NP-MRD: Showing NP-Card for didebromodiscorhabdin C (NP0331924)

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Record Information

Version

2.0

Created at

2023-10-06 01:22:27 UTC

Updated at

2025-02-11 15:44:28 UTC

NP-MRD ID

NP0331924

Natural Product DOI

https://doi.org/10.57994/1257

Secondary Accession Numbers

None

Natural Product Identification

Common Name

didebromodiscorhabdin C

Description

didebromodiscorhabdin C was first documented in 2023 (PMID: 37755087). Based on a literature review very few articles have been published on didebromodiscorhabdin C.

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 10062301222D          

 23 27  0  0  0  0            999 V2000
    4.5994   -0.9970    0.0000 O   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
    2.9168    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  0  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
  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  1  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
  5 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  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
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  2  0  0  0  0
 11 19  1  0  0  0  0
 15 19  1  0  0  0  0
 18 20  1  0  0  0  0
  9 20  1  0  0  0  0
 20 21  2  0  0  0  0
  5 22  1  0  0  0  0
 22 23  2  0  0  0  0
  2 23  1  0  0  0  0
M  CHG  1  12   1
M  END
> <DATABASE_ID>
NP0331924

> <DATABASE_NAME>
NP-MRD

> <SMILES>
O=C1C=CC2(CCNC3=C2C2=[NH+]CCC4=CNC(=C24)C3=O)C=C1

> <INCHI_IDENTIFIER>
InChI=1S/C18H15N3O2/c22-11-1-4-18(5-2-11)6-8-20-16-13(18)14-12-10(3-7-19-14)9-21-15(12)17(16)23/h1-2,4-5,9,20-21H,3,6-8H2/p+1

> <INCHI_KEY>
AROYJUCVKLJDAK-UHFFFAOYSA-O

> <FORMULA>
C18H16N3O2

> <MOLECULAR_WEIGHT>
306.344

> <EXACT_MASS>
306.123703187

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
39

> <JCHEM_AVERAGE_POLARIZABILITY>
31.918665239455592

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
1

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
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>
0.6872329076666666

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
17.227997542068817

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.292386879612412

> <JCHEM_PKA_STRONGEST_BASIC>
8.17863861146387

> <JCHEM_POLAR_SURFACE_AREA>
75.93

> <JCHEM_REFRACTIVITY>
101.77629999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
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  O   UNK     0       8.585  -1.861   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       7.785  -0.546   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       6.245  -0.581   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.445   0.734   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       6.184   2.086   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       6.923   3.437   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       6.122   4.752   0.000  0.00  0.00           C+0
HETATM    8  N   UNK     0       4.582   4.717   0.000  0.00  0.00           N+0
HETATM    9  C   UNK     0       3.843   3.365   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       4.644   2.050   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       3.905   0.699   0.000  0.00  0.00           C+0
HETATM   12  N   UNK     0       4.388  -1.075   0.000  0.00  0.00           N+1
HETATM   13  C   UNK     0       3.385  -2.243   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       1.871  -1.958   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       1.362  -0.505   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -0.059   0.089   0.000  0.00  0.00           C+0
HETATM   17  N   UNK     0       0.066   1.624   0.000  0.00  0.00           N+0
HETATM   18  C   UNK     0       1.565   1.979   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       2.365   0.663   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       2.304   3.330   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       1.503   4.645   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0       7.723   2.121   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       8.524   0.806   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   23                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6   10   22                                             
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10   20                                                  
CONECT   10    9    5   11                                                  
CONECT   11   10   12   19                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16   19                                                  
CONECT   16   15   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19   20                                                  
CONECT   19   18   11   15                                                  
CONECT   20   18    9   21                                                  
CONECT   21   20                                                            
CONECT   22    5   23                                                       
CONECT   23   22    2                                                       
MASTER        0    0    0    0    0    0    0    0   23    0   54    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₈H₁₆N₃O₂

Average Mass

306.3440 Da

Monoisotopic Mass

306.12370 Da

IUPAC Name

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

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

O=C1C=CC2(CCNC3=C2C2=[NH+]CCC4=CNC(=C24)C3=O)C=C1

InChI Identifier

InChI=1S/C18H15N3O2/c22-11-1-4-18(5-2-11)6-8-20-16-13(18)14-12-10(3-7-19-14)9-21-15(12)17(16)23/h1-2,4-5,9,20-21H,3,6-8H2/p+1

InChI Key

AROYJUCVKLJDAK-UHFFFAOYSA-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
HMBC 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
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, C2D6OS, experimental)	maria.orfanoudaki@nih.gov	National Cancer Institute, MD, USA	Maria Orfanoudaki	2024-05-03	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, C2D6OS, simulated)	maria.orfanoudaki@nih.gov	National Cancer Institute, MD, USA	Maria Orfanoudaki	2024-05-03	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, DMSO, simulated)	maria.orfanoudaki@nih.gov	National Cancer Institute, MD, USA	Maria Orfanoudaki	2023-10-30	View Spectrum

Species

Species of Origin

Species Name	Source	Reference
Latrunculia brevis		Not Available

Chemical Taxonomy

Classification

Not classified

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	0.69	ChemAxon
pKa (Strongest Acidic)	13.29	ChemAxon
pKa (Strongest Basic)	8.18	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	101.78 m³·mol⁻¹	ChemAxon
Polarizability	31.92 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 ]
DOI: 10.3390/md21090474

Showing NP-Card for didebromodiscorhabdin C (NP0331924)

MOL for NP0331924 (didebromodiscorhabdin C )

3D MOL for NP0331924 (didebromodiscorhabdin C )

3D SDF for NP0331924 (didebromodiscorhabdin C )

3D-SDF for NP0331924 (didebromodiscorhabdin C )

PDB for NP0331924 (didebromodiscorhabdin C )

3D PDB for NP0331924 (didebromodiscorhabdin C )

SMILES for NP0331924 (didebromodiscorhabdin C )

INCHI for NP0331924 (didebromodiscorhabdin C )

Structure for NP0331924 (didebromodiscorhabdin C )

3D Structure for NP0331924 (didebromodiscorhabdin C )