NP-MRD: Showing NP-Card for (-)-Herbertene (NP0059056)

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Record Information

Version

2.0

Created at

2022-04-28 04:20:02 UTC

Updated at

2022-04-28 04:20:03 UTC

NP-MRD ID

NP0059056

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(-)-Herbertene

Description

Herbertene belongs to the class of organic compounds known as sesquiterpenoids. These are terpenes with three consecutive isoprene units. Thus, herbertene is considered to be an isoprenoid. (-)-Herbertene is found in Herberta adunca, Herbertus aduncus, Herbertus sakuraii, Mastigophora diclados, Metacalypogeia alternifolia and Wettsteinia schusteriana. (-)-Herbertene was first documented in 2003 (PMID: 14629996). Based on a literature review a small amount of articles have been published on Herbertene (PMID: 31293063) (PMID: 25303318) (PMID: 16041439).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 37 38  0  0  0  0  0  0  0  0999 V2000
    3.6127    1.9716   -0.8279 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8262    0.7244   -0.6865 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3959   -0.4477   -1.1321 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6521   -1.6046   -0.9901 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3926   -1.5821   -0.4279 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7992   -0.3966    0.0319 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5429   -0.4441    0.6475 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7165   -1.7195    1.4771 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7199    0.6992    1.6580 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4131    1.8015    0.8984 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7853    1.2765   -0.4493 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6939   -0.2168   -0.2554 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.9615   -0.5936    0.5370 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7081   -1.0028   -1.5282 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5527    0.7519   -0.1150 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7070    1.8072   -0.7523 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3150    2.5308   -1.7170 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3570    2.6028    0.0702 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3881   -0.4865   -1.5821 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1023   -2.5171   -1.3296 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7916   -2.4867   -0.3109 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2980   -1.9923    1.8339 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0188   -2.5381    0.7743 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4198   -1.5286    2.2860 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2623    0.3686    2.5661 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2941    1.0492    1.9205 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8848    2.7586    0.9040 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3729    2.0116    1.4707 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1966    1.6540   -1.2926 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8611    1.5096   -0.6668 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8875   -1.6666    0.8602 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9463    0.0566    1.4345 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8824   -0.3695    0.0044 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7860   -1.0268   -1.8756 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1049   -0.5915   -2.3431 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4635   -2.0468   -1.3014 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1434    1.6843    0.2093 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6 15  2  0
  6  7  1  0
  7  8  1  1
  7  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  1
 12 14  1  0
 15  2  1  0
 12  7  1  0
  1 16  1  0
  1 17  1  0
  1 18  1  0
  3 19  1  0
  4 20  1  0
  5 21  1  0
 15 37  1  0
  8 22  1  0
  8 23  1  0
  8 24  1  0
  9 25  1  0
  9 26  1  0
 10 27  1  0
 10 28  1  0
 11 29  1  0
 11 30  1  0
 13 31  1  0
 13 32  1  0
 13 33  1  0
 14 34  1  0
 14 35  1  0
 14 36  1  0
M  END


  Mrv1652304282206202D          

 15 16  0  0  1  0            999 V2000
    0.5101    2.8480    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0419    2.2349    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8489    2.4065    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1038    3.1911    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5518    3.8042    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2552    3.6327    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8067    4.5888    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4009    1.7934    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.0684    1.3085    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8134    0.5238    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9884    0.5238    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7335    1.3085    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0752    1.1454    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1751    1.9157    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9530    2.4065    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  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  1  6  1  0  0  0  0
  5  7  1  0  0  0  0
  8  3  1  6  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
  8 12  1  0  0  0  0
 12 13  1  0  0  0  0
 12 14  1  0  0  0  0
  8 15  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0059056

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC1=CC=CC(=C1)[C@@]1(C)CCCC1(C)C

> <INCHI_IDENTIFIER>
InChI=1S/C15H22/c1-12-7-5-8-13(11-12)15(4)10-6-9-14(15,2)3/h5,7-8,11H,6,9-10H2,1-4H3/t15-/m1/s1

> <INCHI_KEY>
BBZBREYBGRYINI-OAHLLOKOSA-N

> <FORMULA>
C15H22

> <MOLECULAR_WEIGHT>
202.341

> <EXACT_MASS>
202.172150708

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_ATOM_COUNT>
37

> <JCHEM_AVERAGE_POLARIZABILITY>
25.35660377945529

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
1-methyl-3-[(1S)-1,2,2-trimethylcyclopentyl]benzene

> <ALOGPS_LOGP>
6.07

> <JCHEM_LOGP>
5.044201119666666

> <ALOGPS_LOGS>
-5.87

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_POLAR_SURFACE_AREA>
0.0

> <JCHEM_REFRACTIVITY>
66.1886

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.76e-04 g/l

> <JCHEM_TRADITIONAL_IUPAC>
1-methyl-3-[(1S)-1,2,2-trimethylcyclopentyl]benzene

> <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       0.952   5.316   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -0.078   4.172   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.585   4.492   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -2.060   5.957   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -1.030   7.101   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.476   6.781   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -1.506   8.566   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -2.615   3.348   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -3.861   2.442   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -3.385   0.978   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -1.845   0.978   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -1.369   2.442   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       0.140   2.138   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -0.327   3.576   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -3.646   4.492   0.000  0.00  0.00           C+0
CONECT    1    2    6                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4    8                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6    7                                                  
CONECT    6    5    1                                                       
CONECT    7    5                                                            
CONECT    8    3    9   12   15                                             
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11    8   13   14                                             
CONECT   13   12                                                            
CONECT   14   12                                                            
CONECT   15    8                                                            
MASTER        0    0    0    0    0    0    0    0   15    0   32    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₅H₂₂

Average Mass

202.3410 Da

Monoisotopic Mass

202.17215 Da

IUPAC Name

1-methyl-3-[(1S)-1,2,2-trimethylcyclopentyl]benzene

Traditional Name

1-methyl-3-[(1S)-1,2,2-trimethylcyclopentyl]benzene

CAS Registry Number

Not Available

SMILES

CC1=CC=CC(=C1)[C@@]1(C)CCCC1(C)C

InChI Identifier

InChI=1S/C15H22/c1-12-7-5-8-13(11-12)15(4)10-6-9-14(15,2)3/h5,7-8,11H,6,9-10H2,1-4H3/t15-/m1/s1

InChI Key

BBZBREYBGRYINI-OAHLLOKOSA-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
Herberta adunca	-	KNApSAcK
Herbertus aduncus	LOTUS Database	35616633
Herbertus sakuraii	Plant	KNApSAcK
Mastigophora diclados	-	KNApSAcK
Metacalypogeia alternifolia	LOTUS Database	35616633
Wettsteinia schusteriana	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

Herbertane sesquiterpenoid
Sesquiterpenoid
Toluene
Benzenoid
Monocyclic benzene moiety
Aromatic hydrocarbon
Unsaturated hydrocarbon
Hydrocarbon
Aromatic homomonocyclic compound

Molecular Framework

Aromatic 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	6.07	ALOGPS
logP	5.04	ChemAxon
logS	-5.9	ALOGPS
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	0	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	0 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	66.19 m³·mol⁻¹	ChemAxon
Polarizability	25.36 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	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

C00012541

Chemspider ID

9085850

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

10910593

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Xie YY, Chen ZM, Luo HY, Shao H, Tu YQ, Bao X, Cao RF, Zhang SY, Tian JM: Lewis Base/Bronsted Acid Co-catalyzed Enantioselective Sulfenylation/Semipinacol Rearrangement of Di- and Trisubstituted Allylic Alcohols. Angew Chem Int Ed Engl. 2019 Sep 2;58(36):12491-12496. doi: 10.1002/anie.201907115. Epub 2019 Aug 7. [PubMed:31293063 ]
Luderer MR, Mealy MJ, Bailey WF: Asymmetric intramolecular carbolithiation of achiral substrates: synthesis of enantioenriched (R)-(+)-cuparene and (R)-(+)-herbertene. J Org Chem. 2014 Nov 7;79(21):10722-6. doi: 10.1021/jo502139m. Epub 2014 Oct 23. [PubMed:25303318 ]
Bernard AM, Frongia A, Secci F, Piras PP: 2,2-dimethyl cyclopentanones by acid catalyzed ring expansion of isopropenylcyclobutanols. A short synthesis of (+/-)-alpha-cuparenone and (+/-)-herbertene. Chem Commun (Camb). 2005 Aug 14;(30):3853-5. doi: 10.1039/b505707h. Epub 2005 Jun 23. [PubMed:16041439 ]
Feld H, Zapp J, Becker H: Secondary metabolites from the liverwort Tylimanthus renifolius. Phytochemistry. 2003 Dec;64(8):1335-40. doi: 10.1016/j.phytochem.2003.08.021. [PubMed:14629996 ]

Showing NP-Card for (-)-Herbertene (NP0059056)

MOL for NP0059056 ((-)-Herbertene)

3D MOL for NP0059056 ((-)-Herbertene)

3D SDF for NP0059056 ((-)-Herbertene)

3D-SDF for NP0059056 ((-)-Herbertene)

PDB for NP0059056 ((-)-Herbertene)

3D PDB for NP0059056 ((-)-Herbertene)

SMILES for NP0059056 ((-)-Herbertene)

INCHI for NP0059056 ((-)-Herbertene)

Structure for NP0059056 ((-)-Herbertene)

3D Structure for NP0059056 ((-)-Herbertene)