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Showing NP-Card for Diaminopimelic acid (NP0000674)

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Record Information
Version2.0
Created at2005-11-16 15:48:42 UTC
Updated at2020-11-24 22:17:23 UTC
NP-MRD IDNP0000674
Secondary Accession NumbersNone
Natural Product 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
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0000674 (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 NP0000674 (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 NP0000674 (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>
NP0000674

> <DATABASE_NAME>
NP-MRD

> <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 NP0000674 (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 NP0000674 (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 NP0000674 (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 NP0000674 (Diaminopimelic acid)

N[C@@H](CCC[C@H](N)C(O)=O)C(O)=O
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INCHI for NP0000674 (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 JSmol
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
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, diaminopimelicHMDB
2,6 Diaminopimelic acidHMDB
Acid, 2,6-diaminopimelicHMDB
Diamino-pimelateHMDB
Diaminopimelic acidMeSH
Chemical FormulaC7H14N2O4
Average Mass190.1971 Da
Monoisotopic Mass190.09536 Da
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
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, H2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Abelmoschus esculentusFooDB
Actinidia chinensisFooDB
Agaricus bisporusFooDB
AgaveFooDB
Allium ampeloprasumFooDB
Allium ascalonicumFooDB
Allium cepaFooDB
Allium cepa L.FooDB
Allium fistulosumFooDB
Allium sativumFooDB
Allium schoenoprasumFooDB
Allium tuberosumFooDB
Aloysia triphyllaFooDB
AmaranthusFooDB
Amelanchier alnifoliaFooDB
Anacardium occidentaleFooDB
Ananas comosusFooDB
Anethum graveolensFooDB
Angelica keiskeiFooDB
Annona cherimolaFooDB
Annona muricataFooDB
Annona reticulataFooDB
Annona squamosaFooDB
Anthriscus cerefoliumFooDB
Apium graveolensFooDB
Apium graveolens var. dulceFooDB
Apium graveolens var. rapaceumFooDB
Apium graveolens var. secalinumFooDB
Arabidopsis thalianaPlant
Arachis hypogaeaFooDB
Arctium lappaFooDB
Armoracia rusticanaFooDB
Artemisia dracunculusFooDB
Artemisia vulgarisFooDB
Artocarpus altilisFooDB
Artocarpus heterophyllusFooDB
Asparagus officinalisFooDB
Attalea speciosaFooDB
Auricularia auricula-judaeFooDB
Auricularia polytrichaFooDB
Avena sativa L.FooDB
Averrhoa carambolaFooDB
Basella albaFooDB
Benincasa hispidaFooDB
Bertholletia excelsaFooDB
Beta vulgarisFooDB
Beta vulgaris ssp. ciclaFooDB
Borago officinalisFooDB
Brassica alboglabraFooDB
Brassica junceaFooDB
Brassica napusFooDB
Brassica napus var. napusFooDB
Brassica oleraceaFooDB
Brassica oleracea var. botrytisFooDB
Brassica oleracea var. capitataFooDB
Brassica oleracea var. gemmiferaFooDB
Brassica oleracea var. gongylodesFooDB
Brassica oleracea var. italicaFooDB
Brassica oleracea var. sabaudaFooDB
Brassica oleracea var. viridisFooDB
Brassica rapaFooDB
Brassica rapa ssp. chinensisFooDB
Brassica rapa var. pekinensisFooDB
Brassica rapa var. rapaFooDB
Brassica ruvoFooDB
Brosimum alicastrumFooDB
Byrsonima crassifoliaFooDB
Cajanus cajanFooDB
Canarium ovatumFooDB
Cannabis sativaCannabisDB
      Not Available
Cantharellus cibariusFooDB
Capparis spinosaFooDB
Capsicum annuumFooDB
Capsicum annuum L.FooDB
Capsicum annuum var. annuumFooDB
Capsicum chinenseFooDB
Capsicum pubescensFooDB
Carica papaya L.FooDB
Carissa macrocarpaFooDB
Carthamus tinctoriusFooDB
Carum carviFooDB
CaryaFooDB
Carya illinoinensisFooDB
CastaneaFooDB
Castanea crenataFooDB
Castanea mollissimaFooDB
Castanea sativaFooDB
Ceratonia siliquaFooDB
Chamaemelum nobileFooDB
Chamerion angustifoliumFooDB
Chenopodium albumFooDB
Chenopodium quinoaFooDB
Chrysanthemum coronariumFooDB
Cicer arietinumFooDB
Cichorium endiviaFooDB
Cichorium intybusFooDB
CinnamomumFooDB
Cinnamomum aromaticumFooDB
Cinnamomum verumFooDB
CirsiumFooDB
Citrullus lanatusFooDB
Citrus ×limon (L.) Burm. f. (pro sp.)FooDB
Citrus aurantiifoliaFooDB
Citrus latifoliaFooDB
Citrus limonFooDB
Citrus maximaFooDB
Citrus paradisiFooDB
Citrus reticulataFooDB
Citrus X sinensis (L.) Osbeck (pro. sp.)FooDB
Cocos nuciferaFooDB
Coffea arabica L.FooDB
Coffea canephoraFooDB
Colocasia esculentaFooDB
Corchorus olitoriusFooDB
Coriandrum sativum L.FooDB
CorylusFooDB
Corylus avellanaFooDB
Crateva religiosaFooDB
Crocus sativusFooDB
Cucumis meloFooDB
Cucumis metuliferusFooDB
Cucumis sativus L.FooDB
CucurbitaFooDB
Cucurbita maximaFooDB
Cucurbita moschataFooDB
Cuminum cyminumFooDB
Curcuma longaFooDB
Cydonia oblongaFooDB
Cymbopogon citratusFooDB
Cynara cardunculusFooDB
Cynara scolymusFooDB
Daucus carotaFooDB
Daucus carota ssp. sativusFooDB
Dimocarpus longanFooDB
DioscoreaFooDB
Dioscorea pentaphyllaFooDB
DiospyrosFooDB
Diospyros kakiFooDB
Diospyros virginianaFooDB
Durio zibethinusFooDB
Dysphania ambrosioidesFooDB
ElaeisFooDB
Eleocharis dulcisFooDB
Elettaria cardamomumFooDB
Empetrum nigrumFooDB
Eragrostis tefFooDB
Eriobotrya japonicaFooDB
Eruca vesicaria subsp. SativaFooDB
Escherichia coliBacteria
Eugenia javanicaFooDB
Eugenia unifloraFooDB
Eutrema japonicumFooDB
Fagopyrum esculentumFooDB
Fagopyrum tataricumFooDB
FagusFooDB
Feijoa sellowianaFooDB
Ficus caricaFooDB
Flammulina velutipesFooDB
Foeniculum vulgareFooDB
Fragaria x ananassaFooDB
Garcinia mangostanaFooDB
Gaylussacia baccataFooDB
Ginkgo bilobaFooDB
Glycine maxFooDB
GossypiumFooDB
Grifola frondosaFooDB
Hedysarum alpinumFooDB
Helianthus annuus L.FooDB
Helianthus tuberosusFooDB
Hibiscus sabbariffaFooDB
Hippophae rhamnoidesFooDB
Hordeum vulgareFooDB
Hyssopus officinalis L.FooDB
Illicium verumFooDB
Ipomoea aquaticaFooDB
Ipomoea batatasFooDB
JuglansFooDB
Juglans ailanthifoliaFooDB
Juglans cinereaFooDB
Juglans nigra L.FooDB
Juglans regiaFooDB
Lablab purpureusFooDB
Lactuca sativaFooDB
Lagenaria sicerariaFooDB
Lathyrus sativusFooDB
Laurus nobilis L.FooDB
Lens culinarisFooDB
Lentinus edodesFooDB
Lepidium sativumFooDB
Levisticum officinaleFooDB
Linum usitatissimumFooDB
Litchi chinensisFooDB
Luffa aegyptiacaFooDB
LupinusFooDB
Lupinus albusFooDB
MacadamiaFooDB
Macadamia tetraphyllaFooDB
Malpighia emarginataFooDB
MalusFooDB
Malus pumilaFooDB
Mammea americanaFooDB
Mangifera indicaFooDB
Manihot esculentaFooDB
Manilkara zapotaFooDB
Maranta arundinaceaFooDB
Matricaria recutitaFooDB
Matteuccia struthiopterisFooDB
Medicago sativaFooDB
Melissa officinalis L.FooDB
MenthaFooDB
Mentha aquaticaFooDB
Mentha arvensisFooDB
Mentha spicataFooDB
Mentha x piperitaFooDB
Mespilus germanicaFooDB
Metroxylon saguFooDB
Momordica charantiaFooDB
MorchellaceaeFooDB
Morella rubraFooDB
Moringa oleiferaFooDB
MorusFooDB
Morus nigraFooDB
Musa acuminataFooDB
Musa x paradisiacaFooDB
MyricaFooDB
Myristica fragransFooDB
NelumboFooDB
Nelumbo nuciferaFooDB
Nephelium lappaceumFooDB
Nuphar luteaFooDB
Ocimum basilicumFooDB
Oenothera biennisFooDB
Olea europaeaFooDB
OpuntiaFooDB
Opuntia cochenilliferaFooDB
Opuntia macrorhizaFooDB
Origanum majoranaFooDB
Origanum onitesFooDB
Origanum vulgareFooDB
Origanum X majoricumFooDB
Oryza rufipogonFooDB
Oryza sativaFooDB
Pachyrhizus erosusFooDB
Panax ginsengFooDB
Pangium eduleFooDB
Panicum miliaceumFooDB
Passiflora edulisFooDB
Pastinaca sativaFooDB
Pediomelum esculentumFooDB
Perideridia oreganaFooDB
Persea americanaFooDB
Petasites japonicusFooDB
Petroselinum crispumFooDB
Phaseolus coccineusFooDB
Phaseolus lunatusFooDB
Phaseolus vulgarisFooDB
Phoenix dactyliferaFooDB
Photinia melanocarpaFooDB
Phyllostachys edulisFooDB
PhysalisFooDB
Physalis philadelphica var. immaculataFooDB
Phytolacca americanaFooDB
Pimenta dioicaFooDB
Pimpinella anisumFooDB
PinusFooDB
Pinus edulisFooDB
Piper nigrum L.FooDB
Pistacia veraFooDB
Pisum sativumFooDB
Pleurotus ostreatusFooDB
Polygonum alpinumFooDB
Portulaca oleraceaFooDB
Pouteria sapotaFooDB
Prunus armeniacaFooDB
Prunus aviumFooDB
Prunus avium L.FooDB
Prunus cerasusFooDB
Prunus domesticaFooDB
Prunus dulcisFooDB
Prunus persicaFooDB
Prunus persica var. nucipersicaFooDB
Prunus persica var. persicaFooDB
Prunus tomentosaFooDB
Prunus virginianaFooDB
Psidium cattleianumFooDB
Psidium guajavaFooDB
Psophocarpus tetragonolobusFooDB
Punica granatumFooDB
Pyrus communisFooDB
Pyrus pyrifoliaFooDB
QuercusFooDB
Raphanus sativusFooDB
Raphanus sativus var. longipinnatusFooDB
Raphanus sativus var. sativusFooDB
Rheum rhabarbarumFooDB
Ribes aureumFooDB
Ribes glandulosumFooDB
Ribes nigrumFooDB
Ribes rubrumFooDB
Ribes uva-crispaFooDB
RosaFooDB
Rubus arcticusFooDB
Rubus chamaemorusFooDB
Rubus idaeusFooDB
Rubus occidentalisFooDB
Rubus spectabilisFooDB
RumexFooDB
Rumex acetosaFooDB
Rumex articusFooDB
Sagittaria latifoliaFooDB
Salix pulchraFooDB
Salvia elegansFooDB
Salvia hispanicaFooDB
Salvia officinalisFooDB
Salvia rosmarinusFooDB
Sambucus nigraFooDB
Sambucus nigra L.FooDB
Satureja hortensis L.FooDB
Satureja montanaFooDB
Scorzonera hispanicaFooDB
Secale cerealeFooDB
Sechium eduleFooDB
Sesamum indicumFooDB
Sesbania bispinosaFooDB
Sinapis albaFooDB
SisymbriumFooDB
Solanum lycopersicumFooDB
Solanum lycopersicum var. cerasiformeFooDB
Solanum lycopersicum var. lycopersicumFooDB
Solanum melongenaFooDB
Solanum quitoenseFooDB
Solanum tuberosumFooDB
Sorbus aucupariaFooDB
Sorghum bicolorFooDB
Spinacia oleraceaFooDB
Streptomyces coacervatusLOTUS Database
Streptomyces daliensisLOTUS Database
Streptomyces fenghuangensisLOTUS Database
Streptomyces fildesensisLOTUS Database
Streptomyces fradiaeLOTUS Database
Streptomyces hebeiensisLOTUS Database
Streptomyces indicusLOTUS Database
Syzygium aromaticumFooDB
Syzygium cuminiFooDB
Syzygium jambosFooDB
Tamarindus indicaFooDB
Taraxacum officinaleFooDB
Tetragonia tetragonioidesFooDB
ThelespermaFooDB
Thymus pulegioidesFooDB
Thymus vulgarisFooDB
Tilia cordataFooDB
Tilia L.FooDB
Tragopogon porrifoliusFooDB
Trigonella foenum-graecumFooDB
TriticumFooDB
Triticum aestivumFooDB
Triticum durumFooDB
Triticum speltaFooDB
Triticum turanicumFooDB
Typha angustifoliaFooDB
VacciniumFooDB
Vaccinium angustifoliumFooDB
Vaccinium angustifolium X Vaccinium corymbosumFooDB
Vaccinium arboreumFooDB
Vaccinium corymbosumFooDB
Vaccinium deliciosumFooDB
Vaccinium elliottiiFooDB
Vaccinium macrocarponFooDB
Vaccinium myrtilloidesFooDB
Vaccinium myrtillusFooDB
Vaccinium ovalifoliumFooDB
Vaccinium ovatumFooDB
Vaccinium oxycoccosFooDB
Vaccinium parvifoliumFooDB
Vaccinium reticulatumFooDB
Vaccinium stamineumFooDB
Vaccinium uliginosumFooDB
Vaccinium vitis-idaeaFooDB
Valerianella locustaFooDB
VanillaFooDB
Verbena officinalisFooDB
Viburnum eduleFooDB
Vicia fabaFooDB
Vigna aconitifoliaFooDB
Vigna angularisFooDB
Vigna mungoFooDB
Vigna radiataFooDB
Vigna umbellataFooDB
Vigna unguiculataFooDB
Vigna unguiculata ssp. cylindricaFooDB
Vigna unguiculata ssp. unguiculataFooDB
Vigna unguiculata var. sesquipedalisFooDB
VitisFooDB
Vitis aestivalisFooDB
Vitis labruscaFooDB
Vitis rotundifoliaFooDB
Vitis vinifera L.FooDB
Xanthosoma sagittifoliumFooDB
Zea mays L.FooDB
Zingiber officinaleFooDB
ZizaniaFooDB
Zizania aquaticaFooDB
Ziziphus zizyphusFooDB
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
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting Point300 °CNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted 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
HMDB IDHMDB0001370
DrugBank IDDB03590
Phenol Explorer Compound IDNot Available
FoodDB IDFDB030951
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
Good Scents IDNot Available
References
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 ]