NP-MRD: Showing NP-Card for (-)-Pacificin J (NP0078648)

Jump To Section:

Identification Spectra BioTaxonomy ChemoTaxonomy Physical properties Links References XML

Record Information

Version

2.0

Created at

2022-04-28 23:40:50 UTC

Updated at

2022-04-28 23:40:51 UTC

NP-MRD ID

NP0078648

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(-)-Pacificin J

Description

Pacificin J 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 ). (-)-Pacificin J is found in Nephthea pacifica. Based on a literature review very few articles have been published on Pacificin J.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 53 54  0  0  0  0  0  0  0  0999 V2000
   -2.7042   -2.8811   -0.6066 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6548   -1.8834    0.2406 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8829   -1.1547    0.7287 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3786   -0.2026   -0.2270 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6639    0.5252   -1.2035 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7673    1.4679   -0.9459 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0827    2.1621   -2.0773 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5225    1.7601    0.4410 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1617    1.7013    1.0076 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1788    0.7126    0.5584 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.6105    0.3276    1.8338 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9551    1.3288   -0.2960 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0711    0.3157   -0.4285 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2892    0.5593    0.0014 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3626   -0.4486   -0.1403 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.7035    0.2863   -0.0881 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2905   -1.1394   -1.4989 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3469   -1.4253    0.8239 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6656   -0.5070   -0.1383 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.0595   -1.8400    0.1303 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3281   -1.4525    0.7476 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.6679   -3.2025   -0.9780 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8303   -3.3920   -0.9437 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6259   -2.0017    0.8835 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6564   -0.8778    1.7563 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2518   -0.6997   -0.7628 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9841    0.5751    0.3638 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8454    0.3093   -2.2574 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3641    2.9168   -1.7212 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6064    1.4016   -2.7427 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8800    2.7098   -2.6347 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3207    1.3967    1.1597 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7945    2.8784    0.5263 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6109    2.6995    0.9329 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2543    1.6254    2.1372 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5024   -0.2515    1.6113 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0258   -0.0000    2.6453 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0115    1.3359    2.1693 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3755    2.2187    0.1583 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5890    1.4396   -1.3347 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8637   -0.6434   -0.8924 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4525    1.5477    0.4660 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4874   -0.2870   -0.6361 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5193    1.2641   -0.6103 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9347    0.4488    0.9683 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9415   -2.1833   -1.3972 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2811   -1.1220   -2.0128 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5472   -0.5759   -2.1250 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2218   -1.5937    1.2507 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9272   -0.3478   -1.2047 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0438   -2.5856   -0.6668 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7825   -1.9774    0.8456 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3996   -1.2388    1.8486 H   0  0  0  0  0  0  0  0  0  0  0  0
  7  6  1  0
  6  5  2  0
  5  4  1  0
  4  3  1  0
  3  2  1  0
  2  1  2  3
  2 21  1  0
 21 20  1  0
 20 19  1  0
 19 10  1  0
 10 11  1  1
 10 12  1  0
 12 13  1  0
 13 14  2  0
 14 15  1  0
 15 16  1  0
 15 17  1  0
 15 18  1  1
 10  9  1  0
  9  8  1  0
  8  6  1  0
 19 21  1  0
  7 29  1  0
  7 30  1  0
  7 31  1  0
  5 28  1  0
  4 26  1  0
  4 27  1  0
  3 24  1  0
  3 25  1  0
  1 22  1  0
  1 23  1  0
 21 53  1  1
 20 51  1  0
 20 52  1  0
 19 50  1  6
 11 36  1  0
 11 37  1  0
 11 38  1  0
 12 39  1  0
 12 40  1  0
 13 41  1  0
 14 42  1  0
 16 43  1  0
 16 44  1  0
 16 45  1  0
 17 46  1  0
 17 47  1  0
 17 48  1  0
 18 49  1  0
  9 34  1  0
  9 35  1  0
  8 32  1  0
  8 33  1  0
M  END


  Mrv1652304292201402D          

 21 22  0  0  1  0            999 V2000
    0.6297   -0.6838    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.2773    0.0622    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.7471    0.7403    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.5694    0.6725    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9217   -0.0734    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7439   -0.1412    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0963   -0.8872    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6265   -1.5653    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8043   -1.4975    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4519   -0.7516    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2306   -0.4791    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2138    0.5369    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0858    1.2336    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6720    0.9074    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3333    1.4006    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0911    1.0745    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8489    0.7484    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4173    1.8323    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7650    0.3167    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7862    1.5644    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1925   -0.6159    0.0000 C   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
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  1 10  1  0  0  0  0
 10 11  2  0  0  0  0
  6 12  1  0  0  0  0
  3 13  1  1  0  0  0
 13 14  1  0  0  0  0
 14 15  2  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 16 18  1  0  0  0  0
 16 19  1  0  0  0  0
  3 20  1  6  0  0  0
  2 21  1  6  0  0  0
  1 21  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0078648

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C\C1=C\CCC(=C)[C@H]2C[C@@H]2[C@@](C)(C\C=C\C(C)(C)O)CC1

> <INCHI_IDENTIFIER>
InChI=1S/C20H32O/c1-15-8-6-9-16(2)17-14-18(17)20(5,13-10-15)12-7-11-19(3,4)21/h7-8,11,17-18,21H,2,6,9-10,12-14H2,1,3-5H3/b11-7+,15-8-/t17-,18+,20+/m1/s1

> <INCHI_KEY>
SPKCOCUHKUVJLN-KBPOYXTOSA-N

> <FORMULA>
C20H32O

> <MOLECULAR_WEIGHT>
288.475

> <EXACT_MASS>
288.24531565

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
53

> <JCHEM_AVERAGE_POLARIZABILITY>
35.7754074665665

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(3E)-5-[(1S,2R,5Z,10S)-2,5-dimethyl-9-methylidenebicyclo[8.1.0]undec-5-en-2-yl]-2-methylpent-3-en-2-ol

> <ALOGPS_LOGP>
5.48

> <JCHEM_LOGP>
4.907474266333334

> <ALOGPS_LOGS>
-5.29

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
17.78131010014986

> <JCHEM_PKA_STRONGEST_BASIC>
-1.582254962194451

> <JCHEM_POLAR_SURFACE_AREA>
20.23

> <JCHEM_REFRACTIVITY>
93.2037

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.49e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(3E)-5-[(1S,2R,5Z,10S)-2,5-dimethyl-9-methylidenebicyclo[8.1.0]undec-5-en-2-yl]-2-methylpent-3-en-2-ol

> <JCHEM_VEBER_RULE>
1

$$$$

HEADER    PROTEIN                                 29-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   29-APR-22         0                                  
HETATM    1  C   UNK     0       1.175  -1.276   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.518   0.116   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.395   1.382   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.929   1.255   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       3.587  -0.137   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       5.122  -0.264   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       5.780  -1.656   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.903  -2.922   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       3.368  -2.795   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.710  -1.403   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.164  -0.894   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       5.999   1.002   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       0.160   2.303   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -1.254   1.694   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -2.489   2.615   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -3.903   2.006   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -5.318   1.397   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -4.512   3.420   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      -3.295   0.591   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0       1.468   2.920   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      -0.359  -1.150   0.000  0.00  0.00           C+0
CONECT    1    2   10   21                                                  
CONECT    2    1    3   21                                                  
CONECT    3    2    4   13   20                                             
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7   12                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9    1   11                                                  
CONECT   11   10                                                            
CONECT   12    6                                                            
CONECT   13    3   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17   18   19                                             
CONECT   17   16                                                            
CONECT   18   16                                                            
CONECT   19   16                                                            
CONECT   20    3                                                            
CONECT   21    2    1                                                       
MASTER        0    0    0    0    0    0    0    0   21    0   44    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₀H₃₂O

Average Mass

288.4750 Da

Monoisotopic Mass

288.24532 Da

IUPAC Name

(3E)-5-[(1S,2R,5Z,10S)-2,5-dimethyl-9-methylidenebicyclo[8.1.0]undec-5-en-2-yl]-2-methylpent-3-en-2-ol

Traditional Name

(3E)-5-[(1S,2R,5Z,10S)-2,5-dimethyl-9-methylidenebicyclo[8.1.0]undec-5-en-2-yl]-2-methylpent-3-en-2-ol

CAS Registry Number

Not Available

SMILES

C\C1=C\CCC(=C)[C@H]2C[C@@H]2[C@@](C)(C\C=C\C(C)(C)O)CC1

InChI Identifier

InChI=1S/C20H32O/c1-15-8-6-9-16(2)17-14-18(17)20(5,13-10-15)12-7-11-19(3,4)21/h7-8,11,17-18,21H,2,6,9-10,12-14H2,1,3-5H3/b11-7+,15-8-/t17-,18+,20+/m1/s1

InChI Key

SPKCOCUHKUVJLN-KBPOYXTOSA-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
Nephthea pacifica	-	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

Hydrocarbon derivatives

Substituents

Tertiary 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	5.48	ALOGPS
logP	4.91	ChemAxon
logS	-5.3	ALOGPS
pKa (Strongest Acidic)	17.78	ChemAxon
pKa (Strongest Basic)	-1.6	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	3	ChemAxon
Refractivity	93.2 m³·mol⁻¹	ChemAxon
Polarizability	35.78 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

C00042822

Chemspider ID

9612564

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

11437700

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Showing NP-Card for (-)-Pacificin J (NP0078648)

MOL for NP0078648 ((-)-Pacificin J)

3D MOL for NP0078648 ((-)-Pacificin J)

3D SDF for NP0078648 ((-)-Pacificin J)

3D-SDF for NP0078648 ((-)-Pacificin J)

PDB for NP0078648 ((-)-Pacificin J)

3D PDB for NP0078648 ((-)-Pacificin J)

SMILES for NP0078648 ((-)-Pacificin J)

INCHI for NP0078648 ((-)-Pacificin J)

Structure for NP0078648 ((-)-Pacificin J)

3D Structure for NP0078648 ((-)-Pacificin J)