NP-MRD: Showing NP-Card for (3r,6r)-6-[(1r,3as,3bs,5r,5ar,7s,9ar,9bs,11ar)-5,5a,7-trihydroxy-9a,11a-dimethyl-tetradecahydrocyclopenta[a]phenanthren-1-yl]-2,3-dimethylheptan-2-yl acetate (NP0222953)

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Record Information

Version

2.0

Created at

2022-09-06 00:55:09 UTC

Updated at

2022-09-06 00:55:09 UTC

NP-MRD ID

NP0222953

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(3r,6r)-6-[(1r,3as,3bs,5r,5ar,7s,9ar,9bs,11ar)-5,5a,7-trihydroxy-9a,11a-dimethyl-tetradecahydrocyclopenta[a]phenanthren-1-yl]-2,3-dimethylheptan-2-yl acetate

Description

CHEMBL487588 belongs to the class of organic compounds known as ergosterols and derivatives. These are steroids containing ergosta-5,7,22-trien-3beta-ol or a derivative thereof, which is based on the 3beta-hydroxylated ergostane skeleton. (3r,6r)-6-[(1r,3as,3bs,5r,5ar,7s,9ar,9bs,11ar)-5,5a,7-trihydroxy-9a,11a-dimethyl-tetradecahydrocyclopenta[a]phenanthren-1-yl]-2,3-dimethylheptan-2-yl acetate is found in Sarcophyton crassocaule. Based on a literature review very few articles have been published on CHEMBL487588.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309062202552D          

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M  END

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M  END


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    6.8898   -0.5288    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.4216   -1.1595    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.9534   -1.7902    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    8.7655   -1.6450    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.6731   -2.5662    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8610   -2.7114    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3292   -2.0807    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    6.0489   -2.8566    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5171   -2.2259    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.2368   -3.0018    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    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  2  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
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  5  7  1  0  0  0  0
  5  8  1  0  0  0  0
  8  9  1  6  0  0  0
  8 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  6  0  0  0
 14 12  1  1  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 17 16  1  1  0  0  0
 17 18  1  0  0  0  0
 18 19  1  6  0  0  0
 19 20  1  0  0  0  0
 20 21  1  1  0  0  0
 20 22  1  0  0  0  0
 22 23  1  6  0  0  0
 22 24  1  0  0  0  0
 24 25  1  0  0  0  0
 25 26  1  1  0  0  0
 25 27  1  0  0  0  0
 27 28  1  0  0  0  0
 28 29  1  0  0  0  0
 22 29  1  0  0  0  0
 29 30  1  1  0  0  0
 29 31  1  0  0  0  0
 18 31  1  0  0  0  0
 31 32  1  1  0  0  0
 32 33  1  0  0  0  0
 33 34  1  0  0  0  0
 17 34  1  0  0  0  0
 14 34  1  0  0  0  0
 34 35  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0222953

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C30H52O5/c1-18(8-9-19(2)27(4,5)35-20(3)31)23-10-11-24-22-16-26(33)30(34)17-21(32)12-15-29(30,7)25(22)13-14-28(23,24)6/h18-19,21-26,32-34H,8-17H2,1-7H3/t18-,19-,21+,22+,23-,24+,25+,26-,28-,29-,30+/m1/s1

> <INCHI_KEY>
NTYRSMDNACWFJE-GGCFKELASA-N

> <FORMULA>
C30H52O5

> <MOLECULAR_WEIGHT>
492.741

> <EXACT_MASS>
492.381474774

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
87

> <JCHEM_AVERAGE_POLARIZABILITY>
59.39224342062685

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3R,6R)-2,3-dimethyl-6-[(1S,2R,5S,7R,8R,10S,11S,14R,15R)-5,7,8-trihydroxy-2,15-dimethyltetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadecan-14-yl]heptan-2-yl acetate

> <JCHEM_LOGP>
4.546454685666666

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.715005071511072

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.28748790470204

> <JCHEM_PKA_STRONGEST_BASIC>
-2.728020209621212

> <JCHEM_POLAR_SURFACE_AREA>
86.99000000000001

> <JCHEM_REFRACTIVITY>
138.07169999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(3R,6R)-2,3-dimethyl-6-[(1S,2R,5S,7R,8R,10S,11S,14R,15R)-5,7,8-trihydroxy-2,15-dimethyltetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadecan-14-yl]heptan-2-yl acetate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 06-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-SEP-22         0                                  
HETATM    1  C   UNK     0      -3.575 -10.094   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -2.630  -8.878   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0      -3.210  -7.452   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0      -1.104  -9.089   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0      -0.159  -7.873   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.057  -8.818   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -1.375  -6.928   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.786  -6.657   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.206  -5.231   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.312  -6.868   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       3.257  -5.652   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       5.363  -7.289   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       5.727  -4.647   0.000  0.00  0.00           C+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  C   UNK     0       9.306  -2.978   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       9.829  -1.529   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      11.345  -1.258   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0      11.868   0.190   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0      12.338  -2.436   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0      12.861  -0.987   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0      13.854  -2.164   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      14.846  -3.342   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0      16.362  -3.071   0.000  0.00  0.00           O+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  C   UNK     0      11.814  -3.884   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      11.291  -5.332   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      10.299  -4.155   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       9.775  -5.603   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       8.259  -5.874   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       7.267  -4.697   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       6.595  -6.083   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6    7    8                                             
CONECT    6    5                                                            
CONECT    7    5                                                            
CONECT    8    5    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12   15   34                                                  
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18   34                                                  
CONECT   18   17   19   31                                                  
CONECT   19   18   20                                                       
CONECT   20   19   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20   23   24   29                                             
CONECT   23   22                                                            
CONECT   24   22   25                                                       
CONECT   25   24   26   27                                                  
CONECT   26   25                                                            
CONECT   27   25   28                                                       
CONECT   28   27   29                                                       
CONECT   29   28   22   30   31                                             
CONECT   30   29                                                            
CONECT   31   29   18   32                                                  
CONECT   32   31   33                                                       
CONECT   33   32   34                                                       
CONECT   34   33   17   14   35                                             
CONECT   35   34                                                            
MASTER        0    0    0    0    0    0    0    0   35    0   76    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₃₀H₅₂O₅

Average Mass

492.7410 Da

Monoisotopic Mass

492.38147 Da

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C30H52O5/c1-18(8-9-19(2)27(4,5)35-20(3)31)23-10-11-24-22-16-26(33)30(34)17-21(32)12-15-29(30,7)25(22)13-14-28(23,24)6/h18-19,21-26,32-34H,8-17H2,1-7H3/t18-,19-,21+,22+,23-,24+,25+,26-,28-,29-,30+/m1/s1

InChI Key

NTYRSMDNACWFJE-GGCFKELASA-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
Sarcophyton crassocaule	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as ergosterols and derivatives. These are steroids containing ergosta-5,7,22-trien-3beta-ol or a derivative thereof, which is based on the 3beta-hydroxylated ergostane skeleton.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Steroids and steroid derivatives

Sub Class

Ergostane steroids

Direct Parent

Ergosterols and derivatives

Alternative Parents

Substituents

Ergosterol-skeleton
Steroid ester
3-hydroxysteroid
6-hydroxysteroid
5-hydroxysteroid
Hydroxysteroid
3-beta-hydroxysteroid
Cyclic alcohol
Tertiary alcohol
Carboxylic acid ester
Secondary alcohol
Polyol
Monocarboxylic acid or derivatives
Carboxylic acid derivative
Organooxygen compound
Carbonyl group
Alcohol
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
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	4.55	ChemAxon
pKa (Strongest Acidic)	13.29	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

23326397

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

14034718

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (3r,6r)-6-[(1r,3as,3bs,5r,5ar,7s,9ar,9bs,11ar)-5,5a,7-trihydroxy-9a,11a-dimethyl-tetradecahydrocyclopenta[a]phenanthren-1-yl]-2,3-dimethylheptan-2-yl acetate (NP0222953)

MOL for NP0222953 ((3r,6r)-6-[(1r,3as,3bs,5r,5ar,7s,9ar,9bs,11ar)-5,5a,7-trihydroxy-9a,11a-dimethyl-tetradecahydrocyclopenta[a]phenanthren-1-yl]-2,3-dimethylheptan-2-yl acetate)

3D MOL for NP0222953 ((3r,6r)-6-[(1r,3as,3bs,5r,5ar,7s,9ar,9bs,11ar)-5,5a,7-trihydroxy-9a,11a-dimethyl-tetradecahydrocyclopenta[a]phenanthren-1-yl]-2,3-dimethylheptan-2-yl acetate)

3D SDF for NP0222953 ((3r,6r)-6-[(1r,3as,3bs,5r,5ar,7s,9ar,9bs,11ar)-5,5a,7-trihydroxy-9a,11a-dimethyl-tetradecahydrocyclopenta[a]phenanthren-1-yl]-2,3-dimethylheptan-2-yl acetate)

3D-SDF for NP0222953 ((3r,6r)-6-[(1r,3as,3bs,5r,5ar,7s,9ar,9bs,11ar)-5,5a,7-trihydroxy-9a,11a-dimethyl-tetradecahydrocyclopenta[a]phenanthren-1-yl]-2,3-dimethylheptan-2-yl acetate)

PDB for NP0222953 ((3r,6r)-6-[(1r,3as,3bs,5r,5ar,7s,9ar,9bs,11ar)-5,5a,7-trihydroxy-9a,11a-dimethyl-tetradecahydrocyclopenta[a]phenanthren-1-yl]-2,3-dimethylheptan-2-yl acetate)

3D PDB for NP0222953 ((3r,6r)-6-[(1r,3as,3bs,5r,5ar,7s,9ar,9bs,11ar)-5,5a,7-trihydroxy-9a,11a-dimethyl-tetradecahydrocyclopenta[a]phenanthren-1-yl]-2,3-dimethylheptan-2-yl acetate)

SMILES for NP0222953 ((3r,6r)-6-[(1r,3as,3bs,5r,5ar,7s,9ar,9bs,11ar)-5,5a,7-trihydroxy-9a,11a-dimethyl-tetradecahydrocyclopenta[a]phenanthren-1-yl]-2,3-dimethylheptan-2-yl acetate)

INCHI for NP0222953 ((3r,6r)-6-[(1r,3as,3bs,5r,5ar,7s,9ar,9bs,11ar)-5,5a,7-trihydroxy-9a,11a-dimethyl-tetradecahydrocyclopenta[a]phenanthren-1-yl]-2,3-dimethylheptan-2-yl acetate)

Structure for NP0222953 ((3r,6r)-6-[(1r,3as,3bs,5r,5ar,7s,9ar,9bs,11ar)-5,5a,7-trihydroxy-9a,11a-dimethyl-tetradecahydrocyclopenta[a]phenanthren-1-yl]-2,3-dimethylheptan-2-yl acetate)

3D Structure for NP0222953 ((3r,6r)-6-[(1r,3as,3bs,5r,5ar,7s,9ar,9bs,11ar)-5,5a,7-trihydroxy-9a,11a-dimethyl-tetradecahydrocyclopenta[a]phenanthren-1-yl]-2,3-dimethylheptan-2-yl acetate)