NP-MRD: Showing NP-Card for (2r,3s,4s,5r,6s)-2-(hydroxymethyl)-6-[(2-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]sulfanyl}-1h-indol-3-yl)oxy]oxane-3,4,5-triol (NP0275041)

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Record Information

Version

2.0

Created at

2022-09-08 22:39:22 UTC

Updated at

2022-09-08 22:39:22 UTC

NP-MRD ID

NP0275041

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(2r,3s,4s,5r,6s)-2-(hydroxymethyl)-6-[(2-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]sulfanyl}-1h-indol-3-yl)oxy]oxane-3,4,5-triol

Description

Calanthoside belongs to the class of organic compounds known as thioglycosides. These are glycoside in which a sugar group is bonded through one carbon to another group via a S-glycosidic bond. (2r,3s,4s,5r,6s)-2-(hydroxymethyl)-6-[(2-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]sulfanyl}-1h-indol-3-yl)oxy]oxane-3,4,5-triol is found in Calanthe discolor. It was first documented in 2021 (PMID: 33952856). Based on a literature review very few articles have been published on Calanthoside (PMID: 34774685).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309092200392D          

 33 36  0  0  1  0            999 V2000
    4.1538   -3.6462    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6018   -3.0331    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7948   -3.2047    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.2428   -2.5916    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4358   -2.7631    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.8838   -2.1500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387   -1.3654    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6538   -0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1712   -0.6979    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5837    0.0165    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.4087    0.0165    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8212    0.7310    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.6462    0.7310    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0587    0.0165    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4087    1.4455    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.8212    2.1599    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5837    1.4455    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.1712    2.1599    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1712    0.7310    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.6538    0.7310    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387   -0.0305    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    0.1271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378   -1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1809   -3.5477    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.3739   -3.7192    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7329   -4.1608    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.4780   -4.9454    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5399   -3.9893    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.0919   -4.6024    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  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  6  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
 10  9  1  6  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  6  0  0  0
 13 14  1  0  0  0  0
 12 15  1  0  0  0  0
 15 16  1  1  0  0  0
 15 17  1  0  0  0  0
 17 18  1  6  0  0  0
 17 19  1  0  0  0  0
 10 19  1  0  0  0  0
 19 20  1  1  0  0  0
  8 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  2  0  0  0  0
 23 24  1  0  0  0  0
 24 25  2  0  0  0  0
 25 26  1  0  0  0  0
 26 27  2  0  0  0  0
  7 27  1  0  0  0  0
 22 27  1  0  0  0  0
  5 28  1  0  0  0  0
 28 29  1  1  0  0  0
 28 30  1  0  0  0  0
 30 31  1  6  0  0  0
 30 32  1  0  0  0  0
  3 32  1  0  0  0  0
 32 33  1  1  0  0  0
M  END

     RDKit          3D

 60 63  0  0  0  0  0  0  0  0999 V2000
   -6.2639   -0.8333   -0.1040 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3556   -0.9644   -1.1670 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0005   -1.2332   -0.5518 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.6680   -0.1395    0.2784 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2639   -0.2080    0.4263 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.7559    0.9077    1.0853 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8986    1.7677    0.4624 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4653    1.6717    0.4532 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4787    0.4051    1.2509 S   0  0  0  0  0  0  0  0  0  0  0  0
    3.2519    0.7598    0.9318 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.5755    0.6324   -0.3823 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1392   -0.5257   -0.8055 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.1200   -1.6229   -1.1048 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8724   -2.7332   -1.5234 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.2277   -1.0787    0.0597 C   0  0  1  0  0  0  0  0  0  0  0  0
    6.2486   -0.1199    0.1325 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6763   -1.2545    1.4503 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.8140   -2.3178    1.5739 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1318    0.0526    1.9074 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.2252    0.8857    2.2329 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9151    2.7153   -0.2706 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1112    3.4549   -0.7112 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2112    4.6074   -1.4787 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4185    5.1907   -1.8049 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5900    4.6111   -1.3531 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5088    3.4673   -0.5904 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3012    2.8896   -0.2681 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9764   -1.5028    1.1514 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.1922   -2.3510    0.3614 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2442   -2.2346    1.5486 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.9270   -1.5658    2.5512 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1220   -2.4768    0.3248 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.7045   -3.5956   -0.3739 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0608   -0.2972   -0.3626 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6313   -1.8151   -1.8230 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3714   -0.0236   -1.7408 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2210   -1.3764   -1.3218 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8682   -0.2432   -0.6068 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3477    1.8630    1.1760 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6177   -0.3131   -1.8095 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5141   -1.3249   -1.9970 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4590   -1.8347   -0.2668 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3858   -3.5790   -1.4336 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5971   -2.0085   -0.3888 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.0998   -0.5112    0.4700 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5628   -1.4905    2.1098 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8384   -2.6584    2.4918 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5845   -0.0978    2.8589 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3564    1.5540    1.5059 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9223    2.9596   -0.4884 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7063    5.0854   -1.8488 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4535    6.1049   -2.4161 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5181    5.0933   -1.6268 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4138    3.0051   -0.2321 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3982   -1.2974    2.0648 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4912   -2.8194    0.9050 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9479   -3.2290    1.9332 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7194   -1.0714    2.1724 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1578   -2.6198    0.6933 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3676   -4.3162    0.2330 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
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  8 21  1  0
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 22 23  2  0
 23 24  1  0
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  8  9  1  0
  9 10  1  0
 10 11  1  0
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 12 13  1  0
 13 14  1  0
 12 15  1  0
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 17 18  1  0
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 30 31  1  0
 30 32  1  0
 32 33  1  0
 32  3  1  0
 27  7  1  0
 19 10  1  0
 27 22  1  0
  1 34  1  0
  2 35  1  0
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  3 37  1  6
  5 38  1  6
 21 50  1  0
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 26 54  1  0
 10 39  1  1
 12 40  1  6
 13 41  1  0
 13 42  1  0
 14 43  1  0
 15 44  1  6
 16 45  1  0
 17 46  1  1
 18 47  1  0
 19 48  1  1
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 28 55  1  1
 29 56  1  0
 30 57  1  1
 31 58  1  0
 32 59  1  1
 33 60  1  0
M  END


  Mrv1652309092200392D          

 33 36  0  0  1  0            999 V2000
    4.1538   -3.6462    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6018   -3.0331    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7948   -3.2047    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.2428   -2.5916    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4358   -2.7631    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.8838   -2.1500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387   -1.3654    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6538   -0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1712   -0.6979    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5837    0.0165    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.4087    0.0165    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8212    0.7310    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.6462    0.7310    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0587    0.0165    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -1.8212    2.1599    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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    1.1387   -0.0305    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    0.1271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378   -1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1809   -3.5477    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.3739   -3.7192    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7329   -4.1608    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.4780   -4.9454    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5399   -3.9893    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.0919   -4.6024    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  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  6  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
 10  9  1  6  0  0  0
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 13 14  1  0  0  0  0
 12 15  1  0  0  0  0
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 17 19  1  0  0  0  0
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  3 32  1  0  0  0  0
 32 33  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0275041

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC[C@H]1O[C@@H](OC2=C(NC3=CC=CC=C23)S[C@@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2O)[C@H](O)[C@@H](O)[C@@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C20H27NO11S/c22-5-9-11(24)13(26)15(28)19(30-9)32-17-7-3-1-2-4-8(7)21-18(17)33-20-16(29)14(27)12(25)10(6-23)31-20/h1-4,9-16,19-29H,5-6H2/t9-,10-,11-,12-,13+,14+,15-,16-,19+,20+/m1/s1

> <INCHI_KEY>
RPMOMKUYGKLDSQ-SHJINENGSA-N

> <FORMULA>
C20H27NO11S

> <MOLECULAR_WEIGHT>
489.49

> <EXACT_MASS>
489.130481867

> <JCHEM_ACCEPTOR_COUNT>
11

> <JCHEM_ATOM_COUNT>
60

> <JCHEM_AVERAGE_POLARIZABILITY>
47.382289077494235

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
9

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3S,4S,5R,6S)-2-(hydroxymethyl)-6-[(2-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]sulfanyl}-1H-indol-3-yl)oxy]oxane-3,4,5-triol

> <JCHEM_LOGP>
-2.5841184643333337

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.521196151130386

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.995974383387422

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9810923566020735

> <JCHEM_POLAR_SURFACE_AREA>
205.31999999999996

> <JCHEM_REFRACTIVITY>
111.18510000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(2R,3S,4S,5R,6S)-2-(hydroxymethyl)-6-[(2-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]sulfanyl}-1H-indol-3-yl)oxy]oxane-3,4,5-triol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 09-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   09-SEP-22         0                                  
HETATM    1  O   UNK     0       7.754  -6.806   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       6.723  -5.662   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.217  -5.982   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       4.187  -4.838   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       2.680  -5.158   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       1.650  -4.013   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       2.126  -2.549   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.220  -1.303   0.000  0.00  0.00           C+0
HETATM    9  S   UNK     0      -0.320  -1.303   0.000  0.00  0.00           S+0
HETATM   10  C   UNK     0      -1.090   0.031   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      -2.630   0.031   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0      -3.400   1.365   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -4.940   1.365   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      -5.710   0.031   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0      -2.630   2.698   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0      -3.400   4.032   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0      -1.090   2.698   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      -0.320   4.032   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0      -0.320   1.365   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0       1.220   1.365   0.000  0.00  0.00           O+0
HETATM   21  N   UNK     0       2.126  -0.057   0.000  0.00  0.00           N+0
HETATM   22  C   UNK     0       3.590  -0.533   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       4.924   0.237   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       6.258  -0.533   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       6.258  -2.073   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       4.924  -2.843   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       3.590  -2.073   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       2.204  -6.622   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0       0.698  -6.943   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0       3.235  -7.767   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0       2.759  -9.231   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0       4.741  -7.447   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0       5.772  -8.591   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   32                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6   28                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8   27                                                  
CONECT    8    7    9   21                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11   19                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13   15                                                  
CONECT   13   12   14                                                       
CONECT   14   13                                                            
CONECT   15   12   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17   10   20                                                  
CONECT   20   19                                                            
CONECT   21    8   22                                                       
CONECT   22   21   23   27                                                  
CONECT   23   22   24                                                       
CONECT   24   23   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   27                                                       
CONECT   27   26    7   22                                                  
CONECT   28    5   29   30                                                  
CONECT   29   28                                                            
CONECT   30   28   31   32                                                  
CONECT   31   30                                                            
CONECT   32   30    3   33                                                  
CONECT   33   32                                                            
MASTER        0    0    0    0    0    0    0    0   33    0   72    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₀H₂₇NO₁₁S

Average Mass

489.4900 Da

Monoisotopic Mass

489.13048 Da

IUPAC Name

(2R,3S,4S,5R,6S)-2-(hydroxymethyl)-6-[(2-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]sulfanyl}-1H-indol-3-yl)oxy]oxane-3,4,5-triol

Traditional Name

(2R,3S,4S,5R,6S)-2-(hydroxymethyl)-6-[(2-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]sulfanyl}-1H-indol-3-yl)oxy]oxane-3,4,5-triol

CAS Registry Number

Not Available

SMILES

OC[C@H]1O[C@@H](OC2=C(NC3=CC=CC=C23)S[C@@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2O)[C@H](O)[C@@H](O)[C@@H]1O

InChI Identifier

InChI=1S/C20H27NO11S/c22-5-9-11(24)13(26)15(28)19(30-9)32-17-7-3-1-2-4-8(7)21-18(17)33-20-16(29)14(27)12(25)10(6-23)31-20/h1-4,9-16,19-29H,5-6H2/t9-,10-,11-,12-,13+,14+,15-,16-,19+,20+/m1/s1

InChI Key

RPMOMKUYGKLDSQ-SHJINENGSA-N

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Calanthe discolor	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as thioglycosides. These are glycoside in which a sugar group is bonded through one carbon to another group via a S-glycosidic bond.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Thioglycosides

Alternative Parents

Substituents

O-glycosyl compound
S-glycosyl compound
Indole
Indole or derivatives
Aryl thioether
Monosaccharide
Oxane
Substituted pyrrole
Benzenoid
Monothioacetal
Heteroaromatic compound
Pyrrole
Secondary alcohol
Polyol
Oxacycle
Acetal
Azacycle
Organoheterocyclic compound
Sulfenyl compound
Primary alcohol
Organosulfur compound
Organonitrogen compound
Alcohol
Hydrocarbon derivative
Organopnictogen compound
Organic nitrogen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic 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	-2.6	ChemAxon
pKa (Strongest Acidic)	12	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	11	ChemAxon
Hydrogen Donor Count	9	ChemAxon
Polar Surface Area	205.32 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	111.19 m³·mol⁻¹	ChemAxon
Polarizability	47.38 Å³	ChemAxon
Number of Rings	4	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

C00026980

Chemspider ID

8024093

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

9848380

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Morikawa T, Manse Y, Luo F, Fukui H, Inoue Y, Kaieda T, Ninomiya K, Muraoka O, Yoshikawa M: Indole Glycosides from Calanthe discolor with Proliferative Activity on Human Hair Follicle Dermal Papilla Cells. Chem Pharm Bull (Tokyo). 2021;69(5):464-471. doi: 10.1248/cpb.c21-00006. [PubMed:33952856 ]
Nanjala C, Ren J, Mutie FM, Waswa EN, Mutinda ES, Odago WO, Mutungi MM, Hu GW: Ethnobotany, phytochemistry, pharmacology, and conservation of the genus Calanthe R. Br. (Orchidaceae). J Ethnopharmacol. 2022 Mar 1;285:114822. doi: 10.1016/j.jep.2021.114822. Epub 2021 Nov 11. [PubMed:34774685 ]
LOTUS database [Link]

Showing NP-Card for (2r,3s,4s,5r,6s)-2-(hydroxymethyl)-6-[(2-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]sulfanyl}-1h-indol-3-yl)oxy]oxane-3,4,5-triol (NP0275041)

MOL for NP0275041 ((2r,3s,4s,5r,6s)-2-(hydroxymethyl)-6-[(2-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]sulfanyl}-1h-indol-3-yl)oxy]oxane-3,4,5-triol)

3D MOL for NP0275041 ((2r,3s,4s,5r,6s)-2-(hydroxymethyl)-6-[(2-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]sulfanyl}-1h-indol-3-yl)oxy]oxane-3,4,5-triol)

3D SDF for NP0275041 ((2r,3s,4s,5r,6s)-2-(hydroxymethyl)-6-[(2-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]sulfanyl}-1h-indol-3-yl)oxy]oxane-3,4,5-triol)

3D-SDF for NP0275041 ((2r,3s,4s,5r,6s)-2-(hydroxymethyl)-6-[(2-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]sulfanyl}-1h-indol-3-yl)oxy]oxane-3,4,5-triol)

PDB for NP0275041 ((2r,3s,4s,5r,6s)-2-(hydroxymethyl)-6-[(2-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]sulfanyl}-1h-indol-3-yl)oxy]oxane-3,4,5-triol)

3D PDB for NP0275041 ((2r,3s,4s,5r,6s)-2-(hydroxymethyl)-6-[(2-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]sulfanyl}-1h-indol-3-yl)oxy]oxane-3,4,5-triol)

SMILES for NP0275041 ((2r,3s,4s,5r,6s)-2-(hydroxymethyl)-6-[(2-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]sulfanyl}-1h-indol-3-yl)oxy]oxane-3,4,5-triol)

INCHI for NP0275041 ((2r,3s,4s,5r,6s)-2-(hydroxymethyl)-6-[(2-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]sulfanyl}-1h-indol-3-yl)oxy]oxane-3,4,5-triol)

Structure for NP0275041 ((2r,3s,4s,5r,6s)-2-(hydroxymethyl)-6-[(2-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]sulfanyl}-1h-indol-3-yl)oxy]oxane-3,4,5-triol)

3D Structure for NP0275041 ((2r,3s,4s,5r,6s)-2-(hydroxymethyl)-6-[(2-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]sulfanyl}-1h-indol-3-yl)oxy]oxane-3,4,5-triol)