NP-MRD: Showing NP-Card for Verdinine (NP0070595)

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Record Information

Version

2.0

Created at

2022-04-28 15:59:29 UTC

Updated at

2022-04-28 15:59:29 UTC

NP-MRD ID

NP0070595

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Verdinine

Description

(1R,2R,5S,7R,10R,11S,14R,15R)-14-[(1R)-1-(3-hydroxy-5-methylpyridin-2-yl)ethyl]-2,15-dimethyl-8-oxotetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]Heptadecan-5-yl acetate belongs to the class of organic compounds known as steroid esters. Steroid esters are compounds containing a steroid moiety which bears a carboxylic acid ester group. Verdinine is found in Veratrum album and Veratrum lobelianum . Based on a literature review very few articles have been published on (1R,2R,5S,7R,10R,11S,14R,15R)-14-[(1R)-1-(3-hydroxy-5-methylpyridin-2-yl)ethyl]-2,15-dimethyl-8-oxotetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]Heptadecan-5-yl acetate.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282217592D          

 34 38  0  0  1  0            999 V2000
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M  END

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M  END


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 21 22  1  0  0  0  0
 22 23  2  0  0  0  0
 23 24  1  0  0  0  0
 24 25  2  0  0  0  0
 20 25  1  0  0  0  0
 23 26  1  0  0  0  0
 21 27  1  0  0  0  0
 19 28  1  6  0  0  0
 13 29  1  1  0  0  0
  5 30  1  6  0  0  0
  2 31  1  6  0  0  0
 31 32  1  0  0  0  0
 32 33  2  0  0  0  0
 32 34  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0070595

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@H]([C@H]1CC[C@H]2[C@H]3CC(=O)[C@@H]4C[C@H](CC[C@]4(C)[C@@H]3CC[C@@]12C)OC(C)=O)C1=C(O)C=C(C)C=N1

> <INCHI_IDENTIFIER>
InChI=1S/C29H41NO4/c1-16-12-26(33)27(30-15-16)17(2)21-6-7-22-20-14-25(32)24-13-19(34-18(3)31)8-10-29(24,5)23(20)9-11-28(21,22)4/h12,15,17,19-24,33H,6-11,13-14H2,1-5H3/t17-,19+,20-,21-,22+,23-,24+,28+,29-/m1/s1

> <INCHI_KEY>
GANKTJHOGMIBAJ-MBFWLXSQSA-N

> <FORMULA>
C29H41NO4

> <MOLECULAR_WEIGHT>
467.65

> <EXACT_MASS>
467.303558804

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
75

> <JCHEM_AVERAGE_POLARIZABILITY>
53.67543338312895

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1R,2R,5S,7R,10R,11S,14R,15R)-14-[(1R)-1-(3-hydroxy-5-methylpyridin-2-yl)ethyl]-2,15-dimethyl-8-oxotetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadecan-5-yl acetate

> <ALOGPS_LOGP>
5.17

> <JCHEM_LOGP>
5.226920379666664

> <ALOGPS_LOGS>
-5.60

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.857899588082711

> <JCHEM_PKA_STRONGEST_BASIC>
6.127086194976784

> <JCHEM_POLAR_SURFACE_AREA>
76.49000000000001

> <JCHEM_REFRACTIVITY>
131.19499999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.18e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1R,2R,5S,7R,10R,11S,14R,15R)-14-[(1R)-1-(3-hydroxy-5-methylpyridin-2-yl)ethyl]-2,15-dimethyl-8-oxotetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadecan-5-yl acetate

> <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       7.929   4.020   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       8.452   2.572   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       7.459   1.394   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.943   1.666   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       5.420   3.114   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       6.413   4.291   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       3.904   3.385   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.911   2.208   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       3.434   0.759   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       4.950   0.488   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       5.474  -0.960   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       1.395   2.479   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       0.872   3.927   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       1.865   5.104   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       3.381   4.833   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -0.667   3.877   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -1.095   2.398   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       0.179   1.534   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -1.612   5.093   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -3.138   4.882   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      -3.718   3.456   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      -5.244   3.245   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      -6.189   4.461   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      -5.609   5.887   0.000  0.00  0.00           C+0
HETATM   25  N   UNK     0      -4.083   6.098   0.000  0.00  0.00           N+0
HETATM   26  C   UNK     0      -7.714   4.250   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0      -2.773   2.240   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0      -1.032   6.519   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       0.200   5.313   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       4.897   4.562   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0       9.968   2.301   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0      10.491   0.852   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0      12.007   0.581   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0       9.498  -0.325   0.000  0.00  0.00           C+0
CONECT    1    2    6                                                       
CONECT    2    1    3   31                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   10                                                  
CONECT    5    4    6    7   30                                             
CONECT    6    5    1                                                       
CONECT    7    5    8   15                                                  
CONECT    8    7    9   12                                                  
CONECT    9    8   10                                                       
CONECT   10    9    4   11                                                  
CONECT   11   10                                                            
CONECT   12    8   13   18                                                  
CONECT   13   12   14   16   29                                             
CONECT   14   13   15                                                       
CONECT   15   14    7                                                       
CONECT   16   13   17   19                                                  
CONECT   17   16   18                                                       
CONECT   18   17   12                                                       
CONECT   19   16   20   28                                                  
CONECT   20   19   21   25                                                  
CONECT   21   20   22   27                                                  
CONECT   22   21   23                                                       
CONECT   23   22   24   26                                                  
CONECT   24   23   25                                                       
CONECT   25   24   20                                                       
CONECT   26   23                                                            
CONECT   27   21                                                            
CONECT   28   19                                                            
CONECT   29   13                                                            
CONECT   30    5                                                            
CONECT   31    2   32                                                       
CONECT   32   31   33   34                                                  
CONECT   33   32                                                            
CONECT   34   32                                                            
MASTER        0    0    0    0    0    0    0    0   34    0   76    0
END

View in JSmol

Synonyms

Value	Source
(1R,2R,5S,7R,10R,11S,14R,15R)-14-[(1R)-1-(3-Hydroxy-5-methylpyridin-2-yl)ethyl]-2,15-dimethyl-8-oxotetracyclo[8.7.0.0,.0,]heptadecan-5-yl acetic acid	Generator

Chemical Formula

C₂₉H₄₁NO₄

Average Mass

467.6500 Da

Monoisotopic Mass

467.30356 Da

IUPAC Name

(1R,2R,5S,7R,10R,11S,14R,15R)-14-[(1R)-1-(3-hydroxy-5-methylpyridin-2-yl)ethyl]-2,15-dimethyl-8-oxotetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadecan-5-yl acetate

Traditional Name

(1R,2R,5S,7R,10R,11S,14R,15R)-14-[(1R)-1-(3-hydroxy-5-methylpyridin-2-yl)ethyl]-2,15-dimethyl-8-oxotetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadecan-5-yl acetate

CAS Registry Number

Not Available

SMILES

C[C@H]([C@H]1CC[C@H]2[C@H]3CC(=O)[C@@H]4C[C@H](CC[C@]4(C)[C@@H]3CC[C@@]12C)OC(C)=O)C1=C(O)C=C(C)C=N1

InChI Identifier

InChI=1S/C29H41NO4/c1-16-12-26(33)27(30-15-16)17(2)21-6-7-22-20-14-25(32)24-13-19(34-18(3)31)8-10-29(24,5)23(20)9-11-28(21,22)4/h12,15,17,19-24,33H,6-11,13-14H2,1-5H3/t17-,19+,20-,21-,22+,23-,24+,28+,29-/m1/s1

InChI Key

GANKTJHOGMIBAJ-MBFWLXSQSA-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 album	LOTUS Database	35616633
Veratrum lobelianum	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as steroid esters. Steroid esters are compounds containing a steroid moiety which bears a carboxylic acid ester group.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Steroids and steroid derivatives

Sub Class

Steroid esters

Direct Parent

Steroid esters

Alternative Parents

Substituents

Pregnane-skeleton
Steroid ester
6-oxosteroid
Oxosteroid
Methylpyridine
Hydroxypyridine
Pyridine
Heteroaromatic compound
Ketone
Carboxylic acid ester
Azacycle
Organoheterocyclic compound
Monocarboxylic acid or derivatives
Carboxylic acid derivative
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Carbonyl group
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	5.17	ALOGPS
logP	5.23	ChemAxon
logS	-5.6	ALOGPS
pKa (Strongest Acidic)	9.86	ChemAxon
pKa (Strongest Basic)	6.13	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	76.49 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	131.2 m³·mol⁻¹	ChemAxon
Polarizability	53.68 Å³	ChemAxon
Number of Rings	5	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	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

162879531

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Showing NP-Card for Verdinine (NP0070595)

MOL for NP0070595 (Verdinine)

3D MOL for NP0070595 (Verdinine)

3D SDF for NP0070595 (Verdinine)

3D-SDF for NP0070595 (Verdinine)

PDB for NP0070595 (Verdinine)

3D PDB for NP0070595 (Verdinine)

SMILES for NP0070595 (Verdinine)

INCHI for NP0070595 (Verdinine)

Structure for NP0070595 (Verdinine)

3D Structure for NP0070595 (Verdinine)