NP-MRD: Showing NP-Card for 6-(1-{1,3a,5,5a-tetrahydroxy-9a,11a-dimethyl-9-oxo-2h,3h,3bh,4h,5h,6h,9bh,10h,11h-cyclopenta[a]phenanthren-1-yl}-1-hydroxyethyl)-3,4-dimethyl-5,6-dihydropyran-2-one (NP0147233)

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Record Information

Version

2.0

Created at

2022-09-02 02:47:46 UTC

Updated at

2022-09-02 02:47:46 UTC

NP-MRD ID

NP0147233

Secondary Accession Numbers

None

Natural Product Identification

Common Name

6-(1-{1,3a,5,5a-tetrahydroxy-9a,11a-dimethyl-9-oxo-2h,3h,3bh,4h,5h,6h,9bh,10h,11h-cyclopenta[a]phenanthren-1-yl}-1-hydroxyethyl)-3,4-dimethyl-5,6-dihydropyran-2-one

Description

NSC312620 belongs to the class of organic compounds known as withanolides and derivatives. These are c28 steroids structurally characterized by an ergostane skeleton usually functionalized at carbons 1, 22 and 26 to form a lactone ring. 6-(1-{1,3a,5,5a-tetrahydroxy-9a,11a-dimethyl-9-oxo-2h,3h,3bh,4h,5h,6h,9bh,10h,11h-cyclopenta[a]phenanthren-1-yl}-1-hydroxyethyl)-3,4-dimethyl-5,6-dihydropyran-2-one is found in Physalis cinerascens, Physalis peruviana and Withania somnifera. NSC312620 is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1533004151516562D          

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M  END

     RDKit          3D

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M  END


  Mrv1533004151516562D          

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    4.4247   -3.1470    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8928   -2.5163    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5330   -3.2587    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  3  5  1  0  0  0  0
  5  6  2  0  0  0  0
  5  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  2  9  1  0  0  0  0
  8 10  1  0  0  0  0
 10 11  1  0  0  0  0
 10 12  1  0  0  0  0
 10 13  1  0  0  0  0
 13 14  1  0  0  0  0
 13 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 17 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 21 23  1  0  0  0  0
 23 24  1  0  0  0  0
 23 25  1  0  0  0  0
 25 26  1  0  0  0  0
 26 27  2  0  0  0  0
 27 28  1  0  0  0  0
 28 29  2  0  0  0  0
 28 30  1  0  0  0  0
 23 30  1  0  0  0  0
 30 31  1  0  0  0  0
 30 32  1  0  0  0  0
 19 32  1  0  0  0  0
 32 33  1  0  0  0  0
 33 34  1  0  0  0  0
 34 35  1  0  0  0  0
 13 35  1  0  0  0  0
 17 35  1  0  0  0  0
 35 36  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0147233

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC1=C(C)C(=O)OC(C1)C(C)(O)C1(O)CCC2(O)C3CC(O)C4(O)CC=CC(=O)C4(C)C3CCC12C

> <INCHI_IDENTIFIER>
InChI=1S/C28H40O8/c1-15-13-21(36-22(31)16(15)2)25(5,32)28(35)12-11-26(33)18-14-20(30)27(34)9-6-7-19(29)24(27,4)17(18)8-10-23(26,28)3/h6-7,17-18,20-21,30,32-35H,8-14H2,1-5H3

> <INCHI_KEY>
PQZVBIJEPVKNOZ-UHFFFAOYSA-N

> <FORMULA>
C28H40O8

> <MOLECULAR_WEIGHT>
504.62

> <EXACT_MASS>
504.272318248

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
76

> <JCHEM_AVERAGE_POLARIZABILITY>
54.6253051025988

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
6-(1-hydroxy-1-{7,8,11,14-tetrahydroxy-2,15-dimethyl-3-oxotetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadec-4-en-14-yl}ethyl)-3,4-dimethyl-5,6-dihydro-2H-pyran-2-one

> <ALOGPS_LOGP>
1.16

> <JCHEM_LOGP>
1.5319072006666656

> <ALOGPS_LOGS>
-3.04

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.192277524935626

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.575845134072459

> <JCHEM_PKA_STRONGEST_BASIC>
-3.201006747884332

> <JCHEM_POLAR_SURFACE_AREA>
144.52

> <JCHEM_REFRACTIVITY>
131.92189999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
4.58e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
6-(1-hydroxy-1-{7,8,11,14-tetrahydroxy-2,15-dimethyl-3-oxotetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadec-4-en-14-yl}ethyl)-3,4-dimethyl-5,6-dihydropyran-2-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 15-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   15-APR-15         0                                  
HETATM    1  C   UNK     0       0.133  -8.357   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.656  -6.909   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.336  -5.731   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -1.852  -6.002   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.187  -4.283   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      -0.806  -3.106   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       1.703  -4.012   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       2.696  -5.189   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.172  -6.638   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       4.211  -4.918   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.483  -6.434   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       3.940  -3.402   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       5.727  -4.647   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       5.839  -6.183   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       5.299  -3.168   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       6.574  -2.304   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       7.790  -3.249   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       8.159  -1.754   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       9.306  -2.978   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       9.829  -1.529   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      11.345  -1.258   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0      11.868   0.190   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0      12.338  -2.436   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0      12.861  -0.987   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0      13.854  -2.164   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      14.846  -3.342   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      14.323  -4.790   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      12.807  -5.061   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0      12.284  -6.510   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0      11.814  -3.884   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      11.291  -5.332   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      10.299  -4.155   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       9.775  -5.603   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       8.259  -5.874   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       7.267  -4.697   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0       6.595  -6.083   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    9                                                  
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8                                                       
CONECT    8    7    9   10                                                  
CONECT    9    8    2                                                       
CONECT   10    8   11   12   13                                             
CONECT   11   10                                                            
CONECT   12   10                                                            
CONECT   13   10   14   15   35                                             
CONECT   14   13                                                            
CONECT   15   13   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18   19   35                                             
CONECT   18   17                                                            
CONECT   19   17   20   32                                                  
CONECT   20   19   21                                                       
CONECT   21   20   22   23                                                  
CONECT   22   21                                                            
CONECT   23   21   24   25   30                                             
CONECT   24   23                                                            
CONECT   25   23   26                                                       
CONECT   26   25   27                                                       
CONECT   27   26   28                                                       
CONECT   28   27   29   30                                                  
CONECT   29   28                                                            
CONECT   30   28   23   31   32                                             
CONECT   31   30                                                            
CONECT   32   30   19   33                                                  
CONECT   33   32   34                                                       
CONECT   34   33   35                                                       
CONECT   35   34   13   17   36                                             
CONECT   36   35                                                            
MASTER        0    0    0    0    0    0    0    0   36    0   80    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₈H₄₀O₈

Average Mass

504.6200 Da

Monoisotopic Mass

504.27232 Da

IUPAC Name

6-(1-hydroxy-1-{7,8,11,14-tetrahydroxy-2,15-dimethyl-3-oxotetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadec-4-en-14-yl}ethyl)-3,4-dimethyl-5,6-dihydro-2H-pyran-2-one

Traditional Name

6-(1-hydroxy-1-{7,8,11,14-tetrahydroxy-2,15-dimethyl-3-oxotetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadec-4-en-14-yl}ethyl)-3,4-dimethyl-5,6-dihydropyran-2-one

CAS Registry Number

Not Available

SMILES

CC1=C(C)C(=O)OC(C1)C(C)(O)C1(O)CCC2(O)C3CC(O)C4(O)CC=CC(=O)C4(C)C3CCC12C

InChI Identifier

InChI=1S/C28H40O8/c1-15-13-21(36-22(31)16(15)2)25(5,32)28(35)12-11-26(33)18-14-20(30)27(34)9-6-7-19(29)24(27,4)17(18)8-10-23(26,28)3/h6-7,17-18,20-21,30,32-35H,8-14H2,1-5H3

InChI Key

PQZVBIJEPVKNOZ-UHFFFAOYSA-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
Physalis cinerascens	LOTUS Database	35616633
Physalis peruviana	LOTUS Database	35616633
Withania somnifera	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as withanolides and derivatives. These are c28 steroids structurally characterized by an ergostane skeleton usually functionalized at carbons 1, 22 and 26 to form a lactone ring.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Steroids and steroid derivatives

Sub Class

Steroid lactones

Direct Parent

Withanolides and derivatives

Alternative Parents

Substituents

Withanolide-skeleton
20-hydroxysteroid
14-hydroxysteroid
6-hydroxysteroid
5-hydroxysteroid
Hydroxysteroid
1-oxosteroid
Oxosteroid
17-hydroxysteroid
Cyclohexenone
Dihydropyranone
Pyran
Tertiary alcohol
Alpha,beta-unsaturated carboxylic ester
Enoate ester
Cyclic alcohol
Secondary alcohol
Carboxylic acid ester
Ketone
Lactone
Carboxylic acid derivative
Polyol
Oxacycle
Organoheterocyclic compound
Monocarboxylic acid or derivatives
Carbonyl group
Alcohol
Organic oxygen compound
Hydrocarbon derivative
Organic oxide
Organooxygen 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	1.16	ALOGPS
logP	1.53	ChemAxon
logS	-3	ALOGPS
pKa (Strongest Acidic)	12.58	ChemAxon
pKa (Strongest Basic)	-3.2	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	144.52 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	131.92 m³·mol⁻¹	ChemAxon
Polarizability	54.63 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

329485

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 6-(1-{1,3a,5,5a-tetrahydroxy-9a,11a-dimethyl-9-oxo-2h,3h,3bh,4h,5h,6h,9bh,10h,11h-cyclopenta[a]phenanthren-1-yl}-1-hydroxyethyl)-3,4-dimethyl-5,6-dihydropyran-2-one (NP0147233)

MOL for NP0147233 (6-(1-{1,3a,5,5a-tetrahydroxy-9a,11a-dimethyl-9-oxo-2h,3h,3bh,4h,5h,6h,9bh,10h,11h-cyclopenta[a]phenanthren-1-yl}-1-hydroxyethyl)-3,4-dimethyl-5,6-dihydropyran-2-one)

3D MOL for NP0147233 (6-(1-{1,3a,5,5a-tetrahydroxy-9a,11a-dimethyl-9-oxo-2h,3h,3bh,4h,5h,6h,9bh,10h,11h-cyclopenta[a]phenanthren-1-yl}-1-hydroxyethyl)-3,4-dimethyl-5,6-dihydropyran-2-one)

3D SDF for NP0147233 (6-(1-{1,3a,5,5a-tetrahydroxy-9a,11a-dimethyl-9-oxo-2h,3h,3bh,4h,5h,6h,9bh,10h,11h-cyclopenta[a]phenanthren-1-yl}-1-hydroxyethyl)-3,4-dimethyl-5,6-dihydropyran-2-one)

3D-SDF for NP0147233 (6-(1-{1,3a,5,5a-tetrahydroxy-9a,11a-dimethyl-9-oxo-2h,3h,3bh,4h,5h,6h,9bh,10h,11h-cyclopenta[a]phenanthren-1-yl}-1-hydroxyethyl)-3,4-dimethyl-5,6-dihydropyran-2-one)

PDB for NP0147233 (6-(1-{1,3a,5,5a-tetrahydroxy-9a,11a-dimethyl-9-oxo-2h,3h,3bh,4h,5h,6h,9bh,10h,11h-cyclopenta[a]phenanthren-1-yl}-1-hydroxyethyl)-3,4-dimethyl-5,6-dihydropyran-2-one)

3D PDB for NP0147233 (6-(1-{1,3a,5,5a-tetrahydroxy-9a,11a-dimethyl-9-oxo-2h,3h,3bh,4h,5h,6h,9bh,10h,11h-cyclopenta[a]phenanthren-1-yl}-1-hydroxyethyl)-3,4-dimethyl-5,6-dihydropyran-2-one)

SMILES for NP0147233 (6-(1-{1,3a,5,5a-tetrahydroxy-9a,11a-dimethyl-9-oxo-2h,3h,3bh,4h,5h,6h,9bh,10h,11h-cyclopenta[a]phenanthren-1-yl}-1-hydroxyethyl)-3,4-dimethyl-5,6-dihydropyran-2-one)

INCHI for NP0147233 (6-(1-{1,3a,5,5a-tetrahydroxy-9a,11a-dimethyl-9-oxo-2h,3h,3bh,4h,5h,6h,9bh,10h,11h-cyclopenta[a]phenanthren-1-yl}-1-hydroxyethyl)-3,4-dimethyl-5,6-dihydropyran-2-one)

Structure for NP0147233 (6-(1-{1,3a,5,5a-tetrahydroxy-9a,11a-dimethyl-9-oxo-2h,3h,3bh,4h,5h,6h,9bh,10h,11h-cyclopenta[a]phenanthren-1-yl}-1-hydroxyethyl)-3,4-dimethyl-5,6-dihydropyran-2-one)

3D Structure for NP0147233 (6-(1-{1,3a,5,5a-tetrahydroxy-9a,11a-dimethyl-9-oxo-2h,3h,3bh,4h,5h,6h,9bh,10h,11h-cyclopenta[a]phenanthren-1-yl}-1-hydroxyethyl)-3,4-dimethyl-5,6-dihydropyran-2-one)