NP-MRD: Showing NP-Card for (+)-Domesticulide E (NP0074127)

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Record Information

Version

2.0

Created at

2022-04-28 19:17:58 UTC

Updated at

2022-04-28 19:17:59 UTC

NP-MRD ID

NP0074127

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(+)-Domesticulide E

Description

Methyl (2R)-2-hydroxy-2-[(1R,2R,5R,6R,13S,16S)-6-[(5S)-5-hydroxy-2-oxo-2,5-dihydrofuran-3-yl]-1,5,15,15-tetramethyl-8,14,17-trioxo-7-oxatetracyclo[11.3.1.0²,¹¹.0⁵,¹⁰]Heptadec-10-en-16-yl]acetate belongs to the class of organic compounds known as limonoids. These are highly oxygenated, modified terpenoids with a prototypical structure either containing or derived from a precursor with a 4,4,8-trimethyl-17-furanylsteroid skeleton. All naturally occurring citrus limonoids contain a furan ring attached to the D-ring, at C-17, as well as oxygen containing functional groups at C-3, C-4, C-7, C-16 and C-17. (+)-Domesticulide E is found in Lansium domesticum and Lansium domesticum Corr. . Based on a literature review very few articles have been published on methyl (2R)-2-hydroxy-2-[(1R,2R,5R,6R,13S,16S)-6-[(5S)-5-hydroxy-2-oxo-2,5-dihydrofuran-3-yl]-1,5,15,15-tetramethyl-8,14,17-trioxo-7-oxatetracyclo[11.3.1.0²,¹¹.0⁵,¹⁰]Heptadec-10-en-16-yl]acetate.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282221172D          

 37 41  0  0  1  0            999 V2000
    4.0974    1.2998    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.6417    0.6121    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    2.4505    1.4014    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.9062    2.0891    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7297    2.0383    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6683    1.6635    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.9298    1.2958    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
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    1.0354   -0.2249    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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  1  2  1  0  0  0  0
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 21 22  1  0  0  0  0
 18 23  1  1  0  0  0
  7 24  1  6  0  0  0
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 34 35  2  0  0  0  0
 32 36  1  1  0  0  0
  1 37  1  6  0  0  0
M  END

     RDKit          3D

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M  END


  Mrv1652304282221172D          

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  9 16  1  0  0  0  0
  9 17  1  0  0  0  0
  8 18  1  6  0  0  0
 18 19  1  0  0  0  0
 19 20  2  0  0  0  0
 19 21  1  0  0  0  0
 21 22  1  0  0  0  0
 18 23  1  1  0  0  0
  7 24  1  6  0  0  0
  2 25  1  0  0  0  0
 25 26  1  0  0  0  0
 26 27  2  0  0  0  0
 26 28  1  0  0  0  0
 28 29  1  0  0  0  0
  1 29  1  0  0  0  0
 29 30  1  6  0  0  0
 30 31  2  0  0  0  0
 31 32  1  0  0  0  0
 32 33  1  0  0  0  0
 33 34  1  0  0  0  0
 30 34  1  0  0  0  0
 34 35  2  0  0  0  0
 32 36  1  1  0  0  0
  1 37  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0074127

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC(=O)[C@H](O)[C@H]1C(C)(C)C(=O)[C@@H]2CC3=C4CC(=O)O[C@@H](C5=C[C@@H](O)OC5=O)[C@]4(C)CC[C@H]3[C@@]1(C)C2=O

> <INCHI_IDENTIFIER>
InChI=1S/C27H32O10/c1-25(2)19(18(30)24(34)35-5)27(4)14-6-7-26(3)15(11(14)8-12(20(25)31)21(27)32)10-17(29)36-22(26)13-9-16(28)37-23(13)33/h9,12,14,16,18-19,22,28,30H,6-8,10H2,1-5H3/t12-,14+,16-,18+,19-,22-,26+,27+/m0/s1

> <INCHI_KEY>
ULLMXIDQKKNRAV-RLNJLFLDSA-N

> <FORMULA>
C27H32O10

> <MOLECULAR_WEIGHT>
516.543

> <EXACT_MASS>
516.19954723

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
69

> <JCHEM_AVERAGE_POLARIZABILITY>
51.87334482172214

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
methyl (2R)-2-hydroxy-2-[(1R,2R,5R,6R,13S,16S)-6-[(5S)-5-hydroxy-2-oxo-2,5-dihydrofuran-3-yl]-1,5,15,15-tetramethyl-8,14,17-trioxo-7-oxatetracyclo[11.3.1.0^{2,11}.0^{5,10}]heptadec-10-en-16-yl]acetate

> <ALOGPS_LOGP>
1.75

> <JCHEM_LOGP>
2.104708579333333

> <ALOGPS_LOGS>
-3.15

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
11.838003189999448

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.223871694326725

> <JCHEM_PKA_STRONGEST_BASIC>
-3.933039355051954

> <JCHEM_POLAR_SURFACE_AREA>
153.5

> <JCHEM_REFRACTIVITY>
126.48379999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
3.63e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(R)-(methyl hydroxy[(1R,2R,5R,6R,13S,16S)-6-[(5S)-5-hydroxy-2-oxo-5H-furan-3-yl]-1,5,15,15-tetramethyl-8,14,17-trioxo-7-oxatetracyclo[11.3.1.0^{2,11}.0^{5,10}]heptadec-10-en-16-yl]acetate)

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 28-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   28-APR-22         0                                  
HETATM    1  C   UNK     0       7.648   2.426   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       6.798   1.143   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.261   1.237   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.574   2.616   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       5.425   3.900   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       6.962   3.805   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       3.114   3.105   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.736   2.419   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.246   0.959   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.933  -0.420   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       0.922  -1.582   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       3.393  -0.909   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       4.771  -0.223   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       3.755   1.133   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       5.061   0.316   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0      -0.179   1.543   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -0.084   0.184   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       0.574   3.430   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       0.868   4.941   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0       2.325   5.442   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0      -0.293   5.952   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0       0.001   7.464   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0      -0.882   2.929   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0       3.008   4.642   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       7.484  -0.236   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       9.021  -0.331   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0       9.708  -1.709   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0       9.872   0.953   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0       9.186   2.331   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      10.036   3.615   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       9.498   5.058   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      10.703   6.016   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0      11.987   5.165   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0      11.575   3.682   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0      12.533   2.476   0.000  0.00  0.00           O+0
HETATM   36  O   UNK     0      10.637   7.555   0.000  0.00  0.00           O+0
HETATM   37  C   UNK     0       8.499   3.710   0.000  0.00  0.00           C+0
CONECT    1    2    6   29   37                                             
CONECT    2    1    3   25                                                  
CONECT    3    2    4   13                                                  
CONECT    4    3    5    7                                                  
CONECT    5    4    6                                                       
CONECT    6    5    1                                                       
CONECT    7    4    8   14   24                                             
CONECT    8    7    9   18                                                  
CONECT    9    8   10   16   17                                             
CONECT   10    9   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10   13   14                                                  
CONECT   13   12    3                                                       
CONECT   14   12    7   15                                                  
CONECT   15   14                                                            
CONECT   16    9                                                            
CONECT   17    9                                                            
CONECT   18    8   19   23                                                  
CONECT   19   18   20   21                                                  
CONECT   20   19                                                            
CONECT   21   19   22                                                       
CONECT   22   21                                                            
CONECT   23   18                                                            
CONECT   24    7                                                            
CONECT   25    2   26                                                       
CONECT   26   25   27   28                                                  
CONECT   27   26                                                            
CONECT   28   26   29                                                       
CONECT   29   28    1   30                                                  
CONECT   30   29   31   34                                                  
CONECT   31   30   32                                                       
CONECT   32   31   33   36                                                  
CONECT   33   32   34                                                       
CONECT   34   33   30   35                                                  
CONECT   35   34                                                            
CONECT   36   32                                                            
CONECT   37    1                                                            
MASTER        0    0    0    0    0    0    0    0   37    0   82    0
END

View in JSmol

Synonyms

Value	Source
Methyl (2R)-2-hydroxy-2-[(1R,2R,5R,6R,13S,16S)-6-[(5S)-5-hydroxy-2-oxo-2,5-dihydrofuran-3-yl]-1,5,15,15-tetramethyl-8,14,17-trioxo-7-oxatetracyclo[11.3.1.0,.0,]heptadec-10-en-16-yl]acetic acid	Generator

Chemical Formula

C₂₇H₃₂O₁₀

Average Mass

516.5430 Da

Monoisotopic Mass

516.19955 Da

IUPAC Name

methyl (2R)-2-hydroxy-2-[(1R,2R,5R,6R,13S,16S)-6-[(5S)-5-hydroxy-2-oxo-2,5-dihydrofuran-3-yl]-1,5,15,15-tetramethyl-8,14,17-trioxo-7-oxatetracyclo[11.3.1.0^{2,11}.0^{5,10}]heptadec-10-en-16-yl]acetate

Traditional Name

(R)-(methyl hydroxy[(1R,2R,5R,6R,13S,16S)-6-[(5S)-5-hydroxy-2-oxo-5H-furan-3-yl]-1,5,15,15-tetramethyl-8,14,17-trioxo-7-oxatetracyclo[11.3.1.0^{2,11}.0^{5,10}]heptadec-10-en-16-yl]acetate)

CAS Registry Number

Not Available

SMILES

COC(=O)[C@H](O)[C@H]1C(C)(C)C(=O)[C@@H]2CC3=C4CC(=O)O[C@@H](C5=C[C@@H](O)OC5=O)[C@]4(C)CC[C@H]3[C@@]1(C)C2=O

InChI Identifier

InChI=1S/C27H32O10/c1-25(2)19(18(30)24(34)35-5)27(4)14-6-7-26(3)15(11(14)8-12(20(25)31)21(27)32)10-17(29)36-22(26)13-9-16(28)37-23(13)33/h9,12,14,16,18-19,22,28,30H,6-8,10H2,1-5H3/t12-,14+,16-,18+,19-,22-,26+,27+/m0/s1

InChI Key

ULLMXIDQKKNRAV-RLNJLFLDSA-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, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, 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
Lansium domesticum	LOTUS Database	35616633
Lansium domesticum Corr.	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as limonoids. These are highly oxygenated, modified terpenoids with a prototypical structure either containing or derived from a precursor with a 4,4,8-trimethyl-17-furanylsteroid skeleton. All naturally occurring citrus limonoids contain a furan ring attached to the D-ring, at C-17, as well as oxygen containing functional groups at C-3, C-4, C-7, C-16 and C-17.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Triterpenoids

Direct Parent

Limonoids

Alternative Parents

Substituents

Mexicanolide
Limonoid skeleton
Naphthopyran
Naphthalene
Tricarboxylic acid or derivatives
1,3-diketone
Delta_valerolactone
Delta valerolactone
1,3-dicarbonyl compound
Pyran
Oxane
2-furanone
Alpha,beta-unsaturated carboxylic ester
Enoate ester
Methyl ester
Dihydrofuran
Secondary alcohol
Lactone
Ketone
Hemiacetal
Carboxylic acid ester
Oxacycle
Organoheterocyclic compound
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	1.75	ALOGPS
logP	2.1	ChemAxon
logS	-3.2	ALOGPS
pKa (Strongest Acidic)	11.22	ChemAxon
pKa (Strongest Basic)	-3.9	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	153.5 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	126.48 m³·mol⁻¹	ChemAxon
Polarizability	51.87 Å³	ChemAxon
Number of Rings	5	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	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

163026056

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Showing NP-Card for (+)-Domesticulide E (NP0074127)

MOL for NP0074127 ((+)-Domesticulide E)

3D MOL for NP0074127 ((+)-Domesticulide E)

3D SDF for NP0074127 ((+)-Domesticulide E)

3D-SDF for NP0074127 ((+)-Domesticulide E)

PDB for NP0074127 ((+)-Domesticulide E)

3D PDB for NP0074127 ((+)-Domesticulide E)

SMILES for NP0074127 ((+)-Domesticulide E)

INCHI for NP0074127 ((+)-Domesticulide E)

Structure for NP0074127 ((+)-Domesticulide E)

3D Structure for NP0074127 ((+)-Domesticulide E)