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Showing metabocard for Thiobarbital (HMDB0259001)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 20:53:49 UTC
Update Date2021-09-26 23:16:16 UTC
HMDB IDHMDB0259001
Secondary Accession NumbersNone
Metabolite Identification
Common NameThiobarbital
DescriptionThiobarbital belongs to the class of organic compounds known as thiobarbituric acid derivatives. These are organic compounds containing a 2-thioxodihydropyrimidine-4,6(1H,5H)-dione skeleton. Based on a literature review a significant number of articles have been published on Thiobarbital. This compound has been identified in human blood as reported by (PMID: 31557052 ). Thiobarbital is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Thiobarbital is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0259001 (Thiobarbital)

  Mrv1652309112122542D          

 13 13  0  0  0  0            999 V2000
   -0.6283    1.7262    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1842    1.8695    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2448    1.8695    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9626    2.6447    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  4  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  7  9  1  0  0  0  0
  9 10  1  0  0  0  0
  3 10  1  0  0  0  0
 10 11  2  0  0  0  0
  3 12  1  0  0  0  0
 12 13  1  0  0  0  0
M  END
Download

3D MOL for HMDB0259001 (Thiobarbital)

HMDB0259001
     RDKit          3D
Thiobarbital
 25 25  0  0  0  0  0  0  0  0999 V2000
   -1.0882    2.3267    0.3738 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1464    1.5043   -0.4583 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1929    0.0401   -0.1823 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5491   -0.5774   -0.4243 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5379   -2.0636   -0.1280 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7563   -0.5963   -1.1358 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3362   -1.2282   -2.1510 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1502   -0.5147   -0.9375 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.6497   -0.3104    0.3737 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2707   -0.2050    0.6830 S   0  0  0  0  0  0  0  0  0  0  0  0
    1.7284   -0.1931    1.4529 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.3128   -0.2854    1.1778 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4065   -0.6457    2.1412 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7167    2.3393    1.4104 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0202    3.3730    0.0040 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1435    2.0280    0.2793 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8823    1.8552   -0.2299 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3117    1.7037   -1.5292 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3444   -0.1323    0.1827 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8577   -0.4774   -1.4857 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3523   -2.5374   -0.7152 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5367   -2.4979   -0.3622 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7920   -2.2655    0.9435 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8477   -0.5970   -1.7105 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0621   -0.0430    2.4277 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
  3  6  1  0
  6  7  2  0
  6  8  1  0
  8  9  1  0
  9 10  2  0
  9 11  1  0
 11 12  1  0
 12 13  2  0
 12  3  1  0
  1 14  1  0
  1 15  1  0
  1 16  1  0
  2 17  1  0
  2 18  1  0
  4 19  1  0
  4 20  1  0
  5 21  1  0
  5 22  1  0
  5 23  1  0
  8 24  1  0
 11 25  1  0
M  END
Download

3D SDF for HMDB0259001 (Thiobarbital)

  Mrv1652309112122542D          

 13 13  0  0  0  0            999 V2000
   -0.6283    1.7262    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1842    1.8695    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2448    1.8695    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9626    2.6447    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  4  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  7  9  1  0  0  0  0
  9 10  1  0  0  0  0
  3 10  1  0  0  0  0
 10 11  2  0  0  0  0
  3 12  1  0  0  0  0
 12 13  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0259001

> <DATABASE_NAME>
hmdb

> <SMILES>
CCC1(CC)C(=O)NC(=S)NC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C8H12N2O2S/c1-3-8(4-2)5(11)9-7(13)10-6(8)12/h3-4H2,1-2H3,(H2,9,10,11,12,13)

> <INCHI_KEY>
QGVNJRROSLYGKF-UHFFFAOYSA-N

> <FORMULA>
C8H12N2O2S

> <MOLECULAR_WEIGHT>
200.26

> <EXACT_MASS>
200.061948808

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
25

> <JCHEM_AVERAGE_POLARIZABILITY>
19.886017690733617

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
5,5-diethyl-2-sulfanylidene-1,3-diazinane-4,6-dione

> <ALOGPS_LOGP>
1.71

> <JCHEM_LOGP>
1.6069644046666662

> <ALOGPS_LOGS>
-2.41

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
10.72505882740455

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.2035247127219035

> <JCHEM_PKA_STRONGEST_BASIC>
-8.430728544822246

> <JCHEM_POLAR_SURFACE_AREA>
58.2

> <JCHEM_REFRACTIVITY>
52.2432

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.74e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
thiobarbital

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0259001 (Thiobarbital)

HMDB0259001
     RDKit          3D
Thiobarbital
 25 25  0  0  0  0  0  0  0  0999 V2000
   -1.0882    2.3267    0.3738 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1464    1.5043   -0.4583 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1929    0.0401   -0.1823 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5491   -0.5774   -0.4243 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5379   -2.0636   -0.1280 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7563   -0.5963   -1.1358 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3362   -1.2282   -2.1510 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1502   -0.5147   -0.9375 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.6497   -0.3104    0.3737 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2707   -0.2050    0.6830 S   0  0  0  0  0  0  0  0  0  0  0  0
    1.7284   -0.1931    1.4529 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.3128   -0.2854    1.1778 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4065   -0.6457    2.1412 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7167    2.3393    1.4104 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0202    3.3730    0.0040 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1435    2.0280    0.2793 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8823    1.8552   -0.2299 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3117    1.7037   -1.5292 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3444   -0.1323    0.1827 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8577   -0.4774   -1.4857 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3523   -2.5374   -0.7152 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5367   -2.4979   -0.3622 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7920   -2.2655    0.9435 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8477   -0.5970   -1.7105 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0621   -0.0430    2.4277 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
  3  6  1  0
  6  7  2  0
  6  8  1  0
  8  9  1  0
  9 10  2  0
  9 11  1  0
 11 12  1  0
 12 13  2  0
 12  3  1  0
  1 14  1  0
  1 15  1  0
  1 16  1  0
  2 17  1  0
  2 18  1  0
  4 19  1  0
  4 20  1  0
  5 21  1  0
  5 22  1  0
  5 23  1  0
  8 24  1  0
 11 25  1  0
M  END
Download

PDB for HMDB0259001 (Thiobarbital)

HEADER    PROTEIN                                 11-SEP-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-SEP-21         0                                  
HETATM    1  C   UNK     0      -1.173   3.222   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.344   3.490   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       4.001   2.310   0.000  0.00  0.00           O+0
HETATM    6  N   UNK     0       2.667  -0.000   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    8  S   UNK     0       1.334  -2.310   0.000  0.00  0.00           S+0
HETATM    9  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      -1.334   2.310   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       2.324   3.490   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       1.797   4.937   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   10   12                                             
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7                                                       
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10                                                       
CONECT   10    9    3   11                                                  
CONECT   11   10                                                            
CONECT   12    3   13                                                       
CONECT   13   12                                                            
MASTER        0    0    0    0    0    0    0    0   13    0   26    0
END
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3D PDB for HMDB0259001 (Thiobarbital)

COMPND    HMDB0259001
HETATM    1  C1  UNL     1      -1.088   2.327   0.374  1.00  0.00           C  
HETATM    2  C2  UNL     1      -0.146   1.504  -0.458  1.00  0.00           C  
HETATM    3  C3  UNL     1      -0.193   0.040  -0.182  1.00  0.00           C  
HETATM    4  C4  UNL     1      -1.549  -0.577  -0.424  1.00  0.00           C  
HETATM    5  C5  UNL     1      -1.538  -2.064  -0.128  1.00  0.00           C  
HETATM    6  C6  UNL     1       0.756  -0.596  -1.136  1.00  0.00           C  
HETATM    7  O1  UNL     1       0.336  -1.228  -2.151  1.00  0.00           O  
HETATM    8  N1  UNL     1       2.150  -0.515  -0.937  1.00  0.00           N  
HETATM    9  C7  UNL     1       2.650  -0.310   0.374  1.00  0.00           C  
HETATM   10  S1  UNL     1       4.271  -0.205   0.683  1.00  0.00           S  
HETATM   11  N2  UNL     1       1.728  -0.193   1.453  1.00  0.00           N  
HETATM   12  C8  UNL     1       0.313  -0.285   1.178  1.00  0.00           C  
HETATM   13  O2  UNL     1      -0.407  -0.646   2.141  1.00  0.00           O  
HETATM   14  H1  UNL     1      -0.717   2.339   1.410  1.00  0.00           H  
HETATM   15  H2  UNL     1      -1.020   3.373   0.004  1.00  0.00           H  
HETATM   16  H3  UNL     1      -2.144   2.028   0.279  1.00  0.00           H  
HETATM   17  H4  UNL     1       0.882   1.855  -0.230  1.00  0.00           H  
HETATM   18  H5  UNL     1      -0.312   1.704  -1.529  1.00  0.00           H  
HETATM   19  H6  UNL     1      -2.344  -0.132   0.183  1.00  0.00           H  
HETATM   20  H7  UNL     1      -1.858  -0.477  -1.486  1.00  0.00           H  
HETATM   21  H8  UNL     1      -2.352  -2.537  -0.715  1.00  0.00           H  
HETATM   22  H9  UNL     1      -0.537  -2.498  -0.362  1.00  0.00           H  
HETATM   23  H10 UNL     1      -1.792  -2.265   0.944  1.00  0.00           H  
HETATM   24  H11 UNL     1       2.848  -0.597  -1.711  1.00  0.00           H  
HETATM   25  H12 UNL     1       2.062  -0.043   2.428  1.00  0.00           H  
CONECT    1    2   14   15   16
CONECT    2    3   17   18
CONECT    3    4    6   12
CONECT    4    5   19   20
CONECT    5   21   22   23
CONECT    6    7    7    8
CONECT    8    9   24
CONECT    9   10   10   11
CONECT   11   12   25
CONECT   12   13   13
END
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SMILES for HMDB0259001 (Thiobarbital)

CCC1(CC)C(=O)NC(=S)NC1=O
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INCHI for HMDB0259001 (Thiobarbital)

InChI=1S/C8H12N2O2S/c1-3-8(4-2)5(11)9-7(13)10-6(8)12/h3-4H2,1-2H3,(H2,9,10,11,12,13)
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View in JSmolView Stereo Labels
SynonymsNot Available
Chemical FormulaC8H12N2O2S
Average Molecular Weight200.26
Monoisotopic Molecular Weight200.061948808
IUPAC Name5,5-diethyl-2-sulfanylidene-1,3-diazinane-4,6-dione
Traditional Namethiobarbital
CAS Registry NumberNot Available
SMILES
CCC1(CC)C(=O)NC(=S)NC1=O
InChI Identifier
InChI=1S/C8H12N2O2S/c1-3-8(4-2)5(11)9-7(13)10-6(8)12/h3-4H2,1-2H3,(H2,9,10,11,12,13)
InChI KeyQGVNJRROSLYGKF-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as thiobarbituric acid derivatives. These are organic compounds containing a 2-thioxodihydropyrimidine-4,6(1H,5H)-dione skeleton.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassDiazines
Sub ClassPyrimidines and pyrimidine derivatives
Direct ParentThiobarbituric acid derivatives
Alternative Parents
Substituents
  • Thiobarbiturate
  • 1,3-diazinane
  • Thiourea
  • Azacycle
  • Carboxylic acid derivative
  • Organic nitrogen compound
  • Organic oxygen compound
  • Organopnictogen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organosulfur compound
  • Organooxygen compound
  • Organonitrogen compound
  • Carbonyl group
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
ProcessNot Available
RoleNot Available
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Thiobarbital GC-MS (Non-derivatized) - 70eV, Positivesplash10-004i-9610000000-7c9c4976dd8a1756860e2021-09-23Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Thiobarbital GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID580885
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkThiobarbital
METLIN IDNot Available
PubChem Compound6474
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]