Showing metabocard for L-2,4-diaminobutanoic acid (MMDBc0054529)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2022-06-05 23:16:48 UTC
Update Date2022-08-27 02:16:37 UTC
Metabolite IDMMDBc0054529
Metabolite Identification
Common NameL-2,4-diaminobutanoic 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
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007f124123f398>


  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 #<Metabolite:0x00007f124123f398>

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 #<Metabolite:0x00007f124123f398>


  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>
MMDBc0054529

> <DATABASE_NAME>
MIME

> <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 #<Metabolite:0x00007f124123f398>

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 #<Metabolite:0x00007f124123f398>

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 #<Metabolite:0x00007f124123f398>

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 #<Metabolite:0x00007f124123f398>

NCC[C@H](N)C(O)=O
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INCHI for #<Metabolite:0x00007f124123f398>

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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Synonyms
ValueSource
(S)-2,4-Diaminobutanoic acidChEBI
alpha,gamma-DiaminobutyrateChEBI
DbuChEBI
L-2,4-DiaminobutanoateChEBI
L-2,4-Diaminobutanoic acidChEBI
L-2,4-DiaminobutyrateChEBI
L-DbuChEBI
L-Diaminobutyric acidChEBI
(S)-2,4-DiaminobutanoateGenerator
a,g-DiaminobutyrateGenerator
a,g-Diaminobutyric acidGenerator
alpha,gamma-Diaminobutyric acidGenerator
Α,γ-diaminobutyrateGenerator
Α,γ-diaminobutyric acidGenerator
L-DiaminobutyrateGenerator
(S)-2,4-diamino-ButanoateHMDB
(S)-2,4-diamino-Butanoic acidHMDB
(S)-2,4-Diaminobutyric acidHMDB
L-2,4-diamino-Butyric acidHMDB
L-2,4-diamino-N-Butyric acidHMDB
L-alpha,gamma-Diaminobutyric acidHMDB
L-DABAHMDB
2,4-Diaminobutyric acid dihydrochloride, (+-)-isomerMeSH, HMDB
2,4-Diaminobutyric acid monohydrochloride, (+-)-isomerMeSH, HMDB
2,4-Diaminobutyric acid, (+)-isomerMeSH, HMDB
2,4-Diaminobutyric acid, (+-)-isomerMeSH, HMDB
2,4-Diaminobutyric acid, (R)-isomerMeSH, HMDB
2,4-Diaminobutyric acid, (S)-isomerMeSH, HMDB
2,4-Diaminobutyric acid dihydrochloride, (S)-isomerMeSH, HMDB
2,4-Diaminobutyric acidMeSH, HMDB
2,4-Diaminobutyric acid monohydrochloride, (S)-isomerMeSH, HMDB
Molecular FormulaC4H10N2O2
Average Mass118.1344
Monoisotopic Mass118.074227574
IUPAC Name(2S)-2,4-diaminobutanoic acid
Traditional Name2,4-diaminobutyric acid
CAS Registry NumberNot Available
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