NP-MRD: Showing NP-Card for (1S,2R,5R,9R)-5-((tert¬-Butyldimethylsilyl)oxy)-2-(hydroxymethyl)-10,10-dimethyl-6-methylenebicyclo[7.2.0]undecane-2-ol (NP0331822)

Jump To Section:

Identification Spectra BioTaxonomy ChemoTaxonomy Physical properties Links References XML

Record Information

Version

2.0

Created at

2023-09-13 16:02:47 UTC

Updated at

2024-09-03 04:17:04 UTC

NP-MRD ID

NP0331822

Natural Product DOI

https://doi.org/10.57994/0910

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(1S,2R,5R,9R)-5-((tert¬-Butyldimethylsilyl)oxy)-2-(hydroxymethyl)-10,10-dimethyl-6-methylenebicyclo[7.2.0]undecane-2-ol

Description

Not Available

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 09132316022D          

 27 28  0  0  1  0            999 V2000
   -0.3726   -1.5223    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4524   -1.5223    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4524   -2.3473    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4524   -0.6973    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2774   -0.6973    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.0526   -0.9795    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8077   -0.0654    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.0502    0.2614    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9035    0.7541    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6610    1.0808    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6202    0.0779    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3346   -0.3346    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6168   -1.1098    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.4418   -1.1098    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.8543   -0.3954    0.0000 Si  0  0  0  0  0  0  0  0  0  0  0  0
    5.5688   -0.8079    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1398    0.0171    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2668    0.3191    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6793    1.0336    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9813   -0.0934    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5523    0.7316    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3346   -1.8851    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6202   -2.2976    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8077   -2.1543    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2774   -1.5223    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.9287   -2.2701    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9666   -2.4154    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
  2  4  1  0  0  0  0
  5  4  1  0  0  0  0
  5  6  1  1  0  0  0
  5  7  1  0  0  0  0
  7  8  1  6  0  0  0
  7  9  1  1  0  0  0
  9 10  1  0  0  0  0
  7 11  1  0  0  0  0
 11 12  1  0  0  0  0
 13 12  1  0  0  0  0
 13 14  1  1  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 15 17  1  0  0  0  0
 15 18  1  0  0  0  0
 18 19  1  0  0  0  0
 18 20  1  0  0  0  0
 18 21  1  0  0  0  0
 13 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  1  0  0  0  0
 25 24  1  0  0  0  0
 25  2  1  0  0  0  0
  5 25  1  0  0  0  0
 25 26  1  6  0  0  0
 22 27  2  0  0  0  0
M  END


  Mrv2104 09132316022D          

 27 28  0  0  1  0            999 V2000
   -0.3726   -1.5223    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4524   -1.5223    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4524   -2.3473    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4524   -0.6973    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2774   -0.6973    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.0526   -0.9795    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8077   -0.0654    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.0502    0.2614    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9035    0.7541    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6610    1.0808    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6202    0.0779    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3346   -0.3346    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6168   -1.1098    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.4418   -1.1098    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.8543   -0.3954    0.0000 Si  0  0  0  0  0  0  0  0  0  0  0  0
    5.5688   -0.8079    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1398    0.0171    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2668    0.3191    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6793    1.0336    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9813   -0.0934    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5523    0.7316    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3346   -1.8851    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6202   -2.2976    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8077   -2.1543    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2774   -1.5223    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.9287   -2.2701    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9666   -2.4154    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
  2  4  1  0  0  0  0
  5  4  1  0  0  0  0
  5  6  1  1  0  0  0
  5  7  1  0  0  0  0
  7  8  1  6  0  0  0
  7  9  1  1  0  0  0
  9 10  1  0  0  0  0
  7 11  1  0  0  0  0
 11 12  1  0  0  0  0
 13 12  1  0  0  0  0
 13 14  1  1  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 15 17  1  0  0  0  0
 15 18  1  0  0  0  0
 18 19  1  0  0  0  0
 18 20  1  0  0  0  0
 18 21  1  0  0  0  0
 13 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  1  0  0  0  0
 25 24  1  0  0  0  0
 25  2  1  0  0  0  0
  5 25  1  0  0  0  0
 25 26  1  6  0  0  0
 22 27  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0331822

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H][C@]12CC(C)(C)[C@]1([H])CCC(=C)[C@@H](CC[C@]2(O)CO)O[Si](C)(C)C(C)(C)C

> <INCHI_IDENTIFIER>
InChI=1S/C21H40O3Si/c1-15-9-10-16-17(13-20(16,5)6)21(23,14-22)12-11-18(15)24-25(7,8)19(2,3)4/h16-18,22-23H,1,9-14H2,2-8H3/t16-,17+,18-,21+/m1/s1

> <INCHI_KEY>
VXOBYTXBOMOBRC-IIMDRIAPSA-N

> <FORMULA>
C21H40O3Si

> <MOLECULAR_WEIGHT>
368.633

> <EXACT_MASS>
368.274671683

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
65

> <JCHEM_AVERAGE_POLARIZABILITY>
43.00465954954678

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1S,2R,5R,9R)-5-[(tert-butyldimethylsilyl)oxy]-2-(hydroxymethyl)-10,10-dimethyl-6-methylidenebicyclo[7.2.0]undecan-2-ol

> <JCHEM_LOGP>
3.7826999999999975

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
15.310363195966346

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.688477703469305

> <JCHEM_PKA_STRONGEST_BASIC>
-3.075606983343322

> <JCHEM_POLAR_SURFACE_AREA>
49.69

> <JCHEM_REFRACTIVITY>
101.19179999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(1S,2R,5R,9R)-5-[(tert-butyldimethylsilyl)oxy]-2-(hydroxymethyl)-10,10-dimethyl-6-methylidenebicyclo[7.2.0]undecan-2-ol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 13-SEP-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   13-SEP-23         0                                  
HETATM    1  C   UNK     0      -0.696  -2.842   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.844  -2.842   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.844  -4.382   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.844  -1.302   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.384  -1.302   0.000  0.00  0.00           C+0
HETATM    6  H   UNK     0       3.832  -1.828   0.000  0.00  0.00           H+0
HETATM    7  C   UNK     0       3.374  -0.122   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       1.960   0.488   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       3.553   1.408   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       4.967   2.018   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       4.891   0.145   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       6.225  -0.625   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       6.751  -2.072   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       8.291  -2.072   0.000  0.00  0.00           O+0
HETATM   15 Si   UNK     0       9.061  -0.738   0.000  0.00  0.00          Si+0
HETATM   16  C   UNK     0      10.395  -1.508   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       7.728   0.032   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       9.831   0.596   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      10.601   1.929   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      11.165  -0.174   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       8.498   1.366   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       6.225  -3.519   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       4.891  -4.289   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       3.374  -4.021   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       2.384  -2.842   0.000  0.00  0.00           C+0
HETATM   26  H   UNK     0       1.734  -4.237   0.000  0.00  0.00           H+0
HETATM   27  C   UNK     0       7.404  -4.509   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    4   25                                             
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6    7   25                                             
CONECT    6    5                                                            
CONECT    7    5    8    9   11                                             
CONECT    8    7                                                            
CONECT    9    7   10                                                       
CONECT   10    9                                                            
CONECT   11    7   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14   22                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16   17   18                                             
CONECT   16   15                                                            
CONECT   17   15                                                            
CONECT   18   15   19   20   21                                             
CONECT   19   18                                                            
CONECT   20   18                                                            
CONECT   21   18                                                            
CONECT   22   13   23   27                                                  
CONECT   23   22   24                                                       
CONECT   24   23   25                                                       
CONECT   25   24    2    5   26                                             
CONECT   26   25                                                            
CONECT   27   22                                                            
MASTER        0    0    0    0    0    0    0    0   27    0   56    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₁H₄₀O₃Si

Average Mass

368.6330 Da

Monoisotopic Mass

368.27467 Da

IUPAC Name

(1S,2R,5R,9R)-5-[(tert-butyldimethylsilyl)oxy]-2-(hydroxymethyl)-10,10-dimethyl-6-methylidenebicyclo[7.2.0]undecan-2-ol

Traditional Name

(1S,2R,5R,9R)-5-[(tert-butyldimethylsilyl)oxy]-2-(hydroxymethyl)-10,10-dimethyl-6-methylidenebicyclo[7.2.0]undecan-2-ol

CAS Registry Number

Not Available

SMILES

[H][C@]12CC(C)(C)[C@]1([H])CCC(=C)[C@@H](CC[C@]2(O)CO)O[Si](C)(C)C(C)(C)C

InChI Identifier

InChI=1S/C21H40O3Si/c1-15-9-10-16-17(13-20(16,5)6)21(23,14-22)12-11-18(15)24-25(7,8)19(2,3)4/h16-18,22-23H,1,9-14H2,2-8H3/t16-,17+,18-,21+/m1/s1

InChI Key

VXOBYTXBOMOBRC-IIMDRIAPSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹H NMR Spectrum (1D, 400 MHz, CDCl3, experimental)	Not Available	Latvian Institute of Organic Synthesis	Georgijs Stakanovs	2023-09-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, CDCl3, experimental)	Not Available	Latvian Institute of Organic Synthesis	Georgijs Stakanovs	2023-09-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, CDCl3, experimental)	Not Available	Not Available	Georgijs Stakanovs	2023-09-13	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, CDCl3, experimental)	Not Available	Not Available	Georgijs Stakanovs	2023-09-13	View Spectrum

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View

Chemical Shift Submissions

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 100.578570142, CDCl₃, simulated)	st_george@inbox.lv	Latvian Institute of Organic Synthesis	Georgijs Stakanovs	2024-05-14	View Spectrum

Species

Species of Origin

Not Available

Chemical Taxonomy

Classification

Not classified

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	3.78	ChemAxon
pKa (Strongest Acidic)	13.69	ChemAxon
pKa (Strongest Basic)	-3.1	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	49.69 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	101.19 m³·mol⁻¹	ChemAxon
Polarizability	43 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

Not Available

References

General References

Not Available

Showing NP-Card for (1S,2R,5R,9R)-5-((tert¬-Butyldimethylsilyl)oxy)-2-(hydroxymethyl)-10,10-dimethyl-6-methylenebicyclo[7.2.0]undecane-2-ol (NP0331822)

MOL for NP0331822 ((1S,2R,5R,9R)-5-((tert¬-Butyldimethylsilyl)oxy)-2-(hydroxymethyl)-10,10-dimethyl-6-methylenebicyclo[7.2.0]undecane-2-ol)

3D MOL for NP0331822 ((1S,2R,5R,9R)-5-((tert¬-Butyldimethylsilyl)oxy)-2-(hydroxymethyl)-10,10-dimethyl-6-methylenebicyclo[7.2.0]undecane-2-ol)

3D SDF for NP0331822 ((1S,2R,5R,9R)-5-((tert¬-Butyldimethylsilyl)oxy)-2-(hydroxymethyl)-10,10-dimethyl-6-methylenebicyclo[7.2.0]undecane-2-ol)

3D-SDF for NP0331822 ((1S,2R,5R,9R)-5-((tert¬-Butyldimethylsilyl)oxy)-2-(hydroxymethyl)-10,10-dimethyl-6-methylenebicyclo[7.2.0]undecane-2-ol)

PDB for NP0331822 ((1S,2R,5R,9R)-5-((tert¬-Butyldimethylsilyl)oxy)-2-(hydroxymethyl)-10,10-dimethyl-6-methylenebicyclo[7.2.0]undecane-2-ol)

3D PDB for NP0331822 ((1S,2R,5R,9R)-5-((tert¬-Butyldimethylsilyl)oxy)-2-(hydroxymethyl)-10,10-dimethyl-6-methylenebicyclo[7.2.0]undecane-2-ol)

SMILES for NP0331822 ((1S,2R,5R,9R)-5-((tert¬-Butyldimethylsilyl)oxy)-2-(hydroxymethyl)-10,10-dimethyl-6-methylenebicyclo[7.2.0]undecane-2-ol)

INCHI for NP0331822 ((1S,2R,5R,9R)-5-((tert¬-Butyldimethylsilyl)oxy)-2-(hydroxymethyl)-10,10-dimethyl-6-methylenebicyclo[7.2.0]undecane-2-ol)

Structure for NP0331822 ((1S,2R,5R,9R)-5-((tert¬-Butyldimethylsilyl)oxy)-2-(hydroxymethyl)-10,10-dimethyl-6-methylenebicyclo[7.2.0]undecane-2-ol)

3D Structure for NP0331822 ((1S,2R,5R,9R)-5-((tert¬-Butyldimethylsilyl)oxy)-2-(hydroxymethyl)-10,10-dimethyl-6-methylenebicyclo[7.2.0]undecane-2-ol)