Showing metabocard for (S)-Ureidoglycolic acid (MMDBc0032834)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2021-11-18 21:57:19 UTC
Update Date2022-08-31 18:51:54 UTC
Metabolite IDMMDBc0032834
Metabolite Identification
Common Name(S)-Ureidoglycolic acid
Description(S)-Ureidoglycolic acid is a substrate of enzyme ureidoglycolate dehydrogenase [EC 1.1.1.154] in purine metabolism pathway (KEGG). Enteric bacteria such as Pseudomonas aeruginosa are able to utilize allantoin as a sole source of nitrogen under anaerobic c
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007fdb0ee5d260>


  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
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3D MOL for #<Metabolite:0x00007fdb0ee5d260>

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
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3D SDF for #<Metabolite:0x00007fdb0ee5d260>


  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>
MMDBc0032834

> <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

$$$$
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3D-SDF for #<Metabolite:0x00007fdb0ee5d260>

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
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PDB for #<Metabolite:0x00007fdb0ee5d260>

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
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3D PDB for #<Metabolite:0x00007fdb0ee5d260>

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
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SMILES for #<Metabolite:0x00007fdb0ee5d260>

NC(=O)N[C@@H](O)C(O)=O
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INCHI for #<Metabolite:0x00007fdb0ee5d260>

InChI=1S/C3H6N2O4/c4-3(9)5-1(6)2(7)8/h1,6H,(H,7,8)(H3,4,5,9)/t1-/m0/s1
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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 Number7424-03-5
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