NP-MRD: Showing NP-Card for Rubiarbonone C (NP0080071)

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Record Information

Version

2.0

Created at

2022-04-29 01:08:18 UTC

Updated at

2022-04-29 01:08:18 UTC

NP-MRD ID

NP0080071

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Rubiarbonone C

Description

(1S,2S,5R,6S,8R,9S,10S,14S,19S,21S)-8,21-dihydroxy-2,9,10,14,18,18-hexamethyl-17-oxo-6-(propan-2-yl)pentacyclo[11.8.0.0²,¹⁰.0⁵,⁹.0¹⁴,¹⁹]Henicos-12-en-5-yl acetate belongs to the class of organic compounds known as steroid esters. Steroid esters are compounds containing a steroid moiety which bears a carboxylic acid ester group. Rubiarbonone C is found in Rubia yunnanensis. Based on a literature review very few articles have been published on (1S,2S,5R,6S,8R,9S,10S,14S,19S,21S)-8,21-dihydroxy-2,9,10,14,18,18-hexamethyl-17-oxo-6-(propan-2-yl)pentacyclo[11.8.0.0²,¹⁰.0⁵,⁹.0¹⁴,¹⁹]Henicos-12-en-5-yl acetate.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304292203082D          

 37 41  0  0  1  0            999 V2000
    6.1403    0.7726    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    5.3816    1.0967    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.1979    1.9009    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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  1  2  1  0  0  0  0
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  4  5  1  0  0  0  0
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  4  7  1  0  0  0  0
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  7 14  1  0  0  0  0
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 32 34  1  0  0  0  0
  2 35  1  1  0  0  0
 35 36  1  0  0  0  0
 35 37  1  0  0  0  0
M  END

     RDKit          3D

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M  END


  Mrv1652304292203082D          

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   -0.9353    0.3874    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2912    1.1206    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1161    1.1332    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2966   -1.1330    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3800   -0.7559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9410    1.1457    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2109   -0.9786    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4157    1.1833    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7403    1.2943    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7573   -0.8929    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.4333   -1.6516    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9283   -2.3115    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6142   -1.7503    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.6880   -0.5917    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5288   -1.4012    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.4687   -0.3249    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
  4  5  1  0  0  0  0
  1  5  1  0  0  0  0
  5  6  1  6  0  0  0
  4  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  3 10  1  0  0  0  0
  8 11  1  0  0  0  0
 11 12  1  6  0  0  0
 12 13  2  0  0  0  0
 13 14  1  0  0  0  0
  7 14  1  0  0  0  0
 12 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  6  0  0  0
 17 18  1  0  0  0  0
 11 18  1  0  0  0  0
 18 19  1  1  0  0  0
 16 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  2  0  0  0  0
 21 23  1  0  0  0  0
 23 24  1  0  0  0  0
 15 24  1  0  0  0  0
 20 25  1  0  0  0  0
 20 26  1  0  0  0  0
 15 27  1  1  0  0  0
  8 28  1  6  0  0  0
  7 29  1  1  0  0  0
  4 30  1  6  0  0  0
  3 31  1  1  0  0  0
 31 32  1  0  0  0  0
 32 33  2  0  0  0  0
 32 34  1  0  0  0  0
  2 35  1  1  0  0  0
 35 36  1  0  0  0  0
 35 37  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0080071

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C)[C@@H]1C[C@@H](O)[C@@]2(C)[C@]1(CC[C@@]1(C)[C@@H]3[C@@H](O)C[C@@H]4C(C)(C)C(=O)CC[C@]4(C)C3=CC[C@]21C)OC(C)=O

> <INCHI_IDENTIFIER>
InChI=1S/C32H50O5/c1-18(2)21-16-25(36)31(9)30(8)13-10-20-26(29(30,7)14-15-32(21,31)37-19(3)33)22(34)17-23-27(4,5)24(35)11-12-28(20,23)6/h10,18,21-23,25-26,34,36H,11-17H2,1-9H3/t21-,22-,23+,25+,26-,28+,29-,30-,31+,32+/m0/s1

> <INCHI_KEY>
ICPKCPHJNFFEEO-RXFNVYCBSA-N

> <FORMULA>
C32H50O5

> <MOLECULAR_WEIGHT>
514.747

> <EXACT_MASS>
514.36582471

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
87

> <JCHEM_AVERAGE_POLARIZABILITY>
59.34862023576774

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1S,2S,5R,6S,8R,9S,10S,14S,19S,21S)-8,21-dihydroxy-2,9,10,14,18,18-hexamethyl-17-oxo-6-(propan-2-yl)pentacyclo[11.8.0.0^{2,10}.0^{5,9}.0^{14,19}]henicos-12-en-5-yl acetate

> <ALOGPS_LOGP>
5.74

> <JCHEM_LOGP>
4.773844027666666

> <ALOGPS_LOGS>
-5.43

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
19.689457045896646

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.58994862966345

> <JCHEM_PKA_STRONGEST_BASIC>
-0.4236025913772238

> <JCHEM_POLAR_SURFACE_AREA>
83.83000000000001

> <JCHEM_REFRACTIVITY>
144.8691

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.90e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1S,2S,5R,6S,8R,9S,10S,14S,19S,21S)-8,21-dihydroxy-6-isopropyl-2,9,10,14,18,18-hexamethyl-17-oxopentacyclo[11.8.0.0^{2,10}.0^{5,9}.0^{14,19}]henicos-12-en-5-yl acetate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 29-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   29-APR-22         0                                  
HETATM    1  C   UNK     0      11.462   1.442   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      11.324  -0.092   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       9.823  -0.435   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       9.033   0.887   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      10.046   2.047   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       9.703   3.548   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       7.493   0.864   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       6.743  -0.482   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       7.534  -1.803   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       9.073  -1.780   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       5.204  -0.505   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       4.413   0.817   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       5.163   2.162   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       6.703   2.185   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       2.874   0.793   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       2.124  -0.552   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       2.914  -1.874   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       4.454  -1.850   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       5.244  -3.172   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0       0.584  -0.575   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      -0.206   0.747   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0      -1.746   0.723   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0       0.543   2.092   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       2.083   2.115   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       0.554  -2.115   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      -0.709  -1.411   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       3.623   2.139   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       5.994  -1.827   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       8.243   2.209   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       8.849   2.416   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0      10.747  -1.667   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0      10.142  -3.083   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0      11.066  -4.315   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0       8.613  -3.267   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      12.484  -1.105   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0      12.187  -2.616   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0      13.941  -0.606   0.000  0.00  0.00           C+0
CONECT    1    2    5                                                       
CONECT    2    1    3   35                                                  
CONECT    3    2    4   10   31                                             
CONECT    4    3    5    7   30                                             
CONECT    5    4    1    6                                                  
CONECT    6    5                                                            
CONECT    7    4    8   14   29                                             
CONECT    8    7    9   11   28                                             
CONECT    9    8   10                                                       
CONECT   10    9    3                                                       
CONECT   11    8   12   18                                                  
CONECT   12   11   13   15                                                  
CONECT   13   12   14                                                       
CONECT   14   13    7                                                       
CONECT   15   12   16   24   27                                             
CONECT   16   15   17   20                                                  
CONECT   17   16   18                                                       
CONECT   18   17   11   19                                                  
CONECT   19   18                                                            
CONECT   20   16   21   25   26                                             
CONECT   21   20   22   23                                                  
CONECT   22   21                                                            
CONECT   23   21   24                                                       
CONECT   24   23   15                                                       
CONECT   25   20                                                            
CONECT   26   20                                                            
CONECT   27   15                                                            
CONECT   28    8                                                            
CONECT   29    7                                                            
CONECT   30    4                                                            
CONECT   31    3   32                                                       
CONECT   32   31   33   34                                                  
CONECT   33   32                                                            
CONECT   34   32                                                            
CONECT   35    2   36   37                                                  
CONECT   36   35                                                            
CONECT   37   35                                                            
MASTER        0    0    0    0    0    0    0    0   37    0   82    0
END

View in JSmol

Synonyms

Value	Source
(1S,2S,5R,6S,8R,9S,10S,14S,19S,21S)-8,21-Dihydroxy-2,9,10,14,18,18-hexamethyl-17-oxo-6-(propan-2-yl)pentacyclo[11.8.0.0,.0,.0,]henicos-12-en-5-yl acetic acid	Generator

Chemical Formula

C₃₂H₅₀O₅

Average Mass

514.7470 Da

Monoisotopic Mass

514.36582 Da

IUPAC Name

(1S,2S,5R,6S,8R,9S,10S,14S,19S,21S)-8,21-dihydroxy-2,9,10,14,18,18-hexamethyl-17-oxo-6-(propan-2-yl)pentacyclo[11.8.0.0^{2,10}.0^{5,9}.0^{14,19}]henicos-12-en-5-yl acetate

Traditional Name

(1S,2S,5R,6S,8R,9S,10S,14S,19S,21S)-8,21-dihydroxy-6-isopropyl-2,9,10,14,18,18-hexamethyl-17-oxopentacyclo[11.8.0.0^{2,10}.0^{5,9}.0^{14,19}]henicos-12-en-5-yl acetate

CAS Registry Number

Not Available

SMILES

CC(C)[C@@H]1C[C@@H](O)[C@@]2(C)[C@]1(CC[C@@]1(C)[C@@H]3[C@@H](O)C[C@@H]4C(C)(C)C(=O)CC[C@]4(C)C3=CC[C@]21C)OC(C)=O

InChI Identifier

InChI=1S/C32H50O5/c1-18(2)21-16-25(36)31(9)30(8)13-10-20-26(29(30,7)14-15-32(21,31)37-19(3)33)22(34)17-23-27(4,5)24(35)11-12-28(20,23)6/h10,18,21-23,25-26,34,36H,11-17H2,1-9H3/t21-,22-,23+,25+,26-,28+,29-,30-,31+,32+/m0/s1

InChI Key

ICPKCPHJNFFEEO-RXFNVYCBSA-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, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, 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
Rubia yunnanensis	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as steroid esters. Steroid esters are compounds containing a steroid moiety which bears a carboxylic acid ester group.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Steroids and steroid derivatives

Sub Class

Steroid esters

Direct Parent

Steroid esters

Alternative Parents

Substituents

Steroid ester
1-hydroxysteroid
Hydroxysteroid
15-hydroxysteroid
Delta-5-steroid
Cyclic alcohol
Cyclic ketone
Secondary alcohol
Ketone
Carboxylic acid ester
Monocarboxylic acid or derivatives
Carboxylic acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Carbonyl group
Alcohol
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	5.74	ALOGPS
logP	4.77	ChemAxon
logS	-5.4	ALOGPS
pKa (Strongest Acidic)	14.59	ChemAxon
pKa (Strongest Basic)	-0.42	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	83.83 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	144.87 m³·mol⁻¹	ChemAxon
Polarizability	59.35 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

163104386

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Showing NP-Card for Rubiarbonone C (NP0080071)

MOL for NP0080071 (Rubiarbonone C)

3D MOL for NP0080071 (Rubiarbonone C)

3D SDF for NP0080071 (Rubiarbonone C)

3D-SDF for NP0080071 (Rubiarbonone C)

PDB for NP0080071 (Rubiarbonone C)

3D PDB for NP0080071 (Rubiarbonone C)

SMILES for NP0080071 (Rubiarbonone C)

INCHI for NP0080071 (Rubiarbonone C)

Structure for NP0080071 (Rubiarbonone C)

3D Structure for NP0080071 (Rubiarbonone C)