NP-MRD: Showing NP-Card for RA XIII (NP0071700)

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Record Information

Version

2.0

Created at

2022-04-28 17:02:46 UTC

Updated at

2022-04-28 17:02:46 UTC

NP-MRD ID

NP0071700

Secondary Accession Numbers

None

Natural Product Identification

Common Name

RA XIII

Description

3-[(1R,4R,7S,10S,13S,16S)-2,5,11-trihydroxy-10-[(4-methoxyphenyl)methyl]-4,9,13,15,29-pentamethyl-8,14,30-trioxo-24-{[(2R,3S,4R,5R,6S)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-22-oxa-3,6,9,12,15,29-hexaazatetracyclo[14.12.2.2¹⁸,²¹.1²³,²⁷]Tritriaconta-2,5,11,18,20,23,25,27(31),32-nonaen-7-yl]propanoic acid 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. RA XIII is found in Rubia akane and Rubia cordifolia . Based on a literature review very few articles have been published on 3-[(1R,4R,7S,10S,13S,16S)-2,5,11-trihydroxy-10-[(4-methoxyphenyl)methyl]-4,9,13,15,29-pentamethyl-8,14,30-trioxo-24-{[(2R,3S,4R,5R,6S)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-22-oxa-3,6,9,12,15,29-hexaazatetracyclo[14.12.2.2¹⁸,²¹.1²³,²⁷]Tritriaconta-2,5,11,18,20,23,25,27(31),32-nonaen-7-yl]propanoic acid.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282219022D          

 70 75  0  0  1  0            999 V2000
    2.4297    4.0182    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.2430    3.8438    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.8028    4.4550    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6075    4.2731    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5597    5.2493    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.1170    5.8652    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.8714    6.6558    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4326    7.2605    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0612    6.8427    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.8086    7.6329    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.0018    7.8140    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7472    8.5988    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4519    7.1902    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.6383    7.3679    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.2957    8.1531    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4438    8.5690    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -2.9324    6.4800    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -6.1793    4.5593    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
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   -7.1138    5.6403    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.7379    5.1009    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -5.2449    3.4782    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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    2.7545    5.4287    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  3  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  7  9  1  0  0  0  0
  9 10  1  0  0  0  0
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M  END

     RDKit          3D

130135  0  0  0  0  0  0  0  0999 V2000
   12.3115    2.3171    1.3521 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.0194    2.7598    1.6275 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.8749    2.3969    0.9063 C   0  0  0  0  0  0  0  0  0  0  0  0
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   12.5496    2.1359    0.2968 H   0  0  0  0  0  0  0  0  0  0  0  0
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M  END


  Mrv1652304282219022D          

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M  END
> <DATABASE_ID>
NP0071700

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC1=CC=C(C[C@@H]2N(C)C(=O)[C@H](CCC(O)=O)NC(=O)[C@@H](C)NC(=O)[C@H]3CC4=CC(OC5=CC=C(C[C@H](N(C)C(=O)[C@H](C)NC2=O)C(=O)N3C)C=C5)=C(O[C@H]2O[C@@H](CO)[C@H](O)[C@@H](O)[C@@H]2O)C=C4)C=C1

> <INCHI_IDENTIFIER>
InChI=1S/C48H60N6O16/c1-24-42(61)51-31(16-18-38(56)57)46(65)52(3)32(19-26-7-12-29(67-6)13-8-26)44(63)50-25(2)45(64)54(5)34-20-27-9-14-30(15-10-27)68-36-22-28(21-33(43(62)49-24)53(4)47(34)66)11-17-35(36)69-48-41(60)40(59)39(58)37(23-55)70-48/h7-15,17,22,24-25,31-34,37,39-41,48,55,58-60H,16,18-21,23H2,1-6H3,(H,49,62)(H,50,63)(H,51,61)(H,56,57)/t24-,25+,31+,32+,33-,34+,37+,39+,40-,41+,48+/m1/s1

> <INCHI_KEY>
KGNAXTMQQANFON-JUHJQUNASA-N

> <FORMULA>
C48H60N6O16

> <MOLECULAR_WEIGHT>
977.034

> <EXACT_MASS>
976.406579876

> <JCHEM_ACCEPTOR_COUNT>
15

> <JCHEM_ATOM_COUNT>
130

> <JCHEM_AVERAGE_POLARIZABILITY>
97.69052443004765

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
8

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-[(1R,4R,7S,10S,13S,16S)-10-[(4-methoxyphenyl)methyl]-4,9,13,15,29-pentamethyl-2,5,8,11,14,30-hexaoxo-24-{[(2R,3S,4R,5R,6S)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-22-oxa-3,6,9,12,15,29-hexaazatetracyclo[14.12.2.2^{18,21}.1^{23,27}]tritriaconta-18,20,23,25,27(31),32-hexaen-7-yl]propanoic acid

> <ALOGPS_LOGP>
1.17

> <JCHEM_LOGP>
-1.1345207026666682

> <ALOGPS_LOGS>
-3.81

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
10.43940944726767

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.01494634532202

> <JCHEM_PKA_STRONGEST_BASIC>
-2.981092354914205

> <JCHEM_POLAR_SURFACE_AREA>
303.37

> <JCHEM_REFRACTIVITY>
243.89319999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
9

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.53e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-[(1R,4R,7S,10S,13S,16S)-10-[(4-methoxyphenyl)methyl]-4,9,13,15,29-pentamethyl-2,5,8,11,14,30-hexaoxo-24-{[(2R,3S,4R,5R,6S)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-22-oxa-3,6,9,12,15,29-hexaazatetracyclo[14.12.2.2^{18,21}.1^{23,27}]tritriaconta-18,20,23,25,27(31),32-hexaen-7-yl]propanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 28-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   28-APR-22         0                                  
HETATM    1  N   UNK     0       4.535   7.501   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0       6.054   7.175   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       7.099   8.316   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       8.601   7.976   0.000  0.00  0.00           O+0
HETATM    5  N   UNK     0       6.645   9.799   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0       7.685  10.948   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       7.227  12.424   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       8.274  13.553   0.000  0.00  0.00           O+0
HETATM    9  N   UNK     0       5.714  12.773   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0       5.243  14.248   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       3.737  14.586   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       3.261  16.051   0.000  0.00  0.00           O+0
HETATM   13  N   UNK     0       2.710  13.422   0.000  0.00  0.00           N+0
HETATM   14  C   UNK     0       1.191  13.754   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       0.552  15.219   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -0.828  15.995   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -1.292  14.528   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -2.770  14.068   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -3.936  15.007   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -3.471  16.477   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      -2.071  17.028   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0      -4.967  13.814   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0      -5.474  12.096   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      -6.585  11.026   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      -6.364   9.410   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      -4.898   8.942   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      -3.699   9.879   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      -2.128   9.564   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      -0.601   9.975   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       0.013   8.528   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0      -0.979   7.350   0.000  0.00  0.00           O+0
HETATM   32  N   UNK     0       1.523   8.174   0.000  0.00  0.00           N+0
HETATM   33  C   UNK     0       1.971   6.693   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       3.480   6.368   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0       3.941   4.898   0.000  0.00  0.00           O+0
HETATM   36  C   UNK     0       0.927   5.561   0.000  0.00  0.00           C+0
HETATM   37  N   UNK     0       0.503  11.037   0.000  0.00  0.00           N+0
HETATM   38  C   UNK     0       0.172  12.566   0.000  0.00  0.00           C+0
HETATM   39  O   UNK     0      -1.321  12.944   0.000  0.00  0.00           O+0
HETATM   40  C   UNK     0       1.976  10.588   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0      -4.082  11.409   0.000  0.00  0.00           C+0
HETATM   42  O   UNK     0      -8.039  11.532   0.000  0.00  0.00           O+0
HETATM   43  C   UNK     0      -9.205  10.525   0.000  0.00  0.00           C+0
HETATM   44  C   UNK     0      -8.915   9.012   0.000  0.00  0.00           C+0
HETATM   45  C   UNK     0     -10.080   8.005   0.000  0.00  0.00           C+0
HETATM   46  C   UNK     0     -11.535   8.511   0.000  0.00  0.00           C+0
HETATM   47  C   UNK     0     -11.824  10.023   0.000  0.00  0.00           C+0
HETATM   48  O   UNK     0     -10.659  11.030   0.000  0.00  0.00           O+0
HETATM   49  C   UNK     0     -13.279  10.529   0.000  0.00  0.00           C+0
HETATM   50  O   UNK     0     -14.444   9.522   0.000  0.00  0.00           O+0
HETATM   51  O   UNK     0     -12.700   7.504   0.000  0.00  0.00           O+0
HETATM   52  O   UNK     0      -9.791   6.493   0.000  0.00  0.00           O+0
HETATM   53  O   UNK     0      -7.460   8.507   0.000  0.00  0.00           O+0
HETATM   54  C   UNK     0       3.190  11.958   0.000  0.00  0.00           C+0
HETATM   55  C   UNK     0       6.282  15.384   0.000  0.00  0.00           C+0
HETATM   56  C   UNK     0       9.189  10.617   0.000  0.00  0.00           C+0
HETATM   57  C   UNK     0      10.228  11.753   0.000  0.00  0.00           C+0
HETATM   58  C   UNK     0       9.763  13.222   0.000  0.00  0.00           C+0
HETATM   59  C   UNK     0      10.803  14.358   0.000  0.00  0.00           C+0
HETATM   60  C   UNK     0      12.306  14.026   0.000  0.00  0.00           C+0
HETATM   61  C   UNK     0      12.771  12.558   0.000  0.00  0.00           C+0
HETATM   62  C   UNK     0      11.732  11.422   0.000  0.00  0.00           C+0
HETATM   63  O   UNK     0      13.346  15.163   0.000  0.00  0.00           O+0
HETATM   64  C   UNK     0      12.881  16.631   0.000  0.00  0.00           C+0
HETATM   65  C   UNK     0       5.142  10.134   0.000  0.00  0.00           C+0
HETATM   66  C   UNK     0       6.522   5.708   0.000  0.00  0.00           C+0
HETATM   67  C   UNK     0       5.486   4.569   0.000  0.00  0.00           C+0
HETATM   68  C   UNK     0       5.954   3.102   0.000  0.00  0.00           C+0
HETATM   69  O   UNK     0       4.918   1.963   0.000  0.00  0.00           O+0
HETATM   70  O   UNK     0       7.459   2.774   0.000  0.00  0.00           O+0
CONECT    1    2   34                                                       
CONECT    2    1    3   66                                                  
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6   65                                                  
CONECT    6    5    7   56                                                  
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10                                                       
CONECT   10    9   11   55                                                  
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11   14   54                                                  
CONECT   14   13   15   38                                                  
CONECT   15   14   16                                                       
CONECT   16   15   17   21                                                  
CONECT   17   16   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20   22                                                  
CONECT   20   19   21                                                       
CONECT   21   20   16                                                       
CONECT   22   19   23                                                       
CONECT   23   22   24   41                                                  
CONECT   24   23   25   42                                                  
CONECT   25   24   26                                                       
CONECT   26   25   27                                                       
CONECT   27   26   28   41                                                  
CONECT   28   27   29                                                       
CONECT   29   28   30   37                                                  
CONECT   30   29   31   32                                                  
CONECT   31   30                                                            
CONECT   32   30   33                                                       
CONECT   33   32   34   36                                                  
CONECT   34   33    1   35                                                  
CONECT   35   34                                                            
CONECT   36   33                                                            
CONECT   37   29   38   40                                                  
CONECT   38   37   14   39                                                  
CONECT   39   38                                                            
CONECT   40   37                                                            
CONECT   41   27   23                                                       
CONECT   42   24   43                                                       
CONECT   43   42   44   48                                                  
CONECT   44   43   45   53                                                  
CONECT   45   44   46   52                                                  
CONECT   46   45   47   51                                                  
CONECT   47   46   48   49                                                  
CONECT   48   47   43                                                       
CONECT   49   47   50                                                       
CONECT   50   49                                                            
CONECT   51   46                                                            
CONECT   52   45                                                            
CONECT   53   44                                                            
CONECT   54   13                                                            
CONECT   55   10                                                            
CONECT   56    6   57                                                       
CONECT   57   56   58   62                                                  
CONECT   58   57   59                                                       
CONECT   59   58   60                                                       
CONECT   60   59   61   63                                                  
CONECT   61   60   62                                                       
CONECT   62   61   57                                                       
CONECT   63   60   64                                                       
CONECT   64   63                                                            
CONECT   65    5                                                            
CONECT   66    2   67                                                       
CONECT   67   66   68                                                       
CONECT   68   67   69   70                                                  
CONECT   69   68                                                            
CONECT   70   68                                                            
MASTER        0    0    0    0    0    0    0    0   70    0  150    0
END

View in JSmol

Synonyms

Value	Source
3-[(1R,4R,7S,10S,13S,16S)-2,5,11-Trihydroxy-10-[(4-methoxyphenyl)methyl]-4,9,13,15,29-pentamethyl-8,14,30-trioxo-24-{[(2R,3S,4R,5R,6S)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-22-oxa-3,6,9,12,15,29-hexaazatetracyclo[14.12.2.2,.1,]tritriaconta-2,5,11,18,20,23,25,27(31),32-nonaen-7-yl]propanoate	Generator

Chemical Formula

C₄₈H₆₀N₆O₁₆

Average Mass

977.0340 Da

Monoisotopic Mass

976.40658 Da

IUPAC Name

3-[(1R,4R,7S,10S,13S,16S)-10-[(4-methoxyphenyl)methyl]-4,9,13,15,29-pentamethyl-2,5,8,11,14,30-hexaoxo-24-{[(2R,3S,4R,5R,6S)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-22-oxa-3,6,9,12,15,29-hexaazatetracyclo[14.12.2.2^{18,21}.1^{23,27}]tritriaconta-18,20,23,25,27(31),32-hexaen-7-yl]propanoic acid

Traditional Name

CAS Registry Number

Not Available

SMILES

COC1=CC=C(C[C@@H]2N(C)C(=O)[C@H](CCC(O)=O)NC(=O)[C@@H](C)NC(=O)[C@H]3CC4=CC(OC5=CC=C(C[C@H](N(C)C(=O)[C@H](C)NC2=O)C(=O)N3C)C=C5)=C(O[C@H]2O[C@@H](CO)[C@H](O)[C@@H](O)[C@@H]2O)C=C4)C=C1

InChI Identifier

InChI=1S/C48H60N6O16/c1-24-42(61)51-31(16-18-38(56)57)46(65)52(3)32(19-26-7-12-29(67-6)13-8-26)44(63)50-25(2)45(64)54(5)34-20-27-9-14-30(15-10-27)68-36-22-28(21-33(43(62)49-24)53(4)47(34)66)11-17-35(36)69-48-41(60)40(59)39(58)37(23-55)70-48/h7-15,17,22,24-25,31-34,37,39-41,48,55,58-60H,16,18-21,23H2,1-6H3,(H,49,62)(H,50,63)(H,51,61)(H,56,57)/t24-,25+,31+,32+,33-,34+,37+,39+,40-,41+,48+/m1/s1

InChI Key

KGNAXTMQQANFON-JUHJQUNASA-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, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, 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
Rubia akane	Plant	KNApSAcK
Rubia cordifolia	Plant	KNApSAcK

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
Cyclic alpha peptide
Phenolic glycoside
Macrolactam
Hexose monosaccharide
O-glycosyl compound
Glycosyl compound
Diaryl ether
Alpha-amino acid or derivatives
Phenoxy compound
Methoxybenzene
Phenol ether
Anisole
Alkyl aryl ether
Benzenoid
Oxane
Monosaccharide
Monocyclic benzene moiety
Cyclic carboximidic acid
Tertiary carboxylic acid amide
Secondary alcohol
Lactam
Carboxamide group
Oxacycle
Azacycle
Organoheterocyclic compound
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Polyol
Monocarboxylic acid or derivatives
Ether
Carboxylic acid
Carboxylic acid derivative
Acetal
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Primary alcohol
Organooxygen compound
Organonitrogen 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	1.17	ALOGPS
logP	-1.1	ChemAxon
logS	-3.8	ALOGPS
pKa (Strongest Acidic)	4.01	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	15	ChemAxon
Hydrogen Donor Count	8	ChemAxon
Polar Surface Area	303.37 Å²	ChemAxon
Rotatable Bond Count	9	ChemAxon
Refractivity	243.89 m³·mol⁻¹	ChemAxon
Polarizability	97.69 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

162844525

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for RA XIII (NP0071700)

MOL for NP0071700 (RA XIII)

3D MOL for NP0071700 (RA XIII)

3D SDF for NP0071700 (RA XIII)

3D-SDF for NP0071700 (RA XIII)

PDB for NP0071700 (RA XIII)

3D PDB for NP0071700 (RA XIII)

SMILES for NP0071700 (RA XIII)

INCHI for NP0071700 (RA XIII)

Structure for NP0071700 (RA XIII)

3D Structure for NP0071700 (RA XIII)