NP-MRD: Showing NP-Card for (8z,10z,12e,15z,17r)-5,20-diazapentacyclo[18.12.1.1¹,⁵.0²,¹⁸.0⁴,¹⁶]tetratriaconta-8,10,12,15-tetraen-17-ol (NP0239380)

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Record Information

Version

2.0

Created at

2022-09-06 22:58:10 UTC

Updated at

2022-09-06 22:58:10 UTC

NP-MRD ID

NP0239380

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(8z,10z,12e,15z,17r)-5,20-diazapentacyclo[18.12.1.1¹,⁵.0²,¹⁸.0⁴,¹⁶]tetratriaconta-8,10,12,15-tetraen-17-ol

Description

Madangamine F belongs to the class of organic compounds known as naphthyridines. Naphthyridines are compounds containing a naphthyridine moiety, a naphthalene in which a carbon atom has been replaced by a nitrogen in each of the two rings. The naphthyridine skeleton can also be described as an assembly two fused pyridine rings, which do not share their nitrogen atom. (8z,10z,12e,15z,17r)-5,20-diazapentacyclo[18.12.1.1¹,⁵.0²,¹⁸.0⁴,¹⁶]tetratriaconta-8,10,12,15-tetraen-17-ol was first documented in 2007 (PMID: 17346073). Based on a literature review a small amount of articles have been published on madangamine F (PMID: 25845061).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309072200582D          

 35 39  0  0  1  0            999 V2000
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   -2.3058   -4.0076    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END

     RDKit          3D

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M  END


  Mrv1652309072200582D          

 35 39  0  0  1  0            999 V2000
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    5.7551   -4.1636    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1662   -4.7641    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3279   -4.8508    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5219   -5.1056    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6772   -4.9404    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.9754   -5.4218    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1725   -5.1192    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2245   -4.3136    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4786   -4.0425    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1084   -3.8191    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5185   -4.1049    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  1  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  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  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  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  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  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  1  0  0  0  0
 24 25  1  0  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 27 28  1  0  0  0  0
 28 29  1  0  0  0  0
 29 30  1  0  0  0  0
 30 31  1  0  0  0  0
  2 31  1  0  0  0  0
 31 32  1  0  0  0  0
 16 32  1  0  0  0  0
 32 33  1  0  0  0  0
 33 34  1  0  0  0  0
  3 34  1  0  0  0  0
 14 34  1  0  0  0  0
 29 35  1  0  0  0  0
 16 35  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0239380

> <DATABASE_NAME>
NP-MRD

> <SMILES>
O[C@@H]1C2CN3CC4(CN5CC\C=C/C=C\C=C\C\C=C1\C5CC24)CCCCCCCCCCCC3

> <INCHI_IDENTIFIER>
InChI=1S/C32H50N2O/c35-31-27-19-15-11-7-3-6-10-14-18-22-34-26-32-20-16-12-8-4-1-2-5-9-13-17-21-33(25-32)24-28(31)29(32)23-30(27)34/h3,6-7,10-11,14,19,28-31,35H,1-2,4-5,8-9,12-13,15-18,20-26H2/b6-3-,11-7+,14-10-,27-19-/t28?,29?,30?,31-,32?/m0/s1

> <INCHI_KEY>
DWPHQXKFRKSKCQ-RFLIESTNSA-N

> <FORMULA>
C32H50N2O

> <MOLECULAR_WEIGHT>
478.765

> <EXACT_MASS>
478.392314238

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
85

> <JCHEM_AVERAGE_POLARIZABILITY>
58.10174987917044

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(8Z,10Z,12E,17R)-5,20-diazapentacyclo[18.12.1.1^{1,5}.0^{2,18}.0^{4,16}]tetratriaconta-8,10,12,15-tetraen-17-ol

> <JCHEM_LOGP>
6.238244512000001

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
2

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.26524961556116

> <JCHEM_PKA_STRONGEST_BASIC>
10.327902448618245

> <JCHEM_POLAR_SURFACE_AREA>
26.71

> <JCHEM_REFRACTIVITY>
153.69539999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(8Z,10Z,12E,17R)-5,20-diazapentacyclo[18.12.1.1^{1,5}.0^{2,18}.0^{4,16}]tetratriaconta-8,10,12,15-tetraen-17-ol

> <JCHEM_VEBER_RULE>
1

$$$$

HEADER    PROTEIN                                 07-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   07-SEP-22         0                                  
HETATM    1  O   UNK     0       0.226 -11.469   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       0.639  -9.985   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.491  -8.791   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -1.981  -8.538   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -2.707  -9.899   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -3.981  -9.009   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -4.304  -7.481   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -4.920  -6.056   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -4.525  -4.557   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -3.450  -3.443   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -2.016  -2.873   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -0.476  -2.941   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       0.448  -4.156   0.000  0.00  0.00           C+0
HETATM   14  N   UNK     0       0.633  -5.684   0.000  0.00  0.00           N+0
HETATM   15  C   UNK     0       2.281  -5.580   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       3.258  -6.896   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       4.317  -5.681   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       4.287  -4.115   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       4.308  -2.558   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       5.835  -2.274   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       6.967  -3.342   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       8.281  -4.159   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       8.987  -5.533   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      10.363  -6.258   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      10.743  -7.772   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       9.644  -8.893   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       8.079  -9.055   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       6.574  -9.530   0.000  0.00  0.00           C+0
HETATM   29  N   UNK     0       4.997  -9.222   0.000  0.00  0.00           N+0
HETATM   30  C   UNK     0       3.687 -10.121   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       2.189  -9.556   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       2.286  -8.052   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       0.893  -7.546   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      -0.202  -7.129   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       4.701  -7.662   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   31                                                  
CONECT    3    2    4   34                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15   34                                                  
CONECT   15   14   16                                                       
CONECT   16   15   17   32   35                                             
CONECT   17   16   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   23                                                       
CONECT   23   22   24                                                       
CONECT   24   23   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   27                                                       
CONECT   27   26   28                                                       
CONECT   28   27   29                                                       
CONECT   29   28   30   35                                                  
CONECT   30   29   31                                                       
CONECT   31   30    2   32                                                  
CONECT   32   31   16   33                                                  
CONECT   33   32   34                                                       
CONECT   34   33    3   14                                                  
CONECT   35   29   16                                                       
MASTER        0    0    0    0    0    0    0    0   35    0   78    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₃₂H₅₀N₂O

Average Mass

478.7650 Da

Monoisotopic Mass

478.39231 Da

IUPAC Name

(8Z,10Z,12E,17R)-5,20-diazapentacyclo[18.12.1.1^{1,5}.0^{2,18}.0^{4,16}]tetratriaconta-8,10,12,15-tetraen-17-ol

Traditional Name

(8Z,10Z,12E,17R)-5,20-diazapentacyclo[18.12.1.1^{1,5}.0^{2,18}.0^{4,16}]tetratriaconta-8,10,12,15-tetraen-17-ol

CAS Registry Number

Not Available

SMILES

O[C@@H]1C2CN3CC4(CN5CC\C=C/C=C\C=C\C\C=C1\C5CC24)CCCCCCCCCCCC3

InChI Identifier

InChI=1S/C32H50N2O/c35-31-27-19-15-11-7-3-6-10-14-18-22-34-26-32-20-16-12-8-4-1-2-5-9-13-17-21-33(25-32)24-28(31)29(32)23-30(27)34/h3,6-7,10-11,14,19,28-31,35H,1-2,4-5,8-9,12-13,15-18,20-26H2/b6-3-,11-7+,14-10-,27-19-/t28?,29?,30?,31-,32?/m0/s1

InChI Key

DWPHQXKFRKSKCQ-RFLIESTNSA-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, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Not Available

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as naphthyridines. Naphthyridines are compounds containing a naphthyridine moiety, a naphthalene in which a carbon atom has been replaced by a nitrogen in each of the two rings. The naphthyridine skeleton can also be described as an assembly two fused pyridine rings, which do not share their nitrogen atom.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Diazanaphthalenes

Sub Class

Naphthyridines

Direct Parent

Naphthyridines

Alternative Parents

Substituents

Naphthyridine
Piperidine
Cyclic alcohol
Secondary alcohol
Tertiary amine
Tertiary aliphatic amine
Azacycle
Alcohol
Organopnictogen compound
Organooxygen compound
Organonitrogen compound
Organic oxygen compound
Organic nitrogen compound
Amine
Hydrocarbon derivative
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic 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	6.24	ChemAxon
pKa (Strongest Acidic)	14.27	ChemAxon
pKa (Strongest Basic)	10.33	ChemAxon
Physiological Charge	2	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	26.71 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	153.7 m³·mol⁻¹	ChemAxon
Polarizability	58.1 Å³	ChemAxon
Number of Rings	5	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	Yes	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

C00039698

Chemspider ID

23281370

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

44421333

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

de Oliveira JH, Nascimento AM, Kossuga MH, Cavalcanti BC, Pessoa CO, Moraes MO, Macedo ML, Ferreira AG, Hajdu E, Pinheiro US, Berlinck RG: Cytotoxic alkylpiperidine alkaloids from the Brazilian marine sponge Pachychalina alcaloidifera. J Nat Prod. 2007 Apr;70(4):538-43. doi: 10.1021/np060450q. Epub 2007 Mar 9. [PubMed:17346073 ]
Amat M, Perez M, Ballette R, Proto S, Bosch J: The alkaloids of the madangamine group. Alkaloids Chem Biol. 2015;74:159-99. doi: 10.1016/bs.alkal.2014.10.001. [PubMed:25845061 ]
LOTUS database [Link]

Showing NP-Card for (8z,10z,12e,15z,17r)-5,20-diazapentacyclo[18.12.1.1¹,⁵.0²,¹⁸.0⁴,¹⁶]tetratriaconta-8,10,12,15-tetraen-17-ol (NP0239380)

MOL for NP0239380 ((8z,10z,12e,15z,17r)-5,20-diazapentacyclo[18.12.1.1¹,⁵.0²,¹⁸.0⁴,¹⁶]tetratriaconta-8,10,12,15-tetraen-17-ol)

3D MOL for NP0239380 ((8z,10z,12e,15z,17r)-5,20-diazapentacyclo[18.12.1.1¹,⁵.0²,¹⁸.0⁴,¹⁶]tetratriaconta-8,10,12,15-tetraen-17-ol)

3D SDF for NP0239380 ((8z,10z,12e,15z,17r)-5,20-diazapentacyclo[18.12.1.1¹,⁵.0²,¹⁸.0⁴,¹⁶]tetratriaconta-8,10,12,15-tetraen-17-ol)

3D-SDF for NP0239380 ((8z,10z,12e,15z,17r)-5,20-diazapentacyclo[18.12.1.1¹,⁵.0²,¹⁸.0⁴,¹⁶]tetratriaconta-8,10,12,15-tetraen-17-ol)

PDB for NP0239380 ((8z,10z,12e,15z,17r)-5,20-diazapentacyclo[18.12.1.1¹,⁵.0²,¹⁸.0⁴,¹⁶]tetratriaconta-8,10,12,15-tetraen-17-ol)

3D PDB for NP0239380 ((8z,10z,12e,15z,17r)-5,20-diazapentacyclo[18.12.1.1¹,⁵.0²,¹⁸.0⁴,¹⁶]tetratriaconta-8,10,12,15-tetraen-17-ol)

SMILES for NP0239380 ((8z,10z,12e,15z,17r)-5,20-diazapentacyclo[18.12.1.1¹,⁵.0²,¹⁸.0⁴,¹⁶]tetratriaconta-8,10,12,15-tetraen-17-ol)

INCHI for NP0239380 ((8z,10z,12e,15z,17r)-5,20-diazapentacyclo[18.12.1.1¹,⁵.0²,¹⁸.0⁴,¹⁶]tetratriaconta-8,10,12,15-tetraen-17-ol)

Structure for NP0239380 ((8z,10z,12e,15z,17r)-5,20-diazapentacyclo[18.12.1.1¹,⁵.0²,¹⁸.0⁴,¹⁶]tetratriaconta-8,10,12,15-tetraen-17-ol)

3D Structure for NP0239380 ((8z,10z,12e,15z,17r)-5,20-diazapentacyclo[18.12.1.1¹,⁵.0²,¹⁸.0⁴,¹⁶]tetratriaconta-8,10,12,15-tetraen-17-ol)