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Showing metabocard for Diaminopimelic acid (HMDB0001370)

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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2023-02-21 17:15:38 UTC
HMDB IDHMDB0001370
Secondary Accession Numbers
  • HMDB01370
Metabolite Identification
Common NameDiaminopimelic acid
DescriptionDiaminopimelic acid or DAPA is a lysine-like amino acid derivative that is a key component of the bacterial cell wall. DAPA is incorporated or integrated into peptidoglycan of gram negative bacteria and is the attachment point for Braun's lipoprotein (BLP or Murein Lipoprotein). BLP is found in gram-negative cell walls and is one of the most abundant membrane proteins. BLP is bound at its C-terminal end (a lysine) by a covalent bond to the peptidoglycan layer (specifically to diaminopimelic acid molecules) and is embedded in the outer membrane by its hydrophobic head (a cysteine with lipids attached). BLP tightly links the two layers and provides structural integrity to the bacterial outer membrane. Diaminopimelic acid can be found in human urine or feces due to the lysis or enzymatic breakdown of gram negative gut microbes.
Structure
Data?1676999738
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0001370 (Diaminopimelic acid)


  Mrv1652309042000222D          

 13 12  0  0  1  0            999 V2000
    7.2849    3.3809    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    7.2849    2.5559    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    6.5704    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8559    2.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1414    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4270    2.5559    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.4270    3.3809    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.7125    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9980    2.5559    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7125    1.3184    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.9993    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.7138    2.5559    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.9993    1.3184    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  6  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  1  0  0  0
  6  8  1  0  0  0  0
  8  9  1  0  0  0  0
  8 10  2  0  0  0  0
  2 11  1  0  0  0  0
 11 12  1  0  0  0  0
 11 13  2  0  0  0  0
M  END
Download

3D MOL for HMDB0001370 (Diaminopimelic acid)

HMDB0001370
     RDKit          3D
Diaminopimelic acid
 27 26  0  0  0  0  0  0  0  0999 V2000
   -3.2031   -0.5399   -1.0563 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2633   -0.5062    0.0709 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.9450    0.0743   -0.3717 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0002    0.0960    0.7936 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3705    0.6323    0.4011 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0263   -0.2041   -0.6755 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.1792   -1.5497   -0.1705 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.3798    0.4140   -0.9130 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3963   -0.2789   -0.6570 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5037    1.6943   -1.3942 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8296    0.1699    1.2231 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3441    0.1639    2.3585 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0283    0.8892    1.0274 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2950    0.3712   -1.5147 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9768   -1.3363   -1.6810 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0691   -1.5805    0.3191 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1743    1.0964   -0.7528 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5175   -0.4843   -1.2358 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0915   -0.9038    1.2038 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4102    0.8360    1.5443 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3156    1.6934    0.1501 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0094    0.5273    1.3087 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4496   -0.1882   -1.6261 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9767   -2.2817   -0.8940 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1256   -1.7243    0.2352 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9457    2.4277   -0.8288 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7133    0.4922    0.4227 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
  6  8  1  0
  8  9  2  0
  8 10  1  0
  2 11  1  0
 11 12  2  0
 11 13  1  0
  1 14  1  0
  1 15  1  0
  2 16  1  1
  3 17  1  0
  3 18  1  0
  4 19  1  0
  4 20  1  0
  5 21  1  0
  5 22  1  0
  6 23  1  6
  7 24  1  0
  7 25  1  0
 10 26  1  0
 13 27  1  0
M  END
Download

3D SDF for HMDB0001370 (Diaminopimelic acid)


  Mrv1652309042000222D          

 13 12  0  0  1  0            999 V2000
    7.2849    3.3809    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    7.2849    2.5559    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    6.5704    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8559    2.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1414    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4270    2.5559    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.4270    3.3809    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.7125    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9980    2.5559    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7125    1.3184    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.9993    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.7138    2.5559    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.9993    1.3184    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  6  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  1  0  0  0
  6  8  1  0  0  0  0
  8  9  1  0  0  0  0
  8 10  2  0  0  0  0
  2 11  1  0  0  0  0
 11 12  1  0  0  0  0
 11 13  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0001370

> <DATABASE_NAME>
hmdb

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

> <INCHI_IDENTIFIER>
InChI=1S/C7H14N2O4/c8-4(6(10)11)2-1-3-5(9)7(12)13/h4-5H,1-3,8-9H2,(H,10,11)(H,12,13)/t4-,5-/m0/s1

> <INCHI_KEY>
GMKMEZVLHJARHF-WHFBIAKZSA-N

> <FORMULA>
C7H14N2O4

> <MOLECULAR_WEIGHT>
190.1971

> <EXACT_MASS>
190.095356946

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
27

> <JCHEM_AVERAGE_POLARIZABILITY>
18.933170312561906

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,6S)-2,6-diaminoheptanedioic acid

> <ALOGPS_LOGP>
-4.13

> <JCHEM_LOGP>
-5.545367993935247

> <ALOGPS_LOGS>
-1.13

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
2.585040505515717

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.8470749826619342

> <JCHEM_PKA_STRONGEST_BASIC>
9.827564769536531

> <JCHEM_POLAR_SURFACE_AREA>
126.64000000000001

> <JCHEM_REFRACTIVITY>
43.63940000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.41e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
diamino-pimelic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0001370 (Diaminopimelic acid)

HMDB0001370
     RDKit          3D
Diaminopimelic acid
 27 26  0  0  0  0  0  0  0  0999 V2000
   -3.2031   -0.5399   -1.0563 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2633   -0.5062    0.0709 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.9450    0.0743   -0.3717 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0002    0.0960    0.7936 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3705    0.6323    0.4011 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0263   -0.2041   -0.6755 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.1792   -1.5497   -0.1705 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.3798    0.4140   -0.9130 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3963   -0.2789   -0.6570 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5037    1.6943   -1.3942 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8296    0.1699    1.2231 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3441    0.1639    2.3585 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0283    0.8892    1.0274 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2950    0.3712   -1.5147 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9768   -1.3363   -1.6810 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0691   -1.5805    0.3191 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1743    1.0964   -0.7528 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5175   -0.4843   -1.2358 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0915   -0.9038    1.2038 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4102    0.8360    1.5443 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3156    1.6934    0.1501 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0094    0.5273    1.3087 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4496   -0.1882   -1.6261 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9767   -2.2817   -0.8940 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1256   -1.7243    0.2352 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9457    2.4277   -0.8288 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7133    0.4922    0.4227 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
  6  8  1  0
  8  9  2  0
  8 10  1  0
  2 11  1  0
 11 12  2  0
 11 13  1  0
  1 14  1  0
  1 15  1  0
  2 16  1  1
  3 17  1  0
  3 18  1  0
  4 19  1  0
  4 20  1  0
  5 21  1  0
  5 22  1  0
  6 23  1  6
  7 24  1  0
  7 25  1  0
 10 26  1  0
 13 27  1  0
M  END
Download

PDB for HMDB0001370 (Diaminopimelic acid)

HEADER    PROTEIN                                 04-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-20         0                                  
HETATM    1  N   UNK     0      13.598   6.311   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0      13.598   4.771   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      12.265   4.001   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      10.931   4.771   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       9.597   4.001   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       8.264   4.771   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0       8.264   6.311   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0       6.930   4.001   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       5.596   4.771   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       6.930   2.461   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0      14.932   4.001   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      16.266   4.771   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0      14.932   2.461   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   11                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8                                                            
CONECT   11    2   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11                                                            
MASTER        0    0    0    0    0    0    0    0   13    0   24    0
END
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3D PDB for HMDB0001370 (Diaminopimelic acid)

COMPND    HMDB0001370
HETATM    1  N1  UNL     1      -3.203  -0.540  -1.056  1.00  0.00           N  
HETATM    2  C1  UNL     1      -2.263  -0.506   0.071  1.00  0.00           C  
HETATM    3  C2  UNL     1      -0.945   0.074  -0.372  1.00  0.00           C  
HETATM    4  C3  UNL     1      -0.000   0.096   0.794  1.00  0.00           C  
HETATM    5  C4  UNL     1       1.370   0.632   0.401  1.00  0.00           C  
HETATM    6  C5  UNL     1       2.026  -0.204  -0.676  1.00  0.00           C  
HETATM    7  N2  UNL     1       2.179  -1.550  -0.171  1.00  0.00           N  
HETATM    8  C6  UNL     1       3.380   0.414  -0.913  1.00  0.00           C  
HETATM    9  O1  UNL     1       4.396  -0.279  -0.657  1.00  0.00           O  
HETATM   10  O2  UNL     1       3.504   1.694  -1.394  1.00  0.00           O  
HETATM   11  C7  UNL     1      -2.830   0.170   1.223  1.00  0.00           C  
HETATM   12  O3  UNL     1      -2.344   0.164   2.359  1.00  0.00           O  
HETATM   13  O4  UNL     1      -4.028   0.889   1.027  1.00  0.00           O  
HETATM   14  H1  UNL     1      -3.295   0.371  -1.515  1.00  0.00           H  
HETATM   15  H2  UNL     1      -2.977  -1.336  -1.681  1.00  0.00           H  
HETATM   16  H3  UNL     1      -2.069  -1.581   0.319  1.00  0.00           H  
HETATM   17  H4  UNL     1      -1.174   1.096  -0.753  1.00  0.00           H  
HETATM   18  H5  UNL     1      -0.518  -0.484  -1.236  1.00  0.00           H  
HETATM   19  H6  UNL     1       0.091  -0.904   1.204  1.00  0.00           H  
HETATM   20  H7  UNL     1      -0.410   0.836   1.544  1.00  0.00           H  
HETATM   21  H8  UNL     1       1.316   1.693   0.150  1.00  0.00           H  
HETATM   22  H9  UNL     1       2.009   0.527   1.309  1.00  0.00           H  
HETATM   23  H10 UNL     1       1.450  -0.188  -1.626  1.00  0.00           H  
HETATM   24  H11 UNL     1       1.977  -2.282  -0.894  1.00  0.00           H  
HETATM   25  H12 UNL     1       3.126  -1.724   0.235  1.00  0.00           H  
HETATM   26  H13 UNL     1       3.946   2.428  -0.829  1.00  0.00           H  
HETATM   27  H14 UNL     1      -4.713   0.492   0.423  1.00  0.00           H  
CONECT    1    2   14   15
CONECT    2    3   11   16
CONECT    3    4   17   18
CONECT    4    5   19   20
CONECT    5    6   21   22
CONECT    6    7    8   23
CONECT    7   24   25
CONECT    8    9    9   10
CONECT   10   26
CONECT   11   12   12   13
CONECT   13   27
END
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SMILES for HMDB0001370 (Diaminopimelic acid)

N[C@@H](CCC[C@H](N)C(O)=O)C(O)=O
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INCHI for HMDB0001370 (Diaminopimelic acid)

InChI=1S/C7H14N2O4/c8-4(6(10)11)2-1-3-5(9)7(12)13/h4-5H,1-3,8-9H2,(H,10,11)(H,12,13)/t4-,5-/m0/s1
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
(S,S)-2,6-Diaminopimelic acidChEBI
(S-(R*,r*))-2,6-diaminoheptanedioic acidChEBI
L,L-2,6-Diaminopimelic acidChEBI
LL-2,6-DiaminoheptanedioateChEBI
LL-2,6-DiaminopimelateChEBI
LL-2,6-Diaminopimelic acidKegg
(S,S)-2,6-DiaminopimelateGenerator
(S-(R*,r*))-2,6-diaminoheptanedioateGenerator
L,L-2,6-DiaminopimelateGenerator
LL-2,6-Diaminoheptanedioic acidGenerator
DiaminopimelateGenerator
( (R*,s*)-2,6-diamino-heptanedioateHMDB
( (R*,s*)-2,6-diamino-heptanedioic acidHMDB
(2R,6S)-2,6-diamino-HeptanedioateHMDB
(2R,6S)-2,6-diamino-Heptanedioic acidHMDB
(R*,s*)-2,6-diamino-heptanedioateHMDB
(R*,s*)-2,6-diamino-heptanedioic acidHMDB
2,6-diamino-HeptanedioateHMDB
2,6-diamino-Heptanedioic acidHMDB
2,6-DiaminoheptanedioateHMDB
2,6-Diaminoheptanedioic acidHMDB
2,6-DiaminopimelateHMDB
2,6-Diaminopimelic acidHMDB, MeSH
a,A'-diaminopimelateHMDB
a,A'-diaminopimelic acidHMDB
a,e-DiaminopimelateHMDB
a,e-Diaminopimelic acidHMDB
D,L-DiaminopimelateHMDB
D,L-meso-DiaminoheptanedioateHMDB
D,L-meso-Diaminoheptanedioic acidHMDB
DAPAHMDB
DL-2,6-DiaminoheptanedioateHMDB
DL-2,6-Diaminoheptanedioic acidHMDB
DL-2,6-DiaminopimelateHMDB
DL-2,6-Diaminopimelic acidHMDB
L,L-2,6-DiaminoheptanedioateHMDB
L,L-2,6-Diaminoheptanedioic acidHMDB
L,L-DiaminopimelateHMDB
meso-1-alpha,epsilon-DiaminopimelateHMDB
meso-2,6-diamino-HeptanedioateHMDB
meso-2,6-diamino-Heptanedioic acidHMDB
meso-2,6-DiaminoheptanedioateHMDB
meso-2,6-Diaminoheptanedioic acidHMDB
meso-alpha,Alpha'-diaminopimelateHMDB
meso-alpha,Alpha'-diaminopimelic acidHMDB
meso-alpha,epsilon-DiaminopimelateHMDB
meso-alpha,epsilon-Diaminopimelic acidHMDB
meso-DiaminoheptanedioateHMDB
meso-Diaminoheptanedioic acidHMDB
meso-DiaminopimelateHMDB
Acid, diaminopimelicMeSH, HMDB
2,6 Diaminopimelic acidMeSH, HMDB
Acid, 2,6-diaminopimelicMeSH, HMDB
Diamino-pimelateGenerator, HMDB
Diaminopimelic acidMeSH
Chemical FormulaC7H14N2O4
Average Molecular Weight190.1971
Monoisotopic Molecular Weight190.095356946
IUPAC Name(2S,6S)-2,6-diaminoheptanedioic acid
Traditional Namediamino-pimelic acid
CAS Registry Number583-93-7
SMILES
N[C@@H](CCC[C@H](N)C(O)=O)C(O)=O
InChI Identifier
InChI=1S/C7H14N2O4/c8-4(6(10)11)2-1-3-5(9)7(12)13/h4-5H,1-3,8-9H2,(H,10,11)(H,12,13)/t4-,5-/m0/s1
InChI KeyGMKMEZVLHJARHF-WHFBIAKZSA-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.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassAmino acids, peptides, and analogues
Direct ParentL-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
  • Organopnictogen compound
  • Organic nitrogen compound
  • Amine
  • Organic oxygen compound
  • Primary amine
  • Organooxygen compound
  • Organonitrogen compound
  • Primary aliphatic amine
  • Carbonyl group
  • Hydrocarbon derivative
  • Organic oxide
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
Process
Naturally occurring process
RoleNot Available
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point300 °CNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic Properties

Experimental Collision Cross Sections

Adduct TypeData SourceCCS Value (Å2)Reference
[M-H]-MetCCS_train_neg134.27530932474
[M+H]+MetCCS_train_pos140.84930932474
[M-H]-Not Available137.2http://allccs.zhulab.cn/database/detail?ID=AllCCS00000045
[M+H]+Not Available141.5http://allccs.zhulab.cn/database/detail?ID=AllCCS00000045
Predicted Molecular Properties
PropertyValueSource
Water Solubility14.1 g/LALOGPS
logP-4.1ALOGPS
logP-5.5ChemAxon
logS-1.1ALOGPS
pKa (Strongest Acidic)1.85ChemAxon
pKa (Strongest Basic)9.83ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count6ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area126.64 ŲChemAxon
Rotatable Bond Count6ChemAxon
Refractivity43.64 m³·mol⁻¹ChemAxon
Polarizability18.93 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+144.31831661259
DarkChem[M-H]-141.34631661259
AllCCS[M+H]+141.93332859911
AllCCS[M-H]-136.60432859911
DeepCCS[M+H]+141.78930932474
DeepCCS[M-H]-139.39430932474
DeepCCS[M-2H]-173.66730932474
DeepCCS[M+Na]+148.15730932474
AllCCS[M+H]+141.932859911
AllCCS[M+H-H2O]+138.232859911
AllCCS[M+NH4]+145.432859911
AllCCS[M+Na]+146.432859911
AllCCS[M-H]-136.632859911
AllCCS[M+Na-2H]-137.732859911
AllCCS[M+HCOO]-139.032859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
Diaminopimelic acidN[C@@H](CCC[C@H](N)C(O)=O)C(O)=O2575.2Standard polar33892256
Diaminopimelic acidN[C@@H](CCC[C@H](N)C(O)=O)C(O)=O1598.5Standard non polar33892256
Diaminopimelic acidN[C@@H](CCC[C@H](N)C(O)=O)C(O)=O2131.1Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Diaminopimelic acid,1TMS,isomer #1C[Si](C)(C)OC(=O)[C@@H](N)CCC[C@H](N)C(=O)O1857.9Semi standard non polar33892256
Diaminopimelic acid,1TMS,isomer #2C[Si](C)(C)N[C@@H](CCC[C@H](N)C(=O)O)C(=O)O1958.6Semi standard non polar33892256
Diaminopimelic acid,2TMS,isomer #1C[Si](C)(C)OC(=O)[C@@H](N)CCC[C@H](N)C(=O)O[Si](C)(C)C1834.3Semi standard non polar33892256
Diaminopimelic acid,2TMS,isomer #2C[Si](C)(C)N[C@@H](CCC[C@H](N)C(=O)O)C(=O)O[Si](C)(C)C1925.1Semi standard non polar33892256
Diaminopimelic acid,2TMS,isomer #3C[Si](C)(C)N[C@@H](CCC[C@H](N)C(=O)O[Si](C)(C)C)C(=O)O1925.9Semi standard non polar33892256
Diaminopimelic acid,2TMS,isomer #4C[Si](C)(C)N[C@@H](CCC[C@H](N[Si](C)(C)C)C(=O)O)C(=O)O2009.7Semi standard non polar33892256
Diaminopimelic acid,2TMS,isomer #5C[Si](C)(C)N([C@@H](CCC[C@H](N)C(=O)O)C(=O)O)[Si](C)(C)C2110.6Semi standard non polar33892256
Diaminopimelic acid,3TMS,isomer #1C[Si](C)(C)N[C@@H](CCC[C@H](N)C(=O)O[Si](C)(C)C)C(=O)O[Si](C)(C)C1913.0Semi standard non polar33892256
Diaminopimelic acid,3TMS,isomer #1C[Si](C)(C)N[C@@H](CCC[C@H](N)C(=O)O[Si](C)(C)C)C(=O)O[Si](C)(C)C2024.4Standard non polar33892256
Diaminopimelic acid,3TMS,isomer #1C[Si](C)(C)N[C@@H](CCC[C@H](N)C(=O)O[Si](C)(C)C)C(=O)O[Si](C)(C)C2795.5Standard polar33892256
Diaminopimelic acid,3TMS,isomer #2C[Si](C)(C)N[C@@H](CCC[C@H](N[Si](C)(C)C)C(=O)O[Si](C)(C)C)C(=O)O2004.6Semi standard non polar33892256
Diaminopimelic acid,3TMS,isomer #2C[Si](C)(C)N[C@@H](CCC[C@H](N[Si](C)(C)C)C(=O)O[Si](C)(C)C)C(=O)O2030.2Standard non polar33892256
Diaminopimelic acid,3TMS,isomer #2C[Si](C)(C)N[C@@H](CCC[C@H](N[Si](C)(C)C)C(=O)O[Si](C)(C)C)C(=O)O2572.2Standard polar33892256
Diaminopimelic acid,3TMS,isomer #3C[Si](C)(C)OC(=O)[C@H](CCC[C@H](N)C(=O)O)N([Si](C)(C)C)[Si](C)(C)C2101.4Semi standard non polar33892256
Diaminopimelic acid,3TMS,isomer #3C[Si](C)(C)OC(=O)[C@H](CCC[C@H](N)C(=O)O)N([Si](C)(C)C)[Si](C)(C)C2037.1Standard non polar33892256
Diaminopimelic acid,3TMS,isomer #3C[Si](C)(C)OC(=O)[C@H](CCC[C@H](N)C(=O)O)N([Si](C)(C)C)[Si](C)(C)C3057.0Standard polar33892256
Diaminopimelic acid,3TMS,isomer #4C[Si](C)(C)OC(=O)[C@@H](N)CCC[C@@H](C(=O)O)N([Si](C)(C)C)[Si](C)(C)C2078.5Semi standard non polar33892256
Diaminopimelic acid,3TMS,isomer #4C[Si](C)(C)OC(=O)[C@@H](N)CCC[C@@H](C(=O)O)N([Si](C)(C)C)[Si](C)(C)C2079.8Standard non polar33892256
Diaminopimelic acid,3TMS,isomer #4C[Si](C)(C)OC(=O)[C@@H](N)CCC[C@@H](C(=O)O)N([Si](C)(C)C)[Si](C)(C)C2870.9Standard polar33892256
Diaminopimelic acid,3TMS,isomer #5C[Si](C)(C)N[C@@H](CCC[C@@H](C(=O)O)N([Si](C)(C)C)[Si](C)(C)C)C(=O)O2152.1Semi standard non polar33892256
Diaminopimelic acid,3TMS,isomer #5C[Si](C)(C)N[C@@H](CCC[C@@H](C(=O)O)N([Si](C)(C)C)[Si](C)(C)C)C(=O)O2059.6Standard non polar33892256
Diaminopimelic acid,3TMS,isomer #5C[Si](C)(C)N[C@@H](CCC[C@@H](C(=O)O)N([Si](C)(C)C)[Si](C)(C)C)C(=O)O2707.2Standard polar33892256
Diaminopimelic acid,4TMS,isomer #1C[Si](C)(C)N[C@@H](CCC[C@H](N[Si](C)(C)C)C(=O)O[Si](C)(C)C)C(=O)O[Si](C)(C)C1974.6Semi standard non polar33892256
Diaminopimelic acid,4TMS,isomer #1C[Si](C)(C)N[C@@H](CCC[C@H](N[Si](C)(C)C)C(=O)O[Si](C)(C)C)C(=O)O[Si](C)(C)C2086.6Standard non polar33892256
Diaminopimelic acid,4TMS,isomer #1C[Si](C)(C)N[C@@H](CCC[C@H](N[Si](C)(C)C)C(=O)O[Si](C)(C)C)C(=O)O[Si](C)(C)C2235.1Standard polar33892256
Diaminopimelic acid,4TMS,isomer #2C[Si](C)(C)OC(=O)[C@@H](N)CCC[C@@H](C(=O)O[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C2096.2Semi standard non polar33892256
Diaminopimelic acid,4TMS,isomer #2C[Si](C)(C)OC(=O)[C@@H](N)CCC[C@@H](C(=O)O[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C2133.5Standard non polar33892256
Diaminopimelic acid,4TMS,isomer #2C[Si](C)(C)OC(=O)[C@@H](N)CCC[C@@H](C(=O)O[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C2694.4Standard polar33892256
Diaminopimelic acid,4TMS,isomer #3C[Si](C)(C)N[C@@H](CCC[C@@H](C(=O)O)N([Si](C)(C)C)[Si](C)(C)C)C(=O)O[Si](C)(C)C2124.5Semi standard non polar33892256
Diaminopimelic acid,4TMS,isomer #3C[Si](C)(C)N[C@@H](CCC[C@@H](C(=O)O)N([Si](C)(C)C)[Si](C)(C)C)C(=O)O[Si](C)(C)C2160.6Standard non polar33892256
Diaminopimelic acid,4TMS,isomer #3C[Si](C)(C)N[C@@H](CCC[C@@H](C(=O)O)N([Si](C)(C)C)[Si](C)(C)C)C(=O)O[Si](C)(C)C2385.7Standard polar33892256
Diaminopimelic acid,4TMS,isomer #4C[Si](C)(C)N[C@@H](CCC[C@@H](C(=O)O[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C)C(=O)O2149.3Semi standard non polar33892256
Diaminopimelic acid,4TMS,isomer #4C[Si](C)(C)N[C@@H](CCC[C@@H](C(=O)O[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C)C(=O)O2133.8Standard non polar33892256
Diaminopimelic acid,4TMS,isomer #4C[Si](C)(C)N[C@@H](CCC[C@@H](C(=O)O[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C)C(=O)O2434.1Standard polar33892256
Diaminopimelic acid,4TMS,isomer #5C[Si](C)(C)N([C@@H](CCC[C@@H](C(=O)O)N([Si](C)(C)C)[Si](C)(C)C)C(=O)O)[Si](C)(C)C2272.7Semi standard non polar33892256
Diaminopimelic acid,4TMS,isomer #5C[Si](C)(C)N([C@@H](CCC[C@@H](C(=O)O)N([Si](C)(C)C)[Si](C)(C)C)C(=O)O)[Si](C)(C)C2210.3Standard non polar33892256
Diaminopimelic acid,4TMS,isomer #5C[Si](C)(C)N([C@@H](CCC[C@@H](C(=O)O)N([Si](C)(C)C)[Si](C)(C)C)C(=O)O)[Si](C)(C)C2526.3Standard polar33892256
Diaminopimelic acid,5TMS,isomer #1C[Si](C)(C)N[C@@H](CCC[C@@H](C(=O)O[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C)C(=O)O[Si](C)(C)C2144.3Semi standard non polar33892256
Diaminopimelic acid,5TMS,isomer #1C[Si](C)(C)N[C@@H](CCC[C@@H](C(=O)O[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C)C(=O)O[Si](C)(C)C2183.1Standard non polar33892256
Diaminopimelic acid,5TMS,isomer #1C[Si](C)(C)N[C@@H](CCC[C@@H](C(=O)O[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C)C(=O)O[Si](C)(C)C2158.3Standard polar33892256
Diaminopimelic acid,5TMS,isomer #2C[Si](C)(C)OC(=O)[C@H](CCC[C@@H](C(=O)O)N([Si](C)(C)C)[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C2302.1Semi standard non polar33892256
Diaminopimelic acid,5TMS,isomer #2C[Si](C)(C)OC(=O)[C@H](CCC[C@@H](C(=O)O)N([Si](C)(C)C)[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C2270.0Standard non polar33892256
Diaminopimelic acid,5TMS,isomer #2C[Si](C)(C)OC(=O)[C@H](CCC[C@@H](C(=O)O)N([Si](C)(C)C)[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C2277.6Standard polar33892256
Diaminopimelic acid,6TMS,isomer #1C[Si](C)(C)OC(=O)[C@H](CCC[C@@H](C(=O)O[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C2409.4Semi standard non polar33892256
Diaminopimelic acid,6TMS,isomer #1C[Si](C)(C)OC(=O)[C@H](CCC[C@@H](C(=O)O[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C2283.1Standard non polar33892256
Diaminopimelic acid,6TMS,isomer #1C[Si](C)(C)OC(=O)[C@H](CCC[C@@H](C(=O)O[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C2140.3Standard polar33892256
Diaminopimelic acid,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC(=O)[C@@H](N)CCC[C@H](N)C(=O)O2102.4Semi standard non polar33892256
Diaminopimelic acid,1TBDMS,isomer #2CC(C)(C)[Si](C)(C)N[C@@H](CCC[C@H](N)C(=O)O)C(=O)O2219.9Semi standard non polar33892256
Diaminopimelic acid,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC(=O)[C@@H](N)CCC[C@H](N)C(=O)O[Si](C)(C)C(C)(C)C2290.5Semi standard non polar33892256
Diaminopimelic acid,2TBDMS,isomer #2CC(C)(C)[Si](C)(C)N[C@@H](CCC[C@H](N)C(=O)O)C(=O)O[Si](C)(C)C(C)(C)C2410.7Semi standard non polar33892256
Diaminopimelic acid,2TBDMS,isomer #3CC(C)(C)[Si](C)(C)N[C@@H](CCC[C@H](N)C(=O)O[Si](C)(C)C(C)(C)C)C(=O)O2398.7Semi standard non polar33892256
Diaminopimelic acid,2TBDMS,isomer #4CC(C)(C)[Si](C)(C)N[C@@H](CCC[C@H](N[Si](C)(C)C(C)(C)C)C(=O)O)C(=O)O2496.6Semi standard non polar33892256
Diaminopimelic acid,2TBDMS,isomer #5CC(C)(C)[Si](C)(C)N([C@@H](CCC[C@H](N)C(=O)O)C(=O)O)[Si](C)(C)C(C)(C)C2554.6Semi standard non polar33892256
Diaminopimelic acid,3TBDMS,isomer #1CC(C)(C)[Si](C)(C)N[C@@H](CCC[C@H](N)C(=O)O[Si](C)(C)C(C)(C)C)C(=O)O[Si](C)(C)C(C)(C)C2584.1Semi standard non polar33892256
Diaminopimelic acid,3TBDMS,isomer #1CC(C)(C)[Si](C)(C)N[C@@H](CCC[C@H](N)C(=O)O[Si](C)(C)C(C)(C)C)C(=O)O[Si](C)(C)C(C)(C)C2596.8Standard non polar33892256
Diaminopimelic acid,3TBDMS,isomer #1CC(C)(C)[Si](C)(C)N[C@@H](CCC[C@H](N)C(=O)O[Si](C)(C)C(C)(C)C)C(=O)O[Si](C)(C)C(C)(C)C2919.1Standard polar33892256
Diaminopimelic acid,3TBDMS,isomer #2CC(C)(C)[Si](C)(C)N[C@@H](CCC[C@H](N[Si](C)(C)C(C)(C)C)C(=O)O[Si](C)(C)C(C)(C)C)C(=O)O2677.8Semi standard non polar33892256
Diaminopimelic acid,3TBDMS,isomer #2CC(C)(C)[Si](C)(C)N[C@@H](CCC[C@H](N[Si](C)(C)C(C)(C)C)C(=O)O[Si](C)(C)C(C)(C)C)C(=O)O2570.7Standard non polar33892256
Diaminopimelic acid,3TBDMS,isomer #2CC(C)(C)[Si](C)(C)N[C@@H](CCC[C@H](N[Si](C)(C)C(C)(C)C)C(=O)O[Si](C)(C)C(C)(C)C)C(=O)O2767.6Standard polar33892256
Diaminopimelic acid,3TBDMS,isomer #3CC(C)(C)[Si](C)(C)OC(=O)[C@H](CCC[C@H](N)C(=O)O)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C2756.3Semi standard non polar33892256
Diaminopimelic acid,3TBDMS,isomer #3CC(C)(C)[Si](C)(C)OC(=O)[C@H](CCC[C@H](N)C(=O)O)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C2627.0Standard non polar33892256
Diaminopimelic acid,3TBDMS,isomer #3CC(C)(C)[Si](C)(C)OC(=O)[C@H](CCC[C@H](N)C(=O)O)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C3057.1Standard polar33892256
Diaminopimelic acid,3TBDMS,isomer #4CC(C)(C)[Si](C)(C)OC(=O)[C@@H](N)CCC[C@@H](C(=O)O)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C2733.4Semi standard non polar33892256
Diaminopimelic acid,3TBDMS,isomer #4CC(C)(C)[Si](C)(C)OC(=O)[C@@H](N)CCC[C@@H](C(=O)O)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C2635.1Standard non polar33892256
Diaminopimelic acid,3TBDMS,isomer #4CC(C)(C)[Si](C)(C)OC(=O)[C@@H](N)CCC[C@@H](C(=O)O)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C2951.5Standard polar33892256
Diaminopimelic acid,3TBDMS,isomer #5CC(C)(C)[Si](C)(C)N[C@@H](CCC[C@@H](C(=O)O)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)C(=O)O2833.0Semi standard non polar33892256
Diaminopimelic acid,3TBDMS,isomer #5CC(C)(C)[Si](C)(C)N[C@@H](CCC[C@@H](C(=O)O)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)C(=O)O2613.3Standard non polar33892256
Diaminopimelic acid,3TBDMS,isomer #5CC(C)(C)[Si](C)(C)N[C@@H](CCC[C@@H](C(=O)O)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)C(=O)O2845.2Standard polar33892256
Diaminopimelic acid,4TBDMS,isomer #1CC(C)(C)[Si](C)(C)N[C@@H](CCC[C@H](N[Si](C)(C)C(C)(C)C)C(=O)O[Si](C)(C)C(C)(C)C)C(=O)O[Si](C)(C)C(C)(C)C2852.2Semi standard non polar33892256
Diaminopimelic acid,4TBDMS,isomer #1CC(C)(C)[Si](C)(C)N[C@@H](CCC[C@H](N[Si](C)(C)C(C)(C)C)C(=O)O[Si](C)(C)C(C)(C)C)C(=O)O[Si](C)(C)C(C)(C)C2771.1Standard non polar33892256
Diaminopimelic acid,4TBDMS,isomer #1CC(C)(C)[Si](C)(C)N[C@@H](CCC[C@H](N[Si](C)(C)C(C)(C)C)C(=O)O[Si](C)(C)C(C)(C)C)C(=O)O[Si](C)(C)C(C)(C)C2691.5Standard polar33892256
Diaminopimelic acid,4TBDMS,isomer #2CC(C)(C)[Si](C)(C)OC(=O)[C@@H](N)CCC[C@@H](C(=O)O[Si](C)(C)C(C)(C)C)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C2985.8Semi standard non polar33892256
Diaminopimelic acid,4TBDMS,isomer #2CC(C)(C)[Si](C)(C)OC(=O)[C@@H](N)CCC[C@@H](C(=O)O[Si](C)(C)C(C)(C)C)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C2842.1Standard non polar33892256
Diaminopimelic acid,4TBDMS,isomer #2CC(C)(C)[Si](C)(C)OC(=O)[C@@H](N)CCC[C@@H](C(=O)O[Si](C)(C)C(C)(C)C)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C2907.7Standard polar33892256
Diaminopimelic acid,4TBDMS,isomer #3CC(C)(C)[Si](C)(C)N[C@@H](CCC[C@@H](C(=O)O)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)C(=O)O[Si](C)(C)C(C)(C)C3026.1Semi standard non polar33892256
Diaminopimelic acid,4TBDMS,isomer #3CC(C)(C)[Si](C)(C)N[C@@H](CCC[C@@H](C(=O)O)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)C(=O)O[Si](C)(C)C(C)(C)C2827.2Standard non polar33892256
Diaminopimelic acid,4TBDMS,isomer #3CC(C)(C)[Si](C)(C)N[C@@H](CCC[C@@H](C(=O)O)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)C(=O)O[Si](C)(C)C(C)(C)C2746.3Standard polar33892256
Diaminopimelic acid,4TBDMS,isomer #4CC(C)(C)[Si](C)(C)N[C@@H](CCC[C@@H](C(=O)O[Si](C)(C)C(C)(C)C)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)C(=O)O3049.6Semi standard non polar33892256
Diaminopimelic acid,4TBDMS,isomer #4CC(C)(C)[Si](C)(C)N[C@@H](CCC[C@@H](C(=O)O[Si](C)(C)C(C)(C)C)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)C(=O)O2828.7Standard non polar33892256
Diaminopimelic acid,4TBDMS,isomer #4CC(C)(C)[Si](C)(C)N[C@@H](CCC[C@@H](C(=O)O[Si](C)(C)C(C)(C)C)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)C(=O)O2774.3Standard polar33892256
Diaminopimelic acid,4TBDMS,isomer #5CC(C)(C)[Si](C)(C)N([C@@H](CCC[C@@H](C(=O)O)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)C(=O)O)[Si](C)(C)C(C)(C)C3149.5Semi standard non polar33892256
Diaminopimelic acid,4TBDMS,isomer #5CC(C)(C)[Si](C)(C)N([C@@H](CCC[C@@H](C(=O)O)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)C(=O)O)[Si](C)(C)C(C)(C)C2884.6Standard non polar33892256
Diaminopimelic acid,4TBDMS,isomer #5CC(C)(C)[Si](C)(C)N([C@@H](CCC[C@@H](C(=O)O)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)C(=O)O)[Si](C)(C)C(C)(C)C2812.2Standard polar33892256
Diaminopimelic acid,5TBDMS,isomer #1CC(C)(C)[Si](C)(C)N[C@@H](CCC[C@@H](C(=O)O[Si](C)(C)C(C)(C)C)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)C(=O)O[Si](C)(C)C(C)(C)C3257.9Semi standard non polar33892256
Diaminopimelic acid,5TBDMS,isomer #1CC(C)(C)[Si](C)(C)N[C@@H](CCC[C@@H](C(=O)O[Si](C)(C)C(C)(C)C)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)C(=O)O[Si](C)(C)C(C)(C)C2997.0Standard non polar33892256
Diaminopimelic acid,5TBDMS,isomer #1CC(C)(C)[Si](C)(C)N[C@@H](CCC[C@@H](C(=O)O[Si](C)(C)C(C)(C)C)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)C(=O)O[Si](C)(C)C(C)(C)C2710.0Standard polar33892256
Diaminopimelic acid,5TBDMS,isomer #2CC(C)(C)[Si](C)(C)OC(=O)[C@H](CCC[C@@H](C(=O)O)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C3363.2Semi standard non polar33892256
Diaminopimelic acid,5TBDMS,isomer #2CC(C)(C)[Si](C)(C)OC(=O)[C@H](CCC[C@@H](C(=O)O)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C3063.4Standard non polar33892256
Diaminopimelic acid,5TBDMS,isomer #2CC(C)(C)[Si](C)(C)OC(=O)[C@H](CCC[C@@H](C(=O)O)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C2745.0Standard polar33892256
Diaminopimelic acid,6TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC(=O)[C@H](CCC[C@@H](C(=O)O[Si](C)(C)C(C)(C)C)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C3653.2Semi standard non polar33892256
Diaminopimelic acid,6TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC(=O)[C@H](CCC[C@@H](C(=O)O[Si](C)(C)C(C)(C)C)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C3242.6Standard non polar33892256
Diaminopimelic acid,6TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC(=O)[C@H](CCC[C@@H](C(=O)O[Si](C)(C)C(C)(C)C)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C2764.7Standard polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Experimental GC-MSGC-MS Spectrum - Diaminopimelic acid GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (4 TMS)splash10-0umi-1950000000-749403a0eb6d05c7903e2014-06-16HMDB team, MONA, MassBankView Spectrum
Experimental GC-MSGC-MS Spectrum - Diaminopimelic acid GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (4 TMS)splash10-0uk9-1980000000-1b092f9141e7549bee242014-06-16HMDB team, MONA, MassBankView Spectrum
Experimental GC-MSGC-MS Spectrum - Diaminopimelic acid GC-EI-TOF (Non-derivatized)splash10-0umi-1950000000-749403a0eb6d05c7903e2017-09-12HMDB team, MONA, MassBankView Spectrum
Experimental GC-MSGC-MS Spectrum - Diaminopimelic acid GC-EI-TOF (Non-derivatized)splash10-0uk9-1980000000-1b092f9141e7549bee242017-09-12HMDB team, MONA, MassBankView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Diaminopimelic acid GC-MS (Non-derivatized) - 70eV, Positivesplash10-00dm-9500000000-5d0aafd0747a1090e0552016-09-22Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Diaminopimelic acid GC-MS (2 TMS) - 70eV, Positivesplash10-014i-4590000000-b941e92697a8b78009122017-10-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Diaminopimelic acid GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Experimental LC-MS/MSLC-MS/MS Spectrum - Diaminopimelic acid Quattro_QQQ 10V, Positive-QTOF (Annotated)splash10-004l-0900000000-d85213bd7ac426f10cd72012-07-24HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Diaminopimelic acid Quattro_QQQ 25V, Positive-QTOF (Annotated)splash10-001i-9100000000-add590f1b216bdb403342012-07-24HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Diaminopimelic acid Quattro_QQQ 40V, Positive-QTOF (Annotated)splash10-001i-9000000000-de98ed3bb8c48b6f98522012-07-24HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Diaminopimelic acid 10V, Positive-QTOFsplash10-004i-0900000000-2c8a0ca138ef6ea5ef432021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Diaminopimelic acid 20V, Positive-QTOFsplash10-003r-9600000000-19f54d2417fe44d0eba32021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Diaminopimelic acid 10V, Negative-QTOFsplash10-000i-0900000000-e8b0bbffeaa501a6fedd2021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Diaminopimelic acid 40V, Positive-QTOFsplash10-0a4i-9000000000-91296097628a67dd97ef2021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Diaminopimelic acid 40V, Positive-QTOFsplash10-0a4i-9000000000-e5c4e034dcab0695e0ce2021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Diaminopimelic acid 35V, Negative-QTOFsplash10-002r-0900000000-2a19445fee9eade1d5382021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Diaminopimelic acid 40V, Negative-QTOFsplash10-00di-9000000000-f44538bc8ae3a51cbbc62021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Diaminopimelic acid 20V, Positive-QTOFsplash10-003r-9700000000-3baa36a29b4ed6172da02021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Diaminopimelic acid 10V, Positive-QTOFsplash10-004i-1900000000-cf39d89ce72ac9ddaf512021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Diaminopimelic acid 20V, Negative-QTOFsplash10-0200-6900000000-6f21b7798408480c1bfc2021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Diaminopimelic acid 20V, Positive-QTOFsplash10-001i-9300000000-6e778092666f89ff42112021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Diaminopimelic acid 10V, Positive-QTOFsplash10-004i-0900000000-28fbb202ae5558af75942021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Diaminopimelic acid 35V, Positive-QTOFsplash10-004i-1900000000-8a1ee3da7fbe94f840c22021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Diaminopimelic acid 40V, Positive-QTOFsplash10-0a4i-9000000000-8caae42eda716644fdc12021-09-20HMDB team, MONAView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Diaminopimelic acid 10V, Positive-QTOFsplash10-0005-1900000000-be94a16bee7fad24d5d92016-09-14Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Diaminopimelic acid 20V, Positive-QTOFsplash10-0002-5900000000-896859ce722942f9dd682016-09-14Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Diaminopimelic acid 40V, Positive-QTOFsplash10-006t-9200000000-50c1b5a4f7b19e8ff0db2016-09-14Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Diaminopimelic acid 10V, Negative-QTOFsplash10-000i-0900000000-5ecd829b51ba774883f62016-09-14Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Diaminopimelic acid 20V, Negative-QTOFsplash10-000i-1900000000-53b7aee01233b5b73d3e2016-09-14Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Diaminopimelic acid 40V, Negative-QTOFsplash10-00di-9400000000-2cc35eb21a44b2d472b52016-09-14Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Diaminopimelic acid 10V, Negative-QTOFsplash10-0079-0900000000-a0ce1f9601e9b8d83ccf2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Diaminopimelic acid 20V, Negative-QTOFsplash10-00dj-6900000000-cc22f522673c5549366c2021-09-22Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Experimental 1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, experimental)2012-12-04Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Experimental 2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, H2O, experimental)2012-12-05Wishart LabView Spectrum

IR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M-H]-)2023-02-03FELIX labView Spectrum
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+H]+)2023-02-03FELIX labView Spectrum
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+Na]+)2023-02-03FELIX labView Spectrum
Biological Properties
Cellular Locations
  • Cytoplasm (predicted from logP)
Biospecimen Locations
  • Blood
  • Feces
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot QuantifiedNot AvailableNot Available
Normal
      Not Available
 details
BloodDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothNormal details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
UrineDetected and Quantified0.08 +/-0.03 umol/mmol creatinineAdult (>18 years old)Not SpecifiedNormal details
UrineDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothNormal details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Colorectal cancer		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothColorectal Cancer details
Associated Disorders and Diseases
Disease References
Colorectal cancer
  1. Brown DG, Rao S, Weir TL, O'Malia J, Bazan M, Brown RJ, Ryan EP: Metabolomics and metabolic pathway networks from human colorectal cancers, adjacent mucosa, and stool. Cancer Metab. 2016 Jun 6;4:11. doi: 10.1186/s40170-016-0151-y. eCollection 2016. [PubMed:27275383 ]
  2. Goedert JJ, Sampson JN, Moore SC, Xiao Q, Xiong X, Hayes RB, Ahn J, Shi J, Sinha R: Fecal metabolomics: assay performance and association with colorectal cancer. Carcinogenesis. 2014 Sep;35(9):2089-96. doi: 10.1093/carcin/bgu131. Epub 2014 Jul 18. [PubMed:25037050 ]
Associated OMIM IDs
DrugBank IDDB03590
Phenol Explorer Compound IDNot Available
FooDB IDFDB022583
KNApSAcK IDC00007596
Chemspider ID388416
KEGG Compound IDC00666
BioCyc IDLL-DIAMINOPIMELATE
BiGG IDNot Available
Wikipedia LinkDiaminopimelic acid
METLIN ID352
PubChem Compound439283
PDB IDNot Available
ChEBI ID16026
Food Biomarker OntologyNot Available
VMH ID26DAP_LL
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceGao, Yong. Synthesis of diaminopimelic acid (DAP) and analogues: mechanistic studies on DAP aminotransferase, epimerase and dehydrogenase. (1998), 166 pp.
Material Safety Data Sheet (MSDS)Download (PDF)
General References
  1. Iida S, Taniguchi H, Kageyama A, Yazawa K, Chibana H, Murata S, Nomura F, Kroppenstedt RM, Mikami Y: Gordonia otitidis sp. nov., isolated from a patient with external otitis. Int J Syst Evol Microbiol. 2005 Sep;55(Pt 5):1871-6. [PubMed:16166681 ]
  2. Ladesic B, Tomasic J, Kveder S, Hrsak I: The metabolic fate of 14C-labeled immunoadjuvant peptidoglycan monomer. II. In vitro studies. Biochim Biophys Acta. 1981 Nov 18;678(1):12-7. [PubMed:6118181 ]
  3. Borruat G, Roten CA, Fay LB, Karamata D: A high-performance liquid chromatography method for the detection of diaminopimelic acid in urine. Anal Biochem. 2001 Apr 1;291(1):11-6. [PubMed:11262151 ]
  4. Hamaker BR, Rivera K, Morales E, Graham GG: Effect of dietary fiber and starch on fecal composition in preschool children consuming maize, amaranth, or cassava flours. J Pediatr Gastroenterol Nutr. 1991 Jul;13(1):59-66. [PubMed:1656007 ]