NP-MRD: Showing NP-Card for (1r,5r,8r)-8-[(1r,3as,3bs,5s,5as,9ar,9bs,11as)-5,5a-dihydroxy-9a,11a-dimethyl-9-oxo-1h,2h,3h,3ah,3bh,4h,5h,6h,9bh,10h,11h-cyclopenta[a]phenanthren-1-yl]-5-methyl-4-methylidene-2,6-dioxabicyclo[3.3.1]nonan-3-one (NP0255094)

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Record Information

Version

2.0

Created at

2022-09-07 19:27:42 UTC

Updated at

2022-09-07 19:27:42 UTC

NP-MRD ID

NP0255094

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(1r,5r,8r)-8-[(1r,3as,3bs,5s,5as,9ar,9bs,11as)-5,5a-dihydroxy-9a,11a-dimethyl-9-oxo-1h,2h,3h,3ah,3bh,4h,5h,6h,9bh,10h,11h-cyclopenta[a]phenanthren-1-yl]-5-methyl-4-methylidene-2,6-dioxabicyclo[3.3.1]nonan-3-one

Description

Withametelin O belongs to the class of organic compounds known as steroid lactones. These are sterol lipids containing a lactone moiety linked to the steroid skeleton. (1r,5r,8r)-8-[(1r,3as,3bs,5s,5as,9ar,9bs,11as)-5,5a-dihydroxy-9a,11a-dimethyl-9-oxo-1h,2h,3h,3ah,3bh,4h,5h,6h,9bh,10h,11h-cyclopenta[a]phenanthren-1-yl]-5-methyl-4-methylidene-2,6-dioxabicyclo[3.3.1]nonan-3-one is found in Datura metel. Based on a literature review very few articles have been published on Withametelin O.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309072221272D          

 34 39  0  0  1  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv1652309072221272D          

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 16 15  1  1  0  0  0
 16 17  1  0  0  0  0
 17 18  1  6  0  0  0
 18 19  1  0  0  0  0
 19 20  1  6  0  0  0
 19 21  1  0  0  0  0
 21 22  1  1  0  0  0
 21 23  1  0  0  0  0
 23 24  1  0  0  0  0
 24 25  2  0  0  0  0
 25 26  1  0  0  0  0
 26 27  2  0  0  0  0
 26 28  1  0  0  0  0
 21 28  1  0  0  0  0
 28 29  1  1  0  0  0
 28 30  1  0  0  0  0
 17 30  1  0  0  0  0
 30 31  1  1  0  0  0
 31 32  1  0  0  0  0
 32 33  1  0  0  0  0
 16 33  1  0  0  0  0
 13 33  1  0  0  0  0
 33 34  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0255094

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@]12CC[C@H]3[C@@H](C[C@H](O)[C@]4(O)CC=CC(=O)[C@]34C)[C@@H]1CC[C@@H]2[C@@H]1CO[C@]2(C)C[C@H]1OC(=O)C2=C

> <INCHI_IDENTIFIER>
InChI=1S/C28H38O6/c1-15-24(31)34-21-13-26(15,3)33-14-17(21)19-8-7-18-16-12-23(30)28(32)10-5-6-22(29)27(28,4)20(16)9-11-25(18,19)2/h5-6,16-21,23,30,32H,1,7-14H2,2-4H3/t16-,17-,18-,19+,20-,21+,23-,25-,26+,27-,28+/m0/s1

> <INCHI_KEY>
QDXNBCJROMNCKV-CHVLNEQGSA-N

> <FORMULA>
C28H38O6

> <MOLECULAR_WEIGHT>
470.606

> <EXACT_MASS>
470.266838944

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
72

> <JCHEM_AVERAGE_POLARIZABILITY>
51.80810125437155

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1R,5R,8R)-8-[(1S,2R,7S,8S,10S,11S,14R,15S)-7,8-dihydroxy-2,15-dimethyl-3-oxotetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadec-4-en-14-yl]-5-methyl-4-methylidene-2,6-dioxabicyclo[3.3.1]nonan-3-one

> <JCHEM_LOGP>
3.178163522333333

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.78692424853799

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.132728072644255

> <JCHEM_PKA_STRONGEST_BASIC>
-3.258128803585538

> <JCHEM_POLAR_SURFACE_AREA>
93.06

> <JCHEM_REFRACTIVITY>
126.79799999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(1R,5R,8R)-8-[(1S,2R,7S,8S,10S,11S,14R,15S)-7,8-dihydroxy-2,15-dimethyl-3-oxotetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadec-4-en-14-yl]-5-methyl-4-methylidene-2,6-dioxabicyclo[3.3.1]nonan-3-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 07-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   07-SEP-22         0                                  
HETATM    1  C   UNK     0       1.367 -10.256   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.312  -9.040   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       3.797  -9.448   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       3.989 -10.976   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0       5.136  -8.686   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       5.544  -7.201   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       3.610  -7.951   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.551  -7.701   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.023  -7.893   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       1.959  -6.216   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       3.297  -5.455   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       4.782  -5.863   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       5.727  -4.647   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       5.299  -3.168   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       6.574  -2.304   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       7.790  -3.249   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       9.306  -2.978   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       9.829  -1.529   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      11.345  -1.258   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0      11.868   0.190   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0      12.338  -2.436   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0      12.861  -0.987   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0      13.854  -2.164   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      14.846  -3.342   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      14.323  -4.790   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      12.807  -5.061   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0      12.284  -6.510   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0      11.814  -3.884   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      11.291  -5.332   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      10.299  -4.155   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       9.775  -5.603   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       8.259  -5.874   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       7.267  -4.697   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       6.595  -6.083   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    8                                                  
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6                                                       
CONECT    6    5    7   12                                                  
CONECT    7    6    8                                                       
CONECT    8    7    2    9   10                                             
CONECT    9    8                                                            
CONECT   10    8   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11    6   13                                                  
CONECT   13   12   14   33                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17   33                                                  
CONECT   17   16   18   30                                                  
CONECT   18   17   19                                                       
CONECT   19   18   20   21                                                  
CONECT   20   19                                                            
CONECT   21   19   22   23   28                                             
CONECT   22   21                                                            
CONECT   23   21   24                                                       
CONECT   24   23   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   27   28                                                  
CONECT   27   26                                                            
CONECT   28   26   21   29   30                                             
CONECT   29   28                                                            
CONECT   30   28   17   31                                                  
CONECT   31   30   32                                                       
CONECT   32   31   33                                                       
CONECT   33   32   16   13   34                                             
CONECT   34   33                                                            
MASTER        0    0    0    0    0    0    0    0   34    0   78    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₈H₃₈O₆

Average Mass

470.6060 Da

Monoisotopic Mass

470.26684 Da

IUPAC Name

(1R,5R,8R)-8-[(1S,2R,7S,8S,10S,11S,14R,15S)-7,8-dihydroxy-2,15-dimethyl-3-oxotetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadec-4-en-14-yl]-5-methyl-4-methylidene-2,6-dioxabicyclo[3.3.1]nonan-3-one

Traditional Name

(1R,5R,8R)-8-[(1S,2R,7S,8S,10S,11S,14R,15S)-7,8-dihydroxy-2,15-dimethyl-3-oxotetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadec-4-en-14-yl]-5-methyl-4-methylidene-2,6-dioxabicyclo[3.3.1]nonan-3-one

CAS Registry Number

Not Available

SMILES

C[C@]12CC[C@H]3[C@@H](C[C@H](O)[C@]4(O)CC=CC(=O)[C@]34C)[C@@H]1CC[C@@H]2[C@@H]1CO[C@]2(C)C[C@H]1OC(=O)C2=C

InChI Identifier

InChI=1S/C28H38O6/c1-15-24(31)34-21-13-26(15,3)33-14-17(21)19-8-7-18-16-12-23(30)28(32)10-5-6-22(29)27(28,4)20(16)9-11-25(18,19)2/h5-6,16-21,23,30,32H,1,7-14H2,2-4H3/t16-,17-,18-,19+,20-,21+,23-,25-,26+,27-,28+/m0/s1

InChI Key

QDXNBCJROMNCKV-CHVLNEQGSA-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
Datura metel	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as steroid lactones. These are sterol lipids containing a lactone moiety linked to the steroid skeleton.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Steroids and steroid derivatives

Sub Class

Steroid lactones

Direct Parent

Steroid lactones

Alternative Parents

Substituents

Steroid lactone
Androstane-skeleton
6-hydroxysteroid
5-hydroxysteroid
Hydroxysteroid
1-oxosteroid
Oxosteroid
Delta valerolactone
Cyclohexenone
Delta_valerolactone
Oxane
Cyclic alcohol
Alpha,beta-unsaturated carboxylic ester
Enoate ester
Tertiary alcohol
Secondary alcohol
Lactone
Carboxylic acid ester
Ketone
1,2-diol
Monocarboxylic acid or derivatives
Carboxylic acid derivative
Organoheterocyclic compound
Dialkyl ether
Ether
Oxacycle
Alcohol
Organic oxide
Organooxygen compound
Carbonyl group
Hydrocarbon derivative
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	3.18	ChemAxon
pKa (Strongest Acidic)	13.13	ChemAxon
pKa (Strongest Basic)	-3.3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	93.06 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	126.8 m³·mol⁻¹	ChemAxon
Polarizability	51.81 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

C00040651

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

16757090

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (1r,5r,8r)-8-[(1r,3as,3bs,5s,5as,9ar,9bs,11as)-5,5a-dihydroxy-9a,11a-dimethyl-9-oxo-1h,2h,3h,3ah,3bh,4h,5h,6h,9bh,10h,11h-cyclopenta[a]phenanthren-1-yl]-5-methyl-4-methylidene-2,6-dioxabicyclo[3.3.1]nonan-3-one (NP0255094)

MOL for NP0255094 ((1r,5r,8r)-8-[(1r,3as,3bs,5s,5as,9ar,9bs,11as)-5,5a-dihydroxy-9a,11a-dimethyl-9-oxo-1h,2h,3h,3ah,3bh,4h,5h,6h,9bh,10h,11h-cyclopenta[a]phenanthren-1-yl]-5-methyl-4-methylidene-2,6-dioxabicyclo[3.3.1]nonan-3-one)

3D MOL for NP0255094 ((1r,5r,8r)-8-[(1r,3as,3bs,5s,5as,9ar,9bs,11as)-5,5a-dihydroxy-9a,11a-dimethyl-9-oxo-1h,2h,3h,3ah,3bh,4h,5h,6h,9bh,10h,11h-cyclopenta[a]phenanthren-1-yl]-5-methyl-4-methylidene-2,6-dioxabicyclo[3.3.1]nonan-3-one)

3D SDF for NP0255094 ((1r,5r,8r)-8-[(1r,3as,3bs,5s,5as,9ar,9bs,11as)-5,5a-dihydroxy-9a,11a-dimethyl-9-oxo-1h,2h,3h,3ah,3bh,4h,5h,6h,9bh,10h,11h-cyclopenta[a]phenanthren-1-yl]-5-methyl-4-methylidene-2,6-dioxabicyclo[3.3.1]nonan-3-one)

3D-SDF for NP0255094 ((1r,5r,8r)-8-[(1r,3as,3bs,5s,5as,9ar,9bs,11as)-5,5a-dihydroxy-9a,11a-dimethyl-9-oxo-1h,2h,3h,3ah,3bh,4h,5h,6h,9bh,10h,11h-cyclopenta[a]phenanthren-1-yl]-5-methyl-4-methylidene-2,6-dioxabicyclo[3.3.1]nonan-3-one)

PDB for NP0255094 ((1r,5r,8r)-8-[(1r,3as,3bs,5s,5as,9ar,9bs,11as)-5,5a-dihydroxy-9a,11a-dimethyl-9-oxo-1h,2h,3h,3ah,3bh,4h,5h,6h,9bh,10h,11h-cyclopenta[a]phenanthren-1-yl]-5-methyl-4-methylidene-2,6-dioxabicyclo[3.3.1]nonan-3-one)

3D PDB for NP0255094 ((1r,5r,8r)-8-[(1r,3as,3bs,5s,5as,9ar,9bs,11as)-5,5a-dihydroxy-9a,11a-dimethyl-9-oxo-1h,2h,3h,3ah,3bh,4h,5h,6h,9bh,10h,11h-cyclopenta[a]phenanthren-1-yl]-5-methyl-4-methylidene-2,6-dioxabicyclo[3.3.1]nonan-3-one)

SMILES for NP0255094 ((1r,5r,8r)-8-[(1r,3as,3bs,5s,5as,9ar,9bs,11as)-5,5a-dihydroxy-9a,11a-dimethyl-9-oxo-1h,2h,3h,3ah,3bh,4h,5h,6h,9bh,10h,11h-cyclopenta[a]phenanthren-1-yl]-5-methyl-4-methylidene-2,6-dioxabicyclo[3.3.1]nonan-3-one)

INCHI for NP0255094 ((1r,5r,8r)-8-[(1r,3as,3bs,5s,5as,9ar,9bs,11as)-5,5a-dihydroxy-9a,11a-dimethyl-9-oxo-1h,2h,3h,3ah,3bh,4h,5h,6h,9bh,10h,11h-cyclopenta[a]phenanthren-1-yl]-5-methyl-4-methylidene-2,6-dioxabicyclo[3.3.1]nonan-3-one)

Structure for NP0255094 ((1r,5r,8r)-8-[(1r,3as,3bs,5s,5as,9ar,9bs,11as)-5,5a-dihydroxy-9a,11a-dimethyl-9-oxo-1h,2h,3h,3ah,3bh,4h,5h,6h,9bh,10h,11h-cyclopenta[a]phenanthren-1-yl]-5-methyl-4-methylidene-2,6-dioxabicyclo[3.3.1]nonan-3-one)

3D Structure for NP0255094 ((1r,5r,8r)-8-[(1r,3as,3bs,5s,5as,9ar,9bs,11as)-5,5a-dihydroxy-9a,11a-dimethyl-9-oxo-1h,2h,3h,3ah,3bh,4h,5h,6h,9bh,10h,11h-cyclopenta[a]phenanthren-1-yl]-5-methyl-4-methylidene-2,6-dioxabicyclo[3.3.1]nonan-3-one)