NP-MRD: Showing NP-Card for (9s)-6-(hydroxymethyl)-9-(2-hydroxypropan-2-yl)-2-methylidenecyclodecyl acetate (NP0312148)

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Record Information

Version

2.0

Created at

2022-09-11 08:41:35 UTC

Updated at

2022-09-11 08:41:35 UTC

NP-MRD ID

NP0312148

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(9s)-6-(hydroxymethyl)-9-(2-hydroxypropan-2-yl)-2-methylidenecyclodecyl acetate

Description

(9S)-6-(hydroxymethyl)-9-(2-hydroxypropan-2-yl)-2-methylidenecyclodecyl acetate belongs to the class of organic compounds known as germacrane sesquiterpenoids. These are sesquiterpenoids having the germacrane skeleton, with a structure characterized by a cyclodecane ring substituted with an isopropyl and two methyl groups. (9s)-6-(hydroxymethyl)-9-(2-hydroxypropan-2-yl)-2-methylidenecyclodecyl acetate is found in Trichilia claussenii. Based on a literature review very few articles have been published on (9S)-6-(hydroxymethyl)-9-(2-hydroxypropan-2-yl)-2-methylidenecyclodecyl acetate.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 51 51  0  0  0  0  0  0  0  0999 V2000
   -0.7216   -1.2685   -2.2053 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8089   -1.4202   -0.8921 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0674   -2.5562   -0.2889 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3120   -2.6787   -0.8622 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0451   -1.3297   -0.8512 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2882   -0.9570    0.5634 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.6936   -1.4767    0.9225 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6102   -0.7128    0.2043 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1687    0.4566    0.9265 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5033    1.3892   -0.0001 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0414    1.3636   -0.1470 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.5204    2.7996   -0.1198 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9579    2.7674   -0.5866 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2650    3.6345   -1.1154 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4075    3.3186    1.1504 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7346    0.4816    0.7413 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5941   -0.5319   -0.0294 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.3869   -1.2205    0.9039 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7456   -1.0646    0.9293 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5059   -1.8444    1.9651 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3630   -0.3094    0.1346 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1375   -1.9316   -2.8355 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2273   -0.4715   -2.7481 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1021   -2.5469    0.8163 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6062   -3.5078   -0.5788 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8929   -3.3580   -0.1967 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2725   -3.0867   -1.8790 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5296   -0.5994   -1.4689 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0150   -1.5476   -1.3913 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6275   -1.5658    1.2516 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8022   -2.5435    0.6393 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8566   -1.3608    2.0054 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2591   -1.2789   -0.3076 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7174    0.5639    1.9585 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2147    0.8672    1.0899 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0297    1.3132   -0.9994 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8001    2.4333    0.3327 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1920    1.0459   -1.2096 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6526    2.3182    0.1332 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0098    2.2869   -1.5817 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2923    3.8231   -0.7300 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4115    4.4387   -1.4771 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1010    4.1485   -0.5951 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6314    2.9874   -1.9484 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2462    3.7243    1.4972 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1821   -0.0306    1.5410 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5014    1.1061    1.2957 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2667    0.0926   -0.6615 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5747   -1.9400    1.7040 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0122   -2.8447    2.0422 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4491   -1.3755    2.9584 H   0  0  0  0  0  0  0  0  0  0  0  0
 20 19  1  0
 19 21  2  0
 19 18  1  0
 18 17  1  0
 17 16  1  0
 16 11  1  0
 11 10  1  0
 10  9  1  0
  9  6  1  0
  6  7  1  0
  7  8  1  0
  6  5  1  0
  5  4  1  0
  4  3  1  0
  3  2  1  0
  2  1  2  3
 11 12  1  0
 12 13  1  0
 12 14  1  0
 12 15  1  0
  2 17  1  0
 20 49  1  0
 20 50  1  0
 20 51  1  0
 17 48  1  6
 16 46  1  0
 16 47  1  0
 11 38  1  6
 10 36  1  0
 10 37  1  0
  9 34  1  0
  9 35  1  0
  6 30  1  1
  7 31  1  0
  7 32  1  0
  8 33  1  0
  5 28  1  0
  5 29  1  0
  4 26  1  0
  4 27  1  0
  3 24  1  0
  3 25  1  0
  1 22  1  0
  1 23  1  0
 13 39  1  0
 13 40  1  0
 13 41  1  0
 14 42  1  0
 14 43  1  0
 14 44  1  0
 15 45  1  0
M  END


  Mrv1652309112210412D          

 21 21  0  0  1  0            999 V2000
    0.8889    2.1275    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    1.5039    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2391    1.6598    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7792    1.0361    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5091    0.2566    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6990    0.1007    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2391   -0.5230    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0492   -0.3671    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.6789    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6188   -0.8348    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0787   -0.2111    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7314   -0.3671    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8873    0.4431    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5755   -1.1772    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5415   -0.5230    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3488    0.5684    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1589    0.7243    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6188    1.3480    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1913    1.1921    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4614    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7314    1.8157    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  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
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  6  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  6  0  0  0
 12 13  1  0  0  0  0
 12 14  1  0  0  0  0
 12 15  1  0  0  0  0
 11 16  1  0  0  0  0
 16 17  1  0  0  0  0
  2 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 19 21  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0312148

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(=O)OC1C[C@H](CCC(CO)CCCC1=C)C(C)(C)O

> <INCHI_IDENTIFIER>
InChI=1S/C17H30O4/c1-12-6-5-7-14(11-18)8-9-15(17(3,4)20)10-16(12)21-13(2)19/h14-16,18,20H,1,5-11H2,2-4H3/t14?,15-,16?/m0/s1

> <INCHI_KEY>
UDIIUGFJZWJUKQ-PCKAHOCUSA-N

> <FORMULA>
C17H30O4

> <MOLECULAR_WEIGHT>
298.423

> <EXACT_MASS>
298.214409446

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
51

> <JCHEM_AVERAGE_POLARIZABILITY>
34.11670342125889

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(9S)-6-(hydroxymethyl)-9-(2-hydroxypropan-2-yl)-2-methylidenecyclodecyl acetate

> <JCHEM_LOGP>
2.1491143909999995

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
17.68154633227874

> <JCHEM_PKA_STRONGEST_ACIDIC>
15.063805778907241

> <JCHEM_PKA_STRONGEST_BASIC>
-1.6258898567195539

> <JCHEM_POLAR_SURFACE_AREA>
66.75999999999999

> <JCHEM_REFRACTIVITY>
82.8607

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(9S)-6-(hydroxymethyl)-9-(2-hydroxypropan-2-yl)-2-methylidenecyclodecyl acetate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 11-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-SEP-22         0                                  
HETATM    1  C   UNK     0       1.659   3.971   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.667   2.807   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.180   3.098   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.188   1.934   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.684   0.479   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       3.171   0.188   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       4.180  -0.976   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       5.692  -0.685   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       2.667  -1.267   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.155  -1.558   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       0.147  -0.394   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -1.365  -0.685   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -1.656   0.827   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -1.074  -2.197   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      -2.878  -0.976   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0       0.651   1.061   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       2.163   1.352   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       1.155   2.516   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0      -0.357   2.225   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -0.861   0.770   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0      -1.365   3.389   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   17                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7    9                                                  
CONECT    7    6    8                                                       
CONECT    8    7                                                            
CONECT    9    6   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12   16                                                  
CONECT   12   11   13   14   15                                             
CONECT   13   12                                                            
CONECT   14   12                                                            
CONECT   15   12                                                            
CONECT   16   11   17                                                       
CONECT   17   16    2   18                                                  
CONECT   18   17   19                                                       
CONECT   19   18   20   21                                                  
CONECT   20   19                                                            
CONECT   21   19                                                            
MASTER        0    0    0    0    0    0    0    0   21    0   42    0
END

View in JSmol

Synonyms

Value	Source
(9S)-6-(Hydroxymethyl)-9-(2-hydroxypropan-2-yl)-2-methylidenecyclodecyl acetic acid	Generator

Chemical Formula

C₁₇H₃₀O₄

Average Mass

298.4230 Da

Monoisotopic Mass

298.21441 Da

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

Not Available

SMILES

CC(=O)OC1C[C@H](CCC(CO)CCCC1=C)C(C)(C)O

InChI Identifier

InChI=1S/C17H30O4/c1-12-6-5-7-14(11-18)8-9-15(17(3,4)20)10-16(12)21-13(2)19/h14-16,18,20H,1,5-11H2,2-4H3/t14?,15-,16?/m0/s1

InChI Key

UDIIUGFJZWJUKQ-PCKAHOCUSA-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
Trichilia claussenii	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as germacrane sesquiterpenoids. These are sesquiterpenoids having the germacrane skeleton, with a structure characterized by a cyclodecane ring substituted with an isopropyl and two methyl groups.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Sesquiterpenoids

Direct Parent

Germacrane sesquiterpenoids

Alternative Parents

Substituents

Germacrane sesquiterpenoid
Tertiary alcohol
Carboxylic acid ester
Monocarboxylic acid or derivatives
Carboxylic acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Primary alcohol
Organooxygen compound
Carbonyl group
Alcohol
Aliphatic homomonocyclic compound

Molecular Framework

Aliphatic homomonocyclic 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

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

162820496

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (9s)-6-(hydroxymethyl)-9-(2-hydroxypropan-2-yl)-2-methylidenecyclodecyl acetate (NP0312148)

MOL for NP0312148 ((9s)-6-(hydroxymethyl)-9-(2-hydroxypropan-2-yl)-2-methylidenecyclodecyl acetate)

3D MOL for NP0312148 ((9s)-6-(hydroxymethyl)-9-(2-hydroxypropan-2-yl)-2-methylidenecyclodecyl acetate)

3D SDF for NP0312148 ((9s)-6-(hydroxymethyl)-9-(2-hydroxypropan-2-yl)-2-methylidenecyclodecyl acetate)

3D-SDF for NP0312148 ((9s)-6-(hydroxymethyl)-9-(2-hydroxypropan-2-yl)-2-methylidenecyclodecyl acetate)

PDB for NP0312148 ((9s)-6-(hydroxymethyl)-9-(2-hydroxypropan-2-yl)-2-methylidenecyclodecyl acetate)

3D PDB for NP0312148 ((9s)-6-(hydroxymethyl)-9-(2-hydroxypropan-2-yl)-2-methylidenecyclodecyl acetate)

SMILES for NP0312148 ((9s)-6-(hydroxymethyl)-9-(2-hydroxypropan-2-yl)-2-methylidenecyclodecyl acetate)

INCHI for NP0312148 ((9s)-6-(hydroxymethyl)-9-(2-hydroxypropan-2-yl)-2-methylidenecyclodecyl acetate)

Structure for NP0312148 ((9s)-6-(hydroxymethyl)-9-(2-hydroxypropan-2-yl)-2-methylidenecyclodecyl acetate)

3D Structure for NP0312148 ((9s)-6-(hydroxymethyl)-9-(2-hydroxypropan-2-yl)-2-methylidenecyclodecyl acetate)