NP-MRD: Showing NP-Card for 6-amino-7-[(2e,6e)-9-[(1s)-2,2-dimethyl-6-methylidenecyclohexyl]-3,7-dimethylnona-2,6-dien-1-yl]-9-methylpurin-9-ium (NP0213871)

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Record Information

Version

2.0

Created at

2022-09-05 12:59:10 UTC

Updated at

2022-09-05 12:59:10 UTC

NP-MRD ID

NP0213871

Secondary Accession Numbers

None

Natural Product Identification

Common Name

6-amino-7-[(2e,6e)-9-[(1s)-2,2-dimethyl-6-methylidenecyclohexyl]-3,7-dimethylnona-2,6-dien-1-yl]-9-methylpurin-9-ium

Description

Agelasine E belongs to the class of organic compounds known as diterpenoids. These are terpene compounds formed by four isoprene units. 6-amino-7-[(2e,6e)-9-[(1s)-2,2-dimethyl-6-methylidenecyclohexyl]-3,7-dimethylnona-2,6-dien-1-yl]-9-methylpurin-9-ium is found in Agelas nakamurai. 6-amino-7-[(2e,6e)-9-[(1s)-2,2-dimethyl-6-methylidenecyclohexyl]-3,7-dimethylnona-2,6-dien-1-yl]-9-methylpurin-9-ium was first documented in 2005 (PMID: 15750645). Based on a literature review a small amount of articles have been published on Agelasine E.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309052214592D          

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M  CHG  1  23   1
M  END

     RDKit          3D

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M  CHG  1  23   1
M  END


  Mrv1652309052214592D          

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M  CHG  1  23   1
M  END
> <DATABASE_ID>
NP0213871

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C\C(CC\C=C(/C)CC[C@@H]1C(=C)CCCC1(C)C)=C/CN1C=[N+](C)C2=NC=NC(N)=C12

> <INCHI_IDENTIFIER>
InChI=1S/C26H40N5/c1-19(12-13-22-21(3)11-8-15-26(22,4)5)9-7-10-20(2)14-16-31-18-30(6)25-23(31)24(27)28-17-29-25/h9,14,17-18,22H,3,7-8,10-13,15-16H2,1-2,4-6H3,(H2,27,28,29)/q+1/b19-9+,20-14+/t22-/m1/s1

> <INCHI_KEY>
PPCBHTAMQFLZHZ-DYKJIVJTSA-N

> <FORMULA>
C26H40N5

> <MOLECULAR_WEIGHT>
422.64

> <EXACT_MASS>
422.327822728

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
71

> <JCHEM_AVERAGE_POLARIZABILITY>
50.784544963607416

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
1

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
6-amino-7-[(2E,6E)-9-[(1S)-2,2-dimethyl-6-methylidenecyclohexyl]-3,7-dimethylnona-2,6-dien-1-yl]-9-methyl-7H-purin-9-ium

> <JCHEM_LOGP>
1.8259908638615885

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_ACIDIC>
18.525969084520113

> <JCHEM_PKA_STRONGEST_BASIC>
-1.9632910798058547

> <JCHEM_POLAR_SURFACE_AREA>
60.61

> <JCHEM_REFRACTIVITY>
133.3117

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
6-amino-7-[(2E,6E)-9-[(1S)-2,2-dimethyl-6-methylidenecyclohexyl]-3,7-dimethylnona-2,6-dien-1-yl]-9-methylpurin-9-ium

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 05-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   05-SEP-22         0                                  
HETATM    1  C   UNK     0      -9.449  -3.646   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0     -10.480  -2.501   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0     -11.986  -2.821   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0     -13.017  -1.677   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0     -12.541  -0.212   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0     -11.034   0.108   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0     -11.611   1.536   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -9.728   0.924   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0     -10.004  -1.036   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -8.498  -0.716   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -7.467  -1.861   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -5.961  -1.541   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -5.485  -0.076   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -4.930  -2.685   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -3.424  -2.365   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -2.393  -3.509   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -0.887  -3.189   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -0.411  -1.724   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       0.143  -4.334   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       1.650  -4.013   0.000  0.00  0.00           C+0
HETATM   21  N   UNK     0       2.126  -2.549   0.000  0.00  0.00           N+0
HETATM   22  C   UNK     0       1.220  -1.303   0.000  0.00  0.00           C+0
HETATM   23  N   UNK     0       2.126  -0.057   0.000  0.00  0.00           N+1
HETATM   24  C   UNK     0       1.650   1.408   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       3.590  -0.533   0.000  0.00  0.00           C+0
HETATM   26  N   UNK     0       4.924   0.237   0.000  0.00  0.00           N+0
HETATM   27  C   UNK     0       6.258  -0.533   0.000  0.00  0.00           C+0
HETATM   28  N   UNK     0       6.258  -2.073   0.000  0.00  0.00           N+0
HETATM   29  C   UNK     0       4.924  -2.843   0.000  0.00  0.00           C+0
HETATM   30  N   UNK     0       4.924  -4.383   0.000  0.00  0.00           N+0
HETATM   31  C   UNK     0       3.590  -2.073   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    9                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7    8    9                                             
CONECT    7    6                                                            
CONECT    8    6                                                            
CONECT    9    6    2   10                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   22   31                                                  
CONECT   22   21   23                                                       
CONECT   23   22   24   25                                                  
CONECT   24   23                                                            
CONECT   25   23   26   31                                                  
CONECT   26   25   27                                                       
CONECT   27   26   28                                                       
CONECT   28   27   29                                                       
CONECT   29   28   30   31                                                  
CONECT   30   29                                                            
CONECT   31   29   25   21                                                  
MASTER        0    0    0    0    0    0    0    0   31    0   66    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₆H₄₀N₅

Average Mass

422.6400 Da

Monoisotopic Mass

422.32782 Da

IUPAC Name

6-amino-7-[(2E,6E)-9-[(1S)-2,2-dimethyl-6-methylidenecyclohexyl]-3,7-dimethylnona-2,6-dien-1-yl]-9-methyl-7H-purin-9-ium

Traditional Name

6-amino-7-[(2E,6E)-9-[(1S)-2,2-dimethyl-6-methylidenecyclohexyl]-3,7-dimethylnona-2,6-dien-1-yl]-9-methylpurin-9-ium

CAS Registry Number

Not Available

SMILES

C\C(CC\C=C(/C)CC[C@@H]1C(=C)CCCC1(C)C)=C/CN1C=[N+](C)C2=NC=NC(N)=C12

InChI Identifier

InChI=1S/C26H40N5/c1-19(12-13-22-21(3)11-8-15-26(22,4)5)9-7-10-20(2)14-16-31-18-30(6)25-23(31)24(27)28-17-29-25/h9,14,17-18,22H,3,7-8,10-13,15-16H2,1-2,4-6H3,(H2,27,28,29)/q+1/b19-9+,20-14+/t22-/m1/s1

InChI Key

PPCBHTAMQFLZHZ-DYKJIVJTSA-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

Species Name	Source	Reference
Agelas nakamurai	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as diterpenoids. These are terpene compounds formed by four isoprene units.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Diterpenoids

Direct Parent

Diterpenoids

Alternative Parents

Substituents

Diterpenoid
6-aminopurine
Purine
Imidazopyrimidine
Aminopyrimidine
Imidolactam
Pyrimidine
N-substituted imidazole
Heteroaromatic compound
Azole
Imidazole
Azacycle
Organoheterocyclic compound
Amine
Organic nitrogen compound
Hydrocarbon derivative
Primary amine
Organonitrogen compound
Organic cation
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	1.83	ChemAxon
pKa (Strongest Acidic)	18.53	ChemAxon
pKa (Strongest Basic)	-2	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	60.61 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	133.31 m³·mol⁻¹	ChemAxon
Polarizability	50.78 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00038375

Chemspider ID

9423149

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

11248116

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Bakkestuen AK, Gundersen LL, Petersen D, Utenova BT, Vik A: Synthesis and antimycobacterial activity of agelasine E and analogs. Org Biomol Chem. 2005 Mar 21;3(6):1025-33. doi: 10.1039/b417471b. Epub 2005 Feb 9. [PubMed:15750645 ]
LOTUS database [Link]

Showing NP-Card for 6-amino-7-[(2e,6e)-9-[(1s)-2,2-dimethyl-6-methylidenecyclohexyl]-3,7-dimethylnona-2,6-dien-1-yl]-9-methylpurin-9-ium (NP0213871)

MOL for NP0213871 (6-amino-7-[(2e,6e)-9-[(1s)-2,2-dimethyl-6-methylidenecyclohexyl]-3,7-dimethylnona-2,6-dien-1-yl]-9-methylpurin-9-ium)

3D MOL for NP0213871 (6-amino-7-[(2e,6e)-9-[(1s)-2,2-dimethyl-6-methylidenecyclohexyl]-3,7-dimethylnona-2,6-dien-1-yl]-9-methylpurin-9-ium)

3D SDF for NP0213871 (6-amino-7-[(2e,6e)-9-[(1s)-2,2-dimethyl-6-methylidenecyclohexyl]-3,7-dimethylnona-2,6-dien-1-yl]-9-methylpurin-9-ium)

3D-SDF for NP0213871 (6-amino-7-[(2e,6e)-9-[(1s)-2,2-dimethyl-6-methylidenecyclohexyl]-3,7-dimethylnona-2,6-dien-1-yl]-9-methylpurin-9-ium)

PDB for NP0213871 (6-amino-7-[(2e,6e)-9-[(1s)-2,2-dimethyl-6-methylidenecyclohexyl]-3,7-dimethylnona-2,6-dien-1-yl]-9-methylpurin-9-ium)

3D PDB for NP0213871 (6-amino-7-[(2e,6e)-9-[(1s)-2,2-dimethyl-6-methylidenecyclohexyl]-3,7-dimethylnona-2,6-dien-1-yl]-9-methylpurin-9-ium)

SMILES for NP0213871 (6-amino-7-[(2e,6e)-9-[(1s)-2,2-dimethyl-6-methylidenecyclohexyl]-3,7-dimethylnona-2,6-dien-1-yl]-9-methylpurin-9-ium)

INCHI for NP0213871 (6-amino-7-[(2e,6e)-9-[(1s)-2,2-dimethyl-6-methylidenecyclohexyl]-3,7-dimethylnona-2,6-dien-1-yl]-9-methylpurin-9-ium)

Structure for NP0213871 (6-amino-7-[(2e,6e)-9-[(1s)-2,2-dimethyl-6-methylidenecyclohexyl]-3,7-dimethylnona-2,6-dien-1-yl]-9-methylpurin-9-ium)

3D Structure for NP0213871 (6-amino-7-[(2e,6e)-9-[(1s)-2,2-dimethyl-6-methylidenecyclohexyl]-3,7-dimethylnona-2,6-dien-1-yl]-9-methylpurin-9-ium)