NP-MRD: Showing NP-Card for (+)-(6S) N-13-demethyldiscorhabdin U (NP0331904)

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Record Information

Version

2.0

Created at

2023-10-04 14:57:28 UTC

Updated at

2025-02-11 15:44:27 UTC

NP-MRD ID

NP0331904

Natural Product DOI

https://doi.org/10.57994/1258

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(+)-(6S) N-13-demethyldiscorhabdin U

Description

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

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 10042314572D          

 26 30  0  0  1  0            999 V2000
    4.1044    2.5649    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5333    1.8601    0.0000 S   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
    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
    3.3126    1.1172    0.0000 C   0  0  2  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
  1  2  1  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
  5  7  1  0  0  0  0
  7  8  1  0  0  0  0
  7  9  2  0  0  0  0
 10  9  1  6  0  0  0
 10  3  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  2  0  0  0  0
 10 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  2  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  2  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  2  0  0  0  0
 16 24  1  0  0  0  0
 20 24  1  0  0  0  0
 23 25  1  0  0  0  0
 14 25  1  0  0  0  0
 25 26  2  0  0  0  0
M  CHG  1  17   1
M  END


  Mrv2104 10042314572D          

 26 30  0  0  1  0            999 V2000
    4.1044    2.5649    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5333    1.8601    0.0000 S   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
    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
    3.3126    1.1172    0.0000 C   0  0  2  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
  1  2  1  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
  5  7  1  0  0  0  0
  7  8  1  0  0  0  0
  7  9  2  0  0  0  0
 10  9  1  6  0  0  0
 10  3  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  2  0  0  0  0
 10 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  2  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  2  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  2  0  0  0  0
 16 24  1  0  0  0  0
 20 24  1  0  0  0  0
 23 25  1  0  0  0  0
 14 25  1  0  0  0  0
 25 26  2  0  0  0  0
M  CHG  1  17   1
M  END
> <DATABASE_ID>
NP0331904

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CSC1=CC(=O)C(Br)=C[C@]11C=CNC2=C1C1=[NH+]CCC3=CNC(=C13)C2=O

> <INCHI_IDENTIFIER>
InChI=1S/C19H14BrN3O2S/c1-26-12-6-11(24)10(20)7-19(12)3-5-22-17-14(19)15-13-9(2-4-21-15)8-23-16(13)18(17)25/h3,5-8,22-23H,2,4H2,1H3/p+1/t19-/m1/s1

> <INCHI_KEY>
XCVKIRRNAMQALM-LJQANCHMSA-O

> <FORMULA>
C19H15BrN3O2S

> <MOLECULAR_WEIGHT>
429.31

> <EXACT_MASS>
428.006287

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
41

> <JCHEM_AVERAGE_POLARIZABILITY>
38.97330318108308

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
1

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1S)-3-bromo-6-(methylsulfanyl)-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'),4',5,9'(16'),11'-heptaen-15'-ium

> <JCHEM_LOGP>
1.4825488823333335

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
17.272087973285952

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.266682557172716

> <JCHEM_PKA_STRONGEST_BASIC>
7.684856187971565

> <JCHEM_POLAR_SURFACE_AREA>
75.93

> <JCHEM_REFRACTIVITY>
122.14899999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(1S)-3-bromo-6-(methylsulfanyl)-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'),4',5,9'(16'),11'-heptaen-15'-ium

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 04-OCT-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-OCT-23         0                                  
HETATM    1  C   UNK     0       7.662   4.788   0.000  0.00  0.00           C+0
HETATM    2  S   UNK     0       8.462   3.472   0.000  0.00  0.00           S+0
HETATM    3  C   UNK     0       7.723   2.121   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       8.524   0.806   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       7.785  -0.546   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       8.585  -1.861   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       6.245  -0.581   0.000  0.00  0.00           C+0
HETATM    8 Br   UNK     0       5.506  -1.932   0.000  0.00  0.00          Br+0
HETATM    9  C   UNK     0       5.445   0.734   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       6.184   2.086   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       6.923   3.437   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       6.122   4.752   0.000  0.00  0.00           C+0
HETATM   13  N   UNK     0       4.582   4.717   0.000  0.00  0.00           N+0
HETATM   14  C   UNK     0       3.843   3.365   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       4.644   2.050   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       3.905   0.699   0.000  0.00  0.00           C+0
HETATM   17  N   UNK     0       4.388  -1.075   0.000  0.00  0.00           N+1
HETATM   18  C   UNK     0       3.385  -2.243   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       1.871  -1.958   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       1.362  -0.505   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      -0.059   0.089   0.000  0.00  0.00           C+0
HETATM   22  N   UNK     0       0.066   1.624   0.000  0.00  0.00           N+0
HETATM   23  C   UNK     0       1.565   1.979   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       2.365   0.663   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       2.304   3.330   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0       1.503   4.645   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   10                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10                                                       
CONECT   10    9    3   11   15                                             
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15   25                                                  
CONECT   15   14   10   16                                                  
CONECT   16   15   17   24                                                  
CONECT   17   16   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   21   24                                                  
CONECT   21   20   22                                                       
CONECT   22   21   23                                                       
CONECT   23   22   24   25                                                  
CONECT   24   23   16   20                                                  
CONECT   25   23   14   26                                                  
CONECT   26   25                                                            
MASTER        0    0    0    0    0    0    0    0   26    0   60    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₉H₁₅BrN₃O₂S

Average Mass

429.3100 Da

Monoisotopic Mass

428.00629 Da

IUPAC Name

(1S)-3-bromo-6-(methylsulfanyl)-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'),4',5,9'(16'),11'-heptaen-15'-ium

Traditional Name

(1S)-3-bromo-6-(methylsulfanyl)-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'),4',5,9'(16'),11'-heptaen-15'-ium

CAS Registry Number

Not Available

SMILES

CSC1=CC(=O)C(Br)=C[C@]11C=CNC2=C1C1=[NH+]CCC3=CNC(=C13)C2=O

InChI Identifier

InChI=1S/C19H14BrN3O2S/c1-26-12-6-11(24)10(20)7-19(12)3-5-22-17-14(19)15-13-9(2-4-21-15)8-23-16(13)18(17)25/h3,5-8,22-23H,2,4H2,1H3/p+1/t19-/m1/s1

InChI Key

XCVKIRRNAMQALM-LJQANCHMSA-O

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
HSQC NMR	[¹H, ¹³C] NMR Spectrum (2D, 600 MHz, CD3OD, 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, CD3OD, 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, CD3OD, 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, CD3OD, 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, 600.314502325, C2D6OS, simulated)	maria.orfanoudaki@nih.gov	National Cancer Institute, MD, USA	Maria Orfanoudaki	2024-05-03	View Spectrum
2D NMR	[¹H, ¹³C] NMR Spectrum (2D, 600 MHz, Methanol, simulated)	maria.orfanoudaki@nih.gov	National Cancer Institute, MD, USA	Maria Orfanoudaki	2023-10-04	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, Methanol, simulated)	maria.orfanoudaki@nih.gov	National Cancer Institute, MD, USA	Maria Orfanoudaki	2023-10-04	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, Methanol, simulated)	maria.orfanoudaki@nih.gov	National Cancer Institute, MD, USA	Maria Orfanoudaki	2023-10-04	View Spectrum

Species

Species of Origin

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	1.48	ChemAxon
pKa (Strongest Acidic)	13.27	ChemAxon
pKa (Strongest Basic)	7.68	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	1	ChemAxon
Refractivity	122.15 m³·mol⁻¹	ChemAxon
Polarizability	38.97 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

44409912

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 (+)-(6S) N-13-demethyldiscorhabdin U (NP0331904)

MOL for NP0331904 ((+)-(6S) N-13-demethyldiscorhabdin U)

3D MOL for NP0331904 ((+)-(6S) N-13-demethyldiscorhabdin U)

3D SDF for NP0331904 ((+)-(6S) N-13-demethyldiscorhabdin U)

3D-SDF for NP0331904 ((+)-(6S) N-13-demethyldiscorhabdin U)

PDB for NP0331904 ((+)-(6S) N-13-demethyldiscorhabdin U)

3D PDB for NP0331904 ((+)-(6S) N-13-demethyldiscorhabdin U)

SMILES for NP0331904 ((+)-(6S) N-13-demethyldiscorhabdin U)

INCHI for NP0331904 ((+)-(6S) N-13-demethyldiscorhabdin U)

Structure for NP0331904 ((+)-(6S) N-13-demethyldiscorhabdin U)

3D Structure for NP0331904 ((+)-(6S) N-13-demethyldiscorhabdin U)