NP-MRD: Showing NP-Card for 2-{[3-hydroxy-2-(hydroxymethyl)-6-{5,7',9',13'-tetramethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosan]-18'-eneoxy}-5-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]oxan-4-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol (NP0213685)

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Record Information

Version

2.0

Created at

2022-09-05 12:44:37 UTC

Updated at

2022-09-05 12:44:37 UTC

NP-MRD ID

NP0213685

Secondary Accession Numbers

None

Natural Product Identification

Common Name

2-{[3-hydroxy-2-(hydroxymethyl)-6-{5,7',9',13'-tetramethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosan]-18'-eneoxy}-5-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]oxan-4-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol

Description

Gracillin belongs to the class of organic compounds known as steroidal saponins. These are saponins in which the aglycone moiety is a steroid. The steroidal aglycone is usually a spirostane, furostane, spirosolane, solanidane, or curcubitacin derivative. 2-{[3-hydroxy-2-(hydroxymethyl)-6-{5,7',9',13'-tetramethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosan]-18'-eneoxy}-5-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]oxan-4-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol is found in Clintonia udensis, Dioscorea collettii, Dioscorea gracillima, Dioscorea panthaica, Dioscorea pseudojaponica, Dioscorea sinoparviflora, Dracaena cochinchinensis, Dracaena concinna, Dracaena draco, Lilium regale, Paris mairei, Paris polyphylla, Polygonatum kingianum and Triteleia hyacinthina. Gracillin is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1533004161505112D          

 62 70  0  0  0  0            999 V2000
    4.3030   -3.2858    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1170   -3.1521    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4082   -2.3802    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2223   -2.2464    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7452   -2.8845    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4540   -3.6564    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.6399   -3.7902    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1155   -2.1473    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.9311   -2.2716    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.6640   -1.8929    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.2507   -2.4728    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.0743   -2.4249    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.4446   -1.6877    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.2682   -1.6397    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.7215   -2.3290    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.5451   -2.2811    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.9984   -2.9704    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.6282   -3.7076    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.8046   -3.7555    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.3512   -3.0662    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.9810   -3.8035    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.5276   -3.1142    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.1573   -3.8514    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.3337   -3.8994    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.8804   -3.2101    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.4351   -3.9046    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.0648   -3.0857    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.3319   -3.4645    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2076   -4.2801    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.8221   -2.9224    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.1923   -2.1852    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.7390   -1.4959    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.1093   -0.7587    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.6560   -0.0694    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.0263    0.6679    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.9329   -0.7107    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.3032    0.0265    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.3862   -1.4000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.2098   -1.3521    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.5801   -0.6148    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.1268    0.0745    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.4971    0.8117    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.0438    1.5010    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.2202    1.4530    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.3207    0.8596    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.6910    1.5969    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.7740    0.1703    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.5976    0.2183    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.4037   -0.5669    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.8570   -1.2562    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.0159   -2.1372    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.4693   -2.8265    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.0990   -3.5638    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.2754   -3.6117    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.9051   -4.3489    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.0815   -4.3969    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.3584   -5.0382    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.9881   -5.7755    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.1820   -4.9903    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.6353   -5.6796    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.5523   -4.2531    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.3759   -4.2051    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  2  7  1  0  0  0  0
  5  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  2  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 15 20  1  0  0  0  0
 20 21  1  0  0  0  0
 20 22  1  0  0  0  0
 12 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  1  0  0  0  0
 24 25  1  0  0  0  0
 11 25  1  0  0  0  0
 25 26  1  0  0  0  0
 25 27  1  0  0  0  0
  9 27  1  0  0  0  0
 27 28  1  0  0  0  0
  5 28  1  0  0  0  0
 28 29  1  0  0  0  0
 17 30  1  0  0  0  0
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 31 32  1  0  0  0  0
 32 33  1  0  0  0  0
 33 34  1  0  0  0  0
 34 35  1  0  0  0  0
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 38 51  1  0  0  0  0
 31 51  1  0  0  0  0
 51 52  1  0  0  0  0
 52 53  1  0  0  0  0
 53 54  1  0  0  0  0
 54 55  1  0  0  0  0
 55 56  1  0  0  0  0
 55 57  1  0  0  0  0
 57 58  1  0  0  0  0
 57 59  1  0  0  0  0
 59 60  1  0  0  0  0
 59 61  1  0  0  0  0
 53 61  1  0  0  0  0
 61 62  1  0  0  0  0
M  END

     RDKit          3D

134142  0  0  0  0  0  0  0  0999 V2000
   -2.2826   -4.2607    0.0474 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7449   -3.0461   -0.7280 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.8613   -1.9753    0.1215 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9709   -1.1856   -0.0487 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.9821   -0.2541    0.9907 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9786    1.0688    0.4993 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.7707    1.7549    1.0415 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.1029    2.2780   -0.0904 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8208    1.8063   -0.1991 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.2226    2.8756   -0.2276 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5362    2.2850    0.1719 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9276    1.1382   -0.7382 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.4810    1.8295   -2.0043 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7798    0.3265   -1.1945 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9390   -0.9571   -1.4322 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1928   -1.7096   -1.2828 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3965   -0.8145   -1.0944 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.0456    0.3437   -0.1829 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.8446   -0.2497    1.1731 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2317   -0.6091    1.6695 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0202   -1.4791    0.7521 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.0602   -2.8656    1.4440 C   0  0  0  0  0  0  0  0  0  0  0  0
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    7.9037   -0.5377   -1.0729 O   0  0  0  0  0  0  0  0  0  0  0  0
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   10.6649   -1.1447   -1.2834 C   0  0  0  0  0  0  0  0  0  0  0  0
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   10.1557    1.3178   -1.4238 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.2968    0.1952    0.7403 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.9744   -0.1583    0.8425 O   0  0  0  0  0  0  0  0  0  0  0  0
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    7.9674   -2.3395    2.0785 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5762    0.9172   -1.4048 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0772    2.7599    1.9002 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8874    2.5174    2.9593 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.1677    1.8061    4.0571 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6499    0.5674    3.7213 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -5.2839   -1.9268   -0.0137 C   0  0  2  0  0  0  0  0  0  0  0  0
   -5.8068   -2.0121    1.2822 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2323   -3.2758   -0.6867 C   0  0  2  0  0  0  0  0  0  0  0  0
   -5.2962   -4.2983    0.2270 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -0.0481    3.6689    0.5061 H   0  0  0  0  0  0  0  0  0  0  0  0
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    2.2643   -1.2052    1.1517 H   0  0  0  0  0  0  0  0  0  0  0  0
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M  END


  Mrv1533004161505112D          

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M  END
> <DATABASE_ID>
NP0213685

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC1C2C(CC3C4CC=C5CC(CCC5(C)C4CCC23C)OC2OC(CO)C(O)C(OC3OC(CO)C(O)C(O)C3O)C2OC2OC(C)C(O)C(O)C2O)OC11CCC(C)CO1

> <INCHI_IDENTIFIER>
InChI=1S/C45H72O17/c1-19-8-13-45(55-18-19)20(2)30-27(62-45)15-26-24-7-6-22-14-23(9-11-43(22,4)25(24)10-12-44(26,30)5)57-42-39(61-40-36(53)34(51)31(48)21(3)56-40)38(33(50)29(17-47)59-42)60-41-37(54)35(52)32(49)28(16-46)58-41/h6,19-21,23-42,46-54H,7-18H2,1-5H3

> <INCHI_KEY>
YQEMAEKYNNOCBY-UHFFFAOYSA-N

> <FORMULA>
C45H72O17

> <MOLECULAR_WEIGHT>
885.054

> <EXACT_MASS>
884.476950858

> <JCHEM_ACCEPTOR_COUNT>
17

> <JCHEM_ATOM_COUNT>
134

> <JCHEM_AVERAGE_POLARIZABILITY>
96.3834221979387

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
9

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-{[3-hydroxy-2-(hydroxymethyl)-6-{5,7',9',13'-tetramethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosan]-18'-eneoxy}-5-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]oxan-4-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol

> <ALOGPS_LOGP>
0.82

> <JCHEM_LOGP>
0.661708483666668

> <ALOGPS_LOGS>
-3.36

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
9

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.375797226162028

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.8846738204158

> <JCHEM_PKA_STRONGEST_BASIC>
-2.98109099242616

> <JCHEM_POLAR_SURFACE_AREA>
255.90999999999994

> <JCHEM_REFRACTIVITY>
215.96210000000005

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
3.90e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-{[3-hydroxy-2-(hydroxymethyl)-6-{5,7',9',13'-tetramethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosan]-18'-eneoxy}-5-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]oxan-4-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 16-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   16-APR-15         0                                  
HETATM    1  C   UNK     0       8.032  -6.134   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       9.552  -5.884   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      10.095  -4.443   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      11.615  -4.193   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      12.591  -5.384   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      12.048  -6.825   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0      10.528  -7.075   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      13.282  -4.008   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      14.805  -4.240   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      16.173  -3.533   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      17.268  -4.616   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      18.805  -4.526   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      19.497  -3.150   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      21.034  -3.061   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      21.880  -4.347   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      23.418  -4.258   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      24.264  -5.545   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      23.573  -6.921   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      22.035  -7.010   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      21.189  -5.724   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      20.498  -7.100   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      19.652  -5.813   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      18.960  -7.189   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      17.423  -7.279   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      16.577  -5.992   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      15.746  -7.289   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      15.054  -5.760   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      13.686  -6.467   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      13.454  -7.989   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0      25.801  -5.455   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0      26.492  -4.079   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0      25.646  -2.792   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0      26.337  -1.416   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      25.491  -0.129   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0      26.182   1.247   0.000  0.00  0.00           O+0
HETATM   36  C   UNK     0      27.875  -1.327   0.000  0.00  0.00           C+0
HETATM   37  O   UNK     0      28.566   0.050   0.000  0.00  0.00           O+0
HETATM   38  C   UNK     0      28.721  -2.613   0.000  0.00  0.00           C+0
HETATM   39  O   UNK     0      30.258  -2.524   0.000  0.00  0.00           O+0
HETATM   40  C   UNK     0      30.950  -1.148   0.000  0.00  0.00           C+0
HETATM   41  O   UNK     0      30.103   0.139   0.000  0.00  0.00           O+0
HETATM   42  C   UNK     0      30.795   1.515   0.000  0.00  0.00           C+0
HETATM   43  C   UNK     0      29.948   2.802   0.000  0.00  0.00           C+0
HETATM   44  O   UNK     0      28.411   2.712   0.000  0.00  0.00           O+0
HETATM   45  C   UNK     0      32.332   1.605   0.000  0.00  0.00           C+0
HETATM   46  O   UNK     0      33.023   2.981   0.000  0.00  0.00           O+0
HETATM   47  C   UNK     0      33.178   0.318   0.000  0.00  0.00           C+0
HETATM   48  O   UNK     0      34.716   0.407   0.000  0.00  0.00           O+0
HETATM   49  C   UNK     0      32.487  -1.058   0.000  0.00  0.00           C+0
HETATM   50  O   UNK     0      33.333  -2.345   0.000  0.00  0.00           O+0
HETATM   51  C   UNK     0      28.030  -3.990   0.000  0.00  0.00           C+0
HETATM   52  O   UNK     0      28.876  -5.276   0.000  0.00  0.00           O+0
HETATM   53  C   UNK     0      28.185  -6.652   0.000  0.00  0.00           C+0
HETATM   54  O   UNK     0      26.647  -6.742   0.000  0.00  0.00           O+0
HETATM   55  C   UNK     0      25.956  -8.118   0.000  0.00  0.00           C+0
HETATM   56  C   UNK     0      24.419  -8.208   0.000  0.00  0.00           C+0
HETATM   57  C   UNK     0      26.802  -9.405   0.000  0.00  0.00           C+0
HETATM   58  O   UNK     0      26.111 -10.781   0.000  0.00  0.00           O+0
HETATM   59  C   UNK     0      28.340  -9.315   0.000  0.00  0.00           C+0
HETATM   60  O   UNK     0      29.186 -10.602   0.000  0.00  0.00           O+0
HETATM   61  C   UNK     0      29.031  -7.939   0.000  0.00  0.00           C+0
HETATM   62  O   UNK     0      30.568  -7.850   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    7                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6    8   28                                             
CONECT    6    5    7                                                       
CONECT    7    6    2                                                       
CONECT    8    5    9                                                       
CONECT    9    8   10   27                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12   25                                                  
CONECT   12   11   13   22                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16   20                                                  
CONECT   16   15   17                                                       
CONECT   17   16   18   30                                                  
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   15   21   22                                             
CONECT   21   20                                                            
CONECT   22   20   12   23                                                  
CONECT   23   22   24                                                       
CONECT   24   23   25                                                       
CONECT   25   24   11   26   27                                             
CONECT   26   25                                                            
CONECT   27   25    9   28                                                  
CONECT   28   27    5   29                                                  
CONECT   29   28                                                            
CONECT   30   17   31                                                       
CONECT   31   30   32   51                                                  
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   51                                                  
CONECT   39   38   40                                                       
CONECT   40   39   41   49                                                  
CONECT   41   40   42                                                       
CONECT   42   41   43   45                                                  
CONECT   43   42   44                                                       
CONECT   44   43                                                            
CONECT   45   42   46   47                                                  
CONECT   46   45                                                            
CONECT   47   45   48   49                                                  
CONECT   48   47                                                            
CONECT   49   47   40   50                                                  
CONECT   50   49                                                            
CONECT   51   38   31   52                                                  
CONECT   52   51   53                                                       
CONECT   53   52   54   61                                                  
CONECT   54   53   55                                                       
CONECT   55   54   56   57                                                  
CONECT   56   55                                                            
CONECT   57   55   58   59                                                  
CONECT   58   57                                                            
CONECT   59   57   60   61                                                  
CONECT   60   59                                                            
CONECT   61   59   53   62                                                  
CONECT   62   61                                                            
MASTER        0    0    0    0    0    0    0    0   62    0  140    0
END

View in JSmol

Synonyms

Value	Source
Diosgenyl rhamnopyranosyl-1-2-(glucopyranosyl-1-3)glucopyranoside	MeSH
Gracillin	MeSH

Chemical Formula

C₄₅H₇₂O₁₇

Average Mass

885.0540 Da

Monoisotopic Mass

884.47695 Da

IUPAC Name

Traditional Name

CAS Registry Number

Not Available

SMILES

CC1C2C(CC3C4CC=C5CC(CCC5(C)C4CCC23C)OC2OC(CO)C(O)C(OC3OC(CO)C(O)C(O)C3O)C2OC2OC(C)C(O)C(O)C2O)OC11CCC(C)CO1

InChI Identifier

InChI=1S/C45H72O17/c1-19-8-13-45(55-18-19)20(2)30-27(62-45)15-26-24-7-6-22-14-23(9-11-43(22,4)25(24)10-12-44(26,30)5)57-42-39(61-40-36(53)34(51)31(48)21(3)56-40)38(33(50)29(17-47)59-42)60-41-37(54)35(52)32(49)28(16-46)58-41/h6,19-21,23-42,46-54H,7-18H2,1-5H3

InChI Key

YQEMAEKYNNOCBY-UHFFFAOYSA-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
Clintonia udensis	LOTUS Database	35616633
Dioscorea collettii	LOTUS Database	35616633
Dioscorea gracillima	LOTUS Database	35616633
Dioscorea panthaica	LOTUS Database	35616633
Dioscorea pseudojaponica	LOTUS Database	35616633
Dioscorea sinoparviflora	LOTUS Database	35616633
Dracaena cochinchinensis	LOTUS Database	35616633
Dracaena concinna	LOTUS Database	35616633
Dracaena draco	LOTUS Database	35616633
Lilium regale	LOTUS Database	35616633
Paris mairei	LOTUS Database	35616633
Paris polyphylla	LOTUS Database	35616633
Polygonatum kingianum	LOTUS Database	35616633
Triteleia hyacinthina	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as steroidal saponins. These are saponins in which the aglycone moiety is a steroid. The steroidal aglycone is usually a spirostane, furostane, spirosolane, solanidane, or curcubitacin derivative.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Steroids and steroid derivatives

Sub Class

Steroidal glycosides

Direct Parent

Steroidal saponins

Alternative Parents

Substituents

Steroidal saponin
Triterpenoid
Spirostane skeleton
Oligosaccharide
Delta-5-steroid
Glycosyl compound
O-glycosyl compound
Ketal
Oxane
Tetrahydrofuran
Secondary alcohol
Oxacycle
Polyol
Acetal
Organoheterocyclic compound
Hydrocarbon derivative
Primary alcohol
Organooxygen compound
Alcohol
Organic oxygen compound
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic 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	0.82	ALOGPS
logP	0.66	ChemAxon
logS	-3.4	ALOGPS
pKa (Strongest Acidic)	11.88	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	17	ChemAxon
Hydrogen Donor Count	9	ChemAxon
Polar Surface Area	255.91 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	215.96 m³·mol⁻¹	ChemAxon
Polarizability	96.38 Å³	ChemAxon
Number of Rings	9	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

496769

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 2-{[3-hydroxy-2-(hydroxymethyl)-6-{5,7',9',13'-tetramethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosan]-18'-eneoxy}-5-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]oxan-4-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol (NP0213685)

MOL for NP0213685 (2-{[3-hydroxy-2-(hydroxymethyl)-6-{5,7',9',13'-tetramethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosan]-18'-eneoxy}-5-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]oxan-4-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol)

3D MOL for NP0213685 (2-{[3-hydroxy-2-(hydroxymethyl)-6-{5,7',9',13'-tetramethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosan]-18'-eneoxy}-5-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]oxan-4-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol)

3D SDF for NP0213685 (2-{[3-hydroxy-2-(hydroxymethyl)-6-{5,7',9',13'-tetramethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosan]-18'-eneoxy}-5-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]oxan-4-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol)

3D-SDF for NP0213685 (2-{[3-hydroxy-2-(hydroxymethyl)-6-{5,7',9',13'-tetramethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosan]-18'-eneoxy}-5-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]oxan-4-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol)

PDB for NP0213685 (2-{[3-hydroxy-2-(hydroxymethyl)-6-{5,7',9',13'-tetramethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosan]-18'-eneoxy}-5-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]oxan-4-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol)

3D PDB for NP0213685 (2-{[3-hydroxy-2-(hydroxymethyl)-6-{5,7',9',13'-tetramethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosan]-18'-eneoxy}-5-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]oxan-4-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol)

SMILES for NP0213685 (2-{[3-hydroxy-2-(hydroxymethyl)-6-{5,7',9',13'-tetramethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosan]-18'-eneoxy}-5-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]oxan-4-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol)

INCHI for NP0213685 (2-{[3-hydroxy-2-(hydroxymethyl)-6-{5,7',9',13'-tetramethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosan]-18'-eneoxy}-5-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]oxan-4-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol)

Structure for NP0213685 (2-{[3-hydroxy-2-(hydroxymethyl)-6-{5,7',9',13'-tetramethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosan]-18'-eneoxy}-5-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]oxan-4-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol)

3D Structure for NP0213685 (2-{[3-hydroxy-2-(hydroxymethyl)-6-{5,7',9',13'-tetramethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosan]-18'-eneoxy}-5-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]oxan-4-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol)