NP-MRD: Showing NP-Card for (1r,2s,4r,5s)-1,2,4,5,6,7,8-heptamethyl-3-methylidenebicyclo[3.2.1]oct-6-ene (NP0265556)

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Record Information

Version

2.0

Created at

2022-09-08 09:34:56 UTC

Updated at

2022-09-08 09:34:56 UTC

NP-MRD ID

NP0265556

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(1r,2s,4r,5s)-1,2,4,5,6,7,8-heptamethyl-3-methylidenebicyclo[3.2.1]oct-6-ene

Description

Sodorifen belongs to the class of organic compounds known as branched unsaturated hydrocarbons. These are hydrocarbons that contains one or more unsaturated carbon atoms, and an aliphatic branch. (1r,2s,4r,5s)-1,2,4,5,6,7,8-heptamethyl-3-methylidenebicyclo[3.2.1]oct-6-ene is found in Serratia plymuthica. (1r,2s,4r,5s)-1,2,4,5,6,7,8-heptamethyl-3-methylidenebicyclo[3.2.1]oct-6-ene was first documented in 2018 (PMID: 30307482). Based on a literature review a small amount of articles have been published on Sodorifen (PMID: 33542330) (PMID: 30732610) (PMID: 30133268).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 42 43  0  0  0  0  0  0  0  0999 V2000
   -0.3098    2.8731   -0.7793 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1748    1.5734   -0.6859 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3470    0.6566   -0.4507 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.5729    1.4586   -0.0458 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0274   -0.4424    0.5081 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.1308   -0.7444    1.4816 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6673   -1.6462   -0.3127 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5297   -2.8399   -0.5319 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5537   -1.4037   -0.7781 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1339   -2.1314   -1.9396 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2193   -0.3162    0.0357 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.6194   -0.6893    0.3953 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1568    0.9282   -0.8096 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.2831    1.8923   -0.5134 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2908   -0.2689    1.2198 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.4060    0.8879    2.0965 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5724    3.4760   -0.9497 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2910    3.3590   -0.6890 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5906    0.2591   -1.4819 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3558    2.1854    0.7451 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9547    1.9755   -0.9550 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3499    0.7148    0.2262 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0063   -1.1825    0.9967 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4224    0.1936    1.9687 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7335   -1.4151    2.2552 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9385   -3.7483   -0.7306 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2282   -2.6415   -1.3492 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1443   -2.9459    0.4030 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0617   -1.5918   -2.2351 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4559   -3.1467   -1.5668 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4141   -2.2218   -2.7615 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9818   -0.0900    1.2371 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6196   -1.7547    0.7403 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2374   -0.5995   -0.5258 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2404    0.6174   -1.8926 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1942    1.4014   -0.1369 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5320    2.4375   -1.4623 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9528    2.6030    0.2706 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4646   -1.2056    1.7981 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4703    1.2093    2.1625 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2334    1.7545    1.8928 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1480    0.5692    3.1500 H   0  0  0  0  0  0  0  0  0  0  0  0
 16 15  1  0
 15 11  1  0
 11 12  1  1
 11 13  1  0
 13 14  1  0
 13  2  1  0
  2  1  2  3
  2  3  1  0
  3  4  1  0
  3  5  1  0
  5  6  1  1
  5  7  1  0
  7  8  1  0
  7  9  2  0
  9 10  1  0
  5 15  1  0
  9 11  1  0
 16 40  1  0
 16 41  1  0
 16 42  1  0
 15 39  1  1
 12 32  1  0
 12 33  1  0
 12 34  1  0
 13 35  1  6
 14 36  1  0
 14 37  1  0
 14 38  1  0
  1 17  1  0
  1 18  1  0
  3 19  1  6
  4 20  1  0
  4 21  1  0
  4 22  1  0
  6 23  1  0
  6 24  1  0
  6 25  1  0
  8 26  1  0
  8 27  1  0
  8 28  1  0
 10 29  1  0
 10 30  1  0
 10 31  1  0
M  END


  Mrv1652309082211342D          

 16 17  0  0  1  0            999 V2000
    3.6130    0.6363    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7880    0.6363    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4300    1.3796    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.9444    2.0247    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6257    1.5632    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.4421    2.3675    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9807    1.0488    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2374    1.4068    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9807    0.2238    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2374   -0.1341    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6257   -0.2905    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.4421   -1.0949    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3940    0.6363    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5690    0.6363    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4300   -0.1070    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.9444   -0.7520    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  1  0  0  0
  3  5  1  0  0  0  0
  5  6  1  1  0  0  0
  5  7  1  0  0  0  0
  7  8  1  0  0  0  0
  7  9  2  0  0  0  0
  9 10  1  0  0  0  0
  9 11  1  0  0  0  0
 11 12  1  1  0  0  0
 11 13  1  0  0  0  0
  5 13  1  0  0  0  0
 13 14  1  0  0  0  0
 11 15  1  0  0  0  0
  2 15  1  0  0  0  0
 15 16  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0265556

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC1[C@]2(C)[C@H](C)C(=C)[C@H](C)[C@@]1(C)C(C)=C2C

> <INCHI_IDENTIFIER>
InChI=1S/C16H26/c1-9-10(2)15(7)12(4)13(5)16(8,11(9)3)14(15)6/h10-11,14H,1H2,2-8H3/t10-,11+,14?,15-,16+

> <INCHI_KEY>
GXPHTJFKVOCWKQ-PDLCYRHZSA-N

> <FORMULA>
C16H26

> <MOLECULAR_WEIGHT>
218.384

> <EXACT_MASS>
218.203450837

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_ATOM_COUNT>
42

> <JCHEM_AVERAGE_POLARIZABILITY>
27.54188191676896

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1R,2S,4R,5S)-1,2,4,5,6,7,8-heptamethyl-3-methylidenebicyclo[3.2.1]oct-6-ene

> <JCHEM_LOGP>
4.303049981000001

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_POLAR_SURFACE_AREA>
0.0

> <JCHEM_REFRACTIVITY>
71.5037

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(1R,2S,4R,5S)-1,2,4,5,6,7,8-heptamethyl-3-methylidenebicyclo[3.2.1]oct-6-ene

> <JCHEM_VEBER_RULE>
1

$$$$

HEADER    PROTEIN                                 08-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   08-SEP-22         0                                  
HETATM    1  C   UNK     0       6.744   1.188   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       5.204   1.188   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.536   2.575   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.496   3.779   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       3.035   2.918   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.692   4.419   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.831   1.958   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.443   2.626   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.831   0.418   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.443  -0.250   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       3.035  -0.542   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       2.692  -2.044   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       2.602   1.188   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       1.062   1.188   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       4.536  -0.200   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       5.496  -1.404   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   15                                                  
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6    7   13                                             
CONECT    6    5                                                            
CONECT    7    5    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12   13   15                                             
CONECT   12   11                                                            
CONECT   13   11    5   14                                                  
CONECT   14   13                                                            
CONECT   15   11    2   16                                                  
CONECT   16   15                                                            
MASTER        0    0    0    0    0    0    0    0   16    0   34    0
END

View in JSmol

Synonyms

Value	Source
1,2,4,5,6,7,8-Heptamethyl-3-methylenebicyclo(3.2.1)oct-6-ene	MeSH

Chemical Formula

C₁₆H₂₆

Average Mass

218.3840 Da

Monoisotopic Mass

218.20345 Da

IUPAC Name

(1R,2S,4R,5S)-1,2,4,5,6,7,8-heptamethyl-3-methylidenebicyclo[3.2.1]oct-6-ene

Traditional Name

(1R,2S,4R,5S)-1,2,4,5,6,7,8-heptamethyl-3-methylidenebicyclo[3.2.1]oct-6-ene

CAS Registry Number

Not Available

SMILES

CC1[C@]2(C)[C@H](C)C(=C)[C@H](C)[C@@]1(C)C(C)=C2C

InChI Identifier

InChI=1S/C16H26/c1-9-10(2)15(7)12(4)13(5)16(8,11(9)3)14(15)6/h10-11,14H,1H2,2-8H3/t10-,11+,14?,15-,16+

InChI Key

GXPHTJFKVOCWKQ-PDLCYRHZSA-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
Serratia plymuthica	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as branched unsaturated hydrocarbons. These are hydrocarbons that contains one or more unsaturated carbon atoms, and an aliphatic branch.

Kingdom

Organic compounds

Super Class

Hydrocarbons

Class

Unsaturated hydrocarbons

Sub Class

Branched unsaturated hydrocarbons

Direct Parent

Branched unsaturated hydrocarbons

Alternative Parents

Substituents

Branched unsaturated hydrocarbon
Polycyclic hydrocarbon
Cyclic olefin
Unsaturated aliphatic hydrocarbon
Olefin
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	4.3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	0	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	0 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	71.5 m³·mol⁻¹	ChemAxon
Polarizability	27.54 Å³	ChemAxon
Number of Rings	2	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

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

46187193

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Lemfack MC, Brandt W, Kruger K, Gurowietz A, Djifack J, Jung JP, Hopf M, Noack H, Junker B, von Reuss S, Piechulla B: Reaction mechanism of the farnesyl pyrophosphate C-methyltransferase towards the biosynthesis of pre-sodorifen pyrophosphate by Serratia plymuthica 4Rx13. Sci Rep. 2021 Feb 4;11(1):3182. doi: 10.1038/s41598-021-82521-9. [PubMed:33542330 ]
Duell ER, D'Agostino PM, Shapiro N, Woyke T, Fuchs TM, Gulder TAM: Direct pathway cloning of the sodorifen biosynthetic gene cluster and recombinant generation of its product in E. coli. Microb Cell Fact. 2019 Feb 7;18(1):32. doi: 10.1186/s12934-019-1080-6. [PubMed:30732610 ]
Kai M, Piechulla B: Interspecies interaction of Serratia plymuthica 4Rx13 and Bacillus subtilis B2g alters the emission of sodorifen. FEMS Microbiol Lett. 2018 Nov 1;365(22). pii: 5127042. doi: 10.1093/femsle/fny253. [PubMed:30307482 ]
von Reuss S, Domik D, Lemfack MC, Magnus N, Kai M, Weise T, Piechulla B: Sodorifen Biosynthesis in the Rhizobacterium Serratia plymuthica Involves Methylation and Cyclization of MEP-Derived Farnesyl Pyrophosphate by a SAM-Dependent C-Methyltransferase. J Am Chem Soc. 2018 Sep 19;140(37):11855-11862. doi: 10.1021/jacs.8b08510. Epub 2018 Sep 4. [PubMed:30133268 ]
LOTUS database [Link]

Showing NP-Card for (1r,2s,4r,5s)-1,2,4,5,6,7,8-heptamethyl-3-methylidenebicyclo[3.2.1]oct-6-ene (NP0265556)

MOL for NP0265556 ((1r,2s,4r,5s)-1,2,4,5,6,7,8-heptamethyl-3-methylidenebicyclo[3.2.1]oct-6-ene)

3D MOL for NP0265556 ((1r,2s,4r,5s)-1,2,4,5,6,7,8-heptamethyl-3-methylidenebicyclo[3.2.1]oct-6-ene)

3D SDF for NP0265556 ((1r,2s,4r,5s)-1,2,4,5,6,7,8-heptamethyl-3-methylidenebicyclo[3.2.1]oct-6-ene)

3D-SDF for NP0265556 ((1r,2s,4r,5s)-1,2,4,5,6,7,8-heptamethyl-3-methylidenebicyclo[3.2.1]oct-6-ene)

PDB for NP0265556 ((1r,2s,4r,5s)-1,2,4,5,6,7,8-heptamethyl-3-methylidenebicyclo[3.2.1]oct-6-ene)

3D PDB for NP0265556 ((1r,2s,4r,5s)-1,2,4,5,6,7,8-heptamethyl-3-methylidenebicyclo[3.2.1]oct-6-ene)

SMILES for NP0265556 ((1r,2s,4r,5s)-1,2,4,5,6,7,8-heptamethyl-3-methylidenebicyclo[3.2.1]oct-6-ene)

INCHI for NP0265556 ((1r,2s,4r,5s)-1,2,4,5,6,7,8-heptamethyl-3-methylidenebicyclo[3.2.1]oct-6-ene)

Structure for NP0265556 ((1r,2s,4r,5s)-1,2,4,5,6,7,8-heptamethyl-3-methylidenebicyclo[3.2.1]oct-6-ene)

3D Structure for NP0265556 ((1r,2s,4r,5s)-1,2,4,5,6,7,8-heptamethyl-3-methylidenebicyclo[3.2.1]oct-6-ene)