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Showing NP-Card for Amakusamine (NP0044714)

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Record Information
Version2.0
Created at2022-02-24 21:13:16 UTC
Updated at2026-02-14 00:01:36 UTC
NP-MRD IDNP0044714
Natural Product DOIhttps://doi.org/10.57994/6749
Secondary Accession NumbersNone
Natural Product Identification
Common NameAmakusamine
Description Amakusamine was first documented in 2021 (PMID: 34612636). Based on a literature review very few articles have been published on 4,8-dibromo-2H,5H-[1,3]dioxolo[4,5-f]indole.
Structure
Thumb
MOL3D MOLSDFPDBSMILESInChI

MOL for NP0044714 (Amakusamine)


  Mrv1652302242222132D          

 14 16  0  0  0  0            999 V2000
    3.2789    2.0625    0.0000 Br  0  0  0  0  0  0  0  0  0  0  0  0
    3.2789    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9934    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7780    1.0799    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.2629    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7780   -0.2549    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9934    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2789   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2789   -1.2375    0.0000 Br  0  0  0  0  0  0  0  0  0  0  0  0
    2.5645    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5645    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7798    1.0799    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2949    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7798   -0.2549    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  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
  3  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  8 10  1  0  0  0  0
 10 11  2  0  0  0  0
  2 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
 10 14  1  0  0  0  0
M  END
Download

3D MOL for NP0044714 (Amakusamine)

     RDKit          3D

 19 21  0  0  0  0  0  0  0  0999 V2000
    0.0649   -3.1266    0.9923 Br  0  0  0  0  0  0  0  0  0  0  0  0
   -0.0233   -1.3344    0.3492 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2697   -0.8250    0.0435 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3481    0.4699   -0.4226 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1820    1.2034   -0.5648 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3057    2.9997   -1.2128 Br  0  0  0  0  0  0  0  0  0  0  0  0
    1.0561    0.6964   -0.2608 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2860    1.2359   -0.3279 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.1705    0.2908    0.0955 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4563   -0.8598    0.4308 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1348   -0.5855    0.2008 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7005    0.7404   -0.6544 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4596   -0.1965    0.1138 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5640   -1.3180    0.0878 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5612    2.1970   -0.6403 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2287    0.4489    0.1461 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8901   -1.7783    0.7995 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5753    0.1602    1.1750 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4206   -0.4186   -0.3508 H   0  0  0  0  0  0  0  0  0  0  0  0
  6  5  1  0
  5  4  2  0
  4 12  1  0
 12 13  1  0
 13 14  1  0
 14  3  1  0
  3  2  2  0
  2  1  1  0
  2 11  1  0
 11  7  2  0
  7  8  1  0
  8  9  1  0
  9 10  2  0
  7  5  1  0
  3  4  1  0
 10 11  1  0
 13 18  1  0
 13 19  1  0
  8 15  1  0
  9 16  1  0
 10 17  1  0
M  END
Download

3D SDF for NP0044714 (Amakusamine)


  Mrv1652302242222132D          

 14 16  0  0  0  0            999 V2000
    3.2789    2.0625    0.0000 Br  0  0  0  0  0  0  0  0  0  0  0  0
    3.2789    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9934    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7780    1.0799    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.2629    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7780   -0.2549    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9934    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2789   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2789   -1.2375    0.0000 Br  0  0  0  0  0  0  0  0  0  0  0  0
    2.5645    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5645    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7798    1.0799    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2949    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7798   -0.2549    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  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
  3  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  8 10  1  0  0  0  0
 10 11  2  0  0  0  0
  2 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
 10 14  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0044714

> <DATABASE_NAME>
NP-MRD

> <SMILES>
BrC1=C2OCOC2=C(Br)C2=C1NC=C2

> <INCHI_IDENTIFIER>
InChI=1S/C9H5Br2NO2/c10-5-4-1-2-12-7(4)6(11)9-8(5)13-3-14-9/h1-2,12H,3H2

> <INCHI_KEY>
QLFRWAZASAPKSB-UHFFFAOYSA-N

> <FORMULA>
C9H5Br2NO2

> <MOLECULAR_WEIGHT>
318.952

> <EXACT_MASS>
316.868704

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
19

> <JCHEM_AVERAGE_POLARIZABILITY>
22.84299838391218

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
4,8-dibromo-2H,5H-[1,3]dioxolo[4,5-f]indole

> <ALOGPS_LOGP>
3.22

> <JCHEM_LOGP>
3.232746527333333

> <ALOGPS_LOGS>
-3.71

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
15.456481337515985

> <JCHEM_PKA_STRONGEST_BASIC>
-4.803682781925852

> <JCHEM_POLAR_SURFACE_AREA>
34.25

> <JCHEM_REFRACTIVITY>
58.157

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.28e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
4,8-dibromo-2H,5H-[1,3]dioxolo[4,5-f]indole

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for NP0044714 (Amakusamine)

Download
PDB for NP0044714 (Amakusamine)
HEADER    PROTEIN                                 24-FEB-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-22         0                                  
HETATM    1 Br   UNK     0       6.121   3.850   0.000  0.00  0.00          Br+0
HETATM    2  C   UNK     0       6.121   2.310   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       7.454   1.540   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       8.919   2.016   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       9.824   0.770   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       8.919  -0.476   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       7.454   0.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       6.121  -0.770   0.000  0.00  0.00           C+0
HETATM    9 Br   UNK     0       6.121  -2.310   0.000  0.00  0.00          Br+0
HETATM   10  C   UNK     0       4.787   0.000   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.787   1.540   0.000  0.00  0.00           C+0
HETATM   12  N   UNK     0       3.322   2.016   0.000  0.00  0.00           N+0
HETATM   13  C   UNK     0       2.417   0.770   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       3.322  -0.476   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   11                                                  
CONECT    3    2    4    7                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    3    8                                                  
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11   14                                                  
CONECT   11   10    2   12                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   10                                                       
MASTER        0    0    0    0    0    0    0    0   14    0   32    0
END

Download
3D PDB for NP0044714 (Amakusamine)
Download
SMILES for NP0044714 (Amakusamine)
BrC1=C2OCOC2=C(Br)C2=C1NC=C2
Download
INCHI for NP0044714 (Amakusamine)
InChI=1S/C9H5Br2NO2/c10-5-4-1-2-12-7(4)6(11)9-8(5)13-3-14-9/h1-2,12H,3H2
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View in JSmol
SynonymsNot Available
Chemical FormulaC9H5Br2NO2
Average Mass318.9520 Da
Monoisotopic Mass316.86870 Da
IUPAC Name4,8-dibromo-2H,5H-[1,3]dioxolo[4,5-f]indole
Traditional Name4,8-dibromo-2H,5H-[1,3]dioxolo[4,5-f]indole
CAS Registry NumberNot Available
SMILES
BrC1=C2OCOC2=C(Br)C2=C1NC=C2
InChI Identifier
InChI=1S/C9H5Br2NO2/c10-5-4-1-2-12-7(4)6(11)9-8(5)13-3-14-9/h1-2,12H,3H2
InChI KeyQLFRWAZASAPKSB-UHFFFAOYSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 100 MHz, Chloroform-d, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 125 MHz, Chloroform-d, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 150 MHz, Chloroform-d, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 175 MHz, Chloroform-d, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 200 MHz, Chloroform-d, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 225 MHz, Chloroform-d, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 25 MHz, Chloroform-d, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 250 MHz, Chloroform-d, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, Chloroform-d, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, Chloroform-d, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, Chloroform-d, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, Chloroform-d, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, Chloroform-d, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, Chloroform-d, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, Chloroform-d, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, Chloroform-d, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, Chloroform-d, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, Chloroform-d, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, Chloroform-d, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, Chloroform-d, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 600.0, Chloroform-d, simulated)[email protected]Not AvailableNot Available2026-02-13View Spectrum
1D NMR13C NMR Spectrum (1D, 150.0, Chloroform-d, simulated)[email protected]Not AvailableNot Available2026-02-13View Spectrum
Species
Species of Origin
Species NameSourceReference
Psammocinia sp.
      Not Available
Psammocinia sp.Linington's dataset npmrd_submissions_20220207
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
logP3.22ALOGPS
logP3.23ChemAxon
logS-3.7ALOGPS
pKa (Strongest Acidic)15.46ChemAxon
pKa (Strongest Basic)-4.8ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area34.25 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity58.16 m³·mol⁻¹ChemAxon
Polarizability22.84 ųChemAxon
Number of Rings3ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID114641892  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. Maeyama Y, Nakashima Y, Kato H, Hitora Y, Maki K, Inada N, Murakami S, Inazumi T, Ise Y, Sugimoto Y, Ishikawa H, Tsukamoto S: Amakusamine from a Psammocinia sp. Sponge: Isolation, Synthesis, and SAR Study on the Inhibition of RANKL-Induced Formation of Multinuclear Osteoclasts. J Nat Prod. 2021 Oct 22;84(10):2738-2743. doi: 10.1021/acs.jnatprod.1c00758. Epub 2021 Oct 6. [PubMed:34612636  ] 
  2. DOI: 10.1021/acs.jnatprod.1c00758
  3. PMID: 34612636