NP-MRD: Showing NP-Card for (3r,4as,6ar,12as,12br)-3,4a,8,12a-tetrahydroxy-12b-{[(2s,5s,6s)-5-hydroxy-6-methyloxan-2-yl]oxy}-3-methyl-4,5,6,6a-tetrahydro-2h-tetraphene-1,7,12-trione (NP0256053)

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Record Information

Version

2.0

Created at

2022-09-07 20:45:54 UTC

Updated at

2022-09-07 20:45:54 UTC

NP-MRD ID

NP0256053

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(3r,4as,6ar,12as,12br)-3,4a,8,12a-tetrahydroxy-12b-{[(2s,5s,6s)-5-hydroxy-6-methyloxan-2-yl]oxy}-3-methyl-4,5,6,6a-tetrahydro-2h-tetraphene-1,7,12-trione

Description

(3R,4aS,6aR,12aS,12bR)-3,4a,8,12a-tetrahydroxy-12b-{[(2S,5S,6S)-5-hydroxy-6-methyloxan-2-yl]oxy}-3-methyl-1,2,3,4,4a,5,6,6a,7,12,12a,12b-dodecahydrotetraphene-1,7,12-trione belongs to the class of organic compounds known as anthraquinone glycosides. These are organic compounds containing an anthraquinone moiety glycosidically bound to a carbohydrate moiety. (3r,4as,6ar,12as,12br)-3,4a,8,12a-tetrahydroxy-12b-{[(2s,5s,6s)-5-hydroxy-6-methyloxan-2-yl]oxy}-3-methyl-4,5,6,6a-tetrahydro-2h-tetraphene-1,7,12-trione is found in Streptomyces fradiae. Based on a literature review very few articles have been published on (3R,4aS,6aR,12aS,12bR)-3,4a,8,12a-tetrahydroxy-12b-{[(2S,5S,6S)-5-hydroxy-6-methyloxan-2-yl]oxy}-3-methyl-1,2,3,4,4a,5,6,6a,7,12,12a,12b-dodecahydrotetraphene-1,7,12-trione.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309072222452D          

 35 39  0  0  1  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv1652309072222452D          

 35 39  0  0  1  0            999 V2000
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 28 30  1  0  0  0  0
 18 30  1  0  0  0  0
  6 30  1  0  0  0  0
 30 31  1  6  0  0  0
  4 32  1  0  0  0  0
 32 33  1  0  0  0  0
 33 34  1  0  0  0  0
  2 34  1  0  0  0  0
 34 35  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0256053

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@@H]1O[C@H](CC[C@@H]1O)O[C@]12C(=O)C[C@](C)(O)C[C@@]1(O)CC[C@H]1C(=O)C3=C(O)C=CC=C3C(=O)[C@@]21O

> <INCHI_IDENTIFIER>
InChI=1S/C25H30O10/c1-12-15(26)6-7-18(34-12)35-25-17(28)10-22(2,31)11-23(25,32)9-8-14-20(29)19-13(4-3-5-16(19)27)21(30)24(14,25)33/h3-5,12,14-15,18,26-27,31-33H,6-11H2,1-2H3/t12-,14-,15-,18-,22-,23-,24+,25+/m0/s1

> <INCHI_KEY>
BDZBETDENXLJSX-GDSCQXIYSA-N

> <FORMULA>
C25H30O10

> <MOLECULAR_WEIGHT>
490.505

> <EXACT_MASS>
490.183897166

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_ATOM_COUNT>
65

> <JCHEM_AVERAGE_POLARIZABILITY>
48.31672335782211

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3R,4aS,6aR,12aS,12bR)-3,4a,8,12a-tetrahydroxy-12b-{[(2S,5S,6S)-5-hydroxy-6-methyloxan-2-yl]oxy}-3-methyl-1,2,3,4,4a,5,6,6a,7,12,12a,12b-dodecahydrotetraphene-1,7,12-trione

> <JCHEM_LOGP>
0.5907687070000005

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
9.787894248522885

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.087754348605651

> <JCHEM_PKA_STRONGEST_BASIC>
-2.899240557939863

> <JCHEM_POLAR_SURFACE_AREA>
170.82

> <JCHEM_REFRACTIVITY>
119.50239999999995

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(3R,4aS,6aR,12aS,12bR)-3,4a,8,12a-tetrahydroxy-12b-{[(2S,5S,6S)-5-hydroxy-6-methyloxan-2-yl]oxy}-3-methyl-4,5,6,6a-tetrahydro-2H-tetraphene-1,7,12-trione

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 07-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   07-SEP-22         0                                  
HETATM    1  C   UNK     0       5.156  -8.215   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       6.668  -7.924   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       7.172  -6.469   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       8.685  -6.178   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       9.189  -4.723   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       8.181  -3.559   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       7.677  -5.014   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       7.808  -6.549   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       6.164  -5.305   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       5.156  -4.141   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.185  -5.336   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       3.811  -3.392   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       5.660  -2.686   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       7.172  -2.395   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       6.164  -1.231   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0       7.677  -0.940   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       9.189  -0.649   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      10.197  -1.813   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      11.709  -1.522   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0      12.213  -0.067   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0      12.717  -2.686   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      14.230  -2.395   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0      14.734  -0.940   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0      15.238  -3.559   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      14.734  -5.014   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      13.221  -5.305   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      12.213  -4.141   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      10.701  -4.432   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0      10.197  -5.887   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0       9.693  -3.268   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0      10.140  -4.741   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0       9.693  -7.342   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       9.189  -8.798   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       7.677  -9.089   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0       7.172 -10.544   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   34                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   32                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7   14   30                                             
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10                                                       
CONECT   10    9   11   12   13                                             
CONECT   11   10                                                            
CONECT   12   10                                                            
CONECT   13   10   14                                                       
CONECT   14   13    6   15   16                                             
CONECT   15   14                                                            
CONECT   16   14   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19   30                                                  
CONECT   19   18   20   21                                                  
CONECT   20   19                                                            
CONECT   21   19   22   27                                                  
CONECT   22   21   23   24                                                  
CONECT   23   22                                                            
CONECT   24   22   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   27                                                       
CONECT   27   26   21   28                                                  
CONECT   28   27   29   30                                                  
CONECT   29   28                                                            
CONECT   30   28   18    6   31                                             
CONECT   31   30                                                            
CONECT   32    4   33                                                       
CONECT   33   32   34                                                       
CONECT   34   33    2   35                                                  
CONECT   35   34                                                            
MASTER        0    0    0    0    0    0    0    0   35    0   78    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₅H₃₀O₁₀

Average Mass

490.5050 Da

Monoisotopic Mass

490.18390 Da

IUPAC Name

(3R,4aS,6aR,12aS,12bR)-3,4a,8,12a-tetrahydroxy-12b-{[(2S,5S,6S)-5-hydroxy-6-methyloxan-2-yl]oxy}-3-methyl-1,2,3,4,4a,5,6,6a,7,12,12a,12b-dodecahydrotetraphene-1,7,12-trione

Traditional Name

(3R,4aS,6aR,12aS,12bR)-3,4a,8,12a-tetrahydroxy-12b-{[(2S,5S,6S)-5-hydroxy-6-methyloxan-2-yl]oxy}-3-methyl-4,5,6,6a-tetrahydro-2H-tetraphene-1,7,12-trione

CAS Registry Number

Not Available

SMILES

C[C@@H]1O[C@H](CC[C@@H]1O)O[C@]12C(=O)C[C@](C)(O)C[C@@]1(O)CC[C@H]1C(=O)C3=C(O)C=CC=C3C(=O)[C@@]21O

InChI Identifier

InChI=1S/C25H30O10/c1-12-15(26)6-7-18(34-12)35-25-17(28)10-22(2,31)11-23(25,32)9-8-14-20(29)19-13(4-3-5-16(19)27)21(30)24(14,25)33/h3-5,12,14-15,18,26-27,31-33H,6-11H2,1-2H3/t12-,14-,15-,18-,22-,23-,24+,25+/m0/s1

InChI Key

BDZBETDENXLJSX-GDSCQXIYSA-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
Streptomyces fradiae	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as anthraquinone glycosides. These are organic compounds containing an anthraquinone moiety glycosidically bound to a carbohydrate moiety.

Kingdom

Super Class

Class

Sub Class

Direct Parent

Anthraquinone glycosides

Alternative Parents

Substituents

Anthraquinone glycoside
Hydroxyanthraquinone
Naphthalene
Tetralin
Aryl alkyl ketone
Aryl ketone
Quinone
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Oxane
Cyclic alcohol
Vinylogous acid
Tertiary alcohol
Ketone
Secondary alcohol
Organoheterocyclic compound
Oxacycle
Acetal
Polyol
Organooxygen compound
Hydrocarbon derivative
Organic oxide
Carbonyl group
Organic oxygen compound
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	0.59	ChemAxon
pKa (Strongest Acidic)	8.09	ChemAxon
pKa (Strongest Basic)	-2.9	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	10	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	170.82 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	119.5 m³·mol⁻¹	ChemAxon
Polarizability	48.32 Å³	ChemAxon
Number of Rings	5	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	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

163008471

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (3r,4as,6ar,12as,12br)-3,4a,8,12a-tetrahydroxy-12b-{[(2s,5s,6s)-5-hydroxy-6-methyloxan-2-yl]oxy}-3-methyl-4,5,6,6a-tetrahydro-2h-tetraphene-1,7,12-trione (NP0256053)

MOL for NP0256053 ((3r,4as,6ar,12as,12br)-3,4a,8,12a-tetrahydroxy-12b-{[(2s,5s,6s)-5-hydroxy-6-methyloxan-2-yl]oxy}-3-methyl-4,5,6,6a-tetrahydro-2h-tetraphene-1,7,12-trione)

3D MOL for NP0256053 ((3r,4as,6ar,12as,12br)-3,4a,8,12a-tetrahydroxy-12b-{[(2s,5s,6s)-5-hydroxy-6-methyloxan-2-yl]oxy}-3-methyl-4,5,6,6a-tetrahydro-2h-tetraphene-1,7,12-trione)

3D SDF for NP0256053 ((3r,4as,6ar,12as,12br)-3,4a,8,12a-tetrahydroxy-12b-{[(2s,5s,6s)-5-hydroxy-6-methyloxan-2-yl]oxy}-3-methyl-4,5,6,6a-tetrahydro-2h-tetraphene-1,7,12-trione)

3D-SDF for NP0256053 ((3r,4as,6ar,12as,12br)-3,4a,8,12a-tetrahydroxy-12b-{[(2s,5s,6s)-5-hydroxy-6-methyloxan-2-yl]oxy}-3-methyl-4,5,6,6a-tetrahydro-2h-tetraphene-1,7,12-trione)

PDB for NP0256053 ((3r,4as,6ar,12as,12br)-3,4a,8,12a-tetrahydroxy-12b-{[(2s,5s,6s)-5-hydroxy-6-methyloxan-2-yl]oxy}-3-methyl-4,5,6,6a-tetrahydro-2h-tetraphene-1,7,12-trione)

3D PDB for NP0256053 ((3r,4as,6ar,12as,12br)-3,4a,8,12a-tetrahydroxy-12b-{[(2s,5s,6s)-5-hydroxy-6-methyloxan-2-yl]oxy}-3-methyl-4,5,6,6a-tetrahydro-2h-tetraphene-1,7,12-trione)

SMILES for NP0256053 ((3r,4as,6ar,12as,12br)-3,4a,8,12a-tetrahydroxy-12b-{[(2s,5s,6s)-5-hydroxy-6-methyloxan-2-yl]oxy}-3-methyl-4,5,6,6a-tetrahydro-2h-tetraphene-1,7,12-trione)

INCHI for NP0256053 ((3r,4as,6ar,12as,12br)-3,4a,8,12a-tetrahydroxy-12b-{[(2s,5s,6s)-5-hydroxy-6-methyloxan-2-yl]oxy}-3-methyl-4,5,6,6a-tetrahydro-2h-tetraphene-1,7,12-trione)

Structure for NP0256053 ((3r,4as,6ar,12as,12br)-3,4a,8,12a-tetrahydroxy-12b-{[(2s,5s,6s)-5-hydroxy-6-methyloxan-2-yl]oxy}-3-methyl-4,5,6,6a-tetrahydro-2h-tetraphene-1,7,12-trione)

3D Structure for NP0256053 ((3r,4as,6ar,12as,12br)-3,4a,8,12a-tetrahydroxy-12b-{[(2s,5s,6s)-5-hydroxy-6-methyloxan-2-yl]oxy}-3-methyl-4,5,6,6a-tetrahydro-2h-tetraphene-1,7,12-trione)