NP-MRD: Showing NP-Card for Senecrassidiol (NP0064928)

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Record Information

Version

2.0

Created at

2022-04-28 09:13:45 UTC

Updated at

2022-04-28 09:13:45 UTC

NP-MRD ID

NP0064928

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Senecrassidiol

Description

Senecrassidiol belongs to the class of organic compounds known as tertiary alcohols. Tertiary alcohols are compounds in which a hydroxy group, -OH, is attached to a saturated carbon atom R3COH (R not H ). Senecrassidiol is found in Panax ginseng, Senecio crassissimum and Senecio crassissimus. Senecrassidiol was first documented in 2014 (PMID: 25301666). Based on a literature review very few articles have been published on Senecrassidiol.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 43 45  0  0  0  0  0  0  0  0999 V2000
   -3.0011   -0.9125    1.3141 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5842   -0.3039    0.0249 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.6818   -0.3078   -1.0004 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8890    1.0641    0.1633 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0024    0.6190   -0.9270 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.2253   -0.7873   -0.5097 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.3979   -1.4302    0.4744 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7531   -0.7220    1.0961 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8831   -0.5714    0.1022 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.5801   -1.8838   -0.0627 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2543   -0.1712   -1.2074 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3885    1.0723   -1.0651 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.5574    1.6836   -2.3460 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8750    2.0680   -0.0896 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0650    1.7810    0.7259 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8260    0.5315    0.4317 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.6688    0.2541    1.4969 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4308   -0.5659    2.1998 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0575   -0.5581    1.5019 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0667   -2.0151    1.2347 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2845   -0.3284   -2.0554 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2342   -1.2621   -0.8867 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3363    0.5707   -0.8248 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6693    1.8373   -0.0941 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5828    1.1857    1.1815 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5865    0.7899   -1.8901 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4687   -1.4748   -1.3768 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0449   -1.7853    1.3356 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0239   -2.4092    0.0844 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5331    0.1846    1.6479 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1628   -1.4407    1.8750 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6637   -2.1994   -1.1119 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5683   -1.8274    0.4473 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0310   -2.7181    0.4637 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0709   -0.0658   -1.9338 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6449   -1.0399   -1.5456 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2134    2.6026   -2.2243 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0217    2.2917    0.6242 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0289    3.0975   -0.5484 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8368    2.6134    0.6866 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8316    1.7429    1.8353 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4628    0.7179   -0.4580 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5986    0.0724    1.2106 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  1
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  6
  9 11  1  0
 11 12  1  0
 12 13  1  6
 12 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
  6  2  1  0
 16  9  1  0
 12  5  1  0
  1 18  1  0
  1 19  1  0
  1 20  1  0
  3 21  1  0
  3 22  1  0
  3 23  1  0
  4 24  1  0
  4 25  1  0
  5 26  1  6
  6 27  1  6
  7 28  1  0
  7 29  1  0
  8 30  1  0
  8 31  1  0
 10 32  1  0
 10 33  1  0
 10 34  1  0
 11 35  1  0
 11 36  1  0
 13 37  1  0
 14 38  1  0
 14 39  1  0
 15 40  1  0
 15 41  1  0
 16 42  1  6
 17 43  1  0
M  END


  Mrv1652304282211132D          

 17 19  0  0  1  0            999 V2000
    5.1617    0.1410    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5460    0.6900    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7213    0.7149    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.5455   -0.1905    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8466   -1.3772    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.2804   -0.6755    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    6.0882   -0.8431    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0632   -1.6359    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2968   -1.3305    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9060   -0.6039    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.0737    0.2039    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.2659    0.3715    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0982   -0.4363    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2736   -0.4618    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7466   -1.1826    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3576   -2.0248    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4626    1.4983    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  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
  1  6  1  0  0  0  0
  6  7  1  1  0  0  0
  5  8  1  0  0  0  0
  8  9  1  0  0  0  0
 10  9  1  1  0  0  0
 10 11  1  0  0  0  0
  3 11  1  0  0  0  0
 11 12  1  1  0  0  0
 12 13  1  0  0  0  0
 10 13  1  0  0  0  0
 13 14  1  0  0  0  0
 13 15  1  0  0  0  0
  5 16  1  6  0  0  0
  3 17  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0064928

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC1(C)C[C@@H]2[C@H]1CC[C@@]1(C)C[C@]2(O)CC[C@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C15H26O2/c1-13(2)8-11-10(13)4-6-14(3)9-15(11,17)7-5-12(14)16/h10-12,16-17H,4-9H2,1-3H3/t10-,11-,12-,14+,15-/m1/s1

> <INCHI_KEY>
SFJOMLIUSIKKRA-MYYUVRNCSA-N

> <FORMULA>
C15H26O2

> <MOLECULAR_WEIGHT>
238.371

> <EXACT_MASS>
238.193280077

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
43

> <JCHEM_AVERAGE_POLARIZABILITY>
28.00626104959167

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1R,2R,5R,8S,9R)-4,4,8-trimethyltricyclo[6.3.1.0^{2,5}]dodecane-1,9-diol

> <ALOGPS_LOGP>
2.19

> <JCHEM_LOGP>
2.196222674333333

> <ALOGPS_LOGS>
-3.01

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.931980188317752

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.298007985875216

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9291348809027538

> <JCHEM_POLAR_SURFACE_AREA>
40.46

> <JCHEM_REFRACTIVITY>
68.0174

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.33e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1R,2R,5R,8S,9R)-4,4,8-trimethyltricyclo[6.3.1.0^{2,5}]dodecane-1,9-diol

> <JCHEM_VEBER_RULE>
0

$$$$

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       9.635   0.263   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       8.486   1.288   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       6.946   1.334   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       8.485  -0.356   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       9.047  -2.571   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       9.857  -1.261   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      11.365  -1.574   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       7.585  -3.054   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       6.154  -2.484   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       5.425  -1.127   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       5.738   0.381   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       4.230   0.693   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       3.917  -0.814   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       2.377  -0.862   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       3.260  -2.208   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      10.001  -3.780   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       6.464   2.797   0.000  0.00  0.00           O+0
CONECT    1    2    6                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4   11   17                                             
CONECT    4    3    5                                                       
CONECT    5    4    6    8   16                                             
CONECT    6    5    1    7                                                  
CONECT    7    6                                                            
CONECT    8    5    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11   13                                                  
CONECT   11   10    3   12                                                  
CONECT   12   11   13                                                       
CONECT   13   12   10   14   15                                             
CONECT   14   13                                                            
CONECT   15   13                                                            
CONECT   16    5                                                            
CONECT   17    3                                                            
MASTER        0    0    0    0    0    0    0    0   17    0   38    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₅H₂₆O₂

Average Mass

238.3710 Da

Monoisotopic Mass

238.19328 Da

IUPAC Name

(1R,2R,5R,8S,9R)-4,4,8-trimethyltricyclo[6.3.1.0^{2,5}]dodecane-1,9-diol

Traditional Name

(1R,2R,5R,8S,9R)-4,4,8-trimethyltricyclo[6.3.1.0^{2,5}]dodecane-1,9-diol

CAS Registry Number

Not Available

SMILES

CC1(C)C[C@@H]2[C@H]1CC[C@@]1(C)C[C@]2(O)CC[C@H]1O

InChI Identifier

InChI=1S/C15H26O2/c1-13(2)8-11-10(13)4-6-14(3)9-15(11,17)7-5-12(14)16/h10-12,16-17H,4-9H2,1-3H3/t10-,11-,12-,14+,15-/m1/s1

InChI Key

SFJOMLIUSIKKRA-MYYUVRNCSA-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
Panax ginseng	LOTUS Database	35616633
Senecio crassissimum	Plant	KNApSAcK
Senecio crassissimus	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as tertiary alcohols. Tertiary alcohols are compounds in which a hydroxy group, -OH, is attached to a saturated carbon atom R3COH (R not H ).

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Alcohols and polyols

Direct Parent

Tertiary alcohols

Alternative Parents

Substituents

Tertiary alcohol
Cyclic alcohol
Secondary alcohol
Hydrocarbon derivative
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	2.19	ALOGPS
logP	2.2	ChemAxon
logS	-3	ALOGPS
pKa (Strongest Acidic)	14.3	ChemAxon
pKa (Strongest Basic)	-2.9	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	40.46 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	68.02 m³·mol⁻¹	ChemAxon
Polarizability	28.01 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	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

C00021998

Chemspider ID

113612035

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

102059900

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Fraga BM, Diaz CE, Amador LJ, Reina M, Santana O, Gonzalez-Coloma A: Bioactive compounds from transformed root cultures and aerial parts of Bethencourtia hermosae. Phytochemistry. 2014 Dec;108:220-8. doi: 10.1016/j.phytochem.2014.09.010. Epub 2014 Oct 6. [PubMed:25301666 ]

Showing NP-Card for Senecrassidiol (NP0064928)

MOL for NP0064928 (Senecrassidiol)

3D MOL for NP0064928 (Senecrassidiol)

3D SDF for NP0064928 (Senecrassidiol)

3D-SDF for NP0064928 (Senecrassidiol)

PDB for NP0064928 (Senecrassidiol)

3D PDB for NP0064928 (Senecrassidiol)

SMILES for NP0064928 (Senecrassidiol)

INCHI for NP0064928 (Senecrassidiol)

Structure for NP0064928 (Senecrassidiol)

3D Structure for NP0064928 (Senecrassidiol)