MiMeDB: Showing metabocard for N-Succinyl-L,L-2,6-diaminopimelate (MMDBc0029929)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-17 23:47:13 UTC

Update Date

2022-08-31 17:37:40 UTC

Metabolite ID

MMDBc0029929

Metabolite Identification

Common Name

N-Succinyl-L,L-2,6-diaminopimelate

Description

N-Succinyl-L,L-2,6-diaminopimelate is an intermediate in lysine biosynthesis. It is the third to last step in the synthesis of lysine and is converted from N-Succinyl-2-amino-6-ketopimelate via the enzyme succinyldiaminopimelate transferase (EC 2.6.1.17). It is then converted to L,L-diaminopimelate via the enzyme succinyl-diaminopimelate desuccinylase (EC 3.5.1.18).

Structure

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

HMDB0012267
     RDKit          3D
N-Succinyl-L,L-2,6-diaminopimelate
 38 37  0  0  0  0  0  0  0  0999 V2000
   -4.9483   -1.2917   -0.1323 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5209    0.0678   -0.2268 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1115    0.2175   -0.7390 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1069   -0.4819    0.1629 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7227   -0.3004   -0.3944 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3812   -0.9175    0.3913 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.6164   -0.6138   -0.3146 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.6303    0.1456    0.3004 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4676    0.5746    1.4922 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8905    0.4500   -0.4324 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8019    1.2762    0.4571 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0428    1.5608   -0.3003 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2306    1.1557   -1.4623 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.0376    2.3102    0.3109 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1988   -2.3779    0.4726 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0627   -3.1135   -0.0918 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8460   -2.9750    1.1228 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7101    0.8412    1.0274 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2048    0.2875    2.0419 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3152    2.1757    1.0030 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9590   -1.6698    0.8427 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8730   -1.4524   -0.6028 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1782    0.5666   -0.9906 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8537    1.2951   -0.7483 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9946   -0.1653   -1.7705 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1132   -0.0040    1.1738 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3748   -1.5339    0.3097 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5310    0.8057   -0.4424 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6708   -0.6221   -1.4663 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4055   -0.4696    1.4105 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7367   -0.9637   -1.2723 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4039   -0.5052   -0.6925 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6200    0.9934   -1.3551 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0350    0.7150    1.3731 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3053    2.2434    0.6833 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.5520    1.8913    1.0851 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9574   -2.8455    2.1168 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4266    2.7299    0.1417 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  2  0
  8 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  2  0
 12 14  1  0
  6 15  1  0
 15 16  2  0
 15 17  1  0
  2 18  1  0
 18 19  2  0
 18 20  1  0
  1 21  1  0
  1 22  1  0
  2 23  1  0
  3 24  1  0
  3 25  1  0
  4 26  1  0
  4 27  1  0
  5 28  1  0
  5 29  1  0
  6 30  1  1
  7 31  1  0
 10 32  1  0
 10 33  1  0
 11 34  1  0
 11 35  1  0
 14 36  1  0
 17 37  1  0
 20 38  1  0
M  END


  Mrv0541 02241203542D          

 20 19  0  0  1  0            999 V2000
   11.0481   -6.8862    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.2231   -6.8862    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.4606   -6.1717    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.4606   -4.7428    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.0481   -5.4572    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.8106   -7.6007    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.2856   -6.1717    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   12.2856   -4.7428    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.2231   -5.4572    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.2231   -8.3151    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.6981   -6.8862    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.9855   -7.6007    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   12.6981   -5.4572    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   12.6981   -4.0283    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.8106   -4.7428    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.8106   -6.1717    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.8106   -9.0296    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.0481   -8.3151    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.2856   -7.6007    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.5231   -6.8862    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  2  6  1  0  0  0  0
  7  3  1  6  0  0  0
  4  8  1  0  0  0  0
  4  5  1  0  0  0  0
  5  9  1  0  0  0  0
  6 12  1  0  0  0  0
  6 10  1  0  0  0  0
  7 11  1  0  0  0  0
  7 13  1  0  0  0  0
  8 13  1  0  0  0  0
  8 14  2  0  0  0  0
  9 15  1  0  0  0  0
  9 16  2  0  0  0  0
 10 17  1  0  0  0  0
 10 18  2  0  0  0  0
 11 19  1  0  0  0  0
 11 20  2  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0029929

> <DATABASE_NAME>
MIME

> <SMILES>
NC(CCC[C@H](NC(=O)CCC(O)=O)C(O)=O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C11H18N2O7/c12-6(10(17)18)2-1-3-7(11(19)20)13-8(14)4-5-9(15)16/h6-7H,1-5,12H2,(H,13,14)(H,15,16)(H,17,18)(H,19,20)/t6?,7-/m0/s1

> <INCHI_KEY>
GLXUWZBUPATPBR-MLWJPKLSSA-N

> <FORMULA>
C11H18N2O7

> <MOLECULAR_WEIGHT>
290.2698

> <EXACT_MASS>
290.11140094

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_AVERAGE_POLARIZABILITY>
27.089310391348025

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(6S)-2-amino-6-(3-carboxypropanamido)heptanedioic acid

> <ALOGPS_LOGP>
-3.08

> <JCHEM_LOGP>
-3.767654759825556

> <ALOGPS_LOGS>
-1.70

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
3.5652463088565987

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.887292954138168

> <JCHEM_PKA_STRONGEST_BASIC>
9.526516455366492

> <JCHEM_POLAR_SURFACE_AREA>
167.01999999999998

> <JCHEM_REFRACTIVITY>
63.97650000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
10

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.80e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(6S)-2-amino-6-(3-carboxypropanamido)heptanedioic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0012267
     RDKit          3D
N-Succinyl-L,L-2,6-diaminopimelate
 38 37  0  0  0  0  0  0  0  0999 V2000
   -4.9483   -1.2917   -0.1323 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5209    0.0678   -0.2268 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1115    0.2175   -0.7390 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1069   -0.4819    0.1629 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7227   -0.3004   -0.3944 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3812   -0.9175    0.3913 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.6164   -0.6138   -0.3146 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.6303    0.1456    0.3004 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4676    0.5746    1.4922 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8905    0.4500   -0.4324 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8019    1.2762    0.4571 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0428    1.5608   -0.3003 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2306    1.1557   -1.4623 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.0376    2.3102    0.3109 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1988   -2.3779    0.4726 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0627   -3.1135   -0.0918 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8460   -2.9750    1.1228 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7101    0.8412    1.0274 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2048    0.2875    2.0419 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3152    2.1757    1.0030 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9590   -1.6698    0.8427 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8730   -1.4524   -0.6028 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1782    0.5666   -0.9906 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8537    1.2951   -0.7483 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9946   -0.1653   -1.7705 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1132   -0.0040    1.1738 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3748   -1.5339    0.3097 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5310    0.8057   -0.4424 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6708   -0.6221   -1.4663 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4055   -0.4696    1.4105 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7367   -0.9637   -1.2723 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4039   -0.5052   -0.6925 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6200    0.9934   -1.3551 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0350    0.7150    1.3731 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3053    2.2434    0.6833 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.5520    1.8913    1.0851 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9574   -2.8455    2.1168 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4266    2.7299    0.1417 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  2  0
  8 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  2  0
 12 14  1  0
  6 15  1  0
 15 16  2  0
 15 17  1  0
  2 18  1  0
 18 19  2  0
 18 20  1  0
  1 21  1  0
  1 22  1  0
  2 23  1  0
  3 24  1  0
  3 25  1  0
  4 26  1  0
  4 27  1  0
  5 28  1  0
  5 29  1  0
  6 30  1  1
  7 31  1  0
 10 32  1  0
 10 33  1  0
 11 34  1  0
 11 35  1  0
 14 36  1  0
 17 37  1  0
 20 38  1  0
M  END

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0      20.623 -12.854   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      19.083 -12.854   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      21.393 -11.521   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      21.393  -8.853   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      20.623 -10.187   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      18.313 -14.188   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      22.933 -11.521   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      22.933  -8.853   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      19.083 -10.187   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      19.083 -15.522   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      23.703 -12.854   0.000  0.00  0.00           C+0
HETATM   12  N   UNK     0      16.773 -14.188   0.000  0.00  0.00           N+0
HETATM   13  N   UNK     0      23.703 -10.187   0.000  0.00  0.00           N+0
HETATM   14  O   UNK     0      23.703  -7.519   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0      18.313  -8.853   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0      18.313 -11.521   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0      18.313 -16.855   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0      20.623 -15.522   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0      22.933 -14.188   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0      25.243 -12.854   0.000  0.00  0.00           O+0
CONECT    1    2    3                                                       
CONECT    2    1    6                                                       
CONECT    3    1    7                                                       
CONECT    4    8    5                                                       
CONECT    5    4    9                                                       
CONECT    6    2   12   10                                                  
CONECT    7    3   11   13                                                  
CONECT    8    4   13   14                                                  
CONECT    9    5   15   16                                                  
CONECT   10    6   17   18                                                  
CONECT   11    7   19   20                                                  
CONECT   12    6                                                            
CONECT   13    7    8                                                       
CONECT   14    8                                                            
CONECT   15    9                                                            
CONECT   16    9                                                            
CONECT   17   10                                                            
CONECT   18   10                                                            
CONECT   19   11                                                            
CONECT   20   11                                                            
MASTER        0    0    0    0    0    0    0    0   20    0   38    0
END

COMPND    HMDB0012267
HETATM    1  N1  UNL     1      -4.948  -1.292  -0.132  1.00  0.00           N  
HETATM    2  C1  UNL     1      -4.521   0.068  -0.227  1.00  0.00           C  
HETATM    3  C2  UNL     1      -3.112   0.217  -0.739  1.00  0.00           C  
HETATM    4  C3  UNL     1      -2.107  -0.482   0.163  1.00  0.00           C  
HETATM    5  C4  UNL     1      -0.723  -0.300  -0.394  1.00  0.00           C  
HETATM    6  C5  UNL     1       0.381  -0.918   0.391  1.00  0.00           C  
HETATM    7  N2  UNL     1       1.616  -0.614  -0.315  1.00  0.00           N  
HETATM    8  C6  UNL     1       2.630   0.146   0.300  1.00  0.00           C  
HETATM    9  O1  UNL     1       2.468   0.575   1.492  1.00  0.00           O  
HETATM   10  C7  UNL     1       3.890   0.450  -0.432  1.00  0.00           C  
HETATM   11  C8  UNL     1       4.802   1.276   0.457  1.00  0.00           C  
HETATM   12  C9  UNL     1       6.043   1.561  -0.300  1.00  0.00           C  
HETATM   13  O2  UNL     1       6.231   1.156  -1.462  1.00  0.00           O  
HETATM   14  O3  UNL     1       7.038   2.310   0.311  1.00  0.00           O  
HETATM   15  C10 UNL     1       0.199  -2.378   0.473  1.00  0.00           C  
HETATM   16  O4  UNL     1       1.063  -3.114  -0.092  1.00  0.00           O  
HETATM   17  O5  UNL     1      -0.846  -2.975   1.123  1.00  0.00           O  
HETATM   18  C11 UNL     1      -4.710   0.841   1.027  1.00  0.00           C  
HETATM   19  O6  UNL     1      -5.205   0.288   2.042  1.00  0.00           O  
HETATM   20  O7  UNL     1      -4.315   2.176   1.003  1.00  0.00           O  
HETATM   21  H1  UNL     1      -4.959  -1.670   0.843  1.00  0.00           H  
HETATM   22  H2  UNL     1      -5.873  -1.452  -0.603  1.00  0.00           H  
HETATM   23  H3  UNL     1      -5.178   0.567  -0.991  1.00  0.00           H  
HETATM   24  H4  UNL     1      -2.854   1.295  -0.748  1.00  0.00           H  
HETATM   25  H5  UNL     1      -2.995  -0.165  -1.771  1.00  0.00           H  
HETATM   26  H6  UNL     1      -2.113  -0.004   1.174  1.00  0.00           H  
HETATM   27  H7  UNL     1      -2.375  -1.534   0.310  1.00  0.00           H  
HETATM   28  H8  UNL     1      -0.531   0.806  -0.442  1.00  0.00           H  
HETATM   29  H9  UNL     1      -0.671  -0.622  -1.466  1.00  0.00           H  
HETATM   30  H10 UNL     1       0.405  -0.470   1.410  1.00  0.00           H  
HETATM   31  H11 UNL     1       1.737  -0.964  -1.272  1.00  0.00           H  
HETATM   32  H12 UNL     1       4.404  -0.505  -0.692  1.00  0.00           H  
HETATM   33  H13 UNL     1       3.620   0.993  -1.355  1.00  0.00           H  
HETATM   34  H14 UNL     1       5.035   0.715   1.373  1.00  0.00           H  
HETATM   35  H15 UNL     1       4.305   2.243   0.683  1.00  0.00           H  
HETATM   36  H16 UNL     1       7.552   1.891   1.085  1.00  0.00           H  
HETATM   37  H17 UNL     1      -0.957  -2.845   2.117  1.00  0.00           H  
HETATM   38  H18 UNL     1      -4.427   2.730   0.142  1.00  0.00           H  
CONECT    1    2   21   22
CONECT    2    3   18   23
CONECT    3    4   24   25
CONECT    4    5   26   27
CONECT    5    6   28   29
CONECT    6    7   15   30
CONECT    7    8   31
CONECT    8    9    9   10
CONECT   10   11   32   33
CONECT   11   12   34   35
CONECT   12   13   13   14
CONECT   14   36
CONECT   15   16   16   17
CONECT   17   37
CONECT   18   19   19   20
CONECT   20   38
END

HMDB0012267
     RDKit          3D
N-Succinyl-L,L-2,6-diaminopimelate
 38 37  0  0  0  0  0  0  0  0999 V2000
   -4.9483   -1.2917   -0.1323 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5209    0.0678   -0.2268 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1115    0.2175   -0.7390 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1069   -0.4819    0.1629 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7227   -0.3004   -0.3944 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3812   -0.9175    0.3913 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.6164   -0.6138   -0.3146 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.6303    0.1456    0.3004 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4676    0.5746    1.4922 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8905    0.4500   -0.4324 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8019    1.2762    0.4571 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0428    1.5608   -0.3003 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2306    1.1557   -1.4623 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.0376    2.3102    0.3109 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1988   -2.3779    0.4726 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0627   -3.1135   -0.0918 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8460   -2.9750    1.1228 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7101    0.8412    1.0274 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2048    0.2875    2.0419 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3152    2.1757    1.0030 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9590   -1.6698    0.8427 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8730   -1.4524   -0.6028 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1782    0.5666   -0.9906 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8537    1.2951   -0.7483 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9946   -0.1653   -1.7705 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1132   -0.0040    1.1738 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3748   -1.5339    0.3097 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5310    0.8057   -0.4424 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6708   -0.6221   -1.4663 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4055   -0.4696    1.4105 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7367   -0.9637   -1.2723 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4039   -0.5052   -0.6925 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6200    0.9934   -1.3551 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0350    0.7150    1.3731 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3053    2.2434    0.6833 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.5520    1.8913    1.0851 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9574   -2.8455    2.1168 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4266    2.7299    0.1417 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  2  0
  8 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  2  0
 12 14  1  0
  6 15  1  0
 15 16  2  0
 15 17  1  0
  2 18  1  0
 18 19  2  0
 18 20  1  0
  1 21  1  0
  1 22  1  0
  2 23  1  0
  3 24  1  0
  3 25  1  0
  4 26  1  0
  4 27  1  0
  5 28  1  0
  5 29  1  0
  6 30  1  1
  7 31  1  0
 10 32  1  0
 10 33  1  0
 11 34  1  0
 11 35  1  0
 14 36  1  0
 17 37  1  0
 20 38  1  0
M  END

Synonyms

Value	Source
N-Succinyl-L,L-2,6-diaminopimelic acid	Generator
L,L-Sdap	HMDB
N-Succinyl-L-2,6-diaminoheptanedioate	HMDB
N-Succinyl-L-2,6-diaminoheptanedioic acid	HMDB
N-Succinyl-LL-2,6-diaminoheptanedioate	HMDB
N-Succinyl-LL-2,6-diaminoheptanedioic acid	HMDB
N-Succinyl-LL-2,6-diaminopimelate	HMDB

Molecular Formula

C₁₁H₁₈N₂O₇

Average Mass

290.2698

Monoisotopic Mass

290.11140094

IUPAC Name

(6S)-2-amino-6-(3-carboxypropanamido)heptanedioic acid

Traditional Name

(6S)-2-amino-6-(3-carboxypropanamido)heptanedioic acid

CAS Registry Number

26605-36-7

SMILES

NC(CCC[C@H](NC(=O)CCC(O)=O)C(O)=O)C(O)=O

InChI Identifier

InChI=1S/C11H18N2O7/c12-6(10(17)18)2-1-3-7(11(19)20)13-8(14)4-5-9(15)16/h6-7H,1-5,12H2,(H,13,14)(H,15,16)(H,17,18)(H,19,20)/t6?,7-/m0/s1

InChI Key

GLXUWZBUPATPBR-MLWJPKLSSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as n-acyl-l-alpha-amino acids. These are n-acylated 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

N-acyl-L-alpha-amino acids

Alternative Parents

Substituents

N-acyl-l-alpha-amino acid
Alpha-amino acid
Tricarboxylic acid or derivatives
Amino fatty acid
Fatty amide
N-acyl-amine
Fatty acyl
Carboxamide group
Secondary carboxylic acid amide
Amino acid
Carboxylic acid
Primary amine
Organooxygen compound
Organonitrogen compound
Organic oxide
Primary aliphatic amine
Organopnictogen compound
Carbonyl group
Organic oxygen compound
Organic nitrogen compound
Amine
Hydrocarbon derivative
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Solid

Predicted Properties

Property	Value	Source
Water Solubility	5.8 g/L	ALOGPS
logP	-3.1	ALOGPS
logP	-3.8	ChemAxon
logS	-1.7	ALOGPS
pKa (Strongest Acidic)	1.89	ChemAxon
pKa (Strongest Basic)	9.53	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	167.02 Å²	ChemAxon
Rotatable Bond Count	10	ChemAxon
Refractivity	63.98 m³·mol⁻¹	ChemAxon
Polarizability	27.09 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	splash10-0ukd-7980000000-e443695d136f221c8fcf	2017-09-01	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (3 TMS) - 70eV, Positive	splash10-006x-9303600000-53e79d2abfa0f9ef52dd	2017-10-06	View Spectrum
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	splash10-00fs-0290000000-94b59924e5c6f873d3e9	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0002-1960000000-f57f28932db38b283c8c	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-054k-7900000000-66284b4cc1812fbb9f0c	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0079-0190000000-fa97ecde1f805141dc72	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-00g1-1490000000-777a3c340c9bca9df3ae	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-006y-9800000000-f1025c9e017254c3c356	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-006x-0190000000-2b72340d09586ce940a0	2021-09-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0002-1910000000-e4c34aca88cb0711d6e6	2021-09-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0pb9-8900000000-b3cbfc02281c4466f2de	2021-09-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-000i-0090000000-39bd027060b8d3f96cff	2021-09-25	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-000b-2970000000-0ae78022739fec47a222	2021-09-25	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-00dl-9300000000-79f5f223496e3d1a1274	2021-09-25	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

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

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

Metabolic Reactions

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	Proteobacteria	1	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human stool	Unknown

Exposure Sources

Source Type	Source Sub-type	Species	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference

External Links

HMDB ID

HMDB0012267

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB028905

KNApSAcK ID

Not Available

Chemspider ID

35032427

KEGG Compound ID

C04421

BioCyc ID

N-SUCCINYLLL-2-6-DIAMINOPIMELATE

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

25202447

PDB ID

Not Available

ChEBI ID

165894

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Wishart DS, Li C, Marcu A, Badran H, Pon A, Budinski Z, Patron J, Lipton D, Cao X, Oler E, Li K, Paccoud M, Hong C, Guo AC, Chan C, Wei W, Ramirez-Gaona M: PathBank: a comprehensive pathway database for model organisms. Nucleic Acids Res. 2020 Jan 8;48(D1):D470-D478. doi: 10.1093/nar/gkz861. [PubMed:31602464 ]

Showing metabocard for N-Succinyl-L,L-2,6-diaminopimelate (MMDBc0029929)

MOL for #<Metabolite:0x00007fecdea43198>

3D MOL for #<Metabolite:0x00007fecdea43198>

3D SDF for #<Metabolite:0x00007fecdea43198>

3D-SDF for #<Metabolite:0x00007fecdea43198>

PDB for #<Metabolite:0x00007fecdea43198>

3D PDB for #<Metabolite:0x00007fecdea43198>

SMILES for #<Metabolite:0x00007fecdea43198>

INCHI for #<Metabolite:0x00007fecdea43198>

Structure for #<Metabolite:0x00007fecdea43198>

3D Structure for #<Metabolite:0x00007fecdea43198>