Showing metabocard for Uracil (MMDBc0000095)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2020-10-27 23:30:11 UTC
Update Date2024-04-30 19:31:03 UTC
Metabolite IDMMDBc0000095
Metabolite Identification
Common NameUracil
DescriptionUracil is a common naturally occurring pyrimidine found in RNA, it base pairs with adenine and is replaced by thymine in DNA. Methylation of uracil produces thymine. Uracil's use in the body is to help carry out the synthesis of many enzymes necessary for cell function through bonding with riboses and phosphates. Uracil serves as allosteric regulator and coenzyme for many important biochemical reactions. UDP and UTP regulate CPSase II activity in animals. UDP-glucose regulates the conversion of glucose to galactose in the liver and other tissues in the process of carbohydrate metabolism. Uracil is also involved in the biosynthesis of polysaccharides and the transportation of sugars containing aldehydes. Uracil is found to be associated with argininemia and carbamoyl phosphate synthetase deficiency, which are inborn errors of metabolism.
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007fe2d632b430>


  Mrv1652309042000002D          

  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 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
    0.0000    0.8250    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
    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  2  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:0x00007fe2d632b430>

HMDB0000300
     RDKit          3D
Uracil
 12 12  0  0  0  0  0  0  0  0999 V2000
   -1.5990   -2.0771   -0.0459 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8499   -1.0658   -0.0238 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3309    0.2317   -0.0060 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4747    1.3122    0.0181 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8377    1.0693    0.0237 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2929   -0.1936    0.0063 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5543   -0.3325    0.0133 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4805   -1.2726   -0.0174 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3982    0.3472   -0.0119 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8688    2.3226    0.0318 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4792    1.8921    0.0420 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8769   -2.2335   -0.0302 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  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
  4 10  1  0
  5 11  1  0
  8 12  1  0
M  END
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3D SDF for #<Metabolite:0x00007fe2d632b430>


  Mrv1652309042000002D          

  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 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
    0.0000    0.8250    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
    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  2  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>
MMDBc0000095

> <DATABASE_NAME>
MIME

> <SMILES>
O=C1NC=CC(=O)N1

> <INCHI_IDENTIFIER>
InChI=1S/C4H4N2O2/c7-3-1-2-5-4(8)6-3/h1-2H,(H2,5,6,7,8)

> <INCHI_KEY>
ISAKRJDGNUQOIC-UHFFFAOYSA-N

> <FORMULA>
C4H4N2O2

> <MOLECULAR_WEIGHT>
112.0868

> <EXACT_MASS>
112.027277382

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
12

> <JCHEM_AVERAGE_POLARIZABILITY>
9.36551055096874

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-1.20

> <JCHEM_LOGP>
-0.8552909999999998

> <ALOGPS_LOGS>
-0.63

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.756677870062841

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.803392786213806

> <JCHEM_PKA_STRONGEST_BASIC>
-5.5116186106121114

> <JCHEM_POLAR_SURFACE_AREA>
58.2

> <JCHEM_REFRACTIVITY>
25.9693

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.65e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
uracil

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for #<Metabolite:0x00007fe2d632b430>

HMDB0000300
     RDKit          3D
Uracil
 12 12  0  0  0  0  0  0  0  0999 V2000
   -1.5990   -2.0771   -0.0459 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8499   -1.0658   -0.0238 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3309    0.2317   -0.0060 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4747    1.3122    0.0181 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8377    1.0693    0.0237 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2929   -0.1936    0.0063 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5543   -0.3325    0.0133 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4805   -1.2726   -0.0174 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3982    0.3472   -0.0119 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8688    2.3226    0.0318 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4792    1.8921    0.0420 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8769   -2.2335   -0.0302 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  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
  4 10  1  0
  5 11  1  0
  8 12  1  0
M  END
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PDB for #<Metabolite:0x00007fe2d632b430>

HEADER    PROTEIN                                 04-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-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  N   UNK     0       1.334  -0.770   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+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:0x00007fe2d632b430>

COMPND    HMDB0000300
HETATM    1  O1  UNL     1      -1.599  -2.077  -0.046  1.00  0.00           O  
HETATM    2  C1  UNL     1      -0.850  -1.066  -0.024  1.00  0.00           C  
HETATM    3  C2  UNL     1      -1.331   0.232  -0.006  1.00  0.00           C  
HETATM    4  C3  UNL     1      -0.475   1.312   0.018  1.00  0.00           C  
HETATM    5  N1  UNL     1       0.838   1.069   0.024  1.00  0.00           N  
HETATM    6  C4  UNL     1       1.293  -0.194   0.006  1.00  0.00           C  
HETATM    7  O2  UNL     1       2.554  -0.333   0.013  1.00  0.00           O  
HETATM    8  N2  UNL     1       0.480  -1.273  -0.017  1.00  0.00           N  
HETATM    9  H1  UNL     1      -2.398   0.347  -0.012  1.00  0.00           H  
HETATM   10  H2  UNL     1      -0.869   2.323   0.032  1.00  0.00           H  
HETATM   11  H3  UNL     1       1.479   1.892   0.042  1.00  0.00           H  
HETATM   12  H4  UNL     1       0.877  -2.233  -0.030  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    8
CONECT    3    4    4    9
CONECT    4    5   10
CONECT    5    6   11
CONECT    6    7    7    8
CONECT    8   12
END
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SMILES for #<Metabolite:0x00007fe2d632b430>

O=C1NC=CC(=O)N1
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INCHI for #<Metabolite:0x00007fe2d632b430>

InChI=1S/C4H4N2O2/c7-3-1-2-5-4(8)6-3/h1-2H,(H2,5,6,7,8)
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Synonyms
ValueSource
2,4(1H,3H)-PyrimidinedioneChEBI
2,4-DioxopyrimidineChEBI
2,4-PyrimidinedioneChEBI
UChEBI
UraChEBI
UrazilChEBI
2,4-DihydroxypyrimidineHMDB
2,4-PyrimidinediolHMDB
Hybar XHMDB
PirodHMDB
PyrodHMDB
Molecular FormulaC4H4N2O2
Average Mass112.0868
Monoisotopic Mass112.027277382
IUPAC Name1,2,3,4-tetrahydropyrimidine-2,4-dione
Traditional Nameuracil
CAS Registry Number66-22-8
SMILES
O=C1NC=CC(=O)N1
InChI Identifier
InChI=1S/C4H4N2O2/c7-3-1-2-5-4(8)6-3/h1-2H,(H2,5,6,7,8)
InChI KeyISAKRJDGNUQOIC-UHFFFAOYSA-N