NP-MRD: Showing NP-Card for 4,12-bis[2-(dimethylamino)ethyl]-6,14,15-trimethoxy-13-(methylsulfanyl)-2,9,10-trithiatricyclo[9.4.0.0³,⁸]pentadeca-1(15),3,5,7,11,13-hexaen-7-ol (NP0222983)

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Record Information

Version

2.0

Created at

2022-09-06 00:57:19 UTC

Updated at

2022-09-06 00:57:20 UTC

NP-MRD ID

NP0222983

Secondary Accession Numbers

None

Natural Product Identification

Common Name

4,12-bis[2-(dimethylamino)ethyl]-6,14,15-trimethoxy-13-(methylsulfanyl)-2,9,10-trithiatricyclo[9.4.0.0³,⁸]pentadeca-1(15),3,5,7,11,13-hexaen-7-ol

Description

Lissoclibadin 5 belongs to the class of organic compounds known as phenethylamines. Phenethylamines are compounds containing a phenethylamine moiety, which consists of a phenyl group substituted at the second position by an ethan-1-amine. 4,12-bis[2-(dimethylamino)ethyl]-6,14,15-trimethoxy-13-(methylsulfanyl)-2,9,10-trithiatricyclo[9.4.0.0³,⁸]pentadeca-1(15),3,5,7,11,13-hexaen-7-ol is found in Lissoclinum badium. Lissoclibadin 5 is a very strong basic compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv0541 04121502132D          

 34 36  0  0  0  0            999 V2000
   -0.5541   -2.4098    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3705   -1.6055    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4178   -1.3623    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6014   -0.5580    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3897   -0.3148    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5733    0.4895    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9685    1.0506    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1521    1.8549    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5474    2.4161    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9405    2.0981    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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 11 32  1  0  0  0  0
 32 33  2  0  0  0  0
  3 33  1  0  0  0  0
 33 34  1  0  0  0  0
M  END

     RDKit          3D

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M  END


  Mrv0541 04121502132D          

 34 36  0  0  0  0            999 V2000
   -0.5541   -2.4098    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
> <DATABASE_ID>
NP0222983

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC1=CC(CCN(C)C)=C2SC3=C(OC)C(OC)=C(SC)C(CCN(C)C)=C3SSC2=C1O

> <INCHI_IDENTIFIER>
InChI=1S/C24H34N2O4S4/c1-25(2)11-9-14-13-16(28-5)17(27)23-20(14)32-24-19(30-7)18(29-6)21(31-8)15(10-12-26(3)4)22(24)33-34-23/h13,27H,9-12H2,1-8H3

> <INCHI_KEY>
PGVMTGVDGHUSFT-UHFFFAOYSA-N

> <FORMULA>
C24H34N2O4S4

> <MOLECULAR_WEIGHT>
542.79

> <EXACT_MASS>
542.140142279

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
68

> <JCHEM_AVERAGE_POLARIZABILITY>
59.703126371355694

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
4,12-bis[2-(dimethylamino)ethyl]-6,14,15-trimethoxy-13-(methylsulfanyl)-2,9,10-trithiatricyclo[9.4.0.0³,⁸]pentadeca-1(15),3,5,7,11,13-hexaen-7-ol

> <ALOGPS_LOGP>
4.26

> <JCHEM_LOGP>
3.334659479187186

> <ALOGPS_LOGS>
-5.13

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
2

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.149514276567576

> <JCHEM_PKA_STRONGEST_BASIC>
9.500261663543075

> <JCHEM_POLAR_SURFACE_AREA>
54.400000000000006

> <JCHEM_REFRACTIVITY>
147.47299999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
10

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
4.07e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
4,12-bis[2-(dimethylamino)ethyl]-6,14,15-trimethoxy-13-(methylsulfanyl)-2,9,10-trithiatricyclo[9.4.0.0³,⁸]pentadeca-1(15),3,5,7,11,13-hexaen-7-ol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 12-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   12-APR-15         0                                  
HETATM    1  C   UNK     0      -1.034  -4.498   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0      -0.692  -2.997   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0       0.780  -2.543   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.123  -1.042   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.594  -0.588   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.937   0.914   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.808   1.961   0.000  0.00  0.00           C+0
HETATM    8  N   UNK     0       2.151   3.463   0.000  0.00  0.00           N+0
HETATM    9  C   UNK     0       1.022   4.510   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       3.622   3.916   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       3.723  -1.635   0.000  0.00  0.00           C+0
HETATM   12  S   UNK     0       5.111  -0.967   0.000  0.00  0.00           S+0
HETATM   13  C   UNK     0       6.498  -1.635   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       7.627  -0.588   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       7.284   0.914   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0       8.413   1.961   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       9.099  -1.042   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      10.227   0.006   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0      11.699  -0.448   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       9.441  -2.543   0.000  0.00  0.00           C+0
HETATM   21  S   UNK     0      10.913  -2.997   0.000  0.00  0.00           S+0
HETATM   22  C   UNK     0      11.255  -4.498   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       8.312  -3.590   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       8.655  -5.092   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      10.127  -5.546   0.000  0.00  0.00           C+0
HETATM   26  N   UNK     0      10.469  -7.047   0.000  0.00  0.00           N+0
HETATM   27  C   UNK     0      11.941  -7.501   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       9.340  -8.095   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       6.841  -3.137   0.000  0.00  0.00           C+0
HETATM   30  S   UNK     0       5.881  -4.341   0.000  0.00  0.00           S+0
HETATM   31  S   UNK     0       4.341  -4.341   0.000  0.00  0.00           S+0
HETATM   32  C   UNK     0       3.380  -3.137   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       1.909  -3.590   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0       1.566  -5.092   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   33                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6   11                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8                                                            
CONECT   11    5   12   32                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14   29                                                  
CONECT   14   13   15   17                                                  
CONECT   15   14   16                                                       
CONECT   16   15                                                            
CONECT   17   14   18   20                                                  
CONECT   18   17   19                                                       
CONECT   19   18                                                            
CONECT   20   17   21   23                                                  
CONECT   21   20   22                                                       
CONECT   22   21                                                            
CONECT   23   20   24   29                                                  
CONECT   24   23   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   27   28                                                  
CONECT   27   26                                                            
CONECT   28   26                                                            
CONECT   29   23   13   30                                                  
CONECT   30   29   31                                                       
CONECT   31   30   32                                                       
CONECT   32   31   11   33                                                  
CONECT   33   32    3   34                                                  
CONECT   34   33                                                            
MASTER        0    0    0    0    0    0    0    0   34    0   72    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₄H₃₄N₂O₄S₄

Average Mass

542.7900 Da

Monoisotopic Mass

542.14014 Da

IUPAC Name

4,12-bis[2-(dimethylamino)ethyl]-6,14,15-trimethoxy-13-(methylsulfanyl)-2,9,10-trithiatricyclo[9.4.0.0³,⁸]pentadeca-1(15),3,5,7,11,13-hexaen-7-ol

Traditional Name

4,12-bis[2-(dimethylamino)ethyl]-6,14,15-trimethoxy-13-(methylsulfanyl)-2,9,10-trithiatricyclo[9.4.0.0³,⁸]pentadeca-1(15),3,5,7,11,13-hexaen-7-ol

CAS Registry Number

Not Available

SMILES

COC1=CC(CCN(C)C)=C2SC3=C(OC)C(OC)=C(SC)C(CCN(C)C)=C3SSC2=C1O

InChI Identifier

InChI=1S/C24H34N2O4S4/c1-25(2)11-9-14-13-16(28-5)17(27)23-20(14)32-24-19(30-7)18(29-6)21(31-8)15(10-12-26(3)4)22(24)33-34-23/h13,27H,9-12H2,1-8H3

InChI Key

PGVMTGVDGHUSFT-UHFFFAOYSA-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, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, 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
Lissoclinum badium	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as phenethylamines. Phenethylamines are compounds containing a phenethylamine moiety, which consists of a phenyl group substituted at the second position by an ethan-1-amine.

Kingdom

Organic compounds

Super Class

Benzenoids

Class

Benzene and substituted derivatives

Sub Class

Phenethylamines

Direct Parent

Phenethylamines

Alternative Parents

Substituents

Phenethylamine
Aryl thioether
Anisole
Phenol ether
Thiophenol ether
Alkyl aryl ether
Aralkylamine
Alkylarylthioether
Phenol
Heteroaromatic compound
Tertiary aliphatic amine
Tertiary amine
Ether
Organoheterocyclic compound
Sulfenyl compound
Thioether
Organosulfur compound
Organooxygen compound
Organonitrogen compound
Organic nitrogen compound
Hydrocarbon derivative
Amine
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	4.26	ALOGPS
logP	3.33	ChemAxon
logS	-5.1	ALOGPS
pKa (Strongest Acidic)	8.15	ChemAxon
pKa (Strongest Basic)	9.5	ChemAxon
Physiological Charge	2	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	54.4 Å²	ChemAxon
Rotatable Bond Count	10	ChemAxon
Refractivity	147.47 m³·mol⁻¹	ChemAxon
Polarizability	59.7 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

22833255

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 4,12-bis[2-(dimethylamino)ethyl]-6,14,15-trimethoxy-13-(methylsulfanyl)-2,9,10-trithiatricyclo[9.4.0.0³,⁸]pentadeca-1(15),3,5,7,11,13-hexaen-7-ol (NP0222983)

MOL for NP0222983 (4,12-bis[2-(dimethylamino)ethyl]-6,14,15-trimethoxy-13-(methylsulfanyl)-2,9,10-trithiatricyclo[9.4.0.0³,⁸]pentadeca-1(15),3,5,7,11,13-hexaen-7-ol)

3D MOL for NP0222983 (4,12-bis[2-(dimethylamino)ethyl]-6,14,15-trimethoxy-13-(methylsulfanyl)-2,9,10-trithiatricyclo[9.4.0.0³,⁸]pentadeca-1(15),3,5,7,11,13-hexaen-7-ol)

3D SDF for NP0222983 (4,12-bis[2-(dimethylamino)ethyl]-6,14,15-trimethoxy-13-(methylsulfanyl)-2,9,10-trithiatricyclo[9.4.0.0³,⁸]pentadeca-1(15),3,5,7,11,13-hexaen-7-ol)

3D-SDF for NP0222983 (4,12-bis[2-(dimethylamino)ethyl]-6,14,15-trimethoxy-13-(methylsulfanyl)-2,9,10-trithiatricyclo[9.4.0.0³,⁸]pentadeca-1(15),3,5,7,11,13-hexaen-7-ol)

PDB for NP0222983 (4,12-bis[2-(dimethylamino)ethyl]-6,14,15-trimethoxy-13-(methylsulfanyl)-2,9,10-trithiatricyclo[9.4.0.0³,⁸]pentadeca-1(15),3,5,7,11,13-hexaen-7-ol)

3D PDB for NP0222983 (4,12-bis[2-(dimethylamino)ethyl]-6,14,15-trimethoxy-13-(methylsulfanyl)-2,9,10-trithiatricyclo[9.4.0.0³,⁸]pentadeca-1(15),3,5,7,11,13-hexaen-7-ol)

SMILES for NP0222983 (4,12-bis[2-(dimethylamino)ethyl]-6,14,15-trimethoxy-13-(methylsulfanyl)-2,9,10-trithiatricyclo[9.4.0.0³,⁸]pentadeca-1(15),3,5,7,11,13-hexaen-7-ol)

INCHI for NP0222983 (4,12-bis[2-(dimethylamino)ethyl]-6,14,15-trimethoxy-13-(methylsulfanyl)-2,9,10-trithiatricyclo[9.4.0.0³,⁸]pentadeca-1(15),3,5,7,11,13-hexaen-7-ol)

Structure for NP0222983 (4,12-bis[2-(dimethylamino)ethyl]-6,14,15-trimethoxy-13-(methylsulfanyl)-2,9,10-trithiatricyclo[9.4.0.0³,⁸]pentadeca-1(15),3,5,7,11,13-hexaen-7-ol)

3D Structure for NP0222983 (4,12-bis[2-(dimethylamino)ethyl]-6,14,15-trimethoxy-13-(methylsulfanyl)-2,9,10-trithiatricyclo[9.4.0.0³,⁸]pentadeca-1(15),3,5,7,11,13-hexaen-7-ol)