NP-MRD: Showing NP-Card for polygarinolide A (NP0341996)

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Record Information

Version

2.0

Created at

2024-11-28 14:45:16 UTC

Updated at

2024-11-30 00:03:38 UTC

NP-MRD ID

NP0341996

Natural Product DOI

https://doi.org/10.57994/3488

Secondary Accession Numbers

None

Natural Product Identification

Common Name

polygarinolide A

Description

polygarinolide A was first documented in 2024 (PMID: 39588637). Based on a literature review very few articles have been published on polygarinolide A.

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 02252314552D          

 17 19  0  0  1  0            999 V2000
   -0.3697    1.3419    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5135    1.1712    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7533    1.9980    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6218    2.0176    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.4696    2.2008    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0538    1.5058    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9079    1.6572    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8067    0.5939    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.9822    0.1024    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2183    0.6232    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.8159   -0.2345    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0195   -1.0646    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8116   -1.2951    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6411    1.2442    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.8953    1.4851    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2192    0.7412    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3541    0.9027    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
  4  3  1  1  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  8  6  1  0  0  0  0
  8  9  1  0  0  0  0
 10  9  1  0  0  0  0
 10  2  1  0  0  0  0
 10 11  1  6  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 14 10  1  0  0  0  0
 14  4  1  0  0  0  0
 14 15  1  6  0  0  0
 15 16  1  0  0  0  0
 14 17  1  0  0  0  0
  8 17  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0341996

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OCC[C@@]12C[C@H]3O[C@]1(CO)[C@H](CC3=O)OC2=O

> <INCHI_IDENTIFIER>
InChI=1S/C11H14O6/c12-2-1-10-4-7-6(14)3-8(16-9(10)15)11(10,5-13)17-7/h7-8,12-13H,1-5H2/t7-,8+,10+,11-/m1/s1

> <INCHI_KEY>
CNONPOWQDMYRMG-YKDSUIRESA-N

> <FORMULA>
C11H14O6

> <MOLECULAR_WEIGHT>
242.227

> <EXACT_MASS>
242.079038171

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
31

> <JCHEM_AVERAGE_POLARIZABILITY>
22.523699542563143

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1R,4S,7R,8R)-7-(2-hydroxyethyl)-8-(hydroxymethyl)-5,9-dioxatricyclo[5.2.1.0^{4,8}]decane-2,6-dione

> <JCHEM_LOGP>
-1.241619942666666

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
15.935950696359956

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.235232849545136

> <JCHEM_PKA_STRONGEST_BASIC>
-2.392256498321368

> <JCHEM_POLAR_SURFACE_AREA>
93.06000000000002

> <JCHEM_REFRACTIVITY>
53.5138

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(1R,4S,7R,8R)-7-(2-hydroxyethyl)-8-(hydroxymethyl)-5,9-dioxatricyclo[5.2.1.0^{4,8}]decane-2,6-dione

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 25-FEB-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   25-FEB-23         0                                  
HETATM    1  O   UNK     0      -0.690   2.505   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       0.959   2.186   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       1.406   3.730   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       3.027   3.766   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.610   4.108   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       5.700   2.811   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       7.295   3.093   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       5.239   1.109   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       3.700   0.191   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.274   1.163   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       1.523  -0.438   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       1.903  -1.987   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       3.382  -2.418   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       3.063   2.323   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       1.671   2.772   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       0.409   1.384   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       4.394   1.685   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   10                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   14                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9   17                                                  
CONECT    9    8   10                                                       
CONECT   10    9    2   11   14                                             
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12                                                            
CONECT   14   10    4   15   17                                             
CONECT   15   14   16                                                       
CONECT   16   15                                                            
CONECT   17   14    8                                                       
MASTER        0    0    0    0    0    0    0    0   17    0   38    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₁H₁₄O₆

Average Mass

242.2270 Da

Monoisotopic Mass

242.07904 Da

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

Not Available

SMILES

OCC[C@@]12C[C@H]3O[C@]1(CO)[C@H](CC3=O)OC2=O

InChI Identifier

InChI=1S/C11H14O6/c12-2-1-10-4-7-6(14)3-8(16-9(10)15)11(10,5-13)17-7/h7-8,12-13H,1-5H2/t7-,8+,10+,11-/m1/s1

InChI Key

CNONPOWQDMYRMG-YKDSUIRESA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
HMBC NMR	[¹H, ¹³C] NMR Spectrum (2D, 600 MHz, CD3OD, experimental)	vinhrooney@korea.ac.kr	Korea University, Korea	VINH	2024-11-28	View Spectrum
NOESY NMR	[¹H, ¹H] NMR Spectrum (2D, 500 MHz, CD3OD, experimental)	vinhrooney@korea.ac.kr	Korea University, Korea	VINH	2024-11-28	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, CD3OD, experimental)	vinhrooney@korea.ac.kr	Korea University, Korea	VINH	2024-11-28	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, CD3OD, experimental)	vinhrooney@korea.ac.kr	Korea University, Korea	VINH	2024-11-28	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, CD3OD, experimental)	vinhrooney@korea.ac.kr	Korea University, Korea	VINH	2024-11-28	View Spectrum

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
arillata		Not Available

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

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

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Luyen BTT, Quang TA, Duy LX, Tai BH, Phong NV, Nghi DH, Khoi NM, Van Chinh N, Cuong NC, Thuy TT, Huong TT, Vinh LB, Hong Anh N, Tuan Hiep N: In vitro and in silico anti-inflammatory effect of minor constituents from the roots of Polygala arillata Buch.-Ham. ex D. Don. Nat Prod Res. 2024 Nov 26:1-10. doi: 10.1080/14786419.2024.2429121. [PubMed:39588637 ]

Showing NP-Card for polygarinolide A (NP0341996)

MOL for NP0341996 (polygarinolide A)

3D MOL for NP0341996 (polygarinolide A)

3D SDF for NP0341996 (polygarinolide A)

3D-SDF for NP0341996 (polygarinolide A)

PDB for NP0341996 (polygarinolide A)

3D PDB for NP0341996 (polygarinolide A)

SMILES for NP0341996 (polygarinolide A)

INCHI for NP0341996 (polygarinolide A)

Structure for NP0341996 (polygarinolide A)

3D Structure for NP0341996 (polygarinolide A)