Np mrd loader

Showing NP-Card for Vinaginsenoside R25 (NP0025576)

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Record Information
Version1.0
Created at2021-06-19 17:39:44 UTC
Updated at2021-06-29 23:50:37 UTC
NP-MRD IDNP0025576
Secondary Accession NumbersNone
Natural Product Identification
Common NameVinaginsenoside R25
Provided ByJEOL DatabaseJEOL Logo
DescriptionVina-ginsenoside R25 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. Vinaginsenoside R25 is found in Panax vietnamensis. It was first documented in 2001 (Tran, Q. L., et al.). Based on a literature review very few articles have been published on vina-ginsenoside R25.
Structure
Thumb
MOL3D MOLSDF3D SDFPDBSMILESInChI

MOL for NP0025576 (Vinaginsenoside R25)


  Mrv1652306192119393D          

127132  0  0  0  0            999 V2000
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M  END
Download

3D MOL for NP0025576 (Vinaginsenoside R25)

     RDKit          3D

127132  0  0  0  0  0  0  0  0999 V2000
   -0.5772    3.6066   -3.5928 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0421    3.3224   -4.7500 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4232    4.3909   -5.7327 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4041    1.9152   -5.1522 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9611    1.7302   -6.2352 O   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

3D SDF for NP0025576 (Vinaginsenoside R25)


  Mrv1652306192119393D          

127132  0  0  0  0            999 V2000
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   -1.1499    1.9115    5.4347 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1525   -0.0479    3.7078 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.3834   -0.0386    3.4031 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.1146   -0.5976    4.5012 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5292   -0.3834    4.4398 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.1821   -1.6132    4.1035 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0118   -2.6768    5.0625 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.8864   -3.6114    4.5996 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.1670   -4.0924    3.2848 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8048   -2.1980    6.5090 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.2918   -3.1553    7.4606 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5837   -0.9000    6.6948 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.5201   -0.4631    8.0612 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0249    0.1955    5.7862 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.0584    1.1770    5.5817 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6727   -0.8938    2.1502 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.0734   -0.4642    0.8663 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.5614    0.8820    0.4080 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8673    2.8536   -2.8672 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8248    4.6318   -3.3311 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5061    4.3946   -5.8954 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0755    4.2244   -6.6933 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1390    5.3891   -5.3826 H   0  0  0  0  0  0  0  0  0  0  0  0
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    0.7043    0.9314   -3.3061 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4677   -0.7963   -4.6801 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2189   -0.5771   -5.8628 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0319   -3.3745   -4.7228 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0306   -2.9524   -6.0468 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6628   -3.9161   -4.7207 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8109   -2.0042   -6.4262 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2486   -0.2961   -8.0822 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4671    1.9616   -7.6319 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -4.8736    0.5630   -6.7204 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4567    0.9613   -9.0550 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0891   -2.1880   -7.8169 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2743   -1.4483   -7.7808 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3879   -1.3788   -4.8735 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8995   -3.4849   -5.6089 H   0  0  0  0  0  0  0  0  0  0  0  0
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    1.9831   -1.9903   -2.9630 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4030   -3.4806   -2.2340 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0178   -0.8457   -1.0177 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1086   -2.4253   -0.2513 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -0.3444   -3.7485   -0.5833 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1972   -3.3632    1.0140 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3083   -0.1209   -1.8572 H   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
> <DATABASE_ID>
NP0025576

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]OC([H])([H])[C@@]1([H])O[C@@]([H])(O[C@@]2([H])C([H])([H])[C@]3(C([H])([H])[H])[C@]([H])(C([H])([H])[C@@]([H])(O[H])[C@]4([H])[C@]([H])(C([H])([H])C([H])([H])[C@@]34C([H])([H])[H])[C@](O[C@]3([H])O[C@]([H])(C([H])([H])O[H])[C@@]([H])(O[H])[C@]([H])(O[H])[C@@]3([H])O[H])(C([H])([H])[H])C([H])([H])C([H])([H])C(=O)C(=C([H])[H])C([H])([H])[H])[C@@]3(C([H])([H])[H])C([H])([H])C([H])([H])[C@]([H])(O[H])C(C([H])([H])[H])(C([H])([H])[H])[C@]23[H])[C@]([H])(O[H])[C@@]([H])(O[H])[C@]1([H])O[H]

> <INCHI_IDENTIFIER>
InChI=1S/C42H70O15/c1-19(2)21(45)10-14-42(8,57-37-34(53)32(51)30(49)25(18-44)56-37)20-9-13-40(6)28(20)22(46)15-26-39(5)12-11-27(47)38(3,4)35(39)23(16-41(26,40)7)54-36-33(52)31(50)29(48)24(17-43)55-36/h20,22-37,43-44,46-53H,1,9-18H2,2-8H3/t20-,22+,23-,24+,25+,26+,27-,28-,29+,30+,31-,32-,33+,34+,35-,36+,37-,39+,40+,41+,42-/m0/s1

> <INCHI_KEY>
KJZQRDAZSWKILI-OGGKGQCOSA-N

> <FORMULA>
C42H70O15

> <MOLECULAR_WEIGHT>
815.007

> <EXACT_MASS>
814.471471554

> <JCHEM_ACCEPTOR_COUNT>
15

> <JCHEM_ATOM_COUNT>
127

> <JCHEM_AVERAGE_POLARIZABILITY>
88.44226499162045

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
10

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(6S)-6-[(1R,2R,5S,7R,8S,10R,11R,14S,15R,16R)-5,16-dihydroxy-2,6,6,10,11-pentamethyl-8-{[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}tetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadecan-14-yl]-2-methyl-6-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}hept-1-en-3-one

> <ALOGPS_LOGP>
0.27

> <JCHEM_LOGP>
0.07215202566666551

> <ALOGPS_LOGS>
-3.35

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.430468634722054

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.909332014454609

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9810835428030016

> <JCHEM_POLAR_SURFACE_AREA>
256.28999999999996

> <JCHEM_REFRACTIVITY>
203.27570000000009

> <JCHEM_ROTATABLE_BOND_COUNT>
11

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
3.68e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(6S)-6-[(1R,2R,5S,7R,8S,10R,11R,14S,15R,16R)-5,16-dihydroxy-2,6,6,10,11-pentamethyl-8-{[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}tetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadecan-14-yl]-2-methyl-6-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}hept-1-en-3-one

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0025576 (Vinaginsenoside R25)

     RDKit          3D

127132  0  0  0  0  0  0  0  0999 V2000
   -0.5772    3.6066   -3.5928 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0421    3.3224   -4.7500 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4232    4.3909   -5.7327 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4041    1.9152   -5.1522 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9611    1.7302   -6.2352 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0874    0.7741   -4.1966 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3923   -0.6072   -4.7796 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4264   -1.7949   -4.2021 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.0048   -3.0807   -4.9604 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8462   -1.6077   -4.3700 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3671   -1.4117   -5.6950 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.2814   -0.0243   -6.0234 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7965    0.2785   -7.3229 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.5439    1.7671   -7.5980 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

PDB for NP0025576 (Vinaginsenoside R25)

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      -0.577   3.607  -3.593  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.042   3.322  -4.750  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.423   4.391  -5.733  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.404   1.915  -5.152  0.00  0.00           C+0
HETATM    5  O   UNK     0       0.961   1.730  -6.235  0.00  0.00           O+0
HETATM    6  C   UNK     0       0.087   0.774  -4.197  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.392  -0.607  -4.780  0.00  0.00           C+0
HETATM    8  C   UNK     0      -0.426  -1.795  -4.202  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.005  -3.081  -4.960  0.00  0.00           C+0
HETATM   10  O   UNK     0      -1.846  -1.608  -4.370  0.00  0.00           O+0
HETATM   11  C   UNK     0      -2.367  -1.412  -5.695  0.00  0.00           C+0
HETATM   12  O   UNK     0      -2.281  -0.024  -6.023  0.00  0.00           O+0
HETATM   13  C   UNK     0      -2.797   0.279  -7.323  0.00  0.00           C+0
HETATM   14  C   UNK     0      -2.544   1.767  -7.598  0.00  0.00           C+0
HETATM   15  O   UNK     0      -3.121   2.166  -8.840  0.00  0.00           O+0
HETATM   16  C   UNK     0      -4.293  -0.068  -7.405  0.00  0.00           C+0
HETATM   17  O   UNK     0      -4.836   0.118  -8.718  0.00  0.00           O+0
HETATM   18  C   UNK     0      -4.494  -1.537  -7.032  0.00  0.00           C+0
HETATM   19  O   UNK     0      -5.897  -1.843  -6.968  0.00  0.00           O+0
HETATM   20  C   UNK     0      -3.843  -1.867  -5.691  0.00  0.00           C+0
HETATM   21  O   UNK     0      -3.953  -3.283  -5.467  0.00  0.00           O+0
HETATM   22  C   UNK     0      -0.224  -2.091  -2.668  0.00  0.00           C+0
HETATM   23  C   UNK     0       1.246  -2.396  -2.266  0.00  0.00           C+0
HETATM   24  C   UNK     0       1.476  -1.783  -0.874  0.00  0.00           C+0
HETATM   25  C   UNK     0       0.068  -1.572  -0.285  0.00  0.00           C+0
HETATM   26  C   UNK     0      -0.420  -2.983   0.195  0.00  0.00           C+0
HETATM   27  C   UNK     0      -0.691  -1.097  -1.565  0.00  0.00           C+0
HETATM   28  C   UNK     0      -2.184  -0.913  -1.279  0.00  0.00           C+0
HETATM   29  O   UNK     0      -2.846  -0.301  -2.380  0.00  0.00           O+0
HETATM   30  C   UNK     0      -2.421   0.031  -0.082  0.00  0.00           C+0
HETATM   31  C   UNK     0      -1.608  -0.309   1.193  0.00  0.00           C+0
HETATM   32  C   UNK     0      -1.966   0.558   2.482  0.00  0.00           C+0
HETATM   33  C   UNK     0      -1.707   2.068   2.255  0.00  0.00           C+0
HETATM   34  C   UNK     0      -3.489   0.390   2.769  0.00  0.00           C+0
HETATM   35  C   UNK     0      -3.939   0.935   4.117  0.00  0.00           C+0
HETATM   36  C   UNK     0      -3.155   0.324   5.267  0.00  0.00           C+0
HETATM   37  O   UNK     0      -3.616   0.915   6.483  0.00  0.00           O+0
HETATM   38  C   UNK     0      -1.607   0.469   5.139  0.00  0.00           C+0
HETATM   39  C   UNK     0      -1.017  -0.413   6.278  0.00  0.00           C+0
HETATM   40  C   UNK     0      -1.150   1.912   5.435  0.00  0.00           C+0
HETATM   41  C   UNK     0      -1.153  -0.048   3.708  0.00  0.00           C+0
HETATM   42  C   UNK     0       0.383  -0.039   3.403  0.00  0.00           C+0
HETATM   43  O   UNK     0       1.115  -0.598   4.501  0.00  0.00           O+0
HETATM   44  C   UNK     0       2.529  -0.383   4.440  0.00  0.00           C+0
HETATM   45  O   UNK     0       3.182  -1.613   4.104  0.00  0.00           O+0
HETATM   46  C   UNK     0       3.012  -2.677   5.063  0.00  0.00           C+0
HETATM   47  C   UNK     0       1.886  -3.611   4.600  0.00  0.00           C+0
HETATM   48  O   UNK     0       2.167  -4.092   3.285  0.00  0.00           O+0
HETATM   49  C   UNK     0       2.805  -2.198   6.509  0.00  0.00           C+0
HETATM   50  O   UNK     0       3.292  -3.155   7.461  0.00  0.00           O+0
HETATM   51  C   UNK     0       3.584  -0.900   6.695  0.00  0.00           C+0
HETATM   52  O   UNK     0       3.520  -0.463   8.061  0.00  0.00           O+0
HETATM   53  C   UNK     0       3.025   0.196   5.786  0.00  0.00           C+0
HETATM   54  O   UNK     0       4.058   1.177   5.582  0.00  0.00           O+0
HETATM   55  C   UNK     0       0.673  -0.894   2.150  0.00  0.00           C+0
HETATM   56  C   UNK     0      -0.073  -0.464   0.866  0.00  0.00           C+0
HETATM   57  C   UNK     0       0.561   0.882   0.408  0.00  0.00           C+0
HETATM   58  H   UNK     0      -0.867   2.854  -2.867  0.00  0.00           H+0
HETATM   59  H   UNK     0      -0.825   4.632  -3.331  0.00  0.00           H+0
HETATM   60  H   UNK     0       1.506   4.395  -5.895  0.00  0.00           H+0
HETATM   61  H   UNK     0      -0.076   4.224  -6.693  0.00  0.00           H+0
HETATM   62  H   UNK     0       0.139   5.389  -5.383  0.00  0.00           H+0
HETATM   63  H   UNK     0      -0.971   0.845  -3.935  0.00  0.00           H+0
HETATM   64  H   UNK     0       0.704   0.931  -3.306  0.00  0.00           H+0
HETATM   65  H   UNK     0       1.468  -0.796  -4.680  0.00  0.00           H+0
HETATM   66  H   UNK     0       0.219  -0.577  -5.863  0.00  0.00           H+0
HETATM   67  H   UNK     0       1.032  -3.374  -4.723  0.00  0.00           H+0
HETATM   68  H   UNK     0      -0.031  -2.952  -6.047  0.00  0.00           H+0
HETATM   69  H   UNK     0      -0.663  -3.916  -4.721  0.00  0.00           H+0
HETATM   70  H   UNK     0      -1.811  -2.004  -6.426  0.00  0.00           H+0
HETATM   71  H   UNK     0      -2.249  -0.296  -8.082  0.00  0.00           H+0
HETATM   72  H   UNK     0      -1.467   1.962  -7.632  0.00  0.00           H+0
HETATM   73  H   UNK     0      -2.965   2.388  -6.799  0.00  0.00           H+0
HETATM   74  H   UNK     0      -2.782   3.062  -9.023  0.00  0.00           H+0
HETATM   75  H   UNK     0      -4.874   0.563  -6.720  0.00  0.00           H+0
HETATM   76  H   UNK     0      -4.457   0.961  -9.055  0.00  0.00           H+0
HETATM   77  H   UNK     0      -4.089  -2.188  -7.817  0.00  0.00           H+0
HETATM   78  H   UNK     0      -6.274  -1.448  -7.781  0.00  0.00           H+0
HETATM   79  H   UNK     0      -4.388  -1.379  -4.874  0.00  0.00           H+0
HETATM   80  H   UNK     0      -4.899  -3.485  -5.609  0.00  0.00           H+0
HETATM   81  H   UNK     0      -0.811  -3.005  -2.494  0.00  0.00           H+0
HETATM   82  H   UNK     0       1.983  -1.990  -2.963  0.00  0.00           H+0
HETATM   83  H   UNK     0       1.403  -3.481  -2.234  0.00  0.00           H+0
HETATM   84  H   UNK     0       2.018  -0.846  -1.018  0.00  0.00           H+0
HETATM   85  H   UNK     0       2.109  -2.425  -0.251  0.00  0.00           H+0
HETATM   86  H   UNK     0      -1.460  -2.997   0.521  0.00  0.00           H+0
HETATM   87  H   UNK     0      -0.344  -3.749  -0.583  0.00  0.00           H+0
HETATM   88  H   UNK     0       0.197  -3.363   1.014  0.00  0.00           H+0
HETATM   89  H   UNK     0      -0.308  -0.121  -1.857  0.00  0.00           H+0
HETATM   90  H   UNK     0      -2.671  -1.876  -1.095  0.00  0.00           H+0
HETATM   91  H   UNK     0      -2.649  -0.858  -3.161  0.00  0.00           H+0
HETATM   92  H   UNK     0      -2.222   1.059  -0.406  0.00  0.00           H+0
HETATM   93  H   UNK     0      -3.496   0.009   0.130  0.00  0.00           H+0
HETATM   94  H   UNK     0      -1.959  -1.309   1.478  0.00  0.00           H+0
HETATM   95  H   UNK     0      -2.414   2.704   2.793  0.00  0.00           H+0
HETATM   96  H   UNK     0      -1.815   2.356   1.207  0.00  0.00           H+0
HETATM   97  H   UNK     0      -0.717   2.388   2.584  0.00  0.00           H+0
HETATM   98  H   UNK     0      -3.757  -0.674   2.725  0.00  0.00           H+0
HETATM   99  H   UNK     0      -4.082   0.893   1.996  0.00  0.00           H+0
HETATM  100  H   UNK     0      -5.006   0.712   4.252  0.00  0.00           H+0
HETATM  101  H   UNK     0      -3.884   2.028   4.154  0.00  0.00           H+0
HETATM  102  H   UNK     0      -3.404  -0.744   5.320  0.00  0.00           H+0
HETATM  103  H   UNK     0      -4.572   0.749   6.549  0.00  0.00           H+0
HETATM  104  H   UNK     0      -1.082  -1.479   6.032  0.00  0.00           H+0
HETATM  105  H   UNK     0       0.024  -0.168   6.499  0.00  0.00           H+0
HETATM  106  H   UNK     0      -1.553  -0.267   7.223  0.00  0.00           H+0
HETATM  107  H   UNK     0      -1.687   2.655   4.845  0.00  0.00           H+0
HETATM  108  H   UNK     0      -0.079   2.039   5.247  0.00  0.00           H+0
HETATM  109  H   UNK     0      -1.319   2.172   6.486  0.00  0.00           H+0
HETATM  110  H   UNK     0      -1.424  -1.117   3.737  0.00  0.00           H+0
HETATM  111  H   UNK     0       0.725   0.991   3.271  0.00  0.00           H+0
HETATM  112  H   UNK     0       2.779   0.331   3.646  0.00  0.00           H+0
HETATM  113  H   UNK     0       3.944  -3.253   5.007  0.00  0.00           H+0
HETATM  114  H   UNK     0       1.794  -4.477   5.262  0.00  0.00           H+0
HETATM  115  H   UNK     0       0.919  -3.104   4.564  0.00  0.00           H+0
HETATM  116  H   UNK     0       2.507  -3.322   2.789  0.00  0.00           H+0
HETATM  117  H   UNK     0       1.747  -2.033   6.743  0.00  0.00           H+0
HETATM  118  H   UNK     0       2.745  -3.958   7.388  0.00  0.00           H+0
HETATM  119  H   UNK     0       4.650  -1.067   6.493  0.00  0.00           H+0
HETATM  120  H   UNK     0       3.687  -1.271   8.589  0.00  0.00           H+0
HETATM  121  H   UNK     0       2.208   0.733   6.281  0.00  0.00           H+0
HETATM  122  H   UNK     0       4.346   1.439   6.478  0.00  0.00           H+0
HETATM  123  H   UNK     0       1.750  -0.921   1.947  0.00  0.00           H+0
HETATM  124  H   UNK     0       0.414  -1.921   2.422  0.00  0.00           H+0
HETATM  125  H   UNK     0       1.606   0.761   0.111  0.00  0.00           H+0
HETATM  126  H   UNK     0       0.031   1.348  -0.425  0.00  0.00           H+0
HETATM  127  H   UNK     0       0.601   1.626   1.201  0.00  0.00           H+0
CONECT    1    2   58   59                                                  
CONECT    2    4    1    3                                                  
CONECT    3    2   60   61   62                                             
CONECT    4    6    2    5                                                  
CONECT    5    4                                                            
CONECT    6    7    4   63   64                                             
CONECT    7    6    8   65   66                                             
CONECT    8   22   10    9    7                                             
CONECT    9    8   67   68   69                                             
CONECT   10    8   11                                                       
CONECT   11   20   12   10   70                                             
CONECT   12   13   11                                                       
CONECT   13   16   12   14   71                                             
CONECT   14   15   13   72   73                                             
CONECT   15   14   74                                                       
CONECT   16   18   13   17   75                                             
CONECT   17   16   76                                                       
CONECT   18   20   16   19   77                                             
CONECT   19   18   78                                                       
CONECT   20   11   18   21   79                                             
CONECT   21   20   80                                                       
CONECT   22   23   27    8   81                                             
CONECT   23   24   22   82   83                                             
CONECT   24   25   23   84   85                                             
CONECT   25   56   27   24   26                                             
CONECT   26   25   86   87   88                                             
CONECT   27   28   25   22   89                                             
CONECT   28   27   30   29   90                                             
CONECT   29   28   91                                                       
CONECT   30   31   28   92   93                                             
CONECT   31   30   94   32   56                                             
CONECT   32   33   34   41   31                                             
CONECT   33   32   95   96   97                                             
CONECT   34   35   32   98   99                                             
CONECT   35   36   34  100  101                                             
CONECT   36   37   35   38  102                                             
CONECT   37   36  103                                                       
CONECT   38   39   40   36   41                                             
CONECT   39   38  104  105  106                                             
CONECT   40   38  107  108  109                                             
CONECT   41  110   38   32   42                                             
CONECT   42   43   41   55  111                                             
CONECT   43   44   42                                                       
CONECT   44   45   43   53  112                                             
CONECT   45   44   46                                                       
CONECT   46   45   49   47  113                                             
CONECT   47   48   46  114  115                                             
CONECT   48   47  116                                                       
CONECT   49   46   51   50  117                                             
CONECT   50   49  118                                                       
CONECT   51   52   49   53  119                                             
CONECT   52   51  120                                                       
CONECT   53   54   51   44  121                                             
CONECT   54   53  122                                                       
CONECT   55   42   56  123  124                                             
CONECT   56   25   57   55   31                                             
CONECT   57   56  125  126  127                                             
CONECT   58    1                                                            
CONECT   59    1                                                            
CONECT   60    3                                                            
CONECT   61    3                                                            
CONECT   62    3                                                            
CONECT   63    6                                                            
CONECT   64    6                                                            
CONECT   65    7                                                            
CONECT   66    7                                                            
CONECT   67    9                                                            
CONECT   68    9                                                            
CONECT   69    9                                                            
CONECT   70   11                                                            
CONECT   71   13                                                            
CONECT   72   14                                                            
CONECT   73   14                                                            
CONECT   74   15                                                            
CONECT   75   16                                                            
CONECT   76   17                                                            
CONECT   77   18                                                            
CONECT   78   19                                                            
CONECT   79   20                                                            
CONECT   80   21                                                            
CONECT   81   22                                                            
CONECT   82   23                                                            
CONECT   83   23                                                            
CONECT   84   24                                                            
CONECT   85   24                                                            
CONECT   86   26                                                            
CONECT   87   26                                                            
CONECT   88   26                                                            
CONECT   89   27                                                            
CONECT   90   28                                                            
CONECT   91   29                                                            
CONECT   92   30                                                            
CONECT   93   30                                                            
CONECT   94   31                                                            
CONECT   95   33                                                            
CONECT   96   33                                                            
CONECT   97   33                                                            
CONECT   98   34                                                            
CONECT   99   34                                                            
CONECT  100   35                                                            
CONECT  101   35                                                            
CONECT  102   36                                                            
CONECT  103   37                                                            
CONECT  104   39                                                            
CONECT  105   39                                                            
CONECT  106   39                                                            
CONECT  107   40                                                            
CONECT  108   40                                                            
CONECT  109   40                                                            
CONECT  110   41                                                            
CONECT  111   42                                                            
CONECT  112   44                                                            
CONECT  113   46                                                            
CONECT  114   47                                                            
CONECT  115   47                                                            
CONECT  116   48                                                            
CONECT  117   49                                                            
CONECT  118   50                                                            
CONECT  119   51                                                            
CONECT  120   52                                                            
CONECT  121   53                                                            
CONECT  122   54                                                            
CONECT  123   55                                                            
CONECT  124   55                                                            
CONECT  125   57                                                            
CONECT  126   57                                                            
CONECT  127   57                                                            
MASTER        0    0    0    0    0    0    0    0  127    0  264    0
END
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3D PDB for NP0025576 (Vinaginsenoside R25)

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SMILES for NP0025576 (Vinaginsenoside R25)
[H]OC([H])([H])[C@@]1([H])O[C@@]([H])(O[C@@]2([H])C([H])([H])[C@]3(C([H])([H])[H])[C@]([H])(C([H])([H])[C@@]([H])(O[H])[C@]4([H])[C@]([H])(C([H])([H])C([H])([H])[C@@]34C([H])([H])[H])[C@](O[C@]3([H])O[C@]([H])(C([H])([H])O[H])[C@@]([H])(O[H])[C@]([H])(O[H])[C@@]3([H])O[H])(C([H])([H])[H])C([H])([H])C([H])([H])C(=O)C(=C([H])[H])C([H])([H])[H])[C@@]3(C([H])([H])[H])C([H])([H])C([H])([H])[C@]([H])(O[H])C(C([H])([H])[H])(C([H])([H])[H])[C@]23[H])[C@]([H])(O[H])[C@@]([H])(O[H])[C@]1([H])O[H]
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INCHI for NP0025576 (Vinaginsenoside R25)
InChI=1S/C42H70O15/c1-19(2)21(45)10-14-42(8,57-37-34(53)32(51)30(49)25(18-44)56-37)20-9-13-40(6)28(20)22(46)15-26-39(5)12-11-27(47)38(3,4)35(39)23(16-41(26,40)7)54-36-33(52)31(50)29(48)24(17-43)55-36/h20,22-37,43-44,46-53H,1,9-18H2,2-8H3/t20-,22+,23-,24+,25+,26+,27-,28-,29+,30+,31-,32-,33+,34+,35-,36+,37-,39+,40+,41+,42-/m0/s1
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View in JSmol
SynonymsNot Available
Chemical FormulaC42H70O15
Average Mass815.0070 Da
Monoisotopic Mass814.47147 Da
IUPAC Name(6S)-6-[(1R,2R,5S,7R,8S,10R,11R,14S,15R,16R)-5,16-dihydroxy-2,6,6,10,11-pentamethyl-8-{[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}tetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadecan-14-yl]-2-methyl-6-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}hept-1-en-3-one
Traditional Name(6S)-6-[(1R,2R,5S,7R,8S,10R,11R,14S,15R,16R)-5,16-dihydroxy-2,6,6,10,11-pentamethyl-8-{[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}tetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadecan-14-yl]-2-methyl-6-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}hept-1-en-3-one
CAS Registry NumberNot Available
SMILES
[H]OC([H])([H])[C@@]1([H])O[C@@]([H])(O[C@@]2([H])C([H])([H])[C@]3(C([H])([H])[H])[C@]([H])(C([H])([H])[C@@]([H])(O[H])[C@]4([H])[C@]([H])(C([H])([H])C([H])([H])[C@@]34C([H])([H])[H])[C@](O[C@]3([H])O[C@]([H])(C([H])([H])O[H])[C@@]([H])(O[H])[C@]([H])(O[H])[C@@]3([H])O[H])(C([H])([H])[H])C([H])([H])C([H])([H])C(=O)C(=C([H])[H])C([H])([H])[H])[C@@]3(C([H])([H])[H])C([H])([H])C([H])([H])[C@]([H])(O[H])C(C([H])([H])[H])(C([H])([H])[H])[C@]23[H])[C@]([H])(O[H])[C@@]([H])(O[H])[C@]1([H])O[H]
InChI Identifier
InChI=1S/C42H70O15/c1-19(2)21(45)10-14-42(8,57-37-34(53)32(51)30(49)25(18-44)56-37)20-9-13-40(6)28(20)22(46)15-26-39(5)12-11-27(47)38(3,4)35(39)23(16-41(26,40)7)54-36-33(52)31(50)29(48)24(17-43)55-36/h20,22-37,43-44,46-53H,1,9-18H2,2-8H3/t20-,22+,23-,24+,25+,26+,27-,28-,29+,30+,31-,32-,33+,34+,35-,36+,37-,39+,40+,41+,42-/m0/s1
InChI KeyKJZQRDAZSWKILI-OGGKGQCOSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
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, 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, 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, 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
Panax vietnamensisJEOL database
    • Tran, Q. L., et al, J. Nat. Prod. 64, 456 (2001)
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.
KingdomOrganic compounds  
Super ClassLipids and lipid-like molecules  
ClassPrenol lipids  
Sub ClassTerpene glycosides  
Direct ParentTriterpene saponins  
Alternative Parents
Substituents
  • Triterpene saponin
    • 

  • Triterpenoid
    • 

  • 24-oxosteroid
    • 

  • 3-hydroxysteroid
    • 

  • 12-hydroxysteroid
    • 

  • 14-alpha-methylsteroid
    • 

  • Hydroxysteroid
    • 

  • Oxosteroid
    • 

  • 3-beta-hydroxysteroid
    • 

  • Steroid
    • 

  • Fatty acyl glycoside
    • 

  • Fatty acyl glycoside of mono- or disaccharide
    • 

  • Alkyl glycoside
    • 

  • Glycosyl compound
    • 

  • O-glycosyl compound
    • 

  • Fatty acyl
    • 

  • Oxane
    • 

  • Alpha-branched alpha,beta-unsaturated-ketone
    • 

  • Monosaccharide
    • 

  • Cyclic alcohol
    • 

  • Acryloyl-group
    • 

  • Enone
    • 

  • Alpha,beta-unsaturated ketone
    • 

  • Ketone
    • 

  • Secondary alcohol
    • 

  • Polyol
    • 

  • Oxacycle
    • 

  • Organoheterocyclic compound
    • 

  • Acetal
    • 

  • Primary alcohol
    • 

  • Organic oxygen compound
    • 

  • Carbonyl group
    • 

  • Organic oxide
    • 

  • Alcohol
    • 

  • Hydrocarbon derivative
    • 

  • Organooxygen compound
    • 

  • Aliphatic heteropolycyclic compound
Molecular FrameworkAliphatic heteropolycyclic compounds
External DescriptorsNot Available
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP0.27ALOGPS
logP0.072ChemAxon
logS-3.4ALOGPS
pKa (Strongest Acidic)11.91ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count15ChemAxon
Hydrogen Donor Count10ChemAxon
Polar Surface Area256.29 ŲChemAxon
Rotatable Bond Count11ChemAxon
Refractivity203.28 m³·mol⁻¹ChemAxon
Polarizability88.44 ųChemAxon
Number of Rings6ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDC00046504  
Chemspider ID8804610  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound10629247  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. Tran, Q. L., et al. (2001). Tran, Q. L., et al, J. Nat. Prod. 64, 456 (2001). J. Nat. Prod..