NP-MRD: Showing NP-Card for (2s,3r,12bs)-3-ethenyl-2-{[(1s)-2-methyl-1h,3h,4h,9h-pyrido[3,4-b]indol-1-yl]methyl}-1h,2h,3h,4h,6h,7h,12h,12bh-indolo[2,3-a]quinolizin-10-ol (NP0258491)

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Record Information

Version

2.0

Created at

2022-09-07 23:58:33 UTC

Updated at

2022-09-07 23:58:33 UTC

NP-MRD ID

NP0258491

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(2s,3r,12bs)-3-ethenyl-2-{[(1s)-2-methyl-1h,3h,4h,9h-pyrido[3,4-b]indol-1-yl]methyl}-1h,2h,3h,4h,6h,7h,12h,12bh-indolo[2,3-a]quinolizin-10-ol

Description

11-Hydroxyusambarine belongs to the class of organic compounds known as harmala alkaloids. Harmala alkaloids are compounds with a structure based on harmaline, harmine, harmalol, harman or a derivative of those parents. These parents are beta-carbolines, consisting of a pyrimidine fused to the pyrrole moiety of an indole to form a pyrido[3,4-b]indole. (2s,3r,12bs)-3-ethenyl-2-{[(1s)-2-methyl-1h,3h,4h,9h-pyrido[3,4-b]indol-1-yl]methyl}-1h,2h,3h,4h,6h,7h,12h,12bh-indolo[2,3-a]quinolizin-10-ol is found in Strychnos usambarensis. (2s,3r,12bs)-3-ethenyl-2-{[(1s)-2-methyl-1h,3h,4h,9h-pyrido[3,4-b]indol-1-yl]methyl}-1h,2h,3h,4h,6h,7h,12h,12bh-indolo[2,3-a]quinolizin-10-ol was first documented in 2011 (PMID: 21628087). Based on a literature review very few articles have been published on 11-Hydroxyusambarine.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309082201582D          

 35 41  0  0  1  0            999 V2000
    0.1515   -1.3534    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6555   -1.1819    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -2.0145   -1.6235    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5665   -2.2366    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3735   -2.0651    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9256   -2.6782    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6706   -3.4628    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8636   -3.6343    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7774   -4.4548    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
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 33 34  1  0  0  0  0
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 34 35  1  0  0  0  0
M  END

     RDKit          3D

 69 75  0  0  0  0  0  0  0  0999 V2000
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M  END


  Mrv1652309082201582D          

 35 41  0  0  1  0            999 V2000
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 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 13 15  2  0  0  0  0
 15 16  1  0  0  0  0
 16 17  2  0  0  0  0
  8 17  1  0  0  0  0
 11 17  1  0  0  0  0
 18  9  1  1  0  0  0
  5 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
  3 20  1  0  0  0  0
 20 21  1  1  0  0  0
 22 21  1  1  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  2  0  0  0  0
 26 27  1  0  0  0  0
 27 28  2  0  0  0  0
 28 29  1  0  0  0  0
 29 30  2  0  0  0  0
 25 30  1  0  0  0  0
 30 31  1  0  0  0  0
 23 31  2  0  0  0  0
 31 32  1  0  0  0  0
 32 33  1  0  0  0  0
 33 34  1  0  0  0  0
 22 34  1  0  0  0  0
 34 35  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0258491

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CN1CCC2=C(NC3=CC=CC=C23)[C@@H]1C[C@H]1C[C@@H]2N(CCC3=C2NC2=CC(O)=CC=C32)C[C@@H]1C=C

> <INCHI_IDENTIFIER>
InChI=1S/C30H34N4O/c1-3-18-17-34-13-11-24-22-9-8-20(35)16-26(22)32-30(24)28(34)15-19(18)14-27-29-23(10-12-33(27)2)21-6-4-5-7-25(21)31-29/h3-9,16,18-19,27-28,31-32,35H,1,10-15,17H2,2H3/t18-,19-,27-,28-/m0/s1

> <INCHI_KEY>
DGQWMSVZRIPJMR-HVYZTVOGSA-N

> <FORMULA>
C30H34N4O

> <MOLECULAR_WEIGHT>
466.629

> <EXACT_MASS>
466.273261731

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
69

> <JCHEM_AVERAGE_POLARIZABILITY>
55.5180415147751

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,3R,12bS)-3-ethenyl-2-{[(1S)-2-methyl-1H,2H,3H,4H,9H-pyrido[3,4-b]indol-1-yl]methyl}-1H,2H,3H,4H,6H,7H,12H,12bH-indolo[2,3-a]quinolizin-10-ol

> <JCHEM_LOGP>
4.931963080333333

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
7

> <JCHEM_PHYSIOLOGICAL_CHARGE>
2

> <JCHEM_PKA>
16.326104368577305

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.529615565137028

> <JCHEM_PKA_STRONGEST_BASIC>
7.757073811158987

> <JCHEM_POLAR_SURFACE_AREA>
58.290000000000006

> <JCHEM_REFRACTIVITY>
143.14559999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(2S,3R,12bS)-3-ethenyl-2-{[(1S)-2-methyl-1H,3H,4H,9H-pyrido[3,4-b]indol-1-yl]methyl}-1H,2H,3H,4H,6H,7H,12H,12bH-indolo[2,3-a]quinolizin-10-ol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 08-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   08-SEP-22         0                                  
HETATM    1  C   UNK     0       0.283  -2.526   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -1.224  -2.206   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -2.254  -3.351   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -3.760  -3.031   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0      -4.791  -4.175   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0      -6.297  -3.855   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -7.328  -4.999   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -6.852  -6.464   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -5.345  -6.784   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0      -5.184  -8.316   0.000  0.00  0.00           N+0
HETATM   11  C   UNK     0      -6.591  -8.942   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -7.067 -10.407   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -8.574 -10.727   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      -9.049 -12.191   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0      -9.604  -9.582   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -9.128  -8.118   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -7.622  -7.798   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -4.315  -5.640   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -2.809  -5.960   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -1.778  -4.815   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      -0.272  -5.136   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       0.204  -6.600   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       1.710  -6.920   0.000  0.00  0.00           C+0
HETATM   24  N   UNK     0       2.956  -6.015   0.000  0.00  0.00           N+0
HETATM   25  C   UNK     0       4.202  -6.920   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       5.709  -6.600   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       6.739  -7.745   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       6.263  -9.209   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       4.757  -9.529   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       3.726  -8.385   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       2.186  -8.385   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       1.156  -9.529   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      -0.351  -9.209   0.000  0.00  0.00           C+0
HETATM   34  N   UNK     0      -0.826  -7.745   0.000  0.00  0.00           N+0
HETATM   35  C   UNK     0      -2.333  -7.424   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   20                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6   18                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9   17                                                  
CONECT    9    8   10   18                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12   17                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16    8   11                                                  
CONECT   18    9    5   19                                                  
CONECT   19   18   20                                                       
CONECT   20   19    3   21                                                  
CONECT   21   20   22                                                       
CONECT   22   21   23   34                                                  
CONECT   23   22   24   31                                                  
CONECT   24   23   25                                                       
CONECT   25   24   26   30                                                  
CONECT   26   25   27                                                       
CONECT   27   26   28                                                       
CONECT   28   27   29                                                       
CONECT   29   28   30                                                       
CONECT   30   29   25   31                                                  
CONECT   31   30   23   32                                                  
CONECT   32   31   33                                                       
CONECT   33   32   34                                                       
CONECT   34   33   22   35                                                  
CONECT   35   34                                                            
MASTER        0    0    0    0    0    0    0    0   35    0   82    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₃₀H₃₄N₄O

Average Mass

466.6290 Da

Monoisotopic Mass

466.27326 Da

IUPAC Name

(2S,3R,12bS)-3-ethenyl-2-{[(1S)-2-methyl-1H,2H,3H,4H,9H-pyrido[3,4-b]indol-1-yl]methyl}-1H,2H,3H,4H,6H,7H,12H,12bH-indolo[2,3-a]quinolizin-10-ol

Traditional Name

(2S,3R,12bS)-3-ethenyl-2-{[(1S)-2-methyl-1H,3H,4H,9H-pyrido[3,4-b]indol-1-yl]methyl}-1H,2H,3H,4H,6H,7H,12H,12bH-indolo[2,3-a]quinolizin-10-ol

CAS Registry Number

Not Available

SMILES

CN1CCC2=C(NC3=CC=CC=C23)[C@@H]1C[C@H]1C[C@@H]2N(CCC3=C2NC2=CC(O)=CC=C32)C[C@@H]1C=C

InChI Identifier

InChI=1S/C30H34N4O/c1-3-18-17-34-13-11-24-22-9-8-20(35)16-26(22)32-30(24)28(34)15-19(18)14-27-29-23(10-12-33(27)2)21-6-4-5-7-25(21)31-29/h3-9,16,18-19,27-28,31-32,35H,1,10-15,17H2,2H3/t18-,19-,27-,28-/m0/s1

InChI Key

DGQWMSVZRIPJMR-HVYZTVOGSA-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
Strychnos usambarensis	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as harmala alkaloids. Harmala alkaloids are compounds with a structure based on harmaline, harmine, harmalol, harman or a derivative of those parents. These parents are beta-carbolines, consisting of a pyrimidine fused to the pyrrole moiety of an indole to form a pyrido[3,4-b]indole.

Kingdom

Organic compounds

Super Class

Alkaloids and derivatives

Class

Harmala alkaloids

Sub Class

Not Available

Direct Parent

Harmala alkaloids

Alternative Parents

Substituents

Harman
Beta-carboline
Pyridoindole
Hydroxyindole
3-alkylindole
Quinolizine
Indole
Indole or derivatives
1-hydroxy-2-unsubstituted benzenoid
Aralkylamine
Piperidine
Benzenoid
Heteroaromatic compound
Pyrrole
Tertiary aliphatic amine
Tertiary amine
Organoheterocyclic compound
Azacycle
Organooxygen compound
Organonitrogen compound
Hydrocarbon derivative
Organopnictogen compound
Organic oxygen compound
Organic nitrogen compound
Amine
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	4.93	ChemAxon
pKa (Strongest Acidic)	9.53	ChemAxon
pKa (Strongest Basic)	7.76	ChemAxon
Physiological Charge	2	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	58.29 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	143.15 m³·mol⁻¹	ChemAxon
Polarizability	55.52 Å³	ChemAxon
Number of Rings	7	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	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

Not Available

Chemspider ID

355722

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

401427

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Nistor I, Cao M, Debrus B, Lebrun P, Lecomte F, Rozet E, Angenot L, Frederich M, Oprean R, Hubert P: Application of a new optimization strategy for the separation of tertiary alkaloids extracted from Strychnos usambarensis leaves. J Pharm Biomed Anal. 2011 Aug 25;56(1):30-7. doi: 10.1016/j.jpba.2011.04.027. Epub 2011 May 7. [PubMed:21628087 ]
LOTUS database [Link]

Showing NP-Card for (2s,3r,12bs)-3-ethenyl-2-{[(1s)-2-methyl-1h,3h,4h,9h-pyrido[3,4-b]indol-1-yl]methyl}-1h,2h,3h,4h,6h,7h,12h,12bh-indolo[2,3-a]quinolizin-10-ol (NP0258491)

MOL for NP0258491 ((2s,3r,12bs)-3-ethenyl-2-{[(1s)-2-methyl-1h,3h,4h,9h-pyrido[3,4-b]indol-1-yl]methyl}-1h,2h,3h,4h,6h,7h,12h,12bh-indolo[2,3-a]quinolizin-10-ol)

3D MOL for NP0258491 ((2s,3r,12bs)-3-ethenyl-2-{[(1s)-2-methyl-1h,3h,4h,9h-pyrido[3,4-b]indol-1-yl]methyl}-1h,2h,3h,4h,6h,7h,12h,12bh-indolo[2,3-a]quinolizin-10-ol)

3D SDF for NP0258491 ((2s,3r,12bs)-3-ethenyl-2-{[(1s)-2-methyl-1h,3h,4h,9h-pyrido[3,4-b]indol-1-yl]methyl}-1h,2h,3h,4h,6h,7h,12h,12bh-indolo[2,3-a]quinolizin-10-ol)

3D-SDF for NP0258491 ((2s,3r,12bs)-3-ethenyl-2-{[(1s)-2-methyl-1h,3h,4h,9h-pyrido[3,4-b]indol-1-yl]methyl}-1h,2h,3h,4h,6h,7h,12h,12bh-indolo[2,3-a]quinolizin-10-ol)

PDB for NP0258491 ((2s,3r,12bs)-3-ethenyl-2-{[(1s)-2-methyl-1h,3h,4h,9h-pyrido[3,4-b]indol-1-yl]methyl}-1h,2h,3h,4h,6h,7h,12h,12bh-indolo[2,3-a]quinolizin-10-ol)

3D PDB for NP0258491 ((2s,3r,12bs)-3-ethenyl-2-{[(1s)-2-methyl-1h,3h,4h,9h-pyrido[3,4-b]indol-1-yl]methyl}-1h,2h,3h,4h,6h,7h,12h,12bh-indolo[2,3-a]quinolizin-10-ol)

SMILES for NP0258491 ((2s,3r,12bs)-3-ethenyl-2-{[(1s)-2-methyl-1h,3h,4h,9h-pyrido[3,4-b]indol-1-yl]methyl}-1h,2h,3h,4h,6h,7h,12h,12bh-indolo[2,3-a]quinolizin-10-ol)

INCHI for NP0258491 ((2s,3r,12bs)-3-ethenyl-2-{[(1s)-2-methyl-1h,3h,4h,9h-pyrido[3,4-b]indol-1-yl]methyl}-1h,2h,3h,4h,6h,7h,12h,12bh-indolo[2,3-a]quinolizin-10-ol)

Structure for NP0258491 ((2s,3r,12bs)-3-ethenyl-2-{[(1s)-2-methyl-1h,3h,4h,9h-pyrido[3,4-b]indol-1-yl]methyl}-1h,2h,3h,4h,6h,7h,12h,12bh-indolo[2,3-a]quinolizin-10-ol)

3D Structure for NP0258491 ((2s,3r,12bs)-3-ethenyl-2-{[(1s)-2-methyl-1h,3h,4h,9h-pyrido[3,4-b]indol-1-yl]methyl}-1h,2h,3h,4h,6h,7h,12h,12bh-indolo[2,3-a]quinolizin-10-ol)