MiMeDB: Showing metabocard for N6-Carboxymethyllysine (MMDBc0000750)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2020-12-10 18:54:10 UTC

Update Date

2024-04-30 19:33:37 UTC

Metabolite ID

MMDBc0000750

Metabolite Identification

Common Name

N6-Carboxymethyllysine

Description

N6-Carboxymethyllysine (CML), also known as epsilon-(carboxymethyl)lysine, 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. CML is a Maillard reaction product, or dietary advanced glycation end-products (d-AGE), formed as a result of the thermal treatment of foods. Due to its chemical stability and its ubiquity in foods and in vivo, CML is used as a biomarker for the ingestion of thermally treated foods. CML is metabolized by intestinal bacteria under anaerobic conditions (PMID: 31091091 ).

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI

HMDB0240347
     RDKit          3D
N6-Carboxymethyllysine
 30 29  0  0  0  0  0  0  0  0999 V2000
   -2.0689    1.4026    0.3393 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5920    0.3532   -0.5244 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.6231   -0.7081   -0.7301 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0737   -1.3321    0.4420 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4331   -1.5850    0.3220 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0879   -0.1918    0.4029 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4941   -0.2874    0.5560 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.3463    0.3144   -0.4005 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1467    1.4746    0.0405 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9287    2.6316   -0.1392 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3196    1.1630    0.7463 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9930   -0.0321   -0.1754 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2032   -1.1852    0.2582 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0499    0.8101   -0.3704 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2072    1.1304    1.3729 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6137    2.2548    0.2162 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7118    0.8846   -1.5031 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9203   -0.5057   -1.5249 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3034   -1.5683   -1.2051 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1270   -0.6092    1.3370 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5015   -2.2694    0.7695 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8307   -2.3199    0.9335 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5499   -1.9184   -0.8114 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6629    0.2963    1.2795 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8980    0.3961   -0.5037 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8534   -1.2864    0.7851 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8775   -0.3465   -1.0465 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5534    0.8319   -1.1243 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9354    0.4016    0.5240 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9286    1.8002   -0.2265 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  1  0
  7  8  1  0
  8  9  1  0
  9 10  2  0
  9 11  1  0
  2 12  1  0
 12 13  2  0
 12 14  1  0
  1 15  1  0
  1 16  1  0
  2 17  1  6
  3 18  1  0
  3 19  1  0
  4 20  1  0
  4 21  1  0
  5 22  1  0
  5 23  1  0
  6 24  1  0
  6 25  1  0
  7 26  1  0
  8 27  1  0
  8 28  1  0
 11 29  1  0
 14 30  1  0
M  END


  Mrv1652311141919422D          

 14 13  0  0  0  0            999 V2000
 9988.5629 9987.3135    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9989.2765 9986.9015    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
 9989.9921 9987.3135    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9990.7076 9986.9015    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9989.9921 9988.1384    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9989.2765 9986.0760    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 9987.8453 9986.9015    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9987.1307 9987.3135    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9986.4160 9986.9015    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9985.7013 9987.3135    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 9984.9863 9986.9015    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9984.2715 9987.3135    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9983.5568 9986.9015    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9984.2715 9988.1384    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  7  1  0  0  0  0
  2  3  1  0  0  0  0
  2  6  1  1  0  0  0
  3  4  1  0  0  0  0
  3  5  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 12 14  2  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0000750

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C8H16N2O4/c9-6(8(13)14)3-1-2-4-10-5-7(11)12/h6,10H,1-5,9H2,(H,11,12)(H,13,14)/t6-/m0/s1

> <INCHI_KEY>
NUXSIDPKKIEIMI-LURJTMIESA-N

> <FORMULA>
C8H16N2O4

> <MOLECULAR_WEIGHT>
204.226

> <EXACT_MASS>
204.111007003

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
30

> <JCHEM_AVERAGE_POLARIZABILITY>
21.14567704336736

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-2-amino-6-[(carboxymethyl)amino]hexanoic acid

> <ALOGPS_LOGP>
-2.98

> <JCHEM_LOGP>
-5.533776904144873

> <ALOGPS_LOGS>
-1.24

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
2.5068697826883692

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.6051481211176402

> <JCHEM_PKA_STRONGEST_BASIC>
10.597717437593165

> <JCHEM_POLAR_SURFACE_AREA>
112.65

> <JCHEM_REFRACTIVITY>
48.668699999999994

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.18e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
N(6)-carboxymethyllysine

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0240347
     RDKit          3D
N6-Carboxymethyllysine
 30 29  0  0  0  0  0  0  0  0999 V2000
   -2.0689    1.4026    0.3393 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5920    0.3532   -0.5244 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.6231   -0.7081   -0.7301 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0737   -1.3321    0.4420 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4331   -1.5850    0.3220 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0879   -0.1918    0.4029 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4941   -0.2874    0.5560 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.3463    0.3144   -0.4005 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1467    1.4746    0.0405 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9287    2.6316   -0.1392 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3196    1.1630    0.7463 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9930   -0.0321   -0.1754 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2032   -1.1852    0.2582 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0499    0.8101   -0.3704 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2072    1.1304    1.3729 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6137    2.2548    0.2162 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7118    0.8846   -1.5031 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9203   -0.5057   -1.5249 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3034   -1.5683   -1.2051 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1270   -0.6092    1.3370 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5015   -2.2694    0.7695 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8307   -2.3199    0.9335 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5499   -1.9184   -0.8114 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6629    0.2963    1.2795 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8980    0.3961   -0.5037 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8534   -1.2864    0.7851 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8775   -0.3465   -1.0465 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5534    0.8319   -1.1243 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9354    0.4016    0.5240 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9286    1.8002   -0.2265 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  1  0
  7  8  1  0
  8  9  1  0
  9 10  2  0
  9 11  1  0
  2 12  1  0
 12 13  2  0
 12 14  1  0
  1 15  1  0
  1 16  1  0
  2 17  1  6
  3 18  1  0
  3 19  1  0
  4 20  1  0
  4 21  1  0
  5 22  1  0
  5 23  1  0
  6 24  1  0
  6 25  1  0
  7 26  1  0
  8 27  1  0
  8 28  1  0
 11 29  1  0
 14 30  1  0
M  END

HEADER    PROTEIN                                 14-NOV-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   14-NOV-19         0                                  
HETATM    1  C   UNK     0    8645.3178642.985   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0    8646.6498642.216   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0    8647.9858642.985   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0    8649.3218642.216   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0    8647.9858644.525   0.000  0.00  0.00           O+0
HETATM    6  N   UNK     0    8646.6498640.675   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0    8643.9788642.216   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0    8642.6448642.985   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0    8641.3108642.216   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0    8639.9768642.985   0.000  0.00  0.00           N+0
HETATM   11  C   UNK     0    8638.6418642.216   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0    8637.3078642.985   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0    8635.9738642.216   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0    8637.3078644.525   0.000  0.00  0.00           O+0
CONECT    1    2    7                                                       
CONECT    2    1    3    6                                                  
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3                                                            
CONECT    6    2                                                            
CONECT    7    1    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12                                                            
MASTER        0    0    0    0    0    0    0    0   14    0   26    0
END

COMPND    HMDB0240347
HETATM    1  N1  UNL     1      -2.069   1.403   0.339  1.00  0.00           N  
HETATM    2  C1  UNL     1      -2.592   0.353  -0.524  1.00  0.00           C  
HETATM    3  C2  UNL     1      -1.623  -0.708  -0.730  1.00  0.00           C  
HETATM    4  C3  UNL     1      -1.074  -1.332   0.442  1.00  0.00           C  
HETATM    5  C4  UNL     1       0.433  -1.585   0.322  1.00  0.00           C  
HETATM    6  C5  UNL     1       1.088  -0.192   0.403  1.00  0.00           C  
HETATM    7  N2  UNL     1       2.494  -0.287   0.556  1.00  0.00           N  
HETATM    8  C6  UNL     1       3.346   0.314  -0.400  1.00  0.00           C  
HETATM    9  C7  UNL     1       4.147   1.475   0.040  1.00  0.00           C  
HETATM   10  O1  UNL     1       3.929   2.632  -0.139  1.00  0.00           O  
HETATM   11  O2  UNL     1       5.320   1.163   0.746  1.00  0.00           O  
HETATM   12  C8  UNL     1      -3.993  -0.032  -0.175  1.00  0.00           C  
HETATM   13  O3  UNL     1      -4.203  -1.185   0.258  1.00  0.00           O  
HETATM   14  O4  UNL     1      -5.050   0.810  -0.370  1.00  0.00           O  
HETATM   15  H1  UNL     1      -2.207   1.130   1.373  1.00  0.00           H  
HETATM   16  H2  UNL     1      -2.614   2.255   0.216  1.00  0.00           H  
HETATM   17  H3  UNL     1      -2.712   0.885  -1.503  1.00  0.00           H  
HETATM   18  H4  UNL     1      -0.920  -0.506  -1.525  1.00  0.00           H  
HETATM   19  H5  UNL     1      -2.303  -1.568  -1.205  1.00  0.00           H  
HETATM   20  H6  UNL     1      -1.127  -0.609   1.337  1.00  0.00           H  
HETATM   21  H7  UNL     1      -1.502  -2.269   0.770  1.00  0.00           H  
HETATM   22  H8  UNL     1       0.831  -2.320   0.933  1.00  0.00           H  
HETATM   23  H9  UNL     1       0.550  -1.918  -0.811  1.00  0.00           H  
HETATM   24  H10 UNL     1       0.663   0.296   1.280  1.00  0.00           H  
HETATM   25  H11 UNL     1       0.898   0.396  -0.504  1.00  0.00           H  
HETATM   26  H12 UNL     1       2.853  -1.286   0.785  1.00  0.00           H  
HETATM   27  H13 UNL     1       3.877  -0.347  -1.046  1.00  0.00           H  
HETATM   28  H14 UNL     1       2.553   0.832  -1.124  1.00  0.00           H  
HETATM   29  H15 UNL     1       5.935   0.402   0.524  1.00  0.00           H  
HETATM   30  H16 UNL     1      -4.929   1.800  -0.227  1.00  0.00           H  
CONECT    1    2   15   16
CONECT    2    3   12   17
CONECT    3    4   18   19
CONECT    4    5   20   21
CONECT    5    6   22   23
CONECT    6    7   24   25
CONECT    7    8   26
CONECT    8    9   27   28
CONECT    9   10   10   11
CONECT   11   29
CONECT   12   13   13   14
CONECT   14   30
END

HMDB0240347
     RDKit          3D
N6-Carboxymethyllysine
 30 29  0  0  0  0  0  0  0  0999 V2000
   -2.0689    1.4026    0.3393 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5920    0.3532   -0.5244 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.6231   -0.7081   -0.7301 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0737   -1.3321    0.4420 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4331   -1.5850    0.3220 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0879   -0.1918    0.4029 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4941   -0.2874    0.5560 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.3463    0.3144   -0.4005 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1467    1.4746    0.0405 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9287    2.6316   -0.1392 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3196    1.1630    0.7463 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9930   -0.0321   -0.1754 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2032   -1.1852    0.2582 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0499    0.8101   -0.3704 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2072    1.1304    1.3729 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6137    2.2548    0.2162 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7118    0.8846   -1.5031 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9203   -0.5057   -1.5249 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3034   -1.5683   -1.2051 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1270   -0.6092    1.3370 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5015   -2.2694    0.7695 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8307   -2.3199    0.9335 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5499   -1.9184   -0.8114 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6629    0.2963    1.2795 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8980    0.3961   -0.5037 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8534   -1.2864    0.7851 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8775   -0.3465   -1.0465 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5534    0.8319   -1.1243 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9354    0.4016    0.5240 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9286    1.8002   -0.2265 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  1  0
  7  8  1  0
  8  9  1  0
  9 10  2  0
  9 11  1  0
  2 12  1  0
 12 13  2  0
 12 14  1  0
  1 15  1  0
  1 16  1  0
  2 17  1  6
  3 18  1  0
  3 19  1  0
  4 20  1  0
  4 21  1  0
  5 22  1  0
  5 23  1  0
  6 24  1  0
  6 25  1  0
  7 26  1  0
  8 27  1  0
  8 28  1  0
 11 29  1  0
 14 30  1  0
M  END

Synonyms

Value	Source
N(6)-Carboxymethyllysine	ChEBI
N(epsilon)-(Carboxymethyl)lysine	ChEBI
NECML	ChEBI
N(epsilon)-Carboxymethyl-L-lysine	ChEBI
N(epsilon)-Carboxymethyllysine	HMDB
Carboxymethyllysine	HMDB
Carboxymethyl-lysine	HMDB
(2S)-2-Amino-6-(carboxymethylamino)hexanoic acid	HMDB
N6-(Carboxymethyl)-L-lysine	HMDB
N6-(Carboxymethyl)lysine	HMDB
Nepsilon-(carboxymethyl)lysine	HMDB
Nε-(carboxymethyl)lysine	HMDB
epsilon-(Carboxymethyl)lysine	HMDB
Ε-(carboxymethyl)lysine	HMDB
CML	HMDB
N-epsilon-Carboxymethyllysine	HMDB
N-Ε-carboxymethyllysine	HMDB
N6-Carboxymethyllysine	HMDB

Molecular Formula

C₈H₁₆N₂O₄

Average Mass

204.226

Monoisotopic Mass

204.111007003

IUPAC Name

(2S)-2-amino-6-[(carboxymethyl)amino]hexanoic acid

Traditional Name

N(6)-carboxymethyllysine

CAS Registry Number

Not Available

SMILES

N[C@@H](CCCCNCC(O)=O)C(O)=O

InChI Identifier

InChI=1S/C8H16N2O4/c9-6(8(13)14)3-1-2-4-10-5-7(11)12/h6,10H,1-5,9H2,(H,11,12)(H,13,14)/t6-/m0/s1

InChI Key

NUXSIDPKKIEIMI-LURJTMIESA-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.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

L-alpha-amino acids

Alternative Parents

Substituents

L-alpha-amino acid
Medium-chain fatty acid
Amino fatty acid
Dicarboxylic acid or derivatives
Fatty acid
Fatty acyl
Amino acid
Carboxylic acid
Secondary aliphatic amine
Secondary amine
Organic nitrogen compound
Primary amine
Organooxygen compound
Organonitrogen compound
Primary aliphatic amine
Organic oxygen compound
Amine
Carbonyl group
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

non-proteinogenic L-alpha-amino acid (CHEBI:53014 )
L-lysine derivative (CHEBI:53014 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	11.8 g/L	ALOGPS
logP	-3	ALOGPS
logP	-5.5	ChemAxon
logS	-1.2	ALOGPS
pKa (Strongest Acidic)	1.61	ChemAxon
pKa (Strongest Basic)	10.6	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	112.65 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	48.67 m³·mol⁻¹	ChemAxon
Polarizability	21.15 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0a5i-2960000000-c1f9dc0a5b88f61b10a4	2021-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-001i-9400000000-20449fa8c1f46d91fd42	2021-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0ac0-9000000000-69659eefcdd0c58f02c5	2021-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0udi-0090000000-2cc3f54c600fdcda0c9d	2021-09-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0udi-0970000000-beb54ba3fb5157275eb8	2021-09-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-060c-9000000000-b14887973901def789e6	2021-09-23	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-09-25	View Spectrum

Chromatographic Retention Times and Retention Indices

Retention Times

Chromatography Type	Technique	Column	Deposition Date	Retention Time (s)
Liquid Chromatography	HILIC	Waters Acquity UPLC-BEH Amide column (eluted)	2025-10-23	563.7
Liquid Chromatography	HILIC	Accucore 150 Amide HILIC (eluted)	2025-10-23	473.9
Liquid Chromatography	Reversed-phase	Hypersil Gold 1.9 µm C18 (void)	2025-10-23	44.1
Liquid Chromatography	Reversed-phase	Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) (eluted)	2025-10-23	238.9
Liquid Chromatography	Reversed-phase	XBridge C18 3.5u 2.1x50 mm (eluted)	2025-10-23	296.6
Liquid Chromatography	Reversed-phase	Ascentis Express C18 (void)	2025-10-23	268.6
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (void)	2025-10-23	398.7
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-23	970.6
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC (eluted)	2025-10-23	599.7
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-23	156.7
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-23	654.9
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (void)	2025-10-23	166.6
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-23	42.1
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-23	450.1
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-23	1013.9
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (void)	2025-10-23	69.6
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-23	261.2
Liquid Chromatography	Reversed-phase	Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex (eluted)	2025-10-23	628.8
Liquid Chromatography	Reversed-phase	Waters Atlantis T3 (2.1 x 150 mm, 5 um) (eluted)	2025-10-23	592.1

Retention Indices

Chromatography Type	Peak Label	SMILES	Stationary Phase	Deposition Date	Retention Index
Gas Chromatography	N6-Carboxymethyllysine_TMS_1	C[Si](C)(C)OC(=O)CNCCCC[C@H](N)C(=O)O	standard non polar	2025-10-23	1999.09
Gas Chromatography	N6-Carboxymethyllysine_TMS_2	C[Si](C)(C)OC(=O)[C@@H](N)CCCCNCC(=O)O	standard non polar	2025-10-23	1864.57
Gas Chromatography	N6-Carboxymethyllysine_TMS_3	C[Si](C)(C)N[C@@H](CCCCNCC(=O)O)C(=O)O	standard non polar	2025-10-23	2019.99
Gas Chromatography	N6-Carboxymethyllysine_TMS_4	C[Si](C)(C)N(CCCC[C@H](N)C(=O)O)CC(=O)O	standard non polar	2025-10-23	1948.91
Gas Chromatography	N6-Carboxymethyllysine_TMS_5	C[Si](C)(C)OC(=O)CNCCCC[C@H](N)C(=O)O[Si](C)(C)C	standard non polar	2025-10-23	1834.96
Gas Chromatography	N6-Carboxymethyllysine_TMS_6	C[Si](C)(C)N[C@@H](CCCCNCC(=O)O[Si](C)(C)C)C(=O)O	standard non polar	2025-10-23	2354.43
Gas Chromatography	N6-Carboxymethyllysine_TMS_7	C[Si](C)(C)OC(=O)CN(CCCC[C@H](N)C(=O)O)[Si](C)(C)C	standard non polar	2025-10-23	1771.0
Gas Chromatography	N6-Carboxymethyllysine_TMS_8	C[Si](C)(C)N[C@@H](CCCCNCC(=O)O)C(=O)O[Si](C)(C)C	standard non polar	2025-10-23	1919.1
Gas Chromatography	N6-Carboxymethyllysine_TMS_9	C[Si](C)(C)OC(=O)[C@@H](N)CCCCN(CC(=O)O)[Si](C)(C)C	standard non polar	2025-10-23	1579.61
Gas Chromatography	N6-Carboxymethyllysine_TMS_10	C[Si](C)(C)N([C@@H](CCCCNCC(=O)O)C(=O)O)[Si](C)(C)C	standard non polar	2025-10-23	2190.21
Gas Chromatography	N6-Carboxymethyllysine_TMS_11	C[Si](C)(C)N[C@@H](CCCCN(CC(=O)O)[Si](C)(C)C)C(=O)O	standard non polar	2025-10-23	2499.67
Gas Chromatography	N6-Carboxymethyllysine_TMS_12	C[Si](C)(C)N[C@@H](CCCCNCC(=O)O[Si](C)(C)C)C(=O)O[Si](C)(C)C	standard non polar	2025-10-23	1360.42
Gas Chromatography	N6-Carboxymethyllysine_TMS_13	C[Si](C)(C)OC(=O)CN(CCCC[C@H](N)C(=O)O[Si](C)(C)C)[Si](C)(C)C	standard non polar	2025-10-23	1634.01
Gas Chromatography	N6-Carboxymethyllysine_TMS_14	C[Si](C)(C)OC(=O)CNCCCC[C@@H](C(=O)O)N([Si](C)(C)C)[Si](C)(C)C	standard non polar	2025-10-23	1656.39
Gas Chromatography	N6-Carboxymethyllysine_TMS_15	C[Si](C)(C)N[C@@H](CCCCN(CC(=O)O[Si](C)(C)C)[Si](C)(C)C)C(=O)O	standard non polar	2025-10-23	1915.48
Gas Chromatography	N6-Carboxymethyllysine_TMS_16	C[Si](C)(C)OC(=O)[C@H](CCCCNCC(=O)O)N([Si](C)(C)C)[Si](C)(C)C	standard non polar	2025-10-23	1838.67
Gas Chromatography	N6-Carboxymethyllysine_TMS_17	C[Si](C)(C)N[C@@H](CCCCN(CC(=O)O)[Si](C)(C)C)C(=O)O[Si](C)(C)C	standard non polar	2025-10-23	2581.95
Gas Chromatography	N6-Carboxymethyllysine_TMS_18	C[Si](C)(C)N(CCCC[C@@H](C(=O)O)N([Si](C)(C)C)[Si](C)(C)C)CC(=O)O	standard non polar	2025-10-23	1882.71
Gas Chromatography	N6-Carboxymethyllysine_TMS_19	C[Si](C)(C)OC(=O)CNCCCC[C@@H](C(=O)O[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C	standard non polar	2025-10-23	2246.37
Gas Chromatography	N6-Carboxymethyllysine_TMS_20	C[Si](C)(C)N[C@@H](CCCCN(CC(=O)O[Si](C)(C)C)[Si](C)(C)C)C(=O)O[Si](C)(C)C	standard non polar	2025-10-23	2628.89
Gas Chromatography	N6-Carboxymethyllysine_TMS_21	C[Si](C)(C)OC(=O)CN(CCCC[C@@H](C(=O)O)N([Si](C)(C)C)[Si](C)(C)C)[Si](C)(C)C	standard non polar	2025-10-23	2169.16
Gas Chromatography	N6-Carboxymethyllysine_TMS_22	C[Si](C)(C)OC(=O)[C@H](CCCCN(CC(=O)O)[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C	standard non polar	2025-10-23	2293.67
Gas Chromatography	N6-Carboxymethyllysine_TMS_23	C[Si](C)(C)OC(=O)CN(CCCC[C@@H](C(=O)O[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C)[Si](C)(C)C	standard non polar	2025-10-23	1151.27
Gas Chromatography	N6-Carboxymethyllysine_TMS_1	C[Si](C)(C)OC(=O)CNCCCC[C@H](N)C(=O)O	standard polar	2025-10-23	2129.9
Gas Chromatography	N6-Carboxymethyllysine_TMS_2	C[Si](C)(C)OC(=O)[C@@H](N)CCCCNCC(=O)O	standard polar	2025-10-23	2364.52
Gas Chromatography	N6-Carboxymethyllysine_TMS_3	C[Si](C)(C)N[C@@H](CCCCNCC(=O)O)C(=O)O	standard polar	2025-10-23	2031.9
Gas Chromatography	N6-Carboxymethyllysine_TMS_4	C[Si](C)(C)N(CCCC[C@H](N)C(=O)O)CC(=O)O	standard polar	2025-10-23	1414.91
Gas Chromatography	N6-Carboxymethyllysine_TMS_5	C[Si](C)(C)OC(=O)CNCCCC[C@H](N)C(=O)O[Si](C)(C)C	standard polar	2025-10-23	1768.07
Gas Chromatography	N6-Carboxymethyllysine_TMS_6	C[Si](C)(C)N[C@@H](CCCCNCC(=O)O[Si](C)(C)C)C(=O)O	standard polar	2025-10-23	2004.88
Gas Chromatography	N6-Carboxymethyllysine_TMS_7	C[Si](C)(C)OC(=O)CN(CCCC[C@H](N)C(=O)O)[Si](C)(C)C	standard polar	2025-10-23	1510.33
Gas Chromatography	N6-Carboxymethyllysine_TMS_8	C[Si](C)(C)N[C@@H](CCCCNCC(=O)O)C(=O)O[Si](C)(C)C	standard polar	2025-10-23	2098.48
Gas Chromatography	N6-Carboxymethyllysine_TMS_9	C[Si](C)(C)OC(=O)[C@@H](N)CCCCN(CC(=O)O)[Si](C)(C)C	standard polar	2025-10-23	2272.54
Gas Chromatography	N6-Carboxymethyllysine_TMS_10	C[Si](C)(C)N([C@@H](CCCCNCC(=O)O)C(=O)O)[Si](C)(C)C	standard polar	2025-10-23	1345.1
Gas Chromatography	N6-Carboxymethyllysine_TMS_11	C[Si](C)(C)N[C@@H](CCCCN(CC(=O)O)[Si](C)(C)C)C(=O)O	standard polar	2025-10-23	2455.55
Gas Chromatography	N6-Carboxymethyllysine_TMS_12	C[Si](C)(C)N[C@@H](CCCCNCC(=O)O[Si](C)(C)C)C(=O)O[Si](C)(C)C	standard polar	2025-10-23	1921.76
Gas Chromatography	N6-Carboxymethyllysine_TMS_13	C[Si](C)(C)OC(=O)CN(CCCC[C@H](N)C(=O)O[Si](C)(C)C)[Si](C)(C)C	standard polar	2025-10-23	1906.27
Gas Chromatography	N6-Carboxymethyllysine_TMS_14	C[Si](C)(C)OC(=O)CNCCCC[C@@H](C(=O)O)N([Si](C)(C)C)[Si](C)(C)C	standard polar	2025-10-23	2829.83
Gas Chromatography	N6-Carboxymethyllysine_TMS_15	C[Si](C)(C)N[C@@H](CCCCN(CC(=O)O[Si](C)(C)C)[Si](C)(C)C)C(=O)O	standard polar	2025-10-23	2330.25
Gas Chromatography	N6-Carboxymethyllysine_TMS_16	C[Si](C)(C)OC(=O)[C@H](CCCCNCC(=O)O)N([Si](C)(C)C)[Si](C)(C)C	standard polar	2025-10-23	2127.91
Gas Chromatography	N6-Carboxymethyllysine_TMS_17	C[Si](C)(C)N[C@@H](CCCCN(CC(=O)O)[Si](C)(C)C)C(=O)O[Si](C)(C)C	standard polar	2025-10-23	2123.06
Gas Chromatography	N6-Carboxymethyllysine_TMS_18	C[Si](C)(C)N(CCCC[C@@H](C(=O)O)N([Si](C)(C)C)[Si](C)(C)C)CC(=O)O	standard polar	2025-10-23	3069.08
Gas Chromatography	N6-Carboxymethyllysine_TMS_19	C[Si](C)(C)OC(=O)CNCCCC[C@@H](C(=O)O[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C	standard polar	2025-10-23	2217.12
Gas Chromatography	N6-Carboxymethyllysine_TMS_20	C[Si](C)(C)N[C@@H](CCCCN(CC(=O)O[Si](C)(C)C)[Si](C)(C)C)C(=O)O[Si](C)(C)C	standard polar	2025-10-23	1802.25
Gas Chromatography	N6-Carboxymethyllysine_TMS_21	C[Si](C)(C)OC(=O)CN(CCCC[C@@H](C(=O)O)N([Si](C)(C)C)[Si](C)(C)C)[Si](C)(C)C	standard polar	2025-10-23	2112.43
Gas Chromatography	N6-Carboxymethyllysine_TMS_22	C[Si](C)(C)OC(=O)[C@H](CCCCN(CC(=O)O)[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C	standard polar	2025-10-23	2123.58
Gas Chromatography	N6-Carboxymethyllysine_TMS_23	C[Si](C)(C)OC(=O)CN(CCCC[C@@H](C(=O)O[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C)[Si](C)(C)C	standard polar	2025-10-23	3314.6

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood
Feces
Placenta
Urine

Tissue Locations

Placenta

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species

Human Pathways

Pathways

Name	SMPDB/PathBank

Microbial Pathways

Pathways

Not Available

Metabolic Reactions

Reactions

This table shows at most 20 reactions. For the full list of associated reactions:

See All Associated Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Bacteria/Eubacteria	Verrucomicrobia	1	Human feces; Human ; Human urine	Indirect association between microbiota composition and metabolites measured in host biospecimen
Bacteria/Eubacteria	Bacteroidetes	1	Human feces; Human urine	Indirect association between microbiota composition and metabolites measured in host biospecimen
Bacteria/Eubacteria	Firmicutes	4	Human ; Human feces; Human urine; Human sputum	Indirect association between microbiota composition and metabolites measured in host biospecimen

Exposure Sources

Other Exposures

Source Type	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Age	Sex	Health Condition	Data Source	Reference
Human Placenta	Detected but not Quantified	Not Specified	Not Specified	Normal	HMDB	34986597
Human Feces	Detected but not Quantified	Adult (>18 years old)	Both	Normal	HMDB	29808030
Human Urine	Detected but not Quantified	Adult (>18 years old)	Both	Normal	HMDB	32966057
Human Blood	Detected but not Quantified	Adult (>18 years old)	Both	Normal	HMDB	32966057

External Links

HMDB ID

HMDB0240347

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

110350

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

123800

PDB ID

Not Available

ChEBI ID

53014

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

Not Available

General References

Bui TPN, Troise AD, Fogliano V, de Vos WM: Anaerobic Degradation of N-epsilon-Carboxymethyllysine, a Major Glycation End-Product, by Human Intestinal Bacteria. J Agric Food Chem. 2019 Jun 12;67(23):6594-6602. doi: 10.1021/acs.jafc.9b02208. Epub 2019 May 28. [PubMed:31091091 ]
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 ]

Showing metabocard for N6-Carboxymethyllysine (MMDBc0000750)

MOL for #<Metabolite:0x00007f9af19a3358>

3D MOL for #<Metabolite:0x00007f9af19a3358>

3D SDF for #<Metabolite:0x00007f9af19a3358>

3D-SDF for #<Metabolite:0x00007f9af19a3358>

PDB for #<Metabolite:0x00007f9af19a3358>

3D PDB for #<Metabolite:0x00007f9af19a3358>

SMILES for #<Metabolite:0x00007f9af19a3358>

INCHI for #<Metabolite:0x00007f9af19a3358>

Structure for #<Metabolite:0x00007f9af19a3358>

3D Structure for #<Metabolite:0x00007f9af19a3358>