Showing metabocard for LL-2,6-Diaminoheptanedioate (MMDBc0049924)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2022-04-29 22:46:23 UTC
Update Date2022-12-15 22:52:19 UTC
Metabolite IDMMDBc0049924
Metabolite Identification
Common NameLL-2,6-Diaminoheptanedioate
DescriptionLL-2,6-Diaminoheptanedioate, also known as diaminopimelic 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
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007f9200db6200>


  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 #<Metabolite:0x00007f9200db6200>

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 #<Metabolite:0x00007f9200db6200>


  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>
MMDBc0049924

> <DATABASE_NAME>
MIME

> <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 #<Metabolite:0x00007f9200db6200>

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
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PDB for #<Metabolite:0x00007f9200db6200>

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 #<Metabolite:0x00007f9200db6200>

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 #<Metabolite:0x00007f9200db6200>

N[C@@H](CCC[C@H](N)C(O)=O)C(O)=O
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INCHI for #<Metabolite:0x00007f9200db6200>

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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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
Molecular FormulaC7H14N2O4
Average Mass190.1971
Monoisotopic Mass190.095356946
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