NP-MRD: Showing NP-Card for (5r,6s,7r,12s,13s,18r)-12,18-dihydroxy-7-[(1s,2r)-1-hydroxy-2,3-dimethylbutyl]-6,13-dimethylpentacyclo[10.8.0.0²,⁹.0⁵,⁹.0¹³,¹⁸]icosa-1,19-diene-11,16-dione (NP0320257)

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Record Information

Version

2.0

Created at

2022-09-11 21:48:32 UTC

Updated at

2022-09-11 21:48:32 UTC

NP-MRD ID

NP0320257

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(5r,6s,7r,12s,13s,18r)-12,18-dihydroxy-7-[(1s,2r)-1-hydroxy-2,3-dimethylbutyl]-6,13-dimethylpentacyclo[10.8.0.0²,⁹.0⁵,⁹.0¹³,¹⁸]icosa-1,19-diene-11,16-dione

Description

Emesterone A belongs to the class of organic compounds known as 11-oxosteroids. These are steroid derivatives carrying a C=O group at the 11-position of the steroid skeleton. (5r,6s,7r,12s,13s,18r)-12,18-dihydroxy-7-[(1s,2r)-1-hydroxy-2,3-dimethylbutyl]-6,13-dimethylpentacyclo[10.8.0.0²,⁹.0⁵,⁹.0¹³,¹⁸]icosa-1,19-diene-11,16-dione was first documented in 1998 (PMID: 9851872). Based on a literature review very few articles have been published on Emesterone A.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309112223482D          

 33 37  0  0  1  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv1652309112223482D          

 33 37  0  0  1  0            999 V2000
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 28 30  1  0  0  0  0
 30 31  1  0  0  0  0
 31 32  1  0  0  0  0
 14 32  1  0  0  0  0
 25 32  1  0  0  0  0
 32 33  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0320257

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C)[C@@H](C)[C@H](O)[C@@H]1CC23CC(=O)[C@]4(O)C(C=C[C@]5(O)CC(=O)CC[C@]45C)=C2CC[C@@H]3[C@@H]1C

> <INCHI_IDENTIFIER>
InChI=1S/C28H40O5/c1-15(2)16(3)24(31)19-13-26-14-23(30)28(33)22(21(26)7-6-20(26)17(19)4)9-11-27(32)12-18(29)8-10-25(27,28)5/h9,11,15-17,19-20,24,31-33H,6-8,10,12-14H2,1-5H3/t16-,17-,19-,20-,24+,25+,26?,27+,28-/m1/s1

> <INCHI_KEY>
WFVBCGMGZQZOAE-QJHBJTLGSA-N

> <FORMULA>
C28H40O5

> <MOLECULAR_WEIGHT>
456.623

> <EXACT_MASS>
456.287574388

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
73

> <JCHEM_AVERAGE_POLARIZABILITY>
51.39765095260658

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(5R,6S,7R,12S,13S,18R)-12,18-dihydroxy-7-[(1S,2R)-1-hydroxy-2,3-dimethylbutyl]-6,13-dimethylpentacyclo[10.8.0.0^{2,9}.0^{5,9}.0^{13,18}]icosa-1,19-diene-11,16-dione

> <JCHEM_LOGP>
2.9874898576666657

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.770358203391538

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.02170942660188

> <JCHEM_PKA_STRONGEST_BASIC>
-0.3422697578350743

> <JCHEM_POLAR_SURFACE_AREA>
94.83000000000001

> <JCHEM_REFRACTIVITY>
127.78129999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(5R,6S,7R,12S,13S,18R)-12,18-dihydroxy-7-[(1S,2R)-1-hydroxy-2,3-dimethylbutyl]-6,13-dimethylpentacyclo[10.8.0.0^{2,9}.0^{5,9}.0^{13,18}]icosa-1,19-diene-11,16-dione

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 11-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-SEP-22         0                                  
HETATM    1  C   UNK     0      -1.678   4.262   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -0.167   3.969   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.843   5.131   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.335   2.512   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -0.675   1.350   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.847   2.219   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       2.857   3.381   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       2.348   0.763   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       3.821   0.313   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       3.848  -1.227   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.449   0.190   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       5.978   0.378   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       6.579   1.796   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       6.905  -0.852   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       7.506   0.566   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0       6.303  -2.269   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       4.775  -2.457   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       3.892  -3.719   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       2.419  -3.268   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       2.392  -1.729   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       1.465  -0.499   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      -0.075  -0.526   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       7.230  -3.499   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       8.759  -3.311   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       9.360  -1.894   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0      10.287  -3.123   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0      10.889  -1.706   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      11.490  -0.288   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0      13.019  -0.100   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0      10.563   0.942   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       9.035   0.754   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       8.433  -0.664   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       8.406   0.876   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9   21                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11   17   20                                             
CONECT   11   10   12                                                       
CONECT   12   11   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12   15   16   32                                             
CONECT   15   14                                                            
CONECT   16   14   17   23                                                  
CONECT   17   16   10   18                                                  
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   10   21                                                  
CONECT   21   20    8   22                                                  
CONECT   22   21                                                            
CONECT   23   16   24                                                       
CONECT   24   23   25                                                       
CONECT   25   24   26   27   32                                             
CONECT   26   25                                                            
CONECT   27   25   28                                                       
CONECT   28   27   29   30                                                  
CONECT   29   28                                                            
CONECT   30   28   31                                                       
CONECT   31   30   32                                                       
CONECT   32   31   14   25   33                                             
CONECT   33   32                                                            
MASTER        0    0    0    0    0    0    0    0   33    0   74    0
END

View in JSmol

Synonyms

Value	Source
Emesterone-a	MeSH

Chemical Formula

C₂₈H₄₀O₅

Average Mass

456.6230 Da

Monoisotopic Mass

456.28757 Da

IUPAC Name

(5R,6S,7R,12S,13S,18R)-12,18-dihydroxy-7-[(1S,2R)-1-hydroxy-2,3-dimethylbutyl]-6,13-dimethylpentacyclo[10.8.0.0^{2,9}.0^{5,9}.0^{13,18}]icosa-1,19-diene-11,16-dione

Traditional Name

(5R,6S,7R,12S,13S,18R)-12,18-dihydroxy-7-[(1S,2R)-1-hydroxy-2,3-dimethylbutyl]-6,13-dimethylpentacyclo[10.8.0.0^{2,9}.0^{5,9}.0^{13,18}]icosa-1,19-diene-11,16-dione

CAS Registry Number

Not Available

SMILES

CC(C)[C@@H](C)[C@H](O)[C@@H]1CC23CC(=O)[C@]4(O)C(C=C[C@]5(O)CC(=O)CC[C@]45C)=C2CC[C@@H]3[C@@H]1C

InChI Identifier

InChI=1S/C28H40O5/c1-15(2)16(3)24(31)19-13-26-14-23(30)28(33)22(21(26)7-6-20(26)17(19)4)9-11-27(32)12-18(29)8-10-25(27,28)5/h9,11,15-17,19-20,24,31-33H,6-8,10,12-14H2,1-5H3/t16-,17-,19-,20-,24+,25+,26?,27+,28-/m1/s1

InChI Key

WFVBCGMGZQZOAE-QJHBJTLGSA-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

Not Available

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as 11-oxosteroids. These are steroid derivatives carrying a C=O group at the 11-position of the steroid skeleton.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Steroids and steroid derivatives

Sub Class

Oxosteroids

Direct Parent

11-oxosteroids

Alternative Parents

Substituents

23-hydroxysteroid
3-oxosteroid
5-hydroxysteroid
Hydroxysteroid
11-oxosteroid
Cyclohexenone
Cyclic alcohol
Tertiary alcohol
Cyclic ketone
Secondary alcohol
Ketone
Organic oxygen compound
Hydrocarbon derivative
Organic oxide
Carbonyl group
Alcohol
Organooxygen compound
Aliphatic homopolycyclic compound

Molecular Framework

Aliphatic homopolycyclic 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	2.99	ChemAxon
pKa (Strongest Acidic)	12.02	ChemAxon
pKa (Strongest Basic)	-0.34	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	94.83 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	127.78 m³·mol⁻¹	ChemAxon
Polarizability	51.4 Å³	ChemAxon
Number of Rings	5	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

Not Available

Chemspider ID

420731

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

479495

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Takahashi N, Fukui T, Iwahori A, Kubo Y, Hosoe T, Kawai K: Induction of differentiation and apoptosis in human promyelocytic leukemia HL60 cell line by a new type of steroids. Exp Cell Res. 1998 Dec 15;245(2):313-20. doi: 10.1006/excr.1998.4254. [PubMed:9851872 ]
LOTUS database [Link]

Showing NP-Card for (5r,6s,7r,12s,13s,18r)-12,18-dihydroxy-7-[(1s,2r)-1-hydroxy-2,3-dimethylbutyl]-6,13-dimethylpentacyclo[10.8.0.0²,⁹.0⁵,⁹.0¹³,¹⁸]icosa-1,19-diene-11,16-dione (NP0320257)

MOL for NP0320257 ((5r,6s,7r,12s,13s,18r)-12,18-dihydroxy-7-[(1s,2r)-1-hydroxy-2,3-dimethylbutyl]-6,13-dimethylpentacyclo[10.8.0.0²,⁹.0⁵,⁹.0¹³,¹⁸]icosa-1,19-diene-11,16-dione)

3D MOL for NP0320257 ((5r,6s,7r,12s,13s,18r)-12,18-dihydroxy-7-[(1s,2r)-1-hydroxy-2,3-dimethylbutyl]-6,13-dimethylpentacyclo[10.8.0.0²,⁹.0⁵,⁹.0¹³,¹⁸]icosa-1,19-diene-11,16-dione)

3D SDF for NP0320257 ((5r,6s,7r,12s,13s,18r)-12,18-dihydroxy-7-[(1s,2r)-1-hydroxy-2,3-dimethylbutyl]-6,13-dimethylpentacyclo[10.8.0.0²,⁹.0⁵,⁹.0¹³,¹⁸]icosa-1,19-diene-11,16-dione)

3D-SDF for NP0320257 ((5r,6s,7r,12s,13s,18r)-12,18-dihydroxy-7-[(1s,2r)-1-hydroxy-2,3-dimethylbutyl]-6,13-dimethylpentacyclo[10.8.0.0²,⁹.0⁵,⁹.0¹³,¹⁸]icosa-1,19-diene-11,16-dione)

PDB for NP0320257 ((5r,6s,7r,12s,13s,18r)-12,18-dihydroxy-7-[(1s,2r)-1-hydroxy-2,3-dimethylbutyl]-6,13-dimethylpentacyclo[10.8.0.0²,⁹.0⁵,⁹.0¹³,¹⁸]icosa-1,19-diene-11,16-dione)

3D PDB for NP0320257 ((5r,6s,7r,12s,13s,18r)-12,18-dihydroxy-7-[(1s,2r)-1-hydroxy-2,3-dimethylbutyl]-6,13-dimethylpentacyclo[10.8.0.0²,⁹.0⁵,⁹.0¹³,¹⁸]icosa-1,19-diene-11,16-dione)

SMILES for NP0320257 ((5r,6s,7r,12s,13s,18r)-12,18-dihydroxy-7-[(1s,2r)-1-hydroxy-2,3-dimethylbutyl]-6,13-dimethylpentacyclo[10.8.0.0²,⁹.0⁵,⁹.0¹³,¹⁸]icosa-1,19-diene-11,16-dione)

INCHI for NP0320257 ((5r,6s,7r,12s,13s,18r)-12,18-dihydroxy-7-[(1s,2r)-1-hydroxy-2,3-dimethylbutyl]-6,13-dimethylpentacyclo[10.8.0.0²,⁹.0⁵,⁹.0¹³,¹⁸]icosa-1,19-diene-11,16-dione)

Structure for NP0320257 ((5r,6s,7r,12s,13s,18r)-12,18-dihydroxy-7-[(1s,2r)-1-hydroxy-2,3-dimethylbutyl]-6,13-dimethylpentacyclo[10.8.0.0²,⁹.0⁵,⁹.0¹³,¹⁸]icosa-1,19-diene-11,16-dione)

3D Structure for NP0320257 ((5r,6s,7r,12s,13s,18r)-12,18-dihydroxy-7-[(1s,2r)-1-hydroxy-2,3-dimethylbutyl]-6,13-dimethylpentacyclo[10.8.0.0²,⁹.0⁵,⁹.0¹³,¹⁸]icosa-1,19-diene-11,16-dione)