Showing metabocard for D-Aspartic acid (MMDBc0000256)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2020-10-27 23:41:33 UTC
Update Date2022-08-31 00:16:13 UTC
Metabolite IDMMDBc0000256
Metabolite Identification
Common NameD-Aspartic acid
DescriptionD-Aspartic acid is the D-isomer of aspartic acid. Since its discovery in invertebrates, free D-aspartate (D-Asp) has been identified in a variety of organisms, including microorganisms, plants, and lower animals, mammals and humans. D-Asp in mammalian tissues is present in specific cells, indicating the existence of specific molecular components that regulate D-Asp levels and localization in tissues. In the rat adrenal medulla, D-Asp is closely associated with adrenaline-cells (A-cells), which account for approximately 80% of the total number of chromaffin cells in the tissue, and which make and store adrenaline. D-Asp appears to be absent from noradrenaline-cells (NA-cells), which comprise approximately 20% of the total number of chromaffin cells in the adrenal medulla, and which make and store noradrenaline. D-aspartate oxidase (EC 1.4.3.1, D-AspO), which catalyzes oxidative deamination of D-Asp, appears to be present only in NA-cells, suggesting that the lack of D-Asp in these cells is due to D-Asp oxidase-mediated metabolism of D-Asp. In the rat adrenal cortex, the distribution of D-Asp changes during development. It has been suggested that developmental changes in the localization of D-Asp reflects the participation of D-Asp in the development and maturation of steroidogenesis in rat adrenal cortical cells. D-Asp is involved in steroid hormone synthesis and secretion in mammals as well. D-Asp is synthesized intracellularly, most likely by Asp racemase (EC 5.1.1.13). Endogenous D-Asp apparently has two different intracellular localization patterns: cytoplasmic and vesicular. D-Asp release can occur through three distinct pathways: 1) spontaneous, continuous release of cytoplasmic D-Asp, which is not associated with a specific stimulus; 2) release of cytoplasmic D-Asp via a volume-sensitive organic anion channel that connects the cytoplasm and extracellular space; 3) exocytotic discharge of vesicular D-Asp. D-Asp can be released via a mechanism that involves the L-Glu transporter. D-Asp is thus apparently in dynamic flux at the cellular level to carry out its physiological function(s) in mammals. (PMID: 16755369 ).
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007fe2b0949770>


  Mrv1652305271900072D          

  9  8  0  0  1  0            999 V2000
    1.9520    0.1187    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    0.9437    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.2375    1.3562    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    0.9437    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1914    1.3562    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    0.1187    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664    1.3562    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3809    0.9437    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664    2.1812    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  6  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  4  6  2  0  0  0  0
  2  7  1  0  0  0  0
  7  8  1  0  0  0  0
  7  9  2  0  0  0  0
M  END
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3D MOL for #<Metabolite:0x00007fe2b0949770>

HMDB0006483
     RDKit          3D
D-Aspartic acid
 16 15  0  0  0  0  0  0  0  0999 V2000
   -0.4043   -1.6045   -0.3670 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5110   -0.2452   -0.8551 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.5742    0.6307   -0.2436 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9328    0.2039   -0.5551 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6047    0.7692   -1.4507 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4888   -0.8491    0.1534 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8025    0.3193   -0.4165 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5165   -0.3261    0.3753 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2067    1.5445   -0.8886 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9089   -2.2330   -1.0327 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9254   -1.7213    0.5519 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4342   -0.2128   -1.9390 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3516    1.6712   -0.6125 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4216    0.6368    0.8498 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4872   -1.0170    0.1875 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1514    2.4335   -0.4690 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  2  0
  4  6  1  0
  2  7  1  0
  7  8  2  0
  7  9  1  0
  1 10  1  0
  1 11  1  0
  2 12  1  6
  3 13  1  0
  3 14  1  0
  6 15  1  0
  9 16  1  0
M  END
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3D SDF for #<Metabolite:0x00007fe2b0949770>


  Mrv1652305271900072D          

  9  8  0  0  1  0            999 V2000
    1.9520    0.1187    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    0.9437    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.2375    1.3562    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    0.9437    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1914    1.3562    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    0.1187    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664    1.3562    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3809    0.9437    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664    2.1812    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  6  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  4  6  2  0  0  0  0
  2  7  1  0  0  0  0
  7  8  1  0  0  0  0
  7  9  2  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0000256

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C4H7NO4/c5-2(4(8)9)1-3(6)7/h2H,1,5H2,(H,6,7)(H,8,9)/t2-/m1/s1

> <INCHI_KEY>
CKLJMWTZIZZHCS-UWTATZPHSA-N

> <FORMULA>
C4H7NO4

> <MOLECULAR_WEIGHT>
133.1027

> <EXACT_MASS>
133.037507717

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
16

> <JCHEM_AVERAGE_POLARIZABILITY>
11.347850299850892

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-3.52

> <JCHEM_LOGP>
-3.5037527551764525

> <ALOGPS_LOGS>
0.03

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
5.113750094894903

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.7025435921010494

> <JCHEM_PKA_STRONGEST_BASIC>
9.614153755159162

> <JCHEM_POLAR_SURFACE_AREA>
100.62

> <JCHEM_REFRACTIVITY>
26.532700000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.42e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
D-aspartic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for #<Metabolite:0x00007fe2b0949770>

HMDB0006483
     RDKit          3D
D-Aspartic acid
 16 15  0  0  0  0  0  0  0  0999 V2000
   -0.4043   -1.6045   -0.3670 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5110   -0.2452   -0.8551 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.5742    0.6307   -0.2436 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9328    0.2039   -0.5551 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6047    0.7692   -1.4507 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4888   -0.8491    0.1534 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8025    0.3193   -0.4165 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5165   -0.3261    0.3753 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2067    1.5445   -0.8886 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9089   -2.2330   -1.0327 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9254   -1.7213    0.5519 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4342   -0.2128   -1.9390 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3516    1.6712   -0.6125 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4216    0.6368    0.8498 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4872   -1.0170    0.1875 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1514    2.4335   -0.4690 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  2  0
  4  6  1  0
  2  7  1  0
  7  8  2  0
  7  9  1  0
  1 10  1  0
  1 11  1  0
  2 12  1  6
  3 13  1  0
  3 14  1  0
  6 15  1  0
  9 16  1  0
M  END
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PDB for #<Metabolite:0x00007fe2b0949770>

HEADER    PROTEIN                                 27-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-MAY-19         0                                  
HETATM    1  N   UNK     0       3.644   0.222   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0       3.644   1.762   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.310   2.532   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.976   1.762   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      -0.357   2.532   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0       0.976   0.222   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       4.977   2.532   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       6.311   1.762   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       4.977   4.072   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    7                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4                                                            
CONECT    7    2    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7                                                            
MASTER        0    0    0    0    0    0    0    0    9    0   16    0
END
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3D PDB for #<Metabolite:0x00007fe2b0949770>

COMPND    HMDB0006483
HETATM    1  N1  UNL     1      -0.404  -1.605  -0.367  1.00  0.00           N  
HETATM    2  C1  UNL     1      -0.511  -0.245  -0.855  1.00  0.00           C  
HETATM    3  C2  UNL     1       0.574   0.631  -0.244  1.00  0.00           C  
HETATM    4  C3  UNL     1       1.933   0.204  -0.555  1.00  0.00           C  
HETATM    5  O1  UNL     1       2.605   0.769  -1.451  1.00  0.00           O  
HETATM    6  O2  UNL     1       2.489  -0.849   0.153  1.00  0.00           O  
HETATM    7  C4  UNL     1      -1.802   0.319  -0.417  1.00  0.00           C  
HETATM    8  O3  UNL     1      -2.517  -0.326   0.375  1.00  0.00           O  
HETATM    9  O4  UNL     1      -2.207   1.545  -0.889  1.00  0.00           O  
HETATM   10  H1  UNL     1      -0.909  -2.233  -1.033  1.00  0.00           H  
HETATM   11  H2  UNL     1      -0.925  -1.721   0.552  1.00  0.00           H  
HETATM   12  H3  UNL     1      -0.434  -0.213  -1.939  1.00  0.00           H  
HETATM   13  H4  UNL     1       0.352   1.671  -0.613  1.00  0.00           H  
HETATM   14  H5  UNL     1       0.422   0.637   0.850  1.00  0.00           H  
HETATM   15  H6  UNL     1       3.487  -1.017   0.187  1.00  0.00           H  
HETATM   16  H7  UNL     1      -2.151   2.433  -0.469  1.00  0.00           H  
CONECT    1    2   10   11
CONECT    2    3    7   12
CONECT    3    4   13   14
CONECT    4    5    5    6
CONECT    6   15
CONECT    7    8    8    9
CONECT    9   16
END
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SMILES for #<Metabolite:0x00007fe2b0949770>

N[C@H](CC(O)=O)C(O)=O
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INCHI for #<Metabolite:0x00007fe2b0949770>

InChI=1S/C4H7NO4/c5-2(4(8)9)1-3(6)7/h2H,1,5H2,(H,6,7)(H,8,9)/t2-/m1/s1
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Synonyms
ValueSource
(R)-2-Aminobutanedioic acidChEBI
(R)-2-Aminosuccinic acidChEBI
Aspartic acid D-formChEBI
D-AsparaginsaeureChEBI
DASChEBI
(R)-2-AminobutanedioateGenerator
(R)-2-AminosuccinateGenerator
Aspartate D-formGenerator
D-AspartateGenerator
D AspartateMeSH
D Aspartic acidMeSH
(-)-Aspartic acidHMDB
(2R)-2-AminobutanedioateHMDB
(2R)-2-Aminobutanedioic acidHMDB
(R)-Aspartic acidHMDB
1-amino-1,2-CarboxyethaneHMDB
Aspartic acidHMDB
D-(-)-Aspartic acidHMDB
delta-(-)-Aspartic acidHMDB
delta-AsparaginsaeureHMDB
delta-AspartateHMDB
delta-Aspartic acidHMDB
Lopac-alpha-9256HMDB
Tocris-0213HMDB
Molecular FormulaC4H7NO4
Average Mass133.1027
Monoisotopic Mass133.037507717
IUPAC Name(2R)-2-aminobutanedioic acid
Traditional NameD-aspartic acid
CAS Registry Number1783-96-6
SMILES
N[C@H](CC(O)=O)C(O)=O
InChI Identifier
InChI=1S/C4H7NO4/c5-2(4(8)9)1-3(6)7/h2H,1,5H2,(H,6,7)(H,8,9)/t2-/m1/s1
InChI KeyCKLJMWTZIZZHCS-UWTATZPHSA-N