Showing metabocard for Dihydrouracil (MMDBc0029468)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2021-11-17 23:23:31 UTC
Update Date2024-10-13 14:52:04 UTC
Metabolite IDMMDBc0029468
Metabolite Identification
Common NameDihydrouracil
DescriptionDihydrohuracil is an intermediate breakdown product of uracil. Dihydropyrimidine dehydrogenase catalyzes the reduction of uracil to 5, 6-dihydrouracil then dihydropyrimidinase hydrolyzes 5, 6-dihydrouracil to N-carbamyl-b-alanine. Finally, beta-ureidopropionase catalyzes the conversion of N-carbamyl-b-alanine to beta-alanine.
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007f46d5370370>


  Mrv1652309032023512D          

  8  8  0  0  0  0            999 V2000
    2.1434   -0.4125    0.0000 O   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 C   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
    0.0000    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
    1.4289    0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  6  8  1  0  0  0  0
  2  8  1  0  0  0  0
M  END
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3D MOL for #<Metabolite:0x00007f46d5370370>

HMDB0000076
     RDKit          3D
Dihydrouracil
 14 14  0  0  0  0  0  0  0  0999 V2000
   -1.2394    2.3319   -0.0281 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5909    1.2647   -0.1291 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2889   -0.0302   -0.3106 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4935   -1.0803    0.4364 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8548   -1.1172   -0.0522 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.6125    0.1027   -0.0266 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8661    0.0927    0.0277 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8266    1.3053   -0.0678 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4132   -0.2882   -1.3820 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3129   -0.0228    0.1410 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9951   -2.0552    0.3595 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4709   -0.7289    1.5099 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3077   -2.0009   -0.4269 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3371    2.2263   -0.0512 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  2  0
  6  8  1  0
  8  2  1  0
  3  9  1  0
  3 10  1  0
  4 11  1  0
  4 12  1  0
  5 13  1  0
  8 14  1  0
M  END
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3D SDF for #<Metabolite:0x00007f46d5370370>


  Mrv1652309032023512D          

  8  8  0  0  0  0            999 V2000
    2.1434   -0.4125    0.0000 O   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 C   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
    0.0000    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
    1.4289    0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  6  8  1  0  0  0  0
  2  8  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0029468

> <DATABASE_NAME>
MIME

> <SMILES>
O=C1CCNC(=O)N1

> <INCHI_IDENTIFIER>
InChI=1S/C4H6N2O2/c7-3-1-2-5-4(8)6-3/h1-2H2,(H2,5,6,7,8)

> <INCHI_KEY>
OIVLITBTBDPEFK-UHFFFAOYSA-N

> <FORMULA>
C4H6N2O2

> <MOLECULAR_WEIGHT>
114.1026

> <EXACT_MASS>
114.042927446

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
14

> <JCHEM_AVERAGE_POLARIZABILITY>
10.133629968746801

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1,3-diazinane-2,4-dione

> <ALOGPS_LOGP>
-1.28

> <JCHEM_LOGP>
-1.2132077313333332

> <ALOGPS_LOGS>
-0.64

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
18.605544735996883

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.726846896036472

> <JCHEM_PKA_STRONGEST_BASIC>
-7.628772459765097

> <JCHEM_POLAR_SURFACE_AREA>
58.2

> <JCHEM_REFRACTIVITY>
25.745500000000003

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.59e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
dihydrouracil

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for #<Metabolite:0x00007f46d5370370>

HMDB0000076
     RDKit          3D
Dihydrouracil
 14 14  0  0  0  0  0  0  0  0999 V2000
   -1.2394    2.3319   -0.0281 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5909    1.2647   -0.1291 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2889   -0.0302   -0.3106 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4935   -1.0803    0.4364 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8548   -1.1172   -0.0522 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.6125    0.1027   -0.0266 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8661    0.0927    0.0277 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8266    1.3053   -0.0678 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4132   -0.2882   -1.3820 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3129   -0.0228    0.1410 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9951   -2.0552    0.3595 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4709   -0.7289    1.5099 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3077   -2.0009   -0.4269 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3371    2.2263   -0.0512 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  2  0
  6  8  1  0
  8  2  1  0
  3  9  1  0
  3 10  1  0
  4 11  1  0
  4 12  1  0
  5 13  1  0
  8 14  1  0
M  END
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PDB for #<Metabolite:0x00007f46d5370370>

HEADER    PROTEIN                                 03-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   03-SEP-20         0                                  
HETATM    1  O   UNK     0       4.001  -0.770   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0       0.000   1.540   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       1.334   3.850   0.000  0.00  0.00           O+0
HETATM    8  N   UNK     0       2.667   1.540   0.000  0.00  0.00           N+0
CONECT    1    2                                                            
CONECT    2    1    3    8                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    2                                                       
MASTER        0    0    0    0    0    0    0    0    8    0   16    0
END
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3D PDB for #<Metabolite:0x00007f46d5370370>

COMPND    HMDB0000076
HETATM    1  O1  UNL     1      -1.239   2.332  -0.028  1.00  0.00           O  
HETATM    2  C1  UNL     1      -0.591   1.265  -0.129  1.00  0.00           C  
HETATM    3  C2  UNL     1      -1.289  -0.030  -0.311  1.00  0.00           C  
HETATM    4  C3  UNL     1      -0.493  -1.080   0.436  1.00  0.00           C  
HETATM    5  N1  UNL     1       0.855  -1.117  -0.052  1.00  0.00           N  
HETATM    6  C4  UNL     1       1.612   0.103  -0.027  1.00  0.00           C  
HETATM    7  O2  UNL     1       2.866   0.093   0.028  1.00  0.00           O  
HETATM    8  N2  UNL     1       0.827   1.305  -0.068  1.00  0.00           N  
HETATM    9  H1  UNL     1      -1.413  -0.288  -1.382  1.00  0.00           H  
HETATM   10  H2  UNL     1      -2.313  -0.023   0.141  1.00  0.00           H  
HETATM   11  H3  UNL     1      -0.995  -2.055   0.360  1.00  0.00           H  
HETATM   12  H4  UNL     1      -0.471  -0.729   1.510  1.00  0.00           H  
HETATM   13  H5  UNL     1       1.308  -2.001  -0.427  1.00  0.00           H  
HETATM   14  H6  UNL     1       1.337   2.226  -0.051  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    8
CONECT    3    4    9   10
CONECT    4    5   11   12
CONECT    5    6   13
CONECT    6    7    7    8
CONECT    8   14
END
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SMILES for #<Metabolite:0x00007f46d5370370>

O=C1CCNC(=O)N1
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INCHI for #<Metabolite:0x00007f46d5370370>

InChI=1S/C4H6N2O2/c7-3-1-2-5-4(8)6-3/h1-2H2,(H2,5,6,7,8)
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Synonyms
ValueSource
2,4-DioxotetrahydropyrimidineChEBI
5,6-Dihydro-2,4-dihydroxypyrimidineChEBI
Dihydro-2,4(1H,3H)-pyrimidinedioneChEBI
DIHYDROPYRIMIDINE-2,4(1H,3H)-dioneChEBI
DihydrouracileChEBI
HydrouracilChEBI
5,6-Dihydro-2,4(1H,3H)-pyrimidinedioneHMDB
5,6-DihydrouracilHMDB
Dihydro-pyrimidine-2,4-dioneHMDB
Molecular FormulaC4H6N2O2
Average Mass114.1026
Monoisotopic Mass114.042927446
IUPAC Name1,3-diazinane-2,4-dione
Traditional Namedihydrouracil
CAS Registry Number504-07-4
SMILES
O=C1CCNC(=O)N1
InChI Identifier
InChI=1S/C4H6N2O2/c7-3-1-2-5-4(8)6-3/h1-2H2,(H2,5,6,7,8)
InChI KeyOIVLITBTBDPEFK-UHFFFAOYSA-N