Showing metabocard for D-Glutamic acid (MMDBc0000233)

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Record Information
Version1.0
StatusDetected and Quantified
Creation Date2020-10-27 23:40:43 UTC
Update Date2024-10-11 01:16:55 UTC
Metabolite IDMMDBc0000233
Metabolite Identification
Common NameD-Glutamic acid
DescriptionThere are two forms of glutamic acid found in nature: L-glutamic acid and D-glutamic acid. D-glutamic acid, is not endogenously produced in higher mammals. It is found naturally primarily in the cell walls of certain bacteria. D-glutamate is also present in certain foods e.g., soybeans and also arises from the turnover of the intestinal tract microflora, whose cell walls contain significant D-glutamate. Unlike other D-amino acids, D-glutamate is not oxidized by the D-amino acid oxidases, and therefore this detoxification pathway is not available for handling D-glutamate. Likewise, D-glutamic acid, when ingested, largely escapes most deamination reactions (unlike the L-counterpart). Free D-glutamate is found in mammalian tissue at surprisingly high levels, with D-glutamate accounting for 9% of the total glutamate present in liver. D-glutamate is the most potent natural inhibitor of glutathione synthesis identified to date and this may account for its localization to the liver, since circulating D-glutamate may alter redox stabiity (PMID 11158923 ). Certain eels are known to use D-glutamic acid as a phermone for chemical communication. D-Glutamic acid has been found to be a metabolite of Lactobacillus (PMID: 22754309 ).
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007fd5c413af78>

  Mrv0541 02231219422D          

 10  9  0  0  1  0            999 V2000
   30.5669  -11.1406    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   27.7090  -13.6156    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   29.8525   -9.9031    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   29.1380  -13.6156    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   28.4235  -10.7281    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   29.1380  -11.1406    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   29.1380  -11.9656    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   28.4235  -12.3781    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   29.8525  -10.7281    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   28.4235  -13.2031    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  9  1  0  0  0  0
  2 10  1  0  0  0  0
  3  9  2  0  0  0  0
  4 10  2  0  0  0  0
  6  5  1  1  0  0  0
  6  7  1  0  0  0  0
  6  9  1  0  0  0  0
  7  8  1  0  0  0  0
  8 10  1  0  0  0  0
M  END
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3D MOL for #<Metabolite:0x00007fd5c413af78>

HMDB0003339
     RDKit          3D
D-Glutamic acid
 19 18  0  0  0  0  0  0  0  0999 V2000
    1.7860   -0.6746   -1.1495 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1167   -0.6021    0.1335 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.3370   -0.3304   -0.1409 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1772   -0.2253    1.0889 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5810    0.0434    0.6449 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5208    0.1807    1.4851 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9313    0.1565   -0.6936 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7599    0.4218    0.9539 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4021    0.7181    2.1277 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8341    1.1292    0.4364 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8135   -0.6198   -1.0828 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4677    0.1810   -1.6890 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2242   -1.5762    0.6757 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7249   -1.1791   -0.7434 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4336    0.5808   -0.7292 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9012    0.6129    1.7505 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2169   -1.1785    1.6636 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4881    0.9043   -1.0650 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9080    1.4574   -0.5065 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  2  0
  5  7  1  0
  2  8  1  0
  8  9  2  0
  8 10  1  0
  1 11  1  0
  1 12  1  0
  2 13  1  1
  3 14  1  0
  3 15  1  0
  4 16  1  0
  4 17  1  0
  7 18  1  0
 10 19  1  0
M  END
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3D SDF for #<Metabolite:0x00007fd5c413af78>

  Mrv0541 02231219422D          

 10  9  0  0  1  0            999 V2000
   30.5669  -11.1406    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   27.7090  -13.6156    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   29.8525   -9.9031    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   29.1380  -13.6156    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   28.4235  -10.7281    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   29.1380  -11.1406    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   29.1380  -11.9656    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   28.4235  -12.3781    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   29.8525  -10.7281    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   28.4235  -13.2031    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  9  1  0  0  0  0
  2 10  1  0  0  0  0
  3  9  2  0  0  0  0
  4 10  2  0  0  0  0
  6  5  1  1  0  0  0
  6  7  1  0  0  0  0
  6  9  1  0  0  0  0
  7  8  1  0  0  0  0
  8 10  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0000233

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C5H9NO4/c6-3(5(9)10)1-2-4(7)8/h3H,1-2,6H2,(H,7,8)(H,9,10)/t3-/m1/s1

> <INCHI_KEY>
WHUUTDBJXJRKMK-GSVOUGTGSA-N

> <FORMULA>
C5H9NO4

> <MOLECULAR_WEIGHT>
147.1293

> <EXACT_MASS>
147.053157781

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_AVERAGE_POLARIZABILITY>
13.18676985483213

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R)-2-aminopentanedioic acid

> <ALOGPS_LOGP>
-3.54

> <JCHEM_LOGP>
-3.241447075983049

> <ALOGPS_LOGS>
-0.26

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
4.27124634014693

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.8777772810395925

> <JCHEM_PKA_STRONGEST_BASIC>
9.536217151721162

> <JCHEM_POLAR_SURFACE_AREA>
100.61999999999999

> <JCHEM_REFRACTIVITY>
31.287699999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.06e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
D-glutamic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for #<Metabolite:0x00007fd5c413af78>

HMDB0003339
     RDKit          3D
D-Glutamic acid
 19 18  0  0  0  0  0  0  0  0999 V2000
    1.7860   -0.6746   -1.1495 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1167   -0.6021    0.1335 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.3370   -0.3304   -0.1409 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1772   -0.2253    1.0889 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5810    0.0434    0.6449 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5208    0.1807    1.4851 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9313    0.1565   -0.6936 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7599    0.4218    0.9539 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4021    0.7181    2.1277 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8341    1.1292    0.4364 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8135   -0.6198   -1.0828 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4677    0.1810   -1.6890 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2242   -1.5762    0.6757 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7249   -1.1791   -0.7434 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4336    0.5808   -0.7292 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9012    0.6129    1.7505 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2169   -1.1785    1.6636 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4881    0.9043   -1.0650 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9080    1.4574   -0.5065 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  2  0
  5  7  1  0
  2  8  1  0
  8  9  2  0
  8 10  1  0
  1 11  1  0
  1 12  1  0
  2 13  1  1
  3 14  1  0
  3 15  1  0
  4 16  1  0
  4 17  1  0
  7 18  1  0
 10 19  1  0
M  END
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PDB for #<Metabolite:0x00007fd5c413af78>

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  O   UNK     0      57.058 -20.796   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0      51.723 -25.416   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      55.725 -18.486   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0      54.391 -25.416   0.000  0.00  0.00           O+0
HETATM    5  N   UNK     0      53.057 -20.026   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0      54.391 -20.796   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      54.391 -22.336   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      53.057 -23.106   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      55.725 -20.026   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      53.057 -24.646   0.000  0.00  0.00           C+0
CONECT    1    9                                                            
CONECT    2   10                                                            
CONECT    3    9                                                            
CONECT    4   10                                                            
CONECT    5    6                                                            
CONECT    6    5    7    9                                                  
CONECT    7    6    8                                                       
CONECT    8    7   10                                                       
CONECT    9    1    3    6                                                  
CONECT   10    2    4    8                                                  
MASTER        0    0    0    0    0    0    0    0   10    0   18    0
END
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3D PDB for #<Metabolite:0x00007fd5c413af78>

COMPND    HMDB0003339
HETATM    1  N1  UNL     1       1.786  -0.675  -1.149  1.00  0.00           N  
HETATM    2  C1  UNL     1       1.117  -0.602   0.134  1.00  0.00           C  
HETATM    3  C2  UNL     1      -0.337  -0.330  -0.141  1.00  0.00           C  
HETATM    4  C3  UNL     1      -1.177  -0.225   1.089  1.00  0.00           C  
HETATM    5  C4  UNL     1      -2.581   0.043   0.645  1.00  0.00           C  
HETATM    6  O1  UNL     1      -3.521   0.181   1.485  1.00  0.00           O  
HETATM    7  O2  UNL     1      -2.931   0.156  -0.694  1.00  0.00           O  
HETATM    8  C5  UNL     1       1.760   0.422   0.954  1.00  0.00           C  
HETATM    9  O3  UNL     1       1.402   0.718   2.128  1.00  0.00           O  
HETATM   10  O4  UNL     1       2.834   1.129   0.436  1.00  0.00           O  
HETATM   11  H1  UNL     1       2.814  -0.620  -1.083  1.00  0.00           H  
HETATM   12  H2  UNL     1       1.468   0.181  -1.689  1.00  0.00           H  
HETATM   13  H3  UNL     1       1.224  -1.576   0.676  1.00  0.00           H  
HETATM   14  H4  UNL     1      -0.725  -1.179  -0.743  1.00  0.00           H  
HETATM   15  H5  UNL     1      -0.434   0.581  -0.729  1.00  0.00           H  
HETATM   16  H6  UNL     1      -0.901   0.613   1.750  1.00  0.00           H  
HETATM   17  H7  UNL     1      -1.217  -1.178   1.664  1.00  0.00           H  
HETATM   18  H8  UNL     1      -3.488   0.904  -1.065  1.00  0.00           H  
HETATM   19  H9  UNL     1       2.908   1.457  -0.506  1.00  0.00           H  
CONECT    1    2   11   12
CONECT    2    3    8   13
CONECT    3    4   14   15
CONECT    4    5   16   17
CONECT    5    6    6    7
CONECT    7   18
CONECT    8    9    9   10
CONECT   10   19
END
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SMILES for #<Metabolite:0x00007fd5c413af78>

N[C@H](CCC(O)=O)C(O)=O
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INCHI for #<Metabolite:0x00007fd5c413af78>

InChI=1S/C5H9NO4/c6-3(5(9)10)1-2-4(7)8/h3H,1-2,6H2,(H,7,8)(H,9,10)/t3-/m1/s1
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Synonyms
Molecular FormulaC5H9NO4
Average Mass147.1293
Monoisotopic Mass147.053157781
IUPAC Name(2R)-2-aminopentanedioic acid
Traditional NameD-glutamic acid
CAS Registry Number6893-26-1
SMILES
N[C@H](CCC(O)=O)C(O)=O
InChI Identifier
InChI=1S/C5H9NO4/c6-3(5(9)10)1-2-4(7)8/h3H,1-2,6H2,(H,7,8)(H,9,10)/t3-/m1/s1
InChI KeyWHUUTDBJXJRKMK-GSVOUGTGSA-N