NP-MRD: Showing NP-Card for (10s)-10-{2-[(1s,2r,4ar,8as)-1,2,4a-trimethyl-5-methylidene-hexahydro-2h-naphthalen-1-yl]ethyl}-10-methyl-1,3,5,7,9-pentaazatricyclo[6.4.1.0⁴,¹³]trideca-2,4,6,8(13)-tetraen-9-ol (NP0279034)

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Record Information

Version

2.0

Created at

2022-09-09 04:16:34 UTC

Updated at

2022-09-09 04:16:34 UTC

NP-MRD ID

NP0279034

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(10s)-10-{2-[(1s,2r,4ar,8as)-1,2,4a-trimethyl-5-methylidene-hexahydro-2h-naphthalen-1-yl]ethyl}-10-methyl-1,3,5,7,9-pentaazatricyclo[6.4.1.0⁴,¹³]trideca-2,4,6,8(13)-tetraen-9-ol

Description

Asmarine B belongs to the class of organic compounds known as colensane and clerodane diterpenoids. These are diterpenoids with a structure based on the clerodane or the colensane skeleton. Clerodanes arise from labdanes by two methyl migrations. (10s)-10-{2-[(1s,2r,4ar,8as)-1,2,4a-trimethyl-5-methylidene-hexahydro-2h-naphthalen-1-yl]ethyl}-10-methyl-1,3,5,7,9-pentaazatricyclo[6.4.1.0⁴,¹³]trideca-2,4,6,8(13)-tetraen-9-ol was first documented in 2005 (PMID: 15624923). Based on a literature review very few articles have been published on Asmarine B (PMID: 33940466).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309092206162D          

 31 35  0  0  1  0            999 V2000
    8.6305    2.6262    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.1147    1.9824    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.4143    1.2137    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.8984    0.5699    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0829    0.6947    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7833    1.4634    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.9678    1.5882    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.9865    0.7634    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1588    1.4266    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6143    2.0465    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8053    1.8848    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.8278    2.7095    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1429    1.1321    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7648    0.3988    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9558    0.2372    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.6450   -0.5270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8221   -0.4676    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
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    2.3475    1.5936    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3250    0.7690    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    2.8447    2.8993    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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  1  2  2  0  0  0  0
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  9 10  1  0  0  0  0
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  7 26  1  0  0  0  0
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  2 30  1  0  0  0  0
  6 30  1  0  0  0  0
 30 31  1  6  0  0  0
M  END

     RDKit          3D

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M  END


  Mrv1652309092206162D          

 31 35  0  0  1  0            999 V2000
    8.6305    2.6262    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
> <DATABASE_ID>
NP0279034

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@@H]1CC[C@]2(C)[C@@H](CCCC2=C)[C@@]1(C)CC[C@@]1(C)CCN2C=NC3=NC=NC(N1O)=C23

> <INCHI_IDENTIFIER>
InChI=1S/C25H37N5O/c1-17-7-6-8-19-24(17,4)10-9-18(2)25(19,5)12-11-23(3)13-14-29-16-28-21-20(29)22(30(23)31)27-15-26-21/h15-16,18-19,31H,1,6-14H2,2-5H3/t18-,19-,23+,24+,25+/m1/s1

> <INCHI_KEY>
YUVFIHRLMIHDBO-YNGJRPBFSA-N

> <FORMULA>
C25H37N5O

> <MOLECULAR_WEIGHT>
423.605

> <EXACT_MASS>
423.299810831

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
68

> <JCHEM_AVERAGE_POLARIZABILITY>
47.789898565556314

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(10S)-10-{2-[(1S,2R,4aR,8aS)-1,2,4a-trimethyl-5-methylidene-decahydronaphthalen-1-yl]ethyl}-10-methyl-1,3,5,7,9-pentaazatricyclo[6.4.1.0^{4,13}]trideca-2,4,6,8(13)-tetraen-9-ol

> <JCHEM_LOGP>
5.191166165333335

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.074703328116122

> <JCHEM_PKA_STRONGEST_BASIC>
2.3997289017524746

> <JCHEM_POLAR_SURFACE_AREA>
67.07000000000001

> <JCHEM_REFRACTIVITY>
135.75900000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(10S)-10-{2-[(1S,2R,4aR,8aS)-1,2,4a-trimethyl-5-methylidene-hexahydro-2H-naphthalen-1-yl]ethyl}-10-methyl-1,3,5,7,9-pentaazatricyclo[6.4.1.0^{4,13}]trideca-2,4,6,8(13)-tetraen-9-ol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 09-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   09-SEP-22         0                                  
HETATM    1  C   UNK     0      16.110   4.902   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      15.147   3.700   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      15.707   2.266   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      14.744   1.064   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      13.221   1.297   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      12.662   2.732   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      11.140   2.965   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      11.175   1.425   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       9.630   2.663   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       8.613   3.820   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       7.103   3.518   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       7.145   5.058   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       7.733   2.113   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       7.028   0.744   0.000  0.00  0.00           C+0
HETATM   15  N   UNK     0       5.517   0.443   0.000  0.00  0.00           N+0
HETATM   16  C   UNK     0       4.937  -0.984   0.000  0.00  0.00           C+0
HETATM   17  N   UNK     0       3.401  -0.873   0.000  0.00  0.00           N+0
HETATM   18  C   UNK     0       3.032   0.622   0.000  0.00  0.00           C+0
HETATM   19  N   UNK     0       1.674   1.348   0.000  0.00  0.00           N+0
HETATM   20  C   UNK     0       1.624   2.888   0.000  0.00  0.00           C+0
HETATM   21  N   UNK     0       2.932   3.701   0.000  0.00  0.00           N+0
HETATM   22  C   UNK     0       4.382   2.975   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       4.340   1.435   0.000  0.00  0.00           C+0
HETATM   24  N   UNK     0       5.612   3.902   0.000  0.00  0.00           N+0
HETATM   25  O   UNK     0       5.310   5.412   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0      10.581   4.400   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       9.058   4.633   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      11.544   5.601   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      13.066   5.368   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      13.625   3.933   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      14.588   5.135   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   30                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7   30                                                  
CONECT    7    6    8    9   26                                             
CONECT    8    7                                                            
CONECT    9    7   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12   13   24                                             
CONECT   12   11                                                            
CONECT   13   11   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16   23                                                  
CONECT   16   15   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19   23                                                  
CONECT   19   18   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   23   24                                                  
CONECT   23   22   18   15                                                  
CONECT   24   22   11   25                                                  
CONECT   25   24                                                            
CONECT   26    7   27   28                                                  
CONECT   27   26                                                            
CONECT   28   26   29                                                       
CONECT   29   28   30                                                       
CONECT   30   29    2    6   31                                             
CONECT   31   30                                                            
MASTER        0    0    0    0    0    0    0    0   31    0   70    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₅H₃₇N₅O

Average Mass

423.6050 Da

Monoisotopic Mass

423.29981 Da

IUPAC Name

(10S)-10-{2-[(1S,2R,4aR,8aS)-1,2,4a-trimethyl-5-methylidene-decahydronaphthalen-1-yl]ethyl}-10-methyl-1,3,5,7,9-pentaazatricyclo[6.4.1.0^{4,13}]trideca-2,4,6,8(13)-tetraen-9-ol

Traditional Name

(10S)-10-{2-[(1S,2R,4aR,8aS)-1,2,4a-trimethyl-5-methylidene-hexahydro-2H-naphthalen-1-yl]ethyl}-10-methyl-1,3,5,7,9-pentaazatricyclo[6.4.1.0^{4,13}]trideca-2,4,6,8(13)-tetraen-9-ol

CAS Registry Number

Not Available

SMILES

C[C@@H]1CC[C@]2(C)[C@@H](CCCC2=C)[C@@]1(C)CC[C@@]1(C)CCN2C=NC3=NC=NC(N1O)=C23

InChI Identifier

InChI=1S/C25H37N5O/c1-17-7-6-8-19-24(17,4)10-9-18(2)25(19,5)12-11-23(3)13-14-29-16-28-21-20(29)22(30(23)31)27-15-26-21/h15-16,18-19,31H,1,6-14H2,2-5H3/t18-,19-,23+,24+,25+/m1/s1

InChI Key

YUVFIHRLMIHDBO-YNGJRPBFSA-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 colensane and clerodane diterpenoids. These are diterpenoids with a structure based on the clerodane or the colensane skeleton. Clerodanes arise from labdanes by two methyl migrations.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Diterpenoids

Direct Parent

Colensane and clerodane diterpenoids

Alternative Parents

Substituents

Clerodane diterpenoid
Pyrimidodiazepine
6-alkylaminopurine
Imidazopyrimidine
Purine
Para-diazepine
N-substituted imidazole
Pyrimidine
Imidolactam
Heteroaromatic compound
Imidazole
Azole
Azacycle
N-organohydroxylamine
Organoheterocyclic compound
Hydrocarbon derivative
Organonitrogen compound
Organic nitrogen compound
Organic oxygen 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	5.19	ChemAxon
pKa (Strongest Acidic)	14.07	ChemAxon
pKa (Strongest Basic)	2.4	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	67.07 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	135.76 m³·mol⁻¹	ChemAxon
Polarizability	47.79 Å³	ChemAxon
Number of Rings	5	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	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

C00046623

Chemspider ID

8020923

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

9845209

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Khan S, Al-Fadhli AA, Tilvi S: Discovery of cytotoxic natural products from Red Sea sponges: Structure and synthesis. Eur J Med Chem. 2021 Aug 5;220:113491. doi: 10.1016/j.ejmech.2021.113491. Epub 2021 Apr 24. [PubMed:33940466 ]
Pappo D, Shimony S, Kashman Y: Synthesis of 9-substituted tetrahydrodiazepinopurines: studies toward the total synthesis of asmarines. J Org Chem. 2005 Jan 7;70(1):199-206. doi: 10.1021/jo048622g. [PubMed:15624923 ]
LOTUS database [Link]

Showing NP-Card for (10s)-10-{2-[(1s,2r,4ar,8as)-1,2,4a-trimethyl-5-methylidene-hexahydro-2h-naphthalen-1-yl]ethyl}-10-methyl-1,3,5,7,9-pentaazatricyclo[6.4.1.0⁴,¹³]trideca-2,4,6,8(13)-tetraen-9-ol (NP0279034)

MOL for NP0279034 ((10s)-10-{2-[(1s,2r,4ar,8as)-1,2,4a-trimethyl-5-methylidene-hexahydro-2h-naphthalen-1-yl]ethyl}-10-methyl-1,3,5,7,9-pentaazatricyclo[6.4.1.0⁴,¹³]trideca-2,4,6,8(13)-tetraen-9-ol)

3D MOL for NP0279034 ((10s)-10-{2-[(1s,2r,4ar,8as)-1,2,4a-trimethyl-5-methylidene-hexahydro-2h-naphthalen-1-yl]ethyl}-10-methyl-1,3,5,7,9-pentaazatricyclo[6.4.1.0⁴,¹³]trideca-2,4,6,8(13)-tetraen-9-ol)

3D SDF for NP0279034 ((10s)-10-{2-[(1s,2r,4ar,8as)-1,2,4a-trimethyl-5-methylidene-hexahydro-2h-naphthalen-1-yl]ethyl}-10-methyl-1,3,5,7,9-pentaazatricyclo[6.4.1.0⁴,¹³]trideca-2,4,6,8(13)-tetraen-9-ol)

3D-SDF for NP0279034 ((10s)-10-{2-[(1s,2r,4ar,8as)-1,2,4a-trimethyl-5-methylidene-hexahydro-2h-naphthalen-1-yl]ethyl}-10-methyl-1,3,5,7,9-pentaazatricyclo[6.4.1.0⁴,¹³]trideca-2,4,6,8(13)-tetraen-9-ol)

PDB for NP0279034 ((10s)-10-{2-[(1s,2r,4ar,8as)-1,2,4a-trimethyl-5-methylidene-hexahydro-2h-naphthalen-1-yl]ethyl}-10-methyl-1,3,5,7,9-pentaazatricyclo[6.4.1.0⁴,¹³]trideca-2,4,6,8(13)-tetraen-9-ol)

3D PDB for NP0279034 ((10s)-10-{2-[(1s,2r,4ar,8as)-1,2,4a-trimethyl-5-methylidene-hexahydro-2h-naphthalen-1-yl]ethyl}-10-methyl-1,3,5,7,9-pentaazatricyclo[6.4.1.0⁴,¹³]trideca-2,4,6,8(13)-tetraen-9-ol)

SMILES for NP0279034 ((10s)-10-{2-[(1s,2r,4ar,8as)-1,2,4a-trimethyl-5-methylidene-hexahydro-2h-naphthalen-1-yl]ethyl}-10-methyl-1,3,5,7,9-pentaazatricyclo[6.4.1.0⁴,¹³]trideca-2,4,6,8(13)-tetraen-9-ol)

INCHI for NP0279034 ((10s)-10-{2-[(1s,2r,4ar,8as)-1,2,4a-trimethyl-5-methylidene-hexahydro-2h-naphthalen-1-yl]ethyl}-10-methyl-1,3,5,7,9-pentaazatricyclo[6.4.1.0⁴,¹³]trideca-2,4,6,8(13)-tetraen-9-ol)

Structure for NP0279034 ((10s)-10-{2-[(1s,2r,4ar,8as)-1,2,4a-trimethyl-5-methylidene-hexahydro-2h-naphthalen-1-yl]ethyl}-10-methyl-1,3,5,7,9-pentaazatricyclo[6.4.1.0⁴,¹³]trideca-2,4,6,8(13)-tetraen-9-ol)

3D Structure for NP0279034 ((10s)-10-{2-[(1s,2r,4ar,8as)-1,2,4a-trimethyl-5-methylidene-hexahydro-2h-naphthalen-1-yl]ethyl}-10-methyl-1,3,5,7,9-pentaazatricyclo[6.4.1.0⁴,¹³]trideca-2,4,6,8(13)-tetraen-9-ol)