NP-MRD: Showing NP-Card for Protoxylocarpin H (NP0081679)

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Record Information

Version

2.0

Created at

2022-04-29 02:43:58 UTC

Updated at

2022-04-29 02:43:58 UTC

NP-MRD ID

NP0081679

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Protoxylocarpin H

Description

(1R,2R,7R,9R,10R,14S,15S)-14-[(3S,5R)-5-[(2R)-2-hydroxy-3,3-dimethyloxiran-2-yl]oxolan-3-yl]-2,6,6,10,15-pentamethyl-5-oxotetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]Heptadeca-3,11-dien-9-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. Protoxylocarpin H is found in Xylocarpus granatum . Based on a literature review very few articles have been published on (1R,2R,7R,9R,10R,14S,15S)-14-[(3S,5R)-5-[(2R)-2-hydroxy-3,3-dimethyloxiran-2-yl]oxolan-3-yl]-2,6,6,10,15-pentamethyl-5-oxotetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]Heptadeca-3,11-dien-9-yl acetate.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304292204432D          

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M  END

     RDKit          3D

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M  END


  Mrv1652304292204432D          

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    1.0596   -0.7929    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.2889   -1.5854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6061   -2.0484    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0452   -1.5420    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.2351   -0.7661    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8377   -1.7713    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.6609   -1.7157    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8585   -2.5167    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2012   -1.0307    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4153   -1.3820    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7495   -2.5916    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0307   -0.9107    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9511    1.3835    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2314    2.1594    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5117    2.9353    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9799    3.5660    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3239    3.0805    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5466   -0.5086    0.0000 C   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  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  1  6  1  0  0  0  0
  6  7  2  0  0  0  0
  5  8  1  0  0  0  0
  5  9  1  0  0  0  0
  4 10  1  1  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
  3 13  1  0  0  0  0
 13 14  1  1  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 12 17  1  0  0  0  0
 17 18  2  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 16 20  1  0  0  0  0
 20 21  1  6  0  0  0
 21 22  1  1  0  0  0
 22 23  1  0  0  0  0
 23 24  1  0  0  0  0
 24 25  1  0  0  0  0
 21 25  1  0  0  0  0
 24 26  1  1  0  0  0
 26 27  1  0  0  0  0
 27 28  1  0  0  0  0
 27 29  1  0  0  0  0
 26 29  1  1  0  0  0
 27 30  1  0  0  0  0
 26 31  1  1  0  0  0
 16 32  1  6  0  0  0
 12 33  1  1  0  0  0
 11 34  1  6  0  0  0
 34 35  1  0  0  0  0
 35 36  2  0  0  0  0
 35 37  1  0  0  0  0
  3 38  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0081679

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(=O)O[C@@H]1C[C@H]2C(C)(C)C(=O)C=C[C@]2(C)[C@H]2CC[C@@]3(C)[C@@H](CC=C3[C@]12C)[C@H]1CO[C@H](C1)[C@@]1(O)OC1(C)C

> <INCHI_IDENTIFIER>
InChI=1S/C32H46O6/c1-18(33)37-25-16-23-27(2,3)24(34)12-14-30(23,7)22-11-13-29(6)20(9-10-21(29)31(22,25)8)19-15-26(36-17-19)32(35)28(4,5)38-32/h10,12,14,19-20,22-23,25-26,35H,9,11,13,15-17H2,1-8H3/t19-,20+,22-,23+,25-,26-,29+,30-,31+,32-/m1/s1

> <INCHI_KEY>
VAHZUXRWDAYHCB-OPUCZGIASA-N

> <FORMULA>
C32H46O6

> <MOLECULAR_WEIGHT>
526.714

> <EXACT_MASS>
526.329439201

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
84

> <JCHEM_AVERAGE_POLARIZABILITY>
59.36134426401124

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1R,2R,7R,9R,10R,14S,15S)-14-[(3S,5R)-5-[(2R)-2-hydroxy-3,3-dimethyloxiran-2-yl]oxolan-3-yl]-2,6,6,10,15-pentamethyl-5-oxotetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadeca-3,11-dien-9-yl acetate

> <ALOGPS_LOGP>
5.52

> <JCHEM_LOGP>
5.0816516830000005

> <ALOGPS_LOGS>
-5.93

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
10.306171852315929

> <JCHEM_PKA_STRONGEST_BASIC>
-3.958426011208806

> <JCHEM_POLAR_SURFACE_AREA>
85.36000000000001

> <JCHEM_REFRACTIVITY>
145.75720000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
6.15e-04 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1R,2R,7R,9R,10R,14S,15S)-14-[(3S,5R)-5-[(2R)-2-hydroxy-3,3-dimethyloxiran-2-yl]oxolan-3-yl]-2,6,6,10,15-pentamethyl-5-oxotetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadeca-3,11-dien-9-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      11.519  -0.407   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      10.003  -0.678   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       9.010   0.499   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       9.533   1.947   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      11.049   2.218   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      12.042   1.041   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      13.558   1.312   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      12.191   3.252   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      10.831   3.743   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       8.541   3.125   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       7.025   2.854   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       6.502   1.405   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       7.494   0.228   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       6.971  -1.221   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       5.455  -1.492   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       4.462  -0.314   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       4.986   1.134   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       3.770   2.079   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       2.495   1.215   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       2.923  -0.264   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       1.978  -1.480   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       2.406  -2.959   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0       1.131  -3.824   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0      -0.084  -2.878   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       0.439  -1.430   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      -1.564  -3.306   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      -3.100  -3.203   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      -3.469  -4.698   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0      -2.242  -1.924   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0      -4.509  -2.580   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0      -1.399  -4.838   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0       3.791  -1.700   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       5.509   2.583   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0       6.032   4.031   0.000  0.00  0.00           O+0
HETATM   35  C   UNK     0       6.555   5.479   0.000  0.00  0.00           C+0
HETATM   36  O   UNK     0       5.563   6.657   0.000  0.00  0.00           O+0
HETATM   37  C   UNK     0       8.071   5.750   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0       8.487  -0.949   0.000  0.00  0.00           C+0
CONECT    1    2    6                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4   13   38                                             
CONECT    4    3    5   10                                                  
CONECT    5    4    6    8    9                                             
CONECT    6    5    1    7                                                  
CONECT    7    6                                                            
CONECT    8    5                                                            
CONECT    9    5                                                            
CONECT   10    4   11                                                       
CONECT   11   10   12   34                                                  
CONECT   12   11   13   17   33                                             
CONECT   13   12    3   14                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17   20   32                                             
CONECT   17   16   12   18                                                  
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   16   21                                                  
CONECT   21   20   22   25                                                  
CONECT   22   21   23                                                       
CONECT   23   22   24                                                       
CONECT   24   23   25   26                                                  
CONECT   25   24   21                                                       
CONECT   26   24   27   29   31                                             
CONECT   27   26   28   29   30                                             
CONECT   28   27                                                            
CONECT   29   27   26                                                       
CONECT   30   27                                                            
CONECT   31   26                                                            
CONECT   32   16                                                            
CONECT   33   12                                                            
CONECT   34   11   35                                                       
CONECT   35   34   36   37                                                  
CONECT   36   35                                                            
CONECT   37   35                                                            
CONECT   38    3                                                            
MASTER        0    0    0    0    0    0    0    0   38    0   86    0
END

View in JSmol

Synonyms

Value	Source
(1R,2R,7R,9R,10R,14S,15S)-14-[(3S,5R)-5-[(2R)-2-Hydroxy-3,3-dimethyloxiran-2-yl]oxolan-3-yl]-2,6,6,10,15-pentamethyl-5-oxotetracyclo[8.7.0.0,.0,]heptadeca-3,11-dien-9-yl acetic acid	Generator

Chemical Formula

C₃₂H₄₆O₆

Average Mass

526.7140 Da

Monoisotopic Mass

526.32944 Da

IUPAC Name

(1R,2R,7R,9R,10R,14S,15S)-14-[(3S,5R)-5-[(2R)-2-hydroxy-3,3-dimethyloxiran-2-yl]oxolan-3-yl]-2,6,6,10,15-pentamethyl-5-oxotetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadeca-3,11-dien-9-yl acetate

Traditional Name

(1R,2R,7R,9R,10R,14S,15S)-14-[(3S,5R)-5-[(2R)-2-hydroxy-3,3-dimethyloxiran-2-yl]oxolan-3-yl]-2,6,6,10,15-pentamethyl-5-oxotetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadeca-3,11-dien-9-yl acetate

CAS Registry Number

Not Available

SMILES

CC(=O)O[C@@H]1C[C@H]2C(C)(C)C(=O)C=C[C@]2(C)[C@H]2CC[C@@]3(C)[C@@H](CC=C3[C@]12C)[C@H]1CO[C@H](C1)[C@@]1(O)OC1(C)C

InChI Identifier

InChI=1S/C32H46O6/c1-18(33)37-25-16-23-27(2,3)24(34)12-14-30(23,7)22-11-13-29(6)20(9-10-21(29)31(22,25)8)19-15-26(36-17-19)32(35)28(4,5)38-32/h10,12,14,19-20,22-23,25-26,35H,9,11,13,15-17H2,1-8H3/t19-,20+,22-,23+,25-,26-,29+,30-,31+,32-/m1/s1

InChI Key

VAHZUXRWDAYHCB-OPUCZGIASA-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
Xylocarpus granatum	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

Limonoid skeleton
24-hydroxysteroid
Hydroxy bile acid, alcohol, or derivatives
Monohydroxy bile acid, alcohol, or derivatives
Bile acid, alcohol, or derivatives
Steroid ester
3-oxo-delta-1-steroid
3-oxosteroid
3-oxo-5-alpha-steroid
Oxosteroid
Delta-1-steroid
Steroid
Cyclohexenone
Tetrahydrofuran
Cyclic ketone
Carboxylic acid ester
Ketone
Monocarboxylic acid or derivatives
Carboxylic acid derivative
Organoheterocyclic compound
Dialkyl ether
Oxirane
Ether
Oxacycle
Organic oxygen compound
Organic oxide
Carbonyl group
Organooxygen compound
Hydrocarbon derivative
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	5.52	ALOGPS
logP	5.08	ChemAxon
logS	-5.9	ALOGPS
pKa (Strongest Acidic)	10.31	ChemAxon
pKa (Strongest Basic)	-4	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	85.36 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	145.76 m³·mol⁻¹	ChemAxon
Polarizability	59.36 Å³	ChemAxon
Number of Rings	6	ChemAxon
Bioavailability	No	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

163039830

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Protoxylocarpin H (NP0081679)

MOL for NP0081679 (Protoxylocarpin H)

3D MOL for NP0081679 (Protoxylocarpin H)

3D SDF for NP0081679 (Protoxylocarpin H)

3D-SDF for NP0081679 (Protoxylocarpin H)

PDB for NP0081679 (Protoxylocarpin H)

3D PDB for NP0081679 (Protoxylocarpin H)

SMILES for NP0081679 (Protoxylocarpin H)

INCHI for NP0081679 (Protoxylocarpin H)

Structure for NP0081679 (Protoxylocarpin H)

3D Structure for NP0081679 (Protoxylocarpin H)