Np mrd loader

Showing NP-Card for holothurin B2 (NP0028104)

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Record Information
Version2.0
Created at2021-06-19 20:04:56 UTC
Updated at2021-06-29 23:54:40 UTC
NP-MRD IDNP0028104
Secondary Accession NumbersNone
Natural Product Identification
Common Nameholothurin B2
Provided ByJEOL DatabaseJEOL Logo
Description holothurin B2 is found in Holothuria and Holothuria polii. holothurin B2 was first documented in 2005 (Silchenko, A. S., et al.).
Structure
Thumb
MOL3D MOLSDF3D SDFPDBSMILESInChI

MOL for NP0028104 (holothurin B2)


  Mrv1652306192122043D          

123129  0  0  0  0            999 V2000
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M  CHG  2  51  -1  60   1
M  END
Download

3D MOL for NP0028104 (holothurin B2)

     RDKit          3D

123129  0  0  0  0  0  0  0  0999 V2000
   -2.5820    7.3706   -1.6729 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2324    7.4209   -2.3830 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.3830    7.1401   -3.7838 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1489    5.7757   -4.1624 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.0622    4.9159   -3.4871 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3030    3.6596   -4.1624 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.6530    2.6085   -3.0758 C   0  0  2  0  0  0  0  0  0  0  0  0
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 29 91  1  0
 29 92  1  0
M  CHG  2  51  -1  60   1
M  END
Download

3D SDF for NP0028104 (holothurin B2)


  Mrv1652306192122043D          

123129  0  0  0  0            999 V2000
   -2.5820    7.3706   -1.6729 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2324    7.4209   -2.3830 C   0  0  2  0  0  0  0  0  0  0  0  0
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   -2.3030    3.6596   -4.1624 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.6530    2.6085   -3.0758 C   0  0  2  0  0  0  0  0  0  0  0  0
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   -1.2766   -1.1811   -0.7651 C   0  0  2  0  0  0  0  0  0  0  0  0
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   -0.7002   -4.6139    5.1168 C   0  0  2  0  0  0  0  0  0  0  0  0
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   -3.1390    4.6788   -6.2108 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3283    5.3896   -3.8656 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.1914    5.6036   -5.0021 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9086    6.2162   -2.7105 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.9829    5.5077   -2.0654 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1758    6.5444   -1.6920 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.4022    7.2266   -0.5724 O   0  0  0  0  0  0  0  0  0  0  0  0
   -9.0763   -0.7188    0.8765 Na  0  3  0  0  0 15  0  0  0  0  0  0
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   -2.4966    7.7266   -0.6415 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -0.9010    8.4662   -2.3342 H   0  0  0  0  0  0  0  0  0  0  0  0
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    1.2620   -2.1178   -0.0060 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3599   -0.5499   -0.7599 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -1.2100   -7.5200    5.0393 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1520   -7.8007    3.9302 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2283   -6.4489    7.0435 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2399   -7.7083    5.1116 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0833   -8.5358    6.1721 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2617   -7.8265    8.1365 H   0  0  0  0  0  0  0  0  0  0  0  0
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M  CHG  2  51  -1  60   1
M  END
> <DATABASE_ID>
NP0028104

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[Na+].[H]O[C@@]1([H])C([H])=C2[C@@]([H])(C([H])([H])C([H])([H])[C@]3([H])[C@]2(C([H])([H])[H])C([H])([H])C([H])([H])[C@]([H])(O[C@]2([H])OC([H])([H])[C@@]([H])(O[S]([O-])(=O)=O)[C@]([H])(O[H])[C@@]2([H])O[C@@]2([H])O[C@@]([H])(C([H])([H])[H])[C@]([H])(O[H])[C@@]([H])(O[H])[C@]2([H])O[H])C3(C([H])([H])[H])C([H])([H])[H])[C@]2(C([H])([H])[H])C([H])([H])C([H])([H])[C@]3(O[H])[C@](OC(=O)[C@]123)(C([H])([H])[H])[C@]1([H])OC(C([H])([H])[H])(C([H])([H])[H])C([H])([H])C1([H])[H]

> <INCHI_IDENTIFIER>
InChI=1S/C41H64O17S.Na/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);/q;+1/p-1/t19-,20+,22+,23-,24-,25-,26+,27-,28-,29+,30-,31+,32+,33-,37+,38-,39-,40-,41+;/m0./s1

> <INCHI_KEY>
XPKZSKANINADOD-XZNTVUFASA-M

> <FORMULA>
C41H63NaO17S

> <MOLECULAR_WEIGHT>
882.99

> <EXACT_MASS>
882.36836602

> <JCHEM_ACCEPTOR_COUNT>
15

> <JCHEM_ATOM_COUNT>
123

> <JCHEM_AVERAGE_POLARIZABILITY>
89.19162376270165

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
sodium (3R,4R,5R,6S)-6-{[(1S,2S,5R,6S,9S,10S,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-{[(2R,3S,4R,5R,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}oxan-3-yl sulfate

> <ALOGPS_LOGP>
2.52

> <JCHEM_LOGP>
-0.3270465532451261

> <ALOGPS_LOGS>
-3.30

> <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>
260.26

> <JCHEM_REFRACTIVITY>
202.40500000000003

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
4.38e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
sodium (3R,4R,5R,6S)-6-{[(1S,2S,5R,6S,9S,10S,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-{[(2R,3S,4R,5R,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}oxan-3-yl sulfate

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0028104 (holothurin B2)

     RDKit          3D

123129  0  0  0  0  0  0  0  0999 V2000
   -2.5820    7.3706   -1.6729 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2324    7.4209   -2.3830 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.3830    7.1401   -3.7838 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1489    5.7757   -4.1624 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.0622    4.9159   -3.4871 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3030    3.6596   -4.1624 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.6530    2.6085   -3.0758 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.4154    2.1336   -2.5206 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5936    1.2389   -1.4151 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.1678   -0.1503   -1.8812 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2766   -1.1811   -0.7651 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4427   -0.8367    0.5008 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.0531   -1.0521    0.1568 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7275   -1.8122    1.6877 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3164   -3.0233    1.5246 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3800   -4.1252    2.5606 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.7382   -4.3634    2.9277 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5258   -3.8192    3.7931 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.8938   -4.2580    3.4218 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6592   -3.6996    2.6521 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2182   -5.4445    4.0011 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2197   -5.8546    4.9473 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.5395   -7.0437    4.3162 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9544   -6.3431    6.2268 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.7245   -7.6546    6.0774 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7423   -7.5573    7.1876 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1098   -6.0783    7.1619 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.2673   -5.7873    6.2038 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4317   -5.5452    8.5547 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9492   -5.3886    6.6638 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7002   -4.6139    5.1168 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.0365   -5.0533    5.3882 O   0  0  0  0  0  0  0  0  0  0  0  0
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 29 92  1  0
M  CHG  2  51  -1  60   1
M  END
Download

PDB for NP0028104 (holothurin B2)

HEADER    PROTEIN                                 19-JUN-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   19-JUN-21         0                                  
HETATM    1  C   UNK     0      -2.582   7.371  -1.673  0.00  0.00           C+0
HETATM    2  C   UNK     0      -1.232   7.421  -2.383  0.00  0.00           C+0
HETATM    3  O   UNK     0      -1.383   7.140  -3.784  0.00  0.00           O+0
HETATM    4  C   UNK     0      -1.149   5.776  -4.162  0.00  0.00           C+0
HETATM    5  O   UNK     0      -2.062   4.916  -3.487  0.00  0.00           O+0
HETATM    6  C   UNK     0      -2.303   3.660  -4.162  0.00  0.00           C+0
HETATM    7  C   UNK     0      -2.653   2.608  -3.076  0.00  0.00           C+0
HETATM    8  O   UNK     0      -1.415   2.134  -2.521  0.00  0.00           O+0
HETATM    9  C   UNK     0      -1.594   1.239  -1.415  0.00  0.00           C+0
HETATM   10  C   UNK     0      -1.168  -0.150  -1.881  0.00  0.00           C+0
HETATM   11  C   UNK     0      -1.277  -1.181  -0.765  0.00  0.00           C+0
HETATM   12  C   UNK     0      -0.443  -0.837   0.501  0.00  0.00           C+0
HETATM   13  C   UNK     0       1.053  -1.052   0.157  0.00  0.00           C+0
HETATM   14  C   UNK     0      -0.728  -1.812   1.688  0.00  0.00           C+0
HETATM   15  C   UNK     0      -1.316  -3.023   1.525  0.00  0.00           C+0
HETATM   16  C   UNK     0      -1.380  -4.125   2.561  0.00  0.00           C+0
HETATM   17  O   UNK     0      -2.738  -4.363   2.928  0.00  0.00           O+0
HETATM   18  C   UNK     0      -0.526  -3.819   3.793  0.00  0.00           C+0
HETATM   19  C   UNK     0       0.894  -4.258   3.422  0.00  0.00           C+0
HETATM   20  O   UNK     0       1.659  -3.700   2.652  0.00  0.00           O+0
HETATM   21  O   UNK     0       1.218  -5.444   4.001  0.00  0.00           O+0
HETATM   22  C   UNK     0       0.220  -5.855   4.947  0.00  0.00           C+0
HETATM   23  C   UNK     0      -0.540  -7.044   4.316  0.00  0.00           C+0
HETATM   24  C   UNK     0       0.954  -6.343   6.227  0.00  0.00           C+0
HETATM   25  C   UNK     0       1.724  -7.655   6.077  0.00  0.00           C+0
HETATM   26  C   UNK     0       2.742  -7.557   7.188  0.00  0.00           C+0
HETATM   27  C   UNK     0       3.110  -6.078   7.162  0.00  0.00           C+0
HETATM   28  C   UNK     0       4.267  -5.787   6.204  0.00  0.00           C+0
HETATM   29  C   UNK     0       3.432  -5.545   8.555  0.00  0.00           C+0
HETATM   30  O   UNK     0       1.949  -5.389   6.664  0.00  0.00           O+0
HETATM   31  C   UNK     0      -0.700  -4.614   5.117  0.00  0.00           C+0
HETATM   32  O   UNK     0      -2.037  -5.053   5.388  0.00  0.00           O+0
HETATM   33  C   UNK     0      -0.350  -3.569   6.221  0.00  0.00           C+0
HETATM   34  C   UNK     0       0.111  -2.292   5.505  0.00  0.00           C+0
HETATM   35  C   UNK     0      -0.692  -2.322   4.200  0.00  0.00           C+0
HETATM   36  C   UNK     0      -2.174  -1.947   4.542  0.00  0.00           C+0
HETATM   37  C   UNK     0      -0.168  -1.386   3.063  0.00  0.00           C+0
HETATM   38  C   UNK     0      -0.423   0.102   3.371  0.00  0.00           C+0
HETATM   39  C   UNK     0      -0.037   1.025   2.221  0.00  0.00           C+0
HETATM   40  C   UNK     0      -0.803   0.629   0.942  0.00  0.00           C+0
HETATM   41  C   UNK     0      -0.778   1.737  -0.182  0.00  0.00           C+0
HETATM   42  C   UNK     0      -1.496   3.013   0.346  0.00  0.00           C+0
HETATM   43  C   UNK     0       0.641   2.188  -0.586  0.00  0.00           C+0
HETATM   44  O   UNK     0      -3.459   1.525  -3.534  0.00  0.00           O+0
HETATM   45  C   UNK     0      -3.252   1.215  -4.910  0.00  0.00           C+0
HETATM   46  C   UNK     0      -3.720   2.361  -5.805  0.00  0.00           C+0
HETATM   47  O   UNK     0      -5.125   2.220  -6.006  0.00  0.00           O+0
HETATM   48  S   UNK     0      -5.722   2.633  -7.463  0.00  0.00           S+0
HETATM   49  O   UNK     0      -5.143   1.635  -8.354  0.00  0.00           O+0
HETATM   50  O   UNK     0      -7.163   2.543  -7.279  0.00  0.00           O+0
HETATM   51  O   UNK     0      -5.209   3.989  -7.653  0.00  0.00           O-1
HETATM   52  C   UNK     0      -3.459   3.741  -5.169  0.00  0.00           C+0
HETATM   53  O   UNK     0      -3.139   4.679  -6.211  0.00  0.00           O+0
HETATM   54  C   UNK     0       0.328   5.390  -3.866  0.00  0.00           C+0
HETATM   55  O   UNK     0       1.191   5.604  -5.002  0.00  0.00           O+0
HETATM   56  C   UNK     0       0.909   6.216  -2.711  0.00  0.00           C+0
HETATM   57  O   UNK     0       1.983   5.508  -2.065  0.00  0.00           O+0
HETATM   58  C   UNK     0      -0.176   6.544  -1.692  0.00  0.00           C+0
HETATM   59  O   UNK     0       0.402   7.227  -0.572  0.00  0.00           O+0
HETATM   60 Na   UNK     0      -9.076  -0.719   0.877  0.00  0.00          Na+1
HETATM   61  H   UNK     0      -2.992   6.357  -1.649  0.00  0.00           H+0
HETATM   62  H   UNK     0      -2.497   7.727  -0.642  0.00  0.00           H+0
HETATM   63  H   UNK     0      -3.313   7.994  -2.199  0.00  0.00           H+0
HETATM   64  H   UNK     0      -0.901   8.466  -2.334  0.00  0.00           H+0
HETATM   65  H   UNK     0      -1.315   5.743  -5.241  0.00  0.00           H+0
HETATM   66  H   UNK     0      -1.383   3.359  -4.682  0.00  0.00           H+0
HETATM   67  H   UNK     0      -3.209   3.103  -2.270  0.00  0.00           H+0
HETATM   68  H   UNK     0      -2.653   1.189  -1.125  0.00  0.00           H+0
HETATM   69  H   UNK     0      -0.157  -0.124  -2.303  0.00  0.00           H+0
HETATM   70  H   UNK     0      -1.806  -0.465  -2.716  0.00  0.00           H+0
HETATM   71  H   UNK     0      -0.969  -2.151  -1.178  0.00  0.00           H+0
HETATM   72  H   UNK     0      -2.337  -1.275  -0.494  0.00  0.00           H+0
HETATM   73  H   UNK     0       1.727  -0.719   0.951  0.00  0.00           H+0
HETATM   74  H   UNK     0       1.262  -2.118  -0.006  0.00  0.00           H+0
HETATM   75  H   UNK     0       1.360  -0.550  -0.760  0.00  0.00           H+0
HETATM   76  H   UNK     0      -1.679  -3.329   0.547  0.00  0.00           H+0
HETATM   77  H   UNK     0      -1.031  -5.039   2.065  0.00  0.00           H+0
HETATM   78  H   UNK     0      -3.301  -4.055   2.193  0.00  0.00           H+0
HETATM   79  H   UNK     0      -1.138  -6.741   3.454  0.00  0.00           H+0
HETATM   80  H   UNK     0      -1.210  -7.520   5.039  0.00  0.00           H+0
HETATM   81  H   UNK     0       0.152  -7.801   3.930  0.00  0.00           H+0
HETATM   82  H   UNK     0       0.228  -6.449   7.043  0.00  0.00           H+0
HETATM   83  H   UNK     0       2.240  -7.708   5.112  0.00  0.00           H+0
HETATM   84  H   UNK     0       1.083  -8.536   6.172  0.00  0.00           H+0
HETATM   85  H   UNK     0       2.262  -7.827   8.136  0.00  0.00           H+0
HETATM   86  H   UNK     0       3.597  -8.225   7.047  0.00  0.00           H+0
HETATM   87  H   UNK     0       5.186  -6.293   6.519  0.00  0.00           H+0
HETATM   88  H   UNK     0       4.465  -4.710   6.151  0.00  0.00           H+0
HETATM   89  H   UNK     0       4.031  -6.103   5.182  0.00  0.00           H+0
HETATM   90  H   UNK     0       3.638  -4.469   8.523  0.00  0.00           H+0
HETATM   91  H   UNK     0       2.577  -5.673   9.229  0.00  0.00           H+0
HETATM   92  H   UNK     0       4.298  -6.054   8.990  0.00  0.00           H+0
HETATM   93  H   UNK     0      -2.584  -4.882   4.589  0.00  0.00           H+0
HETATM   94  H   UNK     0       0.387  -3.874   6.958  0.00  0.00           H+0
HETATM   95  H   UNK     0      -1.246  -3.338   6.813  0.00  0.00           H+0
HETATM   96  H   UNK     0       1.190  -2.335   5.315  0.00  0.00           H+0
HETATM   97  H   UNK     0      -0.079  -1.401   6.111  0.00  0.00           H+0
HETATM   98  H   UNK     0      -2.218  -1.024   5.132  0.00  0.00           H+0
HETATM   99  H   UNK     0      -2.780  -1.788   3.644  0.00  0.00           H+0
HETATM  100  H   UNK     0      -2.690  -2.700   5.139  0.00  0.00           H+0
HETATM  101  H   UNK     0       0.923  -1.484   3.009  0.00  0.00           H+0
HETATM  102  H   UNK     0      -1.481   0.290   3.585  0.00  0.00           H+0
HETATM  103  H   UNK     0       0.135   0.394   4.268  0.00  0.00           H+0
HETATM  104  H   UNK     0       1.047   1.002   2.069  0.00  0.00           H+0
HETATM  105  H   UNK     0      -0.282   2.046   2.528  0.00  0.00           H+0
HETATM  106  H   UNK     0      -1.864   0.576   1.241  0.00  0.00           H+0
HETATM  107  H   UNK     0      -0.917   3.519   1.125  0.00  0.00           H+0
HETATM  108  H   UNK     0      -2.482   2.773   0.758  0.00  0.00           H+0
HETATM  109  H   UNK     0      -1.649   3.745  -0.453  0.00  0.00           H+0
HETATM  110  H   UNK     0       1.248   2.451   0.285  0.00  0.00           H+0
HETATM  111  H   UNK     0       1.180   1.436  -1.161  0.00  0.00           H+0
HETATM  112  H   UNK     0       0.601   3.084  -1.218  0.00  0.00           H+0
HETATM  113  H   UNK     0      -3.810   0.299  -5.129  0.00  0.00           H+0
HETATM  114  H   UNK     0      -2.188   1.001  -5.066  0.00  0.00           H+0
HETATM  115  H   UNK     0      -3.200   2.264  -6.766  0.00  0.00           H+0
HETATM  116  H   UNK     0      -4.354   4.133  -4.671  0.00  0.00           H+0
HETATM  117  H   UNK     0      -3.907   4.646  -6.842  0.00  0.00           H+0
HETATM  118  H   UNK     0       0.409   4.322  -3.636  0.00  0.00           H+0
HETATM  119  H   UNK     0       0.866   6.400  -5.463  0.00  0.00           H+0
HETATM  120  H   UNK     0       1.362   7.144  -3.082  0.00  0.00           H+0
HETATM  121  H   UNK     0       2.554   5.189  -2.792  0.00  0.00           H+0
HETATM  122  H   UNK     0      -0.611   5.619  -1.301  0.00  0.00           H+0
HETATM  123  H   UNK     0       1.224   6.729  -0.383  0.00  0.00           H+0
CONECT    1    2   61   62   63                                             
CONECT    2   58    3    1   64                                             
CONECT    3    2    4                                                       
CONECT    4   54    3    5   65                                             
CONECT    5    6    4                                                       
CONECT    6    5   52    7   66                                             
CONECT    7    8    6   44   67                                             
CONECT    8    7    9                                                       
CONECT    9   10   41    8   68                                             
CONECT   10    9   11   69   70                                             
CONECT   11   10   12   71   72                                             
CONECT   12   13   11   40   14                                             
CONECT   13   12   73   74   75                                             
CONECT   14   37   15   12                                                  
CONECT   15   14   16   76                                                  
CONECT   16   18   15   17   77                                             
CONECT   17   16   78                                                       
CONECT   18   16   35   31   19                                             
CONECT   19   21   18   20                                                  
CONECT   20   19                                                            
CONECT   21   22   19                                                       
CONECT   22   31   21   23   24                                             
CONECT   23   22   79   80   81                                             
CONECT   24   22   30   25   82                                             
CONECT   25   26   24   83   84                                             
CONECT   26   27   25   85   86                                             
CONECT   27   30   26   28   29                                             
CONECT   28   27   87   88   89                                             
CONECT   29   27   90   91   92                                             
CONECT   30   24   27                                                       
CONECT   31   33   18   22   32                                             
CONECT   32   31   93                                                       
CONECT   33   34   31   94   95                                             
CONECT   34   35   33   96   97                                             
CONECT   35   37   18   34   36                                             
CONECT   36   35   98   99  100                                             
CONECT   37   14   35   38  101                                             
CONECT   38   39   37  102  103                                             
CONECT   39   40   38  104  105                                             
CONECT   40   41   12   39  106                                             
CONECT   41   42   43    9   40                                             
CONECT   42   41  107  108  109                                             
CONECT   43   41  110  111  112                                             
CONECT   44    7   45                                                       
CONECT   45   44   46  113  114                                             
CONECT   46   45   52   47  115                                             
CONECT   47   48   46                                                       
CONECT   48   47   49   50   51                                             
CONECT   49   48                                                            
CONECT   50   48                                                            
CONECT   51   48                                                            
CONECT   52    6   46   53  116                                             
CONECT   53   52  117                                                       
CONECT   54    4   56   55  118                                             
CONECT   55   54  119                                                       
CONECT   56   54   58   57  120                                             
CONECT   57   56  121                                                       
CONECT   58   56    2   59  122                                             
CONECT   59   58  123                                                       
CONECT   61    1                                                            
CONECT   62    1                                                            
CONECT   63    1                                                            
CONECT   64    2                                                            
CONECT   65    4                                                            
CONECT   66    6                                                            
CONECT   67    7                                                            
CONECT   68    9                                                            
CONECT   69   10                                                            
CONECT   70   10                                                            
CONECT   71   11                                                            
CONECT   72   11                                                            
CONECT   73   13                                                            
CONECT   74   13                                                            
CONECT   75   13                                                            
CONECT   76   15                                                            
CONECT   77   16                                                            
CONECT   78   17                                                            
CONECT   79   23                                                            
CONECT   80   23                                                            
CONECT   81   23                                                            
CONECT   82   24                                                            
CONECT   83   25                                                            
CONECT   84   25                                                            
CONECT   85   26                                                            
CONECT   86   26                                                            
CONECT   87   28                                                            
CONECT   88   28                                                            
CONECT   89   28                                                            
CONECT   90   29                                                            
CONECT   91   29                                                            
CONECT   92   29                                                            
CONECT   93   32                                                            
CONECT   94   33                                                            
CONECT   95   33                                                            
CONECT   96   34                                                            
CONECT   97   34                                                            
CONECT   98   36                                                            
CONECT   99   36                                                            
CONECT  100   36                                                            
CONECT  101   37                                                            
CONECT  102   38                                                            
CONECT  103   38                                                            
CONECT  104   39                                                            
CONECT  105   39                                                            
CONECT  106   40                                                            
CONECT  107   42                                                            
CONECT  108   42                                                            
CONECT  109   42                                                            
CONECT  110   43                                                            
CONECT  111   43                                                            
CONECT  112   43                                                            
CONECT  113   45                                                            
CONECT  114   45                                                            
CONECT  115   46                                                            
CONECT  116   52                                                            
CONECT  117   53                                                            
CONECT  118   54                                                            
CONECT  119   55                                                            
CONECT  120   56                                                            
CONECT  121   57                                                            
CONECT  122   58                                                            
CONECT  123   59                                                            
MASTER        0    0    0    0    0    0    0    0  123    0  258    0
END
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3D PDB for NP0028104 (holothurin B2)

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SMILES for NP0028104 (holothurin B2)
[Na+].[H]O[C@@]1([H])C([H])=C2[C@@]([H])(C([H])([H])C([H])([H])[C@]3([H])[C@]2(C([H])([H])[H])C([H])([H])C([H])([H])[C@]([H])(O[C@]2([H])OC([H])([H])[C@@]([H])(O[S]([O-])(=O)=O)[C@]([H])(O[H])[C@@]2([H])O[C@@]2([H])O[C@@]([H])(C([H])([H])[H])[C@]([H])(O[H])[C@@]([H])(O[H])[C@]2([H])O[H])C3(C([H])([H])[H])C([H])([H])[H])[C@]2(C([H])([H])[H])C([H])([H])C([H])([H])[C@]3(O[H])[C@](OC(=O)[C@]123)(C([H])([H])[H])[C@]1([H])OC(C([H])([H])[H])(C([H])([H])[H])C([H])([H])C1([H])[H]
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INCHI for NP0028104 (holothurin B2)
InChI=1S/C41H64O17S.Na/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);/q;+1/p-1/t19-,20+,22+,23-,24-,25-,26+,27-,28-,29+,30-,31+,32+,33-,37+,38-,39-,40-,41+;/m0./s1
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View in JSmol
SynonymsNot Available
Chemical FormulaC41H63NaO17S
Average Mass882.9900 Da
Monoisotopic Mass882.36837 Da
IUPAC Namesodium (3R,4R,5R,6S)-6-{[(1S,2S,5R,6S,9S,10S,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-{[(2R,3S,4R,5R,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}oxan-3-yl sulfate
Traditional Namesodium (3R,4R,5R,6S)-6-{[(1S,2S,5R,6S,9S,10S,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-{[(2R,3S,4R,5R,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}oxan-3-yl sulfate
CAS Registry NumberNot Available
SMILES
[Na+].[H]O[C@@]1([H])C([H])=C2[C@@]([H])(C([H])([H])C([H])([H])[C@]3([H])[C@]2(C([H])([H])[H])C([H])([H])C([H])([H])[C@]([H])(O[C@]2([H])OC([H])([H])[C@@]([H])(O[S]([O-])(=O)=O)[C@]([H])(O[H])[C@@]2([H])O[C@@]2([H])O[C@@]([H])(C([H])([H])[H])[C@]([H])(O[H])[C@@]([H])(O[H])[C@]2([H])O[H])C3(C([H])([H])[H])C([H])([H])[H])[C@]2(C([H])([H])[H])C([H])([H])C([H])([H])[C@]3(O[H])[C@](OC(=O)[C@]123)(C([H])([H])[H])[C@]1([H])OC(C([H])([H])[H])(C([H])([H])[H])C([H])([H])C1([H])[H]
InChI Identifier
InChI=1S/C41H64O17S.Na/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);/q;+1/p-1/t19-,20+,22+,23-,24-,25-,26+,27-,28-,29+,30-,31+,32+,33-,37+,38-,39-,40-,41+;/m0./s1
InChI KeyXPKZSKANINADOD-XZNTVUFASA-M
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
HolothuriaJEOL database
    • Silchenko, A. S., et al, J. Nat. Prod. 68, 564 (2005)
Holothuria poliiAnimalia
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
logP2.52ALOGPS
logP-0.33ChemAxon
logS-3.3ALOGPS
pKa (Strongest Acidic)-2ChemAxon
pKa (Strongest Basic)-3.3ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count15ChemAxon
Hydrogen Donor Count6ChemAxon
Polar Surface Area260.26 ŲChemAxon
Rotatable Bond Count7ChemAxon
Refractivity202.4 m³·mol⁻¹ChemAxon
Polarizability89.19 ųChemAxon
Number of Rings8ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
External LinksNot Available
References
General References
  1. Silchenko, A. S., et al. (2005). Silchenko, A. S., et al, J. Nat. Prod. 68, 564 (2005). J. Nat. Prod..