NP-MRD: Showing NP-Card for (1R,4R,6R,9R,10S)-9-Hydroxymethyl-4,12,12-trimethyl-5-oxatricyclo[8.2.0.04,6]dodecane-9-ol (NP0331809)

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Record Information

Version

2.0

Created at

2023-09-13 16:00:48 UTC

Updated at

2024-09-03 04:17:01 UTC

NP-MRD ID

NP0331809

Natural Product DOI

https://doi.org/10.57994/0896

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(1R,4R,6R,9R,10S)-9-Hydroxymethyl-4,12,12-trimethyl-5-oxatricyclo[8.2.0.04,6]dodecane-9-ol

Description

(1R,4R,6R,9R,10S)-9-Hydroxymethyl-4,12,12-trimethyl-5-oxatricyclo[8.2.0.04,6]Dodecane-9-ol belongs to the class of organic compounds known as sesquiterpenoids. These are terpenes with three consecutive isoprene units. Based on a literature review very few articles have been published on (1R,4R,6R,9R,10S)-9-Hydroxymethyl-4,12,12-trimethyl-5-oxatricyclo[8.2.0.04,6]Dodecane-9-ol.

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 09132316002D          

 20 22  0  0  1  0            999 V2000
    5.8458    0.9912    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0319    1.1259    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8972    0.3120    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1666    1.9399    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3526    2.0746    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.5417    1.9227    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2179    1.2606    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.4398    0.4660    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5916    0.7237    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7666    0.7150    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1291    1.2386    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.7241    0.5198    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9773    2.0495    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.3509    1.5126    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3822    2.7683    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1544    3.0586    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9326    2.7846    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.1284    3.5861    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6807    3.1325    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3560    2.6585    0.0000 O   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  6  0  0  0
  5  7  1  0  0  0  0
  7  2  1  0  0  0  0
  7  8  1  1  0  0  0
  7  9  1  0  0  0  0
  9 10  1  0  0  0  0
 11 10  1  0  0  0  0
 11 12  1  6  0  0  0
 11 13  1  0  0  0  0
 13 14  1  6  0  0  0
 11 14  1  0  0  0  0
 13 15  1  0  0  0  0
 15 16  1  0  0  0  0
 17 16  1  0  0  0  0
  5 17  1  0  0  0  0
 17 18  1  1  0  0  0
 17 19  1  6  0  0  0
 19 20  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0331809

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C15H26O3/c1-13(2)8-11-10(13)4-6-14(3)12(18-14)5-7-15(11,17)9-16/h10-12,16-17H,4-9H2,1-3H3/t10-,11+,12-,14-,15+/m1/s1

> <INCHI_KEY>
OHDVDXBNIVPOOL-OGMFBOKVSA-N

> <FORMULA>
C15H26O3

> <MOLECULAR_WEIGHT>
254.37

> <EXACT_MASS>
254.188194697

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
44

> <JCHEM_AVERAGE_POLARIZABILITY>
29.011839520407257

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1R,4R,6R,9R,10S)-9-(hydroxymethyl)-4,12,12-trimethyl-5-oxatricyclo[8.2.0.0^{4,6}]dodecan-9-ol

> <JCHEM_LOGP>
1.6040565026666667

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
15.31045939507265

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.688803396051544

> <JCHEM_PKA_STRONGEST_BASIC>
-3.075601029783077

> <JCHEM_POLAR_SURFACE_AREA>
52.989999999999995

> <JCHEM_REFRACTIVITY>
69.6612

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(1R,4R,6R,9R,10S)-9-(hydroxymethyl)-4,12,12-trimethyl-5-oxatricyclo[8.2.0.0^{4,6}]dodecan-9-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      10.912   1.850   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       9.393   2.102   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       9.141   0.582   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       9.644   3.621   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       8.125   3.873   0.000  0.00  0.00           C+0
HETATM    6  H   UNK     0       6.611   3.589   0.000  0.00  0.00           H+0
HETATM    7  C   UNK     0       7.873   2.353   0.000  0.00  0.00           C+0
HETATM    8  H   UNK     0       8.288   0.870   0.000  0.00  0.00           H+0
HETATM    9  C   UNK     0       6.704   1.351   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       5.164   1.335   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       3.974   2.312   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       3.218   0.970   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       3.691   3.826   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       2.522   2.824   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       4.447   5.168   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       5.888   5.709   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       7.341   5.198   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       7.706   6.694   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       8.737   5.847   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0       9.998   4.963   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4    7                                             
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6    7   17                                             
CONECT    6    5                                                            
CONECT    7    5    2    8    9                                             
CONECT    8    7                                                            
CONECT    9    7   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12   13   14                                             
CONECT   12   11                                                            
CONECT   13   11   14   15                                                  
CONECT   14   13   11                                                       
CONECT   15   13   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16    5   18   19                                             
CONECT   18   17                                                            
CONECT   19   17   20                                                       
CONECT   20   19                                                            
MASTER        0    0    0    0    0    0    0    0   20    0   44    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₅H₂₆O₃

Average Mass

254.3700 Da

Monoisotopic Mass

254.18819 Da

IUPAC Name

(1R,4R,6R,9R,10S)-9-(hydroxymethyl)-4,12,12-trimethyl-5-oxatricyclo[8.2.0.0^{4,6}]dodecan-9-ol

Traditional Name

(1R,4R,6R,9R,10S)-9-(hydroxymethyl)-4,12,12-trimethyl-5-oxatricyclo[8.2.0.0^{4,6}]dodecan-9-ol

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C15H26O3/c1-13(2)8-11-10(13)4-6-14(3)12(18-14)5-7-15(11,17)9-16/h10-12,16-17H,4-9H2,1-3H3/t10-,11+,12-,14-,15+/m1/s1

InChI Key

OHDVDXBNIVPOOL-OGMFBOKVSA-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	LIOS	Georgijs Stakanovs	2024-05-08	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, CDCl3, experimental)	Not Available	LIOS	Georgijs Stakanovs	2024-05-08	View Spectrum
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
1D NMR	¹³C NMR Spectrum (1D, 101, CDCl₃, simulated)	st_george@inbox.lv	Latvian Institute of Organic Synthesis	Georgijs Stakanovs	2024-05-08	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101, CDCl₃, simulated)	st_george@inbox.lv	Latvian Institute of Organic Synthesis	Georgijs Stakanovs	2024-05-08	View Spectrum

Species

Species of Origin

Not Available

Chemical Taxonomy

Description

This compound 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

Farsesane sesquiterpenoid
Caryophyllane sesquiterpenoid
Sesquiterpenoid
Long chain fatty alcohol
Fatty alcohol
Fatty acyl
Tertiary alcohol
Cyclic alcohol
Oxacycle
Organoheterocyclic compound
Ether
Oxirane
Dialkyl ether
Organic oxygen compound
Hydrocarbon derivative
Organooxygen compound
Alcohol
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	1.6	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	52.99 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	69.66 m³·mol⁻¹	ChemAxon
Polarizability	29.01 Å³	ChemAxon
Number of Rings	3	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

14543509

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for (1R,4R,6R,9R,10S)-9-Hydroxymethyl-4,12,12-trimethyl-5-oxatricyclo[8.2.0.04,6]dodecane-9-ol (NP0331809)

MOL for NP0331809 ((1R,4R,6R,9R,10S)-9-Hydroxymethyl-4,12,12-trimethyl-5-oxatricyclo[8.2.0.04,6]dodecane-9-ol)

3D MOL for NP0331809 ((1R,4R,6R,9R,10S)-9-Hydroxymethyl-4,12,12-trimethyl-5-oxatricyclo[8.2.0.04,6]dodecane-9-ol)

3D SDF for NP0331809 ((1R,4R,6R,9R,10S)-9-Hydroxymethyl-4,12,12-trimethyl-5-oxatricyclo[8.2.0.04,6]dodecane-9-ol)

3D-SDF for NP0331809 ((1R,4R,6R,9R,10S)-9-Hydroxymethyl-4,12,12-trimethyl-5-oxatricyclo[8.2.0.04,6]dodecane-9-ol)

PDB for NP0331809 ((1R,4R,6R,9R,10S)-9-Hydroxymethyl-4,12,12-trimethyl-5-oxatricyclo[8.2.0.04,6]dodecane-9-ol)

3D PDB for NP0331809 ((1R,4R,6R,9R,10S)-9-Hydroxymethyl-4,12,12-trimethyl-5-oxatricyclo[8.2.0.04,6]dodecane-9-ol)

SMILES for NP0331809 ((1R,4R,6R,9R,10S)-9-Hydroxymethyl-4,12,12-trimethyl-5-oxatricyclo[8.2.0.04,6]dodecane-9-ol)

INCHI for NP0331809 ((1R,4R,6R,9R,10S)-9-Hydroxymethyl-4,12,12-trimethyl-5-oxatricyclo[8.2.0.04,6]dodecane-9-ol)

Structure for NP0331809 ((1R,4R,6R,9R,10S)-9-Hydroxymethyl-4,12,12-trimethyl-5-oxatricyclo[8.2.0.04,6]dodecane-9-ol)

3D Structure for NP0331809 ((1R,4R,6R,9R,10S)-9-Hydroxymethyl-4,12,12-trimethyl-5-oxatricyclo[8.2.0.04,6]dodecane-9-ol)