NP-MRD: Showing NP-Card for (1r,3as,3bs,7s,9ar,9bs,11as)-9a,11a-dimethyl-1-[(1s)-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 (NP0294339)

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Record Information

Version

2.0

Created at

2022-09-10 02:49:57 UTC

Updated at

2022-09-10 02:49:57 UTC

NP-MRD ID

NP0294339

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(1r,3as,3bs,7s,9ar,9bs,11as)-9a,11a-dimethyl-1-[(1s)-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

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, verazine is considered to be a sterol. (1r,3as,3bs,7s,9ar,9bs,11as)-9a,11a-dimethyl-1-[(1s)-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 is found in Anticlea sibirica, Eclipta prostrata and Veratrum dahuricum. (1r,3as,3bs,7s,9ar,9bs,11as)-9a,11a-dimethyl-1-[(1s)-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 2020 (PMID: 33350228). Based on a literature review a small amount of articles have been published on Verazine (PMID: 34641477) (PMID: 33910157) (PMID: 36014585) (PMID: 32202118).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309102204492D          

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M  END

     RDKit          3D

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M  END


  Mrv1652309102204492D          

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M  END
> <DATABASE_ID>
NP0294339

> <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-LURFOZDGSA-N

> <FORMULA>
C27H43NO

> <MOLECULAR_WEIGHT>
397.647

> <EXACT_MASS>
397.334465009

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
72

> <JCHEM_AVERAGE_POLARIZABILITY>
49.12725312524687

> <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-[(1S)-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-[(1S)-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                                 10-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   10-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

(1S,2R,5S,10S,11S,14R,15S)-2,15-dimethyl-14-[(1S)-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

Traditional Name

(1S,2R,5S,10S,11S,14R,15S)-2,15-dimethyl-14-[(1S)-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

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-LURFOZDGSA-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
Anticlea sibirica	LOTUS Database	35616633
Eclipta prostrata	LOTUS Database	35616633
Veratrum dahuricum	LOTUS Database	35616633

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
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	32.59 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	121.83 m³·mol⁻¹	ChemAxon
Polarizability	49.13 Å³	ChemAxon
Number of Rings	5	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	Yes	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

C00028250

Chemspider ID

141486

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

161052

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Dirks ML, Seale JT, Collins JM, McDougal OM: Review: Veratrum californicum Alkaloids. Molecules. 2021 Sep 30;26(19). pii: molecules26195934. doi: 10.3390/molecules26195934. [PubMed:34641477 ]
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 ]
Seale JT, McDougal OM: Veratrum parviflorum: An Underexplored Source for Bioactive Steroidal Alkaloids. Molecules. 2022 Aug 22;27(16). pii: molecules27165349. doi: 10.3390/molecules27165349. [PubMed:36014585 ]
Meng-Zhen Z, Li-Juan G, Shi-Fang XU, Wen-Kang H, Xiao-Yu LI, Yi-Ping YE: [Advances in studies on steroidal alkaloids and their pharmacological activities in genus Veratrum]. Zhongguo Zhong Yao Za Zhi. 2020 Nov;45(21):5129-5142. doi: 10.19540/j.cnki.cjcmm.20200612.201. [PubMed:33350228 ]
Wang Y, Shi Y, Tian WS, Tang P, Zhuang C, Chen FE: Stereoselective Synthesis of (-)-Verazine and Congeners via a Cascade Ring-Switching Process of Furostan-26-acid. Org Lett. 2020 Apr 3;22(7):2761-2765. doi: 10.1021/acs.orglett.0c00747. Epub 2020 Mar 23. [PubMed:32202118 ]
LOTUS database [Link]

Showing NP-Card for (1r,3as,3bs,7s,9ar,9bs,11as)-9a,11a-dimethyl-1-[(1s)-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 (NP0294339)

MOL for NP0294339 ((1r,3as,3bs,7s,9ar,9bs,11as)-9a,11a-dimethyl-1-[(1s)-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 NP0294339 ((1r,3as,3bs,7s,9ar,9bs,11as)-9a,11a-dimethyl-1-[(1s)-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 NP0294339 ((1r,3as,3bs,7s,9ar,9bs,11as)-9a,11a-dimethyl-1-[(1s)-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 NP0294339 ((1r,3as,3bs,7s,9ar,9bs,11as)-9a,11a-dimethyl-1-[(1s)-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 NP0294339 ((1r,3as,3bs,7s,9ar,9bs,11as)-9a,11a-dimethyl-1-[(1s)-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 NP0294339 ((1r,3as,3bs,7s,9ar,9bs,11as)-9a,11a-dimethyl-1-[(1s)-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 NP0294339 ((1r,3as,3bs,7s,9ar,9bs,11as)-9a,11a-dimethyl-1-[(1s)-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 NP0294339 ((1r,3as,3bs,7s,9ar,9bs,11as)-9a,11a-dimethyl-1-[(1s)-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 NP0294339 ((1r,3as,3bs,7s,9ar,9bs,11as)-9a,11a-dimethyl-1-[(1s)-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 NP0294339 ((1r,3as,3bs,7s,9ar,9bs,11as)-9a,11a-dimethyl-1-[(1s)-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)