NP-MRD: Showing NP-Card for 2-[(1s,3z,7z)-4,8-dimethylcyclodeca-3,7-dien-1-yl]propan-2-ol (NP0221291)

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Record Information

Version

2.0

Created at

2022-09-05 22:49:55 UTC

Updated at

2022-09-05 22:49:55 UTC

NP-MRD ID

NP0221291

Secondary Accession Numbers

None

Natural Product Identification

Common Name

2-[(1s,3z,7z)-4,8-dimethylcyclodeca-3,7-dien-1-yl]propan-2-ol

Description

Hedycaryol 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. 2-[(1s,3z,7z)-4,8-dimethylcyclodeca-3,7-dien-1-yl]propan-2-ol is found in Chamaecyparis obtusa, Cryptomeria japonica, Microbiota decussata and Thymus praecox. 2-[(1s,3z,7z)-4,8-dimethylcyclodeca-3,7-dien-1-yl]propan-2-ol was first documented in 2021 (PMID: 33867898). Based on a literature review a small amount of articles have been published on Hedycaryol (PMID: 35239190) (PMID: 34985289) (PMID: 34540881) (PMID: 33496585).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 42 42  0  0  0  0  0  0  0  0999 V2000
    2.0384    3.3415    0.5354 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3204    2.2427   -0.2004 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0258    2.1336   -0.0818 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8129    1.1359   -0.7214 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2467    0.0606    0.2401 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.7281   -0.0683    0.3737 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1339   -1.1564    1.3459 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4429   -0.3374   -0.9204 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2644    1.1178    0.8816 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5521   -1.2117   -0.1443 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7958   -1.2940    0.5872 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8556   -1.8083   -0.2859 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7914   -3.2173   -0.7527 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8571   -1.0235   -0.6525 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9802    0.3917   -0.2217 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0777    1.3133   -1.0371 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3648    3.8726    1.2269 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3240    4.0944   -0.2497 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9343    2.9921    1.0467 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4769    2.8728    0.5707 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7700    1.6681   -1.0160 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4695    0.6989   -1.6626 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8568    0.3360    1.2525 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1170   -2.1605    0.9061 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1998   -0.9192    1.6362 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5652   -1.0931    2.3082 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6568    0.6087   -1.4909 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4468   -0.7400   -0.6605 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9535   -1.0958   -1.5457 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0842    1.2427    1.8422 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3452   -1.2020   -1.2292 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1475   -2.1178    0.0584 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6621   -2.0418    1.4249 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9867   -0.3408    1.0715 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7575   -3.6006   -0.7311 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4478   -3.8515   -0.1262 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2181   -3.2463   -1.7862 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6198   -1.4810   -1.3128 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0716    0.6655   -0.3460 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8130    0.5262    0.8781 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5418    0.7313   -1.7672 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7865    1.9611   -1.6435 H   0  0  0  0  0  0  0  0  0  0  0  0
 13 12  1  0
 12 14  2  0
 14 15  1  0
 15 16  1  0
 16  2  1  0
  2  1  1  0
  2  3  2  0
  3  4  1  0
  4  5  1  0
  5 10  1  0
 10 11  1  0
  5  6  1  0
  6  7  1  0
  6  8  1  0
  6  9  1  0
 11 12  1  0
 13 35  1  0
 13 36  1  0
 13 37  1  0
 14 38  1  0
 15 39  1  0
 15 40  1  0
 16 41  1  0
 16 42  1  0
  1 17  1  0
  1 18  1  0
  1 19  1  0
  3 20  1  0
  4 21  1  0
  4 22  1  0
  5 23  1  1
 10 31  1  0
 10 32  1  0
 11 33  1  0
 11 34  1  0
  7 24  1  0
  7 25  1  0
  7 26  1  0
  8 27  1  0
  8 28  1  0
  8 29  1  0
  9 30  1  0
M  END


  Mrv1652309062200492D          

 16 16  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  1  0  0  0  0  0  0  0  0  0
    3.0492   -0.3671    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5893   -0.9907    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6729    0.1730    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4256   -0.9071    0.0000 O   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
    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
    0.3488   -1.6143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0787   -0.2111    0.0000 C   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
  1  2  1  0  0  0  0
  2  3  2  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
  6  7  1  0  0  0  0
  6  8  1  0  0  0  0
  6  9  1  0  0  0  0
  5 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 12 14  2  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
  2 16  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0221291

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C\C1=C\CC\C(C)=C/C[C@H](CC1)C(C)(C)O

> <INCHI_IDENTIFIER>
InChI=1S/C15H26O/c1-12-6-5-7-13(2)9-11-14(10-8-12)15(3,4)16/h6,9,14,16H,5,7-8,10-11H2,1-4H3/b12-6-,13-9-/t14-/m0/s1

> <INCHI_KEY>
SDMLCXJKAYFHQM-LIJSYYTGSA-N

> <FORMULA>
C15H26O

> <MOLECULAR_WEIGHT>
222.372

> <EXACT_MASS>
222.198365457

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
42

> <JCHEM_AVERAGE_POLARIZABILITY>
27.687662791327774

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
2-[(1S,3Z,7Z)-4,8-dimethylcyclodeca-3,7-dien-1-yl]propan-2-ol

> <JCHEM_LOGP>
3.8340117826666673

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
19.471274743086116

> <JCHEM_PKA_STRONGEST_BASIC>
-0.8430644273741325

> <JCHEM_POLAR_SURFACE_AREA>
20.23

> <JCHEM_REFRACTIVITY>
72.2645

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
2-[(1S,3Z,7Z)-4,8-dimethylcyclodeca-3,7-dien-1-yl]propan-2-ol

> <JCHEM_VEBER_RULE>
1

$$$$

HEADER    PROTEIN                                 06-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-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       5.692  -0.685   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       6.700  -1.849   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       6.856   0.323   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       4.528  -1.693   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       3.171   0.188   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       2.667  -1.267   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       1.155  -1.558   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       0.651  -3.013   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       0.147  -0.394   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       0.651   1.061   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       2.163   1.352   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   16                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6   10                                                  
CONECT    6    5    7    8    9                                             
CONECT    7    6                                                            
CONECT    8    6                                                            
CONECT    9    6                                                            
CONECT   10    5   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15    2                                                       
MASTER        0    0    0    0    0    0    0    0   16    0   32    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₅H₂₆O

Average Mass

222.3720 Da

Monoisotopic Mass

222.19837 Da

IUPAC Name

2-[(1S,3Z,7Z)-4,8-dimethylcyclodeca-3,7-dien-1-yl]propan-2-ol

Traditional Name

2-[(1S,3Z,7Z)-4,8-dimethylcyclodeca-3,7-dien-1-yl]propan-2-ol

CAS Registry Number

Not Available

SMILES

C\C1=C\CC\C(C)=C/C[C@H](CC1)C(C)(C)O

InChI Identifier

InChI=1S/C15H26O/c1-12-6-5-7-13(2)9-11-14(10-8-12)15(3,4)16/h6,9,14,16H,5,7-8,10-11H2,1-4H3/b12-6-,13-9-/t14-/m0/s1

InChI Key

SDMLCXJKAYFHQM-LIJSYYTGSA-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
Chamaecyparis obtusa	LOTUS Database	35616633
Cryptomeria japonica	LOTUS Database	35616633
Microbiota decussata	LOTUS Database	35616633
Thymus praecox	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
Organic oxygen compound
Hydrocarbon derivative
Organooxygen compound
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
logP	3.83	ChemAxon
pKa (Strongest Acidic)	19.47	ChemAxon
pKa (Strongest Basic)	-0.84	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	1	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	20.23 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	72.26 m³·mol⁻¹	ChemAxon
Polarizability	27.69 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	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

C00011710

Chemspider ID

4937499

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

6432240

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Amparo TR, Seibert JB, Silveira BM, Costa FSF, Almeida TC, Braga SFP, da Silva GN, Dos Santos ODH, de Souza GHB: Brazilian essential oils as source for the discovery of new anti-COVID-19 drug: a review guided by in silico study. Phytochem Rev. 2021;20(5):1013-1032. doi: 10.1007/s11101-021-09754-4. Epub 2021 Apr 13. [PubMed:33867898 ]
Xu H, Dickschat JS: Hedycaryol - Central Intermediates in Sesquiterpene Biosynthesis, Part II. Chemistry. 2022 May 6;28(26):e202200405. doi: 10.1002/chem.202200405. Epub 2022 Mar 21. [PubMed:35239190 ]
Xu H, Lackus ND, Kollner TG, Dickschat JS: Isotopic Labeling Experiments Solve the Hedycaryol Problem. Org Lett. 2022 Jan 21;24(2):587-591. doi: 10.1021/acs.orglett.1c04021. Epub 2022 Jan 5. [PubMed:34985289 ]
Yang F, Zhang H, Tian G, Ren W, Li J, Xiao H, Zheng J: Effects of Molecular Distillation on the Chemical Components, Cleaning, and Antibacterial Abilities of Four Different Citrus Oils. Front Nutr. 2021 Sep 1;8:731724. doi: 10.3389/fnut.2021.731724. eCollection 2021. [PubMed:34540881 ]
Schriever K, Saenz-Mendez P, Rudraraju RS, Hendrikse NM, Hudson EP, Biundo A, Schnell R, Syren PO: Engineering of Ancestors as a Tool to Elucidate Structure, Mechanism, and Specificity of Extant Terpene Cyclase. J Am Chem Soc. 2021 Mar 17;143(10):3794-3807. doi: 10.1021/jacs.0c10214. Epub 2021 Jan 26. [PubMed:33496585 ]
LOTUS database [Link]

Showing NP-Card for 2-[(1s,3z,7z)-4,8-dimethylcyclodeca-3,7-dien-1-yl]propan-2-ol (NP0221291)

MOL for NP0221291 (2-[(1s,3z,7z)-4,8-dimethylcyclodeca-3,7-dien-1-yl]propan-2-ol)

3D MOL for NP0221291 (2-[(1s,3z,7z)-4,8-dimethylcyclodeca-3,7-dien-1-yl]propan-2-ol)

3D SDF for NP0221291 (2-[(1s,3z,7z)-4,8-dimethylcyclodeca-3,7-dien-1-yl]propan-2-ol)

3D-SDF for NP0221291 (2-[(1s,3z,7z)-4,8-dimethylcyclodeca-3,7-dien-1-yl]propan-2-ol)

PDB for NP0221291 (2-[(1s,3z,7z)-4,8-dimethylcyclodeca-3,7-dien-1-yl]propan-2-ol)

3D PDB for NP0221291 (2-[(1s,3z,7z)-4,8-dimethylcyclodeca-3,7-dien-1-yl]propan-2-ol)

SMILES for NP0221291 (2-[(1s,3z,7z)-4,8-dimethylcyclodeca-3,7-dien-1-yl]propan-2-ol)

INCHI for NP0221291 (2-[(1s,3z,7z)-4,8-dimethylcyclodeca-3,7-dien-1-yl]propan-2-ol)

Structure for NP0221291 (2-[(1s,3z,7z)-4,8-dimethylcyclodeca-3,7-dien-1-yl]propan-2-ol)

3D Structure for NP0221291 (2-[(1s,3z,7z)-4,8-dimethylcyclodeca-3,7-dien-1-yl]propan-2-ol)