NP-MRD: Showing NP-Card for (-)-Cimicidanol (NP0066506)

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Record Information

Version

1.0

Created at

2022-04-28 10:45:50 UTC

Updated at

2022-04-28 10:45:50 UTC

NP-MRD ID

NP0066506

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(-)-Cimicidanol

Description

Cimicidanol belongs to the class of organic compounds known as cycloartanols and derivatives. These are steroids containing a cycloartanol moiety. (-)-Cimicidanol is found in Cimicifuga foetida L. . Based on a literature review very few articles have been published on Cimicidanol.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282212452D          

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M  END

     RDKit          3D

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M  END


  Mrv1652304282212452D          

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  8 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
  7 14  1  0  0  0  0
 14 15  1  1  0  0  0
 12 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  2  0  0  0  0
 17 19  1  0  0  0  0
 11 19  1  0  0  0  0
 16 20  1  1  0  0  0
 20 21  1  6  0  0  0
 20 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  2  0  0  0  0
 25 23  1  1  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 25 27  1  0  0  0  0
 26 28  1  0  0  0  0
 26 29  1  0  0  0  0
 12 30  1  1  0  0  0
 11 31  1  6  0  0  0
  7 32  1  1  0  0  0
  5 32  1  1  0  0  0
  3 33  1  0  0  0  0
  3 34  1  0  0  0  0
  2 35  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0066506

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@H](CC(=O)[C@@H]1OC1(C)C)[C@H]1C(=O)C[C@@]2(C)C3=CC[C@@H]4[C@]5(C[C@@]35[C@@H](O)C[C@]12C)CC[C@H](O)C4(C)C

> <INCHI_IDENTIFIER>
InChI=1S/C30H44O5/c1-16(12-17(31)24-26(4,5)35-24)23-18(32)13-27(6)20-9-8-19-25(2,3)21(33)10-11-29(19)15-30(20,29)22(34)14-28(23,27)7/h9,16,19,21-24,33-34H,8,10-15H2,1-7H3/t16-,19+,21+,22+,23+,24+,27+,28-,29-,30+/m1/s1

> <INCHI_KEY>
IGPRVRMPUFGMJK-LLGPNKIBSA-N

> <FORMULA>
C30H44O5

> <MOLECULAR_WEIGHT>
484.677

> <EXACT_MASS>
484.318874517

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
79

> <JCHEM_AVERAGE_POLARIZABILITY>
55.87110081610615

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1S,3R,6S,8R,12R,15R,16R,18S)-15-[(2R)-4-[(2R)-3,3-dimethyloxiran-2-yl]-4-oxobutan-2-yl]-6,18-dihydroxy-7,7,12,16-tetramethylpentacyclo[9.7.0.0^{1,3}.0^{3,8}.0^{12,16}]octadec-10-en-14-one

> <ALOGPS_LOGP>
4.28

> <JCHEM_LOGP>
3.345720930333335

> <ALOGPS_LOGS>
-4.88

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
19.554153298064794

> <JCHEM_PKA_STRONGEST_ACIDIC>
18.51865396582177

> <JCHEM_PKA_STRONGEST_BASIC>
-0.1956001824980128

> <JCHEM_POLAR_SURFACE_AREA>
87.13

> <JCHEM_REFRACTIVITY>
134.3676

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.40e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1S,3R,6S,8R,12R,15R,16R,18S)-15-[(2R)-4-[(2R)-3,3-dimethyloxiran-2-yl]-4-oxobutan-2-yl]-6,18-dihydroxy-7,7,12,16-tetramethylpentacyclo[9.7.0.0^{1,3}.0^{3,8}.0^{12,16}]octadec-10-en-14-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 28-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   28-APR-22         0                                  
HETATM    1  C   UNK     0      -0.993  -0.363   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -1.516  -1.811   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.523  -2.988   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.993  -2.717   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.516  -1.269   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.523  -0.092   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       3.032  -0.998   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.025  -2.175   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       3.501  -3.624   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.985  -3.895   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       5.541  -1.904   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       6.064  -0.456   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       5.071   0.722   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       3.555   0.451   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       2.562   1.628   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0       7.603  -0.506   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       8.031  -1.985   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       9.479  -2.508   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       6.756  -2.849   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       8.548   0.710   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       7.968   2.137   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      10.074   0.499   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      11.019   1.715   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0      10.439   3.142   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0      12.544   1.505   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      13.971   2.085   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0      13.760   0.559   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0      14.048   3.623   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      15.443   2.539   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       6.736   0.930   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       5.172  -3.399   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       2.039   0.179   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      -1.665  -4.022   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      -0.305  -4.513   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0      -3.032  -2.082   0.000  0.00  0.00           O+0
CONECT    1    2    6                                                       
CONECT    2    1    3   35                                                  
CONECT    3    2    4   33   34                                             
CONECT    4    3    5   10                                                  
CONECT    5    4    6    7   32                                             
CONECT    6    5    1                                                       
CONECT    7    5    8   14   32                                             
CONECT    8    7    9   11                                                  
CONECT    9    8   10                                                       
CONECT   10    9    4                                                       
CONECT   11    8   12   19   31                                             
CONECT   12   11   13   16   30                                             
CONECT   13   12   14                                                       
CONECT   14   13    7   15                                                  
CONECT   15   14                                                            
CONECT   16   12   17   20                                                  
CONECT   17   16   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17   11                                                       
CONECT   20   16   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20   23                                                       
CONECT   23   22   24   25                                                  
CONECT   24   23                                                            
CONECT   25   23   26   27                                                  
CONECT   26   25   27   28   29                                             
CONECT   27   26   25                                                       
CONECT   28   26                                                            
CONECT   29   26                                                            
CONECT   30   12                                                            
CONECT   31   11                                                            
CONECT   32    7    5                                                       
CONECT   33    3                                                            
CONECT   34    3                                                            
CONECT   35    2                                                            
MASTER        0    0    0    0    0    0    0    0   35    0   80    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₃₀H₄₄O₅

Average Mass

484.6770 Da

Monoisotopic Mass

484.31887 Da

IUPAC Name

(1S,3R,6S,8R,12R,15R,16R,18S)-15-[(2R)-4-[(2R)-3,3-dimethyloxiran-2-yl]-4-oxobutan-2-yl]-6,18-dihydroxy-7,7,12,16-tetramethylpentacyclo[9.7.0.0^{1,3}.0^{3,8}.0^{12,16}]octadec-10-en-14-one

Traditional Name

(1S,3R,6S,8R,12R,15R,16R,18S)-15-[(2R)-4-[(2R)-3,3-dimethyloxiran-2-yl]-4-oxobutan-2-yl]-6,18-dihydroxy-7,7,12,16-tetramethylpentacyclo[9.7.0.0^{1,3}.0^{3,8}.0^{12,16}]octadec-10-en-14-one

CAS Registry Number

Not Available

SMILES

C[C@H](CC(=O)[C@@H]1OC1(C)C)[C@H]1C(=O)C[C@@]2(C)C3=CC[C@@H]4[C@]5(C[C@@]35[C@@H](O)C[C@]12C)CC[C@H](O)C4(C)C

InChI Identifier

InChI=1S/C30H44O5/c1-16(12-17(31)24-26(4,5)35-24)23-18(32)13-27(6)20-9-8-19-25(2,3)21(33)10-11-29(19)15-30(20,29)22(34)14-28(23,27)7/h9,16,19,21-24,33-34H,8,10-15H2,1-7H3/t16-,19+,21+,22+,23+,24+,27+,28-,29-,30+/m1/s1

InChI Key

IGPRVRMPUFGMJK-LLGPNKIBSA-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
Actaea cimicifuga	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as cycloartanols and derivatives. These are steroids containing a cycloartanol moiety.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Steroids and steroid derivatives

Sub Class

Cycloartanols and derivatives

Direct Parent

Cycloartanols and derivatives

Alternative Parents

Substituents

Cycloartanol-skeleton
9b,19-cyclo-lanostane-skeleton
Cycloartane-skeleton
Triterpenoid
23-oxosteroid
3-hydroxysteroid
Hydroxysteroid
16-oxosteroid
Oxosteroid
11-beta-hydroxysteroid
11-hydroxysteroid
3-beta-hydroxysteroid
Cyclic alcohol
Ketone
Secondary alcohol
Cyclic ketone
Oxacycle
Ether
Oxirane
Dialkyl ether
Organoheterocyclic compound
Organooxygen compound
Alcohol
Hydrocarbon derivative
Carbonyl group
Organic oxygen compound
Organic oxide
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	4.28	ALOGPS
logP	3.35	ChemAxon
logS	-4.9	ALOGPS
pKa (Strongest Acidic)	18.52	ChemAxon
pKa (Strongest Basic)	-0.2	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	87.13 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	134.37 m³·mol⁻¹	ChemAxon
Polarizability	55.87 Å³	ChemAxon
Number of Rings	6	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

C00024072

Chemspider ID

8588498

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

10413064

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for (-)-Cimicidanol (NP0066506)

MOL for NP0066506 ((-)-Cimicidanol)

3D MOL for NP0066506 ((-)-Cimicidanol)

3D SDF for NP0066506 ((-)-Cimicidanol)

3D-SDF for NP0066506 ((-)-Cimicidanol)

PDB for NP0066506 ((-)-Cimicidanol)

3D PDB for NP0066506 ((-)-Cimicidanol)

SMILES for NP0066506 ((-)-Cimicidanol)

INCHI for NP0066506 ((-)-Cimicidanol)

Structure for NP0066506 ((-)-Cimicidanol)

3D Structure for NP0066506 ((-)-Cimicidanol)