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Showing metabocard for D-alpha-Aminobutyric acid (HMDB0000650)

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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2022-03-07 02:49:05 UTC
HMDB IDHMDB0000650
Secondary Accession Numbers
  • HMDB00650
Metabolite 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
Data?1582752147
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0000650 (D-alpha-Aminobutyric acid)

  Mrv1652305271900072D          

  7  6  0  0  0  0            999 V2000
 9998.9586 9998.7576    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
 9998.2439 9999.1697    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9997.5292 9998.7576    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9998.2439 9999.9944    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9999.6740 9999.1697    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.3874 9998.7576    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.9586 9997.9323    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  5  1  0  0  0  0
  1  7  1  1  0  0  0
  2  3  1  0  0  0  0
  2  4  2  0  0  0  0
  5  6  1  0  0  0  0
M  END
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3D MOL for HMDB0000650 (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 HMDB0000650 (D-alpha-Aminobutyric acid)

  Mrv1652305271900072D          

  7  6  0  0  0  0            999 V2000
 9998.9586 9998.7576    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
 9998.2439 9999.1697    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9997.5292 9998.7576    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9998.2439 9999.9944    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9999.6740 9999.1697    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.3874 9998.7576    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.9586 9997.9323    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  5  1  0  0  0  0
  1  7  1  1  0  0  0
  2  3  1  0  0  0  0
  2  4  2  0  0  0  0
  5  6  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0000650

> <DATABASE_NAME>
hmdb

> <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

$$$$
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3D-SDF for HMDB0000650 (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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PDB for HMDB0000650 (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 HMDB0000650 (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 HMDB0000650 (D-alpha-Aminobutyric acid)

CC[C@@H](N)C(O)=O
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INCHI for HMDB0000650 (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 JSmolView NMR AssignmentsView Stereo Labels
Synonyms
Chemical FormulaC4H9NO2
Average Molecular Weight103.1198
Monoisotopic Molecular Weight103.063328537
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
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
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
ProcessNot Available
RoleNot Available
Physical Properties
StateSolid
Experimental Molecular 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
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm (predicted from logP)
Biospecimen Locations
  • Blood
  • Feces
  • Saliva
  • Urine
Tissue Locations
  • Placenta
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot QuantifiedNot AvailableNot Available
Normal
      Not Available
 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)FemaleNormal details
SalivaDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothNormal details
UrineDetected and Quantified0.30 umol/mmol creatinineAdult (>18 years old)BothNormal details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothColorectal Cancer details
SalivaDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothOral cancer details
SalivaDetected but not QuantifiedNot QuantifiedAdult (>18 years old)FemaleBreast cancer details
SalivaDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Not SpecifiedPancreatic cancer details
SalivaDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Not SpecifiedPeriodontal diseases details
Associated Disorders and Diseases
Disease References
Colorectal cancer
  1. Brown DG, Rao S, Weir TL, O'Malia J, Bazan M, Brown RJ, Ryan EP: Metabolomics and metabolic pathway networks from human colorectal cancers, adjacent mucosa, and stool. Cancer Metab. 2016 Jun 6;4:11. doi: 10.1186/s40170-016-0151-y. eCollection 2016. [PubMed:27275383 ]
Perillyl alcohol administration for cancer treatment
  1. Sugimoto M, Wong DT, Hirayama A, Soga T, Tomita M: Capillary electrophoresis mass spectrometry-based saliva metabolomics identified oral, breast and pancreatic cancer-specific profiles. Metabolomics. 2010 Mar;6(1):78-95. Epub 2009 Sep 10. [PubMed:20300169 ]
Pancreatic cancer
  1. Sugimoto M, Wong DT, Hirayama A, Soga T, Tomita M: Capillary electrophoresis mass spectrometry-based saliva metabolomics identified oral, breast and pancreatic cancer-specific profiles. Metabolomics. 2010 Mar;6(1):78-95. Epub 2009 Sep 10. [PubMed:20300169 ]
Periodontal disease
  1. Sugimoto M, Wong DT, Hirayama A, Soga T, Tomita M: Capillary electrophoresis mass spectrometry-based saliva metabolomics identified oral, breast and pancreatic cancer-specific profiles. Metabolomics. 2010 Mar;6(1):78-95. Epub 2009 Sep 10. [PubMed:20300169 ]
Associated OMIM IDs
DrugBank IDDB04454
Phenol Explorer Compound IDNot Available
FooDB 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
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1140351
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Download (PDF)
General References
  1. Ohdoi C, Nyhan WL, Kuhara T: Chemical diagnosis of Lesch-Nyhan syndrome using gas chromatography-mass spectrometry detection. J Chromatogr B Analyt Technol Biomed Life Sci. 2003 Jul 15;792(1):123-30. [PubMed:12829005 ]
  2. Ketting D, Wadman SK, Spaapen LJ, Van der Meer SB, Duran M: Gas chromatography method for the separation of amino acids enantiomers in plasma and urine. Application in a case of short bowel syndrome. Clin Chim Acta. 1991 Dec 31;204(1-3):79-86. [PubMed:1819475 ]
  3. 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 ]
  4. Elshenawy S, Pinney SE, Stuart T, Doulias PT, Zura G, Parry S, Elovitz MA, Bennett MJ, Bansal A, Strauss JF 3rd, Ischiropoulos H, Simmons RA: The Metabolomic Signature of the Placenta in Spontaneous Preterm Birth. Int J Mol Sci. 2020 Feb 4;21(3). pii: ijms21031043. doi: 10.3390/ijms21031043. [PubMed:32033212 ]