NP-MRD: Showing NP-Card for (1s,3ar,3br,5s,5ar,7s,9ar,9br,11r,11ar)-1-[(1r)-1-hydroxy-5-methoxy-5-methylhexyl]-3a,3b,6,6,9a-pentamethyl-dodecahydro-1h-cyclopenta[a]phenanthrene-5,7,11-triol (NP0253722)

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Record Information

Version

2.0

Created at

2022-09-07 17:40:24 UTC

Updated at

2022-09-07 17:40:24 UTC

NP-MRD ID

NP0253722

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(1s,3ar,3br,5s,5ar,7s,9ar,9br,11r,11ar)-1-[(1r)-1-hydroxy-5-methoxy-5-methylhexyl]-3a,3b,6,6,9a-pentamethyl-dodecahydro-1h-cyclopenta[a]phenanthrene-5,7,11-triol

Description

CHEMBL1669120 belongs to the class of organic compounds known as 3-beta-hydroxysteroids. These are steroids carrying a beta-hydroxyl group at the 3-position of the steroid backbone. (1s,3ar,3br,5s,5ar,7s,9ar,9br,11r,11ar)-1-[(1r)-1-hydroxy-5-methoxy-5-methylhexyl]-3a,3b,6,6,9a-pentamethyl-dodecahydro-1h-cyclopenta[a]phenanthrene-5,7,11-triol is found in Panax ginseng. Based on a literature review very few articles have been published on CHEMBL1669120.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309072219402D          

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M  END


  Mrv1652309072219402D          

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    3.3737   -2.8825    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.1858   -3.0277    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.9055   -2.2518    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7176   -2.3970    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5297   -2.5422    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8100   -3.3182    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    6.6221   -3.4634    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.2782   -3.9489    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9917   -4.3631    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9942   -4.7234    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4661   -3.8037    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.9343   -4.4344    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.2146   -5.2103    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1221   -4.2891    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8418   -3.5132    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.5309   -4.2774    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  3  5  1  0  0  0  0
  3  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  1  0  0  0
 11  9  1  6  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  1  0  0  0
 16 14  1  1  0  0  0
 11 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  6  0  0  0
 17 19  1  0  0  0  0
 20 19  1  6  0  0  0
 20 21  1  0  0  0  0
 21 22  1  6  0  0  0
 21 23  1  0  0  0  0
 23 24  1  0  0  0  0
 24 25  1  0  0  0  0
 25 26  1  6  0  0  0
 25 27  1  0  0  0  0
 27 28  1  0  0  0  0
 27 29  1  0  0  0  0
 30 27  1  6  0  0  0
 21 30  1  0  0  0  0
 30 31  1  0  0  0  0
 31 32  1  1  0  0  0
 31 33  1  0  0  0  0
 33 34  1  0  0  0  0
 20 34  1  0  0  0  0
 14 34  1  0  0  0  0
 34 35  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0253722

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC(C)(C)CCC[C@@H](O)[C@H]1CC[C@]2(C)[C@@H]1[C@H](O)C[C@@H]1[C@@]3(C)CC[C@H](O)C(C)(C)[C@@H]3[C@@H](O)C[C@@]21C

> <INCHI_IDENTIFIER>
InChI=1S/C30H54O5/c1-26(2,35-8)13-9-10-19(31)18-11-15-29(6)24(18)20(32)16-22-28(5)14-12-23(34)27(3,4)25(28)21(33)17-30(22,29)7/h18-25,31-34H,9-17H2,1-8H3/t18-,19-,20-,21+,22-,23+,24+,25+,28-,29-,30-/m1/s1

> <INCHI_KEY>
YRJCMCBXAVZZTO-HDFOMQQSSA-N

> <FORMULA>
C30H54O5

> <MOLECULAR_WEIGHT>
494.757

> <EXACT_MASS>
494.397124839

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
89

> <JCHEM_AVERAGE_POLARIZABILITY>
59.94499661775777

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1R,2R,5S,7R,8S,10R,11R,14S,15R,16R)-14-[(1R)-1-hydroxy-5-methoxy-5-methylhexyl]-2,6,6,10,11-pentamethyltetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadecane-5,8,16-triol

> <JCHEM_LOGP>
3.5201876396666663

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.684709442565229

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.24889033528494

> <JCHEM_PKA_STRONGEST_BASIC>
-2.8264643413201744

> <JCHEM_POLAR_SURFACE_AREA>
90.15

> <JCHEM_REFRACTIVITY>
139.92749999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(1R,2R,5S,7R,8S,10R,11R,14S,15R,16R)-14-[(1R)-1-hydroxy-5-methoxy-5-methylhexyl]-2,6,6,10,11-pentamethyltetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadecane-5,8,16-triol

> <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      -6.631  -0.657   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0      -5.105  -0.447   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0      -4.160  -1.662   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -5.376  -2.608   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -2.944  -0.717   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -3.215  -2.878   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -1.690  -2.668   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -0.744  -3.883   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.781  -3.673   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       1.362  -2.246   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       1.726  -4.889   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       1.298  -6.368   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       2.573  -7.232   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       3.789  -6.287   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       4.158  -7.782   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       3.266  -4.839   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       4.258  -3.661   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       3.735  -2.213   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       5.774  -3.932   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       6.297  -5.381   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       7.813  -5.652   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       7.290  -4.203   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       8.806  -4.474   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      10.322  -4.746   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      10.845  -6.194   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0      12.361  -6.465   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0       9.853  -7.371   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      11.184  -8.144   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       9.322  -8.817   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       8.337  -7.100   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       7.344  -8.277   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0       7.867  -9.726   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0       5.828  -8.006   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       5.305  -6.558   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       4.724  -7.984   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    5    6                                             
CONECT    4    3                                                            
CONECT    5    3                                                            
CONECT    6    3    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12   16                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15   16   34                                             
CONECT   15   14                                                            
CONECT   16   14   11   17                                                  
CONECT   17   16   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17   20                                                       
CONECT   20   19   21   34                                                  
CONECT   21   20   22   23   30                                             
CONECT   22   21                                                            
CONECT   23   21   24                                                       
CONECT   24   23   25                                                       
CONECT   25   24   26   27                                                  
CONECT   26   25                                                            
CONECT   27   25   28   29   30                                             
CONECT   28   27                                                            
CONECT   29   27                                                            
CONECT   30   27   21   31                                                  
CONECT   31   30   32   33                                                  
CONECT   32   31                                                            
CONECT   33   31   34                                                       
CONECT   34   33   20   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

C₃₀H₅₄O₅

Average Mass

494.7570 Da

Monoisotopic Mass

494.39712 Da

IUPAC Name

(1R,2R,5S,7R,8S,10R,11R,14S,15R,16R)-14-[(1R)-1-hydroxy-5-methoxy-5-methylhexyl]-2,6,6,10,11-pentamethyltetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadecane-5,8,16-triol

Traditional Name

(1R,2R,5S,7R,8S,10R,11R,14S,15R,16R)-14-[(1R)-1-hydroxy-5-methoxy-5-methylhexyl]-2,6,6,10,11-pentamethyltetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadecane-5,8,16-triol

CAS Registry Number

Not Available

SMILES

COC(C)(C)CCC[C@@H](O)[C@H]1CC[C@]2(C)[C@@H]1[C@H](O)C[C@@H]1[C@@]3(C)CC[C@H](O)C(C)(C)[C@@H]3[C@@H](O)C[C@@]21C

InChI Identifier

InChI=1S/C30H54O5/c1-26(2,35-8)13-9-10-19(31)18-11-15-29(6)24(18)20(32)16-22-28(5)14-12-23(34)27(3,4)25(28)21(33)17-30(22,29)7/h18-25,31-34H,9-17H2,1-8H3/t18-,19-,20-,21+,22-,23+,24+,25+,28-,29-,30-/m1/s1

InChI Key

YRJCMCBXAVZZTO-HDFOMQQSSA-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
Panax ginseng	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as 3-beta-hydroxysteroids. These are steroids carrying a beta-hydroxyl group at the 3-position of the steroid backbone.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Steroids and steroid derivatives

Sub Class

Hydroxysteroids

Direct Parent

3-beta-hydroxysteroids

Alternative Parents

Substituents

14-alpha-methylsteroid
3-beta-hydroxysteroid
12-hydroxysteroid
6-hydroxysteroid
Fatty alcohol
Fatty acyl
Cyclic alcohol
Secondary alcohol
Dialkyl ether
Ether
Polyol
Alcohol
Hydrocarbon derivative
Organic oxygen compound
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	3.52	ChemAxon
pKa (Strongest Acidic)	14.25	ChemAxon
pKa (Strongest Basic)	-2.8	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	90.15 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	139.93 m³·mol⁻¹	ChemAxon
Polarizability	59.94 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	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

26387840

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

53316854

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (1s,3ar,3br,5s,5ar,7s,9ar,9br,11r,11ar)-1-[(1r)-1-hydroxy-5-methoxy-5-methylhexyl]-3a,3b,6,6,9a-pentamethyl-dodecahydro-1h-cyclopenta[a]phenanthrene-5,7,11-triol (NP0253722)

MOL for NP0253722 ((1s,3ar,3br,5s,5ar,7s,9ar,9br,11r,11ar)-1-[(1r)-1-hydroxy-5-methoxy-5-methylhexyl]-3a,3b,6,6,9a-pentamethyl-dodecahydro-1h-cyclopenta[a]phenanthrene-5,7,11-triol)

3D MOL for NP0253722 ((1s,3ar,3br,5s,5ar,7s,9ar,9br,11r,11ar)-1-[(1r)-1-hydroxy-5-methoxy-5-methylhexyl]-3a,3b,6,6,9a-pentamethyl-dodecahydro-1h-cyclopenta[a]phenanthrene-5,7,11-triol)

3D SDF for NP0253722 ((1s,3ar,3br,5s,5ar,7s,9ar,9br,11r,11ar)-1-[(1r)-1-hydroxy-5-methoxy-5-methylhexyl]-3a,3b,6,6,9a-pentamethyl-dodecahydro-1h-cyclopenta[a]phenanthrene-5,7,11-triol)

3D-SDF for NP0253722 ((1s,3ar,3br,5s,5ar,7s,9ar,9br,11r,11ar)-1-[(1r)-1-hydroxy-5-methoxy-5-methylhexyl]-3a,3b,6,6,9a-pentamethyl-dodecahydro-1h-cyclopenta[a]phenanthrene-5,7,11-triol)

PDB for NP0253722 ((1s,3ar,3br,5s,5ar,7s,9ar,9br,11r,11ar)-1-[(1r)-1-hydroxy-5-methoxy-5-methylhexyl]-3a,3b,6,6,9a-pentamethyl-dodecahydro-1h-cyclopenta[a]phenanthrene-5,7,11-triol)

3D PDB for NP0253722 ((1s,3ar,3br,5s,5ar,7s,9ar,9br,11r,11ar)-1-[(1r)-1-hydroxy-5-methoxy-5-methylhexyl]-3a,3b,6,6,9a-pentamethyl-dodecahydro-1h-cyclopenta[a]phenanthrene-5,7,11-triol)

SMILES for NP0253722 ((1s,3ar,3br,5s,5ar,7s,9ar,9br,11r,11ar)-1-[(1r)-1-hydroxy-5-methoxy-5-methylhexyl]-3a,3b,6,6,9a-pentamethyl-dodecahydro-1h-cyclopenta[a]phenanthrene-5,7,11-triol)

INCHI for NP0253722 ((1s,3ar,3br,5s,5ar,7s,9ar,9br,11r,11ar)-1-[(1r)-1-hydroxy-5-methoxy-5-methylhexyl]-3a,3b,6,6,9a-pentamethyl-dodecahydro-1h-cyclopenta[a]phenanthrene-5,7,11-triol)

Structure for NP0253722 ((1s,3ar,3br,5s,5ar,7s,9ar,9br,11r,11ar)-1-[(1r)-1-hydroxy-5-methoxy-5-methylhexyl]-3a,3b,6,6,9a-pentamethyl-dodecahydro-1h-cyclopenta[a]phenanthrene-5,7,11-triol)

3D Structure for NP0253722 ((1s,3ar,3br,5s,5ar,7s,9ar,9br,11r,11ar)-1-[(1r)-1-hydroxy-5-methoxy-5-methylhexyl]-3a,3b,6,6,9a-pentamethyl-dodecahydro-1h-cyclopenta[a]phenanthrene-5,7,11-triol)