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Showing NP-Card for 7,8-Diaminononanoate (NP0050503)

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Record Information
Version2.0
Created at2022-04-27 21:46:19 UTC
Updated at2022-04-27 21:46:19 UTC
NP-MRD IDNP0050503
Secondary Accession NumbersNone
Natural Product Identification
Common Name7,8-Diaminononanoate
Description7,8-Diamino-Nonanoic Acid, also known as 7,8-DAP or 7,8-diaminopelargonic acid, 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-Diaminononanoate is found in Bacillus subtilis , Escherichia coli and Paraburkholderia phymatum. 7,8-Diaminononanoate was first documented in 1969 (PMID: 4892372). 7,8-Diamino-Nonanoic Acid is a very strong basic compound (based on its pKa) (PMID: 15937974) (PMID: 19345718).
Structure
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MOLSDFPDBSMILESInChI

MOL for NP0050503 (7,8-Diaminononanoate)


  Mrv0541 02231215402D          

 13 12  0  0  1  0            999 V2000
    2.2836    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9980    2.5559    0.0000 C   0  0  2  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    2.1434    0.0000 C   0  0  2  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
    4.4270    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
    5.8559    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
    7.2849    2.5559    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
    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  6  0  0  0
  2  4  1  0  0  0  0
  4  5  1  1  0  0  0
  4  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 11 13  2  0  0  0  0
M  END
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3D MOL for NP0050503 (7,8-Diaminononanoate)

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3D SDF for NP0050503 (7,8-Diaminononanoate)

  Mrv0541 02231215402D          

 13 12  0  0  1  0            999 V2000
    2.2836    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9980    2.5559    0.0000 C   0  0  2  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    2.1434    0.0000 C   0  0  2  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
    4.4270    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
    5.8559    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
    7.2849    2.5559    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
    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  6  0  0  0
  2  4  1  0  0  0  0
  4  5  1  1  0  0  0
  4  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 11 13  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0050503

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@H](N)[C@H](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)/t7-,8+/m0/s1

> <INCHI_KEY>
KCEGBPIYGIWCDH-JGVFFNPUSA-N

> <FORMULA>
C9H20N2O2

> <MOLECULAR_WEIGHT>
188.2673

> <EXACT_MASS>
188.152477894

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
21.854472267044233

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(7R,8S)-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>
51.299600000000005

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.94e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
DAPA

> <JCHEM_VEBER_RULE>
0

$$$$

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3D-SDF for NP0050503 (7,8-Diaminononanoate)
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PDB for NP0050503 (7,8-Diaminononanoate)
HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-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       5.596   4.771   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0       5.596   6.311   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0       6.930   4.001   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0       6.930   2.461   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0       8.264   4.771   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       9.597   4.001   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      10.931   4.771   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      12.265   4.001   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      13.598   4.771   0.000  0.00  0.00           C+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    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   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 NP0050503 (7,8-Diaminononanoate)
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SMILES for NP0050503 (7,8-Diaminononanoate)
C[C@H](N)[C@H](N)CCCCCC(O)=O
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INCHI for NP0050503 (7,8-Diaminononanoate)
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)/t7-,8+/m0/s1
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View in JSmol
Synonyms
ValueSource
(7R,8S)-7,8-Diaminopelargonic acidChEBI
7,8-DAPChEBI
7,8-DAPAChEBI
7,8-Diaminopelargonic acidChEBI
DAPChEBI
DAPAChEBI
(7R,8S)-7,8-DiaminopelargonateGenerator
7,8-DiaminopelargonateGenerator
7,8-Diamino-nonanoateGenerator
7,8-DIAMINO-nonanoIC ACIDChEBI
(7R,8S)-7,8-DiaminononanoateGenerator
Chemical FormulaC9H20N2O2
Average Mass188.2673 Da
Monoisotopic Mass188.15248 Da
IUPAC Name(7R,8S)-7,8-diaminononanoic acid
Traditional NameDAPA
CAS Registry NumberNot Available
SMILES
C[C@H](N)[C@H](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)/t7-,8+/m0/s1
InChI KeyKCEGBPIYGIWCDH-JGVFFNPUSA-N
Experimental Spectra
Not Available
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Bacillus subtilisBacteria
Escherichia coliBacteria
Paraburkholderia phymatum-
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
Polarizability21.85 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDNot Available
DrugBank IDDB01715  
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound445025  
PDB IDNot Available
ChEBI ID42085  
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. Eisenberg MA, Krell K: Synthesis of desthiobiotin from 7,8-diaminopelargonic acid in biotin auxotrophs of Escherichia coli K-12. J Bacteriol. 1969 Jun;98(3):1227-31. doi: 10.1128/jb.98.3.1227-1231.1969. [PubMed:4892372  ]