NP-MRD: Showing NP-Card for (1r,4s,5r,6s,9r,10s,11s,13s)-11-hydroxy-5-({[(2r)-5-hydroxy-3,4-dihydro-2h-pyrrol-2-yl]oxy}methyl)-5,9-dimethyl-14-methylidene-15-oxotetracyclo[11.2.1.0¹,¹⁰.0⁴,⁹]hexadecan-6-yl acetate (NP0230296)

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Record Information

Version

2.0

Created at

2022-09-06 10:42:19 UTC

Updated at

2022-09-06 10:42:19 UTC

NP-MRD ID

NP0230296

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(1r,4s,5r,6s,9r,10s,11s,13s)-11-hydroxy-5-({[(2r)-5-hydroxy-3,4-dihydro-2h-pyrrol-2-yl]oxy}methyl)-5,9-dimethyl-14-methylidene-15-oxotetracyclo[11.2.1.0¹,¹⁰.0⁴,⁹]hexadecan-6-yl acetate

Description

Excisusin F belongs to the class of organic compounds known as kaurane diterpenoids. These are diterpene alkaloids with a structure that is based on the kaurane skeleton. Kaurane is a tetracyclic compound that arises by cyclisation of a pimarane precursor followed by rearrangement. It possesses a [3,2,1]-bicyclic ring system with C15-C16 bridge connected to C13, forming the five-membered ring D. (1r,4s,5r,6s,9r,10s,11s,13s)-11-hydroxy-5-({[(2r)-5-hydroxy-3,4-dihydro-2h-pyrrol-2-yl]oxy}methyl)-5,9-dimethyl-14-methylidene-15-oxotetracyclo[11.2.1.0¹,¹⁰.0⁴,⁹]hexadecan-6-yl acetate is found in Isodon excisus. (1r,4s,5r,6s,9r,10s,11s,13s)-11-hydroxy-5-({[(2r)-5-hydroxy-3,4-dihydro-2h-pyrrol-2-yl]oxy}methyl)-5,9-dimethyl-14-methylidene-15-oxotetracyclo[11.2.1.0¹,¹⁰.0⁴,⁹]hexadecan-6-yl acetate was first documented in 2011 (PMID: 21273070). Based on a literature review very few articles have been published on Excisusin F.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309062212422D          

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M  END

     RDKit          3D

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M  END


  Mrv1652309062212422D          

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 26 27  1  6  0  0  0
 26 28  1  0  0  0  0
 28  5  1  6  0  0  0
 28 29  1  0  0  0  0
 29 30  1  1  0  0  0
 29 31  1  0  0  0  0
 31 32  1  0  0  0  0
  2 32  1  0  0  0  0
 32 33  1  6  0  0  0
  5 33  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0230296

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(=O)O[C@H]1CC[C@]2(C)[C@H](CC[C@@]34C[C@@H](C[C@H](O)[C@@H]23)C(=C)C4=O)[C@]1(C)CO[C@@H]1CCC(O)=N1

> <INCHI_IDENTIFIER>
InChI=1S/C26H37NO6/c1-14-16-11-17(29)22-24(3)9-8-19(33-15(2)28)25(4,13-32-21-6-5-20(30)27-21)18(24)7-10-26(22,12-16)23(14)31/h16-19,21-22,29H,1,5-13H2,2-4H3,(H,27,30)/t16-,17+,18+,19+,21-,22+,24-,25+,26-/m1/s1

> <INCHI_KEY>
UDIMVRVKHIXRQH-TYORKGSASA-N

> <FORMULA>
C26H37NO6

> <MOLECULAR_WEIGHT>
459.583

> <EXACT_MASS>
459.262087915

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
70

> <JCHEM_AVERAGE_POLARIZABILITY>
50.240560542832796

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1R,4S,5R,6S,9R,10S,11S,13S)-11-hydroxy-5-({[(2R)-5-hydroxy-3,4-dihydro-2H-pyrrol-2-yl]oxy}methyl)-5,9-dimethyl-14-methylidene-15-oxotetracyclo[11.2.1.0^{1,10}.0^{4,9}]hexadecan-6-yl acetate

> <JCHEM_LOGP>
2.8903405509999995

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
14.878256596716927

> <JCHEM_PKA_STRONGEST_ACIDIC>
5.561615267356719

> <JCHEM_PKA_STRONGEST_BASIC>
-1.7981394026729407

> <JCHEM_POLAR_SURFACE_AREA>
105.42

> <JCHEM_REFRACTIVITY>
120.83539999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(1R,4S,5R,6S,9R,10S,11S,13S)-11-hydroxy-5-({[(2R)-5-hydroxy-3,4-dihydro-2H-pyrrol-2-yl]oxy}methyl)-5,9-dimethyl-14-methylidene-15-oxotetracyclo[11.2.1.0^{1,10}.0^{4,9}]hexadecan-6-yl acetate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 06-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-SEP-22         0                                  
HETATM    1  C   UNK     0       0.081  -0.001   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.599  -0.263   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.761   0.870   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       2.508   2.389   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       4.273   0.155   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       4.843   1.624   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       6.354   1.935   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       7.389   0.779   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       8.892   1.111   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       8.304   2.535   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      10.192   1.938   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      10.126   3.476   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       8.760   4.189   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       7.382   3.503   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       6.303   4.602   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       7.015   5.967   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       6.329   7.346   0.000  0.00  0.00           O+0
HETATM   18  N   UNK     0       8.534   5.712   0.000  0.00  0.00           N+0
HETATM   19  C   UNK     0       9.932  -0.025   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0      11.436   0.307   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0      11.900   1.776   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      10.860   2.912   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0      13.404   2.108   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0       9.468  -1.493   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       7.964  -1.825   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       6.924  -0.689   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       6.477  -2.163   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       5.392  -1.066   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       4.934  -2.642   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0       5.969  -3.783   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0       3.356  -2.939   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       2.310  -1.708   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       3.386  -0.839   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   32                                                  
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6   28   33                                             
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9   26                                                  
CONECT    9    8   10   11   19                                             
CONECT   10    9                                                            
CONECT   11    9   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14   18                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17   18                                                  
CONECT   17   16                                                            
CONECT   18   16   13                                                       
CONECT   19    9   20   24                                                  
CONECT   20   19   21                                                       
CONECT   21   20   22   23                                                  
CONECT   22   21                                                            
CONECT   23   21                                                            
CONECT   24   19   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25    8   27   28                                             
CONECT   27   26                                                            
CONECT   28   26    5   29                                                  
CONECT   29   28   30   31                                                  
CONECT   30   29                                                            
CONECT   31   29   32                                                       
CONECT   32   31    2   33                                                  
CONECT   33   32    5                                                       
MASTER        0    0    0    0    0    0    0    0   33    0   74    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₆H₃₇NO₆

Average Mass

459.5830 Da

Monoisotopic Mass

459.26209 Da

IUPAC Name

(1R,4S,5R,6S,9R,10S,11S,13S)-11-hydroxy-5-({[(2R)-5-hydroxy-3,4-dihydro-2H-pyrrol-2-yl]oxy}methyl)-5,9-dimethyl-14-methylidene-15-oxotetracyclo[11.2.1.0^{1,10}.0^{4,9}]hexadecan-6-yl acetate

Traditional Name

(1R,4S,5R,6S,9R,10S,11S,13S)-11-hydroxy-5-({[(2R)-5-hydroxy-3,4-dihydro-2H-pyrrol-2-yl]oxy}methyl)-5,9-dimethyl-14-methylidene-15-oxotetracyclo[11.2.1.0^{1,10}.0^{4,9}]hexadecan-6-yl acetate

CAS Registry Number

Not Available

SMILES

CC(=O)O[C@H]1CC[C@]2(C)[C@H](CC[C@@]34C[C@@H](C[C@H](O)[C@@H]23)C(=C)C4=O)[C@]1(C)CO[C@@H]1CCC(O)=N1

InChI Identifier

InChI=1S/C26H37NO6/c1-14-16-11-17(29)22-24(3)9-8-19(33-15(2)28)25(4,13-32-21-6-5-20(30)27-21)18(24)7-10-26(22,12-16)23(14)31/h16-19,21-22,29H,1,5-13H2,2-4H3,(H,27,30)/t16-,17+,18+,19+,21-,22+,24-,25+,26-/m1/s1

InChI Key

UDIMVRVKHIXRQH-TYORKGSASA-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
Isodon excisus	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as kaurane diterpenoids. These are diterpene alkaloids with a structure that is based on the kaurane skeleton. Kaurane is a tetracyclic compound that arises by cyclisation of a pimarane precursor followed by rearrangement. It possesses a [3,2,1]-bicyclic ring system with C15-C16 bridge connected to C13, forming the five-membered ring D.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Diterpenoids

Direct Parent

Kaurane diterpenoids

Alternative Parents

Substituents

Kaurane diterpenoid
Hydroxysteroid
1-hydroxysteroid
Steroid
Pyrrolidone
2-pyrrolidone
Cyclic alcohol
Pyrrolidine
Carboxamide group
Carboxylic acid ester
Ketone
Lactam
Secondary alcohol
Secondary carboxylic acid amide
Organoheterocyclic compound
Monocarboxylic acid or derivatives
Azacycle
Carboxylic acid derivative
Organooxygen compound
Organonitrogen compound
Organic oxide
Carbonyl group
Organic nitrogen compound
Alcohol
Hydrocarbon derivative
Organic oxygen compound
Organopnictogen compound
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	2.89	ChemAxon
pKa (Strongest Acidic)	5.56	ChemAxon
pKa (Strongest Basic)	-1.8	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	105.42 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	120.84 m³·mol⁻¹	ChemAxon
Polarizability	50.24 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

26386279

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

53323644

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Hong SS, Lee SA, Kim N, Hwang JS, Han XH, Lee MK, Jung JK, Hong JT, Kim Y, Lee D, Hwang BY: Pyrrolidinone diterpenoid from Isodon excisus and inhibition of nitric oxide production in lipopolysaccharide-induced macrophage RAW264.7 cells. Bioorg Med Chem Lett. 2011 Feb 15;21(4):1279-81. doi: 10.1016/j.bmcl.2010.11.095. Epub 2010 Nov 25. [PubMed:21273070 ]
LOTUS database [Link]

Showing NP-Card for (1r,4s,5r,6s,9r,10s,11s,13s)-11-hydroxy-5-({[(2r)-5-hydroxy-3,4-dihydro-2h-pyrrol-2-yl]oxy}methyl)-5,9-dimethyl-14-methylidene-15-oxotetracyclo[11.2.1.0¹,¹⁰.0⁴,⁹]hexadecan-6-yl acetate (NP0230296)

MOL for NP0230296 ((1r,4s,5r,6s,9r,10s,11s,13s)-11-hydroxy-5-({[(2r)-5-hydroxy-3,4-dihydro-2h-pyrrol-2-yl]oxy}methyl)-5,9-dimethyl-14-methylidene-15-oxotetracyclo[11.2.1.0¹,¹⁰.0⁴,⁹]hexadecan-6-yl acetate)

3D MOL for NP0230296 ((1r,4s,5r,6s,9r,10s,11s,13s)-11-hydroxy-5-({[(2r)-5-hydroxy-3,4-dihydro-2h-pyrrol-2-yl]oxy}methyl)-5,9-dimethyl-14-methylidene-15-oxotetracyclo[11.2.1.0¹,¹⁰.0⁴,⁹]hexadecan-6-yl acetate)

3D SDF for NP0230296 ((1r,4s,5r,6s,9r,10s,11s,13s)-11-hydroxy-5-({[(2r)-5-hydroxy-3,4-dihydro-2h-pyrrol-2-yl]oxy}methyl)-5,9-dimethyl-14-methylidene-15-oxotetracyclo[11.2.1.0¹,¹⁰.0⁴,⁹]hexadecan-6-yl acetate)

3D-SDF for NP0230296 ((1r,4s,5r,6s,9r,10s,11s,13s)-11-hydroxy-5-({[(2r)-5-hydroxy-3,4-dihydro-2h-pyrrol-2-yl]oxy}methyl)-5,9-dimethyl-14-methylidene-15-oxotetracyclo[11.2.1.0¹,¹⁰.0⁴,⁹]hexadecan-6-yl acetate)

PDB for NP0230296 ((1r,4s,5r,6s,9r,10s,11s,13s)-11-hydroxy-5-({[(2r)-5-hydroxy-3,4-dihydro-2h-pyrrol-2-yl]oxy}methyl)-5,9-dimethyl-14-methylidene-15-oxotetracyclo[11.2.1.0¹,¹⁰.0⁴,⁹]hexadecan-6-yl acetate)

3D PDB for NP0230296 ((1r,4s,5r,6s,9r,10s,11s,13s)-11-hydroxy-5-({[(2r)-5-hydroxy-3,4-dihydro-2h-pyrrol-2-yl]oxy}methyl)-5,9-dimethyl-14-methylidene-15-oxotetracyclo[11.2.1.0¹,¹⁰.0⁴,⁹]hexadecan-6-yl acetate)

SMILES for NP0230296 ((1r,4s,5r,6s,9r,10s,11s,13s)-11-hydroxy-5-({[(2r)-5-hydroxy-3,4-dihydro-2h-pyrrol-2-yl]oxy}methyl)-5,9-dimethyl-14-methylidene-15-oxotetracyclo[11.2.1.0¹,¹⁰.0⁴,⁹]hexadecan-6-yl acetate)

INCHI for NP0230296 ((1r,4s,5r,6s,9r,10s,11s,13s)-11-hydroxy-5-({[(2r)-5-hydroxy-3,4-dihydro-2h-pyrrol-2-yl]oxy}methyl)-5,9-dimethyl-14-methylidene-15-oxotetracyclo[11.2.1.0¹,¹⁰.0⁴,⁹]hexadecan-6-yl acetate)

Structure for NP0230296 ((1r,4s,5r,6s,9r,10s,11s,13s)-11-hydroxy-5-({[(2r)-5-hydroxy-3,4-dihydro-2h-pyrrol-2-yl]oxy}methyl)-5,9-dimethyl-14-methylidene-15-oxotetracyclo[11.2.1.0¹,¹⁰.0⁴,⁹]hexadecan-6-yl acetate)

3D Structure for NP0230296 ((1r,4s,5r,6s,9r,10s,11s,13s)-11-hydroxy-5-({[(2r)-5-hydroxy-3,4-dihydro-2h-pyrrol-2-yl]oxy}methyl)-5,9-dimethyl-14-methylidene-15-oxotetracyclo[11.2.1.0¹,¹⁰.0⁴,⁹]hexadecan-6-yl acetate)