NP-MRD: Showing NP-Card for (1r,3s,5s,12s,13r)-12-hydroxy-5,9,13-trimethyl-16-methylidene-4,14-dioxatricyclo[11.3.2.0³,⁵]octadec-8-en-15-one (NP0221138)

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Record Information

Version

2.0

Created at

2022-09-05 22:38:12 UTC

Updated at

2022-09-05 22:38:12 UTC

NP-MRD ID

NP0221138

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(1r,3s,5s,12s,13r)-12-hydroxy-5,9,13-trimethyl-16-methylidene-4,14-dioxatricyclo[11.3.2.0³,⁵]octadec-8-en-15-one

Description

Sinulariolide belongs to the class of organic compounds known as macrolides and analogues. These are organic compounds containing a lactone ring of at least twelve members. (1r,3s,5s,12s,13r)-12-hydroxy-5,9,13-trimethyl-16-methylidene-4,14-dioxatricyclo[11.3.2.0³,⁵]octadec-8-en-15-one is found in Sinularia capillosa, Sinularia flexibilis and Sinularia sandensis. (1r,3s,5s,12s,13r)-12-hydroxy-5,9,13-trimethyl-16-methylidene-4,14-dioxatricyclo[11.3.2.0³,⁵]octadec-8-en-15-one was first documented in 2016 (PMID: 27801783). Based on a literature review a small amount of articles have been published on Sinulariolide (PMID: 31783709) (PMID: 30096866) (PMID: 28901434) (PMID: 28767067).

Structure

MOL SDF PDB SMILES InChI


  Mrv1652309062200382D          

 24 26  0  0  1  0            999 V2000
    5.0893    0.6475    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2019    1.4648    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9871    1.7180    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5559    1.1205    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.2787    2.4898    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.8571    3.1989    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    6.6423    3.4521    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0398    3.3115    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4422    2.7427    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5144    1.9208    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.3654    1.7177    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6779    2.1738    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.8530    2.1633    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2564    2.8829    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.4498    3.0563    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1842    3.7048    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4758    4.4765    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0734    5.0453    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8586    5.2985    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7865    6.1204    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6759    5.1860    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3634    4.7299    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7850    4.0208    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    6.5702    4.2740    0.0000 O   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  0  0  0  0
  6  7  1  1  0  0  0
  6  8  1  0  0  0  0
  8  9  1  0  0  0  0
 10  9  1  1  0  0  0
  2 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  6  0  0  0
 13 14  1  0  0  0  0
 12 14  1  0  0  0  0
 14 15  1  6  0  0  0
 14 16  1  0  0  0  0
 16 17  1  0  0  0  0
 18 17  1  4  0  0  0
 18 19  2  0  0  0  0
 19 20  1  0  0  0  0
 19 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
  6 23  1  0  0  0  0
 23 24  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0221138

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC1=CCC[C@]2(C)O[C@H]2C[C@H]2CC[C@@](C)(OC(=O)C2=C)[C@@H](O)CC1

> <INCHI_IDENTIFIER>
InChI=1S/C20H30O4/c1-13-6-5-10-20(4)17(23-20)12-15-9-11-19(3,16(21)8-7-13)24-18(22)14(15)2/h6,15-17,21H,2,5,7-12H2,1,3-4H3/t15-,16+,17+,19-,20+/m1/s1

> <INCHI_KEY>
FONRUOAYELOHDC-QQBOBMDFSA-N

> <FORMULA>
C20H30O4

> <MOLECULAR_WEIGHT>
334.456

> <EXACT_MASS>
334.214409446

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
54

> <JCHEM_AVERAGE_POLARIZABILITY>
36.536478777245925

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1R,3S,5S,12S,13R)-12-hydroxy-5,9,13-trimethyl-16-methylidene-4,14-dioxatricyclo[11.3.2.0^{3,5}]octadec-8-en-15-one

> <JCHEM_LOGP>
3.665471669666667

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.968662970602185

> <JCHEM_PKA_STRONGEST_BASIC>
-3.249906816658605

> <JCHEM_POLAR_SURFACE_AREA>
59.06

> <JCHEM_REFRACTIVITY>
93.34159999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(1R,3S,5S,12S,13R)-12-hydroxy-5,9,13-trimethyl-16-methylidene-4,14-dioxatricyclo[11.3.2.0^{3,5}]octadec-8-en-15-one

> <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       9.500   1.209   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       9.710   2.734   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      11.176   3.207   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      12.238   2.092   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0      11.720   4.648   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      10.933   5.971   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      12.399   6.444   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       9.408   6.181   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       8.292   5.120   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       8.427   3.586   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       6.282   3.206   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       4.999   4.058   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       3.459   4.038   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       4.212   5.381   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       2.706   5.705   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       4.077   6.916   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       4.622   8.356   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       5.737   9.418   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       7.203   9.891   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       7.068  11.425   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       8.728   9.680   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      10.012   8.829   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      10.799   7.505   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0      12.264   7.978   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   10                                                  
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6                                                       
CONECT    6    5    7    8   23                                             
CONECT    7    6                                                            
CONECT    8    6    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9    2   11                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13   14                                                  
CONECT   13   12   14                                                       
CONECT   14   13   12   15   16                                             
CONECT   15   14                                                            
CONECT   16   14   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20   21                                                  
CONECT   20   19                                                            
CONECT   21   19   22                                                       
CONECT   22   21   23                                                       
CONECT   23   22    6   24                                                  
CONECT   24   23                                                            
MASTER        0    0    0    0    0    0    0    0   24    0   52    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₀H₃₀O₄

Average Mass

334.4560 Da

Monoisotopic Mass

334.21441 Da

IUPAC Name

(1R,3S,5S,12S,13R)-12-hydroxy-5,9,13-trimethyl-16-methylidene-4,14-dioxatricyclo[11.3.2.0^{3,5}]octadec-8-en-15-one

Traditional Name

(1R,3S,5S,12S,13R)-12-hydroxy-5,9,13-trimethyl-16-methylidene-4,14-dioxatricyclo[11.3.2.0^{3,5}]octadec-8-en-15-one

CAS Registry Number

Not Available

SMILES

CC1=CCC[C@]2(C)O[C@H]2C[C@H]2CC[C@@](C)(OC(=O)C2=C)[C@@H](O)CC1

InChI Identifier

InChI=1S/C20H30O4/c1-13-6-5-10-20(4)17(23-20)12-15-9-11-19(3,16(21)8-7-13)24-18(22)14(15)2/h6,15-17,21H,2,5,7-12H2,1,3-4H3/t15-,16+,17+,19-,20+/m1/s1

InChI Key

FONRUOAYELOHDC-QQBOBMDFSA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Sinularia capillosa	LOTUS Database	35616633
Sinularia flexibilis	LOTUS Database	35616633
Sinularia sandensis	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as macrolides and analogues. These are organic compounds containing a lactone ring of at least twelve members.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Macrolides and analogues

Sub Class

Not Available

Direct Parent

Macrolides and analogues

Alternative Parents

Substituents

Macrolide
Caprolactone
Oxepane
Alpha,beta-unsaturated carboxylic ester
Enoate ester
Secondary alcohol
Lactone
Carboxylic acid ester
Oxacycle
Organoheterocyclic compound
Monocarboxylic acid or derivatives
Ether
Oxirane
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
logP	3.67	ChemAxon
pKa (Strongest Acidic)	13.97	ChemAxon
pKa (Strongest Basic)	-3.2	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	59.06 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	93.34 m³·mol⁻¹	ChemAxon
Polarizability	36.54 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

C00038285

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

134730293

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Wu YJ, Lin SH, Din ZH, Su JH, Liu CI: Sinulariolide Inhibits Gastric Cancer Cell Migration and Invasion through Downregulation of the EMT Process and Suppression of FAK/PI3K/AKT/mTOR and MAPKs Signaling Pathways. Mar Drugs. 2019 Nov 27;17(12). pii: md17120668. doi: 10.3390/md17120668. [PubMed:31783709 ]
Wu CH, Chao CH, Huang TZ, Huang CY, Hwang TL, Dai CF, Sheu JH: Cembranoid-Related Metabolites and Biological Activities from the Soft Coral Sinularia flexibilis. Mar Drugs. 2018 Aug 9;16(8). pii: md16080278. doi: 10.3390/md16080278. [PubMed:30096866 ]
Chung TW, Li YR, Huang WY, Su JH, Chan HL, Lin SH, Liu CS, Lin SC, Lin CC, Lin CH: Sinulariolide suppresses LPSinduced phenotypic and functional maturation of dendritic cells. Mol Med Rep. 2017 Nov;16(5):6992-7000. doi: 10.3892/mmr.2017.7480. Epub 2017 Sep 13. [PubMed:28901434 ]
Cheng TC, Din ZH, Su JH, Wu YJ, Liu CI: Sinulariolide Suppresses Cell Migration and Invasion by Inhibiting Matrix Metalloproteinase-2/-9 and Urokinase through the PI3K/AKT/mTOR Signaling Pathway in Human Bladder Cancer Cells. Mar Drugs. 2017 Aug 2;15(8). pii: md15080238. doi: 10.3390/md15080238. [PubMed:28767067 ]
Lin JJ, Wang RY, Chen JC, Chiu CC, Liao MH, Wu YJ: Cytotoxicity of 11-epi-Sinulariolide Acetate Isolated from Cultured Soft Corals on HA22T Cells through the Endoplasmic Reticulum Stress Pathway and Mitochondrial Dysfunction. Int J Mol Sci. 2016 Oct 27;17(11). pii: ijms17111787. doi: 10.3390/ijms17111787. [PubMed:27801783 ]
LOTUS database [Link]

Showing NP-Card for (1r,3s,5s,12s,13r)-12-hydroxy-5,9,13-trimethyl-16-methylidene-4,14-dioxatricyclo[11.3.2.0³,⁵]octadec-8-en-15-one (NP0221138)

MOL for NP0221138 ((1r,3s,5s,12s,13r)-12-hydroxy-5,9,13-trimethyl-16-methylidene-4,14-dioxatricyclo[11.3.2.0³,⁵]octadec-8-en-15-one)

3D MOL for NP0221138 ((1r,3s,5s,12s,13r)-12-hydroxy-5,9,13-trimethyl-16-methylidene-4,14-dioxatricyclo[11.3.2.0³,⁵]octadec-8-en-15-one)

3D SDF for NP0221138 ((1r,3s,5s,12s,13r)-12-hydroxy-5,9,13-trimethyl-16-methylidene-4,14-dioxatricyclo[11.3.2.0³,⁵]octadec-8-en-15-one)

3D-SDF for NP0221138 ((1r,3s,5s,12s,13r)-12-hydroxy-5,9,13-trimethyl-16-methylidene-4,14-dioxatricyclo[11.3.2.0³,⁵]octadec-8-en-15-one)

PDB for NP0221138 ((1r,3s,5s,12s,13r)-12-hydroxy-5,9,13-trimethyl-16-methylidene-4,14-dioxatricyclo[11.3.2.0³,⁵]octadec-8-en-15-one)

3D PDB for NP0221138 ((1r,3s,5s,12s,13r)-12-hydroxy-5,9,13-trimethyl-16-methylidene-4,14-dioxatricyclo[11.3.2.0³,⁵]octadec-8-en-15-one)

SMILES for NP0221138 ((1r,3s,5s,12s,13r)-12-hydroxy-5,9,13-trimethyl-16-methylidene-4,14-dioxatricyclo[11.3.2.0³,⁵]octadec-8-en-15-one)

INCHI for NP0221138 ((1r,3s,5s,12s,13r)-12-hydroxy-5,9,13-trimethyl-16-methylidene-4,14-dioxatricyclo[11.3.2.0³,⁵]octadec-8-en-15-one)

Structure for NP0221138 ((1r,3s,5s,12s,13r)-12-hydroxy-5,9,13-trimethyl-16-methylidene-4,14-dioxatricyclo[11.3.2.0³,⁵]octadec-8-en-15-one)

3D Structure for NP0221138 ((1r,3s,5s,12s,13r)-12-hydroxy-5,9,13-trimethyl-16-methylidene-4,14-dioxatricyclo[11.3.2.0³,⁵]octadec-8-en-15-one)