NP-MRD: Showing NP-Card for Plakinidine D (NP0070321)

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Record Information

Version

2.0

Created at

2022-04-28 15:39:11 UTC

Updated at

2022-04-28 15:39:11 UTC

NP-MRD ID

NP0070321

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Plakinidine D

Description

8-Amino-3,10,19-triazapentacyclo[10.7.1.0²,⁷.0⁹,²⁰.0¹³,¹⁸]Icosa-1(19),2(7),8,10,12(20),13,15,17-octaen-6-one 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. Plakinidine D is found in Didemnum rubeum and Didemnum rubeus. Based on a literature review very few articles have been published on 8-amino-3,10,19-triazapentacyclo[10.7.1.0²,⁷.0⁹,²⁰.0¹³,¹⁸]Icosa-1(19),2(7),8,10,12(20),13,15,17-octaen-6-one.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 34 38  0  0  0  0  0  0  0  0999 V2000
   -2.3392    2.9863   -0.8573 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5571    1.8700   -0.5178 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0957    0.7468    0.0650 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3372   -0.3843    0.4151 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0154   -0.3427    0.1509 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8251   -1.3943    0.4573 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1592   -1.2722    0.1617 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0453   -2.3051    0.4460 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3917   -2.1897    0.1508 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9221   -1.0588   -0.4338 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0403   -0.0255   -0.7191 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7047   -0.1476   -0.4231 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8808    0.9191   -0.7334 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5562    0.7742   -0.4296 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1840    1.8733   -0.7693 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7593    2.7765   -1.3309 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.9656    2.2452   -1.3213 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9347   -1.4909    1.0012 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3876   -1.6460    1.0905 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1168   -0.3458    1.1411 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5288    0.7322    0.3324 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2439    1.6297   -0.1243 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3074    3.9073   -0.3519 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0029    2.9214   -1.6604 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6226   -3.1941    0.9066 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0537   -3.0233    0.3899 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9598   -0.9285   -0.6792 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4150    0.8754   -1.1762 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8915    2.6690   -1.6728 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3476   -2.2545    1.4003 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6679   -2.2379    1.9863 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7567   -2.2021    0.1820 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1524   -0.5195    0.7500 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2483    0.0362    2.1731 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3 21  1  0
 21 22  2  0
 21 20  1  0
 20 19  1  0
 19 18  1  0
 18  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  2  0
 11 12  1  0
 12 13  2  0
 13 17  1  0
 17 16  2  0
 16 15  1  0
 15 14  2  0
 15  2  1  0
  4  3  1  0
 14  5  1  0
 12  7  1  0
 14 13  1  0
  1 23  1  0
  1 24  1  0
 20 33  1  0
 20 34  1  0
 19 31  1  0
 19 32  1  0
 18 30  1  0
  8 25  1  0
  9 26  1  0
 10 27  1  0
 11 28  1  0
 17 29  1  0
M  END


  Mrv1652304282217392D          

 22 26  0  0  0  0            999 V2000
    0.5520   -2.2364    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0800   -2.9130    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4301   -3.6601    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2521   -3.7305    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7240   -3.0538    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3739   -2.3067    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1392   -1.6865    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.9286   -1.9262    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1157   -2.7297    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5134   -3.2935    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5293   -4.1184    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7498   -4.3884    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.9051   -2.9695    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5074   -2.4057    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3204   -1.6022    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5310   -1.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0419   -4.3368    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7420   -2.8427    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2139   -3.5193    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0920   -2.0956    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6201   -1.4189    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2019   -1.4893    0.0000 N   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
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  1  6  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  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
  4 12  1  0  0  0  0
  9 13  1  0  0  0  0
 13 14  2  0  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
  8 16  1  0  0  0  0
  3 17  1  0  0  0  0
  2 18  1  0  0  0  0
 18 19  2  0  0  0  0
 18 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
  1 22  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0070321

> <DATABASE_NAME>
NP-MRD

> <SMILES>
NC1=C2C(=O)CCNC2=C2N=C3C=CC=CC3=C3C=NC1=C23

> <INCHI_IDENTIFIER>
InChI=1S/C17H12N4O/c18-14-13-11(22)5-6-19-16(13)17-12-9(7-20-15(12)14)8-3-1-2-4-10(8)21-17/h1-4,7,19H,5-6,18H2

> <INCHI_KEY>
XQMSONSBRQAXNX-UHFFFAOYSA-N

> <FORMULA>
C17H12N4O

> <MOLECULAR_WEIGHT>
288.31

> <EXACT_MASS>
288.101111022

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
34

> <JCHEM_AVERAGE_POLARIZABILITY>
30.53975131532656

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
8-amino-3,10,19-triazapentacyclo[10.7.1.0^{2,7}.0^{9,20}.0^{13,18}]icosa-1,7,9(20),10,12,14,16,18-octaen-6-one

> <ALOGPS_LOGP>
2.49

> <JCHEM_LOGP>
2.847084101333333

> <ALOGPS_LOGS>
-3.63

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
15.140748476225394

> <JCHEM_PKA_STRONGEST_ACIDIC>
10.525220605423138

> <JCHEM_PKA_STRONGEST_BASIC>
2.5943851355451804

> <JCHEM_POLAR_SURFACE_AREA>
80.37

> <JCHEM_REFRACTIVITY>
88.76639999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.80e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
8-amino-3,10,19-triazapentacyclo[10.7.1.0^{2,7}.0^{9,20}.0^{13,18}]icosa-1,7,9(20),10,12,14,16,18-octaen-6-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 28-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   28-APR-22         0                                  
HETATM    1  C   UNK     0       1.030  -4.175   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.149  -5.438   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.803  -6.832   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.337  -6.964   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       3.218  -5.700   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.565  -4.306   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0       3.993  -3.148   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0       5.467  -3.596   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       5.816  -5.096   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       4.692  -6.148   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.721  -7.688   0.000  0.00  0.00           C+0
HETATM   12  N   UNK     0       3.266  -8.192   0.000  0.00  0.00           N+0
HETATM   13  C   UNK     0       7.290  -5.543   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       8.414  -4.491   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       8.065  -2.991   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       6.591  -2.543   0.000  0.00  0.00           C+0
HETATM   17  N   UNK     0      -0.078  -8.095   0.000  0.00  0.00           N+0
HETATM   18  C   UNK     0      -1.385  -5.306   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      -2.266  -6.569   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0      -2.038  -3.912   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      -1.158  -2.649   0.000  0.00  0.00           C+0
HETATM   22  N   UNK     0       0.377  -2.780   0.000  0.00  0.00           N+0
CONECT    1    2    6   22                                                  
CONECT    2    1    3   18                                                  
CONECT    3    2    4   17                                                  
CONECT    4    3    5   12                                                  
CONECT    5    4    6   10                                                  
CONECT    6    5    1    7                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9   16                                                  
CONECT    9    8   10   13                                                  
CONECT   10    9    5   11                                                  
CONECT   11   10   12                                                       
CONECT   12   11    4                                                       
CONECT   13    9   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15    8                                                       
CONECT   17    3                                                            
CONECT   18    2   19   20                                                  
CONECT   19   18                                                            
CONECT   20   18   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21    1                                                       
MASTER        0    0    0    0    0    0    0    0   22    0   52    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₇H₁₂N₄O

Average Mass

288.3100 Da

Monoisotopic Mass

288.10111 Da

IUPAC Name

8-amino-3,10,19-triazapentacyclo[10.7.1.0^{2,7}.0^{9,20}.0^{13,18}]icosa-1,7,9(20),10,12,14,16,18-octaen-6-one

Traditional Name

8-amino-3,10,19-triazapentacyclo[10.7.1.0^{2,7}.0^{9,20}.0^{13,18}]icosa-1,7,9(20),10,12,14,16,18-octaen-6-one

CAS Registry Number

Not Available

SMILES

NC1=C2C(=O)CCNC2=C2N=C3C=CC=CC3=C3C=NC1=C23

InChI Identifier

InChI=1S/C17H12N4O/c18-14-13-11(22)5-6-19-16(13)17-12-9(7-20-15(12)14)8-3-1-2-4-10(8)21-17/h1-4,7,19H,5-6,18H2

InChI Key

XQMSONSBRQAXNX-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, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, 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
Didemnum rubeum	Animalia	KNApSAcK
Didemnum rubeus	Animalia	KNApSAcK

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

Acridine
Benzoquinoline
1,10-phenanthroline
Aminoquinoline
Tetrahydroquinolone
Quinolone
Tetrahydroquinoline
Quinoline
Indole or derivatives
Aryl alkyl ketone
Aryl ketone
Secondary aliphatic/aromatic amine
Benzenoid
Pyridine
Heteroaromatic compound
Vinylogous amide
Ketone
Secondary amine
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Azacycle
Amine
Organonitrogen compound
Organooxygen compound
Imine
Primary amine
Hydrocarbon derivative
Organic oxide
Organic oxygen compound
Organic nitrogen 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	2.49	ALOGPS
logP	2.85	ChemAxon
logS	-3.6	ALOGPS
pKa (Strongest Acidic)	10.53	ChemAxon
pKa (Strongest Basic)	2.59	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	80.37 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	88.77 m³·mol⁻¹	ChemAxon
Polarizability	30.54 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

C00028847

Chemspider ID

10476817

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

Not Available

Showing NP-Card for Plakinidine D (NP0070321)

MOL for NP0070321 (Plakinidine D)

3D MOL for NP0070321 (Plakinidine D)

3D SDF for NP0070321 (Plakinidine D)

3D-SDF for NP0070321 (Plakinidine D)

PDB for NP0070321 (Plakinidine D)

3D PDB for NP0070321 (Plakinidine D)

SMILES for NP0070321 (Plakinidine D)

INCHI for NP0070321 (Plakinidine D)

Structure for NP0070321 (Plakinidine D)

3D Structure for NP0070321 (Plakinidine D)