NP-MRD: Showing NP-Card for 2,3-Dihydroxy-3-deoxymexicanolide (NP0081500)

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Record Information

Version

2.0

Created at

2022-04-29 02:30:33 UTC

Updated at

2022-04-29 02:30:33 UTC

NP-MRD ID

NP0081500

Secondary Accession Numbers

None

Natural Product Identification

Common Name

2,3-Dihydroxy-3-deoxymexicanolide

Description

Methyl 2-[(1R,2S,5R,6R,13R,14S,16S)-6-(furan-2-yl)-13,14-dihydroxy-1,5,15,15-tetramethyl-8,17-dioxo-7-oxatetracyclo[11.3.1.0²,¹¹.0⁵,¹⁰]Heptadec-10-en-16-yl]acetate belongs to the class of organic compounds known as steroid lactones. These are sterol lipids containing a lactone moiety linked to the steroid skeleton. 2,3-Dihydroxy-3-deoxymexicanolide is found in Swietenia mahagoni . Based on a literature review very few articles have been published on methyl 2-[(1R,2S,5R,6R,13R,14S,16S)-6-(furan-2-yl)-13,14-dihydroxy-1,5,15,15-tetramethyl-8,17-dioxo-7-oxatetracyclo[11.3.1.0²,¹¹.0⁵,¹⁰]Heptadec-10-en-16-yl]acetate.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304292204302D          

 35 39  0  0  1  0            999 V2000
    4.0094   -0.1264    0.0000 C   0  0  0  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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    3.7297    2.0383    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    4.9208    1.2490    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
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 18 35  1  6  0  0  0
M  END

     RDKit          3D

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M  END


  Mrv1652304292204302D          

 35 39  0  0  1  0            999 V2000
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 33 34  1  0  0  0  0
 18 35  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0081500

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC(=O)C[C@H]1C(C)(C)[C@H](O)[C@]2(O)CC3=C4CC(=O)O[C@@H](C5=CC=CO5)[C@]4(C)CC[C@@H]3[C@@]1(C)C2=O

> <INCHI_IDENTIFIER>
InChI=1S/C27H34O8/c1-24(2)18(12-19(28)33-5)26(4)15-8-9-25(3)16(14(15)13-27(32,22(24)30)23(26)31)11-20(29)35-21(25)17-7-6-10-34-17/h6-7,10,15,18,21-22,30,32H,8-9,11-13H2,1-5H3/t15-,18-,21-,22-,25+,26+,27+/m0/s1

> <INCHI_KEY>
NEWCLZIYOMDVPL-MRLJFEQKSA-N

> <FORMULA>
C27H34O8

> <MOLECULAR_WEIGHT>
486.561

> <EXACT_MASS>
486.225368055

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
69

> <JCHEM_AVERAGE_POLARIZABILITY>
50.757422132039196

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
2.71

> <JCHEM_LOGP>
2.209812750333331

> <ALOGPS_LOGS>
-3.68

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.223537122125286

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.016126682701328

> <JCHEM_PKA_STRONGEST_BASIC>
-2.931651601350659

> <JCHEM_POLAR_SURFACE_AREA>
123.27000000000002

> <JCHEM_REFRACTIVITY>
123.94079999999995

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.03e-01 g/l

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

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 29-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   29-APR-22         0                                  
HETATM    1  C   UNK     0       7.484  -0.236   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       7.648   2.426   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       9.186   2.331   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       9.872   0.953   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       9.021  -0.331   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       9.708  -1.709   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0      10.036   3.615   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       9.498   5.058   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      10.703   6.016   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      11.987   5.165   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0      11.575   3.682   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       8.499   3.710   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       3.114   3.105   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       1.736   2.419   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       1.246   0.959   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       1.933  -0.420   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       3.393  -0.909   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       4.771  -0.223   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0       3.499  -2.446   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0       3.755   1.133   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0       5.061   0.316   0.000  0.00  0.00           O+0
HETATM   27  O   UNK     0       0.922  -1.582   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0      -0.179   1.543   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      -0.084   0.184   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       0.574   3.430   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       0.868   4.941   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0       2.325   5.442   0.000  0.00  0.00           O+0
HETATM   33  O   UNK     0      -0.293   5.952   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0       0.001   7.464   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       3.008   4.642   0.000  0.00  0.00           C+0
CONECT    1    2   10                                                       
CONECT    2    1    3    7                                                  
CONECT    3    2    4   23                                                  
CONECT    4    3    5   18                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    2    8   17                                             
CONECT    8    7    9   12                                                  
CONECT    9    8   10                                                       
CONECT   10    9    1   11                                                  
CONECT   11   10                                                            
CONECT   12    8   13   16                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   12                                                       
CONECT   17    7                                                            
CONECT   18    4   19   25   35                                             
CONECT   19   18   20   30                                                  
CONECT   20   19   21   28   29                                             
CONECT   21   20   22   27                                                  
CONECT   22   21   23   24   25                                             
CONECT   23   22    3                                                       
CONECT   24   22                                                            
CONECT   25   22   18   26                                                  
CONECT   26   25                                                            
CONECT   27   21                                                            
CONECT   28   20                                                            
CONECT   29   20                                                            
CONECT   30   19   31                                                       
CONECT   31   30   32   33                                                  
CONECT   32   31                                                            
CONECT   33   31   34                                                       
CONECT   34   33                                                            
CONECT   35   18                                                            
MASTER        0    0    0    0    0    0    0    0   35    0   78    0
END

View in JSmol

Synonyms

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

Chemical Formula

C₂₇H₃₄O₈

Average Mass

486.5610 Da

Monoisotopic Mass

486.22537 Da

IUPAC Name

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

Traditional Name

methyl [(1R,2S,5R,6R,13R,14S,16S)-6-(furan-2-yl)-13,14-dihydroxy-1,5,15,15-tetramethyl-8,17-dioxo-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[C@H]1C(C)(C)[C@H](O)[C@]2(O)CC3=C4CC(=O)O[C@@H](C5=CC=CO5)[C@]4(C)CC[C@@H]3[C@@]1(C)C2=O

InChI Identifier

InChI=1S/C27H34O8/c1-24(2)18(12-19(28)33-5)26(4)15-8-9-25(3)16(14(15)13-27(32,22(24)30)23(26)31)11-20(29)35-21(25)17-7-6-10-34-17/h6-7,10,15,18,21-22,30,32H,8-9,11-13H2,1-5H3/t15-,18-,21-,22-,25+,26+,27+/m0/s1

InChI Key

NEWCLZIYOMDVPL-MRLJFEQKSA-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
Swietenia mahagoni	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as steroid lactones. These are sterol lipids containing a lactone moiety linked to the steroid skeleton.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Steroids and steroid derivatives

Sub Class

Steroid lactones

Direct Parent

Steroid lactones

Alternative Parents

Substituents

Steroid lactone
12-alpha-hydroxysteroid
Hydroxysteroid
12-hydroxysteroid
Naphthopyran
Naphthalene
Delta_valerolactone
Delta valerolactone
Pyran
Oxane
Dicarboxylic acid or derivatives
Heteroaromatic compound
Methyl ester
Tertiary alcohol
Furan
Cyclic alcohol
Secondary alcohol
Lactone
Ketone
Carboxylic acid ester
1,2-diol
Oxacycle
Organoheterocyclic compound
Carboxylic acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Carbonyl group
Alcohol
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic 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	2.71	ALOGPS
logP	2.21	ChemAxon
logS	-3.7	ALOGPS
pKa (Strongest Acidic)	12.02	ChemAxon
pKa (Strongest Basic)	-2.9	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	123.27 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	123.94 m³·mol⁻¹	ChemAxon
Polarizability	50.76 Å³	ChemAxon
Number of Rings	5	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	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

163054159

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Showing NP-Card for 2,3-Dihydroxy-3-deoxymexicanolide (NP0081500)

MOL for NP0081500 (2,3-Dihydroxy-3-deoxymexicanolide)

3D MOL for NP0081500 (2,3-Dihydroxy-3-deoxymexicanolide)

3D SDF for NP0081500 (2,3-Dihydroxy-3-deoxymexicanolide)

3D-SDF for NP0081500 (2,3-Dihydroxy-3-deoxymexicanolide)

PDB for NP0081500 (2,3-Dihydroxy-3-deoxymexicanolide)

3D PDB for NP0081500 (2,3-Dihydroxy-3-deoxymexicanolide)

SMILES for NP0081500 (2,3-Dihydroxy-3-deoxymexicanolide)

INCHI for NP0081500 (2,3-Dihydroxy-3-deoxymexicanolide)

Structure for NP0081500 (2,3-Dihydroxy-3-deoxymexicanolide)

3D Structure for NP0081500 (2,3-Dihydroxy-3-deoxymexicanolide)