NP-MRD: Showing NP-Card for (1r,2s)-1-(3,4-dihydroxyphenyl)-3-({[(2r,3r,4r,5r)-5-(2,3-dihydroxypropyl)-3,4-dihydroxyoxolan-2-yl]methoxy}carbonyl)-6,7-dihydroxy-1,2-dihydronaphthalene-2-carboxylic acid (NP0152652)

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Record Information

Version

2.0

Created at

2022-09-02 09:10:45 UTC

Updated at

2022-09-02 09:10:45 UTC

NP-MRD ID

NP0152652

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(1r,2s)-1-(3,4-dihydroxyphenyl)-3-({[(2r,3r,4r,5r)-5-(2,3-dihydroxypropyl)-3,4-dihydroxyoxolan-2-yl]methoxy}carbonyl)-6,7-dihydroxy-1,2-dihydronaphthalene-2-carboxylic acid

Description

Trilobatin B belongs to the class of organic compounds known as lignan glycosides. These are aromatic polycyclic compounds containing a carbohydrate component glycosidically linked to a lignan moiety. They include 1-aryltetralin lactones. (1r,2s)-1-(3,4-dihydroxyphenyl)-3-({[(2r,3r,4r,5r)-5-(2,3-dihydroxypropyl)-3,4-dihydroxyoxolan-2-yl]methoxy}carbonyl)-6,7-dihydroxy-1,2-dihydronaphthalene-2-carboxylic acid is found in Bazzania trilobata. Based on a literature review very few articles have been published on Trilobatin B.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309022211102D          

 39 42  0  0  1  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv1652309022211102D          

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 13 15  1  0  0  0  0
  5 15  1  0  0  0  0
 15 16  1  1  0  0  0
  2 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  1  0  0  0  0
 21 23  2  0  0  0  0
 23 24  1  0  0  0  0
 23 25  1  0  0  0  0
 25 26  2  0  0  0  0
 19 26  1  0  0  0  0
 26 27  1  0  0  0  0
 27 28  1  1  0  0  0
 28 29  2  0  0  0  0
 29 30  1  0  0  0  0
 30 31  2  0  0  0  0
 31 32  1  0  0  0  0
 31 33  1  0  0  0  0
 33 34  1  0  0  0  0
 33 35  2  0  0  0  0
 28 35  1  0  0  0  0
 27 36  1  0  0  0  0
 17 36  1  0  0  0  0
 36 37  1  6  0  0  0
 37 38  2  0  0  0  0
 37 39  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0152652

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OCC(O)C[C@H]1O[C@H](COC(=O)C2=CC3=CC(O)=C(O)C=C3[C@H]([C@@H]2C(O)=O)C2=CC=C(O)C(O)=C2)[C@H](O)[C@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C26H28O13/c27-8-12(28)6-19-23(33)24(34)20(39-19)9-38-26(37)14-3-11-5-17(31)18(32)7-13(11)21(22(14)25(35)36)10-1-2-15(29)16(30)4-10/h1-5,7,12,19-24,27-34H,6,8-9H2,(H,35,36)/t12?,19-,20-,21-,22-,23+,24+/m1/s1

> <INCHI_KEY>
SPXXGPHPASGHLM-DHYIGXGMSA-N

> <FORMULA>
C26H28O13

> <MOLECULAR_WEIGHT>
548.497

> <EXACT_MASS>
548.152990962

> <JCHEM_ACCEPTOR_COUNT>
12

> <JCHEM_ATOM_COUNT>
67

> <JCHEM_AVERAGE_POLARIZABILITY>
53.79981678855169

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
9

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1R,2S)-1-(3,4-dihydroxyphenyl)-3-({[(2R,3R,4R,5R)-5-(2,3-dihydroxypropyl)-3,4-dihydroxyoxolan-2-yl]methoxy}carbonyl)-6,7-dihydroxy-1,2-dihydronaphthalene-2-carboxylic acid

> <ALOGPS_LOGP>
0.74

> <JCHEM_LOGP>
-0.2302474896666663

> <ALOGPS_LOGS>
-2.81

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
8.897437795844796

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.425249960169446

> <JCHEM_PKA_STRONGEST_BASIC>
-3.6139503659175514

> <JCHEM_POLAR_SURFACE_AREA>
234.66999999999996

> <JCHEM_REFRACTIVITY>
131.6923

> <JCHEM_ROTATABLE_BOND_COUNT>
9

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
8.41e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1R,2S)-1-(3,4-dihydroxyphenyl)-3-({[(2R,3R,4R,5R)-5-(2,3-dihydroxypropyl)-3,4-dihydroxyoxolan-2-yl]methoxy}carbonyl)-6,7-dihydroxy-1,2-dihydronaphthalene-2-carboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 02-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   02-SEP-22         0                                  
HETATM    1  O   UNK     0      -1.334  -0.770   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       0.000   1.540   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      -1.334   2.310   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -1.334   3.850   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      -2.580   4.755   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0      -2.104   6.220   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -3.009   7.466   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -2.382   8.873   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      -0.851   9.034   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0      -3.288  10.118   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      -2.661  11.525   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0      -0.564   6.220   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       0.342   7.466   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0      -0.088   4.755   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       1.377   4.279   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0       8.002  -0.000   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0       6.668  -2.310   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0       8.002  -3.080   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       2.667  -4.620   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       4.001  -5.390   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       4.001  -6.930   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       2.667  -7.700   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0       2.667  -9.240   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0       1.334  -6.930   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0       0.000  -7.700   0.000  0.00  0.00           O+0
HETATM   35  C   UNK     0       1.334  -5.390   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0       0.000  -3.080   0.000  0.00  0.00           C+0
HETATM   38  O   UNK     0      -1.334  -2.310   0.000  0.00  0.00           O+0
HETATM   39  O   UNK     0       0.000  -4.620   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   17                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6   15                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8   13                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12                                                       
CONECT   12   11                                                            
CONECT   13    7   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13    5   16                                                  
CONECT   16   15                                                            
CONECT   17    2   18   36                                                  
CONECT   18   17   19                                                       
CONECT   19   18   20   26                                                  
CONECT   20   19   21                                                       
CONECT   21   20   22   23                                                  
CONECT   22   21                                                            
CONECT   23   21   24   25                                                  
CONECT   24   23                                                            
CONECT   25   23   26                                                       
CONECT   26   25   19   27                                                  
CONECT   27   26   28   36                                                  
CONECT   28   27   29   35                                                  
CONECT   29   28   30                                                       
CONECT   30   29   31                                                       
CONECT   31   30   32   33                                                  
CONECT   32   31                                                            
CONECT   33   31   34   35                                                  
CONECT   34   33                                                            
CONECT   35   33   28                                                       
CONECT   36   27   17   37                                                  
CONECT   37   36   38   39                                                  
CONECT   38   37                                                            
CONECT   39   37                                                            
MASTER        0    0    0    0    0    0    0    0   39    0   84    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₆H₂₈O₁₃

Average Mass

548.4970 Da

Monoisotopic Mass

548.15299 Da

IUPAC Name

(1R,2S)-1-(3,4-dihydroxyphenyl)-3-({[(2R,3R,4R,5R)-5-(2,3-dihydroxypropyl)-3,4-dihydroxyoxolan-2-yl]methoxy}carbonyl)-6,7-dihydroxy-1,2-dihydronaphthalene-2-carboxylic acid

Traditional Name

(1R,2S)-1-(3,4-dihydroxyphenyl)-3-({[(2R,3R,4R,5R)-5-(2,3-dihydroxypropyl)-3,4-dihydroxyoxolan-2-yl]methoxy}carbonyl)-6,7-dihydroxy-1,2-dihydronaphthalene-2-carboxylic acid

CAS Registry Number

Not Available

SMILES

OCC(O)C[C@H]1O[C@H](COC(=O)C2=CC3=CC(O)=C(O)C=C3[C@H]([C@@H]2C(O)=O)C2=CC=C(O)C(O)=C2)[C@H](O)[C@H]1O

InChI Identifier

InChI=1S/C26H28O13/c27-8-12(28)6-19-23(33)24(34)20(39-19)9-38-26(37)14-3-11-5-17(31)18(32)7-13(11)21(22(14)25(35)36)10-1-2-15(29)16(30)4-10/h1-5,7,12,19-24,27-34H,6,8-9H2,(H,35,36)/t12?,19-,20-,21-,22-,23+,24+/m1/s1

InChI Key

SPXXGPHPASGHLM-DHYIGXGMSA-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
Bazzania trilobata	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as lignan glycosides. These are aromatic polycyclic compounds containing a carbohydrate component glycosidically linked to a lignan moiety. They include 1-aryltetralin lactones.

Kingdom

Organic compounds

Super Class

Lignans, neolignans and related compounds

Class

Lignan glycosides

Sub Class

Not Available

Direct Parent

Lignan glycosides

Alternative Parents

Substituents

Lignan glycoside
1-aryltetralin lignan
2-naphthalenecarboxylic acid or derivatives
2-naphthalenecarboxylic acid
2-naphthol
Glycosyl compound
C-glycosyl compound
Naphthalene
Catechol
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Phenol
Benzenoid
Monosaccharide
Dicarboxylic acid or derivatives
Monocyclic benzene moiety
Alpha,beta-unsaturated carboxylic ester
Enoate ester
Tetrahydrofuran
Secondary alcohol
Carboxylic acid ester
Oxacycle
Organoheterocyclic compound
Ether
Dialkyl ether
Carboxylic acid
Carboxylic acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Primary alcohol
Organooxygen compound
Carbonyl group
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	0.74	ALOGPS
logP	-0.23	ChemAxon
logS	-2.8	ALOGPS
pKa (Strongest Acidic)	3.43	ChemAxon
pKa (Strongest Basic)	-3.6	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	12	ChemAxon
Hydrogen Donor Count	9	ChemAxon
Polar Surface Area	234.67 Å²	ChemAxon
Rotatable Bond Count	9	ChemAxon
Refractivity	131.69 m³·mol⁻¹	ChemAxon
Polarizability	53.8 Å³	ChemAxon
Number of Rings	4	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

C00043090

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

100918689

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (1r,2s)-1-(3,4-dihydroxyphenyl)-3-({[(2r,3r,4r,5r)-5-(2,3-dihydroxypropyl)-3,4-dihydroxyoxolan-2-yl]methoxy}carbonyl)-6,7-dihydroxy-1,2-dihydronaphthalene-2-carboxylic acid (NP0152652)

MOL for NP0152652 ((1r,2s)-1-(3,4-dihydroxyphenyl)-3-({[(2r,3r,4r,5r)-5-(2,3-dihydroxypropyl)-3,4-dihydroxyoxolan-2-yl]methoxy}carbonyl)-6,7-dihydroxy-1,2-dihydronaphthalene-2-carboxylic acid)

3D MOL for NP0152652 ((1r,2s)-1-(3,4-dihydroxyphenyl)-3-({[(2r,3r,4r,5r)-5-(2,3-dihydroxypropyl)-3,4-dihydroxyoxolan-2-yl]methoxy}carbonyl)-6,7-dihydroxy-1,2-dihydronaphthalene-2-carboxylic acid)

3D SDF for NP0152652 ((1r,2s)-1-(3,4-dihydroxyphenyl)-3-({[(2r,3r,4r,5r)-5-(2,3-dihydroxypropyl)-3,4-dihydroxyoxolan-2-yl]methoxy}carbonyl)-6,7-dihydroxy-1,2-dihydronaphthalene-2-carboxylic acid)

3D-SDF for NP0152652 ((1r,2s)-1-(3,4-dihydroxyphenyl)-3-({[(2r,3r,4r,5r)-5-(2,3-dihydroxypropyl)-3,4-dihydroxyoxolan-2-yl]methoxy}carbonyl)-6,7-dihydroxy-1,2-dihydronaphthalene-2-carboxylic acid)

PDB for NP0152652 ((1r,2s)-1-(3,4-dihydroxyphenyl)-3-({[(2r,3r,4r,5r)-5-(2,3-dihydroxypropyl)-3,4-dihydroxyoxolan-2-yl]methoxy}carbonyl)-6,7-dihydroxy-1,2-dihydronaphthalene-2-carboxylic acid)

3D PDB for NP0152652 ((1r,2s)-1-(3,4-dihydroxyphenyl)-3-({[(2r,3r,4r,5r)-5-(2,3-dihydroxypropyl)-3,4-dihydroxyoxolan-2-yl]methoxy}carbonyl)-6,7-dihydroxy-1,2-dihydronaphthalene-2-carboxylic acid)

SMILES for NP0152652 ((1r,2s)-1-(3,4-dihydroxyphenyl)-3-({[(2r,3r,4r,5r)-5-(2,3-dihydroxypropyl)-3,4-dihydroxyoxolan-2-yl]methoxy}carbonyl)-6,7-dihydroxy-1,2-dihydronaphthalene-2-carboxylic acid)

INCHI for NP0152652 ((1r,2s)-1-(3,4-dihydroxyphenyl)-3-({[(2r,3r,4r,5r)-5-(2,3-dihydroxypropyl)-3,4-dihydroxyoxolan-2-yl]methoxy}carbonyl)-6,7-dihydroxy-1,2-dihydronaphthalene-2-carboxylic acid)

Structure for NP0152652 ((1r,2s)-1-(3,4-dihydroxyphenyl)-3-({[(2r,3r,4r,5r)-5-(2,3-dihydroxypropyl)-3,4-dihydroxyoxolan-2-yl]methoxy}carbonyl)-6,7-dihydroxy-1,2-dihydronaphthalene-2-carboxylic acid)

3D Structure for NP0152652 ((1r,2s)-1-(3,4-dihydroxyphenyl)-3-({[(2r,3r,4r,5r)-5-(2,3-dihydroxypropyl)-3,4-dihydroxyoxolan-2-yl]methoxy}carbonyl)-6,7-dihydroxy-1,2-dihydronaphthalene-2-carboxylic acid)