NP-MRD: Showing NP-Card for (2s,3s,4r,5r,6s)-6-[(9r)-4,5-dihydroxy-2-(hydroxymethyl)-10-oxo-9h-anthracen-9-yl]-3,4,5-trihydroxyoxan-2-yl benzoate (NP0298055)

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Record Information

Version

2.0

Created at

2022-09-10 08:57:42 UTC

Updated at

2022-09-10 08:57:42 UTC

NP-MRD ID

NP0298055

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(2s,3s,4r,5r,6s)-6-[(9r)-4,5-dihydroxy-2-(hydroxymethyl)-10-oxo-9h-anthracen-9-yl]-3,4,5-trihydroxyoxan-2-yl benzoate

Description

Picramnioside A belongs to the class of organic compounds known as anthracenes. These are organic compounds containing a system of three linearly fused benzene rings. (2s,3s,4r,5r,6s)-6-[(9r)-4,5-dihydroxy-2-(hydroxymethyl)-10-oxo-9h-anthracen-9-yl]-3,4,5-trihydroxyoxan-2-yl benzoate is found in Picramnia antidesma and Picramnia sellowii. Based on a literature review very few articles have been published on Picramnioside A.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309102210572D          

 37 41  0  0  1  0            999 V2000
    2.8579    4.9500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724    4.5375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724    3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    3.3000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.8579    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    2.0625    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.1434    1.2375    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.8579    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    4.2868    5.7750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    5.0013    4.5375    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
  4  3  1  6  0  0  0
  4  5  1  0  0  0  0
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  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
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  8 14  1  0  0  0  0
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 32 37  1  0  0  0  0
M  END

     RDKit          3D

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M  END


  Mrv1652309102210572D          

 37 41  0  0  1  0            999 V2000
    2.8579    4.9500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724    4.5375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
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 32 37  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0298055

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OCC1=CC(O)=C2C(=O)C3=C(O)C=CC=C3[C@@H]([C@@H]3O[C@@H](OC(=O)C4=CC=CC=C4)[C@@H](O)[C@H](O)[C@H]3O)C2=C1

> <INCHI_IDENTIFIER>
InChI=1S/C27H24O10/c28-11-12-9-15-18(14-7-4-8-16(29)19(14)21(31)20(15)17(30)10-12)25-23(33)22(32)24(34)27(36-25)37-26(35)13-5-2-1-3-6-13/h1-10,18,22-25,27-30,32-34H,11H2/t18-,22-,23-,24+,25+,27+/m1/s1

> <INCHI_KEY>
ONFRLXXHGVGGCD-OCFOFQISSA-N

> <FORMULA>
C27H24O10

> <MOLECULAR_WEIGHT>
508.479

> <EXACT_MASS>
508.136946973

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
61

> <JCHEM_AVERAGE_POLARIZABILITY>
49.86920954557238

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,3S,4R,5R,6S)-6-[(9R)-4,5-dihydroxy-2-(hydroxymethyl)-10-oxo-9,10-dihydroanthracen-9-yl]-3,4,5-trihydroxyoxan-2-yl benzoate

> <JCHEM_LOGP>
3.176400574666667

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
8.967378756553787

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.305656148842788

> <JCHEM_PKA_STRONGEST_BASIC>
-2.876116218729801

> <JCHEM_POLAR_SURFACE_AREA>
173.98

> <JCHEM_REFRACTIVITY>
128.6825

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(2S,3S,4R,5R,6S)-6-[(9R)-4,5-dihydroxy-2-(hydroxymethyl)-10-oxo-9H-anthracen-9-yl]-3,4,5-trihydroxyoxan-2-yl benzoate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 10-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   10-SEP-22         0                                  
HETATM    1  O   UNK     0       5.335   9.240   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       6.668   8.470   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       6.668   6.930   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       5.335   6.160   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       5.335   4.620   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       4.001   3.850   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       4.001   2.310   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       5.335   1.540   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       6.668   2.310   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       8.002   1.540   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       8.002  -0.000   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       6.668  -2.310   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       4.001  -2.310   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       1.334  -2.310   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      -1.334   2.310   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0      -2.667   1.540   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       2.667   4.620   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0       1.334   3.850   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0       2.667   6.160   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0       1.334   6.930   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0       4.001   6.930   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0       4.001   8.470   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0       8.002   9.240   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       8.002  10.780   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       9.336  11.550   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      10.669  10.780   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0      10.669   9.240   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0       9.336   8.470   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   32                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   30                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7   26                                                  
CONECT    7    6    8   25                                                  
CONECT    8    7    9   14                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12    8   15                                                  
CONECT   15   14   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15   18   25                                                  
CONECT   18   17   19   20                                                  
CONECT   19   18                                                            
CONECT   20   18   21                                                       
CONECT   21   20   22   24                                                  
CONECT   22   21   23                                                       
CONECT   23   22                                                            
CONECT   24   21   25                                                       
CONECT   25   24   17    7                                                  
CONECT   26    6   27   28                                                  
CONECT   27   26                                                            
CONECT   28   26   29   30                                                  
CONECT   29   28                                                            
CONECT   30   28    4   31                                                  
CONECT   31   30                                                            
CONECT   32    2   33   37                                                  
CONECT   33   32   34                                                       
CONECT   34   33   35                                                       
CONECT   35   34   36                                                       
CONECT   36   35   37                                                       
CONECT   37   36   32                                                       
MASTER        0    0    0    0    0    0    0    0   37    0   82    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₇H₂₄O₁₀

Average Mass

508.4790 Da

Monoisotopic Mass

508.13695 Da

IUPAC Name

(2S,3S,4R,5R,6S)-6-[(9R)-4,5-dihydroxy-2-(hydroxymethyl)-10-oxo-9,10-dihydroanthracen-9-yl]-3,4,5-trihydroxyoxan-2-yl benzoate

Traditional Name

(2S,3S,4R,5R,6S)-6-[(9R)-4,5-dihydroxy-2-(hydroxymethyl)-10-oxo-9H-anthracen-9-yl]-3,4,5-trihydroxyoxan-2-yl benzoate

CAS Registry Number

Not Available

SMILES

OCC1=CC(O)=C2C(=O)C3=C(O)C=CC=C3[C@@H]([C@@H]3O[C@@H](OC(=O)C4=CC=CC=C4)[C@@H](O)[C@H](O)[C@H]3O)C2=C1

InChI Identifier

InChI=1S/C27H24O10/c28-11-12-9-15-18(14-7-4-8-16(29)19(14)21(31)20(15)17(30)10-12)25-23(33)22(32)24(34)27(36-25)37-26(35)13-5-2-1-3-6-13/h1-10,18,22-25,27-30,32-34H,11H2/t18-,22-,23-,24+,25+,27+/m1/s1

InChI Key

ONFRLXXHGVGGCD-OCFOFQISSA-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
Picramnia antidesma	LOTUS Database	35616633
Picramnia sellowii	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as anthracenes. These are organic compounds containing a system of three linearly fused benzene rings.

Kingdom

Organic compounds

Super Class

Benzenoids

Class

Anthracenes

Sub Class

Not Available

Direct Parent

Anthracenes

Alternative Parents

Substituents

Anthracene
Benzoate ester
Benzoic acid or derivatives
Benzoyl
Aryl ketone
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Monocyclic benzene moiety
Monosaccharide
Oxane
Vinylogous acid
Secondary alcohol
Carboxylic acid ester
Ketone
Oxacycle
Organoheterocyclic compound
Carboxylic acid derivative
Polyol
Monocarboxylic acid or derivatives
Acetal
Alcohol
Primary alcohol
Hydrocarbon derivative
Aldehyde
Organic oxygen compound
Aromatic alcohol
Organic oxide
Organooxygen compound
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	3.18	ChemAxon
pKa (Strongest Acidic)	8.31	ChemAxon
pKa (Strongest Basic)	-2.9	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	173.98 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	128.68 m³·mol⁻¹	ChemAxon
Polarizability	49.87 Å³	ChemAxon
Number of Rings	5	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

101915965

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (2s,3s,4r,5r,6s)-6-[(9r)-4,5-dihydroxy-2-(hydroxymethyl)-10-oxo-9h-anthracen-9-yl]-3,4,5-trihydroxyoxan-2-yl benzoate (NP0298055)

MOL for NP0298055 ((2s,3s,4r,5r,6s)-6-[(9r)-4,5-dihydroxy-2-(hydroxymethyl)-10-oxo-9h-anthracen-9-yl]-3,4,5-trihydroxyoxan-2-yl benzoate)

3D MOL for NP0298055 ((2s,3s,4r,5r,6s)-6-[(9r)-4,5-dihydroxy-2-(hydroxymethyl)-10-oxo-9h-anthracen-9-yl]-3,4,5-trihydroxyoxan-2-yl benzoate)

3D SDF for NP0298055 ((2s,3s,4r,5r,6s)-6-[(9r)-4,5-dihydroxy-2-(hydroxymethyl)-10-oxo-9h-anthracen-9-yl]-3,4,5-trihydroxyoxan-2-yl benzoate)

3D-SDF for NP0298055 ((2s,3s,4r,5r,6s)-6-[(9r)-4,5-dihydroxy-2-(hydroxymethyl)-10-oxo-9h-anthracen-9-yl]-3,4,5-trihydroxyoxan-2-yl benzoate)

PDB for NP0298055 ((2s,3s,4r,5r,6s)-6-[(9r)-4,5-dihydroxy-2-(hydroxymethyl)-10-oxo-9h-anthracen-9-yl]-3,4,5-trihydroxyoxan-2-yl benzoate)

3D PDB for NP0298055 ((2s,3s,4r,5r,6s)-6-[(9r)-4,5-dihydroxy-2-(hydroxymethyl)-10-oxo-9h-anthracen-9-yl]-3,4,5-trihydroxyoxan-2-yl benzoate)

SMILES for NP0298055 ((2s,3s,4r,5r,6s)-6-[(9r)-4,5-dihydroxy-2-(hydroxymethyl)-10-oxo-9h-anthracen-9-yl]-3,4,5-trihydroxyoxan-2-yl benzoate)

INCHI for NP0298055 ((2s,3s,4r,5r,6s)-6-[(9r)-4,5-dihydroxy-2-(hydroxymethyl)-10-oxo-9h-anthracen-9-yl]-3,4,5-trihydroxyoxan-2-yl benzoate)

Structure for NP0298055 ((2s,3s,4r,5r,6s)-6-[(9r)-4,5-dihydroxy-2-(hydroxymethyl)-10-oxo-9h-anthracen-9-yl]-3,4,5-trihydroxyoxan-2-yl benzoate)

3D Structure for NP0298055 ((2s,3s,4r,5r,6s)-6-[(9r)-4,5-dihydroxy-2-(hydroxymethyl)-10-oxo-9h-anthracen-9-yl]-3,4,5-trihydroxyoxan-2-yl benzoate)