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Showing NP-Card for dl-2-aminopimelic acid (NP0254960)

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Record Information
Version2.0
Created at2022-09-07 19:17:07 UTC
Updated at2022-09-07 19:17:07 UTC
NP-MRD IDNP0254960
Secondary Accession NumbersNone
Natural Product Identification
Common Namedl-2-aminopimelic acid
Description2-Aminoheptanedioic acid, also known as alpha-aminopimelic acid or a-aminopimelate, 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). 2-Aminoheptanedioic acid is a very strong basic compound (based on its pKa). Outside of the human body, 2-Aminoheptanedioic acid has been detected, but not quantified in, beverages and fruits. dl-2-aminopimelic acid is found in Asplenium prolongatum, Indigofera hendecaphylla and Salmonella enterica. dl-2-aminopimelic acid was first documented in 1986 (PMID: 3079832). This could make 2-aminoheptanedioic acid a potential biomarker for the consumption of these foods (PMID: 2019472).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0254960 (dl-2-aminopimelic acid)


  Mrv0541 05061307402D          

 12 11  0  0  0  0            999 V2000
    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
    6.5704    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
    7.2849    2.5559    0.0000 C   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
    7.9993    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2849    3.3809    0.0000 N   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
    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  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  3  1  0  0  0  0
  6  4  1  0  0  0  0
  7  5  1  0  0  0  0
  8  5  1  0  0  0  0
  9  6  2  0  0  0  0
 10  6  1  0  0  0  0
 11  7  2  0  0  0  0
 12  7  1  0  0  0  0
M  END
Download

3D MOL for NP0254960 (dl-2-aminopimelic acid)

     RDKit          3D

 25 24  0  0  0  0  0  0  0  0999 V2000
    1.5322    1.6752    0.8848 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.7355    0.2803    0.6357 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.9462   -0.0727   -0.6251 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5141    0.1948   -0.4675 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0986   -0.6223    0.6745 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5985   -0.3198    0.8069 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2210   -0.6913   -0.4686 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3287   -1.8887   -0.8234 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6991    0.3096   -1.2957 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1576    0.0026    0.3249 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9574    0.9661    0.3252 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6393   -1.2627    0.0361 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2772    2.2536    0.4178 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5182    1.9316    1.9002 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4167   -0.3631    1.4828 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1560   -1.1648   -0.8007 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3895    0.5369   -1.4346 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6744    1.2645   -0.3390 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0144   -0.1515   -1.3930 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0392   -1.7059    0.4473 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6180   -0.3872    1.6403 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7874    0.7007    1.1225 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9455   -1.0063    1.6302 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4726    1.2906   -1.1365 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2857   -1.7701    0.6286 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
  7  9  1  0
  7  8  2  0
  2 10  1  0
 10 12  1  0
 10 11  2  0
  1 13  1  0
  1 14  1  0
  2 15  1  1
  3 16  1  0
  3 17  1  0
  4 18  1  0
  4 19  1  0
  5 20  1  0
  5 21  1  0
  6 22  1  0
  6 23  1  0
  9 24  1  0
 12 25  1  0
M  END
Download

3D SDF for NP0254960 (dl-2-aminopimelic acid)


  Mrv0541 05061307402D          

 12 11  0  0  0  0            999 V2000
    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
    6.5704    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
    7.2849    2.5559    0.0000 C   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
    7.9993    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2849    3.3809    0.0000 N   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
    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  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  3  1  0  0  0  0
  6  4  1  0  0  0  0
  7  5  1  0  0  0  0
  8  5  1  0  0  0  0
  9  6  2  0  0  0  0
 10  6  1  0  0  0  0
 11  7  2  0  0  0  0
 12  7  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0254960

> <DATABASE_NAME>
NP-MRD

> <SMILES>
NC(CCCCC(O)=O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C7H13NO4/c8-5(7(11)12)3-1-2-4-6(9)10/h5H,1-4,8H2,(H,9,10)(H,11,12)

> <INCHI_KEY>
JUQLUIFNNFIIKC-UHFFFAOYSA-N

> <FORMULA>
C7H13NO4

> <MOLECULAR_WEIGHT>
175.1824

> <EXACT_MASS>
175.084457909

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_AVERAGE_POLARIZABILITY>
17.60747945653503

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-aminoheptanedioic acid

> <ALOGPS_LOGP>
-3.18

> <JCHEM_LOGP>
-2.3613308082496256

> <ALOGPS_LOGS>
-1.14

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
4.518793491688202

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.1272745445775825

> <JCHEM_PKA_STRONGEST_BASIC>
9.526567332800782

> <JCHEM_POLAR_SURFACE_AREA>
100.62000000000002

> <JCHEM_REFRACTIVITY>
40.4897

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.26e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-aminopimelic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0254960 (dl-2-aminopimelic acid)

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PDB for NP0254960 (dl-2-aminopimelic acid)
HEADER    PROTEIN                                 06-MAY-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-MAY-13         0                                  
HETATM    1  C   UNK     0      10.931   4.771   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       9.597   4.001   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       8.264   4.771   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      13.598   4.771   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       6.930   4.001   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      14.932   4.001   0.000  0.00  0.00           C+0
HETATM    8  N   UNK     0      13.598   6.311   0.000  0.00  0.00           N+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  O   UNK     0      16.266   4.771   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0      14.932   2.461   0.000  0.00  0.00           O+0
CONECT    1    2    3                                                       
CONECT    2    1    4                                                       
CONECT    3    1    5                                                       
CONECT    4    2    6                                                       
CONECT    5    3    7    8                                                  
CONECT    6    4    9   10                                                  
CONECT    7    5   11   12                                                  
CONECT    8    5                                                            
CONECT    9    6                                                            
CONECT   10    6                                                            
CONECT   11    7                                                            
CONECT   12    7                                                            
MASTER        0    0    0    0    0    0    0    0   12    0   22    0
END

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3D PDB for NP0254960 (dl-2-aminopimelic acid)
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SMILES for NP0254960 (dl-2-aminopimelic acid)
NC(CCCCC(O)=O)C(O)=O
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INCHI for NP0254960 (dl-2-aminopimelic acid)
InChI=1S/C7H13NO4/c8-5(7(11)12)3-1-2-4-6(9)10/h5H,1-4,8H2,(H,9,10)(H,11,12)
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View in JSmol
Synonyms
ValueSource
alpha-Aminopimelic acidChEBI
ApmChEBI
a-AminopimelateGenerator
a-Aminopimelic acidGenerator
alpha-AminopimelateGenerator
Α-aminopimelateGenerator
Α-aminopimelic acidGenerator
2-AminoheptanedioateGenerator
(+-)-2-Aminopimelic acidHMDB
(2S)-2-Aminoheptanedioic acidHMDB
2-Amino-(+-)-heptanedioic acidHMDB
2-Amino-heptanedioic acidHMDB
2-AminopimelateHMDB
2-Aminopimelic acidHMDB
DL-2-AminopimelateHMDB
DL-2-Aminopimelic acidHMDB
DL-2-Aminopimelic acid(alpha-)HMDB
Chemical FormulaC7H13NO4
Average Mass175.1824 Da
Monoisotopic Mass175.08446 Da
IUPAC Name2-aminoheptanedioic acid
Traditional Name2-aminopimelic acid
CAS Registry NumberNot Available
SMILES
NC(CCCCC(O)=O)C(O)=O
InChI Identifier
InChI=1S/C7H13NO4/c8-5(7(11)12)3-1-2-4-6(9)10/h5H,1-4,8H2,(H,9,10)(H,11,12)
InChI KeyJUQLUIFNNFIIKC-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
Asplenium prolongatumLOTUS Database
Indigofera hendecaphyllaLOTUS Database
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-3.2ALOGPS
logP-2.4ChemAxon
logS-1.1ALOGPS
pKa (Strongest Acidic)2.13ChemAxon
pKa (Strongest Basic)9.53ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area100.62 ŲChemAxon
Rotatable Bond Count6ChemAxon
Refractivity40.49 m³·mol⁻¹ChemAxon
Polarizability17.61 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0034252  
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB012568  
KNApSAcK IDNot Available
Chemspider ID91360  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound101122  
PDB IDNot Available
ChEBI ID64305  
Good Scents IDNot Available
References
General References
  1. Le Roux P, Blanot D, Mengin-Lecreulx D, Van Heijenoort J: Peptides containing 2-aminopimelic acid. Synthesis and study of in vitro effects on bacterial cells. Int J Pept Protein Res. 1991 Feb;37(2):103-11. [PubMed:2019472  ] 
  2. Berges DA, DeWolf WE Jr, Dunn GL, Grappel SF, Newman DJ, Taggart JJ, Gilvarg C: Peptides of 2-aminopimelic acid: antibacterial agents that inhibit diaminopimelic acid biosynthesis. J Med Chem. 1986 Jan;29(1):89-95. doi: 10.1021/jm00151a015. [PubMed:3079832  ] 
  3. LOTUS database [Link]