NP-MRD: Showing NP-Card for (+)-(6S)-discorhabdin E (NP0331925)

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Record Information

Version

1.0

Created at

2023-10-06 01:38:12 UTC

Updated at

2024-05-05 00:33:46 UTC

NP-MRD ID

NP0331925

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(+)-(6S)-discorhabdin E

Description

(1R)-5-bromo-4,8'-dioxo-6',10',15'-triazaspiro[cyclohexane-1,3'-tetracyclo[7.6.1.0²,⁷.0¹²,¹⁶]Hexadecane]-1'(15'),2,2'(7'),5,9'(16'),11'-hexaen-15'-ium belongs to the class of organic compounds known as phenanthrolines. These are aromatic polycyclic compounds containing the phenanthroline skeleton, which is a derivative of phenanthrene, and consists of two pyridine rings non-linearly joined by a benzene ring. Based on a literature review very few articles have been published on (1R)-5-bromo-4,8'-dioxo-6',10',15'-triazaspiro[cyclohexane-1,3'-tetracyclo[7.6.1.0²,⁷.0¹²,¹⁶]Hexadecane]-1'(15'),2,2'(7'),5,9'(16'),11'-hexaen-15'-ium.

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 10062301382D          

 24 28  0  0  1  0            999 V2000
    2.9498   -1.0351    0.0000 Br  0  0  0  0  0  0  0  0  0  0  0  0
    3.3457   -0.3113    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9168    0.3934    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3126    1.1172    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.7085    1.8411    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2796    2.5458    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4548    2.5267    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0590    1.8029    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4879    1.0982    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0920    0.3744    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3509   -0.5761    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    1.8132   -1.2017    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0025   -1.0489    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7295   -0.2704    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0317    0.0477    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0355    0.8699    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.8383    1.0600    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2672    0.3553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2342    1.7839    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8053    2.4886    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1374    1.1363    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5663    0.4316    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1705   -0.2922    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5994   -0.9970    0.0000 O   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
  4  3  1  6  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  4  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  2  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  2  0  0  0  0
 10 18  1  0  0  0  0
 14 18  1  0  0  0  0
 17 19  1  0  0  0  0
  8 19  1  0  0  0  0
 19 20  2  0  0  0  0
  4 21  1  0  0  0  0
 21 22  2  0  0  0  0
 22 23  1  0  0  0  0
  2 23  1  0  0  0  0
 23 24  2  0  0  0  0
M  CHG  1  11   1
M  END
> <DATABASE_ID>
NP0331925

> <DATABASE_NAME>
NP-MRD

> <SMILES>
BrC1=C[C@]2(CCNC3=C2C2=[NH+]CCC4=CNC(=C24)C3=O)C=CC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C18H14BrN3O2/c19-10-7-18(3-1-11(10)23)4-6-21-16-13(18)14-12-9(2-5-20-14)8-22-15(12)17(16)24/h1,3,7-8,21-22H,2,4-6H2/p+1/t18-/m1/s1

> <INCHI_KEY>
JDWKHDMGELDYEC-GOSISDBHSA-O

> <FORMULA>
C18H15BrN3O2

> <MOLECULAR_WEIGHT>
385.24

> <EXACT_MASS>
384.034216

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
39

> <JCHEM_AVERAGE_POLARIZABILITY>
35.30497467897437

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
1

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1S)-3-bromo-4,8'-dioxo-6',10',15'-triazaspiro[cyclohexane-1,3'-tetracyclo[7.6.1.0^{2,7}.0^{12,16}]hexadecane]-1'(15'),2,2'(7'),5,9'(16'),11'-hexaen-15'-ium

> <JCHEM_LOGP>
1.2408931733333328

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
17.225730659882068

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.292302909955067

> <JCHEM_PKA_STRONGEST_BASIC>
7.721812419397708

> <JCHEM_POLAR_SURFACE_AREA>
75.93

> <JCHEM_REFRACTIVITY>
109.38559999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(1S)-3-bromo-4,8'-dioxo-6',10',15'-triazaspiro[cyclohexane-1,3'-tetracyclo[7.6.1.0^{2,7}.0^{12,16}]hexadecane]-1'(15'),2,2'(7'),5,9'(16'),11'-hexaen-15'-ium

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 06-OCT-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-OCT-23         0                                  
HETATM    1 Br   UNK     0       5.506  -1.932   0.000  0.00  0.00          Br+0
HETATM    2  C   UNK     0       6.245  -0.581   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.445   0.734   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       6.184   2.086   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       6.923   3.437   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       6.122   4.752   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0       4.582   4.717   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0       3.843   3.365   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       4.644   2.050   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       3.905   0.699   0.000  0.00  0.00           C+0
HETATM   11  N   UNK     0       4.388  -1.075   0.000  0.00  0.00           N+1
HETATM   12  C   UNK     0       3.385  -2.243   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       1.871  -1.958   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       1.362  -0.505   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -0.059   0.089   0.000  0.00  0.00           C+0
HETATM   16  N   UNK     0       0.066   1.624   0.000  0.00  0.00           N+0
HETATM   17  C   UNK     0       1.565   1.979   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       2.365   0.663   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       2.304   3.330   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0       1.503   4.645   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0       7.723   2.121   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       8.524   0.806   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       7.785  -0.546   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0       8.585  -1.861   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   23                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    9   21                                             
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9   19                                                  
CONECT    9    8    4   10                                                  
CONECT   10    9   11   18                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15   18                                                  
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18   19                                                  
CONECT   18   17   10   14                                                  
CONECT   19   17    8   20                                                  
CONECT   20   19                                                            
CONECT   21    4   22                                                       
CONECT   22   21   23                                                       
CONECT   23   22    2   24                                                  
CONECT   24   23                                                            
MASTER        0    0    0    0    0    0    0    0   24    0   56    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₈H₁₅BrN₃O₂

Average Mass

385.2400 Da

Monoisotopic Mass

384.03422 Da

IUPAC Name

(1S)-3-bromo-4,8'-dioxo-6',10',15'-triazaspiro[cyclohexane-1,3'-tetracyclo[7.6.1.0^{2,7}.0^{12,16}]hexadecane]-1'(15'),2,2'(7'),5,9'(16'),11'-hexaen-15'-ium

Traditional Name

(1S)-3-bromo-4,8'-dioxo-6',10',15'-triazaspiro[cyclohexane-1,3'-tetracyclo[7.6.1.0^{2,7}.0^{12,16}]hexadecane]-1'(15'),2,2'(7'),5,9'(16'),11'-hexaen-15'-ium

CAS Registry Number

Not Available

SMILES

BrC1=C[C@]2(CCNC3=C2C2=[NH+]CCC4=CNC(=C24)C3=O)C=CC1=O

InChI Identifier

InChI=1S/C18H14BrN3O2/c19-10-7-18(3-1-11(10)23)4-6-21-16-13(18)14-12-9(2-5-20-14)8-22-15(12)17(16)24/h1,3,7-8,21-22H,2,4-6H2/p+1/t18-/m1/s1

InChI Key

JDWKHDMGELDYEC-GOSISDBHSA-O

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
HSQC NMR	[¹H, ¹³C] NMR Spectrum (2D, 600 MHz, C2D6OS, experimental)	maria.orfanoudaki@nih.gov	National Cancer Institute, MD, USA	Maria Orfanoudaki	2024-05-03	View Spectrum
COSY NMR	[¹H, ¹H] NMR Spectrum (2D, 600 MHz, C2D6OS, experimental)	maria.orfanoudaki@nih.gov	National Cancer Institute, MD, USA	Maria Orfanoudaki	2024-05-03	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, C2D6OS, experimental)	maria.orfanoudaki@nih.gov	National Cancer Institute, MD, USA	Maria Orfanoudaki	2024-05-03	View Spectrum

Predicted Spectra

Not Available

Chemical Shift Submissions

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹H NMR Spectrum (1D, 600.314502325, C2D6OS, simulated)	maria.orfanoudaki@nih.gov	National Cancer Institute, MD, USA	Maria Orfanoudaki	2024-05-03	View Spectrum

Species

Species of Origin

Species Name	Source	Reference
brevis		Not Available

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as phenanthrolines. These are aromatic polycyclic compounds containing the phenanthroline skeleton, which is a derivative of phenanthrene, and consists of two pyridine rings non-linearly joined by a benzene ring.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Phenanthrolines

Sub Class

Not Available

Direct Parent

Phenanthrolines

Alternative Parents

Substituents

1,7-phenanthroline
Pyrrolo[4,3,2-de]quinoline
Pyrroloquinoline
Indole or derivatives
Aryl ketone
Tetrahydropyridine
Alpha-haloketone
Pyrrole
Heteroaromatic compound
Ketone
Cyclic ketone
Secondary aliphatic amine
Enamine
Azacycle
Bromoalkene
Haloalkene
Vinyl bromide
Vinyl halide
Organic oxide
Organooxygen compound
Organonitrogen compound
Organobromide
Organohalogen compound
Hydrocarbon derivative
Carbonyl group
Amine
Organic nitrogen compound
Organic oxygen compound
Organic cation
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	1.24	ChemAxon
pKa (Strongest Acidic)	13.29	ChemAxon
pKa (Strongest Basic)	7.72	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	75.93 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	109.39 m³·mol⁻¹	ChemAxon
Polarizability	35.3 Å³	ChemAxon
Number of Rings	5	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

Not Available

Chemspider ID

10475325

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

21773329

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Orfanoudaki M, Smith EA, Hill NT, Garman KA, Brownell I, Copp BR, Grkovic T, Henrich CJ: An Investigation of Structure-Activity Relationships and Cell Death Mechanisms of the Marine Alkaloids Discorhabdins in Merkel Cell Carcinoma Cells. Mar Drugs. 2023 Aug 29;21(9):474. doi: 10.3390/md21090474. [PubMed:37755087 ]

Showing NP-Card for (+)-(6S)-discorhabdin E (NP0331925)

MOL for NP0331925 ((+)-(6S)-discorhabdin E )

3D MOL for NP0331925 ((+)-(6S)-discorhabdin E )

3D SDF for NP0331925 ((+)-(6S)-discorhabdin E )

3D-SDF for NP0331925 ((+)-(6S)-discorhabdin E )

PDB for NP0331925 ((+)-(6S)-discorhabdin E )

3D PDB for NP0331925 ((+)-(6S)-discorhabdin E )

SMILES for NP0331925 ((+)-(6S)-discorhabdin E )

INCHI for NP0331925 ((+)-(6S)-discorhabdin E )

Structure for NP0331925 ((+)-(6S)-discorhabdin E )

3D Structure for NP0331925 ((+)-(6S)-discorhabdin E )