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Showing NP-Card for D-alpha-Aminobutyric acid (NP0000897)

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Record Information
Version2.0
Created at2005-11-16 15:48:42 UTC
Updated at2021-08-19 23:58:33 UTC
NP-MRD IDNP0000897
Secondary Accession NumbersNone
Natural Product Identification
Common NameD-alpha-Aminobutyric acid
DescriptionD-alpha-Aminobutyric acid (AABA), also known as alpha-aminobutyrate, (R)-2-aminobutanoic acid or D-homoalanine, belongs to the class of organic compounds known as D-alpha-amino acids. These are alpha amino acids which have the D-configuration of the alpha-carbon atom. D-alpha-aminobutyric acid is an optically active form of alpha-aminobutyric acid having D-configuration. It is an enantiomer of a L-alpha-aminobutyric acid and a non-proteinogenic amino acid. Alpha-aminobutyric acid is one of the three isomers of aminobutyric acid. The two others are the neurotransmitter Gamma-Aminobutyric acid (GABA) and Beta-Aminobutyric acid (BABA) which is known for inducing plant disease resistance. Optically active organic compounds found in meteorites typically exist in racemic form, yet life on Earth has almost exclusively selected for L- over D-enantiomers of amino acids. D-enantiomers of non-proteinogenic amino acids are known to inhibit aerobic microorganisms. D-alpha-aminobutyric acid has been shown to inhibit microbial iron reduction by a number of Geobacter strains including Geobacter bemidjiensis, Geobacter metallireducens and Geopsychrobacter electrodiphilus (PMID: 25695622 ). D-alpha-Aminobutyric acid is a known substrate of D-amino acid oxidase (PMID: 6127341 ).
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0000897 (D-alpha-Aminobutyric acid)


     RDKit          2D

 16 15  0  0  0  0  0  0  0  0999 V2000
   -1.6906    1.1651    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5607    0.1785    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5692   -0.8082    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4175   -1.9380    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.5558    0.3217    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2472    1.7896    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0276    0.0322    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7039    2.2949    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6772    0.0352    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8204    2.1517    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6777   -0.8227    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2808    1.4202    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6990   -1.7948    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0677   -3.3574    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9136   -1.8301    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0142    1.1621    0.0000 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
  3  5  1  0
  5  6  2  0
  5  7  1  0
  1  8  1  6
  1  9  1  0
  1 10  1  0
  2 11  1  6
  2 12  1  0
  3 13  1  1
  4 14  1  0
  4 15  1  0
  7 16  1  0
M  END
Download

3D MOL for NP0000897 (D-alpha-Aminobutyric acid)

HMDB0000650
     RDKit          3D
D-alpha-Aminobutyric acid
 16 15  0  0  0  0  0  0  0  0999 V2000
    1.7855    0.0518   -0.2506 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6997   -0.8675    0.2479 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6548   -0.3870   -0.2665 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.6795   -1.2651    0.2114 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8664    1.0160    0.1892 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8700    1.2520    0.9040 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0145    2.0225   -0.1647 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7651   -0.4581   -0.3432 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4767    0.4269   -1.2443 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9595    0.8909    0.4771 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9227   -1.8839   -0.0947 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6949   -0.8386    1.3500 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6778   -0.3818   -1.3671 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5972   -1.0611   -0.2240 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7079   -1.3651    1.2425 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2650    2.8479   -0.6670 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
  3  5  1  0
  5  6  2  0
  5  7  1  0
  1  8  1  0
  1  9  1  0
  1 10  1  0
  2 11  1  0
  2 12  1  0
  3 13  1  6
  4 14  1  0
  4 15  1  0
  7 16  1  0
M  END
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3D SDF for NP0000897 (D-alpha-Aminobutyric acid)


     RDKit          2D

 16 15  0  0  0  0  0  0  0  0999 V2000
   -1.6906    1.1651    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5607    0.1785    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5692   -0.8082    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4175   -1.9380    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.5558    0.3217    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2472    1.7896    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0276    0.0322    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7039    2.2949    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6772    0.0352    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8204    2.1517    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6777   -0.8227    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2808    1.4202    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6990   -1.7948    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0677   -3.3574    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9136   -1.8301    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0142    1.1621    0.0000 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
  3  5  1  0
  5  6  2  0
  5  7  1  0
  1  8  1  6
  1  9  1  0
  1 10  1  0
  2 11  1  6
  2 12  1  0
  3 13  1  1
  4 14  1  0
  4 15  1  0
  7 16  1  0
M  END
> <DATABASE_ID>
NP0000897

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C4H9NO2/c1-2-3(5)4(6)7/h3H,2,5H2,1H3,(H,6,7)/t3-/m1/s1

> <INCHI_KEY>
QWCKQJZIFLGMSD-GSVOUGTGSA-N

> <FORMULA>
C4H9NO2

> <MOLECULAR_WEIGHT>
103.1198

> <EXACT_MASS>
103.063328537

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
16

> <JCHEM_AVERAGE_POLARIZABILITY>
10.38387358105714

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-2.55

> <JCHEM_LOGP>
-2.3181498124844198

> <ALOGPS_LOGS>
0.54

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.615755119614637

> <JCHEM_PKA_STRONGEST_BASIC>
9.53467345401491

> <JCHEM_POLAR_SURFACE_AREA>
63.32

> <JCHEM_REFRACTIVITY>
25.021300000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.58e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
D-2-aminobutyric acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0000897 (D-alpha-Aminobutyric acid)

HMDB0000650
     RDKit          3D
D-alpha-Aminobutyric acid
 16 15  0  0  0  0  0  0  0  0999 V2000
    1.7855    0.0518   -0.2506 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6997   -0.8675    0.2479 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6548   -0.3870   -0.2665 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.6795   -1.2651    0.2114 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8664    1.0160    0.1892 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8700    1.2520    0.9040 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0145    2.0225   -0.1647 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7651   -0.4581   -0.3432 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4767    0.4269   -1.2443 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9595    0.8909    0.4771 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9227   -1.8839   -0.0947 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6949   -0.8386    1.3500 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6778   -0.3818   -1.3671 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5972   -1.0611   -0.2240 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7079   -1.3651    1.2425 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2650    2.8479   -0.6670 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
  3  5  1  0
  5  6  2  0
  5  7  1  0
  1  8  1  0
  1  9  1  0
  1 10  1  0
  2 11  1  0
  2 12  1  0
  3 13  1  6
  4 14  1  0
  4 15  1  0
  7 16  1  0
M  END
Download

PDB for NP0000897 (D-alpha-Aminobutyric acid)

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  C   UNK     0    8664.7238664.348   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0    8663.3898665.117   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0    8662.0558664.348   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0    8663.3898666.656   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0    8666.0588665.117   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0    8667.3908664.348   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0    8664.7238662.807   0.000  0.00  0.00           N+0
CONECT    1    2    5    7                                                  
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2                                                            
CONECT    5    1    6                                                       
CONECT    6    5                                                            
CONECT    7    1                                                            
MASTER        0    0    0    0    0    0    0    0    7    0   12    0
END
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3D PDB for NP0000897 (D-alpha-Aminobutyric acid)

COMPND    HMDB0000650
HETATM    1  C1  UNL     1       1.786   0.052  -0.251  1.00  0.00           C  
HETATM    2  C2  UNL     1       0.700  -0.867   0.248  1.00  0.00           C  
HETATM    3  C3  UNL     1      -0.655  -0.387  -0.267  1.00  0.00           C  
HETATM    4  N1  UNL     1      -1.679  -1.265   0.211  1.00  0.00           N  
HETATM    5  C4  UNL     1      -0.866   1.016   0.189  1.00  0.00           C  
HETATM    6  O1  UNL     1      -1.870   1.252   0.904  1.00  0.00           O  
HETATM    7  O2  UNL     1       0.015   2.023  -0.165  1.00  0.00           O  
HETATM    8  H1  UNL     1       2.765  -0.458  -0.343  1.00  0.00           H  
HETATM    9  H2  UNL     1       1.477   0.427  -1.244  1.00  0.00           H  
HETATM   10  H3  UNL     1       1.959   0.891   0.477  1.00  0.00           H  
HETATM   11  H4  UNL     1       0.923  -1.884  -0.095  1.00  0.00           H  
HETATM   12  H5  UNL     1       0.695  -0.839   1.350  1.00  0.00           H  
HETATM   13  H6  UNL     1      -0.678  -0.382  -1.367  1.00  0.00           H  
HETATM   14  H7  UNL     1      -2.597  -1.061  -0.224  1.00  0.00           H  
HETATM   15  H8  UNL     1      -1.708  -1.365   1.243  1.00  0.00           H  
HETATM   16  H9  UNL     1      -0.265   2.848  -0.667  1.00  0.00           H  
CONECT    1    2    8    9   10
CONECT    2    3   11   12
CONECT    3    4    5   13
CONECT    4   14   15
CONECT    5    6    6    7
CONECT    7   16
END
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SMILES for NP0000897 (D-alpha-Aminobutyric acid)

CC[C@@H](N)C(O)=O
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INCHI for NP0000897 (D-alpha-Aminobutyric acid)

InChI=1S/C4H9NO2/c1-2-3(5)4(6)7/h3H,2,5H2,1H3,(H,6,7)/t3-/m1/s1
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View in JSmol
Synonyms
ValueSource
(2R)-2-Aminobutyric acidChEBI
(R)-2-Aminobutanoic acidChEBI
(R)-2-Aminobutyric acidChEBI
alpha-Aminobutyric acidChEBI
D-(-)-2-Aminobutyric acidChEBI
D-2-Aminobutanoic acidChEBI
D-2-AminobuttersaeureChEBI
D-2-AminobutyrateChEBI
D-2-Aminobutyric acidChEBI
(2R)-2-AminobutyrateGenerator
(R)-2-AminobutanoateGenerator
(R)-2-AminobutyrateGenerator
a-AminobutyrateGenerator
a-Aminobutyric acidGenerator
alpha-AminobutyrateGenerator
Α-aminobutyrateGenerator
Α-aminobutyric acidGenerator
D-(-)-2-AminobutyrateGenerator
D-2-AminobutanoateGenerator
D-a-AminobutyrateGenerator
D-a-Aminobutyric acidGenerator
D-alpha-AminobutyrateGenerator
D-Α-aminobutyrateGenerator
D-Α-aminobutyric acidGenerator
(2R)-2-AminobutanoateHMDB
(2R)-2-Aminobutanoic acidHMDB
(R)-2-Amino-butanoateHMDB
(R)-2-Amino-butanoic acidHMDB
delta-(-)-2-Aminobutyric acidHMDB
delta-2-AminobutanoateHMDB
delta-2-Aminobutanoic acidHMDB
delta-2-AminobuttersaeureHMDB
delta-2-AminobutyrateHMDB
delta-2-Aminobutyric acidHMDB
delta-alpha-Aminobutyric acidHMDB
2R-Amino-butanoateHMDB
(2S)-2-Aminobutanoic acidHMDB
alpha-Aminobutyric acid, (S)-isomerHMDB
Butyrine, (S)-isomerHMDB
L-2-Aminobutyric acidHMDB
HomoalanineHMDB
2-Aminobutyric acidHMDB
2-Aminobutanoic acidHMDB
alpha-Aminobutyric acid, (+-)-isomerHMDB
Butyrine, (R)-isomerHMDB
ButyrineHMDB
Butyrine, (+-)-isomerHMDB
L-HomoalanineHMDB
alpha-Aminobutyric acid, (R)-isomerHMDB
Chemical FormulaC4H9NO2
Average Mass103.1198 Da
Monoisotopic Mass103.06333 Da
IUPAC Name(2R)-2-aminobutanoic acid
Traditional NameD-2-aminobutyric acid
CAS Registry Number2623-91-8
SMILES
CC[C@@H](N)C(O)=O
InChI Identifier
InChI=1S/C4H9NO2/c1-2-3(5)4(6)7/h3H,2,5H2,1H3,(H,6,7)/t3-/m1/s1
InChI KeyQWCKQJZIFLGMSD-GSVOUGTGSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, H2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Predicted Spectra
Not Available
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 d-alpha-amino acids. These are alpha amino acids which have the D-configuration of the alpha-carbon atom.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassAmino acids, peptides, and analogues
Direct ParentD-alpha-amino acids
Alternative Parents
Substituents
  • D-alpha-amino acid
  • Fatty acid
  • Amino acid
  • Carboxylic acid
  • Monocarboxylic acid or derivatives
  • Amine
  • Hydrocarbon derivative
  • Organic oxide
  • Organopnictogen compound
  • Primary amine
  • Organooxygen compound
  • Organonitrogen compound
  • Organic oxygen compound
  • Primary aliphatic amine
  • Organic nitrogen compound
  • Carbonyl group
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling Point215.17 °C. @ 760.00 mm Hg (est)The Good Scents Company Information System
Water Solubility278 mg/mLNot Available
LogP-0.064 (est)The Good Scents Company Information System
Predicted Properties
PropertyValueSource
Water Solubility358 g/LALOGPS
logP-2.6ALOGPS
logP-2.3ChemAxon
logS0.54ALOGPS
pKa (Strongest Acidic)2.62ChemAxon
pKa (Strongest Basic)9.53ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area63.32 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity25.02 m³·mol⁻¹ChemAxon
Polarizability10.38 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0000650
DrugBank IDDB04454
Phenol Explorer Compound IDNot Available
FoodDB IDFDB012680
KNApSAcK IDNot Available
Chemspider ID388757
KEGG Compound IDC02261
BioCyc IDCPD0-1952
BiGG IDNot Available
Wikipedia LinkAlpha-Aminobutyric acid
METLIN IDNot Available
PubChem Compound439691
PDB IDNot Available
ChEBI ID28797
Good Scents IDrw1140351
References
General References
  1. Lange R, Hui Bon Hoa G, Douzou P, Yagi K: Kinetics of primary interaction of D-amino acid oxidase with its substrate. Biochem Int. 1983 May;6(5):693-8. [PubMed:6148943 ]
  2. Nixon SL, Cockell CS: Nonproteinogenic D-amino acids at millimolar concentrations are a toxin for anaerobic microorganisms relevant to early Earth and other anoxic planets. Astrobiology. 2015 Mar;15(3):238-46. doi: 10.1089/ast.2014.1252. Epub 2015 Feb 19. [PubMed:25695622 ]
  3. Fitzpatrick PF, Massey V: The kinetic mechanism of D-amino acid oxidase with D-alpha-aminobutyrate as substrate. Effect of enzyme concentration on the kinetics. J Biol Chem. 1982 Nov 10;257(21):12916-23. [PubMed:6127341 ]