NP-MRD: Showing NP-Card for Ravidomycin (NP0024687)

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Record Information

Version

2.0

Created at

2021-06-19 17:00:05 UTC

Updated at

2021-06-29 23:49:10 UTC

NP-MRD ID

NP0024687

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Ravidomycin

Provided By

JEOL Database JEOL Logo

Description

Ravidomycin is found in Streptomyces ravidus and Streptomyces rochei. Ravidomycin was first documented in 1998 (Yamashita, N. et al.). Based on a literature review very few articles have been published on (2S,3S,4S,5S,6R)-4-(dimethylamino)-6-{5-ethenyl-15-hydroxy-3,17-dimethoxy-8-oxo-9-oxatetracyclo[8.8.0.0²,⁷.0¹¹,¹⁶]Octadeca-1(10),2(7),3,5,11,13,15,17-octaen-12-yl}-5-hydroxy-2-methyloxan-3-yl acetate.

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652306192119003D          

 74 78  0  0  0  0            999 V2000
    5.9385    2.1191   -0.0117 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7264    0.8164    0.2155 C   0  0  0  0  0  0  0  0  0  0  0  0
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    2.4088   -2.9400   -1.5874 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END

     RDKit          3D

 74 78  0  0  0  0  0  0  0  0999 V2000
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    5.7264    0.8164    0.2155 C   0  0  0  0  0  0  0  0  0  0  0  0
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 10  9  2  0
 18 19  1  0
 35 30  1  0
 21 22  1  0
 36 37  1  0
 14 15  1  0
 31 32  1  0
 15  8  1  0
 32 33  1  0
 26 25  1  0
 32 34  2  0
  9 11  1  0
 36 38  1  0
 30 31  1  0
 35 36  1  0
 39 40  1  0
 30 62  1  1
 26 57  1  1
 35 66  1  1
 28 58  1  1
 29 59  1  0
 29 60  1  0
 29 61  1  0
 40 74  1  0
 39 73  1  6
  4 45  1  0
 10 49  1  0
 16 50  1  0
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 19 51  1  0
 19 52  1  0
 19 53  1  0
 22 54  1  0
 37 67  1  0
 37 68  1  0
 37 69  1  0
 33 63  1  0
 33 64  1  0
 33 65  1  0
 38 70  1  0
 38 71  1  0
 38 72  1  0
M  END


  Mrv1652306192119003D          

 74 78  0  0  0  0            999 V2000
    5.9385    2.1191   -0.0117 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7264    0.8164    0.2155 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4114    0.2119    0.4612 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1824   -1.1012    0.0584 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9422   -1.7215    0.2887 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8132   -2.9942   -0.2154 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4088   -2.9400   -1.5874 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9037   -1.0898    1.0070 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1440    0.2467    1.3625 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3780    0.8830    1.1115 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0847    1.0665    1.9815 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2668    2.2250    2.3349 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1517    0.4627    2.0900 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4473   -0.9044    1.8349 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6087   -1.7071    1.3770 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3568   -3.0764    1.3437 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8992   -3.6068    1.6619 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1594   -4.9636    1.6216 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1131   -5.8454    1.2252 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9874   -2.7650    2.0499 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2757   -3.2775    2.3634 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5880   -4.6153    2.3140 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -4.1489   -1.1040    2.8319 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9066   -0.5123    2.5327 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7979    1.0215    2.5867 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.5629    1.4480    1.2322 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2050    2.8329    1.1270 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.7865    3.0729   -0.3179 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3767    3.7281    1.5859 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.5303    3.4745    0.7518 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7774    4.3703   -0.2401 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9755    3.9391   -1.0287 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1289    5.3813   -0.4655 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7052    3.3541    3.0539 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.7417    4.1452    3.7915 N   0  0  1  0  0  0  0  0  0  0  0  0
   -4.2991    5.5234    4.0249 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0712    4.1517    3.1831 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9941    1.8291    3.1676 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.2116    1.5223    4.5548 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7811   -1.3557    2.1434 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1378    2.8509   -0.0397 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.9445    2.4867   -0.1916 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.5754    0.1355    0.2051 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9608   -1.6582   -0.4596 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2084   -2.5341   -2.2162 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2062   -3.9640   -1.9152 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4905   -2.3556   -1.7130 H   0  0  0  0  0  0  0  0  0  0  0  0
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    1.1637   -3.7515    1.0929 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2175   -5.6325    0.2034 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7206   -5.8105    1.9337 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5155   -6.8629    1.2375 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -5.2964   -2.9107    2.9867 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0060   -0.5133    3.1411 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -1.3326    3.0227    1.7641 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5693    2.7708   -1.0211 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9093    2.4617   -0.5592 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5314    4.1224   -0.4905 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0727    4.7800    1.5392 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7867    2.9642   -1.4852 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1668    4.6653   -1.8238 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8521    3.8963   -0.3774 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7835    3.5128    3.6350 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0085    6.0465    4.6763 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2051    6.0954    3.0957 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3339    5.5403    4.5429 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7937    4.5909    3.8812 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1126    4.7394    2.2616 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4330    3.1411    2.9748 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -4.6730    2.3095    4.9130 H   0  0  0  0  0  0  0  0  0  0  0  0
 11 13  1  0  0  0  0
 13 14  1  0  0  0  0
 28 29  1  0  0  0  0
 41 20  1  0  0  0  0
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 30 28  1  0  0  0  0
 17 16  1  0  0  0  0
 16 15  2  0  0  0  0
 14 41  2  0  0  0  0
  9  8  1  0  0  0  0
 28 27  1  0  0  0  0
 24 23  1  0  0  0  0
  8  5  2  0  0  0  0
 23 21  2  0  0  0  0
 21 20  1  0  0  0  0
 41 25  1  0  0  0  0
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 11 12  2  0  0  0  0
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  3  2  1  0  0  0  0
 26 39  1  0  0  0  0
  2  1  2  3  0  0  0
  4  3  2  0  0  0  0
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 39 35  1  0  0  0  0
  6  7  1  0  0  0  0
  3 10  1  0  0  0  0
 17 18  1  0  0  0  0
 10  9  2  0  0  0  0
 18 19  1  0  0  0  0
 35 30  1  0  0  0  0
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 15  8  1  0  0  0  0
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 26 25  1  0  0  0  0
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 39 73  1  6  0  0  0
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 10 49  1  0  0  0  0
 16 50  1  0  0  0  0
 24 56  1  0  0  0  0
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 19 51  1  0  0  0  0
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 22 54  1  0  0  0  0
 37 67  1  0  0  0  0
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 33 63  1  0  0  0  0
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 38 70  1  0  0  0  0
 38 71  1  0  0  0  0
 38 72  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0024687

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]OC1=C([H])C([H])=C(C2=C3OC(=O)C4=C([H])C(C([H])=C([H])[H])=C([H])C(OC([H])([H])[H])=C4C3=C([H])C(OC([H])([H])[H])=C12)[C@@]1([H])O[C@@]([H])(C([H])([H])[H])[C@@]([H])(OC(=O)C([H])([H])[H])[C@@]([H])(N(C([H])([H])[H])C([H])([H])[H])[C@]1([H])O[H]

> <INCHI_IDENTIFIER>
InChI=1S/C31H33NO9/c1-8-16-11-19-23(21(12-16)37-6)18-13-22(38-7)25-20(34)10-9-17(24(25)29(18)41-31(19)36)30-27(35)26(32(4)5)28(14(2)39-30)40-15(3)33/h8-14,26-28,30,34-35H,1H2,2-7H3/t14-,26-,27-,28+,30+/m0/s1

> <INCHI_KEY>
GHLIFBNIGXVDHM-LBUDYNQBSA-N

> <FORMULA>
C31H33NO9

> <MOLECULAR_WEIGHT>
563.603

> <EXACT_MASS>
563.215531647

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
74

> <JCHEM_AVERAGE_POLARIZABILITY>
60.20919353578953

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,3S,4S,5S,6R)-4-(dimethylamino)-6-{5-ethenyl-15-hydroxy-3,17-dimethoxy-8-oxo-9-oxatetracyclo[8.8.0.0^{2,7}.0^{11,16}]octadeca-1(18),2,4,6,10,12,14,16-octaen-12-yl}-5-hydroxy-2-methyloxan-3-yl acetate

> <ALOGPS_LOGP>
3.67

> <JCHEM_LOGP>
2.980296469876598

> <ALOGPS_LOGS>
-3.95

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
13.419974832981008

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.677113497103736

> <JCHEM_PKA_STRONGEST_BASIC>
8.00061001235909

> <JCHEM_POLAR_SURFACE_AREA>
123.99000000000001

> <JCHEM_REFRACTIVITY>
150.4358

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
6.39e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S,3S,4S,5S,6R)-4-(dimethylamino)-6-{5-ethenyl-15-hydroxy-3,17-dimethoxy-8-oxo-9-oxatetracyclo[8.8.0.0^{2,7}.0^{11,16}]octadeca-1(18),2,4,6,10,12,14,16-octaen-12-yl}-5-hydroxy-2-methyloxan-3-yl acetate

> <JCHEM_VEBER_RULE>
0

$$$$

     RDKit          3D

 74 78  0  0  0  0  0  0  0  0999 V2000
    5.9385    2.1191   -0.0117 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7264    0.8164    0.2155 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4114    0.2119    0.4612 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1824   -1.1012    0.0584 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9422   -1.7215    0.2887 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8132   -2.9942   -0.2154 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4088   -2.9400   -1.5874 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9037   -1.0898    1.0070 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1440    0.2467    1.3625 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3780    0.8830    1.1115 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0847    1.0665    1.9815 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2668    2.2250    2.3349 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1517    0.4627    2.0900 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4473   -0.9044    1.8349 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6087   -1.7071    1.3770 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3568   -3.0764    1.3437 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8992   -3.6068    1.6619 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1594   -4.9636    1.6216 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1131   -5.8454    1.2252 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9874   -2.7650    2.0499 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2757   -3.2775    2.3634 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5880   -4.6153    2.3140 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3315   -2.4712    2.7505 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1489   -1.1040    2.8319 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9066   -0.5123    2.5327 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7979    1.0215    2.5867 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.5629    1.4480    1.2322 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2050    2.8329    1.1270 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.7865    3.0729   -0.3179 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3767    3.7281    1.5859 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.5303    3.4745    0.7518 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -5.9755    3.9391   -1.0287 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -4.7417    4.1452    3.7915 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2991    5.5234    4.0249 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0712    4.1517    3.1831 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9941    1.8291    3.1676 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.2116    1.5223    4.5548 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7811   -1.3557    2.1434 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1378    2.8509   -0.0397 H   0  0  0  0  0  0  0  0  0  0  0  0
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    6.5754    0.1355    0.2051 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9608   -1.6582   -0.4596 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2084   -2.5341   -2.2162 H   0  0  0  0  0  0  0  0  0  0  0  0
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    1.4905   -2.3556   -1.7130 H   0  0  0  0  0  0  0  0  0  0  0  0
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    1.1637   -3.7515    1.0929 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -2.5693    2.7708   -1.0211 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9093    2.4617   -0.5592 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5314    4.1224   -0.4905 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -5.7867    2.9642   -1.4852 H   0  0  0  0  0  0  0  0  0  0  0  0
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M  END

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       5.939   2.119  -0.012  0.00  0.00           C+0
HETATM    2  C   UNK     0       5.726   0.816   0.216  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.411   0.212   0.461  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.182  -1.101   0.058  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.942  -1.722   0.289  0.00  0.00           C+0
HETATM    6  O   UNK     0       2.813  -2.994  -0.215  0.00  0.00           O+0
HETATM    7  C   UNK     0       2.409  -2.940  -1.587  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.904  -1.090   1.007  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.144   0.247   1.363  0.00  0.00           C+0
HETATM   10  C   UNK     0       3.378   0.883   1.111  0.00  0.00           C+0
HETATM   11  C   UNK     0       1.085   1.067   1.982  0.00  0.00           C+0
HETATM   12  O   UNK     0       1.267   2.225   2.335  0.00  0.00           O+0
HETATM   13  O   UNK     0      -0.152   0.463   2.090  0.00  0.00           O+0
HETATM   14  C   UNK     0      -0.447  -0.904   1.835  0.00  0.00           C+0
HETATM   15  C   UNK     0       0.609  -1.707   1.377  0.00  0.00           C+0
HETATM   16  C   UNK     0       0.357  -3.076   1.344  0.00  0.00           C+0
HETATM   17  C   UNK     0      -0.899  -3.607   1.662  0.00  0.00           C+0
HETATM   18  O   UNK     0      -1.159  -4.964   1.622  0.00  0.00           O+0
HETATM   19  C   UNK     0      -0.113  -5.845   1.225  0.00  0.00           C+0
HETATM   20  C   UNK     0      -1.987  -2.765   2.050  0.00  0.00           C+0
HETATM   21  C   UNK     0      -3.276  -3.277   2.363  0.00  0.00           C+0
HETATM   22  O   UNK     0      -3.588  -4.615   2.314  0.00  0.00           O+0
HETATM   23  C   UNK     0      -4.332  -2.471   2.751  0.00  0.00           C+0
HETATM   24  C   UNK     0      -4.149  -1.104   2.832  0.00  0.00           C+0
HETATM   25  C   UNK     0      -2.907  -0.512   2.533  0.00  0.00           C+0
HETATM   26  C   UNK     0      -2.798   1.022   2.587  0.00  0.00           C+0
HETATM   27  O   UNK     0      -2.563   1.448   1.232  0.00  0.00           O+0
HETATM   28  C   UNK     0      -2.205   2.833   1.127  0.00  0.00           C+0
HETATM   29  C   UNK     0      -1.787   3.073  -0.318  0.00  0.00           C+0
HETATM   30  C   UNK     0      -3.377   3.728   1.586  0.00  0.00           C+0
HETATM   31  O   UNK     0      -4.530   3.474   0.752  0.00  0.00           O+0
HETATM   32  C   UNK     0      -4.777   4.370  -0.240  0.00  0.00           C+0
HETATM   33  C   UNK     0      -5.976   3.939  -1.029  0.00  0.00           C+0
HETATM   34  O   UNK     0      -4.129   5.381  -0.466  0.00  0.00           O+0
HETATM   35  C   UNK     0      -3.705   3.354   3.054  0.00  0.00           C+0
HETATM   36  N   UNK     0      -4.742   4.145   3.792  0.00  0.00           N+0
HETATM   37  C   UNK     0      -4.299   5.523   4.025  0.00  0.00           C+0
HETATM   38  C   UNK     0      -6.071   4.152   3.183  0.00  0.00           C+0
HETATM   39  C   UNK     0      -3.994   1.829   3.168  0.00  0.00           C+0
HETATM   40  O   UNK     0      -4.212   1.522   4.555  0.00  0.00           O+0
HETATM   41  C   UNK     0      -1.781  -1.356   2.143  0.00  0.00           C+0
HETATM   42  H   UNK     0       5.138   2.851  -0.040  0.00  0.00           H+0
HETATM   43  H   UNK     0       6.944   2.487  -0.192  0.00  0.00           H+0
HETATM   44  H   UNK     0       6.575   0.136   0.205  0.00  0.00           H+0
HETATM   45  H   UNK     0       4.961  -1.658  -0.460  0.00  0.00           H+0
HETATM   46  H   UNK     0       3.208  -2.534  -2.216  0.00  0.00           H+0
HETATM   47  H   UNK     0       2.206  -3.964  -1.915  0.00  0.00           H+0
HETATM   48  H   UNK     0       1.490  -2.356  -1.713  0.00  0.00           H+0
HETATM   49  H   UNK     0       3.520   1.912   1.439  0.00  0.00           H+0
HETATM   50  H   UNK     0       1.164  -3.752   1.093  0.00  0.00           H+0
HETATM   51  H   UNK     0       0.218  -5.633   0.203  0.00  0.00           H+0
HETATM   52  H   UNK     0       0.721  -5.811   1.934  0.00  0.00           H+0
HETATM   53  H   UNK     0      -0.516  -6.863   1.238  0.00  0.00           H+0
HETATM   54  H   UNK     0      -2.773  -5.084   2.053  0.00  0.00           H+0
HETATM   55  H   UNK     0      -5.296  -2.911   2.987  0.00  0.00           H+0
HETATM   56  H   UNK     0      -5.006  -0.513   3.141  0.00  0.00           H+0
HETATM   57  H   UNK     0      -1.940   1.254   3.229  0.00  0.00           H+0
HETATM   58  H   UNK     0      -1.333   3.023   1.764  0.00  0.00           H+0
HETATM   59  H   UNK     0      -2.569   2.771  -1.021  0.00  0.00           H+0
HETATM   60  H   UNK     0      -0.909   2.462  -0.559  0.00  0.00           H+0
HETATM   61  H   UNK     0      -1.531   4.122  -0.491  0.00  0.00           H+0
HETATM   62  H   UNK     0      -3.073   4.780   1.539  0.00  0.00           H+0
HETATM   63  H   UNK     0      -5.787   2.964  -1.485  0.00  0.00           H+0
HETATM   64  H   UNK     0      -6.167   4.665  -1.824  0.00  0.00           H+0
HETATM   65  H   UNK     0      -6.852   3.896  -0.377  0.00  0.00           H+0
HETATM   66  H   UNK     0      -2.784   3.513   3.635  0.00  0.00           H+0
HETATM   67  H   UNK     0      -5.008   6.046   4.676  0.00  0.00           H+0
HETATM   68  H   UNK     0      -4.205   6.095   3.096  0.00  0.00           H+0
HETATM   69  H   UNK     0      -3.334   5.540   4.543  0.00  0.00           H+0
HETATM   70  H   UNK     0      -6.794   4.591   3.881  0.00  0.00           H+0
HETATM   71  H   UNK     0      -6.113   4.739   2.262  0.00  0.00           H+0
HETATM   72  H   UNK     0      -6.433   3.141   2.975  0.00  0.00           H+0
HETATM   73  H   UNK     0      -4.910   1.592   2.615  0.00  0.00           H+0
HETATM   74  H   UNK     0      -4.673   2.309   4.913  0.00  0.00           H+0
CONECT    1    2   42   43                                                  
CONECT    2    3    1   44                                                  
CONECT    3    2    4   10                                                  
CONECT    4    5    3   45                                                  
CONECT    5    8    4    6                                                  
CONECT    6    5    7                                                       
CONECT    7    6   46   47   48                                             
CONECT    8    9    5   15                                                  
CONECT    9    8   10   11                                                  
CONECT   10    3    9   49                                                  
CONECT   11   13   12    9                                                  
CONECT   12   11                                                            
CONECT   13   11   14                                                       
CONECT   14   13   41   15                                                  
CONECT   15   16   14    8                                                  
CONECT   16   17   15   50                                                  
CONECT   17   20   16   18                                                  
CONECT   18   17   19                                                       
CONECT   19   18   51   52   53                                             
CONECT   20   41   17   21                                                  
CONECT   21   23   20   22                                                  
CONECT   22   21   54                                                       
CONECT   23   24   21   55                                                  
CONECT   24   23   25   56                                                  
CONECT   25   41   24   26                                                  
CONECT   26   27   39   25   57                                             
CONECT   27   28   26                                                       
CONECT   28   29   30   27   58                                             
CONECT   29   28   59   60   61                                             
CONECT   30   28   35   31   62                                             
CONECT   31   32   30                                                       
CONECT   32   31   33   34                                                  
CONECT   33   32   63   64   65                                             
CONECT   34   32                                                            
CONECT   35   39   30   36   66                                             
CONECT   36   37   38   35                                                  
CONECT   37   36   67   68   69                                             
CONECT   38   36   70   71   72                                             
CONECT   39   26   35   40   73                                             
CONECT   40   39   74                                                       
CONECT   41   20   14   25                                                  
CONECT   42    1                                                            
CONECT   43    1                                                            
CONECT   44    2                                                            
CONECT   45    4                                                            
CONECT   46    7                                                            
CONECT   47    7                                                            
CONECT   48    7                                                            
CONECT   49   10                                                            
CONECT   50   16                                                            
CONECT   51   19                                                            
CONECT   52   19                                                            
CONECT   53   19                                                            
CONECT   54   22                                                            
CONECT   55   23                                                            
CONECT   56   24                                                            
CONECT   57   26                                                            
CONECT   58   28                                                            
CONECT   59   29                                                            
CONECT   60   29                                                            
CONECT   61   29                                                            
CONECT   62   30                                                            
CONECT   63   33                                                            
CONECT   64   33                                                            
CONECT   65   33                                                            
CONECT   66   35                                                            
CONECT   67   37                                                            
CONECT   68   37                                                            
CONECT   69   37                                                            
CONECT   70   38                                                            
CONECT   71   38                                                            
CONECT   72   38                                                            
CONECT   73   39                                                            
CONECT   74   40                                                            
MASTER        0    0    0    0    0    0    0    0   74    0  156    0
END

RDKit          3D

74 78  0  0  0  0  0  0  0  0999 V2000
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    0.2175   -5.6325    0.2034 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7206   -5.8105    1.9337 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5155   -6.8629    1.2375 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7727   -5.0838    2.0534 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2964   -2.9107    2.9867 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0060   -0.5133    3.1411 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9398    1.2536    3.2290 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3326    3.0227    1.7641 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5693    2.7708   -1.0211 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9093    2.4617   -0.5592 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5314    4.1224   -0.4905 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0727    4.7800    1.5392 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7867    2.9642   -1.4852 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1668    4.6653   -1.8238 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8521    3.8963   -0.3774 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7835    3.5128    3.6350 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0085    6.0465    4.6763 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2051    6.0954    3.0957 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3339    5.5403    4.5429 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7937    4.5909    3.8812 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1126    4.7394    2.2616 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4330    3.1411    2.9748 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9099    1.5921    2.6151 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6730    2.3095    4.9130 H   0  0  0  0  0  0  0  0  0  0  0  0
 11 13  1  0
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M  END

View in JSmol

Synonyms

Value	Source
(2S,3S,4S,5S,6R)-4-(Dimethylamino)-6-{5-ethenyl-15-hydroxy-3,17-dimethoxy-8-oxo-9-oxatetracyclo[8.8.0.0,.0,]octadeca-1(10),2(7),3,5,11,13,15,17-octaen-12-yl}-5-hydroxy-2-methyloxan-3-yl acetic acid	Generator
1-Hydroxy-4-[3-(dimethylamino)-4-O-acetyl-3,6-dideoxy-b-L-galactopyranosyl]-8-vinyl-10,12-dimethoxy-6H-benzo[D]naphtho[1,2-b]pyran-6-one	Generator
1-Hydroxy-4-[3-(dimethylamino)-4-O-acetyl-3,6-dideoxy-β-L-galactopyranosyl]-8-vinyl-10,12-dimethoxy-6H-benzo[D]naphtho[1,2-b]pyran-6-one	Generator

Chemical Formula

C₃₁H₃₃NO₉

Average Mass

563.6030 Da

Monoisotopic Mass

563.21553 Da

IUPAC Name

(2S,3S,4S,5S,6R)-4-(dimethylamino)-6-{5-ethenyl-15-hydroxy-3,17-dimethoxy-8-oxo-9-oxatetracyclo[8.8.0.0^{2,7}.0^{11,16}]octadeca-1(18),2,4,6,10,12,14,16-octaen-12-yl}-5-hydroxy-2-methyloxan-3-yl acetate

Traditional Name

CAS Registry Number

Not Available

SMILES

[H]OC1=C([H])C([H])=C(C2=C3OC(=O)C4=C([H])C(C([H])=C([H])[H])=C([H])C(OC([H])([H])[H])=C4C3=C([H])C(OC([H])([H])[H])=C12)[C@@]1([H])O[C@@]([H])(C([H])([H])[H])[C@@]([H])(OC(=O)C([H])([H])[H])[C@@]([H])(N(C([H])([H])[H])C([H])([H])[H])[C@]1([H])O[H]

InChI Identifier

InChI=1S/C31H33NO9/c1-8-16-11-19-23(21(12-16)37-6)18-13-22(38-7)25-20(34)10-9-17(24(25)29(18)41-31(19)36)30-27(35)26(32(4)5)28(14(2)39-30)40-15(3)33/h8-14,26-28,30,34-35H,1H2,2-7H3/t14-,26-,27-,28+,30+/m0/s1

InChI Key

GHLIFBNIGXVDHM-LBUDYNQBSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, CDCl₃, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, CDCl₃, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, CDCl₃, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, CDCl₃, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, CDCl₃, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, CDCl₃, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, CDCl₃, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, CDCl₃, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, CDCl₃, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, CDCl₃, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, CDCl₃, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, CDCl₃, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, CDCl₃, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, CDCl₃, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, CDCl₃, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, CDCl₃, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, CDCl₃, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, CDCl₃, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, CDCl₃, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, CDCl₃, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Streptomyces ravidus	LOTUS Database	35616633
Streptomyces rochei	JEOL database	Yamashita, N. et al, J. Antibiotics 51, 1105 (1998)

Chemical Taxonomy

Classification

Not classified

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	3.67	ALOGPS
logP	2.98	ChemAxon
logS	-4	ALOGPS
pKa (Strongest Acidic)	8.68	ChemAxon
pKa (Strongest Basic)	8	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	123.99 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	150.44 m³·mol⁻¹	ChemAxon
Polarizability	60.21 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	Yes	ChemAxon

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

9039962

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

10864675

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Yamashita, N. et al. (1998). Yamashita, N. et al, J. Antibiotics 51, 1105 (1998). J. Antibiotics.

Showing NP-Card for Ravidomycin (NP0024687)

MOL for NP0024687 (Ravidomycin)

3D MOL for NP0024687 (Ravidomycin)

3D SDF for NP0024687 (Ravidomycin)

3D-SDF for NP0024687 (Ravidomycin)

PDB for NP0024687 (Ravidomycin)

3D PDB for NP0024687 (Ravidomycin)

SMILES for NP0024687 (Ravidomycin)

INCHI for NP0024687 (Ravidomycin)

Structure for NP0024687 (Ravidomycin)

3D Structure for NP0024687 (Ravidomycin)