NP-MRD: Showing NP-Card for (-)-Holothurin B (NP0078498)

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Record Information

Version

2.0

Created at

2022-04-28 23:34:18 UTC

Updated at

2022-04-28 23:34:19 UTC

NP-MRD ID

NP0078498

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(-)-Holothurin B

Description

[(3R,4S,5R,6S)-6-{[(1S,2R,5R,6R,9S,10R,13S,16S,18R)-6-[(2R)-5,5-dimethyloxolan-2-yl]-5,10-dihydroxy-2,6,13,17,17-pentamethyl-8-oxo-7-oxapentacyclo[10.8.0.0²,⁹.0⁵,⁹.0¹³,¹⁸]Icos-11-en-16-yl]oxy}-4-hydroxy-5-{[(2S,3S,4S,5S,6R)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}oxan-3-yl]oxidanesulfonic acid belongs to the class of organic compounds known as triterpene saponins. These are glycosylated derivatives of triterpene sapogenins. The sapogenin moiety backbone is usually based on the oleanane, ursane, taraxastane, bauerane, lanostane, lupeol, lupane, dammarane, cycloartane, friedelane, hopane, 9b,19-cyclo-lanostane, cycloartane, or cycloartanol skeleton. (-)-Holothurin B is found in Holothuria leucospilota, Holothuria lubrica, Holothuria polii and Holothuria tubulosa. Based on a literature review very few articles have been published on [(3R,4S,5R,6S)-6-{[(1S,2R,5R,6R,9S,10R,13S,16S,18R)-6-[(2R)-5,5-dimethyloxolan-2-yl]-5,10-dihydroxy-2,6,13,17,17-pentamethyl-8-oxo-7-oxapentacyclo[10.8.0.0²,⁹.0⁵,⁹.0¹³,¹⁸]Icos-11-en-16-yl]oxy}-4-hydroxy-5-{[(2S,3S,4S,5S,6R)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}oxan-3-yl]oxidanesulfonic acid.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304292201342D          

 59 66  0  0  1  0            999 V2000
    1.1483   -0.0451    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6448    0.6137    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3226    1.3732    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.5037    1.4738    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.0072    0.8150    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.3294    0.0555    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.1671   -0.6033    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7729    1.0836    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7584    1.9085    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0306    2.1496    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2694    0.4248    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7963   -0.2510    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0073   -0.0099    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6515   -0.5065    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9952    0.0325    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.1044   -0.7853    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9158   -0.9341    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3082   -0.2084    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7392    0.3890    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8612   -1.7573    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5917   -1.4072    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9810    0.8424    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5529    1.3523    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9287    2.1809    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8191    2.0320    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6380    1.9314    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9602    1.1719    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.4637    0.5131    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.7860   -0.2463    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6048   -0.3469    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1014    0.3119    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.7791    1.0713    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5268    1.4199    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9082    1.8862    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9202    0.2113    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.2425   -0.5482    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    6.0613   -0.6488    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.3836   -1.4082    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8870   -2.0671    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.0682   -1.9665    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.7459   -1.2070    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.9271   -1.1064    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4305   -1.7652    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.6117   -1.6646    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.1151   -2.3234    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.4374   -3.0829    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.2562   -3.1835    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.7528   -2.5247    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5785   -3.9429    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9408   -3.7417    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2963   -2.2228    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2894   -0.9052    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5716   -2.6253    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.2093   -2.8265    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.0282   -2.9271    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    7.8470   -3.0278    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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    7.1288   -2.1083    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9671   -0.1457    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  3  2  1  6  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  1  6  1  0  0  0  0
  6  7  1  1  0  0  0
  5  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  4 10  1  0  0  0  0
  8 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
  5 13  1  1  0  0  0
 13 14  2  0  0  0  0
 11 15  1  6  0  0  0
 15 16  1  6  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 15 19  1  0  0  0  0
 17 20  1  0  0  0  0
 17 21  1  0  0  0  0
 11 22  1  1  0  0  0
  8 23  1  6  0  0  0
  4 24  1  1  0  0  0
  3 25  1  0  0  0  0
 25 26  1  0  0  0  0
 27 26  1  1  0  0  0
 27 28  1  0  0  0  0
  2 28  1  0  0  0  0
 28 29  1  0  0  0  0
 29 30  1  0  0  0  0
 30 31  1  0  0  0  0
 31 32  1  0  0  0  0
 27 32  1  0  0  0  0
 32 33  1  0  0  0  0
 32 34  1  0  0  0  0
 31 35  1  1  0  0  0
 36 35  1  6  0  0  0
 36 37  1  0  0  0  0
 37 38  1  0  0  0  0
 38 39  1  0  0  0  0
 39 40  1  0  0  0  0
 40 41  1  0  0  0  0
 36 41  1  0  0  0  0
 41 42  1  1  0  0  0
 43 42  1  6  0  0  0
 43 44  1  0  0  0  0
 44 45  1  0  0  0  0
 45 46  1  0  0  0  0
 46 47  1  0  0  0  0
 47 48  1  0  0  0  0
 43 48  1  0  0  0  0
 47 49  1  6  0  0  0
 46 50  1  1  0  0  0
 45 51  1  6  0  0  0
 44 52  1  6  0  0  0
 40 53  1  1  0  0  0
 39 54  1  1  0  0  0
 54 55  1  0  0  0  0
 55 56  2  0  0  0  0
 55 57  2  0  0  0  0
 55 58  1  0  0  0  0
 28 59  1  1  0  0  0
M  END

     RDKit          3D

123130  0  0  0  0  0  0  0  0999 V2000
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    4.4098   -0.4948   -0.8176 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.3998   -1.0316   -0.0368 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1396   -0.4402   -0.2944 C   0  0  1  0  0  0  0  0  0  0  0  0
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   -1.8885   -1.1526    1.1369 C   0  0  0  0  0  0  0  0  0  0  0  0
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    1.8094   -0.6163    3.0117 H   0  0  0  0  0  0  0  0  0  0  0  0
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 58122  1  6
 59123  1  0
M  END


  Mrv1652304292201342D          

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  1  2  2  0  0  0  0
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  1  6  1  0  0  0  0
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  9 10  1  0  0  0  0
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 11 12  1  0  0  0  0
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  5 13  1  1  0  0  0
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  8 23  1  6  0  0  0
  4 24  1  1  0  0  0
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 25 26  1  0  0  0  0
 27 26  1  1  0  0  0
 27 28  1  0  0  0  0
  2 28  1  0  0  0  0
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 29 30  1  0  0  0  0
 30 31  1  0  0  0  0
 31 32  1  0  0  0  0
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 32 33  1  0  0  0  0
 32 34  1  0  0  0  0
 31 35  1  1  0  0  0
 36 35  1  6  0  0  0
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 37 38  1  0  0  0  0
 38 39  1  0  0  0  0
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 45 46  1  0  0  0  0
 46 47  1  0  0  0  0
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 43 48  1  0  0  0  0
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 44 52  1  6  0  0  0
 40 53  1  1  0  0  0
 39 54  1  1  0  0  0
 54 55  1  0  0  0  0
 55 56  2  0  0  0  0
 55 57  2  0  0  0  0
 55 58  1  0  0  0  0
 28 59  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0078498

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@H]1O[C@@H](O[C@@H]2[C@H](O)[C@@H](CO[C@H]2O[C@H]2CC[C@@]3(C)[C@@H](CC[C@@H]4C3=C[C@@H](O)[C@]35C(=O)O[C@](C)([C@H]6CCC(C)(C)O6)[C@@]3(O)CC[C@]45C)C2(C)C)OS(O)(=O)=O)[C@@H](O)[C@@H](O)[C@@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C41H64O17S/c1-19-27(43)29(45)30(46)32(53-19)55-31-28(44)22(58-59(49,50)51)18-52-33(31)54-25-12-14-37(6)21-17-24(42)41-34(47)57-39(8,26-11-13-35(2,3)56-26)40(41,48)16-15-38(41,7)20(21)9-10-23(37)36(25,4)5/h17,19-20,22-33,42-46,48H,9-16,18H2,1-8H3,(H,49,50,51)/t19-,20-,22-,23+,24-,25+,26-,27-,28-,29+,30+,31-,32+,33+,37-,38-,39-,40+,41-/m1/s1

> <INCHI_KEY>
HZPAESJKKJRHHK-RYCIJELPSA-N

> <FORMULA>
C41H64O17S

> <MOLECULAR_WEIGHT>
861.01

> <EXACT_MASS>
860.386421775

> <JCHEM_ACCEPTOR_COUNT>
15

> <JCHEM_ATOM_COUNT>
123

> <JCHEM_AVERAGE_POLARIZABILITY>
89.89340462355467

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
7

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[(3R,4S,5R,6S)-6-{[(1S,2R,5R,6R,9S,10R,13S,16S,18R)-6-[(2R)-5,5-dimethyloxolan-2-yl]-5,10-dihydroxy-2,6,13,17,17-pentamethyl-8-oxo-7-oxapentacyclo[10.8.0.0^{2,9}.0^{5,9}.0^{13,18}]icos-11-en-16-yl]oxy}-4-hydroxy-5-{[(2S,3S,4S,5S,6R)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}oxan-3-yl]oxidanesulfonic acid

> <ALOGPS_LOGP>
1.16

> <JCHEM_LOGP>
-0.3270465532451261

> <ALOGPS_LOGS>
-3.10

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
8

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
12.07036267473481

> <JCHEM_PKA_STRONGEST_ACIDIC>
-1.965918678351012

> <JCHEM_PKA_STRONGEST_BASIC>
-3.2550538968067153

> <JCHEM_POLAR_SURFACE_AREA>
257.42999999999995

> <JCHEM_REFRACTIVITY>
203.52670000000006

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
6.80e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[(3R,4S,5R,6S)-6-{[(1S,2R,5R,6R,9S,10R,13S,16S,18R)-6-[(2R)-5,5-dimethyloxolan-2-yl]-5,10-dihydroxy-2,6,13,17,17-pentamethyl-8-oxo-7-oxapentacyclo[10.8.0.0^{2,9}.0^{5,9}.0^{13,18}]icos-11-en-16-yl]oxy}-4-hydroxy-5-{[(2S,3S,4S,5S,6R)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}oxan-3-yl]oxidanesulfonic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 29-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   29-APR-22         0                                  
HETATM    1  C   UNK     0       2.143  -0.084   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       3.070   1.146   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.469   2.563   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.940   2.751   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.013   1.521   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.615   0.104   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      -0.312  -1.126   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      -1.443   2.023   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -1.416   3.563   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.057   4.013   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -2.370   0.793   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      -1.486  -0.469   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0      -0.014  -0.018   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       1.216  -0.945   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0      -3.724   0.061   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0      -3.928  -1.466   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0      -5.443  -1.744   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -6.175  -0.389   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -5.113   0.726   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -5.341  -3.280   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      -6.704  -2.627   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      -3.698   1.572   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0      -2.899   2.524   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0       1.734   4.071   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       3.396   3.793   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       4.924   3.605   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       5.526   2.188   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       4.599   0.958   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       5.200  -0.460   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       6.729  -0.648   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       7.656   0.582   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       7.054   2.000   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       8.450   2.651   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       7.295   3.521   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0       9.184   0.394   0.000  0.00  0.00           O+0
HETATM   36  C   UNK     0       9.786  -1.023   0.000  0.00  0.00           C+0
HETATM   37  O   UNK     0      11.314  -1.211   0.000  0.00  0.00           O+0
HETATM   38  C   UNK     0      11.916  -2.629   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0      10.989  -3.859   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0       9.461  -3.671   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0       8.859  -2.253   0.000  0.00  0.00           C+0
HETATM   42  O   UNK     0       7.331  -2.065   0.000  0.00  0.00           O+0
HETATM   43  C   UNK     0       6.404  -3.295   0.000  0.00  0.00           C+0
HETATM   44  C   UNK     0       4.875  -3.107   0.000  0.00  0.00           C+0
HETATM   45  C   UNK     0       3.948  -4.337   0.000  0.00  0.00           C+0
HETATM   46  C   UNK     0       4.550  -5.755   0.000  0.00  0.00           C+0
HETATM   47  C   UNK     0       6.078  -5.943   0.000  0.00  0.00           C+0
HETATM   48  O   UNK     0       7.005  -4.713   0.000  0.00  0.00           O+0
HETATM   49  C   UNK     0       6.680  -7.360   0.000  0.00  0.00           C+0
HETATM   50  O   UNK     0       3.623  -6.985   0.000  0.00  0.00           O+0
HETATM   51  O   UNK     0       2.420  -4.149   0.000  0.00  0.00           O+0
HETATM   52  O   UNK     0       4.274  -1.690   0.000  0.00  0.00           O+0
HETATM   53  O   UNK     0       8.534  -4.901   0.000  0.00  0.00           O+0
HETATM   54  O   UNK     0      11.591  -5.276   0.000  0.00  0.00           O+0
HETATM   55  S   UNK     0      13.119  -5.464   0.000  0.00  0.00           S+0
HETATM   56  O   UNK     0      14.648  -5.652   0.000  0.00  0.00           O+0
HETATM   57  O   UNK     0      12.931  -6.993   0.000  0.00  0.00           O+0
HETATM   58  O   UNK     0      13.307  -3.935   0.000  0.00  0.00           O+0
HETATM   59  C   UNK     0       3.672  -0.272   0.000  0.00  0.00           C+0
CONECT    1    2    6                                                       
CONECT    2    1    3   28                                                  
CONECT    3    2    4   25                                                  
CONECT    4    3    5   10   24                                             
CONECT    5    4    6    8   13                                             
CONECT    6    5    1    7                                                  
CONECT    7    6                                                            
CONECT    8    5    9   11   23                                             
CONECT    9    8   10                                                       
CONECT   10    9    4                                                       
CONECT   11    8   12   15   22                                             
CONECT   12   11   13                                                       
CONECT   13   12    5   14                                                  
CONECT   14   13                                                            
CONECT   15   11   16   19                                                  
CONECT   16   15   17                                                       
CONECT   17   16   18   20   21                                             
CONECT   18   17   19                                                       
CONECT   19   18   15                                                       
CONECT   20   17                                                            
CONECT   21   17                                                            
CONECT   22   11                                                            
CONECT   23    8                                                            
CONECT   24    4                                                            
CONECT   25    3   26                                                       
CONECT   26   25   27                                                       
CONECT   27   26   28   32                                                  
CONECT   28   27    2   29   59                                             
CONECT   29   28   30                                                       
CONECT   30   29   31                                                       
CONECT   31   30   32   35                                                  
CONECT   32   31   27   33   34                                             
CONECT   33   32                                                            
CONECT   34   32                                                            
CONECT   35   31   36                                                       
CONECT   36   35   37   41                                                  
CONECT   37   36   38                                                       
CONECT   38   37   39                                                       
CONECT   39   38   40   54                                                  
CONECT   40   39   41   53                                                  
CONECT   41   40   36   42                                                  
CONECT   42   41   43                                                       
CONECT   43   42   44   48                                                  
CONECT   44   43   45   52                                                  
CONECT   45   44   46   51                                                  
CONECT   46   45   47   50                                                  
CONECT   47   46   48   49                                                  
CONECT   48   47   43                                                       
CONECT   49   47                                                            
CONECT   50   46                                                            
CONECT   51   45                                                            
CONECT   52   44                                                            
CONECT   53   40                                                            
CONECT   54   39   55                                                       
CONECT   55   54   56   57   58                                             
CONECT   56   55                                                            
CONECT   57   55                                                            
CONECT   58   55                                                            
CONECT   59   28                                                            
MASTER        0    0    0    0    0    0    0    0   59    0  132    0
END

View in JSmol

Synonyms

Value	Source
[(3R,4S,5R,6S)-6-{[(1S,2R,5R,6R,9S,10R,13S,16S,18R)-6-[(2R)-5,5-dimethyloxolan-2-yl]-5,10-dihydroxy-2,6,13,17,17-pentamethyl-8-oxo-7-oxapentacyclo[10.8.0.0,.0,.0,]icos-11-en-16-yl]oxy}-4-hydroxy-5-{[(2S,3S,4S,5S,6R)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}oxan-3-yl]oxidanesulfonate	Generator
[(3R,4S,5R,6S)-6-{[(1S,2R,5R,6R,9S,10R,13S,16S,18R)-6-[(2R)-5,5-dimethyloxolan-2-yl]-5,10-dihydroxy-2,6,13,17,17-pentamethyl-8-oxo-7-oxapentacyclo[10.8.0.0,.0,.0,]icos-11-en-16-yl]oxy}-4-hydroxy-5-{[(2S,3S,4S,5S,6R)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}oxan-3-yl]oxidanesulphonate	Generator
[(3R,4S,5R,6S)-6-{[(1S,2R,5R,6R,9S,10R,13S,16S,18R)-6-[(2R)-5,5-dimethyloxolan-2-yl]-5,10-dihydroxy-2,6,13,17,17-pentamethyl-8-oxo-7-oxapentacyclo[10.8.0.0,.0,.0,]icos-11-en-16-yl]oxy}-4-hydroxy-5-{[(2S,3S,4S,5S,6R)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}oxan-3-yl]oxidanesulphonic acid	Generator

Chemical Formula

C₄₁H₆₄O₁₇S

Average Mass

861.0100 Da

Monoisotopic Mass

860.38642 Da

IUPAC Name

Traditional Name

CAS Registry Number

Not Available

SMILES

C[C@H]1O[C@@H](O[C@@H]2[C@H](O)[C@@H](CO[C@H]2O[C@H]2CC[C@@]3(C)[C@@H](CC[C@@H]4C3=C[C@@H](O)[C@]35C(=O)O[C@](C)([C@H]6CCC(C)(C)O6)[C@@]3(O)CC[C@]45C)C2(C)C)OS(O)(=O)=O)[C@@H](O)[C@@H](O)[C@@H]1O

InChI Identifier

InChI=1S/C41H64O17S/c1-19-27(43)29(45)30(46)32(53-19)55-31-28(44)22(58-59(49,50)51)18-52-33(31)54-25-12-14-37(6)21-17-24(42)41-34(47)57-39(8,26-11-13-35(2,3)56-26)40(41,48)16-15-38(41,7)20(21)9-10-23(37)36(25,4)5/h17,19-20,22-33,42-46,48H,9-16,18H2,1-8H3,(H,49,50,51)/t19-,20-,22-,23+,24-,25+,26-,27-,28-,29+,30+,31-,32+,33+,37-,38-,39-,40+,41-/m1/s1

InChI Key

HZPAESJKKJRHHK-RYCIJELPSA-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
Holothuria leucospilota	Animalia	KNApSAcK
Holothuria lubrica	Animalia	KNApSAcK
Holothuria polii	Animalia	KNApSAcK
Holothuria tubulosa	Animalia	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as triterpene saponins. These are glycosylated derivatives of triterpene sapogenins. The sapogenin moiety backbone is usually based on the oleanane, ursane, taraxastane, bauerane, lanostane, lupeol, lupane, dammarane, cycloartane, friedelane, hopane, 9b,19-cyclo-lanostane, cycloartane, or cycloartanol skeleton.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Terpene glycosides

Direct Parent

Triterpene saponins

Alternative Parents

Substituents

Triterpene saponin
Triterpenoid
Steroidal glycoside
Steroid lactone
17-hydroxysteroid
Hydroxysteroid
12-hydroxysteroid
Steroid
O-glycosyl compound
Glycosyl compound
Disaccharide
Sulfuric acid ester
Alkyl sulfate
Sulfate-ester
Sulfuric acid monoester
Oxane
Gamma butyrolactone
Tetrahydrofuran
Tertiary alcohol
Organic sulfuric acid or derivatives
Cyclic alcohol
Secondary alcohol
Lactone
Carboxylic acid ester
Oxacycle
Organoheterocyclic compound
Polyol
Monocarboxylic acid or derivatives
Ether
Dialkyl ether
Carboxylic acid derivative
Acetal
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Carbonyl group
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	1.16	ALOGPS
logP	-0.33	ChemAxon
logS	-3.1	ALOGPS
pKa (Strongest Acidic)	-2	ChemAxon
pKa (Strongest Basic)	-3.3	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	15	ChemAxon
Hydrogen Donor Count	7	ChemAxon
Polar Surface Area	257.43 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	203.53 m³·mol⁻¹	ChemAxon
Polarizability	89.89 Å³	ChemAxon
Number of Rings	8	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

162813306

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for (-)-Holothurin B (NP0078498)

MOL for NP0078498 ((-)-Holothurin B)

3D MOL for NP0078498 ((-)-Holothurin B)

3D SDF for NP0078498 ((-)-Holothurin B)

3D-SDF for NP0078498 ((-)-Holothurin B)

PDB for NP0078498 ((-)-Holothurin B)

3D PDB for NP0078498 ((-)-Holothurin B)

SMILES for NP0078498 ((-)-Holothurin B)

INCHI for NP0078498 ((-)-Holothurin B)

Structure for NP0078498 ((-)-Holothurin B)

3D Structure for NP0078498 ((-)-Holothurin B)