NP-MRD: Showing NP-Card for (-)-1(10),5-Germacradien-4-ol (NP0058335)

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Record Information

Version

2.0

Created at

2022-04-28 03:42:00 UTC

Updated at

2022-04-28 03:42:00 UTC

NP-MRD ID

NP0058335

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(-)-1(10),5-Germacradien-4-ol

Description

Germacra-1(10),5-dien-4beta-ol, also known as (4S,7S)-1(10),5-germacradien-4-ol, 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. (-)-1(10),5-Germacradien-4-ol is found in Chamaecyparis lawsoniana, Cryptomeria japonica, Juniperus sabina, Microbiota decussata, Neodiprion sertifer, Picea koraiensis, Pinus sibirica, Porella swartziana, Pseudobrickellia brasiliensis, Renealmia nicolaioides and Reneilmia cincinnata. Based on a literature review very few articles have been published on germacra-1(10),5-dien-4beta-ol.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 42 42  0  0  0  0  0  0  0  0999 V2000
    1.6537    3.0665   -1.0571 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4509    1.9801   -0.0263 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3672    1.0594    0.2144 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2971   -0.0412    1.1799 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8619   -1.3649    0.6818 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4264   -1.4556   -0.7433 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.3177   -2.5572   -1.3713 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7988   -0.3189   -1.4466 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0079   -1.7959   -0.9359 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0679   -1.2280   -0.4454 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2017   -0.0706    0.4554 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.6539    0.0973    0.9383 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.5554    0.4151   -0.2359 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1257   -1.0888    1.7111 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8359    1.2558   -0.1763 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1520    2.0196    0.6952 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2870    3.9994   -0.5879 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7120    3.1884   -1.3062 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0570    2.8927   -1.9569 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2951    1.1276   -0.3826 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6190    0.2243    2.0518 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2935   -0.1721    1.7196 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0271   -1.8163    1.3070 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7025   -2.1002    0.9072 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3000   -2.5143   -2.4563 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9326   -3.5602   -1.0674 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3389   -2.4839   -1.0006 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5318   -0.4420   -2.3850 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1527   -2.6765   -1.6115 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0479   -1.6744   -0.7444 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6272   -0.1441    1.4011 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6862    0.9774    1.6138 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3115   -0.3836   -0.3843 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9217    0.5405   -1.1578 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0829    1.3861   -0.1143 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7112   -2.0507    1.3547 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2388   -1.1659    1.5448 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9976   -0.9247    2.7860 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4890    1.1534   -1.2256 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7283    1.9455   -0.2718 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1511    3.0984    0.8267 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1721    1.6023    1.7019 H   0  0  0  0  0  0  0  0  0  0  0  0
 13 12  1  0
 12 14  1  0
 12 11  1  0
 11 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  6  1  0
  6  7  1  0
  6  8  1  6
  6  9  1  0
  9 10  2  0
 10 11  1  0
 13 33  1  0
 13 34  1  0
 13 35  1  0
 12 32  1  1
 14 36  1  0
 14 37  1  0
 14 38  1  0
 11 31  1  1
 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  0
  5 24  1  0
  7 25  1  0
  7 26  1  0
  7 27  1  0
  8 28  1  0
  9 29  1  0
 10 30  1  0
M  END


  Mrv1652304282205422D          

 16 16  0  0  1  0            999 V2000
    1.8253    0.2981    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0234   -0.5028    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.0748    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6363   -0.8460    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4381   -0.0451    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.0326    0.5269    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8345    1.3278    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    1.8998    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.2216    1.6710    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4197    0.8701    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8780    2.5139    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6300    2.6999    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3545    0.1837    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9490   -0.3883    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5526    0.9845    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8161   -0.7316    0.0000 C   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  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  1 10  1  0  0  0  0
  8 11  1  1  0  0  0
  8 12  1  6  0  0  0
  5 13  1  1  0  0  0
 13 14  1  0  0  0  0
 13 15  1  0  0  0  0
  2 16  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0058335

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C)[C@@H]1CC\C(C)=C\CC[C@](C)(O)\C=C\1

> <INCHI_IDENTIFIER>
InChI=1S/C15H26O/c1-12(2)14-8-7-13(3)6-5-10-15(4,16)11-9-14/h6,9,11-12,14,16H,5,7-8,10H2,1-4H3/b11-9+,13-6+/t14-,15+/m1/s1

> <INCHI_KEY>
RHCTXHCNRLCYBN-LDKNCKFKSA-N

> <FORMULA>
C15H26O

> <MOLECULAR_WEIGHT>
222.372

> <EXACT_MASS>
222.198365457

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
42

> <JCHEM_AVERAGE_POLARIZABILITY>
27.192638422153102

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1S,2E,4S,7E)-1,7-dimethyl-4-(propan-2-yl)cyclodeca-2,7-dien-1-ol

> <ALOGPS_LOGP>
4.73

> <JCHEM_LOGP>
4.033577067333333

> <ALOGPS_LOGS>
-3.81

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
18.586977272603132

> <JCHEM_PKA_STRONGEST_BASIC>
-1.2298561409633901

> <JCHEM_POLAR_SURFACE_AREA>
20.23

> <JCHEM_REFRACTIVITY>
72.3771

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.47e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1S,2E,4S,7E)-4-isopropyl-1,7-dimethylcyclodeca-2,7-dien-1-ol

> <JCHEM_VEBER_RULE>
1

$$$$

HEADER    PROTEIN                                 28-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   28-APR-22         0                                  
HETATM    1  C   UNK     0       3.407   0.556   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       3.777  -0.938   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.667  -2.006   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.188  -1.579   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.818  -0.084   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.928   0.984   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.558   2.478   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.667   3.546   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       4.147   3.119   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       4.517   1.624   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       1.639   4.693   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       3.043   5.040   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -0.662   0.343   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -1.771  -0.725   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -1.032   1.838   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       5.257  -1.366   0.000  0.00  0.00           C+0
CONECT    1    2   10                                                       
CONECT    2    1    3   16                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6   13                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9   11   12                                             
CONECT    9    8   10                                                       
CONECT   10    9    1                                                       
CONECT   11    8                                                            
CONECT   12    8                                                            
CONECT   13    5   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13                                                            
CONECT   16    2                                                            
MASTER        0    0    0    0    0    0    0    0   16    0   32    0
END

View in JSmol

Synonyms

Value	Source
(-)-1(10),5-Germacradien-4-ol	ChEBI
(-)-Germacra-1(10),5(e)-dien-4beta-ol	ChEBI
(1S,2E,4S,7E)-4-Isopropyl-1,7-dimethylcyclodeca-2,7-dien-1-ol	ChEBI
(4S,7S)-1(10),5-Germacradien-4-ol	ChEBI
cis-1,7-Dimethyl-4-isopropyl-2,7-cyclodeca-2(e),7(e)-dien-1-ol	ChEBI
(-)-Germacra-1(10),5(e)-dien-4b-ol	Generator
(-)-Germacra-1(10),5(e)-dien-4β-ol	Generator
Germacra-1(10),5-dien-4b-ol	Generator
Germacra-1(10),5-dien-4β-ol	Generator

Chemical Formula

C₁₅H₂₆O

Average Mass

222.3720 Da

Monoisotopic Mass

222.19837 Da

IUPAC Name

(1S,2E,4S,7E)-1,7-dimethyl-4-(propan-2-yl)cyclodeca-2,7-dien-1-ol

Traditional Name

(1S,2E,4S,7E)-4-isopropyl-1,7-dimethylcyclodeca-2,7-dien-1-ol

CAS Registry Number

Not Available

SMILES

CC(C)[C@@H]1CC\C(C)=C\CC[C@](C)(O)\C=C\1

InChI Identifier

InChI=1S/C15H26O/c1-12(2)14-8-7-13(3)6-5-10-15(4,16)11-9-14/h6,9,11-12,14,16H,5,7-8,10H2,1-4H3/b11-9+,13-6+/t14-,15+/m1/s1

InChI Key

RHCTXHCNRLCYBN-LDKNCKFKSA-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, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, 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 lawsoniana	LOTUS Database	35616633
Cryptomeria japonica	LOTUS Database	35616633
Juniperus sabina	LOTUS Database	35616633
Microbiota decussata	LOTUS Database	35616633
Neodiprion sertifer	LOTUS Database	35616633
Picea koraiensis	LOTUS Database	35616633
Pinus sibirica	LOTUS Database	35616633
Porella swartziana	LOTUS Database	35616633
Pseudobrickellia brasiliensis	Plant	KNApSAcK
Renealmia nicolaioides	LOTUS Database	35616633
Reneilmia cincinnata	-	KNApSAcK

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	4.73	ALOGPS
logP	4.03	ChemAxon
logS	-3.8	ALOGPS
pKa (Strongest Acidic)	18.59	ChemAxon
pKa (Strongest Basic)	-1.2	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	72.38 m³·mol⁻¹	ChemAxon
Polarizability	27.19 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

Not Available

Chemspider ID

9323883

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

11148775

PDB ID

Not Available

ChEBI ID

176846

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for (-)-1(10),5-Germacradien-4-ol (NP0058335)

MOL for NP0058335 ((-)-1(10),5-Germacradien-4-ol)

3D MOL for NP0058335 ((-)-1(10),5-Germacradien-4-ol)

3D SDF for NP0058335 ((-)-1(10),5-Germacradien-4-ol)

3D-SDF for NP0058335 ((-)-1(10),5-Germacradien-4-ol)

PDB for NP0058335 ((-)-1(10),5-Germacradien-4-ol)

3D PDB for NP0058335 ((-)-1(10),5-Germacradien-4-ol)

SMILES for NP0058335 ((-)-1(10),5-Germacradien-4-ol)

INCHI for NP0058335 ((-)-1(10),5-Germacradien-4-ol)

Structure for NP0058335 ((-)-1(10),5-Germacradien-4-ol)

3D Structure for NP0058335 ((-)-1(10),5-Germacradien-4-ol)