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Showing NP-Card for Aminomalonic acid (NP0086713)

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Record Information
Version2.0
Created at2022-05-11 16:28:55 UTC
Updated at2022-05-11 16:28:55 UTC
NP-MRD IDNP0086713
Secondary Accession NumbersNone
Natural Product Identification
Common NameAminomalonic acid
DescriptionAminomalonic acid, also known as aminomalonate or amino-propanedioate, belongs to the class of organic compounds known as alpha amino acids. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon). Aminomalonic acid is a very strong basic compound (based on its pKa). Aminomalonic acid exists in all living organisms, ranging from bacteria to humans. Outside of the human body, Aminomalonic acid has been detected, but not quantified in, milk (cow). This could make aminomalonic acid a potential biomarker for the consumption of these foods. Aminomalonic acid was first documented in 1984 (PMID: 6366787). An amino dicarboxylic acid that is malonic acid in which one of the methylene hydrogens has been replaced by an amino group (PMID: 1621954).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0086713 (Aminomalonic acid)


  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 NP0086713 (Aminomalonic acid)

     RDKit          3D

 13 12  0  0  0  0  0  0  0  0999 V2000
   -1.3229   -1.0129   -0.7910 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4163   -0.3049    0.0809 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3396    1.1385   -0.2304 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9869    1.6981   -1.1497 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5044    1.9157    0.5487 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9035   -0.9570    0.1456 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1145   -1.9944   -0.5113 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8935   -0.4150    0.9315 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3066   -0.8739   -0.4691 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1963   -0.6959   -1.7798 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8585   -0.3882    1.1172 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1347    2.2649    1.4251 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8765   -0.3750    0.6824 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  5  1  0
  3  4  2  0
  2  6  1  0
  6  8  1  0
  6  7  2  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 NP0086713 (Aminomalonic acid)


  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>
NP0086713

> <DATABASE_NAME>
NP-MRD

> <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 NP0086713 (Aminomalonic acid)

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PDB for NP0086713 (Aminomalonic acid)
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 NP0086713 (Aminomalonic acid)
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SMILES for NP0086713 (Aminomalonic acid)
NC(C(O)=O)C(O)=O
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INCHI for NP0086713 (Aminomalonic acid)
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
Chemical FormulaC3H5NO4
Average Mass119.0761 Da
Monoisotopic Mass119.02186 Da
IUPAC Name2-aminopropanedioic acid
Traditional Nameaminomalonic acid
CAS Registry NumberNot Available
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
Experimental Spectra
Not Available
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Anas platyrhynchosFooDB
AnatidaeFooDB
Anser anserFooDB
Bison bisonFooDB
Bos taurusFooDB
Bos taurus X Bison bisonFooDB
Bubalus bubalisFooDB
Capra aegagrus hircusFooDB
CervidaeFooDB
Cervus canadensisFooDB
ColumbaFooDB
ColumbidaeFooDB
Dromaius novaehollandiaeFooDB
Equus caballusFooDB
Gallus gallusFooDB
Lagopus mutaFooDB
LeporidaeFooDB
Lepus timidusFooDB
Melanitta fuscaFooDB
Meleagris gallopavoFooDB
Numida meleagrisFooDB
OdocoileusFooDB
OryctolagusFooDB
Ovis ariesFooDB
PhasianidaeFooDB
Phasianus colchicusFooDB
Struthio camelusFooDB
Sus scrofaFooDB
Sus scrofa domesticaFooDB
Chemical Taxonomy
Description Belongs to the class of organic compounds known as alpha amino acids. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon).
KingdomOrganic compounds  
Super ClassOrganic acids and derivatives  
ClassCarboxylic acids and derivatives  
Sub ClassAmino acids, peptides, and analogues  
Direct ParentAlpha amino acids  
Alternative Parents
Substituents
  • Alpha-amino acid
    • 

  • Dicarboxylic acid or derivatives
    • 

  • 1,3-dicarbonyl compound
    • 

  • Amino acid
    • 

  • Carboxylic acid
    • 

  • Hydrocarbon derivative
    • 

  • Organopnictogen compound
    • 

  • Primary amine
    • 

  • Organooxygen compound
    • 

  • Organonitrogen compound
    • 

  • Primary aliphatic amine
    • 

  • Organic oxygen compound
    • 

  • Carbonyl group
    • 

  • Amine
    • 

  • Organic nitrogen compound
    • 

  • Organic oxide
    • 

  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP-3.5ALOGPS
logP-3.4ChemAxon
logS0.03ALOGPS
pKa (Strongest Acidic)0.45ChemAxon
pKa (Strongest Basic)8.5ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area100.62 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity21.98 m³·mol⁻¹ChemAxon
Polarizability9.48 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0001147  
DrugBank IDDB02289  
Phenol Explorer Compound IDNot Available
FoodDB IDFDB022451  
KNApSAcK IDNot Available
Chemspider ID90998  
KEGG Compound IDC00872  
BioCyc IDAMINOMALONATE  
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound100714  
PDB IDNot Available
ChEBI ID17475  
Good Scents IDNot Available
References
General References
  1. Copley SD, Frank E, Kirsch WM, Koch TH: Detection and possible origins of aminomalonic acid in protein hydrolysates. Anal Biochem. 1992 Feb 14;201(1):152-7. doi: 10.1016/0003-2697(92)90188-d. [PubMed:1621954  ] 
  2. Van Buskirk JJ, Kirsch WM, Kleyer DL, Barkley RM, Koch TH: Aminomalonic acid: identification in Escherichia coli and atherosclerotic plaque. Proc Natl Acad Sci U S A. 1984 Feb;81(3):722-5. doi: 10.1073/pnas.81.3.722. [PubMed:6366787  ]