Np mrd loader

Showing NP-Card for gymnoside VI (NP0032248)

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Record Information
Version2.0
Created at2021-06-19 23:06:03 UTC
Updated at2021-06-30 00:01:19 UTC
NP-MRD IDNP0032248
Secondary Accession NumbersNone
Natural Product Identification
Common Namegymnoside VI
Provided ByJEOL DatabaseJEOL Logo
Description gymnoside VI is found in Gymnadenia conopsea. gymnoside VI was first documented in 2006 (Morikawa, T., et al.).
Structure
Thumb
MOL3D MOLSDF3D SDFPDBSMILESInChI

MOL for NP0032248 (gymnoside VI)


  Mrv1652306202101063D          

134139  0  0  0  0            999 V2000
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   -3.0335    3.0656   -3.5911 C   0  0  2  0  0  0  0  0  0  0  0  0
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   -2.5417    1.6031   -3.4658 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.1600    0.7273   -2.3329 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.4067   -0.6275   -2.2845 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.6832   -1.4288   -1.0371 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6636   -1.2998   -0.3211 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6894   -2.3395   -0.8573 O   0  0  0  0  0  0  0  0  0  0  0  0
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    1.3553   -2.1584    2.2963 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8478   -1.2722    3.2494 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7891   -0.7306    4.0824 O   0  0  0  0  0  0  0  0  0  0  0  0
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    2.2094    1.6636    6.9297 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.3853    2.1175    7.6189 O   0  0  0  0  0  0  0  0  0  0  0  0
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    3.3383    1.5958    4.8208 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -4.9410   -1.5857   -5.3948 C   0  0  2  0  0  0  0  0  0  0  0  0
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M  END
Download

3D MOL for NP0032248 (gymnoside VI)

     RDKit          3D

134139  0  0  0  0  0  0  0  0999 V2000
   -4.5117    3.1930   -3.9566 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0335    3.0656   -3.5911 C   0  0  2  0  0  0  0  0  0  0  0  0
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M  END
Download

3D SDF for NP0032248 (gymnoside VI)


  Mrv1652306202101063D          

134139  0  0  0  0            999 V2000
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    2.6548   -2.7641   -2.9804 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4979   -2.7743   -3.7651 C   0  0  0  0  0  0  0  0  0  0  0  0
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    0.9899    0.9516    0.2415 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3611    0.8605    0.4909 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9834    1.8049    1.3008 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
> <DATABASE_ID>
NP0032248

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]OC([H])([H])[C@]1([H])O[C@]([H])(OC2=C([H])C([H])=C(C([H])=C2[H])C([H])([H])OC(=O)C([H])([H])[C@@](O[C@]2([H])O[C@]([H])(C([H])([H])OC(=O)C(\[H])=C(/[H])C3=C([H])C([H])=C([H])C([H])=C3[H])[C@@]([H])(O[H])[C@]([H])(O[H])[C@@]2([H])O[H])(C(=O)OC([H])([H])C2=C([H])C([H])=C(O[C@]3([H])O[C@]([H])(C([H])([H])O[H])[C@@]([H])(O[H])[C@]([H])(O[H])[C@@]3([H])O[H])C([H])=C2[H])C([H])([H])C([H])(C([H])([H])[H])C([H])([H])[H])[C@@]([H])(O[H])[C@]([H])(O[H])[C@@]1([H])O[H]

> <INCHI_IDENTIFIER>
InChI=1S/C49H62O23/c1-25(2)18-49(48(63)66-23-28-10-15-30(16-11-28)68-46-43(61)40(58)37(55)32(21-51)70-46,72-47-44(62)41(59)38(56)33(71-47)24-65-34(52)17-12-26-6-4-3-5-7-26)19-35(53)64-22-27-8-13-29(14-9-27)67-45-42(60)39(57)36(54)31(20-50)69-45/h3-17,25,31-33,36-47,50-51,54-62H,18-24H2,1-2H3/b17-12+/t31-,32+,33+,36-,37+,38+,39+,40-,41-,42-,43+,44+,45-,46+,47-,49+/m0/s1

> <INCHI_KEY>
VCCBFXCFLIEPOV-QPJLZBKDSA-N

> <FORMULA>
C49H62O23

> <MOLECULAR_WEIGHT>
1019.012

> <EXACT_MASS>
1018.368188256

> <JCHEM_ACCEPTOR_COUNT>
20

> <JCHEM_ATOM_COUNT>
134

> <JCHEM_AVERAGE_POLARIZABILITY>
100.92598470424332

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
11

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
4-(4-{[(2R,3S,4R,5R,6S)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)methyl 1-(4-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)methyl (2R)-2-(2-methylpropyl)-2-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-({[(2E)-3-phenylprop-2-enoyl]oxy}methyl)oxan-2-yl]oxy}butanedioate

> <ALOGPS_LOGP>
0.84

> <JCHEM_LOGP>
0.4337572033333317

> <ALOGPS_LOGS>
-3.68

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.193902937141482

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.748604424433479

> <JCHEM_PKA_STRONGEST_BASIC>
-3.648395345629174

> <JCHEM_POLAR_SURFACE_AREA>
356.81000000000006

> <JCHEM_REFRACTIVITY>
242.25709999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
24

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.14e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
4-(4-{[(2R,3S,4R,5R,6S)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)methyl 1-(4-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)methyl (2R)-2-(2-methylpropyl)-2-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-({[(2E)-3-phenylprop-2-enoyl]oxy}methyl)oxan-2-yl]oxy}butanedioate

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0032248 (gymnoside VI)

     RDKit          3D

134139  0  0  0  0  0  0  0  0999 V2000
   -4.5117    3.1930   -3.9566 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0335    3.0656   -3.5911 C   0  0  2  0  0  0  0  0  0  0  0  0
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   -2.4067   -0.6275   -2.2845 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6832   -1.4288   -1.0371 C   0  0  0  0  0  0  0  0  0  0  0  0
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    1.3553   -2.1584    2.2963 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8478   -1.2722    3.2494 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7891   -0.7306    4.0824 O   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

PDB for NP0032248 (gymnoside VI)

HEADER    PROTEIN                                 20-JUN-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   20-JUN-21         0                                  
HETATM    1  C   UNK     0      -4.512   3.193  -3.957  0.00  0.00           C+0
HETATM    2  C   UNK     0      -3.034   3.066  -3.591  0.00  0.00           C+0
HETATM    3  C   UNK     0      -2.190   3.786  -4.651  0.00  0.00           C+0
HETATM    4  C   UNK     0      -2.542   1.603  -3.466  0.00  0.00           C+0
HETATM    5  C   UNK     0      -3.160   0.727  -2.333  0.00  0.00           C+0
HETATM    6  C   UNK     0      -2.407  -0.628  -2.285  0.00  0.00           C+0
HETATM    7  C   UNK     0      -2.683  -1.429  -1.037  0.00  0.00           C+0
HETATM    8  O   UNK     0      -3.664  -1.300  -0.321  0.00  0.00           O+0
HETATM    9  O   UNK     0      -1.689  -2.340  -0.857  0.00  0.00           O+0
HETATM   10  C   UNK     0      -1.765  -3.120   0.342  0.00  0.00           C+0
HETATM   11  C   UNK     0      -0.860  -2.503   1.374  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.514  -2.764   1.360  0.00  0.00           C+0
HETATM   13  C   UNK     0       1.355  -2.158   2.296  0.00  0.00           C+0
HETATM   14  C   UNK     0       0.848  -1.272   3.249  0.00  0.00           C+0
HETATM   15  O   UNK     0       1.789  -0.731   4.082  0.00  0.00           O+0
HETATM   16  C   UNK     0       1.334   0.163   5.110  0.00  0.00           C+0
HETATM   17  O   UNK     0       0.591  -0.550   6.103  0.00  0.00           O+0
HETATM   18  C   UNK     0       0.127   0.306   7.163  0.00  0.00           C+0
HETATM   19  C   UNK     0      -0.752  -0.544   8.086  0.00  0.00           C+0
HETATM   20  O   UNK     0      -1.806  -1.135   7.321  0.00  0.00           O+0
HETATM   21  C   UNK     0       1.315   0.911   7.916  0.00  0.00           C+0
HETATM   22  O   UNK     0       0.878   1.812   8.933  0.00  0.00           O+0
HETATM   23  C   UNK     0       2.209   1.664   6.930  0.00  0.00           C+0
HETATM   24  O   UNK     0       3.385   2.118   7.619  0.00  0.00           O+0
HETATM   25  C   UNK     0       2.599   0.781   5.745  0.00  0.00           C+0
HETATM   26  O   UNK     0       3.338   1.596   4.821  0.00  0.00           O+0
HETATM   27  C   UNK     0      -0.522  -1.010   3.266  0.00  0.00           C+0
HETATM   28  C   UNK     0      -1.369  -1.618   2.332  0.00  0.00           C+0
HETATM   29  O   UNK     0      -4.580   0.624  -2.525  0.00  0.00           O+0
HETATM   30  C   UNK     0      -5.095  -0.441  -3.319  0.00  0.00           C+0
HETATM   31  O   UNK     0      -4.483  -0.478  -4.600  0.00  0.00           O+0
HETATM   32  C   UNK     0      -4.941  -1.586  -5.395  0.00  0.00           C+0
HETATM   33  C   UNK     0      -4.114  -1.626  -6.686  0.00  0.00           C+0
HETATM   34  O   UNK     0      -2.723  -1.739  -6.310  0.00  0.00           O+0
HETATM   35  C   UNK     0      -1.909  -0.739  -6.722  0.00  0.00           C+0
HETATM   36  O   UNK     0      -2.178   0.134  -7.533  0.00  0.00           O+0
HETATM   37  C   UNK     0      -0.611  -0.758  -6.012  0.00  0.00           C+0
HETATM   38  C   UNK     0      -0.283  -1.633  -5.049  0.00  0.00           C+0
HETATM   39  C   UNK     0       0.965  -1.581  -4.271  0.00  0.00           C+0
HETATM   40  C   UNK     0       1.600  -0.373  -3.948  0.00  0.00           C+0
HETATM   41  C   UNK     0       2.758  -0.364  -3.165  0.00  0.00           C+0
HETATM   42  C   UNK     0       3.287  -1.559  -2.683  0.00  0.00           C+0
HETATM   43  C   UNK     0       2.655  -2.764  -2.980  0.00  0.00           C+0
HETATM   44  C   UNK     0       1.498  -2.774  -3.765  0.00  0.00           C+0
HETATM   45  C   UNK     0      -6.440  -1.440  -5.676  0.00  0.00           C+0
HETATM   46  O   UNK     0      -6.936  -2.570  -6.396  0.00  0.00           O+0
HETATM   47  C   UNK     0      -7.204  -1.308  -4.353  0.00  0.00           C+0
HETATM   48  O   UNK     0      -8.585  -1.035  -4.635  0.00  0.00           O+0
HETATM   49  C   UNK     0      -6.609  -0.206  -3.476  0.00  0.00           C+0
HETATM   50  O   UNK     0      -7.281  -0.213  -2.208  0.00  0.00           O+0
HETATM   51  C   UNK     0      -2.923   1.470  -0.990  0.00  0.00           C+0
HETATM   52  O   UNK     0      -3.787   1.989  -0.296  0.00  0.00           O+0
HETATM   53  O   UNK     0      -1.592   1.482  -0.692  0.00  0.00           O+0
HETATM   54  C   UNK     0      -1.267   2.087   0.562  0.00  0.00           C+0
HETATM   55  C   UNK     0       0.223   1.986   0.798  0.00  0.00           C+0
HETATM   56  C   UNK     0       0.990   0.952   0.242  0.00  0.00           C+0
HETATM   57  C   UNK     0       2.361   0.861   0.491  0.00  0.00           C+0
HETATM   58  C   UNK     0       2.983   1.805   1.301  0.00  0.00           C+0
HETATM   59  O   UNK     0       4.311   1.769   1.626  0.00  0.00           O+0
HETATM   60  C   UNK     0       5.191   1.478   0.523  0.00  0.00           C+0
HETATM   61  O   UNK     0       5.509   0.079   0.475  0.00  0.00           O+0
HETATM   62  C   UNK     0       6.218  -0.424   1.615  0.00  0.00           C+0
HETATM   63  C   UNK     0       5.275  -1.203   2.538  0.00  0.00           C+0
HETATM   64  O   UNK     0       5.983  -1.722   3.662  0.00  0.00           O+0
HETATM   65  C   UNK     0       7.024   0.636   2.390  0.00  0.00           C+0
HETATM   66  O   UNK     0       8.103   0.042   3.123  0.00  0.00           O+0
HETATM   67  C   UNK     0       7.590   1.625   1.381  0.00  0.00           C+0
HETATM   68  O   UNK     0       8.444   2.577   2.032  0.00  0.00           O+0
HETATM   69  C   UNK     0       6.456   2.364   0.665  0.00  0.00           C+0
HETATM   70  O   UNK     0       6.944   2.785  -0.623  0.00  0.00           O+0
HETATM   71  C   UNK     0       2.228   2.815   1.894  0.00  0.00           C+0
HETATM   72  C   UNK     0       0.857   2.909   1.643  0.00  0.00           C+0
HETATM   73  H   UNK     0      -5.156   2.906  -3.121  0.00  0.00           H+0
HETATM   74  H   UNK     0      -4.764   2.572  -4.823  0.00  0.00           H+0
HETATM   75  H   UNK     0      -4.765   4.230  -4.203  0.00  0.00           H+0
HETATM   76  H   UNK     0      -2.869   3.586  -2.640  0.00  0.00           H+0
HETATM   77  H   UNK     0      -1.127   3.754  -4.392  0.00  0.00           H+0
HETATM   78  H   UNK     0      -2.313   3.324  -5.637  0.00  0.00           H+0
HETATM   79  H   UNK     0      -2.480   4.839  -4.731  0.00  0.00           H+0
HETATM   80  H   UNK     0      -2.697   1.114  -4.433  0.00  0.00           H+0
HETATM   81  H   UNK     0      -1.452   1.635  -3.324  0.00  0.00           H+0
HETATM   82  H   UNK     0      -2.639  -1.265  -3.141  0.00  0.00           H+0
HETATM   83  H   UNK     0      -1.326  -0.439  -2.305  0.00  0.00           H+0
HETATM   84  H   UNK     0      -2.790  -3.231   0.716  0.00  0.00           H+0
HETATM   85  H   UNK     0      -1.419  -4.132   0.100  0.00  0.00           H+0
HETATM   86  H   UNK     0       0.940  -3.432   0.615  0.00  0.00           H+0
HETATM   87  H   UNK     0       2.418  -2.375   2.271  0.00  0.00           H+0
HETATM   88  H   UNK     0       0.731   0.963   4.659  0.00  0.00           H+0
HETATM   89  H   UNK     0      -0.504   1.089   6.723  0.00  0.00           H+0
HETATM   90  H   UNK     0      -1.200   0.056   8.883  0.00  0.00           H+0
HETATM   91  H   UNK     0      -0.180  -1.362   8.536  0.00  0.00           H+0
HETATM   92  H   UNK     0      -1.366  -1.586   6.575  0.00  0.00           H+0
HETATM   93  H   UNK     0       1.900   0.123   8.407  0.00  0.00           H+0
HETATM   94  H   UNK     0       1.687   2.271   9.238  0.00  0.00           H+0
HETATM   95  H   UNK     0       1.705   2.573   6.580  0.00  0.00           H+0
HETATM   96  H   UNK     0       3.982   2.450   6.917  0.00  0.00           H+0
HETATM   97  H   UNK     0       3.284  -0.010   6.075  0.00  0.00           H+0
HETATM   98  H   UNK     0       3.357   1.115   3.970  0.00  0.00           H+0
HETATM   99  H   UNK     0      -0.973  -0.336   3.987  0.00  0.00           H+0
HETATM  100  H   UNK     0      -2.434  -1.388   2.354  0.00  0.00           H+0
HETATM  101  H   UNK     0      -4.930  -1.382  -2.781  0.00  0.00           H+0
HETATM  102  H   UNK     0      -4.737  -2.513  -4.842  0.00  0.00           H+0
HETATM  103  H   UNK     0      -4.367  -2.505  -7.287  0.00  0.00           H+0
HETATM  104  H   UNK     0      -4.305  -0.729  -7.285  0.00  0.00           H+0
HETATM  105  H   UNK     0       0.054   0.043  -6.315  0.00  0.00           H+0
HETATM  106  H   UNK     0      -0.963  -2.439  -4.782  0.00  0.00           H+0
HETATM  107  H   UNK     0       1.203   0.579  -4.290  0.00  0.00           H+0
HETATM  108  H   UNK     0       3.246   0.579  -2.930  0.00  0.00           H+0
HETATM  109  H   UNK     0       4.190  -1.548  -2.078  0.00  0.00           H+0
HETATM  110  H   UNK     0       3.065  -3.699  -2.607  0.00  0.00           H+0
HETATM  111  H   UNK     0       1.023  -3.728  -3.986  0.00  0.00           H+0
HETATM  112  H   UNK     0      -6.629  -0.551  -6.292  0.00  0.00           H+0
HETATM  113  H   UNK     0      -7.911  -2.470  -6.386  0.00  0.00           H+0
HETATM  114  H   UNK     0      -7.198  -2.266  -3.818  0.00  0.00           H+0
HETATM  115  H   UNK     0      -8.976  -0.786  -3.772  0.00  0.00           H+0
HETATM  116  H   UNK     0      -6.802   0.776  -3.926  0.00  0.00           H+0
HETATM  117  H   UNK     0      -6.751   0.371  -1.625  0.00  0.00           H+0
HETATM  118  H   UNK     0      -1.790   1.570   1.375  0.00  0.00           H+0
HETATM  119  H   UNK     0      -1.564   3.143   0.533  0.00  0.00           H+0
HETATM  120  H   UNK     0       0.526   0.192  -0.384  0.00  0.00           H+0
HETATM  121  H   UNK     0       2.915   0.032   0.062  0.00  0.00           H+0
HETATM  122  H   UNK     0       4.713   1.734  -0.432  0.00  0.00           H+0
HETATM  123  H   UNK     0       6.935  -1.157   1.222  0.00  0.00           H+0
HETATM  124  H   UNK     0       4.463  -0.568   2.902  0.00  0.00           H+0
HETATM  125  H   UNK     0       4.821  -2.035   1.989  0.00  0.00           H+0
HETATM  126  H   UNK     0       5.349  -2.268   4.162  0.00  0.00           H+0
HETATM  127  H   UNK     0       6.404   1.166   3.123  0.00  0.00           H+0
HETATM  128  H   UNK     0       7.698  -0.690   3.640  0.00  0.00           H+0
HETATM  129  H   UNK     0       8.232   1.103   0.661  0.00  0.00           H+0
HETATM  130  H   UNK     0       8.979   2.043   2.656  0.00  0.00           H+0
HETATM  131  H   UNK     0       6.198   3.286   1.199  0.00  0.00           H+0
HETATM  132  H   UNK     0       7.755   3.298  -0.441  0.00  0.00           H+0
HETATM  133  H   UNK     0       2.707   3.538   2.550  0.00  0.00           H+0
HETATM  134  H   UNK     0       0.287   3.711   2.108  0.00  0.00           H+0
CONECT    1    2   73   74   75                                             
CONECT    2    4    1    3   76                                             
CONECT    3    2   77   78   79                                             
CONECT    4    5    2   80   81                                             
CONECT    5   51    4   29    6                                             
CONECT    6    7    5   82   83                                             
CONECT    7    8    9    6                                                  
CONECT    8    7                                                            
CONECT    9   10    7                                                       
CONECT   10   11    9   84   85                                             
CONECT   11   12   28   10                                                  
CONECT   12   13   11   86                                                  
CONECT   13   14   12   87                                                  
CONECT   14   15   27   13                                                  
CONECT   15   14   16                                                       
CONECT   16   25   17   15   88                                             
CONECT   17   18   16                                                       
CONECT   18   21   17   19   89                                             
CONECT   19   20   18   90   91                                             
CONECT   20   19   92                                                       
CONECT   21   23   18   22   93                                             
CONECT   22   21   94                                                       
CONECT   23   25   21   24   95                                             
CONECT   24   23   96                                                       
CONECT   25   16   23   26   97                                             
CONECT   26   25   98                                                       
CONECT   27   14   28   99                                                  
CONECT   28   11   27  100                                                  
CONECT   29    5   30                                                       
CONECT   30   31   49   29  101                                             
CONECT   31   32   30                                                       
CONECT   32   45   31   33  102                                             
CONECT   33   34   32  103  104                                             
CONECT   34   33   35                                                       
CONECT   35   36   37   34                                                  
CONECT   36   35                                                            
CONECT   37   35   38  105                                                  
CONECT   38   39   37  106                                                  
CONECT   39   44   40   38                                                  
CONECT   40   39   41  107                                                  
CONECT   41   42   40  108                                                  
CONECT   42   41   43  109                                                  
CONECT   43   42   44  110                                                  
CONECT   44   43   39  111                                                  
CONECT   45   47   32   46  112                                             
CONECT   46   45  113                                                       
CONECT   47   49   45   48  114                                             
CONECT   48   47  115                                                       
CONECT   49   47   50   30  116                                             
CONECT   50   49  117                                                       
CONECT   51    5   53   52                                                  
CONECT   52   51                                                            
CONECT   53   51   54                                                       
CONECT   54   53   55  118  119                                             
CONECT   55   54   56   72                                                  
CONECT   56   55   57  120                                                  
CONECT   57   56   58  121                                                  
CONECT   58   57   71   59                                                  
CONECT   59   58   60                                                       
CONECT   60   69   61   59  122                                             
CONECT   61   62   60                                                       
CONECT   62   65   61   63  123                                             
CONECT   63   64   62  124  125                                             
CONECT   64   63  126                                                       
CONECT   65   67   62   66  127                                             
CONECT   66   65  128                                                       
CONECT   67   69   65   68  129                                             
CONECT   68   67  130                                                       
CONECT   69   60   67   70  131                                             
CONECT   70   69  132                                                       
CONECT   71   58   72  133                                                  
CONECT   72   71   55  134                                                  
CONECT   73    1                                                            
CONECT   74    1                                                            
CONECT   75    1                                                            
CONECT   76    2                                                            
CONECT   77    3                                                            
CONECT   78    3                                                            
CONECT   79    3                                                            
CONECT   80    4                                                            
CONECT   81    4                                                            
CONECT   82    6                                                            
CONECT   83    6                                                            
CONECT   84   10                                                            
CONECT   85   10                                                            
CONECT   86   12                                                            
CONECT   87   13                                                            
CONECT   88   16                                                            
CONECT   89   18                                                            
CONECT   90   19                                                            
CONECT   91   19                                                            
CONECT   92   20                                                            
CONECT   93   21                                                            
CONECT   94   22                                                            
CONECT   95   23                                                            
CONECT   96   24                                                            
CONECT   97   25                                                            
CONECT   98   26                                                            
CONECT   99   27                                                            
CONECT  100   28                                                            
CONECT  101   30                                                            
CONECT  102   32                                                            
CONECT  103   33                                                            
CONECT  104   33                                                            
CONECT  105   37                                                            
CONECT  106   38                                                            
CONECT  107   40                                                            
CONECT  108   41                                                            
CONECT  109   42                                                            
CONECT  110   43                                                            
CONECT  111   44                                                            
CONECT  112   45                                                            
CONECT  113   46                                                            
CONECT  114   47                                                            
CONECT  115   48                                                            
CONECT  116   49                                                            
CONECT  117   50                                                            
CONECT  118   54                                                            
CONECT  119   54                                                            
CONECT  120   56                                                            
CONECT  121   57                                                            
CONECT  122   60                                                            
CONECT  123   62                                                            
CONECT  124   63                                                            
CONECT  125   63                                                            
CONECT  126   64                                                            
CONECT  127   65                                                            
CONECT  128   66                                                            
CONECT  129   67                                                            
CONECT  130   68                                                            
CONECT  131   69                                                            
CONECT  132   70                                                            
CONECT  133   71                                                            
CONECT  134   72                                                            
MASTER        0    0    0    0    0    0    0    0  134    0  278    0
END
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3D PDB for NP0032248 (gymnoside VI)

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SMILES for NP0032248 (gymnoside VI)
[H]OC([H])([H])[C@]1([H])O[C@]([H])(OC2=C([H])C([H])=C(C([H])=C2[H])C([H])([H])OC(=O)C([H])([H])[C@@](O[C@]2([H])O[C@]([H])(C([H])([H])OC(=O)C(\[H])=C(/[H])C3=C([H])C([H])=C([H])C([H])=C3[H])[C@@]([H])(O[H])[C@]([H])(O[H])[C@@]2([H])O[H])(C(=O)OC([H])([H])C2=C([H])C([H])=C(O[C@]3([H])O[C@]([H])(C([H])([H])O[H])[C@@]([H])(O[H])[C@]([H])(O[H])[C@@]3([H])O[H])C([H])=C2[H])C([H])([H])C([H])(C([H])([H])[H])C([H])([H])[H])[C@@]([H])(O[H])[C@]([H])(O[H])[C@@]1([H])O[H]
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INCHI for NP0032248 (gymnoside VI)
InChI=1S/C49H62O23/c1-25(2)18-49(48(63)66-23-28-10-15-30(16-11-28)68-46-43(61)40(58)37(55)32(21-51)70-46,72-47-44(62)41(59)38(56)33(71-47)24-65-34(52)17-12-26-6-4-3-5-7-26)19-35(53)64-22-27-8-13-29(14-9-27)67-45-42(60)39(57)36(54)31(20-50)69-45/h3-17,25,31-33,36-47,50-51,54-62H,18-24H2,1-2H3/b17-12+/t31-,32+,33+,36-,37+,38+,39+,40-,41-,42-,43+,44+,45-,46+,47-,49+/m0/s1
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View in JSmol
SynonymsNot Available
Chemical FormulaC49H62O23
Average Mass1019.0120 Da
Monoisotopic Mass1018.36819 Da
IUPAC Name4-(4-{[(2R,3S,4R,5R,6S)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)methyl 1-(4-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)methyl (2R)-2-(2-methylpropyl)-2-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-({[(2E)-3-phenylprop-2-enoyl]oxy}methyl)oxan-2-yl]oxy}butanedioate
Traditional Name4-(4-{[(2R,3S,4R,5R,6S)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)methyl 1-(4-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)methyl (2R)-2-(2-methylpropyl)-2-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-({[(2E)-3-phenylprop-2-enoyl]oxy}methyl)oxan-2-yl]oxy}butanedioate
CAS Registry NumberNot Available
SMILES
[H]OC([H])([H])[C@]1([H])O[C@]([H])(OC2=C([H])C([H])=C(C([H])=C2[H])C([H])([H])OC(=O)C([H])([H])[C@@](O[C@]2([H])O[C@]([H])(C([H])([H])OC(=O)C(\[H])=C(/[H])C3=C([H])C([H])=C([H])C([H])=C3[H])[C@@]([H])(O[H])[C@]([H])(O[H])[C@@]2([H])O[H])(C(=O)OC([H])([H])C2=C([H])C([H])=C(O[C@]3([H])O[C@]([H])(C([H])([H])O[H])[C@@]([H])(O[H])[C@]([H])(O[H])[C@@]3([H])O[H])C([H])=C2[H])C([H])([H])C([H])(C([H])([H])[H])C([H])([H])[H])[C@@]([H])(O[H])[C@]([H])(O[H])[C@@]1([H])O[H]
InChI Identifier
InChI=1S/C49H62O23/c1-25(2)18-49(48(63)66-23-28-10-15-30(16-11-28)68-46-43(61)40(58)37(55)32(21-51)70-46,72-47-44(62)41(59)38(56)33(71-47)24-65-34(52)17-12-26-6-4-3-5-7-26)19-35(53)64-22-27-8-13-29(14-9-27)67-45-42(60)39(57)36(54)31(20-50)69-45/h3-17,25,31-33,36-47,50-51,54-62H,18-24H2,1-2H3/b17-12+/t31-,32+,33+,36-,37+,38+,39+,40-,41-,42-,43+,44+,45-,46+,47-,49+/m0/s1
InChI KeyVCCBFXCFLIEPOV-QPJLZBKDSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 500 MHz, C5D5N, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, C5D5N, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 100 MHz, C5D5N, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, C5D5N, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 200 MHz, C5D5N, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, C5D5N, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 300 MHz, C5D5N, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, C5D5N, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 400 MHz, C5D5N, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, C5D5N, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 600 MHz, C5D5N, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, C5D5N, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 700 MHz, C5D5N, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, C5D5N, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 800 MHz, C5D5N, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, C5D5N, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 900 MHz, C5D5N, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, C5D5N, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 1000 MHz, C5D5N, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, C5D5N, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Gymnadenia conopseaJEOL database
    • Morikawa, T., et al, J. Nat. Prod. 69, 881 (2006) 
Chemical Taxonomy
ClassificationNot classified
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP0.84ALOGPS
logP0.43ChemAxon
logS-3.7ALOGPS
pKa (Strongest Acidic)11.75ChemAxon
pKa (Strongest Basic)-3.6ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count20ChemAxon
Hydrogen Donor Count11ChemAxon
Polar Surface Area356.81 ŲChemAxon
Rotatable Bond Count24ChemAxon
Refractivity242.26 m³·mol⁻¹ChemAxon
Polarizability100.93 ųChemAxon
Number of Rings6ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
External LinksNot Available
References
General References
  1. Morikawa, T., et al. (2006). Morikawa, T., et al, J. Nat. Prod. 69, 881 (2006) . J. Nat. Prod..