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Showing metabocard for 2-Oxo-4-hydroxy-4-carboxy-5-ureidoimidazole (HMDB0301917)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2021-09-23 03:38:17 UTC
Update Date2021-09-23 03:38:18 UTC
HMDB IDHMDB0301917
Secondary Accession NumbersNone
Metabolite Identification
Common Name2-Oxo-4-hydroxy-4-carboxy-5-ureidoimidazole
Description5-hydroxy-2-oxo-4-ureido-2,5-dihydro-1H-imidazole-5-carboxylate, also known as 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline, belongs to the class of organic compounds known as alpha amino acids and derivatives. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon), or a derivative thereof. 5-hydroxy-2-oxo-4-ureido-2,5-dihydro-1H-imidazole-5-carboxylate is an extremely weak basic (essentially neutral) compound (based on its pKa). 5-hydroxy-2-oxo-4-ureido-2,5-dihydro-1H-imidazole-5-carboxylate exists in all living organisms, ranging from bacteria to humans. Outside of the human body, 5-hydroxy-2-oxo-4-ureido-2,5-dihydro-1H-imidazole-5-carboxylate has been detected, but not quantified in, soy beans. This could make 5-hydroxy-2-oxo-4-ureido-2,5-dihydro-1H-imidazole-5-carboxylate a potential biomarker for the consumption of these foods. 5-hydroxy-2-oxo-4-ureido-2,5-dihydro-1h-imidazole-5-carboxylate is part of the Purine metabolism pathway.
Structure
Thumb
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0301917 (2-Oxo-4-hydroxy-4-carboxy-5-ureidoimidazole)

  Mrv1652309042000402D          

 14 14  0  0  0  0            999 V2000
    0.4520    2.3766    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3182    2.0809    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2750    1.2571    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5219    1.0435    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.9712    1.7354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0532    2.4555    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7452    2.0061    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7020    1.1823    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9669    0.8077    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3939    0.7329    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7951    1.7786    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2750    2.9048    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4601    3.2793    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9669    3.3541    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  5  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  9  3  1  0  0  0  0
  3  2  1  0  0  0  0
  6  2  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  8 10  2  0  0  0  0
  5 11  2  0  0  0  0
  2 12  1  0  0  0  0
 12 13  1  0  0  0  0
 12 14  2  0  0  0  0
M  END
Download

3D MOL for HMDB0301917 (2-Oxo-4-hydroxy-4-carboxy-5-ureidoimidazole)

HMDB0301917
     RDKit          3D
2-Oxo-4-hydroxy-4-carboxy-5-ureidoimidazole
 20 20  0  0  0  0  0  0  0  0999 V2000
    3.4960   -0.7829   -0.3309 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0708   -0.6084   -0.2544 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3415   -1.5307    0.1876 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4670    0.5922   -0.6707 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0577    0.8117   -0.6068 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4411    1.9502   -1.0313 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8315    2.0032   -0.9072 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5980    2.9867   -1.2345 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2257    0.7714   -0.3551 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0345    0.0086   -0.0904 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1175   -1.1840   -0.8406 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9574   -0.3033    1.3714 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7033    0.5570    2.2257 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1854   -1.6044    1.7614 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0663   -0.0435   -0.7499 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9066   -1.6419    0.0353 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1200    1.3370   -1.0395 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2280    0.5096   -0.1884 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0837   -1.4161   -0.8679 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1201   -2.4124    1.1742 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  2  4  1  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  2  0
  7  9  1  0
  9 10  1  0
 10 11  1  0
 10 12  1  0
 12 13  2  0
 12 14  1  0
 10  5  1  0
  1 15  1  0
  1 16  1  0
  4 17  1  0
  9 18  1  0
 11 19  1  0
 14 20  1  0
M  END
Download

3D SDF for HMDB0301917 (2-Oxo-4-hydroxy-4-carboxy-5-ureidoimidazole)

  Mrv1652309042000402D          

 14 14  0  0  0  0            999 V2000
    0.4520    2.3766    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3182    2.0809    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2750    1.2571    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5219    1.0435    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.9712    1.7354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0532    2.4555    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7452    2.0061    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7020    1.1823    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9669    0.8077    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3939    0.7329    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7951    1.7786    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2750    2.9048    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4601    3.2793    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9669    3.3541    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  5  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  9  3  1  0  0  0  0
  3  2  1  0  0  0  0
  6  2  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  8 10  2  0  0  0  0
  5 11  2  0  0  0  0
  2 12  1  0  0  0  0
 12 13  1  0  0  0  0
 12 14  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0301917

> <DATABASE_NAME>
hmdb

> <SMILES>
NC(=O)NC1=NC(=O)NC1(O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C5H6N4O5/c6-3(12)7-1-5(14,2(10)11)9-4(13)8-1/h14H,(H,10,11)(H4,6,7,8,9,12,13)

> <INCHI_KEY>
WHKYNCPIXMNTRQ-UHFFFAOYSA-N

> <FORMULA>
C5H6N4O5

> <MOLECULAR_WEIGHT>
202.1249

> <EXACT_MASS>
202.033819322

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
20

> <JCHEM_AVERAGE_POLARIZABILITY>
16.004617959627303

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
4-(carbamoylamino)-5-hydroxy-2-oxo-2,5-dihydro-1H-imidazole-5-carboxylic acid

> <ALOGPS_LOGP>
-1.86

> <JCHEM_LOGP>
-2.2777762976666662

> <ALOGPS_LOGS>
-1.62

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
9.332369787461557

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.5311433200394338

> <JCHEM_PKA_STRONGEST_BASIC>
-1.1180337776917915

> <JCHEM_POLAR_SURFACE_AREA>
154.10999999999999

> <JCHEM_REFRACTIVITY>
38.66830000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.85e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5-(carbamoylamino)-4-hydroxy-2-oxo-3H-imidazole-4-carboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0301917 (2-Oxo-4-hydroxy-4-carboxy-5-ureidoimidazole)

HMDB0301917
     RDKit          3D
2-Oxo-4-hydroxy-4-carboxy-5-ureidoimidazole
 20 20  0  0  0  0  0  0  0  0999 V2000
    3.4960   -0.7829   -0.3309 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0708   -0.6084   -0.2544 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3415   -1.5307    0.1876 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4670    0.5922   -0.6707 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0577    0.8117   -0.6068 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4411    1.9502   -1.0313 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8315    2.0032   -0.9072 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5980    2.9867   -1.2345 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2257    0.7714   -0.3551 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0345    0.0086   -0.0904 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1175   -1.1840   -0.8406 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9574   -0.3033    1.3714 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7033    0.5570    2.2257 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1854   -1.6044    1.7614 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0663   -0.0435   -0.7499 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9066   -1.6419    0.0353 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1200    1.3370   -1.0395 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2280    0.5096   -0.1884 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0837   -1.4161   -0.8679 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1201   -2.4124    1.1742 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  2  4  1  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  2  0
  7  9  1  0
  9 10  1  0
 10 11  1  0
 10 12  1  0
 12 13  2  0
 12 14  1  0
 10  5  1  0
  1 15  1  0
  1 16  1  0
  4 17  1  0
  9 18  1  0
 11 19  1  0
 14 20  1  0
M  END
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PDB for HMDB0301917 (2-Oxo-4-hydroxy-4-carboxy-5-ureidoimidazole)

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  N   UNK     0       0.844   4.436   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0      -0.594   3.884   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.513   2.347   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0       0.974   1.948   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0       1.813   3.239   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      -1.966   4.584   0.000  0.00  0.00           O+0
HETATM    7  N   UNK     0      -3.258   3.745   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0      -3.177   2.207   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0      -1.805   1.508   0.000  0.00  0.00           N+0
HETATM   10  O   UNK     0      -4.469   1.368   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       3.351   3.320   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0      -0.513   5.422   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       0.859   6.121   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0      -1.805   6.261   0.000  0.00  0.00           O+0
CONECT    1    2    5                                                       
CONECT    2    1    3    6   12                                             
CONECT    3    4    9    2                                                  
CONECT    4    3    5                                                       
CONECT    5    1    4   11                                                  
CONECT    6    2                                                            
CONECT    7    8                                                            
CONECT    8    7    9   10                                                  
CONECT    9    3    8                                                       
CONECT   10    8                                                            
CONECT   11    5                                                            
CONECT   12    2   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12                                                            
MASTER        0    0    0    0    0    0    0    0   14    0   28    0
END
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3D PDB for HMDB0301917 (2-Oxo-4-hydroxy-4-carboxy-5-ureidoimidazole)

COMPND    HMDB0301917
HETATM    1  N1  UNL     1       3.496  -0.783  -0.331  1.00  0.00           N  
HETATM    2  C1  UNL     1       2.071  -0.608  -0.254  1.00  0.00           C  
HETATM    3  O1  UNL     1       1.342  -1.531   0.188  1.00  0.00           O  
HETATM    4  N2  UNL     1       1.467   0.592  -0.671  1.00  0.00           N  
HETATM    5  C2  UNL     1       0.058   0.812  -0.607  1.00  0.00           C  
HETATM    6  N3  UNL     1      -0.441   1.950  -1.031  1.00  0.00           N  
HETATM    7  C3  UNL     1      -1.832   2.003  -0.907  1.00  0.00           C  
HETATM    8  O2  UNL     1      -2.598   2.987  -1.235  1.00  0.00           O  
HETATM    9  N4  UNL     1      -2.226   0.771  -0.355  1.00  0.00           N  
HETATM   10  C4  UNL     1      -1.035   0.009  -0.090  1.00  0.00           C  
HETATM   11  O3  UNL     1      -1.117  -1.184  -0.841  1.00  0.00           O  
HETATM   12  C5  UNL     1      -0.957  -0.303   1.371  1.00  0.00           C  
HETATM   13  O4  UNL     1      -0.703   0.557   2.226  1.00  0.00           O  
HETATM   14  O5  UNL     1      -1.185  -1.604   1.761  1.00  0.00           O  
HETATM   15  H1  UNL     1       4.066  -0.044  -0.750  1.00  0.00           H  
HETATM   16  H2  UNL     1       3.907  -1.642   0.035  1.00  0.00           H  
HETATM   17  H3  UNL     1       2.120   1.337  -1.040  1.00  0.00           H  
HETATM   18  H4  UNL     1      -3.228   0.510  -0.188  1.00  0.00           H  
HETATM   19  H5  UNL     1      -2.084  -1.416  -0.868  1.00  0.00           H  
HETATM   20  H6  UNL     1      -1.120  -2.412   1.174  1.00  0.00           H  
CONECT    1    2   15   16
CONECT    2    3    3    4
CONECT    4    5   17
CONECT    5    6    6   10
CONECT    6    7
CONECT    7    8    8    9
CONECT    9   10   18
CONECT   10   11   12
CONECT   11   19
CONECT   12   13   13   14
CONECT   14   20
END
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SMILES for HMDB0301917 (2-Oxo-4-hydroxy-4-carboxy-5-ureidoimidazole)

NC(=O)NC1=NC(=O)NC1(O)C(O)=O
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INCHI for HMDB0301917 (2-Oxo-4-hydroxy-4-carboxy-5-ureidoimidazole)

InChI=1S/C5H6N4O5/c6-3(12)7-1-5(14,2(10)11)9-4(13)8-1/h14H,(H,10,11)(H4,6,7,8,9,12,13)
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View in JSmolView Stereo Labels
Synonyms
ValueSource
2-oxo-4-Hydroxy-4-carboxy-5-ureidoimidazolineKegg
5-Hydroxy-2-oxo-4-ureido-2,5-dihydro-1H-imidazole-5-carboxylic acidGenerator
Chemical FormulaC5H6N4O5
Average Molecular Weight202.1249
Monoisotopic Molecular Weight202.033819322
IUPAC Name4-(carbamoylamino)-5-hydroxy-2-oxo-2,5-dihydro-1H-imidazole-5-carboxylic acid
Traditional Name5-(carbamoylamino)-4-hydroxy-2-oxo-3H-imidazole-4-carboxylic acid
CAS Registry NumberNot Available
SMILES
NC(=O)NC1=NC(=O)NC1(O)C(O)=O
InChI Identifier
InChI=1S/C5H6N4O5/c6-3(12)7-1-5(14,2(10)11)9-4(13)8-1/h14H,(H,10,11)(H4,6,7,8,9,12,13)
InChI KeyWHKYNCPIXMNTRQ-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as alpha amino acids and derivatives. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon), or a derivative thereof.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassAmino acids, peptides, and analogues
Direct ParentAlpha amino acids and derivatives
Alternative Parents
Substituents
  • Alpha-amino acid or derivatives
  • Alpha-hydroxy acid
  • Hydroxy acid
  • 3-imidazoline
  • Carbonic acid derivative
  • Urea
  • Alkanolamine
  • Amidine
  • Carboxylic acid amidine
  • Carboxylic acid
  • Monocarboxylic acid or derivatives
  • Azacycle
  • Carboximidamide
  • Propargyl-type 1,3-dipolar organic compound
  • Organic 1,3-dipolar compound
  • Organoheterocyclic compound
  • Hydrocarbon derivative
  • Organonitrogen compound
  • Organooxygen compound
  • Carbonyl group
  • Organic nitrogen compound
  • Organic oxygen compound
  • Organopnictogen compound
  • Organic oxide
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Source
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
Biological Properties
Cellular LocationsNot Available
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB001617
KNApSAcK IDNot Available
Chemspider ID391844
KEGG Compound IDC12248
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound443736
PDB IDNot Available
ChEBI ID31132
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 ReferencesNot Available