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Showing NP-Card for (3r)-3,6-diaminohexanimidic acid (NP0250921)

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Record Information
Version2.0
Created at2022-09-07 13:55:48 UTC
Updated at2022-09-07 13:55:49 UTC
NP-MRD IDNP0250921
Secondary Accession NumbersNone
Natural Product Identification
Common Name(3r)-3,6-diaminohexanimidic acid
DescriptionBeta-Lysinamide is also known as β-lysinamide. (3r)-3,6-diaminohexanimidic acid is found in Streptomyces nashvillensis. (3r)-3,6-diaminohexanimidic acid was first documented in 1992 (PMID: 1490885). Based on a literature review very few articles have been published on beta-Lysinamide (PMID: 1468984).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0250921 ((3r)-3,6-diaminohexanimidic acid)


  Mrv1652309072215552D          

 10  9  0  0  1  0            999 V2000
    1.0461    1.4289    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.7605    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7605    2.6664    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895    1.8414    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.1895    2.6664    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0474    1.8414    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  6  0  0  0
  5  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
M  END
Download

3D MOL for NP0250921 ((3r)-3,6-diaminohexanimidic acid)

     RDKit          3D

 25 24  0  0  0  0  0  0  0  0999 V2000
    4.7500   -0.2323   -1.1584 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7698   -0.5171   -1.0363 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.0123   -0.0905   -0.0873 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5840    0.8129    0.8158 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6052   -0.5396    0.0348 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6558    0.6209   -0.0516 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.9263    1.6249    0.9604 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7804    0.2395    0.0642 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2135   -0.8096   -0.9366 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7033   -1.0449   -0.6386 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3880    0.2153   -0.8232 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.2132    0.8015    1.7451 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4701   -1.1246    0.9765 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4171   -1.2545   -0.7895 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8123    1.1089   -1.0354 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3582    2.4651    0.6944 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5206    1.2583    1.8590 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4414    1.1154   -0.0976 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0417   -0.1614    1.0662 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1717   -0.4557   -1.9808 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7095   -1.7859   -0.7781 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8346   -1.3667    0.4326 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1272   -1.8321   -1.2700 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4621    0.7841    0.0299 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2213    0.1678   -1.4118 H   0  0  0  0  0  0  0  0  0  0  0  0
 11 10  1  0
 10  9  1  0
  9  8  1  0
  8  6  1  0
  6  7  1  0
  6  5  1  0
  5  3  1  0
  3  4  1  0
  3  2  2  0
 11 24  1  0
 11 25  1  0
 10 22  1  0
 10 23  1  0
  9 20  1  0
  9 21  1  0
  8 18  1  0
  8 19  1  0
  6 15  1  6
  7 16  1  0
  7 17  1  0
  5 13  1  0
  5 14  1  0
  4 12  1  0
  2  1  1  0
M  END
Download

3D SDF for NP0250921 ((3r)-3,6-diaminohexanimidic acid)


  Mrv1652309072215552D          

 10  9  0  0  1  0            999 V2000
    1.0461    1.4289    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.7605    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7605    2.6664    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895    1.8414    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.1895    2.6664    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0474    1.8414    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  6  0  0  0
  5  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
M  END
> <DATABASE_ID>
NP0250921

> <DATABASE_NAME>
NP-MRD

> <SMILES>
NCCC[C@@H](N)CC(O)=N

> <INCHI_IDENTIFIER>
InChI=1S/C6H15N3O/c7-3-1-2-5(8)4-6(9)10/h5H,1-4,7-8H2,(H2,9,10)/t5-/m1/s1

> <INCHI_KEY>
YHADRABFJIUKLA-RXMQYKEDSA-N

> <FORMULA>
C6H15N3O

> <MOLECULAR_WEIGHT>
145.206

> <EXACT_MASS>
145.121512115

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
25

> <JCHEM_AVERAGE_POLARIZABILITY>
16.106266740837114

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3R)-3,6-diaminohexanimidic acid

> <JCHEM_LOGP>
-3.7269302913176827

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
2

> <JCHEM_PKA_STRONGEST_ACIDIC>
-0.2553745576257791

> <JCHEM_PKA_STRONGEST_BASIC>
13.738127569006982

> <JCHEM_POLAR_SURFACE_AREA>
96.11999999999999

> <JCHEM_REFRACTIVITY>
50.59160000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(3R)-3,6-diaminohexanimidic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0250921 ((3r)-3,6-diaminohexanimidic acid)

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PDB for NP0250921 ((3r)-3,6-diaminohexanimidic acid)
HEADER    PROTEIN                                 07-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   07-SEP-22         0                                  
HETATM    1  N   UNK     0       1.953   2.667   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0       3.286   3.437   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       3.286   4.977   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       4.620   2.667   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       5.954   3.437   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0       5.954   4.977   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0       7.287   2.667   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       8.621   3.437   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       9.955   2.667   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0      11.288   3.437   0.000  0.00  0.00           N+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9                                                            
MASTER        0    0    0    0    0    0    0    0   10    0   18    0
END

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3D PDB for NP0250921 ((3r)-3,6-diaminohexanimidic acid)
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SMILES for NP0250921 ((3r)-3,6-diaminohexanimidic acid)
NCCC[C@@H](N)CC(O)=N
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INCHI for NP0250921 ((3r)-3,6-diaminohexanimidic acid)
InChI=1S/C6H15N3O/c7-3-1-2-5(8)4-6(9)10/h5H,1-4,7-8H2,(H2,9,10)/t5-/m1/s1
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View in JSmol
Synonyms
ValueSource
b-LysinamideGenerator
Β-lysinamideGenerator
D-beta-LysinamideMeSH
Chemical FormulaC6H15N3O
Average Mass145.2060 Da
Monoisotopic Mass145.12151 Da
IUPAC Name(3R)-3,6-diaminohexanimidic acid
Traditional Name(3R)-3,6-diaminohexanimidic acid
CAS Registry NumberNot Available
SMILES
NCCC[C@@H](N)CC(O)=N
InChI Identifier
InChI=1S/C6H15N3O/c7-3-1-2-5(8)4-6(9)10/h5H,1-4,7-8H2,(H2,9,10)/t5-/m1/s1
InChI KeyYHADRABFJIUKLA-RXMQYKEDSA-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
Streptomyces nashvillensisLOTUS Database
Chemical Taxonomy
ClassificationNot classified
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-3.7ChemAxon
pKa (Strongest Acidic)-0.26ChemAxon
pKa (Strongest Basic)13.74ChemAxon
Physiological Charge2ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area96.12 ŲChemAxon
Rotatable Bond Count5ChemAxon
Refractivity50.59 m³·mol⁻¹ChemAxon
Polarizability16.11 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 ID112675  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound126879  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. Ikeda Y, Naganawa H, Kondo S, Takeuchi T: Preparation of 13C and 15N labeled bellenamine and its degradation products. J Antibiot (Tokyo). 1992 Dec;45(12):1925-9. doi: 10.7164/antibiotics.45.1925. [PubMed:1490885  ] 
  2. Ikeda Y, Gomi S, Hamada M, Kondo S, Takeuchi T: Production of bellenamine and new metabolites in a synthetic medium. J Antibiot (Tokyo). 1992 Nov;45(11):1763-6. doi: 10.7164/antibiotics.45.1763. [PubMed:1468984  ] 
  3. LOTUS database [Link]