Showing metabocard for Aminomalonic acid (MMDBc0030367)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2021-11-18 00:05:29 UTC
Update Date2024-04-30 19:46:00 UTC
Metabolite IDMMDBc0030367
Metabolite Identification
Common NameAminomalonic acid
DescriptionAminomalonic acid (Ama) is an amino dicarboxylic acid that is an analog of malonic acid in which one of the methylene hydrogens has been replaced by an amino group. It is a strongly acidic compound that is very water soluble. Aminomalonic acid is a natural occurring, largely non-proteogenic amino acid that was first detected in alkaline hydrolysates of proteins in 1984. In particular, aminomalonic acid was isolated from proteins isolated from Escherichia coli cultures and from human atherosclerotic plaques (PMID: 6366787 ). Aminomalonic acid is a relatively unstable, minor amino acid in complex structures such as bacteria or tissues. The presence of aminomalonic acid has important biological implications because the malonic acid moiety potentially imparts calcium binding properties to proteins. Possible origins of aminomalonic acid in proteins include its introduction via errors in protein synthesis and oxidative damage to amino acid residues in proteins. (PMID: 1621954 , 6366787  ). Aminomalonic acid can be generated naturally via the activity of mammalian and bacterial enzymes on various precursors such as 2-aminomalonamide, diethylaminomalonate and ketomalonic acid (PMID: 35346 ). Free aminomalonic acid appears to be an oxidation product arising from perturbed serine or threonine metabolism. Aminomalonic acid is produced in animals that have been exposed to Cadmium (a strong pro-oxidant) for extended periods of time and it has been proposed to be a potential biomarker of Cadmium toxicity (PMID: 32193438 ). Aminomalonic acid has also been found to be elevated in the urine of individuals with anxiety and major depressive disorders (PMID: 30232320 ). Aminomalonic acid has been reported to be a potential biomarker for hepatocellular carcinoma (PMID: 18767022 ) and it exhibits strong inhibitory effects on L-asparagine synthase (PMID: 35346 ). Several metabolomics studies have also found that altered aminomalonic acid levels in serum are associated with neuropsychiatric disorders, melanoma, ketamine overdose and aortic aneurysm, indicating that aminomalonic acid is an important serum indicator for diseases and toxicities (PMID: 32193438 ).
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007f46ec4cc658>


  Mrv0541 02231216062D          

  8  7  0  0  0  0            999 V2000
    2.0625    0.7145    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    2.1434    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  3  5  2  0  0  0  0
  2  6  1  0  0  0  0
  6  7  1  0  0  0  0
  6  8  2  0  0  0  0
M  END
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3D MOL for #<Metabolite:0x00007f46ec4cc658>

HMDB0001147
     RDKit          3D
Aminomalonic acid
 13 12  0  0  0  0  0  0  0  0999 V2000
    0.0283   -1.1746   -0.8412 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0736    0.2318   -0.5877 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2362    0.6161    0.2281 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4070    1.8102    0.5292 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1273   -0.3281    0.6560 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1995    0.7329    0.0153 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3676    1.9324    0.3138 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2289   -0.1656    0.2511 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1985   -1.7278    0.0372 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8800   -1.4125   -1.2515 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2149    0.7337   -1.5904 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7924   -0.8195    0.0971 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4022   -0.4290    1.2125 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  3  5  1  0
  2  6  1  0
  6  7  2  0
  6  8  1  0
  1  9  1  0
  1 10  1  0
  2 11  1  0
  5 12  1  0
  8 13  1  0
M  END
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3D SDF for #<Metabolite:0x00007f46ec4cc658>


  Mrv0541 02231216062D          

  8  7  0  0  0  0            999 V2000
    2.0625    0.7145    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    2.1434    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  3  5  2  0  0  0  0
  2  6  1  0  0  0  0
  6  7  1  0  0  0  0
  6  8  2  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0030367

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C3H5NO4/c4-1(2(5)6)3(7)8/h1H,4H2,(H,5,6)(H,7,8)

> <INCHI_KEY>
JINBYESILADKFW-UHFFFAOYSA-N

> <FORMULA>
C3H5NO4

> <MOLECULAR_WEIGHT>
119.0761

> <EXACT_MASS>
119.021857653

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_AVERAGE_POLARIZABILITY>
9.47937151561501

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-aminopropanedioic acid

> <ALOGPS_LOGP>
-3.50

> <JCHEM_LOGP>
-3.4290208572044985

> <ALOGPS_LOGS>
0.03

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
3.6755223055219526

> <JCHEM_PKA_STRONGEST_ACIDIC>
0.45162167120244945

> <JCHEM_PKA_STRONGEST_BASIC>
8.495965759301432

> <JCHEM_POLAR_SURFACE_AREA>
100.62

> <JCHEM_REFRACTIVITY>
21.983500000000003

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.26e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
aminomalonic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for #<Metabolite:0x00007f46ec4cc658>

HMDB0001147
     RDKit          3D
Aminomalonic acid
 13 12  0  0  0  0  0  0  0  0999 V2000
    0.0283   -1.1746   -0.8412 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0736    0.2318   -0.5877 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2362    0.6161    0.2281 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4070    1.8102    0.5292 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1273   -0.3281    0.6560 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1995    0.7329    0.0153 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3676    1.9324    0.3138 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2289   -0.1656    0.2511 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1985   -1.7278    0.0372 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8800   -1.4125   -1.2515 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2149    0.7337   -1.5904 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7924   -0.8195    0.0971 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4022   -0.4290    1.2125 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  3  5  1  0
  2  6  1  0
  6  7  2  0
  6  8  1  0
  1  9  1  0
  1 10  1  0
  2 11  1  0
  5 12  1  0
  8 13  1  0
M  END
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PDB for #<Metabolite:0x00007f46ec4cc658>

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  N   UNK     0       3.850   1.334   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0       2.310   1.334   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.540   2.667   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       2.310   4.001   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0       0.000   2.667   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       2.310  -1.334   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    6                                                  
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3                                                            
CONECT    6    2    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6                                                            
MASTER        0    0    0    0    0    0    0    0    8    0   14    0
END
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3D PDB for #<Metabolite:0x00007f46ec4cc658>

COMPND    HMDB0001147
HETATM    1  N1  UNL     1       0.028  -1.175  -0.841  1.00  0.00           N  
HETATM    2  C1  UNL     1       0.074   0.232  -0.588  1.00  0.00           C  
HETATM    3  C2  UNL     1       1.236   0.616   0.228  1.00  0.00           C  
HETATM    4  O1  UNL     1       1.407   1.810   0.529  1.00  0.00           O  
HETATM    5  O2  UNL     1       2.127  -0.328   0.656  1.00  0.00           O  
HETATM    6  C3  UNL     1      -1.200   0.733   0.015  1.00  0.00           C  
HETATM    7  O3  UNL     1      -1.368   1.932   0.314  1.00  0.00           O  
HETATM    8  O4  UNL     1      -2.229  -0.166   0.251  1.00  0.00           O  
HETATM    9  H1  UNL     1       0.199  -1.728   0.037  1.00  0.00           H  
HETATM   10  H2  UNL     1      -0.880  -1.412  -1.251  1.00  0.00           H  
HETATM   11  H3  UNL     1       0.215   0.734  -1.590  1.00  0.00           H  
HETATM   12  H4  UNL     1       2.792  -0.819   0.097  1.00  0.00           H  
HETATM   13  H5  UNL     1      -2.402  -0.429   1.213  1.00  0.00           H  
CONECT    1    2    9   10
CONECT    2    3    6   11
CONECT    3    4    4    5
CONECT    5   12
CONECT    6    7    7    8
CONECT    8   13
END
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SMILES for #<Metabolite:0x00007f46ec4cc658>

NC(C(O)=O)C(O)=O
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INCHI for #<Metabolite:0x00007f46ec4cc658>

InChI=1S/C3H5NO4/c4-1(2(5)6)3(7)8/h1H,4H2,(H,5,6)(H,7,8)
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Synonyms
ValueSource
2-Aminomalonic acidChEBI
AminomalonateChEBI
2-AminomalonateGenerator
a-Aminomalonic acidHMDB
alpha-Aminomalonic acidHMDB
amino-Malonic acidHMDB
amino-PropanedioateHMDB
amino-Propanedioic acidHMDB
AminopropanedioateHMDB
Aminopropanedioic acidHMDB
Molecular FormulaC3H5NO4
Average Mass119.0761
Monoisotopic Mass119.021857653
IUPAC Name2-aminopropanedioic acid
Traditional Nameaminomalonic acid
CAS Registry Number1068-84-4
SMILES
NC(C(O)=O)C(O)=O
InChI Identifier
InChI=1S/C3H5NO4/c4-1(2(5)6)3(7)8/h1H,4H2,(H,5,6)(H,7,8)
InChI KeyJINBYESILADKFW-UHFFFAOYSA-N