NP-MRD: Showing NP-Card for Amathaspiramide D (NP0069557)

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Record Information

Version

2.0

Created at

2022-04-28 14:55:49 UTC

Updated at

2022-04-28 14:55:49 UTC

NP-MRD ID

NP0069557

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Amathaspiramide D

Description

Amathaspiramide D belongs to the class of organic compounds known as phenylpyrrolidines. These are polycyclic aromatic compounds containing a benzene ring linked to a pyrrolidine ring through a CC or CN bond. Pyrrolidine is a five-membered saturated aliphatic heterocycle with one nitrogen atom and four carbon atoms. Amathaspiramide D is found in Amathia wilsoni. Amathaspiramide D was first documented in 2016 (PMID: 27064857). Based on a literature review very few articles have been published on Amathaspiramide D.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 39 41  0  0  0  0  0  0  0  0999 V2000
    3.7022    1.0742    2.1506 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9326    1.4819    0.8076 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0551    1.1229   -0.2041 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9218    0.3599    0.0225 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0341   -0.0044   -0.9974 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1658   -0.7649   -0.7250 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.1074   -1.5643    0.5803 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.2396   -0.7432    1.6881 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4366   -2.2086    0.4304 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7003   -3.5988    0.6052 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2755   -1.1180    0.0929 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5089   -1.0918    0.2050 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4198    0.0033   -0.4248 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.0743    0.7127   -1.5632 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2098    1.4527   -0.8137 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5883    1.6901    0.5174 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0906    2.3124    1.5015 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2740    1.0793    0.5164 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2894    0.4064   -2.2850 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1871   -0.0978   -3.7878 Br  0  0  0  0  0  0  0  0  0  0  0  0
    2.4290    1.1749   -2.5128 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2903    1.5247   -1.4986 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8516    2.5889   -1.8724 Br  0  0  0  0  0  0  0  0  0  0  0  0
    2.6720    1.2904    2.4835 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9144   -0.0303    2.2298 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4016    1.5654    2.8509 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7654    0.0561    1.0474 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4023   -1.4869   -1.5220 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7004   -2.2861    0.6141 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1477   -0.7161    2.0712 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7480   -4.1655   -0.3672 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6457   -3.8216    1.1174 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8711   -4.0980    1.1710 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4823    0.0867   -2.3478 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4116    1.5416   -1.8739 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1367    0.8912   -0.7990 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3510    2.4680   -1.2881 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4822    1.4157    1.0844 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6222    1.4970   -3.5358 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
  9 11  1  0
 11 12  2  0
 13 11  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  2  0
 16 18  1  0
  5 19  2  0
 19 20  1  0
 19 21  1  0
 21 22  2  0
 22 23  1  0
 22  3  1  0
 13  6  1  0
 13 18  1  1
  1 24  1  0
  1 25  1  0
  1 26  1  0
  4 27  1  0
  6 28  1  6
  7 29  1  1
  8 30  1  0
 10 31  1  0
 10 32  1  0
 10 33  1  0
 14 34  1  0
 14 35  1  0
 15 36  1  0
 15 37  1  0
 18 38  1  0
 21 39  1  0
M  END


  Mrv1652304282216552D          

 23 25  0  0  1  0            999 V2000
    1.8465   -1.2111    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1015   -1.9957    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5494   -2.6088    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7425   -2.4373    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4875   -1.6527    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0396   -1.0396    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7846   -0.2549    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0000   -0.0000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.0000    0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7846    1.0799    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0396    1.8646    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2695    0.4125    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.7545    1.0799    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5391    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5391   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2065   -0.4849    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7545   -0.2549    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6674    1.3099    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6674   -0.4849    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3194   -1.4811    0.0000 Br  0  0  0  0  0  0  0  0  0  0  0  0
    1.8044   -3.3934    0.0000 Br  0  0  0  0  0  0  0  0  0  0  0  0
    2.9084   -2.1672    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1634   -2.9519    0.0000 C   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
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  1  6  1  0  0  0  0
  7  6  1  1  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  2  0  0  0  0
 10 12  1  0  0  0  0
  7 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
 15 17  1  0  0  0  0
 12 17  1  1  0  0  0
  9 18  1  0  0  0  0
  8 19  1  1  0  0  0
  5 20  1  0  0  0  0
  3 21  1  0  0  0  0
  2 22  1  0  0  0  0
 22 23  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0069557

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC1=CC([C@H]2[C@@H](O)N(C)C(=O)[C@]22CCC(=O)N2)=C(Br)C=C1Br

> <INCHI_IDENTIFIER>
InChI=1S/C15H16Br2N2O4/c1-19-13(21)12(15(14(19)22)4-3-11(20)18-15)7-5-10(23-2)9(17)6-8(7)16/h5-6,12-13,21H,3-4H2,1-2H3,(H,18,20)/t12-,13+,15-/m0/s1

> <INCHI_KEY>
MSSHNEUEONPAKC-GUTXKFCHSA-N

> <FORMULA>
C15H16Br2N2O4

> <MOLECULAR_WEIGHT>
448.111

> <EXACT_MASS>
445.947683

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
39

> <JCHEM_AVERAGE_POLARIZABILITY>
35.89122234499652

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(5S,8R,9R)-9-(2,4-dibromo-5-methoxyphenyl)-8-hydroxy-7-methyl-1,7-diazaspiro[4.4]nonane-2,6-dione

> <ALOGPS_LOGP>
2.02

> <JCHEM_LOGP>
1.4490418086666672

> <ALOGPS_LOGS>
-3.44

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.048363504274892

> <JCHEM_PKA_STRONGEST_ACIDIC>
10.094121162359976

> <JCHEM_PKA_STRONGEST_BASIC>
-1.8644063806261646

> <JCHEM_POLAR_SURFACE_AREA>
78.87

> <JCHEM_REFRACTIVITY>
89.60780000000003

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.61e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(5S,8R,9R)-9-(2,4-dibromo-5-methoxyphenyl)-8-hydroxy-7-methyl-1,7-diazaspiro[4.4]nonane-2,6-dione

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 28-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   28-APR-22         0                                  
HETATM    1  C   UNK     0       3.447  -2.261   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       3.923  -3.725   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.892  -4.870   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.386  -4.550   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.910  -3.085   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.941  -1.941   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.465  -0.476   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.000  -0.000   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0      -0.000   1.540   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0       1.465   2.016   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       1.941   3.481   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       2.370   0.770   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       3.275   2.016   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       4.740   1.540   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       4.740  -0.000   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       5.986  -0.905   0.000  0.00  0.00           O+0
HETATM   17  N   UNK     0       3.275  -0.476   0.000  0.00  0.00           N+0
HETATM   18  C   UNK     0      -1.246   2.445   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      -1.246  -0.905   0.000  0.00  0.00           O+0
HETATM   20 Br   UNK     0      -0.596  -2.765   0.000  0.00  0.00          Br+0
HETATM   21 Br   UNK     0       3.368  -6.334   0.000  0.00  0.00          Br+0
HETATM   22  O   UNK     0       5.429  -4.046   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0       5.905  -5.510   0.000  0.00  0.00           C+0
CONECT    1    2    6                                                       
CONECT    2    1    3   22                                                  
CONECT    3    2    4   21                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6   20                                                  
CONECT    6    5    1    7                                                  
CONECT    7    6    8   12                                                  
CONECT    8    7    9   19                                                  
CONECT    9    8   10   18                                                  
CONECT   10    9   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10    7   13   17                                             
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15   12                                                       
CONECT   18    9                                                            
CONECT   19    8                                                            
CONECT   20    5                                                            
CONECT   21    3                                                            
CONECT   22    2   23                                                       
CONECT   23   22                                                            
MASTER        0    0    0    0    0    0    0    0   23    0   50    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₅H₁₆Br₂N₂O₄

Average Mass

448.1110 Da

Monoisotopic Mass

445.94768 Da

IUPAC Name

(5S,8R,9R)-9-(2,4-dibromo-5-methoxyphenyl)-8-hydroxy-7-methyl-1,7-diazaspiro[4.4]nonane-2,6-dione

Traditional Name

(5S,8R,9R)-9-(2,4-dibromo-5-methoxyphenyl)-8-hydroxy-7-methyl-1,7-diazaspiro[4.4]nonane-2,6-dione

CAS Registry Number

Not Available

SMILES

COC1=CC([C@H]2[C@@H](O)N(C)C(=O)[C@]22CCC(=O)N2)=C(Br)C=C1Br

InChI Identifier

InChI=1S/C15H16Br2N2O4/c1-19-13(21)12(15(14(19)22)4-3-11(20)18-15)7-5-10(23-2)9(17)6-8(7)16/h5-6,12-13,21H,3-4H2,1-2H3,(H,18,20)/t12-,13+,15-/m0/s1

InChI Key

MSSHNEUEONPAKC-GUTXKFCHSA-N

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Amathia wilsoni	Animalia	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as phenylpyrrolidines. These are polycyclic aromatic compounds containing a benzene ring linked to a pyrrolidine ring through a CC or CN bond. Pyrrolidine is a five-membered saturated aliphatic heterocycle with one nitrogen atom and four carbon atoms.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Pyrrolidines

Sub Class

Phenylpyrrolidines

Direct Parent

Phenylpyrrolidines

Alternative Parents

Substituents

3-phenylpyrrolidine
Alpha-amino acid or derivatives
Diazaspirononane
Phenoxy compound
Phenol ether
Anisole
Methoxybenzene
Halobenzene
Bromobenzene
Alkyl aryl ether
2-pyrrolidone
Pyrrolidone
Aryl bromide
Aryl halide
Monocyclic benzene moiety
N-alkylpyrrolidine
Benzenoid
Pyrrole
Tertiary carboxylic acid amide
Secondary carboxylic acid amide
Lactam
Carboxamide group
Azacycle
Alkanolamine
Carboxylic acid derivative
Ether
Organic nitrogen compound
Carbonyl group
Organohalogen compound
Organobromide
Organonitrogen compound
Organooxygen compound
Hydrocarbon derivative
Organic oxide
Organic oxygen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Physical Properties

State

Not Available

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
logP	2.02	ALOGPS
logP	1.45	ChemAxon
logS	-3.4	ALOGPS
pKa (Strongest Acidic)	10.09	ChemAxon
pKa (Strongest Basic)	-1.9	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	78.87 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	89.61 m³·mol⁻¹	ChemAxon
Polarizability	35.89 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00027840

Chemspider ID

8702832

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

10527436

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Cai SL, Song R, Dong HQ, Lin GQ, Sun XW: Practical Asymmetric Synthesis of Amathaspiramides B, D, and F. Org Lett. 2016 May 6;18(9):1996-9. doi: 10.1021/acs.orglett.6b00588. Epub 2016 Apr 11. [PubMed:27064857 ]

Showing NP-Card for Amathaspiramide D (NP0069557)

MOL for NP0069557 (Amathaspiramide D)

3D MOL for NP0069557 (Amathaspiramide D)

3D SDF for NP0069557 (Amathaspiramide D)

3D-SDF for NP0069557 (Amathaspiramide D)

PDB for NP0069557 (Amathaspiramide D)

3D PDB for NP0069557 (Amathaspiramide D)

SMILES for NP0069557 (Amathaspiramide D)

INCHI for NP0069557 (Amathaspiramide D)

Structure for NP0069557 (Amathaspiramide D)

3D Structure for NP0069557 (Amathaspiramide D)