NP-MRD: Showing NP-Card for (1r,5r)-1-[(2s)-6-methylhept-5-en-2-yl]-4-methylidenebicyclo[3.1.0]hexane (NP0319827)

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Record Information

Version

2.0

Created at

2022-09-11 21:03:58 UTC

Updated at

2022-09-11 21:03:58 UTC

NP-MRD ID

NP0319827

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(1r,5r)-1-[(2s)-6-methylhept-5-en-2-yl]-4-methylidenebicyclo[3.1.0]hexane

Description

Sesquisabinene B belongs to the class of organic compounds known as sesquiterpenoids. These are terpenes with three consecutive isoprene units. (1r,5r)-1-[(2s)-6-methylhept-5-en-2-yl]-4-methylidenebicyclo[3.1.0]hexane is found in Haplocarpha lyrata. It was first documented in 2004 (PMID: 15075399). Based on a literature review a significant number of articles have been published on sesquisabinene B (PMID: 29996001) (PMID: 30977996) (PMID: 25624157) (PMID: 18785666).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 39 40  0  0  0  0  0  0  0  0999 V2000
   -3.6048    1.3209   -2.2195 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2600    0.7398   -1.1072 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0425   -0.2302   -0.3346 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1000   -0.8343    0.6898 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9038    0.0799    0.7593 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.5957   -0.5081    1.2316 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.5581   -1.9600    0.8711 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5275    0.2816    0.6311 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8885   -0.2183    1.0747 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8941    0.6762    0.3869 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7932    0.1853   -0.4422 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8119   -1.2712   -0.6993 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7787    1.0521   -1.1180 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1753    1.5180    1.0038 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9736    0.9637   -0.4023 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.9489    2.0203   -2.7034 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5582    1.1066   -2.6722 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9042    0.1855    0.2009 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4398   -0.9989   -1.0394 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5777   -1.0089    1.6528 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7610   -1.7913    0.2436 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5225   -0.3889    2.3495 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4397   -2.4208    1.0361 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3170   -2.4890    1.4885 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8123   -2.1530   -0.1874 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5277    0.1987   -0.4751 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4426    1.3271    0.9899 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0409   -0.0712    2.1548 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0908   -1.2542    0.7693 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8948    1.7462    0.5638 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5582   -1.5429   -1.4805 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8119   -1.5397   -1.1175 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0578   -1.8602    0.2108 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8156    0.8044   -0.8099 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7673    0.9162   -2.2361 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5861    2.1307   -0.9590 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3948    2.2116    1.3165 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1807    1.7690    1.3565 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0963    1.3077   -0.9774 H   0  0  0  0  0  0  0  0  0  0  0  0
  7  6  1  0
  6  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  2  3
 11 12  1  0
 11 13  1  0
  6  5  1  0
  5 14  1  1
 14 15  1  0
 15  2  1  0
  2  1  2  3
  2  3  1  0
  3  4  1  0
 15  5  1  0
  4  5  1  0
  7 23  1  0
  7 24  1  0
  7 25  1  0
  6 22  1  1
  8 26  1  0
  8 27  1  0
  9 28  1  0
  9 29  1  0
 10 30  1  0
 12 31  1  0
 12 32  1  0
 12 33  1  0
 13 34  1  0
 13 35  1  0
 13 36  1  0
 14 37  1  0
 14 38  1  0
 15 39  1  6
  1 16  1  0
  1 17  1  0
  3 18  1  0
  3 19  1  0
  4 20  1  0
  4 21  1  0
M  END


  Mrv1652309112223032D          

 15 16  0  0  1  0            999 V2000
    2.4975    2.3383    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2425    1.5536    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7275    0.8862    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2425    0.2188    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4579    0.4737    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.1224   -0.2800    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.3019   -0.3662    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6073   -0.9474    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2717   -1.7011    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7566   -2.3685    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4211   -3.1222    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9060   -3.7896    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6006   -3.2084    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7434    0.8862    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4579    1.2987    0.0000 C   0  0  2  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  1  0  0  0
  6  7  1  6  0  0  0
  6  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
 11 12  1  0  0  0  0
 11 13  1  0  0  0  0
  5 14  1  0  0  0  0
 15 14  1  6  0  0  0
  2 15  1  0  0  0  0
  5 15  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0319827

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@@H](CCC=C(C)C)[C@@]12C[C@@H]1C(=C)CC2

> <INCHI_IDENTIFIER>
InChI=1S/C15H24/c1-11(2)6-5-7-13(4)15-9-8-12(3)14(15)10-15/h6,13-14H,3,5,7-10H2,1-2,4H3/t13-,14+,15+/m0/s1

> <INCHI_KEY>
DYUSFBWNOCHOFP-RRFJBIMHSA-N

> <FORMULA>
C15H24

> <MOLECULAR_WEIGHT>
204.357

> <EXACT_MASS>
204.187800773

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_ATOM_COUNT>
39

> <JCHEM_AVERAGE_POLARIZABILITY>
26.325804528016825

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1R,5R)-1-[(2S)-6-methylhept-5-en-2-yl]-4-methylidenebicyclo[3.1.0]hexane

> <JCHEM_LOGP>
4.519309391666669

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_POLAR_SURFACE_AREA>
0.0

> <JCHEM_REFRACTIVITY>
67.4524

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(1R,5R)-1-[(2S)-6-methylhept-5-en-2-yl]-4-methylidenebicyclo[3.1.0]hexane

> <JCHEM_VEBER_RULE>
1

$$$$

HEADER    PROTEIN                                 11-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-SEP-22         0                                  
HETATM    1  C   UNK     0       4.662   4.365   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.186   2.900   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.091   1.654   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.186   0.408   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.721   0.884   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.095  -0.523   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.563  -0.684   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       3.000  -1.768   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.374  -3.175   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       3.279  -4.421   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       2.653  -5.828   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       3.558  -7.074   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       1.121  -5.989   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       1.388   1.654   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       2.721   2.424   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   15                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6   14   15                                             
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11                                                            
CONECT   14    5   15                                                       
CONECT   15   14    2    5                                                  
MASTER        0    0    0    0    0    0    0    0   15    0   32    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₅H₂₄

Average Mass

204.3570 Da

Monoisotopic Mass

204.18780 Da

IUPAC Name

(1R,5R)-1-[(2S)-6-methylhept-5-en-2-yl]-4-methylidenebicyclo[3.1.0]hexane

Traditional Name

(1R,5R)-1-[(2S)-6-methylhept-5-en-2-yl]-4-methylidenebicyclo[3.1.0]hexane

CAS Registry Number

Not Available

SMILES

C[C@@H](CCC=C(C)C)[C@@]12C[C@@H]1C(=C)CC2

InChI Identifier

InChI=1S/C15H24/c1-11(2)6-5-7-13(4)15-9-8-12(3)14(15)10-15/h6,13-14H,3,5,7-10H2,1-2,4H3/t13-,14+,15+/m0/s1

InChI Key

DYUSFBWNOCHOFP-RRFJBIMHSA-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
Haplocarpha lyrata	LOTUS Database	35616633

Chemical Taxonomy

Description

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

Sesquisabinane sesquiterpenoid
Sesquiterpenoid
Branched unsaturated hydrocarbon
Polycyclic hydrocarbon
Cyclic olefin
Unsaturated aliphatic hydrocarbon
Unsaturated hydrocarbon
Olefin
Hydrocarbon
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	4.52	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	0	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	0 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	67.45 m³·mol⁻¹	ChemAxon
Polarizability	26.33 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

58837653

KEGG Compound ID

Not Available

BioCyc ID

CPD-13872

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

90658542

PDB ID

Not Available

ChEBI ID

143550

Good Scents ID

Not Available

References

General References

Chen D, Du Z, Lin Z, Su P, Huang H, Ou Z, Pan W, Huang S, Zhang K, Zheng X, Lin L, Zhang L: The Chemical Compositions of Angelica pubescens Oil and Its Prevention of UV-B Radiation-Induced Cutaneous Photoaging. Chem Biodivers. 2018 Oct;15(10):e1800235. doi: 10.1002/cbdv.201800235. Epub 2018 Oct 7. [PubMed:29996001 ]
Blank PN, Shinsky SA, Christianson DW: Structure of Sesquisabinene Synthase 1, a Terpenoid Cyclase That Generates a Strained [3.1.0] Bridged-Bicyclic Product. ACS Chem Biol. 2019 May 17;14(5):1011-1019. doi: 10.1021/acschembio.9b00218. Epub 2019 Apr 17. [PubMed:30977996 ]
Moniodis J, Jones CG, Barbour EL, Plummer JA, Ghisalberti EL, Bohlmann J: The transcriptome of sesquiterpenoid biosynthesis in heartwood xylem of Western Australian sandalwood (Santalum spicatum). Phytochemistry. 2015 May;113:79-86. doi: 10.1016/j.phytochem.2014.12.009. Epub 2015 Jan 24. [PubMed:25624157 ]
Furstner A, Schlecker A: A gold-catalyzed entry into the sesquisabinene and sesquithujene families of terpenoids and formal total syntheses of cedrene and cedrol. Chemistry. 2008;14(30):9181-91. doi: 10.1002/chem.200801382. [PubMed:18785666 ]
Kollner TG, Schnee C, Gershenzon J, Degenhardt J: The variability of sesquiterpenes emitted from two Zea mays cultivars is controlled by allelic variation of two terpene synthase genes encoding stereoselective multiple product enzymes. Plant Cell. 2004 May;16(5):1115-31. doi: 10.1105/tpc.019877. Epub 2004 Apr 9. [PubMed:15075399 ]
LOTUS database [Link]

Showing NP-Card for (1r,5r)-1-[(2s)-6-methylhept-5-en-2-yl]-4-methylidenebicyclo[3.1.0]hexane (NP0319827)

MOL for NP0319827 ((1r,5r)-1-[(2s)-6-methylhept-5-en-2-yl]-4-methylidenebicyclo[3.1.0]hexane)

3D MOL for NP0319827 ((1r,5r)-1-[(2s)-6-methylhept-5-en-2-yl]-4-methylidenebicyclo[3.1.0]hexane)

3D SDF for NP0319827 ((1r,5r)-1-[(2s)-6-methylhept-5-en-2-yl]-4-methylidenebicyclo[3.1.0]hexane)

3D-SDF for NP0319827 ((1r,5r)-1-[(2s)-6-methylhept-5-en-2-yl]-4-methylidenebicyclo[3.1.0]hexane)

PDB for NP0319827 ((1r,5r)-1-[(2s)-6-methylhept-5-en-2-yl]-4-methylidenebicyclo[3.1.0]hexane)

3D PDB for NP0319827 ((1r,5r)-1-[(2s)-6-methylhept-5-en-2-yl]-4-methylidenebicyclo[3.1.0]hexane)

SMILES for NP0319827 ((1r,5r)-1-[(2s)-6-methylhept-5-en-2-yl]-4-methylidenebicyclo[3.1.0]hexane)

INCHI for NP0319827 ((1r,5r)-1-[(2s)-6-methylhept-5-en-2-yl]-4-methylidenebicyclo[3.1.0]hexane)

Structure for NP0319827 ((1r,5r)-1-[(2s)-6-methylhept-5-en-2-yl]-4-methylidenebicyclo[3.1.0]hexane)

3D Structure for NP0319827 ((1r,5r)-1-[(2s)-6-methylhept-5-en-2-yl]-4-methylidenebicyclo[3.1.0]hexane)