Showing metabocard for Thymine (MMDBc0000089)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2020-10-27 23:29:58 UTC
Update Date2024-10-10 00:56:01 UTC
Metabolite IDMMDBc0000089
Metabolite Identification
Common NameThymine
DescriptionOne of the pyrimidine bases of living matter. Derivation: Hydrolysis of deoxyribonucleic acid, from methylcyanoacetylurea by catalytic reduction. Use: Biochemical research. (Hawley's Condensed Chemical Dictionary). Thymine is a pyrimidine nucleobase. As the name implies, thymine may be derived by methylation of uracil at the 5th carbon. Thymine is found in the nucleic acid DNA. In RNA thymine is replaced with uracil in most cases. In DNA, thymine binds to adenine via two hydrogen bonds to assist in stabilizing the nucleic acid structures.
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007f923974eb68>


  Mrv1652309191922122D          

  9  9  0  0  0  0            999 V2000
    2.1434    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
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 N   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
    0.7145    2.0625    0.0000 O   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
  3  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  0  0  0  0
  2  8  1  0  0  0  0
  8  9  2  0  0  0  0
M  END
Download

3D MOL for #<Metabolite:0x00007f923974eb68>

HMDB0000262
     RDKit          3D
Thymine
 15 15  0  0  0  0  0  0  0  0999 V2000
    2.1857   -0.1429    0.1090 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6847   -0.0612    0.0291 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0879   -1.1958    0.0414 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4245   -1.0978   -0.0309 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0276    0.1023   -0.1159 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2770    0.1910   -0.1834 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2737    1.2157   -0.1282 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0673    1.1679   -0.0580 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7712    2.2093   -0.0695 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6199   -0.3949   -0.8600 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5008   -0.8698    0.8921 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5414    0.8597    0.4760 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4203   -2.1670    0.1112 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9813   -1.9832   -0.0190 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7193    2.1669   -0.1940 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  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
  3 13  1  0
  4 14  1  0
  7 15  1  0
M  END
Download

3D SDF for #<Metabolite:0x00007f923974eb68>


  Mrv1652309191922122D          

  9  9  0  0  0  0            999 V2000
    2.1434    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
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 N   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
    0.7145    2.0625    0.0000 O   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
  3  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  0  0  0  0
  2  8  1  0  0  0  0
  8  9  2  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0000089

> <DATABASE_NAME>
MIME

> <SMILES>
CC1=CNC(=O)NC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C5H6N2O2/c1-3-2-6-5(9)7-4(3)8/h2H,1H3,(H2,6,7,8,9)

> <INCHI_KEY>
RWQNBRDOKXIBIV-UHFFFAOYSA-N

> <FORMULA>
C5H6N2O2

> <MOLECULAR_WEIGHT>
126.1133

> <EXACT_MASS>
126.042927446

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
15

> <JCHEM_AVERAGE_POLARIZABILITY>
11.422204494643946

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
5-methyl-1,2,3,4-tetrahydropyrimidine-2,4-dione

> <ALOGPS_LOGP>
-0.99

> <JCHEM_LOGP>
-0.45974051066666644

> <ALOGPS_LOGS>
-1.07

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.002512971014774

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.057944384019686

> <JCHEM_PKA_STRONGEST_BASIC>
-4.998777587344984

> <JCHEM_POLAR_SURFACE_AREA>
58.2

> <JCHEM_REFRACTIVITY>
30.326400000000003

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.08e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
thymine

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for #<Metabolite:0x00007f923974eb68>

HMDB0000262
     RDKit          3D
Thymine
 15 15  0  0  0  0  0  0  0  0999 V2000
    2.1857   -0.1429    0.1090 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6847   -0.0612    0.0291 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0879   -1.1958    0.0414 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4245   -1.0978   -0.0309 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0276    0.1023   -0.1159 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2770    0.1910   -0.1834 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2737    1.2157   -0.1282 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0673    1.1679   -0.0580 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7712    2.2093   -0.0695 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6199   -0.3949   -0.8600 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5008   -0.8698    0.8921 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5414    0.8597    0.4760 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4203   -2.1670    0.1112 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9813   -1.9832   -0.0190 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7193    2.1669   -0.1940 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  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
  3 13  1  0
  4 14  1  0
  7 15  1  0
M  END
Download

PDB for #<Metabolite:0x00007f923974eb68>

HEADER    PROTEIN                                 19-SEP-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   19-SEP-19         0                                  
HETATM    1  C   UNK     0       4.001   2.310   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0       1.334  -0.770   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      -1.334  -0.770   0.000  0.00  0.00           O+0
HETATM    7  N   UNK     0       0.000   1.540   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       1.334   3.850   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    8                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8                                                       
CONECT    8    7    2    9                                                  
CONECT    9    8                                                            
MASTER        0    0    0    0    0    0    0    0    9    0   18    0
END
Download

3D PDB for #<Metabolite:0x00007f923974eb68>

COMPND    HMDB0000262
HETATM    1  C1  UNL     1       2.186  -0.143   0.109  1.00  0.00           C  
HETATM    2  C2  UNL     1       0.685  -0.061   0.029  1.00  0.00           C  
HETATM    3  C3  UNL     1      -0.088  -1.196   0.041  1.00  0.00           C  
HETATM    4  N1  UNL     1      -1.424  -1.098  -0.031  1.00  0.00           N  
HETATM    5  C4  UNL     1      -2.028   0.102  -0.116  1.00  0.00           C  
HETATM    6  O1  UNL     1      -3.277   0.191  -0.183  1.00  0.00           O  
HETATM    7  N2  UNL     1      -1.274   1.216  -0.128  1.00  0.00           N  
HETATM    8  C5  UNL     1       0.067   1.168  -0.058  1.00  0.00           C  
HETATM    9  O2  UNL     1       0.771   2.209  -0.069  1.00  0.00           O  
HETATM   10  H1  UNL     1       2.620  -0.395  -0.860  1.00  0.00           H  
HETATM   11  H2  UNL     1       2.501  -0.870   0.892  1.00  0.00           H  
HETATM   12  H3  UNL     1       2.541   0.860   0.476  1.00  0.00           H  
HETATM   13  H4  UNL     1       0.420  -2.167   0.111  1.00  0.00           H  
HETATM   14  H5  UNL     1      -1.981  -1.983  -0.019  1.00  0.00           H  
HETATM   15  H6  UNL     1      -1.719   2.167  -0.194  1.00  0.00           H  
CONECT    1    2   10   11   12
CONECT    2    3    3    8
CONECT    3    4   13
CONECT    4    5   14
CONECT    5    6    6    7
CONECT    7    8   15
CONECT    8    9    9
END
Download

SMILES for #<Metabolite:0x00007f923974eb68>

CC1=CNC(=O)NC1=O
Download

INCHI for #<Metabolite:0x00007f923974eb68>

InChI=1S/C5H6N2O2/c1-3-2-6-5(9)7-4(3)8/h2H,1H3,(H2,6,7,8,9)
Download
Synonyms
ValueSource
2,4-Dihydroxy-5-methylpyrimidineChEBI
5-Methyl-2,4(1H,3H)-pyrimidinedioneChEBI
5-Methylpyrimidine-2,4(1H,3H)-dioneChEBI
5-MethyluracilChEBI
TChEBI
ThyChEBI
ThyminChEBI
4-Hydroxy-5-methylpyrimidin-2(1H)-oneHMDB
5-Methyl-1,2,3,4-tetrahydropyrimidine-2,4-dioneHMDB
5-Methyl-2,4-dihydroxypyrimidineHMDB
5-Methylpyrimidine-2,4-dioneHMDB
5 MethyluracilHMDB
Molecular FormulaC5H6N2O2
Average Mass126.1133
Monoisotopic Mass126.042927446
IUPAC Name5-methyl-1,2,3,4-tetrahydropyrimidine-2,4-dione
Traditional Namethymine
CAS Registry Number65-71-4
SMILES
CC1=CNC(=O)NC1=O
InChI Identifier
InChI=1S/C5H6N2O2/c1-3-2-6-5(9)7-4(3)8/h2H,1H3,(H2,6,7,8,9)
InChI KeyRWQNBRDOKXIBIV-UHFFFAOYSA-N