NP-MRD: Showing NP-Card for (1s,3r,6s,8r,9r,10s,12r,13r)-10-hydroxy-13-isopropyl-9,12-dimethyl-4-methylidene-7-oxapentacyclo[7.6.0.0¹,¹².0³,⁸.0⁶,⁸]pentadecane-5,11-dione (NP0304863)

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Record Information

Version

2.0

Created at

2022-09-10 20:15:05 UTC

Updated at

2022-09-10 20:15:05 UTC

NP-MRD ID

NP0304863

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(1s,3r,6s,8r,9r,10s,12r,13r)-10-hydroxy-13-isopropyl-9,12-dimethyl-4-methylidene-7-oxapentacyclo[7.6.0.0¹,¹².0³,⁸.0⁶,⁸]pentadecane-5,11-dione

Description

Crinipellin B belongs to the class of organic compounds known as angular triquinanes. These are triquinane with a structure based on a [6.3.0.0^1,5] Undecane carbon skeleton. (1s,3r,6s,8r,9r,10s,12r,13r)-10-hydroxy-13-isopropyl-9,12-dimethyl-4-methylidene-7-oxapentacyclo[7.6.0.0¹,¹².0³,⁸.0⁶,⁸]pentadecane-5,11-dione is found in Crinipellis scabella. (1s,3r,6s,8r,9r,10s,12r,13r)-10-hydroxy-13-isopropyl-9,12-dimethyl-4-methylidene-7-oxapentacyclo[7.6.0.0¹,¹².0³,⁸.0⁶,⁸]pentadecane-5,11-dione was first documented in 2006 (PMID: 17268633). Based on a literature review very few articles have been published on Crinipellin B (PMID: 29797755).

Structure

MOL SDF PDB SMILES InChI


  Mrv1652309102222152D          

 24 28  0  0  1  0            999 V2000
    2.2422   -2.9598    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3950   -2.1491    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1407   -1.7961    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8645   -2.1919    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0354   -0.9779    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.7624   -0.1994    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2247   -0.8251    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.8289   -1.5489    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.0182   -1.3962    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9129   -0.5779    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.5171   -1.3018    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2936   -1.1490    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3989   -0.3307    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.1227    0.0651    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8274   -0.3639    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1419    0.8899    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3468    0.0222    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.2193    0.6223    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7426    0.7461    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3897    1.4917    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5534    0.5933    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.1535    1.1594    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6586   -0.2250    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.4043    0.1280    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
  3  5  1  0  0  0  0
  5  6  1  6  0  0  0
  7  6  1  6  0  0  0
  5  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  2  1  1  0  0  0
  8  9  1  0  0  0  0
 10  9  1  6  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  6  0  0  0
 14 15  1  0  0  0  0
 14 16  1  0  0  0  0
 13 17  1  0  0  0  0
 10 17  1  0  0  0  0
 17 18  1  6  0  0  0
 17 19  1  0  0  0  0
 19 20  2  0  0  0  0
 19 21  1  0  0  0  0
 21 22  1  1  0  0  0
 21 23  1  0  0  0  0
 10 23  1  0  0  0  0
  7 23  1  0  0  0  0
 23 24  1  1  0  0  0
M  END


  Mrv1652309102222152D          

 24 28  0  0  1  0            999 V2000
    2.2422   -2.9598    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3950   -2.1491    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1407   -1.7961    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8645   -2.1919    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0354   -0.9779    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.7624   -0.1994    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2247   -0.8251    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.8289   -1.5489    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.0182   -1.3962    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9129   -0.5779    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.5171   -1.3018    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2936   -1.1490    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3989   -0.3307    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.1227    0.0651    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8274   -0.3639    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1419    0.8899    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3468    0.0222    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.2193    0.6223    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7426    0.7461    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3897    1.4917    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5534    0.5933    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.1535    1.1594    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6586   -0.2250    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.4043    0.1280    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
  3  5  1  0  0  0  0
  5  6  1  6  0  0  0
  7  6  1  6  0  0  0
  5  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  2  1  1  0  0  0
  8  9  1  0  0  0  0
 10  9  1  6  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  6  0  0  0
 14 15  1  0  0  0  0
 14 16  1  0  0  0  0
 13 17  1  0  0  0  0
 10 17  1  0  0  0  0
 17 18  1  6  0  0  0
 17 19  1  0  0  0  0
 19 20  2  0  0  0  0
 19 21  1  0  0  0  0
 21 22  1  1  0  0  0
 21 23  1  0  0  0  0
 10 23  1  0  0  0  0
  7 23  1  0  0  0  0
 23 24  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0304863

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C)[C@H]1CC[C@]23C[C@@H]4C(=C)C(=O)[C@H]5O[C@@]45[C@@]2(C)[C@H](O)C(=O)[C@]13C

> <INCHI_IDENTIFIER>
InChI=1S/C20H26O4/c1-9(2)11-6-7-19-8-12-10(3)13(21)16-20(12,24-16)18(19,5)15(23)14(22)17(11,19)4/h9,11-12,15-16,23H,3,6-8H2,1-2,4-5H3/t11-,12-,15-,16-,17+,18+,19-,20+/m1/s1

> <INCHI_KEY>
PBZBBNIYZKWVGM-GCMPBZKXSA-N

> <FORMULA>
C20H26O4

> <MOLECULAR_WEIGHT>
330.424

> <EXACT_MASS>
330.183109317

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
50

> <JCHEM_AVERAGE_POLARIZABILITY>
35.46664195390795

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1S,3R,6S,8R,9R,10S,12R,13R)-10-hydroxy-9,12-dimethyl-4-methylidene-13-(propan-2-yl)-7-oxapentacyclo[7.6.0.0^{1,12}.0^{3,8}.0^{6,8}]pentadecane-5,11-dione

> <JCHEM_LOGP>
2.9299699499999994

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
18.46735450392292

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.845669970384542

> <JCHEM_PKA_STRONGEST_BASIC>
-3.741019214632563

> <JCHEM_POLAR_SURFACE_AREA>
66.9

> <JCHEM_REFRACTIVITY>
87.4438

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(1S,3R,6S,8R,9R,10S,12R,13R)-10-hydroxy-13-isopropyl-9,12-dimethyl-4-methylidene-7-oxapentacyclo[7.6.0.0^{1,12}.0^{3,8}.0^{6,8}]pentadecane-5,11-dione

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 10-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   10-SEP-22         0                                  
HETATM    1  C   UNK     0       4.185  -5.525   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.471  -4.012   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.863  -3.353   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       7.214  -4.092   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       5.666  -1.825   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       5.156  -0.372   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       4.153  -1.540   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       3.414  -2.891   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.901  -2.606   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.704  -1.079   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       0.965  -2.430   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -0.548  -2.145   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -0.745  -0.617   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -2.096   0.121   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -3.411  -0.679   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -2.131   1.661   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       0.647   0.041   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -0.409   1.162   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       1.386   1.393   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0       0.727   2.785   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0       2.900   1.107   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0       4.020   2.164   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0       3.096  -0.420   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       4.488   0.239   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    8                                                  
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6    7                                                  
CONECT    6    5    7                                                       
CONECT    7    6    5    8   23                                             
CONECT    8    7    2    9                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11   17   23                                             
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14   17                                                  
CONECT   14   13   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14                                                            
CONECT   17   13   10   18   19                                             
CONECT   18   17                                                            
CONECT   19   17   20   21                                                  
CONECT   20   19                                                            
CONECT   21   19   22   23                                                  
CONECT   22   21                                                            
CONECT   23   21   10    7   24                                             
CONECT   24   23                                                            
MASTER        0    0    0    0    0    0    0    0   24    0   56    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₀H₂₆O₄

Average Mass

330.4240 Da

Monoisotopic Mass

330.18311 Da

IUPAC Name

(1S,3R,6S,8R,9R,10S,12R,13R)-10-hydroxy-9,12-dimethyl-4-methylidene-13-(propan-2-yl)-7-oxapentacyclo[7.6.0.0^{1,12}.0^{3,8}.0^{6,8}]pentadecane-5,11-dione

Traditional Name

(1S,3R,6S,8R,9R,10S,12R,13R)-10-hydroxy-13-isopropyl-9,12-dimethyl-4-methylidene-7-oxapentacyclo[7.6.0.0^{1,12}.0^{3,8}.0^{6,8}]pentadecane-5,11-dione

CAS Registry Number

Not Available

SMILES

CC(C)[C@H]1CC[C@]23C[C@@H]4C(=C)C(=O)[C@H]5O[C@@]45[C@@]2(C)[C@H](O)C(=O)[C@]13C

InChI Identifier

InChI=1S/C20H26O4/c1-9(2)11-6-7-19-8-12-10(3)13(21)16-20(12,24-16)18(19,5)15(23)14(22)17(11,19)4/h9,11-12,15-16,23H,3,6-8H2,1-2,4-5H3/t11-,12-,15-,16-,17+,18+,19-,20+/m1/s1

InChI Key

PBZBBNIYZKWVGM-GCMPBZKXSA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Crinipellis scabella	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as angular triquinanes. These are triquinane with a structure based on a [6.3.0.0^1,5] Undecane carbon skeleton.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Sesquiterpenoids

Direct Parent

Angular triquinanes

Alternative Parents

Substituents

Angular triquinane sesquiterpenoid
Oxane
Cyclic alcohol
Secondary alcohol
Ketone
Oxacycle
Organoheterocyclic compound
Ether
Oxirane
Dialkyl ether
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Carbonyl group
Alcohol
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic 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	2.93	ChemAxon
pKa (Strongest Acidic)	12.85	ChemAxon
pKa (Strongest Basic)	-3.7	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	66.9 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	87.44 m³·mol⁻¹	ChemAxon
Polarizability	35.47 Å³	ChemAxon
Number of Rings	5	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

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

102050673

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Huang Z, Huang J, Qu Y, Zhang W, Gong J, Yang Z: Total Syntheses of Crinipellins Enabled by Cobalt-Mediated and Palladium-Catalyzed Intramolecular Pauson-Khand Reactions. Angew Chem Int Ed Engl. 2018 Jul 9;57(28):8744-8748. doi: 10.1002/anie.201805143. Epub 2018 Jun 12. [PubMed:29797755 ]
Chappell D, Russell AT: From alpha-cedrene to crinipellin B and onward: 25 years of the alkene-arene meta-photocycloaddition reaction in natural product synthesis. Org Biomol Chem. 2006 Dec 21;4(24):4409-30. doi: 10.1039/b614011b. Epub 2006 Nov 3. [PubMed:17268633 ]
LOTUS database [Link]

Showing NP-Card for (1s,3r,6s,8r,9r,10s,12r,13r)-10-hydroxy-13-isopropyl-9,12-dimethyl-4-methylidene-7-oxapentacyclo[7.6.0.0¹,¹².0³,⁸.0⁶,⁸]pentadecane-5,11-dione (NP0304863)

MOL for NP0304863 ((1s,3r,6s,8r,9r,10s,12r,13r)-10-hydroxy-13-isopropyl-9,12-dimethyl-4-methylidene-7-oxapentacyclo[7.6.0.0¹,¹².0³,⁸.0⁶,⁸]pentadecane-5,11-dione)

3D MOL for NP0304863 ((1s,3r,6s,8r,9r,10s,12r,13r)-10-hydroxy-13-isopropyl-9,12-dimethyl-4-methylidene-7-oxapentacyclo[7.6.0.0¹,¹².0³,⁸.0⁶,⁸]pentadecane-5,11-dione)

3D SDF for NP0304863 ((1s,3r,6s,8r,9r,10s,12r,13r)-10-hydroxy-13-isopropyl-9,12-dimethyl-4-methylidene-7-oxapentacyclo[7.6.0.0¹,¹².0³,⁸.0⁶,⁸]pentadecane-5,11-dione)

3D-SDF for NP0304863 ((1s,3r,6s,8r,9r,10s,12r,13r)-10-hydroxy-13-isopropyl-9,12-dimethyl-4-methylidene-7-oxapentacyclo[7.6.0.0¹,¹².0³,⁸.0⁶,⁸]pentadecane-5,11-dione)

PDB for NP0304863 ((1s,3r,6s,8r,9r,10s,12r,13r)-10-hydroxy-13-isopropyl-9,12-dimethyl-4-methylidene-7-oxapentacyclo[7.6.0.0¹,¹².0³,⁸.0⁶,⁸]pentadecane-5,11-dione)

3D PDB for NP0304863 ((1s,3r,6s,8r,9r,10s,12r,13r)-10-hydroxy-13-isopropyl-9,12-dimethyl-4-methylidene-7-oxapentacyclo[7.6.0.0¹,¹².0³,⁸.0⁶,⁸]pentadecane-5,11-dione)

SMILES for NP0304863 ((1s,3r,6s,8r,9r,10s,12r,13r)-10-hydroxy-13-isopropyl-9,12-dimethyl-4-methylidene-7-oxapentacyclo[7.6.0.0¹,¹².0³,⁸.0⁶,⁸]pentadecane-5,11-dione)

INCHI for NP0304863 ((1s,3r,6s,8r,9r,10s,12r,13r)-10-hydroxy-13-isopropyl-9,12-dimethyl-4-methylidene-7-oxapentacyclo[7.6.0.0¹,¹².0³,⁸.0⁶,⁸]pentadecane-5,11-dione)

Structure for NP0304863 ((1s,3r,6s,8r,9r,10s,12r,13r)-10-hydroxy-13-isopropyl-9,12-dimethyl-4-methylidene-7-oxapentacyclo[7.6.0.0¹,¹².0³,⁸.0⁶,⁸]pentadecane-5,11-dione)

3D Structure for NP0304863 ((1s,3r,6s,8r,9r,10s,12r,13r)-10-hydroxy-13-isopropyl-9,12-dimethyl-4-methylidene-7-oxapentacyclo[7.6.0.0¹,¹².0³,⁸.0⁶,⁸]pentadecane-5,11-dione)