NP-MRD: Showing NP-Card for germacradienol (NP0196005)

Jump To Section:

Identification Spectra BioTaxonomy ChemoTaxonomy Physical properties Links References XML

Record Information

Version

2.0

Created at

2022-09-04 13:59:06 UTC

Updated at

2022-09-04 13:59:07 UTC

NP-MRD ID

NP0196005

Secondary Accession Numbers

None

Natural Product Identification

Common Name

germacradienol

Description

(1E,4S,5E,7R)-germacra-1(10),5-dien-11-ol, also known as germacradienol, 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. Thus, (1E,4S,5E,7R)-germacra-1(10),5-dien-11-ol is considered to be an isoprenoid. germacradienol is found in Dumortiera hirsuta, Mentha piperita, Porella swartziana and Streptomyces albidoflavus. germacradienol was first documented in 2004 (PMID: 14995166). Based on a literature review a small amount of articles have been published on (1E,4S,5E,7R)-germacra-1(10),5-dien-11-ol (PMID: 17080683) (PMID: 16787064).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 42 42  0  0  0  0  0  0  0  0999 V2000
   -1.6121    3.4271    0.4708 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6502    2.0087   -0.0453 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7218    1.2645    0.1469 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8696   -0.1387   -0.3151 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3494   -1.0897    0.7532 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2016   -1.9154    0.2127 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.7485   -3.3170    0.0023 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0358   -1.9238    1.1472 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0277   -1.1693    1.0196 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2506   -0.1826   -0.0727 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.7271    0.0741   -0.3038 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4897   -1.1724   -0.6372 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8591    1.1242   -1.3786 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2935    0.6096    0.8676 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6370    1.1684    0.2496 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4269    1.5486   -0.7562 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2816    4.1000   -0.3455 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8589    3.4183    1.2994 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5843    3.7152    0.8886 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5828    1.6911    0.6864 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9612   -0.3509   -0.5147 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3624   -0.3106   -1.2720 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9775   -0.5471    1.6466 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1946   -1.7163    1.1069 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9009   -1.5406   -0.7693 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8116   -3.2514   -0.3211 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2132   -3.8632   -0.7806 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7706   -3.8729    0.9838 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1212   -2.6285    1.9855 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8336   -1.2424    1.7520 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8304   -0.4988   -1.0389 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7449   -1.7404    0.3035 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9477   -1.8353   -1.3253 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4774   -0.8542   -1.0502 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7550    0.8808   -1.9904 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9672    1.0409   -2.0326 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9417    2.1338   -0.9282 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6051    0.7959    1.5548 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1397    1.0566    1.2544 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3746    1.9651    0.3666 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6258    0.7349   -1.4794 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0395    2.4036   -1.3412 H   0  0  0  0  0  0  0  0  0  0  0  0
  7  6  1  0
  6  5  1  0
  5  4  1  0
  4  3  1  0
  3  2  2  0
  2  1  1  0
  2 16  1  0
 16 15  1  0
 15 10  1  0
 10  9  1  0
  9  8  2  0
 10 11  1  0
 11 12  1  0
 11 13  1  0
 11 14  1  0
  8  6  1  0
  7 26  1  0
  7 27  1  0
  7 28  1  0
  6 25  1  6
  5 23  1  0
  5 24  1  0
  4 21  1  0
  4 22  1  0
  3 20  1  0
  1 17  1  0
  1 18  1  0
  1 19  1  0
 16 41  1  0
 16 42  1  0
 15 39  1  0
 15 40  1  0
 10 31  1  6
  9 30  1  0
  8 29  1  0
 12 32  1  0
 12 33  1  0
 12 34  1  0
 13 35  1  0
 13 36  1  0
 13 37  1  0
 14 38  1  0
M  END

  Mrv1652309042215592D          

 16 16  0  0  1  0            999 V2000
    0.9440    0.1576    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.1434   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000    0.0000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1270    0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3020   -1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    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  0  0  0  0
  6  7  1  6  0  0  0
  6  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  6  0  0  0
 11 12  1  0  0  0  0
 11 13  1  0  0  0  0
 11 14  1  0  0  0  0
 10 15  1  0  0  0  0
 15 16  1  0  0  0  0
  2 16  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0196005

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@H]1CC\C=C(C)\CC[C@H](\C=C\1)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/h6,9,11,13-14,16H,5,7-8,10H2,1-4H3/b11-9+,12-6+/t13-,14+/m0/s1

> <INCHI_KEY>
ZVZPKUXZGROCDB-IFRRKGDKSA-N

> <FORMULA>
C15H26O

> <MOLECULAR_WEIGHT>
222.372

> <EXACT_MASS>
222.198365457

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
42

> <JCHEM_AVERAGE_POLARIZABILITY>
27.288295458913126

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

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

> <JCHEM_LOGP>
3.877669607333332

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
19.29647510280105

> <JCHEM_PKA_STRONGEST_BASIC>
-0.9195217900348193

> <JCHEM_POLAR_SURFACE_AREA>
20.23

> <JCHEM_REFRACTIVITY>
72.5311

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
germacradienol

> <JCHEM_VEBER_RULE>
1

$$$$

HEADER    PROTEIN                                 04-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-22         0                                  
HETATM    1  C   UNK     0       1.762   0.294   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.001   2.310   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.335   1.540   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       5.335  -0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -0.000   0.000   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -2.667  -1.540   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -2.104   0.564   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      -0.564  -2.104   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0      -0.000   1.540   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       1.334   2.310   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                                                       
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11   15                                                  
CONECT   11   10   12   13   14                                             
CONECT   12   11                                                            
CONECT   13   11                                                            
CONECT   14   11                                                            
CONECT   15   10   16                                                       
CONECT   16   15    2                                                       
MASTER        0    0    0    0    0    0    0    0   16    0   32    0
END

View in JSmol

Synonyms

Value	Source
(4S,7R)-Germacra-1(10)e,5E-diene-11-ol	ChEBI
Germacradienol	ChEBI

Chemical Formula

C₁₅H₂₆O

Average Mass

222.3720 Da

Monoisotopic Mass

222.19837 Da

IUPAC Name

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

Traditional Name

germacradienol

CAS Registry Number

Not Available

SMILES

C[C@H]1CC\C=C(C)\CC[C@H](\C=C\1)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/h6,9,11,13-14,16H,5,7-8,10H2,1-4H3/b11-9+,12-6+/t13-,14+/m0/s1

InChI Key

ZVZPKUXZGROCDB-IFRRKGDKSA-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
Dumortiera hirsuta	LOTUS Database	35616633
Mentha piperita	LOTUS Database	35616633
Porella swartziana	LOTUS Database	35616633
Streptomyces albidoflavus	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

germacrane sesquiterpenoid (CHEBI:46734 )
Germacrane sesquiterpenoids (LMPR0103090009 )

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	3.88	ChemAxon
pKa (Strongest Acidic)	19.3	ChemAxon
pKa (Strongest Basic)	-0.92	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	72.53 m³·mol⁻¹	ChemAxon
Polarizability	27.29 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

17600421

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

16667385

PDB ID

Not Available

ChEBI ID

46734

Good Scents ID

Not Available

References

General References

Cane DE, He X, Kobayashi S, Omura S, Ikeda H: Geosmin biosynthesis in Streptomyces avermitilis. Molecular cloning, expression, and mechanistic study of the germacradienol/geosmin synthase. J Antibiot (Tokyo). 2006 Aug;59(8):471-9. doi: 10.1038/ja.2006.66. [PubMed:17080683 ]
Jiang J, He X, Cane DE: Geosmin biosynthesis. Streptomyces coelicolor germacradienol/germacrene D synthase converts farnesyl diphosphate to geosmin. J Am Chem Soc. 2006 Jun 28;128(25):8128-9. doi: 10.1021/ja062669x. [PubMed:16787064 ]
He X, Cane DE: Mechanism and stereochemistry of the germacradienol/germacrene D synthase of Streptomyces coelicolor A3(2). J Am Chem Soc. 2004 Mar 10;126(9):2678-9. doi: 10.1021/ja039929k. [PubMed:14995166 ]
LOTUS database [Link]

Showing NP-Card for germacradienol (NP0196005)

MOL for NP0196005 (germacradienol)

3D MOL for NP0196005 (germacradienol)

3D SDF for NP0196005 (germacradienol)

3D-SDF for NP0196005 (germacradienol)

PDB for NP0196005 (germacradienol)

3D PDB for NP0196005 (germacradienol)

SMILES for NP0196005 (germacradienol)

INCHI for NP0196005 (germacradienol)

Structure for NP0196005 (germacradienol)

3D Structure for NP0196005 (germacradienol)