NP-MRD: Showing NP-Card for (1r,3as,3bs,7s,9ar,9bs,11as)-9a,11a-dimethyl-1-[(1r)-1-[(5s)-5-methyl-3,4,5,6-tetrahydropyridin-2-yl]ethyl]-1h,2h,3h,3ah,3bh,4h,6h,7h,8h,9h,9bh,10h,11h-cyclopenta[a]phenanthren-7-ol (NP0209388)

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Record Information

Version

2.0

Created at

2022-09-05 06:46:50 UTC

Updated at

2022-09-05 06:46:50 UTC

NP-MRD ID

NP0209388

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(1r,3as,3bs,7s,9ar,9bs,11as)-9a,11a-dimethyl-1-[(1r)-1-[(5s)-5-methyl-3,4,5,6-tetrahydropyridin-2-yl]ethyl]-1h,2h,3h,3ah,3bh,4h,6h,7h,8h,9h,9bh,10h,11h-cyclopenta[a]phenanthren-7-ol

Description

20-Epi-verazine belongs to the class of organic compounds known as 22,26-epiminocholestanes. These are steroid alkaloids obtained by reduction of spirosolane through opening of the E-ring. Thus, 20-epi-verazine is considered to be a sterol. (1r,3as,3bs,7s,9ar,9bs,11as)-9a,11a-dimethyl-1-[(1r)-1-[(5s)-5-methyl-3,4,5,6-tetrahydropyridin-2-yl]ethyl]-1h,2h,3h,3ah,3bh,4h,6h,7h,8h,9h,9bh,10h,11h-cyclopenta[a]phenanthren-7-ol was first documented in 2021 (PMID: 33910157). Based on a literature review very few articles have been published on 20-epi-verazine.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309052208462D          

 29 33  0  0  1  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv1652309052208462D          

 29 33  0  0  1  0            999 V2000
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M  END
> <DATABASE_ID>
NP0209388

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@H]([C@H]1CC[C@H]2[C@@H]3CC=C4C[C@@H](O)CC[C@]4(C)[C@H]3CC[C@]12C)C1=NC[C@@H](C)CC1

> <INCHI_IDENTIFIER>
InChI=1S/C27H43NO/c1-17-5-10-25(28-16-17)18(2)22-8-9-23-21-7-6-19-15-20(29)11-13-26(19,3)24(21)12-14-27(22,23)4/h6,17-18,20-24,29H,5,7-16H2,1-4H3/t17-,18+,20-,21-,22+,23-,24-,26-,27+/m0/s1

> <INCHI_KEY>
VRBNGKPRTHBEIQ-RWWNDWOOSA-N

> <FORMULA>
C27H43NO

> <MOLECULAR_WEIGHT>
397.647

> <EXACT_MASS>
397.334465009

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
72

> <JCHEM_AVERAGE_POLARIZABILITY>
49.40810132944182

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1S,2R,5S,10S,11S,14R,15S)-2,15-dimethyl-14-[(1R)-1-[(5S)-5-methyl-3,4,5,6-tetrahydropyridin-2-yl]ethyl]tetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadec-7-en-5-ol

> <JCHEM_LOGP>
5.585828248333333

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
18.20428950550382

> <JCHEM_PKA_STRONGEST_BASIC>
4.123824449894225

> <JCHEM_POLAR_SURFACE_AREA>
32.59

> <JCHEM_REFRACTIVITY>
121.82799999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(1S,2R,5S,10S,11S,14R,15S)-2,15-dimethyl-14-[(1R)-1-[(5S)-5-methyl-3,4,5,6-tetrahydropyridin-2-yl]ethyl]tetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadec-7-en-5-ol

> <JCHEM_VEBER_RULE>
1

$$$$

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      -1.320  -5.020   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.206  -5.231   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.151  -4.015   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.676  -4.226   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       3.257  -5.652   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       4.782  -5.863   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       5.363  -7.289   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       5.727  -4.647   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       5.299  -3.168   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       6.574  -2.304   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       7.790  -3.249   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       9.306  -2.978   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       9.829  -1.529   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      11.345  -1.258   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      12.338  -2.436   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      13.854  -2.164   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      14.846  -3.342   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      16.362  -3.071   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0      14.323  -4.790   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      12.807  -5.061   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      11.814  -3.884   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      11.291  -5.332   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      10.299  -4.155   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       9.775  -5.603   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       8.259  -5.874   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       7.267  -4.697   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       6.595  -6.083   0.000  0.00  0.00           C+0
HETATM   28  N   UNK     0       2.312  -6.868   0.000  0.00  0.00           N+0
HETATM   29  C   UNK     0       0.786  -6.657   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   29                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6   28                                                  
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9   26                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12   26                                                  
CONECT   12   11   13   23                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16   21                                                  
CONECT   16   15   17                                                       
CONECT   17   16   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   15   22   23                                             
CONECT   22   21                                                            
CONECT   23   21   12   24                                                  
CONECT   24   23   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   11    8   27                                             
CONECT   27   26                                                            
CONECT   28    5   29                                                       
CONECT   29   28    2                                                       
MASTER        0    0    0    0    0    0    0    0   29    0   66    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₇H₄₃NO

Average Mass

397.6470 Da

Monoisotopic Mass

397.33447 Da

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

Not Available

SMILES

C[C@H]([C@H]1CC[C@H]2[C@@H]3CC=C4C[C@@H](O)CC[C@]4(C)[C@H]3CC[C@]12C)C1=NC[C@@H](C)CC1

InChI Identifier

InChI=1S/C27H43NO/c1-17-5-10-25(28-16-17)18(2)22-8-9-23-21-7-6-19-15-20(29)11-13-26(19,3)24(21)12-14-27(22,23)4/h6,17-18,20-24,29H,5,7-16H2,1-4H3/t17-,18+,20-,21-,22+,23-,24-,26-,27+/m0/s1

InChI Key

VRBNGKPRTHBEIQ-RWWNDWOOSA-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 22,26-epiminocholestanes. These are steroid alkaloids obtained by reduction of spirosolane through opening of the E-ring.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Steroids and steroid derivatives

Sub Class

Steroidal alkaloids

Direct Parent

22,26-epiminocholestanes

Alternative Parents

Substituents

22,26-epiminocholestane skeleton
Progestogin-skeleton
Pregnane-skeleton
3-hydroxy-delta-5-steroid
3-hydroxysteroid
Hydroxysteroid
3-beta-hydroxysteroid
3-beta-hydroxy-delta-5-steroid
Delta-5-steroid
Tetrahydropyridine
Hydropyridine
Cyclic alcohol
Secondary alcohol
Ketimine
Azacycle
Organoheterocyclic compound
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Organopnictogen compound
Organic oxygen compound
Organic nitrogen compound
Hydrocarbon derivative
Alcohol
Imine
Organooxygen compound
Organonitrogen compound
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	5.59	ChemAxon
pKa (Strongest Acidic)	18.2	ChemAxon
pKa (Strongest Basic)	4.12	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	1	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

24690523

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

44584077

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Gao LJ, Zhang MZ, Li XY, Huang WK, Xu SF, Ye YP: Steroidal alkaloids isolated from Veratrum grandiflorum Loes. as novel Smoothened inhibitors with anti-proliferation effects on DAOY medulloblastoma cells. Bioorg Med Chem. 2021 Jun 1;39:116166. doi: 10.1016/j.bmc.2021.116166. Epub 2021 Apr 21. [PubMed:33910157 ]
LOTUS database [Link]

Showing NP-Card for (1r,3as,3bs,7s,9ar,9bs,11as)-9a,11a-dimethyl-1-[(1r)-1-[(5s)-5-methyl-3,4,5,6-tetrahydropyridin-2-yl]ethyl]-1h,2h,3h,3ah,3bh,4h,6h,7h,8h,9h,9bh,10h,11h-cyclopenta[a]phenanthren-7-ol (NP0209388)

MOL for NP0209388 ((1r,3as,3bs,7s,9ar,9bs,11as)-9a,11a-dimethyl-1-[(1r)-1-[(5s)-5-methyl-3,4,5,6-tetrahydropyridin-2-yl]ethyl]-1h,2h,3h,3ah,3bh,4h,6h,7h,8h,9h,9bh,10h,11h-cyclopenta[a]phenanthren-7-ol)

3D MOL for NP0209388 ((1r,3as,3bs,7s,9ar,9bs,11as)-9a,11a-dimethyl-1-[(1r)-1-[(5s)-5-methyl-3,4,5,6-tetrahydropyridin-2-yl]ethyl]-1h,2h,3h,3ah,3bh,4h,6h,7h,8h,9h,9bh,10h,11h-cyclopenta[a]phenanthren-7-ol)

3D SDF for NP0209388 ((1r,3as,3bs,7s,9ar,9bs,11as)-9a,11a-dimethyl-1-[(1r)-1-[(5s)-5-methyl-3,4,5,6-tetrahydropyridin-2-yl]ethyl]-1h,2h,3h,3ah,3bh,4h,6h,7h,8h,9h,9bh,10h,11h-cyclopenta[a]phenanthren-7-ol)

3D-SDF for NP0209388 ((1r,3as,3bs,7s,9ar,9bs,11as)-9a,11a-dimethyl-1-[(1r)-1-[(5s)-5-methyl-3,4,5,6-tetrahydropyridin-2-yl]ethyl]-1h,2h,3h,3ah,3bh,4h,6h,7h,8h,9h,9bh,10h,11h-cyclopenta[a]phenanthren-7-ol)

PDB for NP0209388 ((1r,3as,3bs,7s,9ar,9bs,11as)-9a,11a-dimethyl-1-[(1r)-1-[(5s)-5-methyl-3,4,5,6-tetrahydropyridin-2-yl]ethyl]-1h,2h,3h,3ah,3bh,4h,6h,7h,8h,9h,9bh,10h,11h-cyclopenta[a]phenanthren-7-ol)

3D PDB for NP0209388 ((1r,3as,3bs,7s,9ar,9bs,11as)-9a,11a-dimethyl-1-[(1r)-1-[(5s)-5-methyl-3,4,5,6-tetrahydropyridin-2-yl]ethyl]-1h,2h,3h,3ah,3bh,4h,6h,7h,8h,9h,9bh,10h,11h-cyclopenta[a]phenanthren-7-ol)

SMILES for NP0209388 ((1r,3as,3bs,7s,9ar,9bs,11as)-9a,11a-dimethyl-1-[(1r)-1-[(5s)-5-methyl-3,4,5,6-tetrahydropyridin-2-yl]ethyl]-1h,2h,3h,3ah,3bh,4h,6h,7h,8h,9h,9bh,10h,11h-cyclopenta[a]phenanthren-7-ol)

INCHI for NP0209388 ((1r,3as,3bs,7s,9ar,9bs,11as)-9a,11a-dimethyl-1-[(1r)-1-[(5s)-5-methyl-3,4,5,6-tetrahydropyridin-2-yl]ethyl]-1h,2h,3h,3ah,3bh,4h,6h,7h,8h,9h,9bh,10h,11h-cyclopenta[a]phenanthren-7-ol)

Structure for NP0209388 ((1r,3as,3bs,7s,9ar,9bs,11as)-9a,11a-dimethyl-1-[(1r)-1-[(5s)-5-methyl-3,4,5,6-tetrahydropyridin-2-yl]ethyl]-1h,2h,3h,3ah,3bh,4h,6h,7h,8h,9h,9bh,10h,11h-cyclopenta[a]phenanthren-7-ol)

3D Structure for NP0209388 ((1r,3as,3bs,7s,9ar,9bs,11as)-9a,11a-dimethyl-1-[(1r)-1-[(5s)-5-methyl-3,4,5,6-tetrahydropyridin-2-yl]ethyl]-1h,2h,3h,3ah,3bh,4h,6h,7h,8h,9h,9bh,10h,11h-cyclopenta[a]phenanthren-7-ol)