
Krasowski MD, Harrison NL: General anaesthetic actions on ligand-gated ion channels. Cell Mol Life Sci. 1999 Aug 15;55(10):1278-303. [PubMed:10487207 ]
Yamakura T, Bertaccini E, Trudell JR, Harris RA: Anesthetics and ion channels: molecular models and sites of action. Annu Rev Pharmacol Toxicol. 2001;41:23-51. [PubMed:11264449 ]
Davies DL, McCauley LD, Bolger MB, Alkana RL: Pressure-sensitive and -insensitive coupling in gamma-aminobutyric acid(A) receptors. Psychopharmacology (Berl). 2001 Oct;157(4):401-10. [PubMed:11605100 ]
Rahman M, Zhu D, Lindblad C, Johansson IM, Holmberg E, Isaksson M, Taube M, Backstrom T, Wang MD: GABA-site antagonism and pentobarbital actions do not depend on the alpha-subunit type in the recombinant rat GABA receptor. Acta Physiol (Oxf). 2006 Aug;187(4):479-88. [PubMed:16866778 ]
Feigenspan A, Weiler R: Electrophysiological properties of mouse horizontal cell GABAA receptors. J Neurophysiol. 2004 Nov;92(5):2789-801. Epub 2004 Jul 7. [PubMed:15240758 ]
Chen X, Ji ZL, Chen YZ: TTD: Therapeutic Target Database. Nucleic Acids Res. 2002 Jan 1;30(1):412-5. [PubMed:11752352 ]
Overington JP, Al-Lazikani B, Hopkins AL: How many drug targets are there? Nat Rev Drug Discov. 2006 Dec;5(12):993-6. [PubMed:17139284 ]
Imming P, Sinning C, Meyer A: Drugs, their targets and the nature and number of drug targets. Nat Rev Drug Discov. 2006 Oct;5(10):821-34. [PubMed:17016423 ]

Enzyme Details

6. Gamma-aminobutyric acid receptor subunit alpha-2

General function:: Involved in ion transport
Specific function:: GABA, the major inhibitory neurotransmitter in the vertebrate brain, mediates neuronal inhibition by binding to the GABA/benzodiazepine receptor and opening an integral chloride channel
Gene Name:: GABRA2
Uniprot ID:: P47869
Molecular weight:: 51325.9

References

Yamakura T, Bertaccini E, Trudell JR, Harris RA: Anesthetics and ion channels: molecular models and sites of action. Annu Rev Pharmacol Toxicol. 2001;41:23-51. [PubMed:11264449 ]
Mehta AK, Ticku MK: An update on GABAA receptors. Brain Res Brain Res Rev. 1999 Apr;29(2-3):196-217. [PubMed:10209232 ]

Enzyme Details

7. Gamma-aminobutyric acid receptor subunit alpha-3

General function:: Involved in ion transport
Specific function:: GABA, the major inhibitory neurotransmitter in the vertebrate brain, mediates neuronal inhibition by binding to the GABA/benzodiazepine receptor and opening an integral chloride channel
Gene Name:: GABRA3
Uniprot ID:: P34903
Molecular weight:: 55164.1

References

Yamakura T, Bertaccini E, Trudell JR, Harris RA: Anesthetics and ion channels: molecular models and sites of action. Annu Rev Pharmacol Toxicol. 2001;41:23-51. [PubMed:11264449 ]
Mehta AK, Ticku MK: An update on GABAA receptors. Brain Res Brain Res Rev. 1999 Apr;29(2-3):196-217. [PubMed:10209232 ]

Enzyme Details

8. Gamma-aminobutyric acid receptor subunit alpha-4

General function:: Involved in ion transport
Specific function:: GABA, the major inhibitory neurotransmitter in the vertebrate brain, mediates neuronal inhibition by binding to the GABA/benzodiazepine receptor and opening an integral chloride channel
Gene Name:: GABRA4
Uniprot ID:: P48169
Molecular weight:: 61622.6

References

Mehta AK, Ticku MK: An update on GABAA receptors. Brain Res Brain Res Rev. 1999 Apr;29(2-3):196-217. [PubMed:10209232 ]

Enzyme Details

9. Gamma-aminobutyric acid receptor subunit alpha-5

General function:: Involved in ion transport
Specific function:: GABA, the major inhibitory neurotransmitter in the vertebrate brain, mediates neuronal inhibition by binding to the GABA/benzodiazepine receptor and opening an integral chloride channel
Gene Name:: GABRA5
Uniprot ID:: P31644
Molecular weight:: 52145.6

References

Yamakura T, Bertaccini E, Trudell JR, Harris RA: Anesthetics and ion channels: molecular models and sites of action. Annu Rev Pharmacol Toxicol. 2001;41:23-51. [PubMed:11264449 ]
Mehta AK, Ticku MK: An update on GABAA receptors. Brain Res Brain Res Rev. 1999 Apr;29(2-3):196-217. [PubMed:10209232 ]

Enzyme Details

10. Gamma-aminobutyric acid receptor subunit alpha-6

General function:: Involved in ion transport
Specific function:: GABA, the major inhibitory neurotransmitter in the vertebrate brain, mediates neuronal inhibition by binding to the GABA/benzodiazepine receptor and opening an integral chloride channel
Gene Name:: GABRA6
Uniprot ID:: Q16445
Molecular weight:: 51023.7

References

Mehta AK, Ticku MK: An update on GABAA receptors. Brain Res Brain Res Rev. 1999 Apr;29(2-3):196-217. [PubMed:10209232 ]
Yamakura T, Bertaccini E, Trudell JR, Harris RA: Anesthetics and ion channels: molecular models and sites of action. Annu Rev Pharmacol Toxicol. 2001;41:23-51. [PubMed:11264449 ]

Showing metabocard for Pentobarbital (HMDB0014457)

MOL for HMDB0014457 (Pentobarbital)

3D MOL for HMDB0014457 (Pentobarbital)

3D SDF for HMDB0014457 (Pentobarbital)

3D-SDF for HMDB0014457 (Pentobarbital)

PDB for HMDB0014457 (Pentobarbital)

3D PDB for HMDB0014457 (Pentobarbital)

SMILES for HMDB0014457 (Pentobarbital)

INCHI for HMDB0014457 (Pentobarbital)

Structure for HMDB0014457 (Pentobarbital)

3D Structure for HMDB0014457 (Pentobarbital)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

Enzymes

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