Showing metabocard for L-Allysine (MMDBc0033099)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2021-11-19 04:34:44 UTC
Update Date2024-04-20 06:12:49 UTC
Metabolite IDMMDBc0033099
Metabolite Identification
Common NameL-Allysine
Description(S)-2-amino-6-oxohexanoate, also known as allysine or L-2-aminoadipate 6-semialdehyde, 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 (S)-2-amino-6-oxohexanoate is a very strong basic compound (based on its pKa) (S)-2-amino-6-oxohexanoate exists in all living species, ranging from bacteria to humans. Outside of the human body, (S)-2-amino-6-oxohexanoate has been detected, but not quantified in, several different foods, such as winged beans, wasabis, common verbena, arrowhead, and oats. This could make (S)-2-amino-6-oxohexanoate a potential biomarker for the consumption of these foods. An optically active form of (S)-2-amino-6-oxohexanoate having L-configuration.
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007fe2af7e0bc8>


  Mrv1652306222023452D          

 11 10  0  0  1  0            999 V2000
    3.1895    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7605    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    1.8414    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.3329    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    2.6664    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.0461    1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0474    1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    1.0164    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  3  1  0  0  0  0
  6  5  1  0  0  0  0
  5  7  1  1  0  0  0
  8  4  2  0  0  0  0
  9  6  2  0  0  0  0
 10  6  1  0  0  0  0
  5 11  1  1  0  0  0
M  END
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3D MOL for #<Metabolite:0x00007fe2af7e0bc8>

HMDB0001263
     RDKit          3D
Allysine
 21 20  0  0  0  0  0  0  0  0999 V2000
    1.0379   -1.2244   -1.0501 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.8705    0.0339   -0.3542 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.2721   -0.2858    0.9977 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0522   -0.9700    0.7965 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0520   -0.1528    0.0476 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3876    1.1228    0.7014 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9017    1.4714    1.7416 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1629    0.7077   -0.2759 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1752    0.1630   -0.7772 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3253    1.9416    0.3368 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3889   -1.9217   -0.3376 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7764   -1.0906   -1.7986 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1533    0.7053   -0.8705 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2495    0.5637    1.6795 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9431   -1.0537    1.4835 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4841   -1.3420    1.7449 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8445   -1.8816    0.1757 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9918   -0.7772    0.0002 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7605    0.0200   -1.0011 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1067    1.7662    0.2112 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2259    2.2042    0.7471 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
  5  6  1  0
  6  7  2  0
  2  8  1  0
  8  9  2  0
  8 10  1  0
  1 11  1  0
  1 12  1  0
  2 13  1  6
  3 14  1  0
  3 15  1  0
  4 16  1  0
  4 17  1  0
  5 18  1  0
  5 19  1  0
  6 20  1  0
 10 21  1  0
M  END
Download

3D SDF for #<Metabolite:0x00007fe2af7e0bc8>


  Mrv1652306222023452D          

 11 10  0  0  1  0            999 V2000
    3.1895    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7605    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    1.8414    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.3329    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    2.6664    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.0461    1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0474    1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    1.0164    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  3  1  0  0  0  0
  6  5  1  0  0  0  0
  5  7  1  1  0  0  0
  8  4  2  0  0  0  0
  9  6  2  0  0  0  0
 10  6  1  0  0  0  0
  5 11  1  1  0  0  0
M  END
> <DATABASE_ID>
MMDBc0033099

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C6H11NO3/c7-5(6(9)10)3-1-2-4-8/h4-5H,1-3,7H2,(H,9,10)/t5-/m0/s1

> <INCHI_KEY>
GFXYTQPNNXGICT-YFKPBYRVSA-N

> <FORMULA>
C6H11NO3

> <MOLECULAR_WEIGHT>
145.1564

> <EXACT_MASS>
145.073893223

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
21

> <JCHEM_AVERAGE_POLARIZABILITY>
14.583357065587663

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-2-amino-6-oxohexanoic acid

> <ALOGPS_LOGP>
-2.20

> <JCHEM_LOGP>
-2.9081307009163337

> <ALOGPS_LOGS>
-0.47

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
17.588756721963396

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.249930329891744

> <JCHEM_PKA_STRONGEST_BASIC>
9.326170574223008

> <JCHEM_POLAR_SURFACE_AREA>
80.39000000000001

> <JCHEM_REFRACTIVITY>
34.963300000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.94e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-amino-6-oxo-hexanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for #<Metabolite:0x00007fe2af7e0bc8>

HMDB0001263
     RDKit          3D
Allysine
 21 20  0  0  0  0  0  0  0  0999 V2000
    1.0379   -1.2244   -1.0501 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.8705    0.0339   -0.3542 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.2721   -0.2858    0.9977 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0522   -0.9700    0.7965 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0520   -0.1528    0.0476 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3876    1.1228    0.7014 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9017    1.4714    1.7416 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1629    0.7077   -0.2759 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1752    0.1630   -0.7772 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3253    1.9416    0.3368 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3889   -1.9217   -0.3376 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7764   -1.0906   -1.7986 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1533    0.7053   -0.8705 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2495    0.5637    1.6795 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9431   -1.0537    1.4835 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4841   -1.3420    1.7449 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8445   -1.8816    0.1757 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9918   -0.7772    0.0002 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7605    0.0200   -1.0011 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1067    1.7662    0.2112 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2259    2.2042    0.7471 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
  5  6  1  0
  6  7  2  0
  2  8  1  0
  8  9  2  0
  8 10  1  0
  1 11  1  0
  1 12  1  0
  2 13  1  6
  3 14  1  0
  3 15  1  0
  4 16  1  0
  4 17  1  0
  5 18  1  0
  5 19  1  0
  6 20  1  0
 10 21  1  0
M  END
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PDB for #<Metabolite:0x00007fe2af7e0bc8>

HEADER    PROTEIN                                 22-JUN-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   22-JUN-20         0                                  
HETATM    1  C   UNK     0       5.954   3.437   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.620   2.667   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       7.287   2.667   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       3.286   3.437   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       8.621   3.437   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       9.955   2.667   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0       8.621   4.977   0.000  0.00  0.00           N+0
HETATM    8  O   UNK     0       1.953   2.667   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      11.288   3.437   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       9.955   1.127   0.000  0.00  0.00           O+0
HETATM   11  H   UNK     0       8.621   1.897   0.000  0.00  0.00           H+0
CONECT    1    2    3                                                       
CONECT    2    1    4                                                       
CONECT    3    1    5                                                       
CONECT    4    2    8                                                       
CONECT    5    3    6    7   11                                             
CONECT    6    5    9   10                                                  
CONECT    7    5                                                            
CONECT    8    4                                                            
CONECT    9    6                                                            
CONECT   10    6                                                            
CONECT   11    5                                                            
MASTER        0    0    0    0    0    0    0    0   11    0   20    0
END
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3D PDB for #<Metabolite:0x00007fe2af7e0bc8>

COMPND    HMDB0001263
HETATM    1  N1  UNL     1       1.038  -1.224  -1.050  1.00  0.00           N  
HETATM    2  C1  UNL     1       0.870   0.034  -0.354  1.00  0.00           C  
HETATM    3  C2  UNL     1       0.272  -0.286   0.998  1.00  0.00           C  
HETATM    4  C3  UNL     1      -1.052  -0.970   0.797  1.00  0.00           C  
HETATM    5  C4  UNL     1      -2.052  -0.153   0.048  1.00  0.00           C  
HETATM    6  C5  UNL     1      -2.388   1.123   0.701  1.00  0.00           C  
HETATM    7  O1  UNL     1      -1.902   1.471   1.742  1.00  0.00           O  
HETATM    8  C6  UNL     1       2.163   0.708  -0.276  1.00  0.00           C  
HETATM    9  O2  UNL     1       3.175   0.163  -0.777  1.00  0.00           O  
HETATM   10  O3  UNL     1       2.325   1.942   0.337  1.00  0.00           O  
HETATM   11  H1  UNL     1       1.389  -1.922  -0.338  1.00  0.00           H  
HETATM   12  H2  UNL     1       1.776  -1.091  -1.799  1.00  0.00           H  
HETATM   13  H3  UNL     1       0.153   0.705  -0.871  1.00  0.00           H  
HETATM   14  H4  UNL     1       0.249   0.564   1.680  1.00  0.00           H  
HETATM   15  H5  UNL     1       0.943  -1.054   1.484  1.00  0.00           H  
HETATM   16  H6  UNL     1      -1.484  -1.342   1.745  1.00  0.00           H  
HETATM   17  H7  UNL     1      -0.844  -1.882   0.176  1.00  0.00           H  
HETATM   18  H8  UNL     1      -2.992  -0.777   0.000  1.00  0.00           H  
HETATM   19  H9  UNL     1      -1.761   0.020  -1.001  1.00  0.00           H  
HETATM   20  H10 UNL     1      -3.107   1.766   0.211  1.00  0.00           H  
HETATM   21  H11 UNL     1       3.226   2.204   0.747  1.00  0.00           H  
CONECT    1    2   11   12
CONECT    2    3    8   13
CONECT    3    4   14   15
CONECT    4    5   16   17
CONECT    5    6   18   19
CONECT    6    7    7   20
CONECT    8    9    9   10
CONECT   10   21
END
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SMILES for #<Metabolite:0x00007fe2af7e0bc8>

[H][C@](N)(CCCC=O)C(O)=O
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INCHI for #<Metabolite:0x00007fe2af7e0bc8>

InChI=1S/C6H11NO3/c7-5(6(9)10)3-1-2-4-8/h4-5H,1-3,7H2,(H,9,10)/t5-/m0/s1
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Synonyms
ValueSource
2-AMINO-6-oxo-hexanoIC ACIDChEBI
6-oxo-L-NorleucineChEBI
AllysineChEBI
L-2-Aminoadipate 6-semialdehydeChEBI
L-6-OxonorleucineChEBI
2-Aminoadipate 6-semialdehydeKegg
L-AllysineKegg
2-AMINO-6-oxo-hexanoateGenerator
L-2-Aminoadipic acid 6-semialdehydeGenerator
2-Aminoadipic acid 6-semialdehydeGenerator
(S)-2-Amino-6-oxohexanoic acidGenerator
2-Aminoadipate semialdehydeHMDB
alpha-AASAHMDB
alpha-Aminoadipate semialdehydeHMDB
2-Aminoadipic semialdehydeHMDB
2-Amino-5-formylvaleric acidHMDB
2-Amino-6-oxohexanoateHMDB
6-OxonorleucineHMDB
L-Homoglutamic semialdehydeHMDB
alpha-Aminoadipic acid delta-semialdehydeHMDB
alpha-Aminoadipic delta-semialdehydeHMDB
α-Aminoadipic acid δ-semialdehydeHMDB
α-Aminoadipic δ-semialdehydeHMDB
Molecular FormulaC6H11NO3
Average Mass145.1564
Monoisotopic Mass145.073893223
IUPAC Name(2S)-2-amino-6-oxohexanoic acid
Traditional Name2-amino-6-oxo-hexanoic acid
CAS Registry Number1962-83-0
SMILES
[H][C@](N)(CCCC=O)C(O)=O
InChI Identifier
InChI=1S/C6H11NO3/c7-5(6(9)10)3-1-2-4-8/h4-5H,1-3,7H2,(H,9,10)/t5-/m0/s1
InChI KeyGFXYTQPNNXGICT-YFKPBYRVSA-N