NP-MRD: Showing NP-Card for RA VI (NP0071694)

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Record Information

Version

2.0

Created at

2022-04-28 17:02:20 UTC

Updated at

2022-04-28 17:02:20 UTC

NP-MRD ID

NP0071694

Secondary Accession Numbers

None

Natural Product Identification

Common Name

RA VI

Description

RA-III belongs to the class of organic compounds known as lignans, neolignans and related compounds. These are plant products of low molecular weight formed primarily from oxidative coupling of two p-propylphenol moieties. They can also be described as micromolecules with two phenylpropanoid units coupled together. They can be attached in various manners, like C5-C5', C8-C8'. Most known natural lignans are oxidized at C9 and C9´ and, based upon the way in which oxygen is incorporated into the skeleton and on the cyclization patterns, a wide range of lignans of very different structural types can be formed. RA VI is found in Rubia akane and Rubia cordifolia . RA VI was first documented in 2006 (PMID: 16827808). Based on a literature review a small amount of articles have been published on RA-III (PMID: 30334345) (PMID: 26913941).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282219022D          

 57 61  0  0  1  0            999 V2000
    2.4297    4.0182    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.2430    3.8438    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.8028    4.4550    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6075    4.2731    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5597    5.2493    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.1170    5.8652    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.8714    6.6558    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4326    7.2605    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0612    6.8427    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.8086    7.6329    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.0018    7.8140    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7472    8.5988    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4519    7.1902    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.6383    7.3679    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.2957    8.1531    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4438    8.5690    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6922    7.7830    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4839    7.5363    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1086    8.0393    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8594    8.8271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1096    9.1221    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6611    7.4003    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9324    6.4800    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5276    5.9070    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4095    5.0412    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6241    4.7902    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9816    5.2924    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1401    5.1234    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3219    5.3440    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0070    4.5684    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5243    3.9373    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8161    4.3791    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.0557    3.5856    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.8642    3.4113    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1113    2.6242    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4964    2.9791    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2696    5.9128    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0923    6.7317    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7074    6.9342    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0587    5.6722    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1866    6.1118    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3069    6.1777    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9310    5.6383    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7087    6.4062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3655    8.2415    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9227    5.6876    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4794    6.2964    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2304    7.0830    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7871    7.6918    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5928    7.5142    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8417    6.7276    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2850    6.1187    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1494    8.1230    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.9005    8.9096    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7545    5.4287    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4939    3.0579    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9387    2.4477    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  3  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  7  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 11 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  6  0  0  0
 15 16  1  0  0  0  0
 16 17  2  0  0  0  0
 17 18  1  0  0  0  0
 18 19  2  0  0  0  0
 19 20  1  0  0  0  0
 20 21  2  0  0  0  0
 16 21  1  0  0  0  0
 19 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  2  0  0  0  0
 24 25  1  0  0  0  0
 25 26  2  0  0  0  0
 26 27  1  0  0  0  0
 27 28  1  0  0  0  0
 28 29  1  0  0  0  0
 29 30  1  0  0  0  0
 30 31  2  0  0  0  0
 30 32  1  0  0  0  0
 32 33  1  0  0  0  0
 33 34  1  0  0  0  0
  1 34  1  0  0  0  0
 34 35  2  0  0  0  0
 33 36  1  1  0  0  0
 29 37  1  6  0  0  0
 37 38  1  0  0  0  0
 14 38  1  0  0  0  0
 38 39  2  0  0  0  0
 37 40  1  0  0  0  0
 27 41  2  0  0  0  0
 23 41  1  0  0  0  0
 24 42  1  0  0  0  0
 42 43  1  0  0  0  0
 13 44  1  0  0  0  0
 10 45  1  6  0  0  0
  6 46  1  6  0  0  0
 46 47  1  0  0  0  0
 47 48  2  0  0  0  0
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 47 52  1  0  0  0  0
 50 53  1  0  0  0  0
 53 54  1  0  0  0  0
  5 55  1  0  0  0  0
  2 56  1  6  0  0  0
 56 57  1  0  0  0  0
M  END

     RDKit          3D

107111  0  0  0  0  0  0  0  0999 V2000
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   -9.3030   -0.1740    3.0494 O   0  0  0  0  0  0  0  0  0  0  0  0
   -8.0792   -0.4769    2.4609 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -5.6295   -1.1019    1.1738 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3092   -1.4591    0.6307 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3608   -0.3662    0.3722 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.9593   -0.7493    0.2026 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2346   -0.6533    1.2677 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2701   -1.2062   -0.9417 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5150   -2.3497   -1.7464 C   0  0  1  0  0  0  0  0  0  0  0  0
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    3.9478   -3.6259   -0.9130 C   0  0  0  0  0  0  0  0  0  0  0  0
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    0.2755    3.2137   -1.1437 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.3922    4.0886   -1.6040 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5670    4.0420   -0.2118 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0880    4.9730    0.3910 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -2.6434    2.7143    0.4761 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.8822    3.1947    1.2416 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4555    3.9399    2.3097 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1467    1.9256   -0.6487 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -0.4191   -0.6329   -1.2890 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -2.3734   -2.3788   -3.7825 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6849   -2.6391   -4.9194 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2083   -0.9913   -4.3403 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3315   -2.3902   -4.3964 H   0  0  0  0  0  0  0  0  0  0  0  0
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    2.3831    3.8655   -1.2263 H   0  0  0  0  0  0  0  0  0  0  0  0
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    1.1408    5.1831   -1.4427 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5210    4.7708   -0.1103 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0722    2.1167    1.2153 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4388    2.3171    1.6136 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5692    3.7442    0.5625 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0053    4.7473    2.3858 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9671   -0.6311   -1.8289 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5162    0.9163   -2.5310 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7200    0.9715   -1.2493 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6089    1.4165   -2.9514 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1811    2.1490   -2.6612 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0192    0.7581   -3.8353 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8344   -1.2608   -0.5813 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.9440   -0.6940    0.5492 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  1  0
  8 50  1  0
 50 51  1  0
 50 48  1  0
 48 49  2  0
 48 45  1  0
 45 46  1  0
 46 47  1  0
 45 44  1  0
 44 42  1  0
 42 43  2  0
 42 40  1  0
 40 41  1  0
 40 39  1  0
 39 37  1  0
 37 38  2  0
 37 36  1  0
 36 35  1  0
 35 29  1  0
 29 28  2  0
 28 27  1  0
 27 26  1  0
 26 23  1  0
 23 22  2  0
 22 21  1  0
 21 20  2  0
 20 19  1  0
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 18 16  1  0
 16 17  1  0
 16 14  1  0
 14 15  2  0
 14 12  1  0
 12 13  1  0
 12 11  1  0
 11  9  1  0
  9 10  2  0
 18 54  1  0
 54 55  2  0
 54 52  1  0
 52 53  1  0
 20 25  1  0
 25 24  2  0
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 32 31  1  0
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  6 56  1  0
 56 57  2  0
 57  3  1  0
  9  8  1  0
 52 36  1  0
 30 29  1  0
 24 23  1  0
  1 58  1  0
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  1 60  1  0
  4 61  1  0
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  7 64  1  0
  8 65  1  1
 51100  1  0
 51101  1  0
 51102  1  0
 45 96  1  1
 46 97  1  0
 46 98  1  0
 47 99  1  0
 44 95  1  0
 40 91  1  6
 41 92  1  0
 41 93  1  0
 41 94  1  0
 39 90  1  0
 36 89  1  1
 35 87  1  0
 35 88  1  0
 28 81  1  0
 22 78  1  0
 21 77  1  0
 19 75  1  0
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 18 74  1  1
 17 71  1  0
 17 72  1  0
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 13 70  1  0
 11 66  1  0
 53103  1  0
 53104  1  0
 53105  1  0
 25 80  1  0
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 34 84  1  0
 34 85  1  0
 34 86  1  0
 31 83  1  0
 30 82  1  0
 56106  1  0
 57107  1  0
M  END


  Mrv1652304282219022D          

 57 61  0  0  1  0            999 V2000
    2.4297    4.0182    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.2430    3.8438    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.8028    4.4550    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6075    4.2731    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5597    5.2493    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.1170    5.8652    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.8714    6.6558    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4326    7.2605    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0612    6.8427    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.8086    7.6329    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.0018    7.8140    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7472    8.5988    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4519    7.1902    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.6383    7.3679    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.2957    8.1531    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4438    8.5690    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6922    7.7830    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4839    7.5363    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1086    8.0393    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8594    8.8271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1096    9.1221    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6611    7.4003    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9324    6.4800    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5276    5.9070    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4095    5.0412    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6241    4.7902    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9816    5.2924    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1401    5.1234    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3219    5.3440    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0070    4.5684    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5243    3.9373    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8161    4.3791    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.0557    3.5856    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.8642    3.4113    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1113    2.6242    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4964    2.9791    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2696    5.9128    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0923    6.7317    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7074    6.9342    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0587    5.6722    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1866    6.1118    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3069    6.1777    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9310    5.6383    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7087    6.4062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3655    8.2415    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9227    5.6876    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4794    6.2964    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2304    7.0830    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7871    7.6918    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5928    7.5142    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8417    6.7276    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2850    6.1187    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1494    8.1230    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.9005    8.9096    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7545    5.4287    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4939    3.0579    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9387    2.4477    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  3  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  7  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 11 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  6  0  0  0
 15 16  1  0  0  0  0
 16 17  2  0  0  0  0
 17 18  1  0  0  0  0
 18 19  2  0  0  0  0
 19 20  1  0  0  0  0
 20 21  2  0  0  0  0
 16 21  1  0  0  0  0
 19 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  2  0  0  0  0
 24 25  1  0  0  0  0
 25 26  2  0  0  0  0
 26 27  1  0  0  0  0
 27 28  1  0  0  0  0
 28 29  1  0  0  0  0
 29 30  1  0  0  0  0
 30 31  2  0  0  0  0
 30 32  1  0  0  0  0
 32 33  1  0  0  0  0
 33 34  1  0  0  0  0
  1 34  1  0  0  0  0
 34 35  2  0  0  0  0
 33 36  1  1  0  0  0
 29 37  1  6  0  0  0
 37 38  1  0  0  0  0
 14 38  1  0  0  0  0
 38 39  2  0  0  0  0
 37 40  1  0  0  0  0
 27 41  2  0  0  0  0
 23 41  1  0  0  0  0
 24 42  1  0  0  0  0
 42 43  1  0  0  0  0
 13 44  1  0  0  0  0
 10 45  1  6  0  0  0
  6 46  1  6  0  0  0
 46 47  1  0  0  0  0
 47 48  2  0  0  0  0
 48 49  1  0  0  0  0
 49 50  2  0  0  0  0
 50 51  1  0  0  0  0
 51 52  2  0  0  0  0
 47 52  1  0  0  0  0
 50 53  1  0  0  0  0
 53 54  1  0  0  0  0
  5 55  1  0  0  0  0
  2 56  1  6  0  0  0
 56 57  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0071694

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC1=CC=C(C[C@@H]2N(C)C(=O)[C@H](CO)NC(=O)[C@@H](C)NC(=O)[C@@H]3CC4=CC(OC5=CC=C(C[C@H](N(C)C(=O)[C@H](C)NC2=O)C(=O)N3C)C=C5)=C(OC)C=C4)C=C1

> <INCHI_IDENTIFIER>
InChI=1S/C41H50N6O10/c1-23-36(49)44-30(22-48)40(53)45(3)31(18-25-8-13-28(55-6)14-9-25)38(51)43-24(2)39(52)47(5)33-19-26-10-15-29(16-11-26)57-35-21-27(12-17-34(35)56-7)20-32(37(50)42-23)46(4)41(33)54/h8-17,21,23-24,30-33,48H,18-20,22H2,1-7H3,(H,42,50)(H,43,51)(H,44,49)/t23-,24+,30+,31+,32+,33+/m1/s1

> <INCHI_KEY>
WASXNYRXXQONPG-YQPHQQCRSA-N

> <FORMULA>
C41H50N6O10

> <MOLECULAR_WEIGHT>
786.883

> <EXACT_MASS>
786.358841834

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
107

> <JCHEM_AVERAGE_POLARIZABILITY>
79.01494038629659

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1S,4R,7S,10S,13S,16S)-7-(hydroxymethyl)-24-methoxy-10-[(4-methoxyphenyl)methyl]-4,9,13,15,29-pentamethyl-22-oxa-3,6,9,12,15,29-hexaazatetracyclo[14.12.2.2^{18,21}.1^{23,27}]tritriaconta-18,20,23,25,27(31),32-hexaene-2,5,8,11,14,30-hexone

> <ALOGPS_LOGP>
2.57

> <JCHEM_LOGP>
0.5856821850000008

> <ALOGPS_LOGS>
-4.65

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
10.995512168471505

> <JCHEM_PKA_STRONGEST_ACIDIC>
10.306822139520436

> <JCHEM_PKA_STRONGEST_BASIC>
-2.8445806715247848

> <JCHEM_POLAR_SURFACE_AREA>
196.14999999999998

> <JCHEM_REFRACTIVITY>
206.9843999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.75e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1S,4R,7S,10S,13S,16S)-7-(hydroxymethyl)-24-methoxy-10-[(4-methoxyphenyl)methyl]-4,9,13,15,29-pentamethyl-22-oxa-3,6,9,12,15,29-hexaazatetracyclo[14.12.2.2^{18,21}.1^{23,27}]tritriaconta-18,20,23,25,27(31),32-hexaene-2,5,8,11,14,30-hexone

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 28-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   28-APR-22         0                                  
HETATM    1  N   UNK     0       4.535   7.501   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0       6.054   7.175   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       7.099   8.316   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       8.601   7.976   0.000  0.00  0.00           O+0
HETATM    5  N   UNK     0       6.645   9.799   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0       7.685  10.948   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       7.227  12.424   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       8.274  13.553   0.000  0.00  0.00           O+0
HETATM    9  N   UNK     0       5.714  12.773   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0       5.243  14.248   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       3.737  14.586   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       3.261  16.051   0.000  0.00  0.00           O+0
HETATM   13  N   UNK     0       2.710  13.422   0.000  0.00  0.00           N+0
HETATM   14  C   UNK     0       1.191  13.754   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       0.552  15.219   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -0.828  15.995   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -1.292  14.528   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -2.770  14.068   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -3.936  15.007   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -3.471  16.477   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      -2.071  17.028   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0      -4.967  13.814   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0      -5.474  12.096   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      -6.585  11.026   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      -6.364   9.410   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      -4.898   8.942   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      -3.699   9.879   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      -2.128   9.564   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      -0.601   9.975   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       0.013   8.528   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0      -0.979   7.350   0.000  0.00  0.00           O+0
HETATM   32  N   UNK     0       1.523   8.174   0.000  0.00  0.00           N+0
HETATM   33  C   UNK     0       1.971   6.693   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       3.480   6.368   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0       3.941   4.898   0.000  0.00  0.00           O+0
HETATM   36  C   UNK     0       0.927   5.561   0.000  0.00  0.00           C+0
HETATM   37  N   UNK     0       0.503  11.037   0.000  0.00  0.00           N+0
HETATM   38  C   UNK     0       0.172  12.566   0.000  0.00  0.00           C+0
HETATM   39  O   UNK     0      -1.321  12.944   0.000  0.00  0.00           O+0
HETATM   40  C   UNK     0       1.976  10.588   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0      -4.082  11.409   0.000  0.00  0.00           C+0
HETATM   42  O   UNK     0      -8.039  11.532   0.000  0.00  0.00           O+0
HETATM   43  C   UNK     0      -9.205  10.525   0.000  0.00  0.00           C+0
HETATM   44  C   UNK     0       3.190  11.958   0.000  0.00  0.00           C+0
HETATM   45  C   UNK     0       6.282  15.384   0.000  0.00  0.00           C+0
HETATM   46  C   UNK     0       9.189  10.617   0.000  0.00  0.00           C+0
HETATM   47  C   UNK     0      10.228  11.753   0.000  0.00  0.00           C+0
HETATM   48  C   UNK     0       9.763  13.222   0.000  0.00  0.00           C+0
HETATM   49  C   UNK     0      10.803  14.358   0.000  0.00  0.00           C+0
HETATM   50  C   UNK     0      12.306  14.026   0.000  0.00  0.00           C+0
HETATM   51  C   UNK     0      12.771  12.558   0.000  0.00  0.00           C+0
HETATM   52  C   UNK     0      11.732  11.422   0.000  0.00  0.00           C+0
HETATM   53  O   UNK     0      13.346  15.163   0.000  0.00  0.00           O+0
HETATM   54  C   UNK     0      12.881  16.631   0.000  0.00  0.00           C+0
HETATM   55  C   UNK     0       5.142  10.134   0.000  0.00  0.00           C+0
HETATM   56  C   UNK     0       6.522   5.708   0.000  0.00  0.00           C+0
HETATM   57  O   UNK     0       5.486   4.569   0.000  0.00  0.00           O+0
CONECT    1    2   34                                                       
CONECT    2    1    3   56                                                  
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6   55                                                  
CONECT    6    5    7   46                                                  
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10                                                       
CONECT   10    9   11   45                                                  
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11   14   44                                                  
CONECT   14   13   15   38                                                  
CONECT   15   14   16                                                       
CONECT   16   15   17   21                                                  
CONECT   17   16   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20   22                                                  
CONECT   20   19   21                                                       
CONECT   21   20   16                                                       
CONECT   22   19   23                                                       
CONECT   23   22   24   41                                                  
CONECT   24   23   25   42                                                  
CONECT   25   24   26                                                       
CONECT   26   25   27                                                       
CONECT   27   26   28   41                                                  
CONECT   28   27   29                                                       
CONECT   29   28   30   37                                                  
CONECT   30   29   31   32                                                  
CONECT   31   30                                                            
CONECT   32   30   33                                                       
CONECT   33   32   34   36                                                  
CONECT   34   33    1   35                                                  
CONECT   35   34                                                            
CONECT   36   33                                                            
CONECT   37   29   38   40                                                  
CONECT   38   37   14   39                                                  
CONECT   39   38                                                            
CONECT   40   37                                                            
CONECT   41   27   23                                                       
CONECT   42   24   43                                                       
CONECT   43   42                                                            
CONECT   44   13                                                            
CONECT   45   10                                                            
CONECT   46    6   47                                                       
CONECT   47   46   48   52                                                  
CONECT   48   47   49                                                       
CONECT   49   48   50                                                       
CONECT   50   49   51   53                                                  
CONECT   51   50   52                                                       
CONECT   52   51   47                                                       
CONECT   53   50   54                                                       
CONECT   54   53                                                            
CONECT   55    5                                                            
CONECT   56    2   57                                                       
CONECT   57   56                                                            
MASTER        0    0    0    0    0    0    0    0   57    0  122    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₄₁H₅₀N₆O₁₀

Average Mass

786.8830 Da

Monoisotopic Mass

786.35884 Da

IUPAC Name

(1S,4R,7S,10S,13S,16S)-7-(hydroxymethyl)-24-methoxy-10-[(4-methoxyphenyl)methyl]-4,9,13,15,29-pentamethyl-22-oxa-3,6,9,12,15,29-hexaazatetracyclo[14.12.2.2^{18,21}.1^{23,27}]tritriaconta-18,20,23,25,27(31),32-hexaene-2,5,8,11,14,30-hexone

Traditional Name

CAS Registry Number

Not Available

SMILES

COC1=CC=C(C[C@@H]2N(C)C(=O)[C@H](CO)NC(=O)[C@@H](C)NC(=O)[C@@H]3CC4=CC(OC5=CC=C(C[C@H](N(C)C(=O)[C@H](C)NC2=O)C(=O)N3C)C=C5)=C(OC)C=C4)C=C1

InChI Identifier

InChI=1S/C41H50N6O10/c1-23-36(49)44-30(22-48)40(53)45(3)31(18-25-8-13-28(55-6)14-9-25)38(51)43-24(2)39(52)47(5)33-19-26-10-15-29(16-11-26)57-35-21-27(12-17-34(35)56-7)20-32(37(50)42-23)46(4)41(33)54/h8-17,21,23-24,30-33,48H,18-20,22H2,1-7H3,(H,42,50)(H,43,51)(H,44,49)/t23-,24+,30+,31+,32+,33+/m1/s1

InChI Key

WASXNYRXXQONPG-YQPHQQCRSA-N

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Rubia akane	Plant	KNApSAcK
Rubia cordifolia	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as lignans, neolignans and related compounds. These are plant products of low molecular weight formed primarily from oxidative coupling of two p-propylphenol moieties. They can also be described as micromolecules with two phenylpropanoid units coupled together. They can be attached in various manners, like C5-C5', C8-C8'. Most known natural lignans are oxidized at C9 and C9´ and, based upon the way in which oxygen is incorporated into the skeleton and on the cyclization patterns, a wide range of lignans of very different structural types can be formed.

Kingdom

Organic compounds

Super Class

Lignans, neolignans and related compounds

Class

Not Available

Sub Class

Not Available

Direct Parent

Lignans, neolignans and related compounds

Alternative Parents

Substituents

Oxyneolignan skeleton
Macrolactam
Diaryl ether
Alpha-amino acid or derivatives
Phenoxy compound
Anisole
Methoxybenzene
Phenol ether
Alkyl aryl ether
Monocyclic benzene moiety
Benzenoid
Tertiary carboxylic acid amide
Carboxamide group
Lactam
Secondary carboxylic acid amide
Organoheterocyclic compound
Azacycle
Ether
Oxacycle
Carboxylic acid derivative
Organonitrogen compound
Organic nitrogen compound
Alcohol
Carbonyl group
Hydrocarbon derivative
Organic oxide
Organooxygen compound
Organic oxygen compound
Primary alcohol
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	2.57	ALOGPS
logP	0.59	ChemAxon
logS	-4.6	ALOGPS
pKa (Strongest Acidic)	10.31	ChemAxon
pKa (Strongest Basic)	-2.8	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	196.15 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	206.98 m³·mol⁻¹	ChemAxon
Polarizability	79.01 Å³	ChemAxon
Number of Rings	5	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

10270338

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

14390141

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Hu YY, Feng L, Wang J, Zhang XJ, Wang Z, Tan NH: Rubipodanin B, a New Cytotoxic Cyclopeptide from Rubia podantha. Chem Biodivers. 2019 Jan;16(1):e1800438. doi: 10.1002/cbdv.201800438. Epub 2018 Dec 13. [PubMed:30334345 ]
Figueiredo PO, Matos Mde F, Perdomo RT, Kato WH Jr, Barros MV, Garcez FR, Garcez WS: Rubiaceae-Type Cyclopeptides from Galianthe thalictroides. J Nat Prod. 2016 Apr 22;79(4):1165-9. doi: 10.1021/acs.jnatprod.5b00849. Epub 2016 Feb 25. [PubMed:26913941 ]
Koizumi T, Abe M, Yamakuni T, Ohizumi Y, Hitotsuyanagi Y, Takeya K, Sato Y: Metronomic scheduling of a cyclic hexapeptide Ra-VII for anti-angiogenesis, tumor vessel maturation and anti-tumor activity. Cancer Sci. 2006 Jul;97(7):665-74. doi: 10.1111/j.1349-7006.2006.00229.x. [PubMed:16827808 ]

Showing NP-Card for RA VI (NP0071694)

MOL for NP0071694 (RA VI)

3D MOL for NP0071694 (RA VI)

3D SDF for NP0071694 (RA VI)

3D-SDF for NP0071694 (RA VI)

PDB for NP0071694 (RA VI)

3D PDB for NP0071694 (RA VI)

SMILES for NP0071694 (RA VI)

INCHI for NP0071694 (RA VI)

Structure for NP0071694 (RA VI)

3D Structure for NP0071694 (RA VI)