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Showing NP-Card for 7,8-diaminopelargonic acid (NP0325513)

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Record Information
Version2.0
Created at2022-09-12 06:19:23 UTC
Updated at2022-09-12 06:19:23 UTC
NP-MRD IDNP0325513
Secondary Accession NumbersNone
Natural Product Identification
Common Name7,8-diaminopelargonic acid
Description7,8-Diaminononanoate, also known as 7,8-DAP or DAPA, belongs to the class of organic compounds known as medium-chain fatty acids. These are fatty acids with an aliphatic tail that contains between 4 and 12 carbon atoms. 7,8-diaminopelargonic acid is found in Daphnia pulex. 7,8-diaminopelargonic acid was first documented in 2005 (PMID: 15937974). 7,8-Diaminononanoate is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral (PMID: 19345718).
Structure
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MOLSDFPDBSMILESInChI

MOL for NP0325513 (7,8-diaminopelargonic acid)

Structure #1
  Mrv0541 02241207002D          

 13 12  0  0  0  0            999 V2000
    2.2836    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
    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
    2.9980    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
    2.9980    3.3809    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.7125    1.3184    0.0000 N   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  7  1  0  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  3  5  1  0  0  0  0
  4  6  1  0  0  0  0
  5  8  1  0  0  0  0
  6  9  1  0  0  0  0
  7  8  1  0  0  0  0
  7 10  1  0  0  0  0
  8 11  1  0  0  0  0
  9 12  2  0  0  0  0
  9 13  1  0  0  0  0
M  END
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3D MOL for NP0325513 (7,8-diaminopelargonic acid)

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3D SDF for NP0325513 (7,8-diaminopelargonic acid)
Structure #1
  Mrv0541 02241207002D          

 13 12  0  0  0  0            999 V2000
    2.2836    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
    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
    2.9980    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
    2.9980    3.3809    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.7125    1.3184    0.0000 N   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  7  1  0  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  3  5  1  0  0  0  0
  4  6  1  0  0  0  0
  5  8  1  0  0  0  0
  6  9  1  0  0  0  0
  7  8  1  0  0  0  0
  7 10  1  0  0  0  0
  8 11  1  0  0  0  0
  9 12  2  0  0  0  0
  9 13  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0325513

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(N)C(N)CCCCCC(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C9H20N2O2/c1-7(10)8(11)5-3-2-4-6-9(12)13/h7-8H,2-6,10-11H2,1H3,(H,12,13)

> <INCHI_KEY>
KCEGBPIYGIWCDH-UHFFFAOYSA-N

> <FORMULA>
C9H20N2O2

> <MOLECULAR_WEIGHT>
188.2673

> <EXACT_MASS>
188.152477894

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
21.871489528943158

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
7,8-diaminononanoic acid

> <ALOGPS_LOGP>
-2.11

> <JCHEM_LOGP>
-1.9209886615753784

> <ALOGPS_LOGS>
-1.58

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.728429829552393

> <JCHEM_PKA_STRONGEST_BASIC>
9.969554860988813

> <JCHEM_POLAR_SURFACE_AREA>
89.34

> <JCHEM_REFRACTIVITY>
51.29959999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.94e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
7,8-diaminopelargonic acid

> <JCHEM_VEBER_RULE>
0

$$$$

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3D-SDF for NP0325513 (7,8-diaminopelargonic acid)
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PDB for NP0325513 (7,8-diaminopelargonic acid)
HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: Structure #1                                      
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0       4.263   4.001   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      10.931   4.771   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       9.597   4.001   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      12.265   4.001   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       8.264   4.771   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      13.598   4.771   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       5.596   4.771   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       6.930   4.001   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      14.932   4.001   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0       5.596   6.311   0.000  0.00  0.00           N+0
HETATM   11  N   UNK     0       6.930   2.461   0.000  0.00  0.00           N+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    7                                                            
CONECT    2    3    4                                                       
CONECT    3    2    5                                                       
CONECT    4    2    6                                                       
CONECT    5    3    8                                                       
CONECT    6    4    9                                                       
CONECT    7    1    8   10                                                  
CONECT    8    5    7   11                                                  
CONECT    9    6   12   13                                                  
CONECT   10    7                                                            
CONECT   11    8                                                            
CONECT   12    9                                                            
CONECT   13    9                                                            
MASTER        0    0    0    0    0    0    0    0   13    0   24    0
END

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3D PDB for NP0325513 (7,8-diaminopelargonic acid)
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SMILES for NP0325513 (7,8-diaminopelargonic acid)
CC(N)C(N)CCCCCC(O)=O
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INCHI for NP0325513 (7,8-diaminopelargonic acid)
InChI=1S/C9H20N2O2/c1-7(10)8(11)5-3-2-4-6-9(12)13/h7-8H,2-6,10-11H2,1H3,(H,12,13)
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Synonyms
ValueSource
7,8-DAPChEBI
7,8-DAPAChEBI
7,8-Diaminopelargonic acidChEBI
DAPChEBI
DAPAChEBI
7,8-DiaminopelargonateGenerator
7,8-Diaminononanoic acidGenerator
7,8-DiaminononanoateChEBI, Generator
Chemical FormulaC9H20N2O2
Average Mass188.2673 Da
Monoisotopic Mass188.15248 Da
IUPAC Name7,8-diaminononanoic acid
Traditional Name7,8-diaminopelargonic acid
CAS Registry NumberNot Available
SMILES
CC(N)C(N)CCCCCC(O)=O
InChI Identifier
InChI=1S/C9H20N2O2/c1-7(10)8(11)5-3-2-4-6-9(12)13/h7-8H,2-6,10-11H2,1H3,(H,12,13)
InChI KeyKCEGBPIYGIWCDH-UHFFFAOYSA-N
Experimental Spectra
Not Available
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Daphnia pulexLOTUS Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as medium-chain fatty acids. These are fatty acids with an aliphatic tail that contains between 4 and 12 carbon atoms.
KingdomOrganic compounds  
Super ClassLipids and lipid-like molecules  
ClassFatty Acyls  
Sub ClassFatty acids and conjugates  
Direct ParentMedium-chain fatty acids  
Alternative Parents
Substituents
  • Medium-chain fatty acid
    • 

  • Amino fatty acid
    • 

  • Branched fatty acid
    • 

  • Methyl-branched fatty acid
    • 

  • Amino acid or derivatives
    • 

  • Amino acid
    • 

  • Carboxylic acid derivative
    • 

  • Carboxylic acid
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Amine
    • 

  • Organooxygen compound
    • 

  • Organonitrogen compound
    • 

  • Primary amine
    • 

  • Primary aliphatic amine
    • 

  • Hydrocarbon derivative
    • 

  • Organic oxide
    • 

  • Carbonyl group
    • 

  • Organopnictogen compound
    • 

  • Organic oxygen compound
    • 

  • Organic nitrogen compound
    • 

  • 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-2.1ALOGPS
logP-1.9ChemAxon
logS-1.6ALOGPS
pKa (Strongest Acidic)4.73ChemAxon
pKa (Strongest Basic)9.97ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area89.34 ŲChemAxon
Rotatable Bond Count7ChemAxon
Refractivity51.3 m³·mol⁻¹ChemAxon
Polarizability21.87 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 IDFDB030615  
KNApSAcK IDC00000759  
Chemspider IDNot Available
KEGG Compound IDC01037  
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound652  
PDB IDNot Available
ChEBI ID2247  
Good Scents IDNot Available
References
General References
  1. Ashkenazi T, Widberg A, Nudelman A, Wittenbach V, Flint D: Inhibitors of biotin biosynthesis as potential herbicides: part 2. Pest Manag Sci. 2005 Oct;61(10):1024-33. doi: 10.1002/ps.1075. [PubMed:15937974  ] 
  2. Mann S, Colliandre L, Labesse G, Ploux O: Inhibition of 7,8-diaminopelargonic acid aminotransferase from Mycobacterium tuberculosis by chiral and achiral anologs of its substrate: biological implications. Biochimie. 2009 Jul;91(7):826-34. doi: 10.1016/j.biochi.2009.03.019. Epub 2009 Apr 2. [PubMed:19345718  ] 
  3. LOTUS database [Link]