NP-MRD: Showing NP-Card for Madangamine D (NP0070081)

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Record Information

Version

2.0

Created at

2022-04-28 15:20:58 UTC

Updated at

2022-04-28 15:20:58 UTC

NP-MRD ID

NP0070081

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Madangamine D

Description

Madangamine D 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 Naphthyridines are compounds containing a naphthyridine moiety, a naphthalene in which a carbon atom has been replaced by a nitrogen in each of the two rings.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. Madangamine D is found in Xestospongia ingens. Madangamine D was first documented in 2013 (PMID: 23474469). Based on a literature review a small amount of articles have been published on Madangamine D (PMID: 29182290) (PMID: 25845061) (PMID: 24798407).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282217202D          

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M  END

     RDKit          3D

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M  END


  Mrv1652304282217202D          

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  5 31  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0070081

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C1[C@@H]2N3C[C@@]45CN(C[C@@H](C\C2=C\C\C=C/CCCC3)[C@@H]14)CCCCCCCCCCC5

> <INCHI_IDENTIFIER>
InChI=1S/C29H48N2/c1-2-5-9-13-17-29-23-30(18-14-10-6-3-1)22-26-20-25-16-12-8-4-7-11-15-19-31(24-29)28(25)21-27(26)29/h4,8,16,26-28H,1-3,5-7,9-15,17-24H2/b8-4-,25-16-/t26-,27-,28+,29-/m1/s1

> <INCHI_KEY>
AXZOZMSDLYMXPA-RXYVIUDFSA-N

> <FORMULA>
C29H48N2

> <MOLECULAR_WEIGHT>
424.717

> <EXACT_MASS>
424.381749554

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
79

> <JCHEM_AVERAGE_POLARIZABILITY>
53.71061809931741

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1R,2R,4S,10Z,16S)-5,18-diazapentacyclo[16.11.1.1^{1,5}.0^{2,16}.0^{4,14}]hentriaconta-10,13-diene

> <ALOGPS_LOGP>
7.01

> <JCHEM_LOGP>
6.8176361703333335

> <ALOGPS_LOGS>
-5.70

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
2

> <JCHEM_PKA_STRONGEST_BASIC>
10.732595983751287

> <JCHEM_POLAR_SURFACE_AREA>
6.48

> <JCHEM_REFRACTIVITY>
136.24249999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
8.45e-04 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1R,2R,4S,10Z,16S)-5,18-diazapentacyclo[16.11.1.1^{1,5}.0^{2,16}.0^{4,14}]hentriaconta-10,13-diene

> <JCHEM_VEBER_RULE>
1

$$$$

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       7.068  -6.052   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0       7.371  -4.493   0.000  0.00  0.00           N+0
HETATM    3  C   UNK     0       6.014  -3.656   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.494  -4.220   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.596  -5.710   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       5.630  -6.830   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       6.744  -7.973   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       7.007  -9.556   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       7.156 -11.151   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       8.325 -12.225   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       9.754 -11.548   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      10.803 -10.347   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      11.762  -9.071   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      11.986  -7.481   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      11.431  -5.945   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      10.566  -4.557   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       8.982  -4.191   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       4.760  -8.227   0.000  0.00  0.00           C+0
HETATM   19  N   UNK     0       3.107  -8.208   0.000  0.00  0.00           N+0
HETATM   20  C   UNK     0       2.171  -6.762   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       1.761  -5.088   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       0.177  -4.749   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      -1.284  -5.445   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      -1.598  -7.019   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      -1.281  -8.573   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      -0.556  -9.947   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       0.655 -10.875   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       2.173 -11.096   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       2.983  -9.783   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       2.920  -3.871   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       3.247  -6.348   0.000  0.00  0.00           C+0
CONECT    1    2    6                                                       
CONECT    2    1    3   17                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   30                                                  
CONECT    5    4    6   31                                                  
CONECT    6    5    1    7   18                                             
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                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16    2                                                       
CONECT   18    6   19                                                       
CONECT   19   18   20   29                                                  
CONECT   20   19   21   31                                                  
CONECT   21   20   22   30                                                  
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   19                                                       
CONECT   30   21    4                                                       
CONECT   31   20    5                                                       
MASTER        0    0    0    0    0    0    0    0   31    0   70    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₉H₄₈N₂

Average Mass

424.7170 Da

Monoisotopic Mass

424.38175 Da

IUPAC Name

(1R,2R,4S,10Z,16S)-5,18-diazapentacyclo[16.11.1.1^{1,5}.0^{2,16}.0^{4,14}]hentriaconta-10,13-diene

Traditional Name

(1R,2R,4S,10Z,16S)-5,18-diazapentacyclo[16.11.1.1^{1,5}.0^{2,16}.0^{4,14}]hentriaconta-10,13-diene

CAS Registry Number

Not Available

SMILES

C1[C@@H]2N3C[C@@]45CN(C[C@@H](C\C2=C\C\C=C/CCCC3)[C@@H]14)CCCCCCCCCCC5

InChI Identifier

InChI=1S/C29H48N2/c1-2-5-9-13-17-29-23-30(18-14-10-6-3-1)22-26-20-25-16-12-8-4-7-11-15-19-31(24-29)28(25)21-27(26)29/h4,8,16,26-28H,1-3,5-7,9-15,17-24H2/b8-4-,25-16-/t26-,27-,28+,29-/m1/s1

InChI Key

AXZOZMSDLYMXPA-RXYVIUDFSA-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
Xestospongia ingens	Animalia	KNApSAcK

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
Tertiary aliphatic amine
Tertiary amine
Azacycle
Organic nitrogen compound
Hydrocarbon derivative
Organonitrogen compound
Amine
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	7.01	ALOGPS
logP	6.82	ChemAxon
logS	-5.7	ALOGPS
pKa (Strongest Basic)	10.73	ChemAxon
Physiological Charge	2	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	6.48 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	136.24 m³·mol⁻¹	ChemAxon
Polarizability	53.71 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

C00028541

Chemspider ID

10237032

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

21604142

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Bhattacharjee A, Gerasimov MV, DeJong S, Wardrop DJ: Oxamidation of Unsaturated O-Alkyl Hydroxamates: Synthesis of the Madangamine Diazatricylic (ABC Rings) Skeleton. Org Lett. 2017 Dec 15;19(24):6570-6573. doi: 10.1021/acs.orglett.7b03283. Epub 2017 Nov 28. [PubMed:29182290 ]
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 ]
Ballette R, Perez M, Proto S, Amat M, Bosch J: Total synthesis of (+)-madangamine D. Angew Chem Int Ed Engl. 2014 Jun 10;53(24):6202-5. doi: 10.1002/anie.201402263. Epub 2014 May 2. [PubMed:24798407 ]
Amat M, Ballette R, Proto S, Perez M, Bosch J: First enantioselective synthesis of tetracyclic intermediates en route to madangamine D. Chem Commun (Camb). 2013 Apr 18;49(30):3149-51. doi: 10.1039/c3cc41104d. Epub 2013 Mar 11. [PubMed:23474469 ]

Showing NP-Card for Madangamine D (NP0070081)

MOL for NP0070081 (Madangamine D)

3D MOL for NP0070081 (Madangamine D)

3D SDF for NP0070081 (Madangamine D)

3D-SDF for NP0070081 (Madangamine D)

PDB for NP0070081 (Madangamine D)

3D PDB for NP0070081 (Madangamine D)

SMILES for NP0070081 (Madangamine D)

INCHI for NP0070081 (Madangamine D)

Structure for NP0070081 (Madangamine D)

3D Structure for NP0070081 (Madangamine D)