Showing metabocard for (-)-Ureidoglycolate (MMDBc0049930)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2022-04-29 22:46:31 UTC
Update Date2022-12-15 22:52:19 UTC
Metabolite IDMMDBc0049930
Metabolite Identification
Common Name(-)-Ureidoglycolate
Description(S)-Ureidoglycolic acid, also known as (S)-ureidoglycolate, belongs to the class of organic compounds known as n-carbamoyl-alpha amino acids. N-carbamoyl-alpha amino acids are compounds containing an alpha amino acid which bears an carbamoyl group at its terminal nitrogen atom (S)-Ureidoglycolic acid exists in all living species, ranging from bacteria to plants to humans (S)-Ureidoglycolic acid has been detected, but not quantified in, several different foods, such as daikon radishes (Raphanus sativus var. longipinnatus), juniperus communis (Juniperus communis), common cabbages (Brassica oleracea), canada blueberries (Vaccinium myrtilloides), and wax apples (Eugenia javanica). This could make (S)-ureidoglycolic acid a potential biomarker for the consumption of these foods (S)-Ureidoglycolic acid is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. Based on a literature review very few articles have been published on (S)-Ureidoglycolic acid.
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007f12409a1308>


  Mrv1652307172022052D          

  9  8  0  0  1  0            999 V2000
   -0.3572   -0.2062    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.3572    0.2062    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0717    0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3572   -1.0313    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0716   -0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7862   -0.2062    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0717    1.0313    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7862    0.2062    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.0716   -1.0313    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  1  0  0  0
  2  5  1  0  0  0  0
  3  6  1  0  0  0  0
  3  7  2  0  0  0  0
  5  8  1  0  0  0  0
  5  9  2  0  0  0  0
M  END
Download

3D MOL for #<Metabolite:0x00007f12409a1308>

HMDB0001005
     RDKit          3D
(S)-Ureidoglycolic acid
 15 14  0  0  0  0  0  0  0  0999 V2000
   -2.6737   -0.3824   -0.5997 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4297    0.2672   -0.5780 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1923    1.1695   -1.4138 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4378   -0.0791    0.3720 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.8606    0.6060    0.3871 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.9933    1.1815    1.6405 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9126   -0.3985    0.1859 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7449   -0.6151    1.0793 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9776   -1.1001   -0.9914 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8924   -1.0605   -1.3422 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3706   -0.1796    0.1303 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6044   -0.8242    1.0794 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9043    1.3731   -0.4155 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2319    2.1373    1.5265 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9757   -2.0953   -1.0604 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  1  0
  5  7  1  0
  7  8  2  0
  7  9  1  0
  1 10  1  0
  1 11  1  0
  4 12  1  0
  5 13  1  6
  6 14  1  0
  9 15  1  0
M  END
Download

3D SDF for #<Metabolite:0x00007f12409a1308>


  Mrv1652307172022052D          

  9  8  0  0  1  0            999 V2000
   -0.3572   -0.2062    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.3572    0.2062    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0717    0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3572   -1.0313    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0716   -0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7862   -0.2062    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0717    1.0313    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7862    0.2062    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.0716   -1.0313    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  1  0  0  0
  2  5  1  0  0  0  0
  3  6  1  0  0  0  0
  3  7  2  0  0  0  0
  5  8  1  0  0  0  0
  5  9  2  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0049930

> <DATABASE_NAME>
MIME

> <SMILES>
NC(=O)N[C@@H](O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C3H6N2O4/c4-3(9)5-1(6)2(7)8/h1,6H,(H,7,8)(H3,4,5,9)/t1-/m0/s1

> <INCHI_KEY>
NWZYYCVIOKVTII-SFOWXEAESA-N

> <FORMULA>
C3H6N2O4

> <MOLECULAR_WEIGHT>
134.0907

> <EXACT_MASS>
134.03275669

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
15

> <JCHEM_AVERAGE_POLARIZABILITY>
10.801086227324335

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-2-(carbamoylamino)-2-hydroxyacetic acid

> <ALOGPS_LOGP>
-2.06

> <JCHEM_LOGP>
-1.9509141746666665

> <ALOGPS_LOGS>
-0.30

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
12.093003710609045

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.9435169172851916

> <JCHEM_PKA_STRONGEST_BASIC>
-3.8235949501629993

> <JCHEM_POLAR_SURFACE_AREA>
112.65

> <JCHEM_REFRACTIVITY>
25.3223

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.79e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
ureidoglycolate

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for #<Metabolite:0x00007f12409a1308>

HMDB0001005
     RDKit          3D
(S)-Ureidoglycolic acid
 15 14  0  0  0  0  0  0  0  0999 V2000
   -2.6737   -0.3824   -0.5997 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4297    0.2672   -0.5780 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1923    1.1695   -1.4138 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4378   -0.0791    0.3720 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.8606    0.6060    0.3871 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.9933    1.1815    1.6405 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9126   -0.3985    0.1859 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7449   -0.6151    1.0793 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9776   -1.1001   -0.9914 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8924   -1.0605   -1.3422 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3706   -0.1796    0.1303 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6044   -0.8242    1.0794 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9043    1.3731   -0.4155 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2319    2.1373    1.5265 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9757   -2.0953   -1.0604 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  1  0
  5  7  1  0
  7  8  2  0
  7  9  1  0
  1 10  1  0
  1 11  1  0
  4 12  1  0
  5 13  1  6
  6 14  1  0
  9 15  1  0
M  END
Download

PDB for #<Metabolite:0x00007f12409a1308>

HEADER    PROTEIN                                 17-JUL-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-JUL-20         0                                  
HETATM    1  C   UNK     0      -0.667  -0.385   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0       0.667   0.385   0.000  0.00  0.00           N+0
HETATM    3  C   UNK     0      -2.001   0.385   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      -0.667  -1.925   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       2.000  -0.385   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      -3.334  -0.385   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0      -2.001   1.925   0.000  0.00  0.00           O+0
HETATM    8  N   UNK     0       3.334   0.385   0.000  0.00  0.00           N+0
HETATM    9  O   UNK     0       2.000  -1.925   0.000  0.00  0.00           O+0
CONECT    1    2    3    4                                                  
CONECT    2    1    5                                                       
CONECT    3    1    6    7                                                  
CONECT    4    1                                                            
CONECT    5    2    8    9                                                  
CONECT    6    3                                                            
CONECT    7    3                                                            
CONECT    8    5                                                            
CONECT    9    5                                                            
MASTER        0    0    0    0    0    0    0    0    9    0   16    0
END
Download

3D PDB for #<Metabolite:0x00007f12409a1308>

COMPND    HMDB0001005
HETATM    1  N1  UNL     1      -2.674  -0.382  -0.600  1.00  0.00           N  
HETATM    2  C1  UNL     1      -1.430   0.267  -0.578  1.00  0.00           C  
HETATM    3  O1  UNL     1      -1.192   1.170  -1.414  1.00  0.00           O  
HETATM    4  N2  UNL     1      -0.438  -0.079   0.372  1.00  0.00           N  
HETATM    5  C2  UNL     1       0.861   0.606   0.387  1.00  0.00           C  
HETATM    6  O2  UNL     1       0.993   1.182   1.641  1.00  0.00           O  
HETATM    7  C3  UNL     1       1.913  -0.398   0.186  1.00  0.00           C  
HETATM    8  O3  UNL     1       2.745  -0.615   1.079  1.00  0.00           O  
HETATM    9  O4  UNL     1       1.978  -1.100  -0.991  1.00  0.00           O  
HETATM   10  H1  UNL     1      -2.892  -1.060  -1.342  1.00  0.00           H  
HETATM   11  H2  UNL     1      -3.371  -0.180   0.130  1.00  0.00           H  
HETATM   12  H3  UNL     1      -0.604  -0.824   1.079  1.00  0.00           H  
HETATM   13  H4  UNL     1       0.904   1.373  -0.416  1.00  0.00           H  
HETATM   14  H5  UNL     1       1.232   2.137   1.527  1.00  0.00           H  
HETATM   15  H6  UNL     1       1.976  -2.095  -1.060  1.00  0.00           H  
CONECT    1    2   10   11
CONECT    2    3    3    4
CONECT    4    5   12
CONECT    5    6    7   13
CONECT    6   14
CONECT    7    8    8    9
CONECT    9   15
END
Download

SMILES for #<Metabolite:0x00007f12409a1308>

NC(=O)N[C@@H](O)C(O)=O
Download

INCHI for #<Metabolite:0x00007f12409a1308>

InChI=1S/C3H6N2O4/c4-3(9)5-1(6)2(7)8/h1,6H,(H,7,8)(H3,4,5,9)/t1-/m0/s1
Download
Synonyms
ValueSource
(-)-UreidoglycolateChEBI
(S)-UreidoglycolateChEBI
(-)-Ureidoglycolic acidGenerator
(S)-[(Aminocarbonyl)amino]hydroxy-acetic acidHMDB
S-(-)-Ureidoglycolic acidHMDB
UreidoglycolateHMDB
Molecular FormulaC3H6N2O4
Average Mass134.0907
Monoisotopic Mass134.03275669
IUPAC Name(2S)-2-(carbamoylamino)-2-hydroxyacetic acid
Traditional Nameureidoglycolate
CAS Registry NumberNot Available
SMILES
NC(=O)N[C@@H](O)C(O)=O
InChI Identifier
InChI=1S/C3H6N2O4/c4-3(9)5-1(6)2(7)8/h1,6H,(H,7,8)(H3,4,5,9)/t1-/m0/s1
InChI KeyNWZYYCVIOKVTII-SFOWXEAESA-N