Showing metabocard for L-Allysine (MMDBc0033099)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2021-11-19 04:34:44 UTC
Update Date2025-01-15 19:03:30 UTC
Metabolite IDMMDBc0033099
Metabolite Identification
Common NameL-Allysine
DescriptionAllysine (CAS: 1962-83-0), also known as 2-amino-6-oxohexanoic acid or 6-oxonorleucine, belongs to the class of organic compounds known as alpha-amino acids. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon). Outside of the human body, allysine has been detected, but not quantified in, several different foods, such as winged beans, wasabi, common verbena, arrowhead, and oats. This could make allysine a potential biomarker for the consumption of these foods. Allysine is a derivative of lysine used in the production of elastin and collagen. It is produced by the actions of the enzyme lysyl oxidase in the extracellular matrix and is essential in the crosslink formation that stabilizes collagen and elastin.
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007f3e00526620>


  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:0x00007f3e00526620>

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:0x00007f3e00526620>


  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:0x00007f3e00526620>

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:0x00007f3e00526620>

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:0x00007f3e00526620>

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:0x00007f3e00526620>

[H][C@](N)(CCCC=O)C(O)=O
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INCHI for #<Metabolite:0x00007f3e00526620>

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