NP-MRD: Showing NP-Card for (+)-(6S)-N-13-methyldiscorhabdin E (NP0332105)

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Record Information

Version

2.0

Created at

2023-11-14 00:02:09 UTC

Updated at

2024-09-03 04:18:03 UTC

NP-MRD ID

NP0332105

Natural Product DOI

https://doi.org/10.57994/1262

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(+)-(6S)-N-13-methyldiscorhabdin E

Description

(+)-(6S)-N-13-methyldiscorhabdin E 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. (+)-(6S)-N-13-methyldiscorhabdin E was first documented in 2023 (PMID: 37755087). Based on a literature review very few articles have been published on (+)-(6S)-N-13-methyldiscorhabdin E.

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 11142300022D          

 25 29  0  0  1  0            999 V2000
    0.8053    2.4886    0.0000 O   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
    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
   -0.5902    1.4076    0.0000 C   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
    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
    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
    3.3457   -0.3113    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9498   -1.0351    0.0000 Br  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
    4.5994   -0.9970    0.0000 O   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
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 11 13  1  0  0  0  0
  2 13  1  0  0  0  0
 13 14  2  0  0  0  0
  5 14  1  0  0  0  0
  9 14  1  0  0  0  0
 15  4  1  1  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
  3 18  1  0  0  0  0
 15 19  1  0  0  0  0
 19 20  2  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 22 24  2  0  0  0  0
 15 24  1  0  0  0  0
 21 25  2  0  0  0  0
M  CHG  1   6   1
M  END


  Mrv2104 11142300022D          

 25 29  0  0  1  0            999 V2000
    0.8053    2.4886    0.0000 O   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
    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
   -0.5902    1.4076    0.0000 C   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
    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
    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
    3.3457   -0.3113    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9498   -1.0351    0.0000 Br  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
    4.5994   -0.9970    0.0000 O   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
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 11 13  1  0  0  0  0
  2 13  1  0  0  0  0
 13 14  2  0  0  0  0
  5 14  1  0  0  0  0
  9 14  1  0  0  0  0
 15  4  1  1  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
  3 18  1  0  0  0  0
 15 19  1  0  0  0  0
 19 20  2  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 22 24  2  0  0  0  0
 15 24  1  0  0  0  0
 21 25  2  0  0  0  0
M  CHG  1   6   1
M  END
> <DATABASE_ID>
NP0332105

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CN1C=C2CC[NH+]=C3C2=C1C(=O)C1=C3[C@@]2(CCN1)C=CC(=O)C(Br)=C2

> <INCHI_IDENTIFIER>
InChI=1S/C19H16BrN3O2/c1-23-9-10-3-6-21-15-13(10)17(23)18(25)16-14(15)19(5-7-22-16)4-2-12(24)11(20)8-19/h2,4,8-9,22H,3,5-7H2,1H3/p+1/t19-/m1/s1

> <INCHI_KEY>
CVZLRMWAEUMAFO-LJQANCHMSA-O

> <FORMULA>
C19H17BrN3O2

> <MOLECULAR_WEIGHT>
399.267

> <EXACT_MASS>
398.049866

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
42

> <JCHEM_AVERAGE_POLARIZABILITY>
37.53404007438613

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
1

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1S)-3-bromo-10'-methyl-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>
1.4645692389999996

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_ACIDIC>
17.04046335167621

> <JCHEM_PKA_STRONGEST_BASIC>
7.749663469078798

> <JCHEM_POLAR_SURFACE_AREA>
65.07

> <JCHEM_REFRACTIVITY>
114.28229999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(1S)-3-bromo-10'-methyl-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                                 14-NOV-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   14-NOV-23         0                                  
HETATM    1  O   UNK     0       1.503   4.645   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       2.304   3.330   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       3.843   3.365   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.644   2.050   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       3.905   0.699   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0       4.388  -1.075   0.000  0.00  0.00           N+1
HETATM    7  C   UNK     0       3.385  -2.243   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.871  -1.958   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.362  -0.505   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -0.059   0.089   0.000  0.00  0.00           C+0
HETATM   11  N   UNK     0       0.066   1.624   0.000  0.00  0.00           N+0
HETATM   12  C   UNK     0      -1.102   2.628   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       1.565   1.979   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       2.365   0.663   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       6.184   2.086   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       6.923   3.437   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       6.122   4.752   0.000  0.00  0.00           C+0
HETATM   18  N   UNK     0       4.582   4.717   0.000  0.00  0.00           N+0
HETATM   19  C   UNK     0       7.723   2.121   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       8.524   0.806   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       7.785  -0.546   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       6.245  -0.581   0.000  0.00  0.00           C+0
HETATM   23 Br   UNK     0       5.506  -1.932   0.000  0.00  0.00          Br+0
HETATM   24  C   UNK     0       5.445   0.734   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0       8.585  -1.861   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   13                                                  
CONECT    3    2    4   18                                                  
CONECT    4    3    5   15                                                  
CONECT    5    4    6   14                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10   14                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11    2   14                                                  
CONECT   14   13    5    9                                                  
CONECT   15    4   16   19   24                                             
CONECT   16   15   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17    3                                                       
CONECT   19   15   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   22   25                                                  
CONECT   22   21   23   24                                                  
CONECT   23   22                                                            
CONECT   24   22   15                                                       
CONECT   25   21                                                            
MASTER        0    0    0    0    0    0    0    0   25    0   58    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₉H₁₇BrN₃O₂

Average Mass

399.2670 Da

Monoisotopic Mass

398.04987 Da

IUPAC Name

(1S)-3-bromo-10'-methyl-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-10'-methyl-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

CN1C=C2CC[NH+]=C3C2=C1C(=O)C1=C3[C@@]2(CCN1)C=CC(=O)C(Br)=C2

InChI Identifier

InChI=1S/C19H16BrN3O2/c1-23-9-10-3-6-21-15-13(10)17(23)18(25)16-14(15)19(5-7-22-16)4-2-12(24)11(20)8-19/h2,4,8-9,22H,3,5-7H2,1H3/p+1/t19-/m1/s1

InChI Key

CVZLRMWAEUMAFO-LJQANCHMSA-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
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
HSQC NMR	[¹H, ¹³C] NMR Spectrum (2D, 600 MHz, C2D6OS, experimental)	maria.orfanoudaki@nih.gov	National Cancer Institute, MD, USA	Maria Orfanoudaki	2023-11-14	View Spectrum
HMBC NMR	[¹H, ¹³C] NMR Spectrum (2D, 600 MHz, C2D6OS, experimental)	maria.orfanoudaki@nih.gov	National Cancer Institute, MD, USA	Maria Orfanoudaki	2023-11-14	View Spectrum
COSY NMR	[¹H, ¹H] NMR Spectrum (2D, 600 MHz, C2D6OS, experimental)	maria.orfanoudaki@nih.gov	National Cancer Institute, MD, USA	Maria Orfanoudaki	2023-11-14	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, C2D6OS, experimental)	maria.orfanoudaki@nih.gov	National Cancer Institute, MD, USA	Maria Orfanoudaki	2023-11-14	View Spectrum

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View

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

Not Available

Chemical Taxonomy

Description

This compound 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
Pyrroloquinoline
Pyrrolo[4,3,2-de]quinoline
Indole or derivatives
Aryl ketone
Tetrahydropyridine
Alpha-branched alpha,beta-unsaturated-ketone
Substituted pyrrole
N-methylpyrrole
Alpha-haloketone
Heteroaromatic compound
Alpha,beta-unsaturated ketone
Secondary ketimine
Enone
Alpha-aminoketone
Acryloyl-group
Cyclic ketone
Tertiary aliphatic amine
Tertiary amine
Ketone
Azacycle
Bromoalkene
Haloalkene
Vinyl halide
Vinyl bromide
Secondary amine
Enamine
Secondary aliphatic amine
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Organobromide
Organohalogen compound
Carbonyl group
Amine
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	1.46	ChemAxon
pKa (Strongest Acidic)	17.04	ChemAxon
pKa (Strongest Basic)	7.75	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	65.07 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	114.28 m³·mol⁻¹	ChemAxon
Polarizability	37.53 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

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

Not Available

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)-N-13-methyldiscorhabdin E (NP0332105)

MOL for NP0332105 ((+)-(6S)-N-13-methyldiscorhabdin E)

3D MOL for NP0332105 ((+)-(6S)-N-13-methyldiscorhabdin E)

3D SDF for NP0332105 ((+)-(6S)-N-13-methyldiscorhabdin E)

3D-SDF for NP0332105 ((+)-(6S)-N-13-methyldiscorhabdin E)

PDB for NP0332105 ((+)-(6S)-N-13-methyldiscorhabdin E)

3D PDB for NP0332105 ((+)-(6S)-N-13-methyldiscorhabdin E)

SMILES for NP0332105 ((+)-(6S)-N-13-methyldiscorhabdin E)

INCHI for NP0332105 ((+)-(6S)-N-13-methyldiscorhabdin E)

Structure for NP0332105 ((+)-(6S)-N-13-methyldiscorhabdin E)

3D Structure for NP0332105 ((+)-(6S)-N-13-methyldiscorhabdin E)