NP-MRD: Showing NP-Card for (5r,9s,11s)-5-hydroxy-11-(hydroxymethyl)-11-methyl-4,8-dimethylidenebicyclo[7.2.0]undecan-3-one (NP0329059)

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Record Information

Version

2.0

Created at

2022-09-12 13:05:09 UTC

Updated at

2022-09-12 13:05:09 UTC

NP-MRD ID

NP0329059

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(5r,9s,11s)-5-hydroxy-11-(hydroxymethyl)-11-methyl-4,8-dimethylidenebicyclo[7.2.0]undecan-3-one

Description

(5R,9S,11S)-5-hydroxy-11-(hydroxymethyl)-11-methyl-4,8-dimethylidenebicyclo[7.2.0]Undecan-3-one belongs to the class of organic compounds known as sesquiterpenoids. These are terpenes with three consecutive isoprene units. (5r,9s,11s)-5-hydroxy-11-(hydroxymethyl)-11-methyl-4,8-dimethylidenebicyclo[7.2.0]undecan-3-one is found in Pulicaria arabica. Based on a literature review very few articles have been published on (5R,9S,11S)-5-hydroxy-11-(hydroxymethyl)-11-methyl-4,8-dimethylidenebicyclo[7.2.0]Undecan-3-one.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 40 41  0  0  0  0  0  0  0  0999 V2000
    0.7092   -2.2535    1.1865 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5270   -1.7169    0.0158 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6543   -1.6863   -0.9484 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2505   -0.3296   -1.1309 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7459    0.1765    0.2001 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.1144    0.0386    0.3245 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3626    1.6047    0.3402 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3063    2.5090    0.4685 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9415    1.9674    0.3313 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6496    3.1256   -0.0562 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0676    0.9732    0.7707 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8472    0.3566   -0.3385 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7559   -1.1545   -0.3954 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.9019   -1.1855    0.5821 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3264    0.1602   -0.0517 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.9200    1.0467    0.9913 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2192   -0.0552   -1.2182 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4166   -0.6547   -0.7772 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0833   -2.3056    1.9041 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6725   -2.6600    1.4561 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3620   -2.1628   -1.9133 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4782   -2.3373   -0.5456 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1567   -0.4697   -1.7749 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5893    0.3977   -1.6419 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2925   -0.3790    1.0680 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4988   -0.0552   -0.5940 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0171    3.5536    0.5706 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3374    2.1997    0.4700 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3701    0.2313    1.4787 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8027    1.5538    1.4021 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7181    0.8740   -1.3039 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0782   -1.4688   -1.4363 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5710   -1.0643    1.6231 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6416   -1.9786    0.3975 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6823    0.6979    2.0269 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0260    0.9727    0.9046 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6805    2.1233    0.8458 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5376    0.9380   -1.6251 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8178   -0.6245   -2.0522 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9420   -0.9585   -1.5549 H   0  0  0  0  0  0  0  0  0  0  0  0
 15 16  1  1
 15 17  1  0
 17 18  1  0
 15 14  1  0
 14 13  1  0
 13 12  1  0
 12 11  1  0
 11  9  1  0
  9 10  2  0
  9  7  1  0
  7  8  2  3
  7  5  1  0
  5  6  1  0
  5  4  1  0
  4  3  1  0
  3  2  1  0
  2  1  2  3
 12 15  1  0
  2 13  1  0
 16 35  1  0
 16 36  1  0
 16 37  1  0
 17 38  1  0
 17 39  1  0
 18 40  1  0
 14 33  1  0
 14 34  1  0
 13 32  1  6
 12 31  1  6
 11 29  1  0
 11 30  1  0
  8 27  1  0
  8 28  1  0
  5 25  1  1
  6 26  1  0
  4 23  1  0
  4 24  1  0
  3 21  1  0
  3 22  1  0
  1 19  1  0
  1 20  1  0
M  END


  Mrv1652309122215052D          

 18 19  0  0  1  0            999 V2000
    2.4366    0.8327    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8491    0.1183    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6615    0.2615    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3760   -0.1510    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6582   -0.9262    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.4832   -0.9262    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3760   -1.7015    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0080   -2.2318    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6615   -2.1140    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8048   -2.9264    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8491   -1.9707    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3188   -1.3387    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3188   -0.5137    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.4938   -0.5137    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4938   -1.3387    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.6915   -1.5313    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3012   -2.1409    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8996   -2.7088    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  1  0  0  0
  5  7  1  0  0  0  0
  7  8  2  0  0  0  0
  7  9  1  0  0  0  0
  9 10  2  0  0  0  0
  9 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
  2 13  1  0  0  0  0
 13 14  1  6  0  0  0
 14 15  1  0  0  0  0
 12 15  1  0  0  0  0
 15 16  1  6  0  0  0
 15 17  1  1  0  0  0
 17 18  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0329059

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@]1(CO)C[C@H]2C1CC(=O)C(=C)[C@H](O)CCC2=C

> <INCHI_IDENTIFIER>
InChI=1S/C15H22O3/c1-9-4-5-13(17)10(2)14(18)6-12-11(9)7-15(12,3)8-16/h11-13,16-17H,1-2,4-8H2,3H3/t11-,12?,13-,15-/m1/s1

> <INCHI_KEY>
JOPKITGVIQRWBI-HTYKBFHYSA-N

> <FORMULA>
C15H22O3

> <MOLECULAR_WEIGHT>
250.338

> <EXACT_MASS>
250.156894568

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
40

> <JCHEM_AVERAGE_POLARIZABILITY>
27.669546888151576

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(5R,9S,11S)-5-hydroxy-11-(hydroxymethyl)-11-methyl-4,8-dimethylidenebicyclo[7.2.0]undecan-3-one

> <JCHEM_LOGP>
1.3983774770000004

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
18.231922456362074

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.41604500480777

> <JCHEM_PKA_STRONGEST_BASIC>
-1.385145708053233

> <JCHEM_POLAR_SURFACE_AREA>
57.53

> <JCHEM_REFRACTIVITY>
70.3633

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(5R,9S,11S)-5-hydroxy-11-(hydroxymethyl)-11-methyl-4,8-dimethylidenebicyclo[7.2.0]undecan-3-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 12-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   12-SEP-22         0                                  
HETATM    1  C   UNK     0       4.548   1.554   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       5.318   0.221   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       6.835   0.488   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       8.169  -0.282   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       8.695  -1.729   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      10.235  -1.729   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       8.169  -3.176   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       9.348  -4.166   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       6.835  -3.946   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       7.102  -5.463   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       5.318  -3.679   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       4.328  -2.499   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       4.328  -0.959   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       2.788  -0.959   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       2.788  -2.499   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       1.291  -2.858   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       2.429  -3.996   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       3.546  -5.056   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   13                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12                                                       
CONECT   12   11   13   15                                                  
CONECT   13   12    2   14                                                  
CONECT   14   13   15                                                       
CONECT   15   14   12   16   17                                             
CONECT   16   15                                                            
CONECT   17   15   18                                                       
CONECT   18   17                                                            
MASTER        0    0    0    0    0    0    0    0   18    0   38    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₅H₂₂O₃

Average Mass

250.3380 Da

Monoisotopic Mass

250.15689 Da

IUPAC Name

(5R,9S,11S)-5-hydroxy-11-(hydroxymethyl)-11-methyl-4,8-dimethylidenebicyclo[7.2.0]undecan-3-one

Traditional Name

(5R,9S,11S)-5-hydroxy-11-(hydroxymethyl)-11-methyl-4,8-dimethylidenebicyclo[7.2.0]undecan-3-one

CAS Registry Number

Not Available

SMILES

C[C@]1(CO)C[C@H]2C1CC(=O)C(=C)[C@H](O)CCC2=C

InChI Identifier

InChI=1S/C15H22O3/c1-9-4-5-13(17)10(2)14(18)6-12-11(9)7-15(12,3)8-16/h11-13,16-17H,1-2,4-8H2,3H3/t11-,12?,13-,15-/m1/s1

InChI Key

JOPKITGVIQRWBI-HTYKBFHYSA-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
Pulicaria arabica	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as sesquiterpenoids. These are terpenes with three consecutive isoprene units.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Sesquiterpenoids

Direct Parent

Sesquiterpenoids

Alternative Parents

Substituents

Caryophyllane sesquiterpenoid
Sesquiterpenoid
Cyclic alcohol
Cyclic ketone
Secondary alcohol
Ketone
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Primary alcohol
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	1.4	ChemAxon
pKa (Strongest Acidic)	14.42	ChemAxon
pKa (Strongest Basic)	-1.4	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	57.53 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	70.36 m³·mol⁻¹	ChemAxon
Polarizability	27.67 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

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

162929008

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (5r,9s,11s)-5-hydroxy-11-(hydroxymethyl)-11-methyl-4,8-dimethylidenebicyclo[7.2.0]undecan-3-one (NP0329059)

MOL for NP0329059 ((5r,9s,11s)-5-hydroxy-11-(hydroxymethyl)-11-methyl-4,8-dimethylidenebicyclo[7.2.0]undecan-3-one)

3D MOL for NP0329059 ((5r,9s,11s)-5-hydroxy-11-(hydroxymethyl)-11-methyl-4,8-dimethylidenebicyclo[7.2.0]undecan-3-one)

3D SDF for NP0329059 ((5r,9s,11s)-5-hydroxy-11-(hydroxymethyl)-11-methyl-4,8-dimethylidenebicyclo[7.2.0]undecan-3-one)

3D-SDF for NP0329059 ((5r,9s,11s)-5-hydroxy-11-(hydroxymethyl)-11-methyl-4,8-dimethylidenebicyclo[7.2.0]undecan-3-one)

PDB for NP0329059 ((5r,9s,11s)-5-hydroxy-11-(hydroxymethyl)-11-methyl-4,8-dimethylidenebicyclo[7.2.0]undecan-3-one)

3D PDB for NP0329059 ((5r,9s,11s)-5-hydroxy-11-(hydroxymethyl)-11-methyl-4,8-dimethylidenebicyclo[7.2.0]undecan-3-one)

SMILES for NP0329059 ((5r,9s,11s)-5-hydroxy-11-(hydroxymethyl)-11-methyl-4,8-dimethylidenebicyclo[7.2.0]undecan-3-one)

INCHI for NP0329059 ((5r,9s,11s)-5-hydroxy-11-(hydroxymethyl)-11-methyl-4,8-dimethylidenebicyclo[7.2.0]undecan-3-one)

Structure for NP0329059 ((5r,9s,11s)-5-hydroxy-11-(hydroxymethyl)-11-methyl-4,8-dimethylidenebicyclo[7.2.0]undecan-3-one)

3D Structure for NP0329059 ((5r,9s,11s)-5-hydroxy-11-(hydroxymethyl)-11-methyl-4,8-dimethylidenebicyclo[7.2.0]undecan-3-one)