NP-MRD: Showing NP-Card for Ligureside B (NP0332029)

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Record Information

Version

2.0

Created at

2023-10-25 20:00:39 UTC

Updated at

2024-09-03 04:17:45 UTC

NP-MRD ID

NP0332029

Natural Product DOI

https://doi.org/10.57994/1157

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Ligureside B

Description

Ligureside B was first documented in 2023 (PMID: 37852389). Based on a literature review very few articles have been published on Ligureside B.

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 10252320002D          

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M  END


  Mrv2104 10252320002D          

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 36 33  1  0  0  0  0
 36 37  1  1  0  0  0
 36 38  1  0  0  0  0
 38 39  1  6  0  0  0
 38 40  1  0  0  0  0
 40 31  1  0  0  0  0
 40 41  1  1  0  0  0
 29 42  1  0  0  0  0
 42 43  1  0  0  0  0
 43 44  2  0  0  0  0
 27 44  1  0  0  0  0
 44 45  1  0  0  0  0
 45 46  1  0  0  0  0
 46 47  1  0  0  0  0
 45 48  2  0  0  0  0
 28 49  2  0  0  0  0
 49 50  1  0  0  0  0
 25 51  2  0  0  0  0
 22 52  1  0  0  0  0
 15 52  1  0  0  0  0
 11 53  1  0  0  0  0
 53 54  2  0  0  0  0
  8 54  1  0  0  0  0
  6 55  2  0  0  0  0
  4 56  1  0  0  0  0
 56 57  1  0  0  0  0
 57 58  1  0  0  0  0
 58 59  1  0  0  0  0
 57 60  2  0  0  0  0
 56 61  2  0  0  0  0
 61 62  1  0  0  0  0
  2 62  1  0  0  0  0
  3 63  2  0  0  0  0
 63 64  1  0  0  0  0
 65 64  1  6  0  0  0
 65 66  1  0  0  0  0
 67 66  1  0  0  0  0
 67 68  1  6  0  0  0
 68 69  1  0  0  0  0
 70 67  1  0  0  0  0
 70 71  1  1  0  0  0
 70 72  1  0  0  0  0
 72 73  1  6  0  0  0
 72 74  1  0  0  0  0
 74 65  1  0  0  0  0
 74 75  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0332029

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC(=O)C1=CO[C@H](C)\C(=C\O[C@@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2O)[C@@H]1CC(=O)OC1=CC=C(CCO[C@@H]2O[C@H](COC(=O)C[C@H]3\C(=C/C)[C@H](O[C@@H]4O[C@H](CO)[C@@H](O)[C@H](O)[C@H]4O)OC=C3C(=O)OC)[C@@H](O)[C@H](O)[C@H]2O)C=C1

> <INCHI_IDENTIFIER>
InChI=1S/C48H64O27/c1-5-23-24(28(44(63)65-4)18-69-45(23)75-48-42(61)38(57)35(54)30(15-50)73-48)12-32(51)68-19-31-36(55)39(58)40(59)46(74-31)66-11-10-21-6-8-22(9-7-21)71-33(52)13-25-26(20(2)67-17-27(25)43(62)64-3)16-70-47-41(60)37(56)34(53)29(14-49)72-47/h5-9,16-18,20,24-25,29-31,34-42,45-50,53-61H,10-15,19H2,1-4H3/b23-5+,26-16-/t20-,24+,25+,29-,30-,31-,34-,35-,36-,37+,38+,39+,40-,41-,42-,45+,46-,47-,48+/m1/s1

> <INCHI_KEY>
CJIOQIHHXFXTFL-DPZUOURJSA-N

> <FORMULA>
C48H64O27

> <MOLECULAR_WEIGHT>
1073.013

> <EXACT_MASS>
1072.363496801

> <JCHEM_ACCEPTOR_COUNT>
23

> <JCHEM_ATOM_COUNT>
139

> <JCHEM_AVERAGE_POLARIZABILITY>
104.74363152395274

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
11

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
methyl (2R,3E,4S)-4-{2-[4-(2-{[(2R,3R,4S,5S,6R)-6-[({2-[(2S,3E,4S)-3-ethylidene-5-(methoxycarbonyl)-2-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,4-dihydro-2H-pyran-4-yl]acetyl}oxy)methyl]-3,4,5-trihydroxyoxan-2-yl]oxy}ethyl)phenoxy]-2-oxoethyl}-2-methyl-3-({[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methylidene)-3,4-dihydro-2H-pyran-5-carboxylate

> <JCHEM_LOGP>
-3.388992151000001

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.067503836295604

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.652724767776933

> <JCHEM_PKA_STRONGEST_BASIC>
-3.6490848644049554

> <JCHEM_POLAR_SURFACE_AREA>
401.5700000000001

> <JCHEM_REFRACTIVITY>
244.97120000000015

> <JCHEM_ROTATABLE_BOND_COUNT>
23

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
methyl (4S,5E,6R)-4-{2-[4-(2-{[(2R,3R,4S,5S,6R)-6-[({2-[(2S,3E,4S)-3-ethylidene-5-(methoxycarbonyl)-2-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-2,4-dihydropyran-4-yl]acetyl}oxy)methyl]-3,4,5-trihydroxyoxan-2-yl]oxy}ethyl)phenoxy]-2-oxoethyl}-6-methyl-5-({[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methylidene)-4,6-dihydropyran-3-carboxylate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 25-OCT-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   25-OCT-23         0                                  
HETATM    1  C   UNK     0       0.000  -3.080   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000  -4.620   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.334  -5.390   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.334  -6.930   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.667  -7.700   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.667  -9.240   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       4.001 -10.010   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       4.001 -11.550   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       5.335 -12.320   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       5.335 -13.860   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.001 -14.630   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       4.001 -16.170   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       5.335 -16.940   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       5.335 -18.480   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       6.668 -19.250   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       8.002 -18.480   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       8.002 -16.940   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0       9.336 -19.250   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      10.669 -18.480   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0       9.336 -20.790   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0      10.669 -21.560   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0       8.002 -21.560   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       8.002 -23.100   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0       9.336 -23.870   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0       9.336 -25.410   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      10.669 -26.180   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      10.669 -27.720   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      12.003 -28.490   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      12.003 -30.030   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0      13.337 -30.800   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0      13.337 -32.340   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0      14.670 -33.110   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0      14.670 -34.650   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      16.004 -35.420   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0      16.004 -36.960   0.000  0.00  0.00           O+0
HETATM   36  C   UNK     0      13.337 -35.420   0.000  0.00  0.00           C+0
HETATM   37  O   UNK     0      13.337 -36.960   0.000  0.00  0.00           O+0
HETATM   38  C   UNK     0      12.003 -34.650   0.000  0.00  0.00           C+0
HETATM   39  O   UNK     0      10.669 -35.420   0.000  0.00  0.00           O+0
HETATM   40  C   UNK     0      12.003 -33.110   0.000  0.00  0.00           C+0
HETATM   41  O   UNK     0      10.669 -32.340   0.000  0.00  0.00           O+0
HETATM   42  O   UNK     0      10.669 -30.800   0.000  0.00  0.00           O+0
HETATM   43  C   UNK     0       9.336 -30.030   0.000  0.00  0.00           C+0
HETATM   44  C   UNK     0       9.336 -28.490   0.000  0.00  0.00           C+0
HETATM   45  C   UNK     0       8.002 -27.720   0.000  0.00  0.00           C+0
HETATM   46  O   UNK     0       6.668 -28.490   0.000  0.00  0.00           O+0
HETATM   47  C   UNK     0       5.335 -27.720   0.000  0.00  0.00           C+0
HETATM   48  O   UNK     0       8.002 -26.180   0.000  0.00  0.00           O+0
HETATM   49  C   UNK     0      13.337 -27.720   0.000  0.00  0.00           C+0
HETATM   50  C   UNK     0      13.337 -26.180   0.000  0.00  0.00           C+0
HETATM   51  O   UNK     0       7.804 -25.249   0.000  0.00  0.00           O+0
HETATM   52  O   UNK     0       6.668 -20.790   0.000  0.00  0.00           O+0
HETATM   53  C   UNK     0       2.667 -13.860   0.000  0.00  0.00           C+0
HETATM   54  C   UNK     0       2.667 -12.320   0.000  0.00  0.00           C+0
HETATM   55  O   UNK     0       1.334 -10.010   0.000  0.00  0.00           O+0
HETATM   56  C   UNK     0       0.000  -7.700   0.000  0.00  0.00           C+0
HETATM   57  C   UNK     0       0.000  -9.240   0.000  0.00  0.00           C+0
HETATM   58  O   UNK     0      -1.334 -10.010   0.000  0.00  0.00           O+0
HETATM   59  C   UNK     0      -1.334 -11.550   0.000  0.00  0.00           C+0
HETATM   60  O   UNK     0       0.626 -10.647   0.000  0.00  0.00           O+0
HETATM   61  C   UNK     0      -1.334  -6.930   0.000  0.00  0.00           C+0
HETATM   62  O   UNK     0      -1.334  -5.390   0.000  0.00  0.00           O+0
HETATM   63  C   UNK     0       2.667  -4.620   0.000  0.00  0.00           C+0
HETATM   64  O   UNK     0       4.001  -5.390   0.000  0.00  0.00           O+0
HETATM   65  C   UNK     0       5.335  -4.620   0.000  0.00  0.00           C+0
HETATM   66  O   UNK     0       5.335  -3.080   0.000  0.00  0.00           O+0
HETATM   67  C   UNK     0       6.668  -2.310   0.000  0.00  0.00           C+0
HETATM   68  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM   69  O   UNK     0       5.335  -0.000   0.000  0.00  0.00           O+0
HETATM   70  C   UNK     0       8.002  -3.080   0.000  0.00  0.00           C+0
HETATM   71  O   UNK     0       9.336  -2.310   0.000  0.00  0.00           O+0
HETATM   72  C   UNK     0       8.002  -4.620   0.000  0.00  0.00           C+0
HETATM   73  O   UNK     0       9.336  -5.390   0.000  0.00  0.00           O+0
HETATM   74  C   UNK     0       6.668  -5.390   0.000  0.00  0.00           C+0
HETATM   75  O   UNK     0       6.668  -6.930   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   62                                                  
CONECT    3    2    4   63                                                  
CONECT    4    3    5   56                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7   55                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9   54                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12   53                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16   52                                                  
CONECT   16   15   17   18                                                  
CONECT   17   16                                                            
CONECT   18   16   19   20                                                  
CONECT   19   18                                                            
CONECT   20   18   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20   23   52                                                  
CONECT   23   22   24                                                       
CONECT   24   23   25                                                       
CONECT   25   24   26   51                                                  
CONECT   26   25   27                                                       
CONECT   27   26   28   44                                                  
CONECT   28   27   29   49                                                  
CONECT   29   28   30   42                                                  
CONECT   30   29   31                                                       
CONECT   31   30   32   40                                                  
CONECT   32   31   33                                                       
CONECT   33   32   34   36                                                  
CONECT   34   33   35                                                       
CONECT   35   34                                                            
CONECT   36   33   37   38                                                  
CONECT   37   36                                                            
CONECT   38   36   39   40                                                  
CONECT   39   38                                                            
CONECT   40   38   31   41                                                  
CONECT   41   40                                                            
CONECT   42   29   43                                                       
CONECT   43   42   44                                                       
CONECT   44   43   27   45                                                  
CONECT   45   44   46   48                                                  
CONECT   46   45   47                                                       
CONECT   47   46                                                            
CONECT   48   45                                                            
CONECT   49   28   50                                                       
CONECT   50   49                                                            
CONECT   51   25                                                            
CONECT   52   22   15                                                       
CONECT   53   11   54                                                       
CONECT   54   53    8                                                       
CONECT   55    6                                                            
CONECT   56    4   57   61                                                  
CONECT   57   56   58   60                                                  
CONECT   58   57   59                                                       
CONECT   59   58                                                            
CONECT   60   57                                                            
CONECT   61   56   62                                                       
CONECT   62   61    2                                                       
CONECT   63    3   64                                                       
CONECT   64   63   65                                                       
CONECT   65   64   66   74                                                  
CONECT   66   65   67                                                       
CONECT   67   66   68   70                                                  
CONECT   68   67   69                                                       
CONECT   69   68                                                            
CONECT   70   67   71   72                                                  
CONECT   71   70                                                            
CONECT   72   70   73   74                                                  
CONECT   73   72                                                            
CONECT   74   72   65   75                                                  
CONECT   75   74                                                            
MASTER        0    0    0    0    0    0    0    0   75    0  160    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₄₈H₆₄O₂₇

Average Mass

1073.0130 Da

Monoisotopic Mass

1072.36350 Da

IUPAC Name

methyl (2R,3E,4S)-4-{2-[4-(2-{[(2R,3R,4S,5S,6R)-6-[({2-[(2S,3E,4S)-3-ethylidene-5-(methoxycarbonyl)-2-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,4-dihydro-2H-pyran-4-yl]acetyl}oxy)methyl]-3,4,5-trihydroxyoxan-2-yl]oxy}ethyl)phenoxy]-2-oxoethyl}-2-methyl-3-({[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methylidene)-3,4-dihydro-2H-pyran-5-carboxylate

Traditional Name

methyl (4S,5E,6R)-4-{2-[4-(2-{[(2R,3R,4S,5S,6R)-6-[({2-[(2S,3E,4S)-3-ethylidene-5-(methoxycarbonyl)-2-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-2,4-dihydropyran-4-yl]acetyl}oxy)methyl]-3,4,5-trihydroxyoxan-2-yl]oxy}ethyl)phenoxy]-2-oxoethyl}-6-methyl-5-({[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methylidene)-4,6-dihydropyran-3-carboxylate

CAS Registry Number

Not Available

SMILES

COC(=O)C1=CO[C@H](C)\C(=C\O[C@@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2O)[C@@H]1CC(=O)OC1=CC=C(CCO[C@@H]2O[C@H](COC(=O)C[C@H]3\C(=C/C)[C@H](O[C@@H]4O[C@H](CO)[C@@H](O)[C@H](O)[C@H]4O)OC=C3C(=O)OC)[C@@H](O)[C@H](O)[C@H]2O)C=C1

InChI Identifier

InChI=1S/C48H64O27/c1-5-23-24(28(44(63)65-4)18-69-45(23)75-48-42(61)38(57)35(54)30(15-50)73-48)12-32(51)68-19-31-36(55)39(58)40(59)46(74-31)66-11-10-21-6-8-22(9-7-21)71-33(52)13-25-26(20(2)67-17-27(25)43(62)64-3)16-70-47-41(60)37(56)34(53)29(14-49)72-47/h5-9,16-18,20,24-25,29-31,34-42,45-50,53-61H,10-15,19H2,1-4H3/b23-5+,26-16-/t20-,24+,25+,29-,30-,31-,34-,35-,36-,37+,38+,39+,40-,41-,42-,45+,46-,47-,48+/m1/s1

InChI Key

CJIOQIHHXFXTFL-DPZUOURJSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View

Predicted Spectra

Not Available

Chemical Shift Submissions

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹H NMR Spectrum (1D, 600, CD₃OD, simulated)	wangying_cpu@163.com	Jinan University	Ying Wang	2024-05-09	View Spectrum

Species

Species of Origin

Species Name	Source	Reference
lucidum		Not Available

Chemical Taxonomy

Classification

Not classified

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	-3.4	ChemAxon
pKa (Strongest Acidic)	11.65	ChemAxon
pKa (Strongest Basic)	-3.6	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	23	ChemAxon
Hydrogen Donor Count	11	ChemAxon
Polar Surface Area	401.57 Å²	ChemAxon
Rotatable Bond Count	23	ChemAxon
Refractivity	244.97 m³·mol⁻¹	ChemAxon
Polarizability	104.74 Å³	ChemAxon
Number of Rings	6	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

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Peng YS, Liu JX, Jiao J, Qiu ML, Tang W, Song JG, Ye WC, Wang Y, Huang XJ: Secoiridoid glycosides from the fruits of Ligustrum lucidum and their in vitro anti-inflammatory activity. Fitoterapia. 2023 Dec;171:105705. doi: 10.1016/j.fitote.2023.105705. Epub 2023 Oct 16. [PubMed:37852389 ]

Showing NP-Card for Ligureside B (NP0332029)

MOL for NP0332029 (Ligureside B)

3D MOL for NP0332029 (Ligureside B)

3D SDF for NP0332029 (Ligureside B)

3D-SDF for NP0332029 (Ligureside B)

PDB for NP0332029 (Ligureside B)

3D PDB for NP0332029 (Ligureside B)

SMILES for NP0332029 (Ligureside B)

INCHI for NP0332029 (Ligureside B)

Structure for NP0332029 (Ligureside B)

3D Structure for NP0332029 (Ligureside B)