NP-MRD: Showing NP-Card for 6'-ethenyl-7'-({2-methyl-1h,3h,4h,9h-pyrido[3,4-b]indol-1-yl}methyl)-3',5',6',7',8',8'a-hexahydro-2'h-spiro[indole-3,1'-indolizine]-2,6-diol (NP0243482)

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Record Information

Version

2.0

Created at

2022-09-07 04:02:36 UTC

Updated at

2022-09-07 04:02:36 UTC

NP-MRD ID

NP0243482

Secondary Accession Numbers

None

Natural Product Identification

Common Name

6'-ethenyl-7'-({2-methyl-1h,3h,4h,9h-pyrido[3,4-b]indol-1-yl}methyl)-3',5',6',7',8',8'a-hexahydro-2'h-spiro[indole-3,1'-indolizine]-2,6-diol

Description

AC1L4DZY 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. 6'-ethenyl-7'-({2-methyl-1h,3h,4h,9h-pyrido[3,4-b]indol-1-yl}methyl)-3',5',6',7',8',8'a-hexahydro-2'h-spiro[indole-3,1'-indolizine]-2,6-diol is found in Strychnos usambarensis. AC1L4DZY is a very strong basic compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1533004171522122D          

 36 42  0  0  0  0            999 V2000
    4.5783    1.7715    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9652    2.3235    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.5783    2.8756    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4067    3.6825    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6221    3.9375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0090    3.3854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2945    3.7979    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.4661    4.6049    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9812    5.2724    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3167    6.0260    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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 16 34  1  0  0  0  0
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 35 36  2  0  0  0  0
M  END

     RDKit          3D

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M  END


  Mrv1533004171522122D          

 36 42  0  0  0  0            999 V2000
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 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
 18 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  2  0  0  0  0
 23 25  1  0  0  0  0
 25 26  1  0  0  0  0
 26 27  2  0  0  0  0
 27 28  1  0  0  0  0
 28 29  1  0  0  0  0
 28 30  2  0  0  0  0
 30 31  1  0  0  0  0
 31 32  2  0  0  0  0
 22 32  1  0  0  0  0
 26 32  1  0  0  0  0
 19 33  1  0  0  0  0
 33 34  1  0  0  0  0
 16 34  1  0  0  0  0
 34 35  1  0  0  0  0
 35 36  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0243482

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CN1CCC2=C(NC3=CC=CC=C23)C1CC1CC2N(CCC22C(=O)NC3=CC(O)=CC=C23)CC1C=C

> <INCHI_IDENTIFIER>
InChI=1S/C30H34N4O2/c1-3-18-17-34-13-11-30(23-9-8-20(35)16-25(23)32-29(30)36)27(34)15-19(18)14-26-28-22(10-12-33(26)2)21-6-4-5-7-24(21)31-28/h3-9,16,18-19,26-27,31,35H,1,10-15,17H2,2H3,(H,32,36)

> <INCHI_KEY>
YAXAQXBFDAJGGS-UHFFFAOYSA-N

> <FORMULA>
C30H34N4O2

> <MOLECULAR_WEIGHT>
482.628

> <EXACT_MASS>
482.268176351

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
70

> <JCHEM_AVERAGE_POLARIZABILITY>
55.489158533231326

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
6'-ethenyl-6-hydroxy-7'-({2-methyl-1H,2H,3H,4H,9H-pyrido[3,4-b]indol-1-yl}methyl)-1,2,3',5',6',7',8',8'a-octahydro-2'H-spiro[indole-3,1'-indolizine]-2-one

> <ALOGPS_LOGP>
4.22

> <JCHEM_LOGP>
2.7657135239046324

> <ALOGPS_LOGS>
-4.28

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
7

> <JCHEM_PHYSIOLOGICAL_CHARGE>
2

> <JCHEM_PKA>
13.364939392062833

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.179453794876412

> <JCHEM_PKA_STRONGEST_BASIC>
10.799761763010181

> <JCHEM_POLAR_SURFACE_AREA>
71.60000000000001

> <JCHEM_REFRACTIVITY>
144.70159999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.54e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
6'-ethenyl-6-hydroxy-7'-({2-methyl-1H,3H,4H,9H-pyrido[3,4-b]indol-1-yl}methyl)-3',5',6',7',8',8'a-hexahydro-1H,2'H-spiro[indole-3,1'-indolizine]-2-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 17-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-APR-15         0                                  
HETATM    1  C   UNK     0       8.546   3.307   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0       7.402   4.337   0.000  0.00  0.00           N+0
HETATM    3  C   UNK     0       8.546   5.368   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       8.226   6.874   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       6.761   7.350   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       5.617   6.320   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0       4.283   7.090   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0       4.603   8.596   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       3.698   9.842   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       4.325  11.249   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       5.856  11.410   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       6.761  10.164   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       6.135   8.757   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       5.937   4.813   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       4.793   3.783   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       5.113   2.276   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       3.968   1.246   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       4.289  -0.260   0.000  0.00  0.00           C+0
HETATM   19  N   UNK     0       5.753  -0.736   0.000  0.00  0.00           N+0
HETATM   20  C   UNK     0       5.753  -2.276   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       4.289  -2.752   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       3.383  -1.506   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       2.478  -2.752   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0       2.954  -4.217   0.000  0.00  0.00           O+0
HETATM   25  N   UNK     0       1.013  -2.276   0.000  0.00  0.00           N+0
HETATM   26  C   UNK     0       1.013  -0.736   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      -0.131   0.294   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       0.189   1.800   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0      -0.955   2.831   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0       1.654   2.276   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       2.798   1.246   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       2.478  -0.260   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       6.898   0.294   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       6.577   1.800   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       7.722   2.831   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0       9.186   2.355   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   14                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6   13                                                  
CONECT    6    5    7   14                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9   13                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12    5    8                                                  
CONECT   14    6    2   15                                                  
CONECT   15   14   16                                                       
CONECT   16   15   17   34                                                  
CONECT   17   16   18                                                       
CONECT   18   17   19   22                                                  
CONECT   19   18   20   33                                                  
CONECT   20   19   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   18   23   32                                             
CONECT   23   22   24   25                                                  
CONECT   24   23                                                            
CONECT   25   23   26                                                       
CONECT   26   25   27   32                                                  
CONECT   27   26   28                                                       
CONECT   28   27   29   30                                                  
CONECT   29   28                                                            
CONECT   30   28   31                                                       
CONECT   31   30   32                                                       
CONECT   32   31   22   26                                                  
CONECT   33   19   34                                                       
CONECT   34   33   16   35                                                  
CONECT   35   34   36                                                       
CONECT   36   35                                                            
MASTER        0    0    0    0    0    0    0    0   36    0   84    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₃₀H₃₄N₄O₂

Average Mass

482.6280 Da

Monoisotopic Mass

482.26818 Da

IUPAC Name

6'-ethenyl-6-hydroxy-7'-({2-methyl-1H,2H,3H,4H,9H-pyrido[3,4-b]indol-1-yl}methyl)-1,2,3',5',6',7',8',8'a-octahydro-2'H-spiro[indole-3,1'-indolizine]-2-one

Traditional Name

6'-ethenyl-6-hydroxy-7'-({2-methyl-1H,3H,4H,9H-pyrido[3,4-b]indol-1-yl}methyl)-3',5',6',7',8',8'a-hexahydro-1H,2'H-spiro[indole-3,1'-indolizine]-2-one

CAS Registry Number

Not Available

SMILES

CN1CCC2=C(NC3=CC=CC=C23)C1CC1CC2N(CCC22C(=O)NC3=CC(O)=CC=C23)CC1C=C

InChI Identifier

InChI=1S/C30H34N4O2/c1-3-18-17-34-13-11-30(23-9-8-20(35)16-25(23)32-29(30)36)27(34)15-19(18)14-26-28-22(10-12-33(26)2)21-6-4-5-7-24(21)31-28/h3-9,16,18-19,26-27,31,35H,1,10-15,17H2,2H3,(H,32,36)

InChI Key

YAXAQXBFDAJGGS-UHFFFAOYSA-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
3-alkylindole
Indole
Indole or derivatives
Dihydroindole
Indolizidine
1-hydroxy-2-unsubstituted benzenoid
Aralkylamine
Piperidine
Benzenoid
N-alkylpyrrolidine
Heteroaromatic compound
Pyrrole
Pyrrolidine
Tertiary aliphatic amine
Amino acid or derivatives
Tertiary amine
Secondary carboxylic acid amide
Lactam
Carboxamide group
Organoheterocyclic compound
Azacycle
Carboxylic acid derivative
Organooxygen compound
Organic oxide
Organopnictogen compound
Organic oxygen compound
Hydrocarbon derivative
Amine
Carbonyl group
Organic nitrogen compound
Organonitrogen 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	4.22	ALOGPS
logP	2.77	ChemAxon
logS	-4.3	ALOGPS
pKa (Strongest Acidic)	9.18	ChemAxon
pKa (Strongest Basic)	10.8	ChemAxon
Physiological Charge	2	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	71.6 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	144.7 m³·mol⁻¹	ChemAxon
Polarizability	55.49 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

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

155297

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 6'-ethenyl-7'-({2-methyl-1h,3h,4h,9h-pyrido[3,4-b]indol-1-yl}methyl)-3',5',6',7',8',8'a-hexahydro-2'h-spiro[indole-3,1'-indolizine]-2,6-diol (NP0243482)

MOL for NP0243482 (6'-ethenyl-7'-({2-methyl-1h,3h,4h,9h-pyrido[3,4-b]indol-1-yl}methyl)-3',5',6',7',8',8'a-hexahydro-2'h-spiro[indole-3,1'-indolizine]-2,6-diol)

3D MOL for NP0243482 (6'-ethenyl-7'-({2-methyl-1h,3h,4h,9h-pyrido[3,4-b]indol-1-yl}methyl)-3',5',6',7',8',8'a-hexahydro-2'h-spiro[indole-3,1'-indolizine]-2,6-diol)

3D SDF for NP0243482 (6'-ethenyl-7'-({2-methyl-1h,3h,4h,9h-pyrido[3,4-b]indol-1-yl}methyl)-3',5',6',7',8',8'a-hexahydro-2'h-spiro[indole-3,1'-indolizine]-2,6-diol)

3D-SDF for NP0243482 (6'-ethenyl-7'-({2-methyl-1h,3h,4h,9h-pyrido[3,4-b]indol-1-yl}methyl)-3',5',6',7',8',8'a-hexahydro-2'h-spiro[indole-3,1'-indolizine]-2,6-diol)

PDB for NP0243482 (6'-ethenyl-7'-({2-methyl-1h,3h,4h,9h-pyrido[3,4-b]indol-1-yl}methyl)-3',5',6',7',8',8'a-hexahydro-2'h-spiro[indole-3,1'-indolizine]-2,6-diol)

3D PDB for NP0243482 (6'-ethenyl-7'-({2-methyl-1h,3h,4h,9h-pyrido[3,4-b]indol-1-yl}methyl)-3',5',6',7',8',8'a-hexahydro-2'h-spiro[indole-3,1'-indolizine]-2,6-diol)

SMILES for NP0243482 (6'-ethenyl-7'-({2-methyl-1h,3h,4h,9h-pyrido[3,4-b]indol-1-yl}methyl)-3',5',6',7',8',8'a-hexahydro-2'h-spiro[indole-3,1'-indolizine]-2,6-diol)

INCHI for NP0243482 (6'-ethenyl-7'-({2-methyl-1h,3h,4h,9h-pyrido[3,4-b]indol-1-yl}methyl)-3',5',6',7',8',8'a-hexahydro-2'h-spiro[indole-3,1'-indolizine]-2,6-diol)

Structure for NP0243482 (6'-ethenyl-7'-({2-methyl-1h,3h,4h,9h-pyrido[3,4-b]indol-1-yl}methyl)-3',5',6',7',8',8'a-hexahydro-2'h-spiro[indole-3,1'-indolizine]-2,6-diol)

3D Structure for NP0243482 (6'-ethenyl-7'-({2-methyl-1h,3h,4h,9h-pyrido[3,4-b]indol-1-yl}methyl)-3',5',6',7',8',8'a-hexahydro-2'h-spiro[indole-3,1'-indolizine]-2,6-diol)