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Showing NP-Card for 2,6-diaminopimelic acid (NP0312422)

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Record Information
Version2.0
Created at2022-09-11 09:11:52 UTC
Updated at2022-09-11 09:11:53 UTC
NP-MRD IDNP0312422
Secondary Accession NumbersNone
Natural Product Identification
Common Name2,6-diaminopimelic acid
Description 2,6-diaminopimelic acid is found in Salmonella enterica. 2,6-diaminopimelic acid was first documented in 1963 (PMID: 13984704).
Structure
Thumb
MOL3D MOLSDFPDBSMILESInChI

MOL for NP0312422 (2,6-diaminopimelic acid)


  Mrv1533005011519272D          

 13 12  0  0  0  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  0  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  0  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
  1  2  1  0  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  0  0  0  0
  6  8  1  0  0  0  0
  8  9  2  0  0  0  0
  8 10  1  0  0  0  0
  2 11  1  0  0  0  0
 11 12  2  0  0  0  0
 11 13  1  0  0  0  0
M  END
Download

3D MOL for NP0312422 (2,6-diaminopimelic acid)

     RDKit          3D

 27 26  0  0  0  0  0  0  0  0999 V2000
    2.6145   -1.1305    0.2740 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.4435   -0.0943   -0.7118 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.0963   -0.3042   -1.3576 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0343   -0.2298   -0.3560 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3266   -0.4580   -1.1423 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5055   -0.3956   -0.1920 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.4295   -1.3859    0.8365 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5824    0.9757    0.3689 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5723    1.1045    1.6174 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6608    2.0317   -0.5233 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6239    1.2549   -0.1737 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5192    2.2993   -0.8614 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9283    1.4072    1.1708 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4818   -1.6862    0.1274 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4998   -0.7996    1.2539 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2013   -0.2295   -1.5274 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9366    0.3592   -2.2138 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0930   -1.3463   -1.7541 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1156    0.7397    0.1483 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0881   -1.0065    0.4251 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4395    0.3239   -1.9189 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3317   -1.4436   -1.6478 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4347   -0.5529   -0.7842 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3354   -2.3160    0.3929 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3358   -1.3804    1.3549 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2852    2.8101   -0.4149 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8631    1.4532    1.5327 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 10  1  0
  8  9  2  0
  2 11  1  0
 11 13  1  0
 11 12  2  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  6
  7 24  1  0
  7 25  1  0
 10 26  1  0
 13 27  1  0
M  END
Download

3D SDF for NP0312422 (2,6-diaminopimelic acid)


  Mrv1533005011519272D          

 13 12  0  0  0  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  0  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  0  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
  1  2  1  0  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  0  0  0  0
  6  8  1  0  0  0  0
  8  9  2  0  0  0  0
  8 10  1  0  0  0  0
  2 11  1  0  0  0  0
 11 12  2  0  0  0  0
 11 13  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0312422

> <DATABASE_NAME>
NP-MRD

> <SMILES>
NC(CCCC(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)

> <INCHI_KEY>
GMKMEZVLHJARHF-UHFFFAOYSA-N

> <FORMULA>
C7H14N2O4

> <MOLECULAR_WEIGHT>
190.199

> <EXACT_MASS>
190.095356939

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
27

> <JCHEM_AVERAGE_POLARIZABILITY>
18.89107397242082

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
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>
Dpm

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0312422 (2,6-diaminopimelic acid)

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PDB for NP0312422 (2,6-diaminopimelic acid)
HEADER    PROTEIN                                 01-MAY-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   01-MAY-15         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 NP0312422 (2,6-diaminopimelic acid)
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SMILES for NP0312422 (2,6-diaminopimelic acid)
NC(CCCC(N)C(O)=O)C(O)=O
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INCHI for NP0312422 (2,6-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)
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View in JSmol
Synonyms
ValueSource
alpha,epsilon-Diaminopimelic acidChEBI
Diaminopimelic acidChEBI
DpmChEBI
a,epsilon-DiaminopimelateGenerator
a,epsilon-Diaminopimelic acidGenerator
alpha,epsilon-DiaminopimelateGenerator
Α,epsilon-diaminopimelateGenerator
Α,epsilon-diaminopimelic acidGenerator
DiaminopimelateGenerator
Meso-diaminopimelic acidGenerator
2,6 Diaminopimelic acidMeSH
Acid, 2,6-diaminopimelicMeSH
Acid, diaminopimelicMeSH
Chemical FormulaC7H14N2O4
Average Mass190.1990 Da
Monoisotopic Mass190.09536 Da
IUPAC Name2,6-diaminoheptanedioic acid
Traditional NameDpm
CAS Registry NumberNot Available
SMILES
NC(CCCC(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)
InChI KeyGMKMEZVLHJARHF-UHFFFAOYSA-N
Experimental Spectra
Not Available
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Salmonella entericaLOTUS Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as alpha amino acids. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon).
KingdomOrganic compounds  
Super ClassOrganic acids and derivatives  
ClassCarboxylic acids and derivatives  
Sub ClassAmino acids, peptides, and analogues  
Direct ParentAlpha amino acids  
Alternative Parents
Substituents
  • Alpha-amino acid
    • 

  • Medium-chain fatty acid
    • 

  • Amino fatty acid
    • 

  • Dicarboxylic acid or derivatives
    • 

  • Fatty acid
    • 

  • Fatty acyl
    • 

  • Amino acid
    • 

  • Carboxylic acid
    • 

  • Organic oxide
    • 

  • Primary amine
    • 

  • Organooxygen compound
    • 

  • Organonitrogen compound
    • 

  • Primary aliphatic amine
    • 

  • Organopnictogen compound
    • 

  • Carbonyl group
    • 

  • Organic oxygen compound
    • 

  • Amine
    • 

  • Organic nitrogen compound
    • 

  • 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
Polarizability18.89 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 IDFDB030997  
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkDiaminopimelic acid  
METLIN IDNot Available
PubChem Compound865  
PDB IDNot Available
ChEBI ID23673  
Good Scents IDNot Available
References
General References
  1. TAKEYA K, HISATSUNE K, INOUE Y: Mycobacterial cell walls. II. Chemical composition of the "basal layer". J Bacteriol. 1963 Jan;85(1):24-30. doi: 10.1128/jb.85.1.24-30.1963. [PubMed:13984704  ] 
  2. Mingma R, Pathom-aree W, Trakulnaleamsai S, Thamchaipenet A, Duangmal K: Isolation of rhizospheric and roots endophytic actinomycetes from Leguminosae plant and their activities to inhibit soybean pathogen, Xanthomonas campestris pv. glycine. World J Microbiol Biotechnol. 2014 Jan;30(1):271-80. doi:  10.1007/s11274-013-1451-9. Epub 2013 Aug 4. [PubMed:23913026  ] 
  3. LOTUS database [Link]