Showing metabocard for Dihydrothymine (MMDBc0000493)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2020-12-10 18:39:01 UTC
Update Date2022-08-31 06:07:10 UTC
MiMeDB IDMMDBc0000493
Metabolite Identification
Common NameDihydrothymine
DescriptionDihydrothymine (CAS: 696-04-8) is an intermediate breakdown product of thymine. Dihydropyrimidine dehydrogenase catalyzes the reduction of thymine into 5,6-dihydrothymine; then dihydropyrimidinase hydrolyzes 5,6-dihydrothymine into N-carbamyl-beta-alanine. Finally, beta-ureidopropionase catalyzes the conversion of N-carbamyl-beta-alanine into beta-alanine. When present at abnormally high levels, dihydrothymine can be toxic, although the mechanism of toxicity is not clear. In particular, patients with dihydropyrimidinase deficiency exhibit highly increased concentrations of 5,6-dihydrouracil and 5,6-dihydrothymine; and moderately increased concentrations of uracil and thymine can be detected in urine. Dihydropyrimidinase deficiency is a disorder that can cause neurological and gastrointestinal problems in some affected individuals. The most common neurological abnormalities that occur are intellectual disability, seizures, weak muscle tone (hypotonia), abnormally small head size (microcephaly), and autistic behaviours that affect communication and social interaction. Gastrointestinal problems that occur in dihydropyrimidinase deficiency include the backflow of acidic stomach contents into the esophagus (gastroesophageal reflux) and recurrent episodes of vomiting.
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x0000564abfbe9960>


  Mrv1652305082019302D          

  9  9  0  0  0  0            999 V2000
    0.1786   -1.1344    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.8931   -0.7219    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6077   -1.1344    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8931    0.1031    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.1785    0.5157    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1786    1.3407    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5359    0.1031    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.2504    0.5157    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5359   -0.7219    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  5  7  1  0  0  0  0
  7  8  1  6  0  0  0
  7  9  1  0  0  0  0
  1  9  1  0  0  0  0
M  END
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3D MOL for #<Metabolite:0x0000564abfbe9960>

HMDB0000079
     RDKit          3D
Dihydrothymine
 17 17  0  0  0  0  0  0  0  0999 V2000
   -1.6124   -0.3251   -0.7091 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8151    0.6099    0.2068 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.1905   -0.2549    1.2674 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7845   -1.1125    0.6736 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.8124   -0.5551   -0.1410 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9161   -1.1238   -0.3149 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4938    0.7119   -0.7529 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.2356    1.3209   -0.5312 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0051    2.4725   -0.9619 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0301    0.2257   -1.5541 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4311   -0.7316   -0.0743 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9484   -1.1647   -1.0430 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5468    1.2939    0.6938 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3114    0.4438    1.9991 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9788   -0.8119    1.7934 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7956   -2.1620    0.8012 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1988    1.1629   -1.3529 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
  5  6  2  0
  5  7  1  0
  7  8  1  0
  8  9  2  0
  8  2  1  0
  1 10  1  0
  1 11  1  0
  1 12  1  0
  2 13  1  1
  3 14  1  0
  3 15  1  0
  4 16  1  0
  7 17  1  0
M  END
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3D SDF for #<Metabolite:0x0000564abfbe9960>


  Mrv1652305082019302D          

  9  9  0  0  0  0            999 V2000
    0.1786   -1.1344    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.8931   -0.7219    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6077   -1.1344    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8931    0.1031    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.1785    0.5157    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1786    1.3407    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5359    0.1031    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.2504    0.5157    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5359   -0.7219    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  5  7  1  0  0  0  0
  7  8  1  6  0  0  0
  7  9  1  0  0  0  0
  1  9  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0000493

> <DATABASE_NAME>
MIME

> <SMILES>
C[C@H]1CNC(=O)NC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C5H8N2O2/c1-3-2-6-5(9)7-4(3)8/h3H,2H2,1H3,(H2,6,7,8,9)/t3-/m0/s1

> <INCHI_KEY>
NBAKTGXDIBVZOO-VKHMYHEASA-N

> <FORMULA>
C5H8N2O2

> <MOLECULAR_WEIGHT>
128.131

> <EXACT_MASS>
128.058577506

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
17

> <JCHEM_AVERAGE_POLARIZABILITY>
12.032355612950356

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(5S)-5-methyl-1,3-diazinane-2,4-dione

> <ALOGPS_LOGP>
-0.80

> <JCHEM_LOGP>
-0.670221453

> <ALOGPS_LOGS>
-0.84

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
18.799734416362337

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.699408342323004

> <JCHEM_PKA_STRONGEST_BASIC>
-7.380677679727569

> <JCHEM_POLAR_SURFACE_AREA>
58.2

> <JCHEM_REFRACTIVITY>
30.320000000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.87e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(5S)-5-methyl-1,3-diazinane-2,4-dione

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for #<Metabolite:0x0000564abfbe9960>

HMDB0000079
     RDKit          3D
Dihydrothymine
 17 17  0  0  0  0  0  0  0  0999 V2000
   -1.6124   -0.3251   -0.7091 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8151    0.6099    0.2068 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.1905   -0.2549    1.2674 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7845   -1.1125    0.6736 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.8124   -0.5551   -0.1410 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9161   -1.1238   -0.3149 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4938    0.7119   -0.7529 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.2356    1.3209   -0.5312 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0051    2.4725   -0.9619 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0301    0.2257   -1.5541 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4311   -0.7316   -0.0743 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9484   -1.1647   -1.0430 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5468    1.2939    0.6938 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3114    0.4438    1.9991 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9788   -0.8119    1.7934 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7956   -2.1620    0.8012 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1988    1.1629   -1.3529 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
  5  6  2  0
  5  7  1  0
  7  8  1  0
  8  9  2  0
  8  2  1  0
  1 10  1  0
  1 11  1  0
  1 12  1  0
  2 13  1  1
  3 14  1  0
  3 15  1  0
  4 16  1  0
  7 17  1  0
M  END
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PDB for #<Metabolite:0x0000564abfbe9960>

HEADER    PROTEIN                                 08-MAY-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   08-MAY-20         0                                  
HETATM    1  N   UNK     0       0.333  -2.118   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0       1.667  -1.347   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       3.001  -2.118   0.000  0.00  0.00           O+0
HETATM    4  N   UNK     0       1.667   0.192   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0       0.333   0.963   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       0.333   2.503   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0      -1.000   0.192   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -2.334   0.963   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -1.000  -1.347   0.000  0.00  0.00           C+0
CONECT    1    2    9                                                       
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7    1                                                       
MASTER        0    0    0    0    0    0    0    0    9    0   18    0
END
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3D PDB for #<Metabolite:0x0000564abfbe9960>

COMPND    HMDB0000079
HETATM    1  C1  UNL     1      -1.612  -0.325  -0.709  1.00  0.00           C  
HETATM    2  C2  UNL     1      -0.815   0.610   0.207  1.00  0.00           C  
HETATM    3  C3  UNL     1      -0.190  -0.255   1.267  1.00  0.00           C  
HETATM    4  N1  UNL     1       0.784  -1.112   0.674  1.00  0.00           N  
HETATM    5  C4  UNL     1       1.812  -0.555  -0.141  1.00  0.00           C  
HETATM    6  O1  UNL     1       2.916  -1.124  -0.315  1.00  0.00           O  
HETATM    7  N2  UNL     1       1.494   0.712  -0.753  1.00  0.00           N  
HETATM    8  C5  UNL     1       0.236   1.321  -0.531  1.00  0.00           C  
HETATM    9  O2  UNL     1       0.005   2.472  -0.962  1.00  0.00           O  
HETATM   10  H1  UNL     1      -2.030   0.226  -1.554  1.00  0.00           H  
HETATM   11  H2  UNL     1      -2.431  -0.732  -0.074  1.00  0.00           H  
HETATM   12  H3  UNL     1      -0.948  -1.165  -1.043  1.00  0.00           H  
HETATM   13  H4  UNL     1      -1.547   1.294   0.694  1.00  0.00           H  
HETATM   14  H5  UNL     1       0.311   0.444   1.999  1.00  0.00           H  
HETATM   15  H6  UNL     1      -0.979  -0.812   1.793  1.00  0.00           H  
HETATM   16  H7  UNL     1       0.796  -2.162   0.801  1.00  0.00           H  
HETATM   17  H8  UNL     1       2.199   1.163  -1.353  1.00  0.00           H  
CONECT    1    2   10   11   12
CONECT    2    3    8   13
CONECT    3    4   14   15
CONECT    4    5   16
CONECT    5    6    6    7
CONECT    7    8   17
CONECT    8    9    9
END
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SMILES for #<Metabolite:0x0000564abfbe9960>

C[C@H]1CNC(=O)NC1=O
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INCHI for #<Metabolite:0x0000564abfbe9960>

InChI=1S/C5H8N2O2/c1-3-2-6-5(9)7-4(3)8/h3H,2H2,1H3,(H2,6,7,8,9)/t3-/m0/s1
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Synonyms
ValueSource
(-)-(S)-5,6-DihydrothymineHMDB
(5S)-5-Methyl-1,3-diazinane-2,4-dioneHMDB
5,6-Dihydro-5-methyluracilHMDB
5,6-DihydrothymineHMDB
5-Methyl-5,6-dihydrouracilHMDB
5-Methyldihydropyrimidine-2,4(1H,3H)-dioneHMDB
Dihydro-5-methyl-2,4(1H,3H)-pyrimidinedioneHMDB
DihydrothymineHMDB
Chemical FormulaC5H8N2O2
Average Molecular Weight128.131
Monoisotopic Molecular Weight128.058577506
IUPAC Name(5S)-5-methyl-1,3-diazinane-2,4-dione
Traditional Name(5S)-5-methyl-1,3-diazinane-2,4-dione
CAS Registry NumberNot Available
SMILES
C[C@H]1CNC(=O)NC1=O
InChI Identifier
InChI=1S/C5H8N2O2/c1-3-2-6-5(9)7-4(3)8/h3H,2H2,1H3,(H2,6,7,8,9)/t3-/m0/s1
InChI KeyNBAKTGXDIBVZOO-VKHMYHEASA-N