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Showing metabocard for L-2,4-diaminobutyric acid (HMDB0006284)

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IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesenzymes (1) Show 1 proteinXML
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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2007-05-22 21:17:54 UTC
Update Date2021-09-14 15:45:29 UTC
HMDB IDHMDB0006284
Secondary Accession Numbers
  • HMDB06284
Metabolite Identification
Common NameL-2,4-diaminobutyric acid
DescriptionL-2,4-diaminobutyric acid, also known as alpha,gamma-diaminobutyrate or Dbu, belongs to the class of organic compounds known as l-alpha-amino acids. These are alpha amino acids which have the L-configuration of the alpha-carbon atom. L-2,4-diaminobutyric acid has been detected, but not quantified in, several different foods, such as pummelos (Citrus maxima), pepper (c. baccatum), celeriacs (Apium graveolens var. rapaceum), pineapples (Ananas comosus), and pot marjorams (Origanum onites). This could make L-2,4-diaminobutyric acid a potential biomarker for the consumption of these foods. L-2,4-diaminobutyric acid is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. Based on a literature review a significant number of articles have been published on L-2,4-diaminobutyric acid.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0006284 (L-2,4-diaminobutyric acid)

  Mrv0541 02231217122D          

  8  7  0  0  1  0            999 V2000
   -0.1914    0.7145    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    1.1270    0.0000 C   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
    1.9520    1.1270    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.9520    1.9520    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3809    1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664   -0.1105    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
  4  5  1  6  0  0  0
  4  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 HMDB0006284 (L-2,4-diaminobutyric acid)

HMDB0006284
     RDKit          3D
L-2,4-diaminobutyric acid
 18 17  0  0  0  0  0  0  0  0999 V2000
   -2.8693   -0.0483   -0.0415 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5653   -0.6163   -0.0272 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5773    0.3998    0.4390 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8352   -0.0633    0.5023 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.6467    1.0425    0.9705 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4012   -0.5951   -0.7130 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9556   -1.5576   -1.3907 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5561   -0.0202   -1.2285 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9384    0.9541   -0.1772 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5974   -0.5341    0.4609 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3666   -1.0007   -1.0447 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5605   -1.4671    0.6850 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6469    1.3333   -0.1695 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8758    0.7007    1.4700 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9126   -0.8452    1.3155 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5435    1.8542    0.2975 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6615    0.7780    1.0752 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4851   -0.3147   -0.9279 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  1  0
  4  6  1  0
  6  7  2  0
  6  8  1  0
  1  9  1  0
  1 10  1  0
  2 11  1  0
  2 12  1  0
  3 13  1  0
  3 14  1  0
  4 15  1  1
  5 16  1  0
  5 17  1  0
  8 18  1  0
M  END
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3D SDF for HMDB0006284 (L-2,4-diaminobutyric acid)

  Mrv0541 02231217122D          

  8  7  0  0  1  0            999 V2000
   -0.1914    0.7145    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    1.1270    0.0000 C   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
    1.9520    1.1270    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.9520    1.9520    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3809    1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664   -0.1105    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
  4  5  1  6  0  0  0
  4  6  1  0  0  0  0
  6  7  1  0  0  0  0
  6  8  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0006284

> <DATABASE_NAME>
hmdb

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

> <INCHI_IDENTIFIER>
InChI=1S/C4H10N2O2/c5-2-1-3(6)4(7)8/h3H,1-2,5-6H2,(H,7,8)/t3-/m0/s1

> <INCHI_KEY>
OGNSCSPNOLGXSM-VKHMYHEASA-N

> <FORMULA>
C4H10N2O2

> <MOLECULAR_WEIGHT>
118.1344

> <EXACT_MASS>
118.074227574

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
11.890036673420415

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-2,4-diaminobutanoic acid

> <ALOGPS_LOGP>
-3.66

> <JCHEM_LOGP>
-4.025544175769902

> <ALOGPS_LOGS>
0.36

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.5466043382409564

> <JCHEM_PKA_STRONGEST_BASIC>
10.25230176518907

> <JCHEM_POLAR_SURFACE_AREA>
89.34

> <JCHEM_REFRACTIVITY>
28.563900000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.70e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2,4-diaminobutyric acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0006284 (L-2,4-diaminobutyric acid)

HMDB0006284
     RDKit          3D
L-2,4-diaminobutyric acid
 18 17  0  0  0  0  0  0  0  0999 V2000
   -2.8693   -0.0483   -0.0415 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5653   -0.6163   -0.0272 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5773    0.3998    0.4390 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8352   -0.0633    0.5023 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.6467    1.0425    0.9705 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4012   -0.5951   -0.7130 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9556   -1.5576   -1.3907 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5561   -0.0202   -1.2285 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9384    0.9541   -0.1772 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5974   -0.5341    0.4609 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3666   -1.0007   -1.0447 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5605   -1.4671    0.6850 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6469    1.3333   -0.1695 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8758    0.7007    1.4700 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9126   -0.8452    1.3155 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5435    1.8542    0.2975 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6615    0.7780    1.0752 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4851   -0.3147   -0.9279 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  1  0
  4  6  1  0
  6  7  2  0
  6  8  1  0
  1  9  1  0
  1 10  1  0
  2 11  1  0
  2 12  1  0
  3 13  1  0
  3 14  1  0
  4 15  1  1
  5 16  1  0
  5 17  1  0
  8 18  1  0
M  END
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PDB for HMDB0006284 (L-2,4-diaminobutyric 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      -0.357   1.334   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0       0.976   2.104   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.310   1.334   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       3.644   2.104   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0       3.644   3.644   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0       4.977   1.334   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       6.311   2.104   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       4.977  -0.206   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    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 HMDB0006284 (L-2,4-diaminobutyric acid)

COMPND    HMDB0006284
HETATM    1  N1  UNL     1      -2.869  -0.048  -0.041  1.00  0.00           N  
HETATM    2  C1  UNL     1      -1.565  -0.616  -0.027  1.00  0.00           C  
HETATM    3  C2  UNL     1      -0.577   0.400   0.439  1.00  0.00           C  
HETATM    4  C3  UNL     1       0.835  -0.063   0.502  1.00  0.00           C  
HETATM    5  N2  UNL     1       1.647   1.042   0.971  1.00  0.00           N  
HETATM    6  C4  UNL     1       1.401  -0.595  -0.713  1.00  0.00           C  
HETATM    7  O1  UNL     1       0.956  -1.558  -1.391  1.00  0.00           O  
HETATM    8  O2  UNL     1       2.556  -0.020  -1.228  1.00  0.00           O  
HETATM    9  H1  UNL     1      -2.938   0.954  -0.177  1.00  0.00           H  
HETATM   10  H2  UNL     1      -3.597  -0.534   0.461  1.00  0.00           H  
HETATM   11  H3  UNL     1      -1.367  -1.001  -1.045  1.00  0.00           H  
HETATM   12  H4  UNL     1      -1.560  -1.467   0.685  1.00  0.00           H  
HETATM   13  H5  UNL     1      -0.647   1.333  -0.170  1.00  0.00           H  
HETATM   14  H6  UNL     1      -0.876   0.701   1.470  1.00  0.00           H  
HETATM   15  H7  UNL     1       0.913  -0.845   1.315  1.00  0.00           H  
HETATM   16  H8  UNL     1       1.543   1.854   0.297  1.00  0.00           H  
HETATM   17  H9  UNL     1       2.661   0.778   1.075  1.00  0.00           H  
HETATM   18  H10 UNL     1       3.485  -0.315  -0.928  1.00  0.00           H  
CONECT    1    2    9   10
CONECT    2    3   11   12
CONECT    3    4   13   14
CONECT    4    5    6   15
CONECT    5   16   17
CONECT    6    7    7    8
CONECT    8   18
END
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SMILES for HMDB0006284 (L-2,4-diaminobutyric acid)

NCC[C@H](N)C(O)=O
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INCHI for HMDB0006284 (L-2,4-diaminobutyric acid)

InChI=1S/C4H10N2O2/c5-2-1-3(6)4(7)8/h3H,1-2,5-6H2,(H,7,8)/t3-/m0/s1
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
Chemical FormulaC4H10N2O2
Average Molecular Weight118.1344
Monoisotopic Molecular Weight118.074227574
IUPAC Name(2S)-2,4-diaminobutanoic acid
Traditional Name2,4-diaminobutyric acid
CAS Registry Number1758-80-1
SMILES
NCC[C@H](N)C(O)=O
InChI Identifier
InChI=1S/C4H10N2O2/c5-2-1-3(6)4(7)8/h3H,1-2,5-6H2,(H,7,8)/t3-/m0/s1
InChI KeyOGNSCSPNOLGXSM-VKHMYHEASA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as l-alpha-amino acids. These are alpha amino acids which have the L-configuration of the alpha-carbon atom.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassAmino acids, peptides, and analogues
Direct ParentL-alpha-amino acids
Alternative Parents
Substituents
  • L-alpha-amino acid
  • Amino fatty acid
  • Fatty acid
  • Fatty acyl
  • Amino acid
  • Carboxylic acid
  • Monocarboxylic acid or derivatives
  • Amine
  • Hydrocarbon derivative
  • Organic oxide
  • Primary amine
  • Organooxygen compound
  • Organonitrogen compound
  • Organopnictogen compound
  • Primary aliphatic amine
  • Organic oxygen compound
  • Carbonyl group
  • Organic nitrogen compound
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Source
ProcessNot Available
RoleNot Available
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
  • Mitochondria
Biospecimen Locations
  • Blood
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified116.35 +/- 10.0 uMAdult (>18 years old)BothAlzheimer's disease details
UrineDetected and Quantified36.0 +/- 5.0 umol/mmol creatinineAdult (>18 years old)BothAlzheimer's disease details
Associated Disorders and Diseases
Disease References
Alzheimer's disease
  1. Fonteh AN, Harrington RJ, Tsai A, Liao P, Harrington MG: Free amino acid and dipeptide changes in the body fluids from Alzheimer's disease subjects. Amino Acids. 2007 Feb;32(2):213-24. Epub 2006 Oct 10. [PubMed:17031479 ]
Associated OMIM IDs
DrugBank IDDB03817
Phenol Explorer Compound IDNot Available
FooDB IDFDB012588
KNApSAcK IDC00001353
Chemspider ID118548
KEGG Compound IDC03283
BioCyc IDCPD-470
BiGG ID41559
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound134490
PDB IDDAB
ChEBI ID48950
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available

Enzymes

Enzyme Details
1. 4-aminobutyrate aminotransferase, mitochondrial
General function:
Involved in 4-aminobutyrate transaminase activity
Specific function:
Catalyzes the conversion of gamma-aminobutyrate and L-beta-aminoisobutyrate to succinate semialdehyde and methylmalonate semialdehyde, respectively. Can also convert delta-aminovalerate and beta-alanine.
Gene Name:
ABAT
Uniprot ID:
P80404
Molecular weight:
56438.405