NP-MRD: Showing NP-Card for Rubivirine (NP0070387)

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Record Information

Version

2.0

Created at

2022-04-28 15:45:32 UTC

Updated at

2022-04-28 15:45:33 UTC

NP-MRD ID

NP0070387

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Rubivirine

Description

Rubivirine belongs to the class of organic compounds known as solanidines and derivatives. These are steroids with a structure based on the solanidane skeleton. Solanidane arises from the conversion of a cholestane side-chain into a bicyclic system. Rubivirine is found in Veratrum viride and Veratrum viride Ait. . Based on a literature review very few articles have been published on Rubivirine.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282217452D          

 31 36  0  0  1  0            999 V2000
    5.4488   -0.7004    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.7755   -0.2237    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.0208    0.5640    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.8457    0.5741    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.1103   -0.2073    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    6.9193   -0.3689    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.4637    0.2509    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1992    1.0323    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    6.3902    1.1939    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.7436    1.6522    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3474    1.0406    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6860    0.5475    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.9505   -0.2339    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.4061   -0.8537    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.5971   -0.6921    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3325    0.0893    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.8770    0.7091    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.6124    1.4906    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8034    1.6522    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2589    1.0323    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    0.9790   -0.3689    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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  2  1  1  6  0  0  0
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  2 13  1  0  0  0  0
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 16 21  1  0  0  0  0
 21 22  1  0  0  0  0
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 21 27  1  6  0  0  0
 14 28  1  6  0  0  0
 13 29  1  6  0  0  0
 29 30  1  0  0  0  0
  1 31  1  1  0  0  0
M  END

     RDKit          3D

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    1.7615   -1.3043   -1.2011 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3901   -0.9800   -1.7298 C   0  0  1  0  0  0  0  0  0  0  0  0
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   -1.3666    1.0127   -1.8808 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -0.5947    2.2295    1.2207 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9521    0.6348    1.9140 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3876    1.4143   -0.7377 H   0  0  0  0  0  0  0  0  0  0  0  0
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    1.9837    2.3586    0.7167 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4075    1.5981    2.2895 H   0  0  0  0  0  0  0  0  0  0  0  0
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 30  9  1  0
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  8 45  1  6
M  END


  Mrv1652304282217452D          

 31 36  0  0  1  0            999 V2000
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 29 30  1  0  0  0  0
  1 31  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0070387

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@@H]1[C@H]2CC[C@H](C)CN2[C@H]2C[C@H]3[C@@H]4CC=C5C[C@@H](O)CC[C@]5(C)[C@H]4C[C@@H](O)[C@]3(CO)[C@@H]12

> <INCHI_IDENTIFIER>
InChI=1S/C27H43NO3/c1-15-4-7-22-16(2)25-23(28(22)13-15)11-21-19-6-5-17-10-18(30)8-9-26(17,3)20(19)12-24(31)27(21,25)14-29/h5,15-16,18-25,29-31H,4,6-14H2,1-3H3/t15-,16+,18-,19+,20-,21-,22+,23-,24+,25-,26-,27+/m0/s1

> <INCHI_KEY>
SUXOAOUIWWNLHR-CHKTXLTHSA-N

> <FORMULA>
C27H43NO3

> <MOLECULAR_WEIGHT>
429.645

> <EXACT_MASS>
429.324294249

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
74

> <JCHEM_AVERAGE_POLARIZABILITY>
52.04511579562741

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1S,2R,7S,10R,11S,13R,14S,15R,16S,17R,20S,23S)-14-(hydroxymethyl)-10,16,20-trimethyl-22-azahexacyclo[12.10.0.0^{2,11}.0^{5,10}.0^{15,23}.0^{17,22}]tetracos-4-ene-7,13-diol

> <ALOGPS_LOGP>
2.93

> <JCHEM_LOGP>
2.3709529979999995

> <ALOGPS_LOGS>
-3.82

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
15.247777023475741

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.459363246756645

> <JCHEM_PKA_STRONGEST_BASIC>
11.635735758555159

> <JCHEM_POLAR_SURFACE_AREA>
63.93000000000001

> <JCHEM_REFRACTIVITY>
124.14759999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.53e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1S,2R,7S,10R,11S,13R,14S,15R,16S,17R,20S,23S)-14-(hydroxymethyl)-10,16,20-trimethyl-22-azahexacyclo[12.10.0.0^{2,11}.0^{5,10}.0^{15,23}.0^{17,22}]tetracos-4-ene-7,13-diol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 28-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   28-APR-22         0                                  
HETATM    1  C   UNK     0      10.171  -1.307   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       8.914  -0.418   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       9.372   1.053   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0      10.912   1.072   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0      11.406  -0.387   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      12.916  -0.689   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      13.932   0.468   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      13.438   1.927   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      11.928   2.229   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      14.455   3.084   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       8.115   1.943   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       6.881   1.022   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       7.374  -0.437   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       6.358  -1.594   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       4.848  -1.292   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       4.354   0.167   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       5.370   1.324   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       4.876   2.782   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       3.366   3.084   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       2.350   1.927   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       2.844   0.468   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       1.828  -0.689   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       0.317  -0.387   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      -0.176   1.072   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       0.840   2.229   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0      -1.687   1.373   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0       3.338  -0.990   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0       6.852  -3.052   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0       8.018  -1.836   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0       9.551  -1.978   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0      10.190  -2.847   0.000  0.00  0.00           C+0
CONECT    1    2    5   31                                                  
CONECT    2    1    3   13                                                  
CONECT    3    2    4   11                                                  
CONECT    4    3    5    9                                                  
CONECT    5    4    1    6                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9   10                                                  
CONECT    9    8    4                                                       
CONECT   10    8                                                            
CONECT   11    3   12                                                       
CONECT   12   11   13   17                                                  
CONECT   13   12    2   14   29                                             
CONECT   14   13   15   28                                                  
CONECT   15   14   16                                                       
CONECT   16   15   17   21                                                  
CONECT   17   16   12   18                                                  
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   21   25                                                  
CONECT   21   20   16   22   27                                             
CONECT   22   21   23                                                       
CONECT   23   22   24                                                       
CONECT   24   23   25   26                                                  
CONECT   25   24   20                                                       
CONECT   26   24                                                            
CONECT   27   21                                                            
CONECT   28   14                                                            
CONECT   29   13   30                                                       
CONECT   30   29                                                            
CONECT   31    1                                                            
MASTER        0    0    0    0    0    0    0    0   31    0   72    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₇H₄₃NO₃

Average Mass

429.6450 Da

Monoisotopic Mass

429.32429 Da

IUPAC Name

(1S,2R,7S,10R,11S,13R,14S,15R,16S,17R,20S,23S)-14-(hydroxymethyl)-10,16,20-trimethyl-22-azahexacyclo[12.10.0.0^{2,11}.0^{5,10}.0^{15,23}.0^{17,22}]tetracos-4-ene-7,13-diol

Traditional Name

(1S,2R,7S,10R,11S,13R,14S,15R,16S,17R,20S,23S)-14-(hydroxymethyl)-10,16,20-trimethyl-22-azahexacyclo[12.10.0.0^{2,11}.0^{5,10}.0^{15,23}.0^{17,22}]tetracos-4-ene-7,13-diol

CAS Registry Number

Not Available

SMILES

C[C@@H]1[C@H]2CC[C@H](C)CN2[C@H]2C[C@H]3[C@@H]4CC=C5C[C@@H](O)CC[C@]5(C)[C@H]4C[C@@H](O)[C@]3(CO)[C@@H]12

InChI Identifier

InChI=1S/C27H43NO3/c1-15-4-7-22-16(2)25-23(28(22)13-15)11-21-19-6-5-17-10-18(30)8-9-26(17,3)20(19)12-24(31)27(21,25)14-29/h5,15-16,18-25,29-31H,4,6-14H2,1-3H3/t15-,16+,18-,19+,20-,21-,22+,23-,24+,25-,26-,27+/m0/s1

InChI Key

SUXOAOUIWWNLHR-CHKTXLTHSA-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, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, 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
Veratrum viride	LOTUS Database	35616633
Veratrum viride Ait.	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as solanidines and derivatives. These are steroids with a structure based on the solanidane skeleton. Solanidane arises from the conversion of a cholestane side-chain into a bicyclic system.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Steroids and steroid derivatives

Sub Class

Steroidal alkaloids

Direct Parent

Solanidines and derivatives

Alternative Parents

Substituents

Solanidane skeleton
18-hydroxysteroid
3-hydroxy-delta-5-steroid
3-hydroxysteroid
12-hydroxysteroid
Hydroxysteroid
3-beta-hydroxysteroid
3-beta-hydroxy-delta-5-steroid
Azasteroid
Delta-5-steroid
Alkaloid or derivatives
Indolizidine
N-alkylpyrrolidine
Piperidine
Pyrrolidine
Cyclic alcohol
Secondary alcohol
Tertiary amine
Tertiary aliphatic amine
Azacycle
Organoheterocyclic compound
Primary alcohol
Organic nitrogen compound
Organonitrogen compound
Hydrocarbon derivative
Organooxygen compound
Organopnictogen compound
Amine
Alcohol
Organic oxygen 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	2.93	ALOGPS
logP	2.37	ChemAxon
logS	-3.8	ALOGPS
pKa (Strongest Acidic)	14.46	ChemAxon
pKa (Strongest Basic)	11.64	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	63.93 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	124.15 m³·mol⁻¹	ChemAxon
Polarizability	52.05 Å³	ChemAxon
Number of Rings	6	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

C00028947

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

101919102

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Rubivirine (NP0070387)

MOL for NP0070387 (Rubivirine)

3D MOL for NP0070387 (Rubivirine)

3D SDF for NP0070387 (Rubivirine)

3D-SDF for NP0070387 (Rubivirine)

PDB for NP0070387 (Rubivirine)

3D PDB for NP0070387 (Rubivirine)

SMILES for NP0070387 (Rubivirine)

INCHI for NP0070387 (Rubivirine)

Structure for NP0070387 (Rubivirine)

3D Structure for NP0070387 (Rubivirine)