NP-MRD: Showing NP-Card for protoxylocarpin a (NP0210080)

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Record Information

Version

2.0

Created at

2022-09-05 07:44:41 UTC

Updated at

2022-09-05 07:44:41 UTC

NP-MRD ID

NP0210080

Secondary Accession Numbers

None

Natural Product Identification

Common Name

protoxylocarpin a

Description

Protoxylocarpin A 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 a is found in Xylocarpus granatum. Based on a literature review very few articles have been published on Protoxylocarpin A.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309052209442D          

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M  END

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M  END


  Mrv1652309052209442D          

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    3.0934   -2.1066    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3737   -2.8825    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.1858   -3.0277    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.9055   -2.2518    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7176   -2.3970    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5297   -2.5422    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8100   -3.3182    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.6221   -3.4634    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.2782   -3.9489    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9917   -4.3631    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9942   -4.7234    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4661   -3.8037    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.9343   -4.4344    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1221   -4.2891    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.5903   -4.9199    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8418   -3.5132    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.3100   -4.1439    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  4  3  1  6  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  1  0  0  0
  7  8  1  6  0  0  0
  7  9  1  0  0  0  0
  9 10  1  0  0  0  0
  9 11  1  0  0  0  0
  9 12  1  0  0  0  0
  6 13  1  0  0  0  0
 13 14  1  0  0  0  0
  4 14  1  0  0  0  0
 14 15  1  1  0  0  0
 15 16  1  1  0  0  0
 16 17  1  0  0  0  0
 17 18  2  0  0  0  0
 18 19  1  0  0  0  0
 15 19  1  0  0  0  0
 19 20  1  1  0  0  0
 19 21  1  0  0  0  0
 21 22  1  0  0  0  0
 23 22  1  6  0  0  0
 23 24  1  0  0  0  0
 24 25  1  6  0  0  0
 24 26  1  0  0  0  0
 26 27  2  0  0  0  0
 27 28  1  0  0  0  0
 28 29  2  0  0  0  0
 28 30  1  0  0  0  0
 30 31  1  0  0  0  0
 30 32  1  0  0  0  0
 30 33  1  0  0  0  0
 24 33  1  0  0  0  0
 33 34  1  6  0  0  0
 34 35  1  0  0  0  0
 35 36  1  1  0  0  0
 35 37  1  0  0  0  0
 18 37  1  0  0  0  0
 23 37  1  0  0  0  0
 37 38  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0210080

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CCO[C@@H]1O[C@H](C[C@H]1[C@@H]1CC=C2[C@@]1(C)CC[C@@H]1[C@@]3(C)C=CC(=O)C(C)(C)[C@@H]3C[C@@H](O)[C@@]21C)[C@@H](O)C(C)(C)O

> <INCHI_IDENTIFIER>
InChI=1S/C32H50O6/c1-9-37-27-18(16-20(38-27)26(35)29(4,5)36)19-10-11-21-30(19,6)14-12-22-31(7)15-13-24(33)28(2,3)23(31)17-25(34)32(21,22)8/h11,13,15,18-20,22-23,25-27,34-36H,9-10,12,14,16-17H2,1-8H3/t18-,19-,20+,22+,23-,25+,26+,27+,30-,31+,32-/m0/s1

> <INCHI_KEY>
SXUJYCUCLFTRKW-CPFPZXGTSA-N

> <FORMULA>
C32H50O6

> <MOLECULAR_WEIGHT>
530.746

> <EXACT_MASS>
530.36073933

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
88

> <JCHEM_AVERAGE_POLARIZABILITY>
60.81944660598458

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1R,2R,7R,9R,10R,14S,15S)-14-[(2R,3S,5R)-5-[(1R)-1,2-dihydroxy-2-methylpropyl]-2-ethoxyoxolan-3-yl]-9-hydroxy-2,6,6,10,15-pentamethyltetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadeca-3,11-dien-5-one

> <JCHEM_LOGP>
4.189866525666666

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
15.099421248664218

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.050987117432257

> <JCHEM_PKA_STRONGEST_BASIC>
-0.3036995494618039

> <JCHEM_POLAR_SURFACE_AREA>
96.22000000000001

> <JCHEM_REFRACTIVITY>
149.2334

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(1R,2R,7R,9R,10R,14S,15S)-14-[(2R,3S,5R)-5-[(1R)-1,2-dihydroxy-2-methylpropyl]-2-ethoxyoxolan-3-yl]-9-hydroxy-2,6,6,10,15-pentamethyltetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadeca-3,11-dien-5-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 05-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   05-SEP-22         0                                  
HETATM    1  C   UNK     0      -1.815  -7.658   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -0.950  -6.383   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0      -1.622  -4.997   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      -0.758  -3.723   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      -1.281  -2.274   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      -0.065  -1.329   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -0.115   0.210   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       1.193   1.023   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      -1.473   0.936   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -2.831   1.662   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -2.200  -0.422   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      -0.747   2.294   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       1.209  -2.193   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       0.781  -3.673   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       1.726  -4.889   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       1.298  -6.368   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       2.573  -7.232   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       3.789  -6.287   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       3.266  -4.839   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       2.594  -3.453   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       4.258  -3.661   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       5.774  -3.932   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       6.297  -5.381   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       7.813  -5.652   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       7.290  -4.203   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       8.806  -4.474   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      10.322  -4.746   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      10.845  -6.194   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0      12.361  -6.465   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0       9.853  -7.371   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      11.184  -8.144   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       9.322  -8.817   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       8.337  -7.100   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       7.344  -8.277   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       5.828  -8.006   0.000  0.00  0.00           C+0
HETATM   36  O   UNK     0       4.835  -9.184   0.000  0.00  0.00           O+0
HETATM   37  C   UNK     0       5.305  -6.558   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0       4.312  -7.735   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5   14                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7   13                                                  
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10   11   12                                             
CONECT   10    9                                                            
CONECT   11    9                                                            
CONECT   12    9                                                            
CONECT   13    6   14                                                       
CONECT   14   13    4   15                                                  
CONECT   15   14   16   19                                                  
CONECT   16   15   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19   37                                                  
CONECT   19   18   15   20   21                                             
CONECT   20   19                                                            
CONECT   21   19   22                                                       
CONECT   22   21   23                                                       
CONECT   23   22   24   37                                                  
CONECT   24   23   25   26   33                                             
CONECT   25   24                                                            
CONECT   26   24   27                                                       
CONECT   27   26   28                                                       
CONECT   28   27   29   30                                                  
CONECT   29   28                                                            
CONECT   30   28   31   32   33                                             
CONECT   31   30                                                            
CONECT   32   30                                                            
CONECT   33   30   24   34                                                  
CONECT   34   33   35                                                       
CONECT   35   34   36   37                                                  
CONECT   36   35                                                            
CONECT   37   35   18   23   38                                             
CONECT   38   37                                                            
MASTER        0    0    0    0    0    0    0    0   38    0   84    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₃₂H₅₀O₆

Average Mass

530.7460 Da

Monoisotopic Mass

530.36074 Da

IUPAC Name

(1R,2R,7R,9R,10R,14S,15S)-14-[(2R,3S,5R)-5-[(1R)-1,2-dihydroxy-2-methylpropyl]-2-ethoxyoxolan-3-yl]-9-hydroxy-2,6,6,10,15-pentamethyltetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadeca-3,11-dien-5-one

Traditional Name

(1R,2R,7R,9R,10R,14S,15S)-14-[(2R,3S,5R)-5-[(1R)-1,2-dihydroxy-2-methylpropyl]-2-ethoxyoxolan-3-yl]-9-hydroxy-2,6,6,10,15-pentamethyltetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadeca-3,11-dien-5-one

CAS Registry Number

Not Available

SMILES

CCO[C@@H]1O[C@H](C[C@H]1[C@@H]1CC=C2[C@@]1(C)CC[C@@H]1[C@@]3(C)C=CC(=O)C(C)(C)[C@@H]3C[C@@H](O)[C@@]21C)[C@@H](O)C(C)(C)O

InChI Identifier

InChI=1S/C32H50O6/c1-9-37-27-18(16-20(38-27)26(35)29(4,5)36)19-10-11-21-30(19,6)14-12-22-31(7)15-13-24(33)28(2,3)23(31)17-25(34)32(21,22)8/h11,13,15,18-20,22-23,25-27,34-36H,9-10,12,14,16-17H2,1-8H3/t18-,19-,20+,22+,23-,25+,26+,27+,30-,31+,32-/m0/s1

InChI Key

SXUJYCUCLFTRKW-CPFPZXGTSA-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
Xylocarpus granatum	LOTUS Database	35616633

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
Dihydroxy bile acid, alcohol, or derivatives
24-hydroxysteroid
Hydroxy bile acid, alcohol, or derivatives
Bile acid, alcohol, or derivatives
3-oxo-delta-1-steroid
3-oxosteroid
3-oxo-5-alpha-steroid
7-hydroxysteroid
Hydroxysteroid
Oxosteroid
Delta-1-steroid
Steroid
Cyclohexenone
Cyclic alcohol
Tetrahydrofuran
Tertiary alcohol
Cyclic ketone
Ketone
Secondary alcohol
Acetal
Organoheterocyclic compound
Oxacycle
Organic oxide
Organic oxygen compound
Carbonyl group
Hydrocarbon derivative
Alcohol
Organooxygen compound
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic compounds

External Descriptors

limonoid (CHEBI:66780 )

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	4.19	ChemAxon
pKa (Strongest Acidic)	13.05	ChemAxon
pKa (Strongest Basic)	-0.3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	96.22 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	149.23 m³·mol⁻¹	ChemAxon
Polarizability	60.82 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

35518030

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

25222951

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for protoxylocarpin a (NP0210080)

MOL for NP0210080 (protoxylocarpin a)

3D MOL for NP0210080 (protoxylocarpin a)

3D SDF for NP0210080 (protoxylocarpin a)

3D-SDF for NP0210080 (protoxylocarpin a)

PDB for NP0210080 (protoxylocarpin a)

3D PDB for NP0210080 (protoxylocarpin a)

SMILES for NP0210080 (protoxylocarpin a)

INCHI for NP0210080 (protoxylocarpin a)

Structure for NP0210080 (protoxylocarpin a)

3D Structure for NP0210080 (protoxylocarpin a)