NP-MRD: Showing NP-Card for methyl (1s,2r,3r,4s,5r,8r,9s,10r,13r,15s)-10-(acetyloxy)-3,4-dihydroxy-1,16-dimethyl-11,19-dioxo-6,12,20-trioxahexacyclo[13.7.0.0²,⁸.0⁵,⁹.0⁸,¹³.0¹⁷,²¹]docosa-17,21-diene-5-carboxylate (NP0262456)

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Record Information

Version

2.0

Created at

2022-09-08 05:15:50 UTC

Updated at

2022-09-08 05:15:50 UTC

NP-MRD ID

NP0262456

Secondary Accession Numbers

None

Natural Product Identification

Common Name

methyl (1s,2r,3r,4s,5r,8r,9s,10r,13r,15s)-10-(acetyloxy)-3,4-dihydroxy-1,16-dimethyl-11,19-dioxo-6,12,20-trioxahexacyclo[13.7.0.0²,⁸.0⁵,⁹.0⁸,¹³.0¹⁷,²¹]docosa-17,21-diene-5-carboxylate

Description

Sergiolide belongs to the class of organic compounds known as quassinoids. These are a group of compounds chemically degraded from triterpenes. According to their basic skeleton, quassinoids are categorized into five distinct groups, C-18, C-19, C-20, C-22 and C-25 types. The C-20 quassinoids can be further classified into two types, tetracyclic and the pentacyclic. The tetracyclic variety does not have oxygenation at C-20, while the pentacyclic quassinoids possess additional oxygenation at C-20 that allows for the formation of an additional ring. methyl (1s,2r,3r,4s,5r,8r,9s,10r,13r,15s)-10-(acetyloxy)-3,4-dihydroxy-1,16-dimethyl-11,19-dioxo-6,12,20-trioxahexacyclo[13.7.0.0²,⁸.0⁵,⁹.0⁸,¹³.0¹⁷,²¹]docosa-17,21-diene-5-carboxylate was first documented in 1992 (PMID: 1517739). Based on a literature review very few articles have been published on Sergiolide.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309082207152D          

 36 41  0  0  1  0            999 V2000
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M  END

     RDKit          2D

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M  END


  Mrv1652309082207152D          

 36 41  0  0  1  0            999 V2000
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 32 33  1  0  0  0  0
 33 34  1  1  0  0  0
 33 35  1  0  0  0  0
  5 35  1  0  0  0  0
 35 36  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0262456

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC(=O)[C@@]12OC[C@@]34[C@H]1[C@@H](OC(C)=O)C(=O)O[C@@H]3C[C@H]1C(C)C3=CC(=O)OC3=C[C@]1(C)[C@H]4[C@@H](O)[C@@H]2O

> <INCHI_IDENTIFIER>
InChI=1S/C25H28O11/c1-9-11-5-15(27)35-13(11)7-23(3)12(9)6-14-24-8-33-25(22(31)32-4,20(29)16(28)18(23)24)19(24)17(21(30)36-14)34-10(2)26/h5,7,9,12,14,16-20,28-29H,6,8H2,1-4H3/t9?,12-,14+,16+,17+,18+,19+,20-,23-,24+,25+/m0/s1

> <INCHI_KEY>
ZZKFDOQILIXHHH-MFRMQFBLSA-N

> <FORMULA>
C25H28O11

> <MOLECULAR_WEIGHT>
504.488

> <EXACT_MASS>
504.163161722

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
64

> <JCHEM_AVERAGE_POLARIZABILITY>
34.664963662976206

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
methyl (1S,2R,3R,4S,5R,8R,9S,10R,13R,15S)-10-(acetyloxy)-3,4-dihydroxy-1,16-dimethyl-11,19-dioxo-6,12,20-trioxahexacyclo[13.7.0.0^{2,8}.0^{5,9}.0^{8,13}.0^{17,21}]docosa-17,21-diene-5-carboxylate

> <JCHEM_LOGP>
-0.9373660656666667

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.657570746106888

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.744111006360086

> <JCHEM_PKA_STRONGEST_BASIC>
-3.3259639455881267

> <JCHEM_POLAR_SURFACE_AREA>
154.89000000000001

> <JCHEM_REFRACTIVITY>
118.03700000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
methyl (1S,2R,3R,4S,5R,8R,9S,10R,13R,15S)-10-(acetyloxy)-3,4-dihydroxy-1,16-dimethyl-11,19-dioxo-6,12,20-trioxahexacyclo[13.7.0.0^{2,8}.0^{5,9}.0^{8,13}.0^{17,21}]docosa-17,21-diene-5-carboxylate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 08-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   08-SEP-22         0                                  
HETATM    1  C   UNK     0      -0.918  -4.412   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0      -1.265  -2.912   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0      -0.139  -1.861   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      -1.557  -1.260   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       3.185  -2.437   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       3.391  -1.143   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -0.000   0.000   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      -1.334  -0.770   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0      -2.667   0.000   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      -2.667   1.540   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0      -1.334   2.310   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       1.334   2.310   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       4.001   2.310   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       5.335   1.540   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       6.668   2.310   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       6.668   3.850   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       8.002   1.540   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       9.467   2.016   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      10.372   0.770   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0      11.912   0.770   0.000  0.00  0.00           O+0
HETATM   27  O   UNK     0       9.467  -0.476   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0       8.002   0.000   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       5.335  -1.540   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0       5.335  -3.080   0.000  0.00  0.00           O+0
HETATM   35  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   36  O   UNK     0       2.667  -4.620   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6    9   35                                             
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9   18   32                                             
CONECT    9    8    5   10                                                  
CONECT   10    9   11   15                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12                                                            
CONECT   15   10   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15   18                                                       
CONECT   18   17    8   19                                                  
CONECT   19   18   20                                                       
CONECT   20   19   21   30                                                  
CONECT   21   20   22   23                                                  
CONECT   22   21                                                            
CONECT   23   21   24   28                                                  
CONECT   24   23   25                                                       
CONECT   25   24   26   27                                                  
CONECT   26   25                                                            
CONECT   27   25   28                                                       
CONECT   28   27   23   29                                                  
CONECT   29   28   30                                                       
CONECT   30   29   20   31   32                                             
CONECT   31   30                                                            
CONECT   32   30    8   33                                                  
CONECT   33   32   34   35                                                  
CONECT   34   33                                                            
CONECT   35   33    5   36                                                  
CONECT   36   35                                                            
MASTER        0    0    0    0    0    0    0    0   36    0   82    0
END

View in JSmol

Synonyms

Value	Source
Sergeolide	MeSH

Chemical Formula

C₂₅H₂₈O₁₁

Average Mass

504.4880 Da

Monoisotopic Mass

504.16316 Da

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

Not Available

SMILES

COC(=O)[C@@]12OC[C@@]34[C@H]1[C@@H](OC(C)=O)C(=O)O[C@@H]3C[C@H]1C(C)C3=CC(=O)OC3=C[C@]1(C)[C@H]4[C@@H](O)[C@@H]2O

InChI Identifier

InChI=1S/C25H28O11/c1-9-11-5-15(27)35-13(11)7-23(3)12(9)6-14-24-8-33-25(22(31)32-4,20(29)16(28)18(23)24)19(24)17(21(30)36-14)34-10(2)26/h5,7,9,12,14,16-20,28-29H,6,8H2,1-4H3/t9?,12-,14+,16+,17+,18+,19+,20-,23-,24+,25+/m0/s1

InChI Key

ZZKFDOQILIXHHH-MFRMQFBLSA-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

Not Available

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as quassinoids. These are a group of compounds chemically degraded from triterpenes. According to their basic skeleton, quassinoids are categorized into five distinct groups, C-18, C-19, C-20, C-22 and C-25 types. The C-20 quassinoids can be further classified into two types, tetracyclic and the pentacyclic. The tetracyclic variety does not have oxygenation at C-20, while the pentacyclic quassinoids possess additional oxygenation at C-20 that allows for the formation of an additional ring.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Terpene lactones

Direct Parent

Quassinoids

Alternative Parents

Substituents

Polycyclic triterpenoid
Triterpenoid
C-20 quassinoid skeleton
Quassinoid
Naphthopyran
Tetracarboxylic acid or derivatives
Naphthofuran
Naphthalene
Furopyran
Oxepane
Delta_valerolactone
Delta valerolactone
Beta-hydroxy acid
Pyran
Oxane
Hydroxy acid
2-furanone
Alpha,beta-unsaturated carboxylic ester
Enoate ester
Methyl ester
Tetrahydrofuran
Furan
Enol ester
Dihydrofuran
Cyclic alcohol
Secondary alcohol
Lactone
Carboxylic acid ester
1,2-diol
Oxacycle
Organoheterocyclic compound
Ether
Dialkyl ether
Carboxylic acid derivative
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

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

4572686

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

5458791

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Tischler M, Cardellina JH 2nd, Boyd MR, Cragg GM: Cytotoxic quassinoids from Cedronia granatensis. J Nat Prod. 1992 May;55(5):667-71. doi: 10.1021/np50083a018. [PubMed:1517739 ]
LOTUS database [Link]

Showing NP-Card for methyl (1s,2r,3r,4s,5r,8r,9s,10r,13r,15s)-10-(acetyloxy)-3,4-dihydroxy-1,16-dimethyl-11,19-dioxo-6,12,20-trioxahexacyclo[13.7.0.0²,⁸.0⁵,⁹.0⁸,¹³.0¹⁷,²¹]docosa-17,21-diene-5-carboxylate (NP0262456)

MOL for NP0262456 (methyl (1s,2r,3r,4s,5r,8r,9s,10r,13r,15s)-10-(acetyloxy)-3,4-dihydroxy-1,16-dimethyl-11,19-dioxo-6,12,20-trioxahexacyclo[13.7.0.0²,⁸.0⁵,⁹.0⁸,¹³.0¹⁷,²¹]docosa-17,21-diene-5-carboxylate)

3D MOL for NP0262456 (methyl (1s,2r,3r,4s,5r,8r,9s,10r,13r,15s)-10-(acetyloxy)-3,4-dihydroxy-1,16-dimethyl-11,19-dioxo-6,12,20-trioxahexacyclo[13.7.0.0²,⁸.0⁵,⁹.0⁸,¹³.0¹⁷,²¹]docosa-17,21-diene-5-carboxylate)

3D SDF for NP0262456 (methyl (1s,2r,3r,4s,5r,8r,9s,10r,13r,15s)-10-(acetyloxy)-3,4-dihydroxy-1,16-dimethyl-11,19-dioxo-6,12,20-trioxahexacyclo[13.7.0.0²,⁸.0⁵,⁹.0⁸,¹³.0¹⁷,²¹]docosa-17,21-diene-5-carboxylate)

3D-SDF for NP0262456 (methyl (1s,2r,3r,4s,5r,8r,9s,10r,13r,15s)-10-(acetyloxy)-3,4-dihydroxy-1,16-dimethyl-11,19-dioxo-6,12,20-trioxahexacyclo[13.7.0.0²,⁸.0⁵,⁹.0⁸,¹³.0¹⁷,²¹]docosa-17,21-diene-5-carboxylate)

PDB for NP0262456 (methyl (1s,2r,3r,4s,5r,8r,9s,10r,13r,15s)-10-(acetyloxy)-3,4-dihydroxy-1,16-dimethyl-11,19-dioxo-6,12,20-trioxahexacyclo[13.7.0.0²,⁸.0⁵,⁹.0⁸,¹³.0¹⁷,²¹]docosa-17,21-diene-5-carboxylate)

3D PDB for NP0262456 (methyl (1s,2r,3r,4s,5r,8r,9s,10r,13r,15s)-10-(acetyloxy)-3,4-dihydroxy-1,16-dimethyl-11,19-dioxo-6,12,20-trioxahexacyclo[13.7.0.0²,⁸.0⁵,⁹.0⁸,¹³.0¹⁷,²¹]docosa-17,21-diene-5-carboxylate)

SMILES for NP0262456 (methyl (1s,2r,3r,4s,5r,8r,9s,10r,13r,15s)-10-(acetyloxy)-3,4-dihydroxy-1,16-dimethyl-11,19-dioxo-6,12,20-trioxahexacyclo[13.7.0.0²,⁸.0⁵,⁹.0⁸,¹³.0¹⁷,²¹]docosa-17,21-diene-5-carboxylate)

INCHI for NP0262456 (methyl (1s,2r,3r,4s,5r,8r,9s,10r,13r,15s)-10-(acetyloxy)-3,4-dihydroxy-1,16-dimethyl-11,19-dioxo-6,12,20-trioxahexacyclo[13.7.0.0²,⁸.0⁵,⁹.0⁸,¹³.0¹⁷,²¹]docosa-17,21-diene-5-carboxylate)

Structure for NP0262456 (methyl (1s,2r,3r,4s,5r,8r,9s,10r,13r,15s)-10-(acetyloxy)-3,4-dihydroxy-1,16-dimethyl-11,19-dioxo-6,12,20-trioxahexacyclo[13.7.0.0²,⁸.0⁵,⁹.0⁸,¹³.0¹⁷,²¹]docosa-17,21-diene-5-carboxylate)

3D Structure for NP0262456 (methyl (1s,2r,3r,4s,5r,8r,9s,10r,13r,15s)-10-(acetyloxy)-3,4-dihydroxy-1,16-dimethyl-11,19-dioxo-6,12,20-trioxahexacyclo[13.7.0.0²,⁸.0⁵,⁹.0⁸,¹³.0¹⁷,²¹]docosa-17,21-diene-5-carboxylate)