Np mrd loader

Showing NP-Card for DL-alpha,epsilon-Diaminopimelic acid (NP0002726)

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Record Information
Version1.0
Created at2020-11-23 19:38:55 UTC
Updated at2021-08-12 19:51:58 UTC
NP-MRD IDNP0002726
Secondary Accession NumbersNone
Natural Product Identification
Common NameDL-alpha,epsilon-Diaminopimelic acid
Provided ByBMRBBMRB logo
DescriptionMeso-diaminopimelate 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. It was first documented in 2001 (PMID: 11262151). Based on a literature review a significant number of articles have been published on meso-diaminopimelate (PMID: 17984079) (PMID: 20803494) (PMID: 22339732) (PMID: 23325104).
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0002726 (DL-alpha,epsilon-Diaminopimelic acid)


     RDKit          2D

 27 26  0  0  0  0  0  0  0  0999 V2000
   -2.5974    2.1222    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9268    0.6588    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4634    0.3294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4634   -0.3294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9268   -0.6588    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5974   -2.1222    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.2562    0.8046    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2857    1.9484    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6882    1.2510    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2562   -0.8046    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2857   -1.9484    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6882   -1.2510    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7000    3.1391    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2304    2.7398    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3902    0.9882    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9581    1.7417    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6119   -1.1632    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3294    1.4634    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3294   -1.4634    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9581   -1.7417    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6119    1.1632    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3902   -0.9882    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7000   -3.1391    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2304   -2.7398    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0176    2.7144    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0176   -2.7144    0.0000 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  6
  3 17  1  1
  3 18  1  0
  4 19  1  1
  4 20  1  0
  5 21  1  1
  5 22  1  0
  6 23  1  1
  7 24  1  0
  7 25  1  0
 10 26  1  0
 13 27  1  0
M  END
Download

3D MOL for NP0002726 (DL-alpha,epsilon-Diaminopimelic acid)

NP0002726
     RDKit          3D

 27 26  0  0  0  0  0  0  0  0999 V2000
   -2.2558    1.8621    0.7455 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4642    0.9244   -0.0674 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.1461   -0.2498    0.7807 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3666   -1.3328    0.2160 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9532   -1.2190   -0.3624 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1224   -0.7225    0.4214 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.3272   -0.7863   -0.4792 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0541    0.7191    0.7537 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3829    1.2304    1.6553 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8256    1.6047   -0.0294 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3349    0.5772   -1.2294 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8522   -0.2281   -2.0732 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5938    1.0708   -1.4248 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6779    2.1940    1.5631 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0054    1.2546    1.1866 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6147    1.4713   -0.4679 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8873    0.0169    1.8159 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2039   -0.7169    0.9610 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2924   -2.1469    1.0242 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0057   -1.9020   -0.5513 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2575   -2.2893   -0.6462 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9864   -0.7411   -1.3895 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3833   -1.3616    1.2812 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6798   -1.7836   -0.4618 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9387   -0.5482   -1.4192 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8872    1.4508   -1.0156 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0976    1.6520   -0.7873 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  6
  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  1
  7 24  1  0
  7 25  1  0
 10 26  1  0
 13 27  1  0
M  END
Download

3D SDF for NP0002726 (DL-alpha,epsilon-Diaminopimelic acid)


     RDKit          2D

 27 26  0  0  0  0  0  0  0  0999 V2000
   -2.5974    2.1222    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9268    0.6588    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4634    0.3294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4634   -0.3294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9268   -0.6588    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5974   -2.1222    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.2562    0.8046    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2857    1.9484    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6882    1.2510    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2562   -0.8046    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2857   -1.9484    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6882   -1.2510    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7000    3.1391    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2304    2.7398    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3902    0.9882    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9581    1.7417    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6119   -1.1632    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3294    1.4634    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3294   -1.4634    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9581   -1.7417    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6119    1.1632    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3902   -0.9882    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7000   -3.1391    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2304   -2.7398    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0176    2.7144    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0176   -2.7144    0.0000 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  6
  3 17  1  1
  3 18  1  0
  4 19  1  1
  4 20  1  0
  5 21  1  1
  5 22  1  0
  6 23  1  1
  7 24  1  0
  7 25  1  0
 10 26  1  0
 13 27  1  0
M  END
> <DATABASE_ID>
NP0002726

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H][C@](N)(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+

> <INCHI_KEY>
GMKMEZVLHJARHF-SYDPRGILSA-N

> <FORMULA>
C7H14N2O4

> <MOLECULAR_WEIGHT>
190.1971

> <EXACT_MASS>
190.095356946

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_AVERAGE_POLARIZABILITY>
18.68414320863363

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,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>
2.585040505515713

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.8470749826619342

> <JCHEM_PKA_STRONGEST_BASIC>
9.827564769536531

> <JCHEM_POLAR_SURFACE_AREA>
126.64

> <JCHEM_REFRACTIVITY>
43.6394

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.41e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
diaminopimelic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0002726 (DL-alpha,epsilon-Diaminopimelic acid)

NP0002726
     RDKit          3D

 27 26  0  0  0  0  0  0  0  0999 V2000
   -2.2558    1.8621    0.7455 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4642    0.9244   -0.0674 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.1461   -0.2498    0.7807 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3666   -1.3328    0.2160 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9532   -1.2190   -0.3624 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1224   -0.7225    0.4214 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.3272   -0.7863   -0.4792 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0541    0.7191    0.7537 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3829    1.2304    1.6553 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8256    1.6047   -0.0294 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3349    0.5772   -1.2294 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8522   -0.2281   -2.0732 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5938    1.0708   -1.4248 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6779    2.1940    1.5631 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0054    1.2546    1.1866 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6147    1.4713   -0.4679 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8873    0.0169    1.8159 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2039   -0.7169    0.9610 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2924   -2.1469    1.0242 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0057   -1.9020   -0.5513 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2575   -2.2893   -0.6462 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9864   -0.7411   -1.3895 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3833   -1.3616    1.2812 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6798   -1.7836   -0.4618 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9387   -0.5482   -1.4192 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8872    1.4508   -1.0156 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0976    1.6520   -0.7873 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  6
  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  1
  7 24  1  0
  7 25  1  0
 10 26  1  0
 13 27  1  0
M  END
Download

PDB for NP0002726 (DL-alpha,epsilon-Diaminopimelic acid)

HEADER    PROTEIN                                 19-OCT-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   19-OCT-12         0                                  
HETATM    1  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    8  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM    9  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   10  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   14  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   15  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
CONECT    1    2    3                                                       
CONECT    2    1    4                                                       
CONECT    3    1    5                                                       
CONECT    4    2    6    8   14                                             
CONECT    5    3    7    9   15                                             
CONECT    6    4   10   11                                                  
CONECT    7    5   12   13                                                  
CONECT    8    4                                                            
CONECT    9    5                                                            
CONECT   10    6                                                            
CONECT   11    6                                                            
CONECT   12    7                                                            
CONECT   13    7                                                            
CONECT   14    4                                                            
CONECT   15    5                                                            
MASTER        0    0    0    0    0    0    0    0   15    0   28    0
END
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3D PDB for NP0002726 (DL-alpha,epsilon-Diaminopimelic acid)

COMPND    NP0002726
HETATM    1  N1  UNL     1      -2.256   1.862   0.745  1.00  0.00           N  
HETATM    2  C1  UNL     1      -1.464   0.924  -0.067  1.00  0.00           C  
HETATM    3  C2  UNL     1      -1.146  -0.250   0.781  1.00  0.00           C  
HETATM    4  C3  UNL     1      -0.367  -1.333   0.216  1.00  0.00           C  
HETATM    5  C4  UNL     1       0.953  -1.219  -0.362  1.00  0.00           C  
HETATM    6  C5  UNL     1       2.122  -0.723   0.421  1.00  0.00           C  
HETATM    7  N2  UNL     1       3.327  -0.786  -0.479  1.00  0.00           N  
HETATM    8  C6  UNL     1       2.054   0.719   0.754  1.00  0.00           C  
HETATM    9  O1  UNL     1       1.383   1.230   1.655  1.00  0.00           O  
HETATM   10  O2  UNL     1       2.826   1.605  -0.029  1.00  0.00           O  
HETATM   11  C7  UNL     1      -2.335   0.577  -1.229  1.00  0.00           C  
HETATM   12  O3  UNL     1      -1.852  -0.228  -2.073  1.00  0.00           O  
HETATM   13  O4  UNL     1      -3.594   1.071  -1.425  1.00  0.00           O  
HETATM   14  H1  UNL     1      -1.678   2.194   1.563  1.00  0.00           H  
HETATM   15  H2  UNL     1      -3.005   1.255   1.187  1.00  0.00           H  
HETATM   16  H3  UNL     1      -0.615   1.471  -0.468  1.00  0.00           H  
HETATM   17  H4  UNL     1      -0.887   0.017   1.816  1.00  0.00           H  
HETATM   18  H5  UNL     1      -2.204  -0.717   0.961  1.00  0.00           H  
HETATM   19  H6  UNL     1      -0.292  -2.147   1.024  1.00  0.00           H  
HETATM   20  H7  UNL     1      -1.006  -1.902  -0.551  1.00  0.00           H  
HETATM   21  H8  UNL     1       1.258  -2.289  -0.646  1.00  0.00           H  
HETATM   22  H9  UNL     1       0.986  -0.741  -1.389  1.00  0.00           H  
HETATM   23  H10 UNL     1       2.383  -1.362   1.281  1.00  0.00           H  
HETATM   24  H11 UNL     1       3.680  -1.784  -0.462  1.00  0.00           H  
HETATM   25  H12 UNL     1       2.939  -0.548  -1.419  1.00  0.00           H  
HETATM   26  H13 UNL     1       2.887   1.451  -1.016  1.00  0.00           H  
HETATM   27  H14 UNL     1      -4.098   1.652  -0.787  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 NP0002726 (DL-alpha,epsilon-Diaminopimelic acid)

[H][C@](N)(CCC[C@@]([H])(N)C(O)=O)C(O)=O
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INCHI for NP0002726 (DL-alpha,epsilon-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+
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View in JSmol
Synonyms
ValueSource
Meso-diaminoheptanedioic acidChEBI
Meso-2,6-diaminopimelateKegg
Meso-2,6-diaminopimelic acidKegg
Meso-diaminoheptanedioateKegg
Meso-diaminopimelic acidGenerator
meso-2,6-Diaminoheptanedioic acidGenerator
Chemical FormulaC7H14N2O4
Average Mass190.1971 Da
Monoisotopic Mass190.09536 Da
IUPAC Name(2R,6S)-2,6-diaminoheptanedioic acid
Traditional Namediaminopimelic acid
CAS Registry NumberNot Available
SMILES
[H][C@](N)(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+
InChI KeyGMKMEZVLHJARHF-SYDPRGILSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of OriginNot Available
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
  • D-alpha-amino acid
  • 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
  • Organic oxide
  • Hydrocarbon derivative
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
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
Polarizability18.68 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID89700
KEGG Compound IDC00680
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkDiaminopimelic_acid
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI ID16488
Good Scents IDNot Available
References
General References
  1. 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 ]
  2. Ulrich EL, Akutsu H, Doreleijers JF, Harano Y, Ioannidis YE, Lin J, Livny M, Mading S, Maziuk D, Miller Z, Nakatani E, Schulte CF, Tolmie DE, Kent Wenger R, Yao H, Markley JL: BioMagResBank. Nucleic Acids Res. 2008 Jan;36(Database issue):D402-8. doi: 10.1093/nar/gkm957. Epub 2007 Nov 4. [PubMed:17984079 ]
  3. Toth GK, Hetenyi A, Ilisz I, Peter A: A simple chromatographic route for the isolation of meso diaminopimelic acid. Chirality. 2011 Feb;23(2):133-7. doi: 10.1002/chir.20888. Epub 2010 Aug 27. [PubMed:20803494 ]
  4. Usha V, Lloyd AJ, Lovering AL, Besra GS: Structure and function of Mycobacterium tuberculosis meso-diaminopimelic acid (DAP) biosynthetic enzymes. FEMS Microbiol Lett. 2012 May;330(1):10-6. doi: 10.1111/j.1574-6968.2012.02527.x. Epub 2012 Mar 7. [PubMed:22339732 ]
  5. Saito Y, Yoshimura Y, Wakamatsu H, Takahata H: A facile synthesis of fully protected meso-diaminopimelic acid (DAP) and its application to the preparation of lipophilic N-acyl iE-DAP. Molecules. 2013 Jan 16;18(1):1162-73. doi: 10.3390/molecules18011162. [PubMed:23325104 ]