NP-MRD: Showing NP-Card for (+)-Suberedamine B (NP0080906)

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Record Information

Version

2.0

Created at

2022-04-29 01:52:55 UTC

Updated at

2022-04-29 01:52:55 UTC

NP-MRD ID

NP0080906

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(+)-Suberedamine B

Description

Suberedamine B belongs to the class of organic compounds known as phenylalanine and derivatives. Phenylalanine and derivatives are compounds containing phenylalanine or a derivative thereof resulting from reaction of phenylalanine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. (+)-Suberedamine B is found in Suberea sp. (+)-Suberedamine B was first documented in 2012 (PMID: 22620987). Based on a literature review very few articles have been published on suberedamine B.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304292203522D          

 33 34  0  0  1  0            999 V2000
   -6.9020   -4.4270    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0770   -4.4270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6645   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8395   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4270   -2.9980    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6020   -2.9980    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1895   -2.2836    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3645   -2.2836    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9520   -2.9980    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3645   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1895   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6020   -4.4270    0.0000 Br  0  0  0  0  0  0  0  0  0  0  0  0
   -1.1270   -2.9980    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1105   -3.7125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230   -4.4270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1105   -5.1414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3480   -4.4270    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.7605   -5.1414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5855   -5.1414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9980   -4.4270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8230   -4.4270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2355   -5.1414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8230   -5.8559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9980   -5.8559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0605   -5.1414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.4730   -5.8559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2355   -3.7125    0.0000 Br  0  0  0  0  0  0  0  0  0  0  0  0
    1.7605   -3.7125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.5855   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6020   -1.5691    0.0000 Br  0  0  0  0  0  0  0  0  0  0  0  0
   -7.3145   -5.1414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3145   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
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  7 31  1  0  0  0  0
  1 32  1  0  0  0  0
  1 33  1  0  0  0  0
M  END

     RDKit          3D

 65 66  0  0  0  0  0  0  0  0999 V2000
    4.4370    4.5827   -1.1272 C   0  0  0  0  0  0  0  0  0  0  0  0
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    4.1040    2.2518   -0.6309 C   0  0  1  0  0  0  0  0  0  0  0  0
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    6.8212   -0.7971    1.9085 C   0  0  0  0  0  0  0  0  0  0  0  0
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    6.0649    0.3939    1.7874 C   0  0  0  0  0  0  0  0  0  0  0  0
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    2.6560    0.6520   -1.5634 O   0  0  0  0  0  0  0  0  0  0  0  0
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    0.0354    0.7714   -0.4435 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2989    0.1212   -0.2666 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5595   -1.2197   -0.4154 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8250   -1.7489   -0.3236 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0740   -3.6505   -0.5190 Br  0  0  0  0  0  0  0  0  0  0  0  0
   -3.8928   -0.8858   -0.0733 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1842   -1.4290    0.0039 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6715   -2.0184    1.1852 C   0  0  0  0  0  0  0  0  0  0  0  0
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 33 65  1  0
M  END


  Mrv1652304292203522D          

 33 34  0  0  1  0            999 V2000
   -6.9020   -4.4270    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0770   -4.4270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -4.8395   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4270   -2.9980    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
> <DATABASE_ID>
NP0080906

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CN[C@@H](CC1=CC(Br)=C(OC)C=C1)C(=O)NCCC1=CC(Br)=C(OCCCN(C)C)C(Br)=C1

> <INCHI_IDENTIFIER>
InChI=1S/C24H32Br3N3O3/c1-28-21(15-16-6-7-22(32-4)18(25)12-16)24(31)29-9-8-17-13-19(26)23(20(27)14-17)33-11-5-10-30(2)3/h6-7,12-14,21,28H,5,8-11,15H2,1-4H3,(H,29,31)/t21-/m0/s1

> <INCHI_KEY>
MNNHZXNEKPRDII-NRFANRHFSA-N

> <FORMULA>
C24H32Br3N3O3

> <MOLECULAR_WEIGHT>
650.25

> <EXACT_MASS>
646.999381

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
65

> <JCHEM_AVERAGE_POLARIZABILITY>
58.31292868164009

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-3-(3-bromo-4-methoxyphenyl)-N-(2-{3,5-dibromo-4-[3-(dimethylamino)propoxy]phenyl}ethyl)-2-(methylamino)propanamide

> <ALOGPS_LOGP>
4.66

> <JCHEM_LOGP>
5.009582826999999

> <ALOGPS_LOGS>
-6.13

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
2

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.3518573455883

> <JCHEM_PKA_STRONGEST_BASIC>
9.340656237375484

> <JCHEM_POLAR_SURFACE_AREA>
62.83

> <JCHEM_REFRACTIVITY>
144.6567

> <JCHEM_ROTATABLE_BOND_COUNT>
13

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
4.83e-04 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S)-3-(3-bromo-4-methoxyphenyl)-N-(2-{3,5-dibromo-4-[3-(dimethylamino)propoxy]phenyl}ethyl)-2-(methylamino)propanamide

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 29-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   29-APR-22         0                                  
HETATM    1  N   UNK     0     -12.884  -8.264   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0     -11.344  -8.264   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0     -10.574  -6.930   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -9.034  -6.930   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      -8.264  -5.596   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      -6.724  -5.596   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -5.954  -4.263   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -4.414  -4.263   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -3.644  -5.596   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -4.414  -6.930   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -5.954  -6.930   0.000  0.00  0.00           C+0
HETATM   12 Br   UNK     0      -6.724  -8.264   0.000  0.00  0.00          Br+0
HETATM   13  C   UNK     0      -2.104  -5.596   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -1.334  -6.930   0.000  0.00  0.00           C+0
HETATM   15  N   UNK     0       0.206  -6.930   0.000  0.00  0.00           N+0
HETATM   16  C   UNK     0       0.976  -8.264   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       0.206  -9.597   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0       2.516  -8.264   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       3.286  -9.597   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       4.826  -9.597   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       5.596  -8.264   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       7.136  -8.264   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       7.906  -9.597   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       7.136 -10.931   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       5.596 -10.931   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0       9.446  -9.597   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0      10.216 -10.931   0.000  0.00  0.00           C+0
HETATM   28 Br   UNK     0       7.906  -6.930   0.000  0.00  0.00          Br+0
HETATM   29  N   UNK     0       3.286  -6.930   0.000  0.00  0.00           N+0
HETATM   30  C   UNK     0       4.826  -6.930   0.000  0.00  0.00           C+0
HETATM   31 Br   UNK     0      -6.724  -2.929   0.000  0.00  0.00          Br+0
HETATM   32  C   UNK     0     -13.654  -9.597   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0     -13.654  -6.930   0.000  0.00  0.00           C+0
CONECT    1    2   32   33                                                  
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7   11                                                  
CONECT    7    6    8   31                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10   13                                                  
CONECT   10    9   11                                                       
CONECT   11   10    6   12                                                  
CONECT   12   11                                                            
CONECT   13    9   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17   18                                                  
CONECT   17   16                                                            
CONECT   18   16   19   29                                                  
CONECT   19   18   20                                                       
CONECT   20   19   21   25                                                  
CONECT   21   20   22                                                       
CONECT   22   21   23   28                                                  
CONECT   23   22   24   26                                                  
CONECT   24   23   25                                                       
CONECT   25   24   20                                                       
CONECT   26   23   27                                                       
CONECT   27   26                                                            
CONECT   28   22                                                            
CONECT   29   18   30                                                       
CONECT   30   29                                                            
CONECT   31    7                                                            
CONECT   32    1                                                            
CONECT   33    1                                                            
MASTER        0    0    0    0    0    0    0    0   33    0   68    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₄H₃₂Br₃N₃O₃

Average Mass

650.2500 Da

Monoisotopic Mass

646.99938 Da

IUPAC Name

(2S)-3-(3-bromo-4-methoxyphenyl)-N-(2-{3,5-dibromo-4-[3-(dimethylamino)propoxy]phenyl}ethyl)-2-(methylamino)propanamide

Traditional Name

(2S)-3-(3-bromo-4-methoxyphenyl)-N-(2-{3,5-dibromo-4-[3-(dimethylamino)propoxy]phenyl}ethyl)-2-(methylamino)propanamide

CAS Registry Number

Not Available

SMILES

CN[C@@H](CC1=CC(Br)=C(OC)C=C1)C(=O)NCCC1=CC(Br)=C(OCCCN(C)C)C(Br)=C1

InChI Identifier

InChI=1S/C24H32Br3N3O3/c1-28-21(15-16-6-7-22(32-4)18(25)12-16)24(31)29-9-8-17-13-19(26)23(20(27)14-17)33-11-5-10-30(2)3/h6-7,12-14,21,28H,5,8-11,15H2,1-4H3,(H,29,31)/t21-/m0/s1

InChI Key

MNNHZXNEKPRDII-NRFANRHFSA-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
Suberea sp.	-	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as phenylalanine and derivatives. Phenylalanine and derivatives are compounds containing phenylalanine or a derivative thereof resulting from reaction of phenylalanine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Phenylalanine and derivatives

Alternative Parents

Substituents

Phenylalanine or derivatives
Alpha-amino acid amide
Amphetamine or derivatives
Phenoxy compound
Anisole
Methoxybenzene
Phenol ether
Alkyl aryl ether
Bromobenzene
Aralkylamine
Halobenzene
Aryl bromide
Aryl halide
Monocyclic benzene moiety
Fatty acyl
Fatty amide
Benzenoid
Tertiary amine
Secondary carboxylic acid amide
Tertiary aliphatic amine
Carboxamide group
Secondary amine
Ether
Secondary aliphatic amine
Organobromide
Carbonyl group
Organic oxide
Amine
Organic oxygen compound
Organic nitrogen compound
Organonitrogen compound
Organooxygen compound
Hydrocarbon derivative
Organohalogen compound
Aromatic homomonocyclic compound

Molecular Framework

Aromatic homomonocyclic 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	4.66	ALOGPS
logP	5.01	ChemAxon
logS	-6.1	ALOGPS
pKa (Strongest Acidic)	14.35	ChemAxon
pKa (Strongest Basic)	9.34	ChemAxon
Physiological Charge	2	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	62.83 Å²	ChemAxon
Rotatable Bond Count	13	ChemAxon
Refractivity	144.66 m³·mol⁻¹	ChemAxon
Polarizability	58.31 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	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

C00046440

Chemspider ID

8434200

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

10258717

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Kottakota SK, Evangelopoulos D, Alnimr A, Bhakta S, McHugh TD, Gray M, Groundwater PW, Marrs EC, Perry JD, Spilling CD, Harburn JJ: Synthesis and biological evaluation of purpurealidin E-derived marine sponge metabolites: aplysamine-2, aplyzanzine A, and suberedamines A and B. J Nat Prod. 2012 Jun 22;75(6):1090-101. doi: 10.1021/np300102z. Epub 2012 May 23. [PubMed:22620987 ]

Showing NP-Card for (+)-Suberedamine B (NP0080906)

MOL for NP0080906 ((+)-Suberedamine B)

3D MOL for NP0080906 ((+)-Suberedamine B)

3D SDF for NP0080906 ((+)-Suberedamine B)

3D-SDF for NP0080906 ((+)-Suberedamine B)

PDB for NP0080906 ((+)-Suberedamine B)

3D PDB for NP0080906 ((+)-Suberedamine B)

SMILES for NP0080906 ((+)-Suberedamine B)

INCHI for NP0080906 ((+)-Suberedamine B)

Structure for NP0080906 ((+)-Suberedamine B)

3D Structure for NP0080906 ((+)-Suberedamine B)