NP-MRD: Showing NP-Card for (2s,3s,4r,4ar,10br)-3,8,9,10-tetrahydroxy-2-(hydroxymethyl)-6-oxo-1h,2h,3h,4h,4ah,10bh-benzo[c]chromen-4-yl 4-hydroxy-3,5-dimethoxybenzoate (NP0180334)

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Record Information

Version

2.0

Created at

2022-09-03 18:40:52 UTC

Updated at

2022-09-03 18:40:52 UTC

NP-MRD ID

NP0180334

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(2s,3s,4r,4ar,10br)-3,8,9,10-tetrahydroxy-2-(hydroxymethyl)-6-oxo-1h,2h,3h,4h,4ah,10bh-benzo[c]chromen-4-yl 4-hydroxy-3,5-dimethoxybenzoate

Description

(2S,3S,4R,4aR,10bR)-3,8,9,10-tetrahydroxy-2-(hydroxymethyl)-6-oxo-1H,2H,3H,4H,4aH,6H,10bH-benzo[c]chromen-4-yl 4-hydroxy-3,5-dimethoxybenzoate belongs to the class of organic compounds known as steroid lactones. These are sterol lipids containing a lactone moiety linked to the steroid skeleton. (2s,3s,4r,4ar,10br)-3,8,9,10-tetrahydroxy-2-(hydroxymethyl)-6-oxo-1h,2h,3h,4h,4ah,10bh-benzo[c]chromen-4-yl 4-hydroxy-3,5-dimethoxybenzoate is found in Diospyros sanza-minika. Based on a literature review very few articles have been published on (2S,3S,4R,4aR,10bR)-3,8,9,10-tetrahydroxy-2-(hydroxymethyl)-6-oxo-1H,2H,3H,4H,4aH,6H,10bH-benzo[c]chromen-4-yl 4-hydroxy-3,5-dimethoxybenzoate.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309032220402D          

 35 38  0  0  1  0            999 V2000
   -1.3480    2.9388    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9355    2.2243    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3480    1.5099    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9355    0.7954    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3480    0.0809    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9355   -0.6336    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3480   -1.3480    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1105   -0.6336    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3020   -1.3480    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.1105   -2.0625    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.9355   -2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3020   -2.7770    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.1105   -3.4914    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    1.1270   -2.7770    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -2.1730    1.5099    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END

     RDKit          3D

 59 62  0  0  0  0  0  0  0  0999 V2000
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M  END


  Mrv1652309032220402D          

 35 38  0  0  1  0            999 V2000
   -1.3480    2.9388    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9355    2.2243    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -0.9355   -0.6336    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
> <DATABASE_ID>
NP0180334

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC1=CC(=CC(OC)=C1O)C(=O)O[C@@H]1[C@@H](O)[C@H](CO)C[C@H]2[C@H]1OC(=O)C1=C2C(O)=C(O)C(O)=C1

> <INCHI_IDENTIFIER>
InChI=1S/C23H24O12/c1-32-13-4-8(5-14(33-2)18(13)28)22(30)35-21-16(26)9(7-24)3-10-15-11(23(31)34-20(10)21)6-12(25)17(27)19(15)29/h4-6,9-10,16,20-21,24-29H,3,7H2,1-2H3/t9-,10+,16-,20+,21+/m0/s1

> <INCHI_KEY>
GJJGOLFDGWSPQJ-NBECYXMCSA-N

> <FORMULA>
C23H24O12

> <MOLECULAR_WEIGHT>
492.433

> <EXACT_MASS>
492.126776213

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_ATOM_COUNT>
59

> <JCHEM_AVERAGE_POLARIZABILITY>
48.2190474065331

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,3S,4R,4aR,10bR)-3,8,9,10-tetrahydroxy-2-(hydroxymethyl)-6-oxo-1H,2H,3H,4H,4aH,6H,10bH-benzo[c]chromen-4-yl 4-hydroxy-3,5-dimethoxybenzoate

> <JCHEM_LOGP>
0.8872640480000012

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
8.543260049814075

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.808836234364804

> <JCHEM_PKA_STRONGEST_BASIC>
-2.6307494751429736

> <JCHEM_POLAR_SURFACE_AREA>
192.43999999999997

> <JCHEM_REFRACTIVITY>
117.30259999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(2S,3S,4R,4aR,10bR)-3,8,9,10-tetrahydroxy-2-(hydroxymethyl)-6-oxo-1H,2H,3H,4H,4aH,10bH-benzo[c]chromen-4-yl 4-hydroxy-3,5-dimethoxybenzoate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 03-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   03-SEP-22         0                                  
HETATM    1  C   UNK     0      -2.516   5.486   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0      -1.746   4.152   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0      -2.516   2.818   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -1.746   1.485   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -2.516   0.151   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -1.746  -1.183   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      -2.516  -2.516   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      -0.206  -1.183   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       0.564  -2.516   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -0.206  -3.850   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      -1.746  -3.850   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       0.564  -5.184   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -0.206  -6.517   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       0.564  -7.851   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       2.104  -5.184   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       2.874  -3.850   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       4.414  -3.850   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       5.184  -2.516   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       6.724  -2.516   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       7.494  -3.850   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       9.034  -3.850   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0       6.724  -5.184   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0       7.494  -6.517   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0       5.184  -5.184   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0       4.414  -6.517   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0       4.414  -1.183   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0       5.184   0.151   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0       2.874  -1.183   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0       2.104  -2.516   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      -4.056   0.151   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      -4.826   1.485   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0      -6.366   1.485   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0      -7.136   2.818   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      -4.056   2.818   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0      -4.826   4.152   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   34                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6   30                                                  
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9                                                       
CONECT    9    8   10   29                                                  
CONECT   10    9   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10   13   15                                                  
CONECT   13   12   14                                                       
CONECT   14   13                                                            
CONECT   15   12   16                                                       
CONECT   16   15   17   29                                                  
CONECT   17   16   18   24                                                  
CONECT   18   17   19   26                                                  
CONECT   19   18   20                                                       
CONECT   20   19   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20   23   24                                                  
CONECT   23   22                                                            
CONECT   24   22   17   25                                                  
CONECT   25   24                                                            
CONECT   26   18   27   28                                                  
CONECT   27   26                                                            
CONECT   28   26   29                                                       
CONECT   29   28   16    9                                                  
CONECT   30    5   31                                                       
CONECT   31   30   32   34                                                  
CONECT   32   31   33                                                       
CONECT   33   32                                                            
CONECT   34   31    3   35                                                  
CONECT   35   34                                                            
MASTER        0    0    0    0    0    0    0    0   35    0   76    0
END

View in JSmol

Synonyms

Value	Source
(2S,3S,4R,4AR,10BR)-3,8,9,10-tetrahydroxy-2-(hydroxymethyl)-6-oxo-1H,2H,3H,4H,4ah,6H,10BH-benzo[c]chromen-4-yl 4-hydroxy-3,5-dimethoxybenzoic acid	Generator

Chemical Formula

C₂₃H₂₄O₁₂

Average Mass

492.4330 Da

Monoisotopic Mass

492.12678 Da

IUPAC Name

(2S,3S,4R,4aR,10bR)-3,8,9,10-tetrahydroxy-2-(hydroxymethyl)-6-oxo-1H,2H,3H,4H,4aH,6H,10bH-benzo[c]chromen-4-yl 4-hydroxy-3,5-dimethoxybenzoate

Traditional Name

(2S,3S,4R,4aR,10bR)-3,8,9,10-tetrahydroxy-2-(hydroxymethyl)-6-oxo-1H,2H,3H,4H,4aH,10bH-benzo[c]chromen-4-yl 4-hydroxy-3,5-dimethoxybenzoate

CAS Registry Number

Not Available

SMILES

COC1=CC(=CC(OC)=C1O)C(=O)O[C@@H]1[C@@H](O)[C@H](CO)C[C@H]2[C@H]1OC(=O)C1=C2C(O)=C(O)C(O)=C1

InChI Identifier

InChI=1S/C23H24O12/c1-32-13-4-8(5-14(33-2)18(13)28)22(30)35-21-16(26)9(7-24)3-10-15-11(23(31)34-20(10)21)6-12(25)17(27)19(15)29/h4-6,9-10,16,20-21,24-29H,3,7H2,1-2H3/t9-,10+,16-,20+,21+/m0/s1

InChI Key

GJJGOLFDGWSPQJ-NBECYXMCSA-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
Diospyros sanza-minika	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as steroid lactones. These are sterol lipids containing a lactone moiety linked to the steroid skeleton.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Steroids and steroid derivatives

Sub Class

Steroid lactones

Direct Parent

Steroid lactones

Alternative Parents

Substituents

Hydrolyzable tannin
Steroid lactone
3-hydroxysteroid
2-hydroxysteroid
Hydroxysteroid
1-hydroxysteroid
16-oxosteroid
Oxosteroid
Tannin
Gallic acid or derivatives
P-hydroxybenzoic acid alkyl ester
P-hydroxybenzoic acid ester
M-methoxybenzoic acid or derivatives
Benzoate ester
Benzopyran
Isochromane
Methoxyphenol
M-dimethoxybenzene
Dimethoxybenzene
2-benzopyran
Benzoic acid or derivatives
Phenol ether
Methoxybenzene
Phenoxy compound
Anisole
Benzoyl
Phenol
Alkyl aryl ether
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Benzenoid
Monocyclic benzene moiety
Dicarboxylic acid or derivatives
Cyclic alcohol
Carboxylic acid ester
Secondary alcohol
Lactone
Ether
Polyol
Carboxylic acid derivative
Oxacycle
Organoheterocyclic compound
Hydrocarbon derivative
Organooxygen compound
Alcohol
Primary alcohol
Organic oxide
Organic oxygen 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	0.89	ChemAxon
pKa (Strongest Acidic)	7.81	ChemAxon
pKa (Strongest Basic)	-2.6	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	10	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	192.44 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	117.3 m³·mol⁻¹	ChemAxon
Polarizability	48.22 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	Yes	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

162978021

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,4ar,10br)-3,8,9,10-tetrahydroxy-2-(hydroxymethyl)-6-oxo-1h,2h,3h,4h,4ah,10bh-benzo[c]chromen-4-yl 4-hydroxy-3,5-dimethoxybenzoate (NP0180334)

MOL for NP0180334 ((2s,3s,4r,4ar,10br)-3,8,9,10-tetrahydroxy-2-(hydroxymethyl)-6-oxo-1h,2h,3h,4h,4ah,10bh-benzo[c]chromen-4-yl 4-hydroxy-3,5-dimethoxybenzoate)

3D MOL for NP0180334 ((2s,3s,4r,4ar,10br)-3,8,9,10-tetrahydroxy-2-(hydroxymethyl)-6-oxo-1h,2h,3h,4h,4ah,10bh-benzo[c]chromen-4-yl 4-hydroxy-3,5-dimethoxybenzoate)

3D SDF for NP0180334 ((2s,3s,4r,4ar,10br)-3,8,9,10-tetrahydroxy-2-(hydroxymethyl)-6-oxo-1h,2h,3h,4h,4ah,10bh-benzo[c]chromen-4-yl 4-hydroxy-3,5-dimethoxybenzoate)

3D-SDF for NP0180334 ((2s,3s,4r,4ar,10br)-3,8,9,10-tetrahydroxy-2-(hydroxymethyl)-6-oxo-1h,2h,3h,4h,4ah,10bh-benzo[c]chromen-4-yl 4-hydroxy-3,5-dimethoxybenzoate)

PDB for NP0180334 ((2s,3s,4r,4ar,10br)-3,8,9,10-tetrahydroxy-2-(hydroxymethyl)-6-oxo-1h,2h,3h,4h,4ah,10bh-benzo[c]chromen-4-yl 4-hydroxy-3,5-dimethoxybenzoate)

3D PDB for NP0180334 ((2s,3s,4r,4ar,10br)-3,8,9,10-tetrahydroxy-2-(hydroxymethyl)-6-oxo-1h,2h,3h,4h,4ah,10bh-benzo[c]chromen-4-yl 4-hydroxy-3,5-dimethoxybenzoate)

SMILES for NP0180334 ((2s,3s,4r,4ar,10br)-3,8,9,10-tetrahydroxy-2-(hydroxymethyl)-6-oxo-1h,2h,3h,4h,4ah,10bh-benzo[c]chromen-4-yl 4-hydroxy-3,5-dimethoxybenzoate)

INCHI for NP0180334 ((2s,3s,4r,4ar,10br)-3,8,9,10-tetrahydroxy-2-(hydroxymethyl)-6-oxo-1h,2h,3h,4h,4ah,10bh-benzo[c]chromen-4-yl 4-hydroxy-3,5-dimethoxybenzoate)

Structure for NP0180334 ((2s,3s,4r,4ar,10br)-3,8,9,10-tetrahydroxy-2-(hydroxymethyl)-6-oxo-1h,2h,3h,4h,4ah,10bh-benzo[c]chromen-4-yl 4-hydroxy-3,5-dimethoxybenzoate)

3D Structure for NP0180334 ((2s,3s,4r,4ar,10br)-3,8,9,10-tetrahydroxy-2-(hydroxymethyl)-6-oxo-1h,2h,3h,4h,4ah,10bh-benzo[c]chromen-4-yl 4-hydroxy-3,5-dimethoxybenzoate)