NP-MRD: Showing NP-Card for (1r,3r,8s,12s,13s,14r,15r,16s,17s)-12,15,16-trihydroxy-9,13,17-trimethyl-4,11-dioxo-5,18-dioxapentacyclo[12.5.0.0¹,⁶.0²,¹⁷.0⁸,¹³]nonadec-9-en-3-yl (2r)-2-methylbutanoate (NP0329486)

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Record Information

Version

2.0

Created at

2022-09-12 13:54:44 UTC

Updated at

2022-09-12 13:54:45 UTC

NP-MRD ID

NP0329486

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(1r,3r,8s,12s,13s,14r,15r,16s,17s)-12,15,16-trihydroxy-9,13,17-trimethyl-4,11-dioxo-5,18-dioxapentacyclo[12.5.0.0¹,⁶.0²,¹⁷.0⁸,¹³]nonadec-9-en-3-yl (2r)-2-methylbutanoate

Description

Simalikalactone D 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. (1r,3r,8s,12s,13s,14r,15r,16s,17s)-12,15,16-trihydroxy-9,13,17-trimethyl-4,11-dioxo-5,18-dioxapentacyclo[12.5.0.0¹,⁶.0²,¹⁷.0⁸,¹³]nonadec-9-en-3-yl (2r)-2-methylbutanoate is found in Leitneria floridana, Quassia africana, Simaba guianensis and Simaba orinocensis. (1r,3r,8s,12s,13s,14r,15r,16s,17s)-12,15,16-trihydroxy-9,13,17-trimethyl-4,11-dioxo-5,18-dioxapentacyclo[12.5.0.0¹,⁶.0²,¹⁷.0⁸,¹³]nonadec-9-en-3-yl (2r)-2-methylbutanoate was first documented in 2009 (PMID: 19667291). Based on a literature review a small amount of articles have been published on Simalikalactone D (PMID: 31940804) (PMID: 25392586) (PMID: 22374406).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309122215542D          

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M  END

     RDKit          3D

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M  END


  Mrv1652309122215542D          

 34 38  0  0  1  0            999 V2000
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 14 22  1  0  0  0  0
 22 23  1  1  0  0  0
 22 24  1  0  0  0  0
 24 25  1  0  0  0  0
 25 26  1  1  0  0  0
 25 27  1  0  0  0  0
 27 28  1  6  0  0  0
 27 29  1  0  0  0  0
 29 30  1  6  0  0  0
 29 31  1  0  0  0  0
 31 32  1  0  0  0  0
 33 32  1  1  0  0  0
 12 33  1  0  0  0  0
 24 33  1  1  0  0  0
 33 34  1  0  0  0  0
  8 34  1  0  0  0  0
 29 34  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0329486

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC[C@@H](C)C(=O)O[C@@H]1C2[C@]3(C)OC[C@]22C(C[C@H]4C(C)=CC(=O)[C@@H](O)[C@]4(C)[C@H]2[C@@H](O)[C@@H]3O)OC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C25H34O9/c1-6-10(2)21(30)34-16-18-24(5)20(29)15(27)17-23(4)12(11(3)7-13(26)19(23)28)8-14(33-22(16)31)25(17,18)9-32-24/h7,10,12,14-20,27-29H,6,8-9H2,1-5H3/t10-,12+,14?,15-,16-,17-,18?,19-,20+,23+,24+,25-/m1/s1

> <INCHI_KEY>
OKIKYYZNNZCZRX-FDYLVKMGSA-N

> <FORMULA>
C25H34O9

> <MOLECULAR_WEIGHT>
478.538

> <EXACT_MASS>
478.220282675

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
68

> <JCHEM_AVERAGE_POLARIZABILITY>
49.40902592806496

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1R,3R,8S,12S,13S,14R,15R,16S,17S)-12,15,16-trihydroxy-9,13,17-trimethyl-4,11-dioxo-5,18-dioxapentacyclo[12.5.0.0^{1,6}.0^{2,17}.0^{8,13}]nonadec-9-en-3-yl (2R)-2-methylbutanoate

> <JCHEM_LOGP>
0.5388179093333324

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.257162559532738

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.66032395199369

> <JCHEM_PKA_STRONGEST_BASIC>
-3.3139924370582197

> <JCHEM_POLAR_SURFACE_AREA>
139.59

> <JCHEM_REFRACTIVITY>
117.23200000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(1R,3R,8S,12S,13S,14R,15R,16S,17S)-12,15,16-trihydroxy-9,13,17-trimethyl-4,11-dioxo-5,18-dioxapentacyclo[12.5.0.0^{1,6}.0^{2,17}.0^{8,13}]nonadec-9-en-3-yl (2R)-2-methylbutanoate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 12-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   12-SEP-22         0                                  
HETATM    1  C   UNK     0      -0.574   9.007   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -1.162   7.584   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.224   6.363   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.303   6.565   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -0.812   4.940   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      -2.338   4.737   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       0.127   3.719   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       1.654   3.921   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.299   5.303   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       1.878   6.784   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       3.837   5.378   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       4.675   4.083   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       6.204   4.411   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       7.220   3.260   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       8.740   3.509   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       9.284   4.949   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       9.715   2.317   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       9.171   0.876   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      10.146  -0.315   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0       7.651   0.627   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       7.107  -0.813   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0       6.676   1.819   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       6.114   0.385   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       5.143   1.605   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       4.832   0.108   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0       5.978  -0.920   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0       3.385  -0.362   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0       2.964  -1.844   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0       2.372   0.831   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       1.446  -0.400   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0       1.035   1.432   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0       1.831   2.794   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       3.884   2.676   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       2.763   2.606   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8                                                       
CONECT    8    7    9   34                                                  
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12                                                       
CONECT   12   11   13   33                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15   22                                                  
CONECT   15   14   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15   18                                                       
CONECT   18   17   19   20                                                  
CONECT   19   18                                                            
CONECT   20   18   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20   14   23   24                                             
CONECT   23   22                                                            
CONECT   24   22   25   33                                                  
CONECT   25   24   26   27                                                  
CONECT   26   25                                                            
CONECT   27   25   28   29                                                  
CONECT   28   27                                                            
CONECT   29   27   30   31   34                                             
CONECT   30   29                                                            
CONECT   31   29   32                                                       
CONECT   32   31   33                                                       
CONECT   33   32   12   24   34                                             
CONECT   34   33    8   29                                                  
MASTER        0    0    0    0    0    0    0    0   34    0   76    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₅H₃₄O₉

Average Mass

478.5380 Da

Monoisotopic Mass

478.22028 Da

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

Not Available

SMILES

CC[C@@H](C)C(=O)O[C@@H]1C2[C@]3(C)OC[C@]22C(C[C@H]4C(C)=CC(=O)[C@@H](O)[C@]4(C)[C@H]2[C@@H](O)[C@@H]3O)OC1=O

InChI Identifier

InChI=1S/C25H34O9/c1-6-10(2)21(30)34-16-18-24(5)20(29)15(27)17-23(4)12(11(3)7-13(26)19(23)28)8-14(33-22(16)31)25(17,18)9-32-24/h7,10,12,14-20,27-29H,6,8-9H2,1-5H3/t10-,12+,14?,15-,16-,17-,18?,19-,20+,23+,24+,25-/m1/s1

InChI Key

OKIKYYZNNZCZRX-FDYLVKMGSA-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
Leitneria floridana	LOTUS Database	35616633
Quassia africana	LOTUS Database	35616633
Simaba guianensis	LOTUS Database	35616633
Simaba orinocensis	LOTUS Database	35616633

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

C-20 quassinoid skeleton
Quassinoid
Naphthopyran
Naphthalene
Furopyran
Cyclohexenone
Oxepane
Delta_valerolactone
Fatty acid ester
Delta valerolactone
Fatty acyl
Pyran
Oxane
Dicarboxylic acid or derivatives
Tetrahydrofuran
Furan
Cyclic alcohol
Cyclic ketone
Secondary alcohol
Lactone
Ketone
Carboxylic acid ester
Oxacycle
Organoheterocyclic compound
Polyol
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

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

118701222

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Mendez B, Reyes J, Conde I, Ramos Z, Lozada E, Cruz AM, Asencio G, Carvajal A, Dharmawardhane S, Pinero-Cruz DM, Hernandez E, Vivas P, Ospina CA: Simalikalactone D, a Potential Anticancer Compound from Simarouba tulae, an Endemic Plant of Puerto Rico. Plants (Basel). 2020 Jan 11;9(1). pii: plants9010093. doi: 10.3390/plants9010093. [PubMed:31940804 ]
Sama W, Ajaiyeoba EO, Choudhary MI: Larvicidal properties of simalikalactone D from Quassia africana (Simaroubaceae) Baill and Baill, on the malaria vector Anopheles gambiae. Afr J Tradit Complement Altern Med. 2014 Jun 4;11(4):84-8. eCollection 2014. [PubMed:25392586 ]
Bertani S, Houel E, Jullian V, Bourdy G, Valentin A, Stien D, Deharo E: New findings on Simalikalactone D, an antimalarial compound from Quassia amara L. (Simaroubaceae). Exp Parasitol. 2012 Apr;130(4):341-7. doi: 10.1016/j.exppara.2012.02.013. Epub 2012 Feb 21. [PubMed:22374406 ]
Cachet N, Hoakwie F, Bertani S, Bourdy G, Deharo E, Stien D, Houel E, Gornitzka H, Fillaux J, Chevalley S, Valentin A, Jullian V: Antimalarial activity of simalikalactone E, a new quassinoid from Quassia amara L. (Simaroubaceae). Antimicrob Agents Chemother. 2009 Oct;53(10):4393-8. doi: 10.1128/AAC.00951-09. Epub 2009 Aug 10. [PubMed:19667291 ]
LOTUS database [Link]

Showing NP-Card for (1r,3r,8s,12s,13s,14r,15r,16s,17s)-12,15,16-trihydroxy-9,13,17-trimethyl-4,11-dioxo-5,18-dioxapentacyclo[12.5.0.0¹,⁶.0²,¹⁷.0⁸,¹³]nonadec-9-en-3-yl (2r)-2-methylbutanoate (NP0329486)

MOL for NP0329486 ((1r,3r,8s,12s,13s,14r,15r,16s,17s)-12,15,16-trihydroxy-9,13,17-trimethyl-4,11-dioxo-5,18-dioxapentacyclo[12.5.0.0¹,⁶.0²,¹⁷.0⁸,¹³]nonadec-9-en-3-yl (2r)-2-methylbutanoate)

3D MOL for NP0329486 ((1r,3r,8s,12s,13s,14r,15r,16s,17s)-12,15,16-trihydroxy-9,13,17-trimethyl-4,11-dioxo-5,18-dioxapentacyclo[12.5.0.0¹,⁶.0²,¹⁷.0⁸,¹³]nonadec-9-en-3-yl (2r)-2-methylbutanoate)

3D SDF for NP0329486 ((1r,3r,8s,12s,13s,14r,15r,16s,17s)-12,15,16-trihydroxy-9,13,17-trimethyl-4,11-dioxo-5,18-dioxapentacyclo[12.5.0.0¹,⁶.0²,¹⁷.0⁸,¹³]nonadec-9-en-3-yl (2r)-2-methylbutanoate)

3D-SDF for NP0329486 ((1r,3r,8s,12s,13s,14r,15r,16s,17s)-12,15,16-trihydroxy-9,13,17-trimethyl-4,11-dioxo-5,18-dioxapentacyclo[12.5.0.0¹,⁶.0²,¹⁷.0⁸,¹³]nonadec-9-en-3-yl (2r)-2-methylbutanoate)

PDB for NP0329486 ((1r,3r,8s,12s,13s,14r,15r,16s,17s)-12,15,16-trihydroxy-9,13,17-trimethyl-4,11-dioxo-5,18-dioxapentacyclo[12.5.0.0¹,⁶.0²,¹⁷.0⁸,¹³]nonadec-9-en-3-yl (2r)-2-methylbutanoate)

3D PDB for NP0329486 ((1r,3r,8s,12s,13s,14r,15r,16s,17s)-12,15,16-trihydroxy-9,13,17-trimethyl-4,11-dioxo-5,18-dioxapentacyclo[12.5.0.0¹,⁶.0²,¹⁷.0⁸,¹³]nonadec-9-en-3-yl (2r)-2-methylbutanoate)

SMILES for NP0329486 ((1r,3r,8s,12s,13s,14r,15r,16s,17s)-12,15,16-trihydroxy-9,13,17-trimethyl-4,11-dioxo-5,18-dioxapentacyclo[12.5.0.0¹,⁶.0²,¹⁷.0⁸,¹³]nonadec-9-en-3-yl (2r)-2-methylbutanoate)

INCHI for NP0329486 ((1r,3r,8s,12s,13s,14r,15r,16s,17s)-12,15,16-trihydroxy-9,13,17-trimethyl-4,11-dioxo-5,18-dioxapentacyclo[12.5.0.0¹,⁶.0²,¹⁷.0⁸,¹³]nonadec-9-en-3-yl (2r)-2-methylbutanoate)

Structure for NP0329486 ((1r,3r,8s,12s,13s,14r,15r,16s,17s)-12,15,16-trihydroxy-9,13,17-trimethyl-4,11-dioxo-5,18-dioxapentacyclo[12.5.0.0¹,⁶.0²,¹⁷.0⁸,¹³]nonadec-9-en-3-yl (2r)-2-methylbutanoate)

3D Structure for NP0329486 ((1r,3r,8s,12s,13s,14r,15r,16s,17s)-12,15,16-trihydroxy-9,13,17-trimethyl-4,11-dioxo-5,18-dioxapentacyclo[12.5.0.0¹,⁶.0²,¹⁷.0⁸,¹³]nonadec-9-en-3-yl (2r)-2-methylbutanoate)