NP-MRD: Showing NP-Card for Gracillin (NP0052116)

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Record Information

Version

2.0

Created at

2022-04-27 23:17:13 UTC

Updated at

2022-04-27 23:17:14 UTC

NP-MRD ID

NP0052116

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Gracillin

Description

(2S,3R,4R,5R,6S)-2-{[(2S,3R,4S,5R,6S)-5-hydroxy-6-(hydroxymethyl)-2-[(1'S,2R,2'S,4'S,5R,7'S,8'R,9'S,12'S,13'R,16'S)-5,7',9',13'-tetramethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]Icosan]-18'-eneoxy]-4-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxan-3-yl]oxy}-6-methyloxane-3,4,5-triol 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. Gracillin is found in Costus speciosus , Dioscorea althaeoides, Dioscorea cayenensis , Dioscorea collettii var.hypoglauca, Dioscorea fustchauensis, Dioscorea futschauensis , Dioscorea gracillima, Dioscorea nipponica , Dioscorea panthaica , Dioscorea parviflora, Dioscorea pseudojaponica, Dioscorea spongiosa, Dioscorea spp., Dioscorea villosa , Dioscorea zingiberensis, Polygonatum zanlanscianense, Smilax china and Tribulus terrestris . Based on a literature review very few articles have been published on (2S,3R,4R,5R,6S)-2-{[(2S,3R,4S,5R,6S)-5-hydroxy-6-(hydroxymethyl)-2-[(1'S,2R,2'S,4'S,5R,7'S,8'R,9'S,12'S,13'R,16'S)-5,7',9',13'-tetramethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]Icosan]-18'-eneoxy]-4-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxan-3-yl]oxy}-6-methyloxane-3,4,5-triol.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282201172D          

 62 70  0  0  1  0            999 V2000
   10.8476    1.2881    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.2179    2.0253    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   10.7645    2.7146    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.9409    2.6667    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.4876    3.3559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.6640    3.3080    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.2937    2.5708    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    8.7470    1.8815    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    9.5707    1.9294    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   10.0240    1.2401    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.2004    1.1922    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.3768    1.1442    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.5532    1.0963    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0998    1.7856    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    7.4701    2.5228    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    6.8834    3.1028    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1505    2.7240    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    6.2843    1.9099    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.5514    1.5312    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.9646    2.1111    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.3349    2.8484    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6734    1.3392    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8594    1.2055    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3365    1.8436    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.6277    2.6155    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4417    2.7493    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5224    1.7098    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4270    0.7156    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.6545    1.0911    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.0415    2.0732    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.4948    1.3840    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   13.3184    1.4319    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   13.7717    0.7426    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   13.4014    0.0054    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   12.5778   -0.0426    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   12.1245    0.6467    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.2075   -0.7798    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.3839   -0.8278    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.8548   -0.6839    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.5953    0.7905    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.0486    0.1012    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   15.8723    0.1492    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   16.3256   -0.5401    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   15.9553   -1.2773    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   15.1317   -1.3253    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   14.6784   -0.6360    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.7614   -2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.2147   -2.7518    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.4086   -1.9666    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.1492   -0.4922    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.2425    0.8864    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.6887    2.1691    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.2354    2.8584    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   13.6056    3.5957    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   13.1523    4.2849    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   12.3287    4.2370    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   11.9584    3.4998    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   12.4118    2.8105    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.1348    3.4518    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.8754    4.9263    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.5226    5.0222    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.4293    3.6436    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  2  0  0  0  0
  5  6  1  0  0  0  0
  7  6  1  6  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  4  9  1  0  0  0  0
  9 10  1  0  0  0  0
  1 10  1  0  0  0  0
  9 11  1  1  0  0  0
  8 12  1  1  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
  7 15  1  0  0  0  0
 15 16  1  1  0  0  0
 16 17  1  0  0  0  0
 18 17  1  1  0  0  0
 14 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  6  0  0  0
 17 21  1  1  0  0  0
 20 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
 25 26  1  0  0  0  0
 20 26  1  0  0  0  0
 24 27  1  6  0  0  0
 19 28  1  6  0  0  0
 14 29  1  1  0  0  0
  2 30  1  1  0  0  0
 31 30  1  6  0  0  0
 31 32  1  0  0  0  0
 32 33  1  0  0  0  0
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 57 59  1  1  0  0  0
 56 60  1  6  0  0  0
 55 61  1  1  0  0  0
 54 62  1  1  0  0  0
M  END

     RDKit          3D

134142  0  0  0  0  0  0  0  0999 V2000
   -3.1580   -2.3901    3.1316 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2629   -1.6021    2.4518 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.2515   -0.2631    2.8243 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -4.2907    1.7893    0.3577 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.8674    2.1050    0.0229 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.2014    0.9565   -0.3895 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0259    0.7480    0.3590 C   0  0  1  0  0  0  0  0  0  0  0  0
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    0.3656   -1.3895    0.7531 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5004   -0.7166   -0.0022 C   0  0  1  0  0  0  0  0  0  0  0  0
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M  END


  Mrv1652304282201172D          

 62 70  0  0  1  0            999 V2000
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   10.0240    1.2401    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.2004    1.1922    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.3768    1.1442    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   16.3256   -0.5401    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
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  1  2  1  0  0  0  0
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 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
  7 15  1  0  0  0  0
 15 16  1  1  0  0  0
 16 17  1  0  0  0  0
 18 17  1  1  0  0  0
 14 18  1  0  0  0  0
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 20 26  1  0  0  0  0
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 19 28  1  6  0  0  0
 14 29  1  1  0  0  0
  2 30  1  1  0  0  0
 31 30  1  6  0  0  0
 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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 31 36  1  0  0  0  0
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 47 48  1  0  0  0  0
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 43 50  1  1  0  0  0
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 53 54  1  0  0  0  0
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 55 56  1  0  0  0  0
 56 57  1  0  0  0  0
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 53 58  1  0  0  0  0
 57 59  1  1  0  0  0
 56 60  1  6  0  0  0
 55 61  1  1  0  0  0
 54 62  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0052116

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@H]1[C@H]2[C@H](C[C@H]3[C@@H]4CC=C5C[C@H](CC[C@]5(C)[C@H]4CC[C@]23C)O[C@H]2O[C@@H](CO)[C@@H](O)[C@H](O[C@@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@H]3O)[C@H]2O[C@@H]2O[C@@H](C)[C@H](O)[C@@H](O)[C@H]2O)O[C@]11CC[C@@H](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/t19-,20+,21+,23+,24-,25+,26+,27+,28-,29+,30+,31+,32-,33-,34-,35+,36-,37-,38+,39-,40+,41+,42+,43+,44+,45-/m1/s1

> <INCHI_KEY>
YQEMAEKYNNOCBY-RTDDWJOOSA-N

> <FORMULA>
C45H72O17

> <MOLECULAR_WEIGHT>
885.054

> <EXACT_MASS>
884.476950858

> <JCHEM_ACCEPTOR_COUNT>
17

> <JCHEM_ATOM_COUNT>
134

> <JCHEM_AVERAGE_POLARIZABILITY>
96.54962804956025

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
9

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,3R,4S,5S,6R)-2-{[(2S,3R,4S,5R,6S)-3-hydroxy-2-(hydroxymethyl)-6-[(1'S,2R,2'S,4'S,5R,7'S,8'R,9'S,12'S,13'R,16'S)-5,7',9',13'-tetramethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icosan]-18'-eneoxy]-5-{[(2S,3R,4R,5R,6S)-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>
215.96210000000008

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
3.90e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S,3R,4S,5S,6R)-2-{[(2S,3R,4S,5R,6S)-3-hydroxy-2-(hydroxymethyl)-6-[(1'S,2R,2'S,4'S,5R,7'S,8'R,9'S,12'S,13'R,16'S)-5,7',9',13'-tetramethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icosan]-18'-eneoxy]-5-{[(2S,3R,4R,5R,6S)-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                                 28-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   28-APR-22         0                                  
HETATM    1  C   UNK     0      20.249   2.404   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      20.940   3.781   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      20.094   5.067   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      18.556   4.978   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      17.710   6.264   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      16.173   6.175   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      15.482   4.799   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      16.328   3.512   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      17.865   3.602   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      18.711   2.315   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      17.174   2.225   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      15.637   2.136   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      14.099   2.046   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      13.253   3.333   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      13.944   4.709   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      12.849   5.792   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      11.481   5.085   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      11.731   3.565   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      10.363   2.858   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       9.267   3.941   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       9.959   5.317   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0       8.724   2.500   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0       7.204   2.250   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       6.228   3.441   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       6.772   4.882   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       8.291   5.132   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       4.708   3.192   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      10.130   1.336   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      12.422   2.037   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0      22.477   3.870   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0      23.324   2.583   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      24.861   2.673   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      25.707   1.386   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      25.016   0.010   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      23.479  -0.079   0.000  0.00  0.00           C+0
HETATM   36  O   UNK     0      22.632   1.207   0.000  0.00  0.00           O+0
HETATM   37  C   UNK     0      22.787  -1.456   0.000  0.00  0.00           C+0
HETATM   38  O   UNK     0      21.250  -1.545   0.000  0.00  0.00           O+0
HETATM   39  O   UNK     0      25.862  -1.277   0.000  0.00  0.00           O+0
HETATM   40  O   UNK     0      27.245   1.476   0.000  0.00  0.00           O+0
HETATM   41  C   UNK     0      28.091   0.189   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0      29.628   0.278   0.000  0.00  0.00           C+0
HETATM   43  C   UNK     0      30.474  -1.008   0.000  0.00  0.00           C+0
HETATM   44  C   UNK     0      29.783  -2.384   0.000  0.00  0.00           C+0
HETATM   45  C   UNK     0      28.246  -2.474   0.000  0.00  0.00           C+0
HETATM   46  O   UNK     0      27.400  -1.187   0.000  0.00  0.00           O+0
HETATM   47  C   UNK     0      27.555  -3.850   0.000  0.00  0.00           C+0
HETATM   48  O   UNK     0      28.401  -5.137   0.000  0.00  0.00           O+0
HETATM   49  O   UNK     0      30.629  -3.671   0.000  0.00  0.00           O+0
HETATM   50  O   UNK     0      32.012  -0.919   0.000  0.00  0.00           O+0
HETATM   51  O   UNK     0      30.319   1.655   0.000  0.00  0.00           O+0
HETATM   52  O   UNK     0      25.552   4.049   0.000  0.00  0.00           O+0
HETATM   53  C   UNK     0      24.706   5.336   0.000  0.00  0.00           C+0
HETATM   54  C   UNK     0      25.397   6.712   0.000  0.00  0.00           C+0
HETATM   55  C   UNK     0      24.551   7.999   0.000  0.00  0.00           C+0
HETATM   56  C   UNK     0      23.014   7.909   0.000  0.00  0.00           C+0
HETATM   57  C   UNK     0      22.322   6.533   0.000  0.00  0.00           C+0
HETATM   58  O   UNK     0      23.169   5.246   0.000  0.00  0.00           O+0
HETATM   59  C   UNK     0      20.785   6.443   0.000  0.00  0.00           C+0
HETATM   60  O   UNK     0      22.167   9.196   0.000  0.00  0.00           O+0
HETATM   61  O   UNK     0      25.242   9.375   0.000  0.00  0.00           O+0
HETATM   62  O   UNK     0      26.935   6.801   0.000  0.00  0.00           O+0
CONECT    1    2   10                                                       
CONECT    2    1    3   30                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    9                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8   15                                                  
CONECT    8    7    9   12                                                  
CONECT    9    8    4   10   11                                             
CONECT   10    9    1                                                       
CONECT   11    9                                                            
CONECT   12    8   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15   18   29                                             
CONECT   15   14    7   16                                                  
CONECT   16   15   17                                                       
CONECT   17   16   18   21                                                  
CONECT   18   17   14   19                                                  
CONECT   19   18   20   28                                                  
CONECT   20   19   21   22   26                                             
CONECT   21   20   17                                                       
CONECT   22   20   23                                                       
CONECT   23   22   24                                                       
CONECT   24   23   25   27                                                  
CONECT   25   24   26                                                       
CONECT   26   25   20                                                       
CONECT   27   24                                                            
CONECT   28   19                                                            
CONECT   29   14                                                            
CONECT   30    2   31                                                       
CONECT   31   30   32   36                                                  
CONECT   32   31   33   52                                                  
CONECT   33   32   34   40                                                  
CONECT   34   33   35   39                                                  
CONECT   35   34   36   37                                                  
CONECT   36   35   31                                                       
CONECT   37   35   38                                                       
CONECT   38   37                                                            
CONECT   39   34                                                            
CONECT   40   33   41                                                       
CONECT   41   40   42   46                                                  
CONECT   42   41   43   51                                                  
CONECT   43   42   44   50                                                  
CONECT   44   43   45   49                                                  
CONECT   45   44   46   47                                                  
CONECT   46   45   41                                                       
CONECT   47   45   48                                                       
CONECT   48   47                                                            
CONECT   49   44                                                            
CONECT   50   43                                                            
CONECT   51   42                                                            
CONECT   52   32   53                                                       
CONECT   53   52   54   58                                                  
CONECT   54   53   55   62                                                  
CONECT   55   54   56   61                                                  
CONECT   56   55   57   60                                                  
CONECT   57   56   58   59                                                  
CONECT   58   57   53                                                       
CONECT   59   57                                                            
CONECT   60   56                                                            
CONECT   61   55                                                            
CONECT   62   54                                                            
MASTER        0    0    0    0    0    0    0    0   62    0  140    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₄₅H₇₂O₁₇

Average Mass

885.0540 Da

Monoisotopic Mass

884.47695 Da

IUPAC Name

(2S,3R,4S,5S,6R)-2-{[(2S,3R,4S,5R,6S)-3-hydroxy-2-(hydroxymethyl)-6-[(1'S,2R,2'S,4'S,5R,7'S,8'R,9'S,12'S,13'R,16'S)-5,7',9',13'-tetramethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icosan]-18'-eneoxy]-5-{[(2S,3R,4R,5R,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}oxan-4-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol

Traditional Name

CAS Registry Number

Not Available

SMILES

C[C@H]1[C@H]2[C@H](C[C@H]3[C@@H]4CC=C5C[C@H](CC[C@]5(C)[C@H]4CC[C@]23C)O[C@H]2O[C@@H](CO)[C@@H](O)[C@H](O[C@@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@H]3O)[C@H]2O[C@@H]2O[C@@H](C)[C@H](O)[C@@H](O)[C@H]2O)O[C@]11CC[C@@H](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/t19-,20+,21+,23+,24-,25+,26+,27+,28-,29+,30+,31+,32-,33-,34-,35+,36-,37-,38+,39-,40+,41+,42+,43+,44+,45-/m1/s1

InChI Key

YQEMAEKYNNOCBY-RTDDWJOOSA-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
Costus speciosus	Plant	KNApSAcK
Dioscorea althaeoides	Plant	KNApSAcK
Dioscorea cayenensis	Plant	KNApSAcK
Dioscorea collettii var.hypoglauca	Plant	KNApSAcK
Dioscorea fustchauensis	Plant	KNApSAcK
Dioscorea futschauensis	Plant	KNApSAcK
Dioscorea gracillima	Plant	KNApSAcK
Dioscorea nipponica	Plant	KNApSAcK
Dioscorea panthaica	Plant	KNApSAcK
Dioscorea parviflora	Plant	KNApSAcK
Dioscorea pseudojaponica	Plant	KNApSAcK
Dioscorea spongiosa	Plant	KNApSAcK
Dioscorea spp.	Plant	KNApSAcK
Dioscorea villosa	Plant	KNApSAcK
Dioscorea zingiberensis	Plant	KNApSAcK
Polygonatum zanlanscianense	Plant	KNApSAcK
Smilax china	Plant	KNApSAcK
Tribulus terrestris	Plant	KNApSAcK

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
O-glycosyl compound
Glycosyl compound
Ketal
Oxane
Tetrahydrofuran
Secondary alcohol
Oxacycle
Organoheterocyclic compound
Polyol
Acetal
Organic oxygen compound
Hydrocarbon derivative
Primary alcohol
Organooxygen compound
Alcohol
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	96.55 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

154496695

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Gracillin (NP0052116)

MOL for NP0052116 (Gracillin)

3D MOL for NP0052116 (Gracillin)

3D SDF for NP0052116 (Gracillin)

3D-SDF for NP0052116 (Gracillin)

PDB for NP0052116 (Gracillin)

3D PDB for NP0052116 (Gracillin)

SMILES for NP0052116 (Gracillin)

INCHI for NP0052116 (Gracillin)

Structure for NP0052116 (Gracillin)

3D Structure for NP0052116 (Gracillin)