NP-MRD: Showing NP-Card for Xylomolone C (NP0084475)

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Record Information

Version

2.0

Created at

2022-04-29 05:12:00 UTC

Updated at

2022-04-29 05:12:00 UTC

NP-MRD ID

NP0084475

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Xylomolone C

Description

Methyl (1S,2R,5S,7R)-7-[(1R,6S,8aR)-1-(furan-3-yl)-8a-methyl-5-methylidene-3-oxo-3,5,6,7,8,8a-hexahydro-1H-isochromen-6-yl]-5-hydroxy-7,8,8-trimethyl-4,6-dioxo-3-oxabicyclo[3.2.2]Nonane-2-carboxylate belongs to the class of organic compounds known as tricarboxylic acids and derivatives. These are carboxylic acids containing exactly three carboxyl groups. Xylomolone C is found in Xylocarpus moluccensis . Based on a literature review very few articles have been published on methyl (1S,2R,5S,7R)-7-[(1R,6S,8aR)-1-(furan-3-yl)-8a-methyl-5-methylidene-3-oxo-3,5,6,7,8,8a-hexahydro-1H-isochromen-6-yl]-5-hydroxy-7,8,8-trimethyl-4,6-dioxo-3-oxabicyclo[3.2.2]Nonane-2-carboxylate.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304292207122D          

 38 42  0  0  1  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv1652304292207122D          

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  8  9  1  0  0  0  0
  9 10  1  6  0  0  0
  9 11  1  0  0  0  0
 11 12  1  0  0  0  0
  5 12  1  0  0  0  0
  8 13  2  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
  9 16  1  0  0  0  0
 16 17  1  6  0  0  0
 17 18  2  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  2  0  0  0  0
 17 21  1  0  0  0  0
 14 22  2  0  0  0  0
  7 23  2  0  0  0  0
  4 24  1  1  0  0  0
 25  4  1  1  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 26 28  1  0  0  0  0
 25 29  1  0  0  0  0
 29 30  1  6  0  0  0
 30 31  1  0  0  0  0
 31 32  1  0  0  0  0
 30 33  2  0  0  0  0
 29 34  1  0  0  0  0
  3 35  2  0  0  0  0
  2 36  1  0  0  0  0
 26 36  1  0  0  0  0
  2 37  1  0  0  0  0
 34 37  1  0  0  0  0
 37 38  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0084475

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H][C@@]1(CC[C@@]2(C)[C@@H](OC(=O)C=C2C1=C)C1=COC=C1)[C@]1(C)[C@H]2[C@@H](OC(=O)[C@](O)(CC2(C)C)C1=O)C(=O)OC

> <INCHI_IDENTIFIER>
InChI=1S/C28H32O9/c1-14-16(7-9-26(4)17(14)11-18(29)36-21(26)15-8-10-35-12-15)27(5)20-19(22(30)34-6)37-24(32)28(33,23(27)31)13-25(20,2)3/h8,10-12,16,19-21,33H,1,7,9,13H2,2-6H3/t16-,19+,20-,21-,26+,27+,28-/m0/s1

> <INCHI_KEY>
GBCRJPZDUCULRH-BZYPKZEDSA-N

> <FORMULA>
C28H32O9

> <MOLECULAR_WEIGHT>
512.555

> <EXACT_MASS>
512.20463261

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
69

> <JCHEM_AVERAGE_POLARIZABILITY>
52.33117901883842

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
methyl (1S,2R,5S,7R)-7-[(1R,6S,8aR)-1-(furan-3-yl)-8a-methyl-5-methylidene-3-oxo-3,5,6,7,8,8a-hexahydro-1H-isochromen-6-yl]-5-hydroxy-7,8,8-trimethyl-4,6-dioxo-3-oxabicyclo[3.2.2]nonane-2-carboxylate

> <ALOGPS_LOGP>
3.00

> <JCHEM_LOGP>
3.6251518276666657

> <ALOGPS_LOGS>
-4.21

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
10.65624516610207

> <JCHEM_PKA_STRONGEST_BASIC>
-2.888871072552219

> <JCHEM_POLAR_SURFACE_AREA>
129.34

> <JCHEM_REFRACTIVITY>
128.76599999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
3.14e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
methyl (1S,2R,5S,7R)-7-[(1R,6S,8aR)-1-(furan-3-yl)-8a-methyl-5-methylidene-3-oxo-1,6,7,8-tetrahydroisochromen-6-yl]-5-hydroxy-7,8,8-trimethyl-4,6-dioxo-3-oxabicyclo[3.2.2]nonane-2-carboxylate

> <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      -0.988  -8.556   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      -0.645  -7.055   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.849  -6.095   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -1.849  -4.555   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -3.351  -4.898   0.000  0.00  0.00           C+0
HETATM    6  H   UNK     0      -2.303  -6.027   0.000  0.00  0.00           H+0
HETATM    7  C   UNK     0      -4.398  -3.769   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -5.900  -4.111   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -6.354  -5.583   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -6.808  -7.055   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -5.306  -6.712   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -3.805  -6.369   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -6.947  -2.982   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -8.449  -3.325   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      -8.903  -4.797   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0      -7.855  -5.926   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -8.309  -7.397   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -7.385  -8.629   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      -8.272  -9.889   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0      -9.743  -9.435   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      -9.766  -7.895   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0      -9.496  -2.196   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0      -3.944  -2.297   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      -2.518  -3.167   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      -0.645  -3.595   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      -0.357  -4.748   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       1.180  -4.658   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       0.763  -5.805   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       0.856  -3.937   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       1.816  -2.733   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0       3.339  -2.963   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0       4.299  -1.759   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0       1.253  -1.300   0.000  0.00  0.00           O+0
HETATM   34  O   UNK     0       1.524  -5.325   0.000  0.00  0.00           O+0
HETATM   35  O   UNK     0      -3.237  -6.763   0.000  0.00  0.00           O+0
HETATM   36  C   UNK     0      -0.357  -5.902   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0       0.856  -6.712   0.000  0.00  0.00           C+0
HETATM   38  O   UNK     0       1.816  -7.916   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   36   37                                             
CONECT    3    2    4   35                                                  
CONECT    4    3    5   24   25                                             
CONECT    5    4    6    7   12                                             
CONECT    6    5                                                            
CONECT    7    5    8   23                                                  
CONECT    8    7    9   13                                                  
CONECT    9    8   10   11   16                                             
CONECT   10    9                                                            
CONECT   11    9   12                                                       
CONECT   12   11    5                                                       
CONECT   13    8   14                                                       
CONECT   14   13   15   22                                                  
CONECT   15   14   16                                                       
CONECT   16   15    9   17                                                  
CONECT   17   16   18   21                                                  
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   17                                                       
CONECT   22   14                                                            
CONECT   23    7                                                            
CONECT   24    4                                                            
CONECT   25    4   26   29                                                  
CONECT   26   25   27   28   36                                             
CONECT   27   26                                                            
CONECT   28   26                                                            
CONECT   29   25   30   34                                                  
CONECT   30   29   31   33                                                  
CONECT   31   30   32                                                       
CONECT   32   31                                                            
CONECT   33   30                                                            
CONECT   34   29   37                                                       
CONECT   35    3                                                            
CONECT   36    2   26                                                       
CONECT   37    2   34   38                                                  
CONECT   38   37                                                            
MASTER        0    0    0    0    0    0    0    0   38    0   84    0
END

View in JSmol

Synonyms

Value	Source
Methyl (1S,2R,5S,7R)-7-[(1R,6S,8ar)-1-(furan-3-yl)-8a-methyl-5-methylidene-3-oxo-3,5,6,7,8,8a-hexahydro-1H-isochromen-6-yl]-5-hydroxy-7,8,8-trimethyl-4,6-dioxo-3-oxabicyclo[3.2.2]nonane-2-carboxylic acid	Generator

Chemical Formula

C₂₈H₃₂O₉

Average Mass

512.5550 Da

Monoisotopic Mass

512.20463 Da

IUPAC Name

methyl (1S,2R,5S,7R)-7-[(1R,6S,8aR)-1-(furan-3-yl)-8a-methyl-5-methylidene-3-oxo-3,5,6,7,8,8a-hexahydro-1H-isochromen-6-yl]-5-hydroxy-7,8,8-trimethyl-4,6-dioxo-3-oxabicyclo[3.2.2]nonane-2-carboxylate

Traditional Name

methyl (1S,2R,5S,7R)-7-[(1R,6S,8aR)-1-(furan-3-yl)-8a-methyl-5-methylidene-3-oxo-1,6,7,8-tetrahydroisochromen-6-yl]-5-hydroxy-7,8,8-trimethyl-4,6-dioxo-3-oxabicyclo[3.2.2]nonane-2-carboxylate

CAS Registry Number

Not Available

SMILES

[H][C@@]1(CC[C@@]2(C)[C@@H](OC(=O)C=C2C1=C)C1=COC=C1)[C@]1(C)[C@H]2[C@@H](OC(=O)[C@](O)(CC2(C)C)C1=O)C(=O)OC

InChI Identifier

InChI=1S/C28H32O9/c1-14-16(7-9-26(4)17(14)11-18(29)36-21(26)15-8-10-35-12-15)27(5)20-19(22(30)34-6)37-24(32)28(33,23(27)31)13-25(20,2)3/h8,10-12,16,19-21,33H,1,7,9,13H2,2-6H3/t16-,19+,20-,21-,26+,27+,28-/m0/s1

InChI Key

GBCRJPZDUCULRH-BZYPKZEDSA-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 moluccensis	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as tricarboxylic acids and derivatives. These are carboxylic acids containing exactly three carboxyl groups.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Tricarboxylic acids and derivatives

Direct Parent

Tricarboxylic acids and derivatives

Alternative Parents

Substituents

Tricarboxylic acid or derivatives
Caprolactone
Oxepane
Dihydropyranone
Pyran
Heteroaromatic compound
Alpha,beta-unsaturated carboxylic ester
Enoate ester
Methyl ester
Tertiary alcohol
Furan
Cyclic alcohol
Lactone
Ketone
Carboxylic acid ester
Oxacycle
Organoheterocyclic compound
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	3	ALOGPS
logP	3.63	ChemAxon
logS	-4.2	ALOGPS
pKa (Strongest Acidic)	10.66	ChemAxon
pKa (Strongest Basic)	-2.9	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	129.34 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	128.77 m³·mol⁻¹	ChemAxon
Polarizability	52.33 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

C00053907

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

163184193

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Xylomolone C (NP0084475)

MOL for NP0084475 (Xylomolone C)

3D MOL for NP0084475 (Xylomolone C)

3D SDF for NP0084475 (Xylomolone C)

3D-SDF for NP0084475 (Xylomolone C)

PDB for NP0084475 (Xylomolone C)

3D PDB for NP0084475 (Xylomolone C)

SMILES for NP0084475 (Xylomolone C)

INCHI for NP0084475 (Xylomolone C)

Structure for NP0084475 (Xylomolone C)

3D Structure for NP0084475 (Xylomolone C)