NP-MRD: Showing NP-Card for Xerophenone C (NP0084466)

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Record Information

Version

2.0

Created at

2022-04-29 05:11:15 UTC

Updated at

2022-04-29 05:11:15 UTC

NP-MRD ID

NP0084466

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Xerophenone C

Description

Xerophenone C is found in Garcinia bracteata.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304292207112D          

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M  END

     RDKit          3D

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M  END


  Mrv1652304292207112D          

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    1.5134    4.6786    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4647    2.0851    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1697    2.5136    0.0000 O   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  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
  5 10  1  0  0  0  0
  4 11  1  0  0  0  0
  2 12  1  0  0  0  0
 12 13  1  1  0  0  0
 13 14  1  0  0  0  0
 14 15  2  0  0  0  0
 15 16  1  0  0  0  0
 15 17  1  0  0  0  0
 12 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  6  0  0  0
 20 21  1  0  0  0  0
 21 22  2  0  0  0  0
 22 23  1  0  0  0  0
 22 24  1  0  0  0  0
 19 25  1  0  0  0  0
 25 26  1  1  0  0  0
 25 27  1  0  0  0  0
 27 28  1  0  0  0  0
 12 28  1  0  0  0  0
 28 29  1  1  0  0  0
 28 30  1  0  0  0  0
 30 31  1  0  0  0  0
 25 31  1  0  0  0  0
 30 32  1  1  0  0  0
 32 33  1  0  0  0  0
 33 34  2  0  0  0  0
 34 35  1  0  0  0  0
 34 36  1  0  0  0  0
 30 37  1  0  0  0  0
  3 37  1  0  0  0  0
 37 38  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0084466

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C)=CC[C@@H]1C[C@]2(CC=C(C)C)C(=O)\C(=C(\O)C3=CC=CC=C3)C(=O)[C@]3(CC=C(C)C)C[C@@]1(C)O[C@]23O

> <INCHI_IDENTIFIER>
InChI=1S/C33H42O5/c1-21(2)13-14-25-19-31(17-15-22(3)4)28(35)26(27(34)24-11-9-8-10-12-24)29(36)32(18-16-23(5)6)20-30(25,7)38-33(31,32)37/h8-13,15-16,25,34,37H,14,17-20H2,1-7H3/b27-26-/t25-,30-,31-,32+,33-/m1/s1

> <INCHI_KEY>
ZMDQKBXRAVFXOB-WEXSKNODSA-N

> <FORMULA>
C33H42O5

> <MOLECULAR_WEIGHT>
518.694

> <EXACT_MASS>
518.303224452

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
80

> <JCHEM_AVERAGE_POLARIZABILITY>
58.91212793477446

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1R,2R,4R,6Z,8S,9R)-9-hydroxy-6-[hydroxy(phenyl)methylidene]-1-methyl-2,4,8-tris(3-methylbut-2-en-1-yl)-10-oxatricyclo[6.2.1.0^{4,9}]undecane-5,7-dione

> <ALOGPS_LOGP>
4.86

> <JCHEM_LOGP>
7.546606930333334

> <ALOGPS_LOGS>
-5.60

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
11.124926349899816

> <JCHEM_PKA_STRONGEST_ACIDIC>
6.106494157162053

> <JCHEM_PKA_STRONGEST_BASIC>
-4.39254567841642

> <JCHEM_POLAR_SURFACE_AREA>
83.83000000000001

> <JCHEM_REFRACTIVITY>
154.23290000000003

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.31e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1R,2R,4R,6Z,8S,9R)-9-hydroxy-6-[hydroxy(phenyl)methylidene]-1-methyl-2,4,8-tris(3-methylbut-2-en-1-yl)-10-oxatricyclo[6.2.1.0^{4,9}]undecane-5,7-dione

> <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  O   UNK     0       0.047  -0.186   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       0.246   1.341   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.024   2.271   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -2.430   1.642   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -2.587   0.110   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -1.339  -0.792   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -1.497  -2.324   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -2.903  -2.954   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -4.150  -2.051   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -3.993  -0.519   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      -3.678   2.544   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       1.642   1.886   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       1.869   0.363   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       3.302  -0.203   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       3.528  -1.726   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       2.323  -2.684   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       4.961  -2.291   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       3.381   1.753   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       4.120   3.167   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       5.643   3.392   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       6.600   2.185   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       8.124   2.411   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       8.690   3.843   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       9.081   1.204   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       3.011   4.297   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       4.138   5.346   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0       1.856   3.047   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0       1.002   3.507   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0      -0.423   2.923   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0       0.470   4.759   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       1.965   5.480   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      -0.285   6.101   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       0.500   7.426   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       2.040   7.408   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       2.795   6.066   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0       2.825   8.733   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0      -0.867   3.892   0.000  0.00  0.00           C+0
HETATM   38  O   UNK     0      -2.183   4.692   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   12                                                  
CONECT    3    2    4   37                                                  
CONECT    4    3    5   11                                                  
CONECT    5    4    6   10                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9    5                                                       
CONECT   11    4                                                            
CONECT   12    2   13   18   28                                             
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15                                                            
CONECT   18   12   19                                                       
CONECT   19   18   20   25                                                  
CONECT   20   19   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   23   24                                                  
CONECT   23   22                                                            
CONECT   24   22                                                            
CONECT   25   19   26   27   31                                             
CONECT   26   25                                                            
CONECT   27   25   28                                                       
CONECT   28   27   12   29   30                                             
CONECT   29   28                                                            
CONECT   30   28   31   32   37                                             
CONECT   31   30   25                                                       
CONECT   32   30   33                                                       
CONECT   33   32   34                                                       
CONECT   34   33   35   36                                                  
CONECT   35   34                                                            
CONECT   36   34                                                            
CONECT   37   30    3   38                                                  
CONECT   38   37                                                            
MASTER        0    0    0    0    0    0    0    0   38    0   82    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₃₃H₄₂O₅

Average Mass

518.6940 Da

Monoisotopic Mass

518.30322 Da

IUPAC Name

(1R,2R,4R,6Z,8S,9R)-9-hydroxy-6-[hydroxy(phenyl)methylidene]-1-methyl-2,4,8-tris(3-methylbut-2-en-1-yl)-10-oxatricyclo[6.2.1.0^{4,9}]undecane-5,7-dione

Traditional Name

(1R,2R,4R,6Z,8S,9R)-9-hydroxy-6-[hydroxy(phenyl)methylidene]-1-methyl-2,4,8-tris(3-methylbut-2-en-1-yl)-10-oxatricyclo[6.2.1.0^{4,9}]undecane-5,7-dione

CAS Registry Number

Not Available

SMILES

CC(C)=CC[C@@H]1C[C@]2(CC=C(C)C)C(=O)\C(=C(\O)C3=CC=CC=C3)C(=O)[C@]3(CC=C(C)C)C[C@@]1(C)O[C@]23O

InChI Identifier

InChI=1S/C33H42O5/c1-21(2)13-14-25-19-31(17-15-22(3)4)28(35)26(27(34)24-11-9-8-10-12-24)29(36)32(18-16-23(5)6)20-30(25,7)38-33(31,32)37/h8-13,15-16,25,34,37H,14,17-20H2,1-7H3/b27-26-/t25-,30-,31-,32+,33-/m1/s1

InChI Key

ZMDQKBXRAVFXOB-WEXSKNODSA-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
Garcinia bracteata (nom. inval.)	Plant	KNApSAcK

Chemical Taxonomy

Classification

Not classified

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	4.86	ALOGPS
logP	7.55	ChemAxon
logS	-5.6	ALOGPS
pKa (Strongest Acidic)	6.11	ChemAxon
pKa (Strongest Basic)	-4.4	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	83.83 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	154.23 m³·mol⁻¹	ChemAxon
Polarizability	58.91 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

External Links

Not Available

References

General References

Not Available

Showing NP-Card for Xerophenone C (NP0084466)

MOL for NP0084466 (Xerophenone C)

3D MOL for NP0084466 (Xerophenone C)

3D SDF for NP0084466 (Xerophenone C)

3D-SDF for NP0084466 (Xerophenone C)

PDB for NP0084466 (Xerophenone C)

3D PDB for NP0084466 (Xerophenone C)

SMILES for NP0084466 (Xerophenone C)

INCHI for NP0084466 (Xerophenone C)

Structure for NP0084466 (Xerophenone C)

3D Structure for NP0084466 (Xerophenone C)