NP-MRD: Showing NP-Card for (10r)-1,8-dihydroxy-3-(hydroxymethyl)-10-[(2s,3r,4r,5s,6r)-3,4,5-trihydroxy-6-({[(2e)-3-(4-hydroxyphenyl)prop-2-en-1-yl]oxy}methyl)oxan-2-yl]-10h-anthracen-9-one (NP0258640)

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Record Information

Version

2.0

Created at

2022-09-08 00:11:46 UTC

Updated at

2022-09-08 00:11:46 UTC

NP-MRD ID

NP0258640

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(10r)-1,8-dihydroxy-3-(hydroxymethyl)-10-[(2s,3r,4r,5s,6r)-3,4,5-trihydroxy-6-({[(2e)-3-(4-hydroxyphenyl)prop-2-en-1-yl]oxy}methyl)oxan-2-yl]-10h-anthracen-9-one

Description

Microdontin B belongs to the class of organic compounds known as anthracenes. These are organic compounds containing a system of three linearly fused benzene rings. Based on a literature review a small amount of articles have been published on Microdontin B.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309082202112D          

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M  END

     RDKit          3D

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M  END


  Mrv1652309082202112D          

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  4  5  1  0  0  0  0
  4  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  3  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  1  0  0  0
 11 12  1  6  0  0  0
 12 13  1  0  0  0  0
 13 14  1  6  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  2  0  0  0  0
 18 19  1  0  0  0  0
 19 20  2  0  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
 24 25  2  0  0  0  0
 19 25  1  0  0  0  0
 13 26  1  0  0  0  0
 26 27  1  1  0  0  0
 26 28  1  0  0  0  0
 28 29  1  6  0  0  0
 28 30  1  0  0  0  0
 11 30  1  0  0  0  0
 30 31  1  1  0  0  0
 10 32  1  0  0  0  0
 32 33  2  0  0  0  0
 33 34  1  0  0  0  0
 34 35  1  0  0  0  0
 35 36  1  0  0  0  0
 34 37  2  0  0  0  0
 37 38  1  0  0  0  0
 38 39  1  0  0  0  0
 38 40  2  0  0  0  0
 32 40  1  0  0  0  0
  2 40  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0258640

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C30H30O10/c31-13-16-11-19-23(18-4-1-5-20(33)24(18)27(36)25(19)21(34)12-16)30-29(38)28(37)26(35)22(40-30)14-39-10-2-3-15-6-8-17(32)9-7-15/h1-9,11-12,22-23,26,28-35,37-38H,10,13-14H2/b3-2+/t22-,23-,26-,28+,29-,30+/m1/s1

> <INCHI_KEY>
DDCAYMMIVGRVHF-QTTNIMKZSA-N

> <FORMULA>
C30H30O10

> <MOLECULAR_WEIGHT>
550.56

> <EXACT_MASS>
550.183897166

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_ATOM_COUNT>
70

> <JCHEM_AVERAGE_POLARIZABILITY>
56.651709334197974

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
7

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(10R)-1,8-dihydroxy-3-(hydroxymethyl)-10-[(2S,3R,4R,5S,6R)-3,4,5-trihydroxy-6-({[(2E)-3-(4-hydroxyphenyl)prop-2-en-1-yl]oxy}methyl)oxan-2-yl]-9,10-dihydroanthracen-9-one

> <JCHEM_LOGP>
3.0889396983333333

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
8.884440567214813

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.279524800073826

> <JCHEM_PKA_STRONGEST_BASIC>
-2.876095093458619

> <JCHEM_POLAR_SURFACE_AREA>
177.14

> <JCHEM_REFRACTIVITY>
145.45640000000003

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(10R)-1,8-dihydroxy-3-(hydroxymethyl)-10-[(2S,3R,4R,5S,6R)-3,4,5-trihydroxy-6-({[(2E)-3-(4-hydroxyphenyl)prop-2-en-1-yl]oxy}methyl)oxan-2-yl]-10H-anthracen-9-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 08-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   08-SEP-22         0                                  
HETATM    1  O   UNK     0       4.001   3.850   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       4.001   2.310   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.335   1.540   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       6.668   2.310   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       6.668   3.850   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       8.002   1.540   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       8.002  -0.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       5.335  -3.080   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       5.335  -4.620   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       6.668  -5.390   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       6.668  -6.930   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0       8.002  -7.700   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       8.002  -9.240   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       9.336 -10.010   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       9.336 -11.550   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      10.669 -12.320   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      10.669 -13.860   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       9.336 -14.630   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0       9.336 -16.170   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0       8.002 -13.860   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       8.002 -12.320   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       4.001  -5.390   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0       4.001  -6.930   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0       2.667  -4.620   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0       1.334  -5.390   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0       1.334  -2.310   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   36  O   UNK     0      -1.334  -2.310   0.000  0.00  0.00           O+0
HETATM   37  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM   39  O   UNK     0       1.334   3.850   0.000  0.00  0.00           O+0
HETATM   40  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   40                                                  
CONECT    3    2    4    9                                                  
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8    3   10                                                  
CONECT   10    9   11   32                                                  
CONECT   11   10   12   30                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14   26                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   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   25                                                       
CONECT   25   24   19                                                       
CONECT   26   13   27   28                                                  
CONECT   27   26                                                            
CONECT   28   26   29   30                                                  
CONECT   29   28                                                            
CONECT   30   28   11   31                                                  
CONECT   31   30                                                            
CONECT   32   10   33   40                                                  
CONECT   33   32   34                                                       
CONECT   34   33   35   37                                                  
CONECT   35   34   36                                                       
CONECT   36   35                                                            
CONECT   37   34   38                                                       
CONECT   38   37   39   40                                                  
CONECT   39   38                                                            
CONECT   40   38   32    2                                                  
MASTER        0    0    0    0    0    0    0    0   40    0   88    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₃₀H₃₀O₁₀

Average Mass

550.5600 Da

Monoisotopic Mass

550.18390 Da

IUPAC Name

(10R)-1,8-dihydroxy-3-(hydroxymethyl)-10-[(2S,3R,4R,5S,6R)-3,4,5-trihydroxy-6-({[(2E)-3-(4-hydroxyphenyl)prop-2-en-1-yl]oxy}methyl)oxan-2-yl]-9,10-dihydroanthracen-9-one

Traditional Name

(10R)-1,8-dihydroxy-3-(hydroxymethyl)-10-[(2S,3R,4R,5S,6R)-3,4,5-trihydroxy-6-({[(2E)-3-(4-hydroxyphenyl)prop-2-en-1-yl]oxy}methyl)oxan-2-yl]-10H-anthracen-9-one

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C30H30O10/c31-13-16-11-19-23(18-4-1-5-20(33)24(18)27(36)25(19)21(34)12-16)30-29(38)28(37)26(35)22(40-30)14-39-10-2-3-15-6-8-17(32)9-7-15/h1-9,11-12,22-23,26,28-35,37-38H,10,13-14H2/b3-2+/t22-,23-,26-,28+,29-,30+/m1/s1

InChI Key

DDCAYMMIVGRVHF-QTTNIMKZSA-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

Not Available

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
C-glycosyl compound
Glycosyl compound
Aryl ketone
Styrene
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Phenol
Monocyclic benzene moiety
Monosaccharide
Oxane
Vinylogous acid
Ketone
Secondary alcohol
Dialkyl ether
Ether
Oxacycle
Organoheterocyclic compound
Polyol
Organic oxygen compound
Alcohol
Organic oxide
Aromatic alcohol
Organooxygen compound
Primary alcohol
Hydrocarbon derivative
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	3.09	ChemAxon
pKa (Strongest Acidic)	8.28	ChemAxon
pKa (Strongest Basic)	-2.9	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	10	ChemAxon
Hydrogen Donor Count	7	ChemAxon
Polar Surface Area	177.14 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	145.46 m³·mol⁻¹	ChemAxon
Polarizability	56.65 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	Yes	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

101629132

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (10r)-1,8-dihydroxy-3-(hydroxymethyl)-10-[(2s,3r,4r,5s,6r)-3,4,5-trihydroxy-6-({[(2e)-3-(4-hydroxyphenyl)prop-2-en-1-yl]oxy}methyl)oxan-2-yl]-10h-anthracen-9-one (NP0258640)

MOL for NP0258640 ((10r)-1,8-dihydroxy-3-(hydroxymethyl)-10-[(2s,3r,4r,5s,6r)-3,4,5-trihydroxy-6-({[(2e)-3-(4-hydroxyphenyl)prop-2-en-1-yl]oxy}methyl)oxan-2-yl]-10h-anthracen-9-one)

3D MOL for NP0258640 ((10r)-1,8-dihydroxy-3-(hydroxymethyl)-10-[(2s,3r,4r,5s,6r)-3,4,5-trihydroxy-6-({[(2e)-3-(4-hydroxyphenyl)prop-2-en-1-yl]oxy}methyl)oxan-2-yl]-10h-anthracen-9-one)

3D SDF for NP0258640 ((10r)-1,8-dihydroxy-3-(hydroxymethyl)-10-[(2s,3r,4r,5s,6r)-3,4,5-trihydroxy-6-({[(2e)-3-(4-hydroxyphenyl)prop-2-en-1-yl]oxy}methyl)oxan-2-yl]-10h-anthracen-9-one)

3D-SDF for NP0258640 ((10r)-1,8-dihydroxy-3-(hydroxymethyl)-10-[(2s,3r,4r,5s,6r)-3,4,5-trihydroxy-6-({[(2e)-3-(4-hydroxyphenyl)prop-2-en-1-yl]oxy}methyl)oxan-2-yl]-10h-anthracen-9-one)

PDB for NP0258640 ((10r)-1,8-dihydroxy-3-(hydroxymethyl)-10-[(2s,3r,4r,5s,6r)-3,4,5-trihydroxy-6-({[(2e)-3-(4-hydroxyphenyl)prop-2-en-1-yl]oxy}methyl)oxan-2-yl]-10h-anthracen-9-one)

3D PDB for NP0258640 ((10r)-1,8-dihydroxy-3-(hydroxymethyl)-10-[(2s,3r,4r,5s,6r)-3,4,5-trihydroxy-6-({[(2e)-3-(4-hydroxyphenyl)prop-2-en-1-yl]oxy}methyl)oxan-2-yl]-10h-anthracen-9-one)

SMILES for NP0258640 ((10r)-1,8-dihydroxy-3-(hydroxymethyl)-10-[(2s,3r,4r,5s,6r)-3,4,5-trihydroxy-6-({[(2e)-3-(4-hydroxyphenyl)prop-2-en-1-yl]oxy}methyl)oxan-2-yl]-10h-anthracen-9-one)

INCHI for NP0258640 ((10r)-1,8-dihydroxy-3-(hydroxymethyl)-10-[(2s,3r,4r,5s,6r)-3,4,5-trihydroxy-6-({[(2e)-3-(4-hydroxyphenyl)prop-2-en-1-yl]oxy}methyl)oxan-2-yl]-10h-anthracen-9-one)

Structure for NP0258640 ((10r)-1,8-dihydroxy-3-(hydroxymethyl)-10-[(2s,3r,4r,5s,6r)-3,4,5-trihydroxy-6-({[(2e)-3-(4-hydroxyphenyl)prop-2-en-1-yl]oxy}methyl)oxan-2-yl]-10h-anthracen-9-one)

3D Structure for NP0258640 ((10r)-1,8-dihydroxy-3-(hydroxymethyl)-10-[(2s,3r,4r,5s,6r)-3,4,5-trihydroxy-6-({[(2e)-3-(4-hydroxyphenyl)prop-2-en-1-yl]oxy}methyl)oxan-2-yl]-10h-anthracen-9-one)