NP-MRD: Showing NP-Card for Rakicidin A (NP0023048)

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Record Information

Version

1.0

Created at

2021-01-06 08:10:48 UTC

Updated at

2021-07-15 17:40:41 UTC

NP-MRD ID

NP0023048

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Rakicidin A

Provided By

NPAtlas

Description

Rakicidin A is found in Micromonospora sp. and Micromonospora sp. No. R385-2. It was first documented in 1995 (PMID: 8557602). Based on a literature review a significant number of articles have been published on Rakicidin A (PMID: 33660974) (PMID: 29656202) (PMID: 26814890) (PMID: 26637117).

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652307042108133D          

 97 97  0  0  0  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv1652307042108133D          

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 30 74  1  0  0  0  0
 30 75  1  0  0  0  0
 31 76  1  0  0  0  0
 31 77  1  0  0  0  0
 32 78  1  0  0  0  0
 32 79  1  0  0  0  0
 33 80  1  0  0  0  0
 33 81  1  0  0  0  0
 34 82  1  0  0  0  0
 34 83  1  0  0  0  0
 35 84  1  0  0  0  0
 35 85  1  0  0  0  0
 36 86  1  1  0  0  0
 37 87  1  0  0  0  0
 37 88  1  0  0  0  0
 37 89  1  0  0  0  0
 38 90  1  0  0  0  0
 38 91  1  0  0  0  0
 38 92  1  0  0  0  0
 39 93  1  6  0  0  0
 40 94  1  0  0  0  0
 40 95  1  0  0  0  0
 40 96  1  0  0  0  0
 43 97  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0023048

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]O[C@@]([H])(C(=O)N([H])[H])[C@@]1([H])N([H])C(=O)C([H])([H])N(C(=O)\C([H])=C([H])/C(=C([H])[H])N([H])C(=O)[C@]([H])(C([H])([H])[H])[C@]([H])(OC1=O)[C@@]([H])(C([H])([H])[H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])(C([H])([H])[H])C([H])([H])[H])C([H])([H])[H]

> <INCHI_IDENTIFIER>
InChI=1S/C32H54N4O7/c1-21(2)16-14-12-10-8-7-9-11-13-15-17-22(3)29-24(5)31(41)34-23(4)18-19-26(38)36(6)20-25(37)35-27(32(42)43-29)28(39)30(33)40/h18-19,21-22,24,27-29,39H,4,7-17,20H2,1-3,5-6H3,(H2,33,40)(H,34,41)(H,35,37)/b19-18-/t22-,24+,27+,28+,29+/m0/s1

> <INCHI_KEY>
NODOLTRBPIFGCQ-HNENSFHCSA-N

> <FORMULA>
C32H54N4O7

> <MOLECULAR_WEIGHT>
606.805

> <EXACT_MASS>
606.399250095

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
97

> <JCHEM_AVERAGE_POLARIZABILITY>
67.7820171879782

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R)-2-[(3R,9Z,14R,15R)-7,14-dimethyl-11-methylidene-15-[(2S)-14-methylpentadecan-2-yl]-2,5,8,13-tetraoxo-1-oxa-4,7,12-triazacyclopentadec-9-en-3-yl]-2-hydroxyacetamide

> <ALOGPS_LOGP>
4.75

> <JCHEM_LOGP>
3.542078019000002

> <ALOGPS_LOGS>
-5.53

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.238852387492374

> <JCHEM_PKA_STRONGEST_ACIDIC>
10.65538558210932

> <JCHEM_PKA_STRONGEST_BASIC>
-0.5728208359309485

> <JCHEM_POLAR_SURFACE_AREA>
168.12999999999997

> <JCHEM_REFRACTIVITY>
165.4559000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
15

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.78e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2R)-2-[(3R,9Z,14R,15R)-7,14-dimethyl-11-methylidene-15-[(2S)-14-methylpentadecan-2-yl]-2,5,8,13-tetraoxo-1-oxa-4,7,12-triazacyclopentadec-9-en-3-yl]-2-hydroxyacetamide

> <JCHEM_VEBER_RULE>
0

$$$$

     RDKit          3D

 97 97  0  0  0  0  0  0  0  0999 V2000
   -4.1051   -3.3712   -2.9840 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7693   -2.1358   -2.5577 C   0  0  0  0  0  0  0  0  0  0  0  0
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  1  2  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  5  7  1  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
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 12 13  1  0
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 35 36  1  0
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 22 39  1  0
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 41 43  1  0
 43  2  1  0
  1 44  1  0
  1 45  1  0
  3 46  1  0
  4 47  1  0
  8 48  1  0
  8 49  1  0
  8 50  1  0
  9 51  1  0
  9 52  1  0
 12 53  1  0
 13 54  1  1
 14 55  1  1
 15 56  1  0
 17 57  1  0
 17 58  1  0
 22 59  1  1
 23 60  1  6
 24 61  1  0
 24 62  1  0
 24 63  1  0
 25 64  1  0
 25 65  1  0
 26 66  1  0
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 27 68  1  0
 27 69  1  0
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 29 72  1  0
 29 73  1  0
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 31 76  1  0
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 33 80  1  0
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 34 83  1  0
 35 84  1  0
 35 85  1  0
 36 86  1  1
 37 87  1  0
 37 88  1  0
 37 89  1  0
 38 90  1  0
 38 91  1  0
 38 92  1  0
 39 93  1  6
 40 94  1  0
 40 95  1  0
 40 96  1  0
 43 97  1  0
M  END

HEADER    PROTEIN                                 04-JUL-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-JUL-21         0                                  
HETATM    1  C   UNK     0      -4.105  -3.371  -2.984  0.00  0.00           C+0
HETATM    2  C   UNK     0      -3.769  -2.136  -2.558  0.00  0.00           C+0
HETATM    3  C   UNK     0      -3.727  -1.146  -3.598  0.00  0.00           C+0
HETATM    4  C   UNK     0      -4.229   0.065  -3.619  0.00  0.00           C+0
HETATM    5  C   UNK     0      -4.951   0.668  -2.563  0.00  0.00           C+0
HETATM    6  O   UNK     0      -4.487   1.890  -2.303  0.00  0.00           O+0
HETATM    7  N   UNK     0      -6.007   0.403  -1.696  0.00  0.00           N+0
HETATM    8  C   UNK     0      -6.787   1.545  -1.068  0.00  0.00           C+0
HETATM    9  C   UNK     0      -6.581  -0.836  -1.250  0.00  0.00           C+0
HETATM   10  C   UNK     0      -6.620  -1.068   0.205  0.00  0.00           C+0
HETATM   11  O   UNK     0      -7.830  -1.371   0.596  0.00  0.00           O+0
HETATM   12  N   UNK     0      -5.695  -1.044   1.226  0.00  0.00           N+0
HETATM   13  C   UNK     0      -4.969  -0.048   1.938  0.00  0.00           C+0
HETATM   14  C   UNK     0      -5.722   0.543   3.131  0.00  0.00           C+0
HETATM   15  O   UNK     0      -6.885   1.115   2.654  0.00  0.00           O+0
HETATM   16  C   UNK     0      -5.993  -0.470   4.153  0.00  0.00           C+0
HETATM   17  N   UNK     0      -7.326  -0.768   4.555  0.00  0.00           N+0
HETATM   18  O   UNK     0      -5.067  -1.107   4.705  0.00  0.00           O+0
HETATM   19  C   UNK     0      -4.272   0.979   1.114  0.00  0.00           C+0
HETATM   20  O   UNK     0      -4.741   2.158   1.360  0.00  0.00           O+0
HETATM   21  O   UNK     0      -3.305   0.804   0.231  0.00  0.00           O+0
HETATM   22  C   UNK     0      -1.868   0.844   0.221  0.00  0.00           C+0
HETATM   23  C   UNK     0      -1.455   2.034  -0.578  0.00  0.00           C+0
HETATM   24  C   UNK     0      -2.212   3.277   0.071  0.00  0.00           C+0
HETATM   25  C   UNK     0      -0.033   2.476  -0.620  0.00  0.00           C+0
HETATM   26  C   UNK     0       0.648   2.983   0.553  0.00  0.00           C+0
HETATM   27  C   UNK     0       1.015   2.221   1.746  0.00  0.00           C+0
HETATM   28  C   UNK     0       2.070   1.159   1.536  0.00  0.00           C+0
HETATM   29  C   UNK     0       3.361   1.824   1.064  0.00  0.00           C+0
HETATM   30  C   UNK     0       4.409   0.746   0.904  0.00  0.00           C+0
HETATM   31  C   UNK     0       4.069  -0.308  -0.093  0.00  0.00           C+0
HETATM   32  C   UNK     0       5.167  -1.324  -0.172  0.00  0.00           C+0
HETATM   33  C   UNK     0       6.506  -0.737  -0.595  0.00  0.00           C+0
HETATM   34  C   UNK     0       7.465  -1.896  -0.641  0.00  0.00           C+0
HETATM   35  C   UNK     0       8.848  -1.604  -1.060  0.00  0.00           C+0
HETATM   36  C   UNK     0       9.640  -0.651  -0.239  0.00  0.00           C+0
HETATM   37  C   UNK     0      11.041  -0.605  -0.923  0.00  0.00           C+0
HETATM   38  C   UNK     0       9.114   0.772  -0.235  0.00  0.00           C+0
HETATM   39  C   UNK     0      -1.523  -0.373  -0.740  0.00  0.00           C+0
HETATM   40  C   UNK     0      -0.221  -1.013  -0.358  0.00  0.00           C+0
HETATM   41  C   UNK     0      -2.545  -1.408  -0.428  0.00  0.00           C+0
HETATM   42  O   UNK     0      -2.430  -1.741   0.822  0.00  0.00           O+0
HETATM   43  N   UNK     0      -3.515  -2.023  -1.184  0.00  0.00           N+0
HETATM   44  H   UNK     0      -4.320  -3.591  -4.014  0.00  0.00           H+0
HETATM   45  H   UNK     0      -4.179  -4.185  -2.308  0.00  0.00           H+0
HETATM   46  H   UNK     0      -3.195  -1.415  -4.568  0.00  0.00           H+0
HETATM   47  H   UNK     0      -4.048   0.674  -4.591  0.00  0.00           H+0
HETATM   48  H   UNK     0      -7.033   1.320  -0.041  0.00  0.00           H+0
HETATM   49  H   UNK     0      -6.162   2.457  -1.059  0.00  0.00           H+0
HETATM   50  H   UNK     0      -7.715   1.690  -1.643  0.00  0.00           H+0
HETATM   51  H   UNK     0      -7.692  -0.718  -1.573  0.00  0.00           H+0
HETATM   52  H   UNK     0      -6.317  -1.735  -1.830  0.00  0.00           H+0
HETATM   53  H   UNK     0      -5.456  -2.051   1.607  0.00  0.00           H+0
HETATM   54  H   UNK     0      -4.082  -0.514   2.498  0.00  0.00           H+0
HETATM   55  H   UNK     0      -5.045   1.353   3.520  0.00  0.00           H+0
HETATM   56  H   UNK     0      -6.976   2.069   2.894  0.00  0.00           H+0
HETATM   57  H   UNK     0      -7.686  -1.726   4.419  0.00  0.00           H+0
HETATM   58  H   UNK     0      -7.952  -0.035   4.988  0.00  0.00           H+0
HETATM   59  H   UNK     0      -1.370   0.695   1.122  0.00  0.00           H+0
HETATM   60  H   UNK     0      -1.860   2.011  -1.589  0.00  0.00           H+0
HETATM   61  H   UNK     0      -2.208   3.198   1.144  0.00  0.00           H+0
HETATM   62  H   UNK     0      -3.151   3.349  -0.459  0.00  0.00           H+0
HETATM   63  H   UNK     0      -1.591   4.130  -0.245  0.00  0.00           H+0
HETATM   64  H   UNK     0       0.083   3.271  -1.441  0.00  0.00           H+0
HETATM   65  H   UNK     0       0.626   1.652  -1.058  0.00  0.00           H+0
HETATM   66  H   UNK     0       0.097   3.920   0.976  0.00  0.00           H+0
HETATM   67  H   UNK     0       1.623   3.535   0.240  0.00  0.00           H+0
HETATM   68  H   UNK     0       0.186   1.764   2.335  0.00  0.00           H+0
HETATM   69  H   UNK     0       1.536   2.925   2.519  0.00  0.00           H+0
HETATM   70  H   UNK     0       1.785   0.357   0.857  0.00  0.00           H+0
HETATM   71  H   UNK     0       2.231   0.701   2.553  0.00  0.00           H+0
HETATM   72  H   UNK     0       3.736   2.559   1.784  0.00  0.00           H+0
HETATM   73  H   UNK     0       3.138   2.290   0.073  0.00  0.00           H+0
HETATM   74  H   UNK     0       4.503   0.257   1.909  0.00  0.00           H+0
HETATM   75  H   UNK     0       5.351   1.269   0.629  0.00  0.00           H+0
HETATM   76  H   UNK     0       3.141  -0.877   0.158  0.00  0.00           H+0
HETATM   77  H   UNK     0       3.976   0.151  -1.117  0.00  0.00           H+0
HETATM   78  H   UNK     0       5.330  -1.865   0.770  0.00  0.00           H+0
HETATM   79  H   UNK     0       4.848  -2.088  -0.933  0.00  0.00           H+0
HETATM   80  H   UNK     0       6.454  -0.235  -1.562  0.00  0.00           H+0
HETATM   81  H   UNK     0       6.774  -0.021   0.211  0.00  0.00           H+0
HETATM   82  H   UNK     0       7.523  -2.372   0.392  0.00  0.00           H+0
HETATM   83  H   UNK     0       7.028  -2.698  -1.306  0.00  0.00           H+0
HETATM   84  H   UNK     0       9.445  -2.566  -1.076  0.00  0.00           H+0
HETATM   85  H   UNK     0       8.814  -1.191  -2.115  0.00  0.00           H+0
HETATM   86  H   UNK     0       9.778  -1.015   0.789  0.00  0.00           H+0
HETATM   87  H   UNK     0      10.826  -0.339  -1.982  0.00  0.00           H+0
HETATM   88  H   UNK     0      11.692   0.099  -0.405  0.00  0.00           H+0
HETATM   89  H   UNK     0      11.402  -1.653  -0.922  0.00  0.00           H+0
HETATM   90  H   UNK     0       8.736   1.082   0.749  0.00  0.00           H+0
HETATM   91  H   UNK     0      10.005   1.461  -0.427  0.00  0.00           H+0
HETATM   92  H   UNK     0       8.457   0.958  -1.087  0.00  0.00           H+0
HETATM   93  H   UNK     0      -1.603  -0.083  -1.769  0.00  0.00           H+0
HETATM   94  H   UNK     0      -0.093  -0.992   0.767  0.00  0.00           H+0
HETATM   95  H   UNK     0      -0.265  -2.141  -0.548  0.00  0.00           H+0
HETATM   96  H   UNK     0       0.652  -0.695  -0.920  0.00  0.00           H+0
HETATM   97  H   UNK     0      -4.259  -2.551  -0.590  0.00  0.00           H+0
CONECT    1    2   44   45                                                  
CONECT    2    1    3   43                                                  
CONECT    3    2    4   46                                                  
CONECT    4    3    5   47                                                  
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8    9                                                  
CONECT    8    7   48   49   50                                             
CONECT    9    7   10   51   52                                             
CONECT   10    9   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10   13   53                                                  
CONECT   13   12   14   19   54                                             
CONECT   14   13   15   16   55                                             
CONECT   15   14   56                                                       
CONECT   16   14   17   18                                                  
CONECT   17   16   57   58                                                  
CONECT   18   16                                                            
CONECT   19   13   20   21                                                  
CONECT   20   19                                                            
CONECT   21   19   22                                                       
CONECT   22   21   23   39   59                                             
CONECT   23   22   24   25   60                                             
CONECT   24   23   61   62   63                                             
CONECT   25   23   26   64   65                                             
CONECT   26   25   27   66   67                                             
CONECT   27   26   28   68   69                                             
CONECT   28   27   29   70   71                                             
CONECT   29   28   30   72   73                                             
CONECT   30   29   31   74   75                                             
CONECT   31   30   32   76   77                                             
CONECT   32   31   33   78   79                                             
CONECT   33   32   34   80   81                                             
CONECT   34   33   35   82   83                                             
CONECT   35   34   36   84   85                                             
CONECT   36   35   37   38   86                                             
CONECT   37   36   87   88   89                                             
CONECT   38   36   90   91   92                                             
CONECT   39   22   40   41   93                                             
CONECT   40   39   94   95   96                                             
CONECT   41   39   42   43                                                  
CONECT   42   41                                                            
CONECT   43   41    2   97                                                  
CONECT   44    1                                                            
CONECT   45    1                                                            
CONECT   46    3                                                            
CONECT   47    4                                                            
CONECT   48    8                                                            
CONECT   49    8                                                            
CONECT   50    8                                                            
CONECT   51    9                                                            
CONECT   52    9                                                            
CONECT   53   12                                                            
CONECT   54   13                                                            
CONECT   55   14                                                            
CONECT   56   15                                                            
CONECT   57   17                                                            
CONECT   58   17                                                            
CONECT   59   22                                                            
CONECT   60   23                                                            
CONECT   61   24                                                            
CONECT   62   24                                                            
CONECT   63   24                                                            
CONECT   64   25                                                            
CONECT   65   25                                                            
CONECT   66   26                                                            
CONECT   67   26                                                            
CONECT   68   27                                                            
CONECT   69   27                                                            
CONECT   70   28                                                            
CONECT   71   28                                                            
CONECT   72   29                                                            
CONECT   73   29                                                            
CONECT   74   30                                                            
CONECT   75   30                                                            
CONECT   76   31                                                            
CONECT   77   31                                                            
CONECT   78   32                                                            
CONECT   79   32                                                            
CONECT   80   33                                                            
CONECT   81   33                                                            
CONECT   82   34                                                            
CONECT   83   34                                                            
CONECT   84   35                                                            
CONECT   85   35                                                            
CONECT   86   36                                                            
CONECT   87   37                                                            
CONECT   88   37                                                            
CONECT   89   37                                                            
CONECT   90   38                                                            
CONECT   91   38                                                            
CONECT   92   38                                                            
CONECT   93   39                                                            
CONECT   94   40                                                            
CONECT   95   40                                                            
CONECT   96   40                                                            
CONECT   97   43                                                            
MASTER        0    0    0    0    0    0    0    0   97    0  194    0
END

RDKit          3D

97 97  0  0  0  0  0  0  0  0999 V2000
   -4.1051   -3.3712   -2.9840 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7693   -2.1358   -2.5577 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7268   -1.1464   -3.5977 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2286    0.0654   -3.6194 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9507    0.6678   -2.5635 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4871    1.8897   -2.3031 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0071    0.4032   -1.6965 N   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7874    1.5452   -1.0676 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5811   -0.8364   -1.2497 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6196   -1.0684    0.2049 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.8301   -1.3709    0.5958 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6949   -1.0443    1.2261 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9687   -0.0479    1.9383 C   0  0  2  0  0  0  0  0  0  0  0  0
   -5.7224    0.5427    3.1306 C   0  0  1  0  0  0  0  0  0  0  0  0
   -6.8854    1.1150    2.6535 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9934   -0.4702    4.1526 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3260   -0.7679    4.5552 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0674   -1.1065    4.7051 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2725    0.9785    1.1138 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7412    2.1580    1.3597 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3053    0.8041    0.2310 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8682    0.8438    0.2212 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.4548    2.0337   -0.5776 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.2123    3.2767    0.0705 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0326    2.4758   -0.6199 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6481    2.9827    0.5533 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0149    2.2208    1.7459 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0704    1.1591    1.5356 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3608    1.8241    1.0640 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4092    0.7461    0.9039 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0693   -0.3084   -0.0934 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1666   -1.3242   -0.1724 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5065   -0.7365   -0.5952 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.4650   -1.8957   -0.6411 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.8484   -1.6044   -1.0604 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.6403   -0.6510   -0.2391 C   0  0  1  0  0  0  0  0  0  0  0  0
   11.0409   -0.6045   -0.9234 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.1137    0.7715   -0.2351 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5229   -0.3730   -0.7398 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.2207   -1.0130   -0.3576 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5454   -1.4081   -0.4279 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4295   -1.7412    0.8215 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5149   -2.0230   -1.1835 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3198   -3.5913   -4.0139 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1789   -4.1848   -2.3079 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1945   -1.4152   -4.5677 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0484    0.6736   -4.5911 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0327    1.3203   -0.0411 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1622    2.4569   -1.0594 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.7149    1.6904   -1.6430 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.6924   -0.7181   -1.5729 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3171   -1.7348   -1.8303 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4564   -2.0509    1.6067 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0819   -0.5135    2.4978 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0446    1.3533    3.5196 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9756    2.0694    2.8935 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.6857   -1.7264    4.4192 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.9518   -0.0349    4.9876 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3697    0.6953    1.1217 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8596    2.0110   -1.5886 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2085    3.1983    1.1440 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1514    3.3491   -0.4594 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5908    4.1302   -0.2452 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0826    3.2708   -1.4411 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6262    1.6519   -1.0581 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0971    3.9199    0.9763 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6225    3.5353    0.2397 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1863    1.7635    2.3350 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5357    2.9254    2.5193 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7850    0.3572    0.8574 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2309    0.7014    2.5531 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7361    2.5589    1.7840 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1375    2.2904    0.0727 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5033    0.2567    1.9090 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3511    1.2694    0.6285 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1409   -0.8772    0.1581 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9760    0.1514   -1.1173 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3304   -1.8646    0.7704 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8478   -2.0879   -0.9326 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4537   -0.2347   -1.5617 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.7742   -0.0209    0.2114 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.5230   -2.3724    0.3915 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.0284   -2.6981   -1.3055 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.4449   -2.5658   -1.0760 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.8138   -1.1911   -2.1152 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.7777   -1.0147    0.7888 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.8257   -0.3390   -1.9816 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.6924    0.0994   -0.4052 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.4022   -1.6526   -0.9215 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.7355    1.0819    0.7490 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.0050    1.4607   -0.4270 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.4565    0.9583   -1.0868 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6025   -0.0831   -1.7693 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0930   -0.9921    0.7665 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2653   -2.1413   -0.5480 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6518   -0.6950   -0.9200 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2593   -2.5505   -0.5897 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  5  7  1  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
 10 11  2  0
 10 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 14 16  1  0
 16 17  1  0
 16 18  2  0
 13 19  1  0
 19 20  2  0
 19 21  1  0
 21 22  1  0
 22 23  1  0
 23 24  1  0
 23 25  1  0
 25 26  1  0
 26 27  1  0
 27 28  1  0
 28 29  1  0
 29 30  1  0
 30 31  1  0
 31 32  1  0
 32 33  1  0
 33 34  1  0
 34 35  1  0
 35 36  1  0
 36 37  1  0
 36 38  1  0
 22 39  1  0
 39 40  1  0
 39 41  1  0
 41 42  2  0
 41 43  1  0
 43  2  1  0
  1 44  1  0
  1 45  1  0
  3 46  1  0
  4 47  1  0
  8 48  1  0
  8 49  1  0
  8 50  1  0
  9 51  1  0
  9 52  1  0
 12 53  1  0
 13 54  1  1
 14 55  1  1
 15 56  1  0
 17 57  1  0
 17 58  1  0
 22 59  1  1
 23 60  1  6
 24 61  1  0
 24 62  1  0
 24 63  1  0
 25 64  1  0
 25 65  1  0
 26 66  1  0
 26 67  1  0
 27 68  1  0
 27 69  1  0
 28 70  1  0
 28 71  1  0
 29 72  1  0
 29 73  1  0
 30 74  1  0
 30 75  1  0
 31 76  1  0
 31 77  1  0
 32 78  1  0
 32 79  1  0
 33 80  1  0
 33 81  1  0
 34 82  1  0
 34 83  1  0
 35 84  1  0
 35 85  1  0
 36 86  1  1
 37 87  1  0
 37 88  1  0
 37 89  1  0
 38 90  1  0
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 38 92  1  0
 39 93  1  6
 40 94  1  0
 40 95  1  0
 40 96  1  0
 43 97  1  0
M  END

View in JSmol View NMR Assignments

Synonyms

Value	Source
2-[(9Z)-5,13-Dihydroxy-7,14-dimethyl-11-methylidene-15-(14-methylpentadecan-2-yl)-2,8-dioxo-1-oxa-4,7,12-triazacyclopentadeca-4,9,12-trien-3-yl]-2-hydroxyethanimidate	Generator

Chemical Formula

C₃₂H₅₄N₄O₇

Average Mass

606.8050 Da

Monoisotopic Mass

606.39925 Da

IUPAC Name

(2R)-2-[(3R,9Z,14R,15R)-7,14-dimethyl-11-methylidene-15-[(2S)-14-methylpentadecan-2-yl]-2,5,8,13-tetraoxo-1-oxa-4,7,12-triazacyclopentadec-9-en-3-yl]-2-hydroxyacetamide

Traditional Name

(2R)-2-[(3R,9Z,14R,15R)-7,14-dimethyl-11-methylidene-15-[(2S)-14-methylpentadecan-2-yl]-2,5,8,13-tetraoxo-1-oxa-4,7,12-triazacyclopentadec-9-en-3-yl]-2-hydroxyacetamide

CAS Registry Number

Not Available

SMILES

CC(C)CCCCCCCCCCCC(C)C1OC(=O)C(NC(=O)CN(C)C(=O)\C=C/C(=C)NC(=O)C1C)C(O)C(N)=O

InChI Identifier

InChI=1S/C32H54N4O7/c1-21(2)16-14-12-10-8-7-9-11-13-15-17-22(3)29-24(5)31(41)34-23(4)18-19-26(38)36(6)20-25(37)35-27(32(42)43-29)28(39)30(33)40/h18-19,21-22,24,27-29,39H,4,7-17,20H2,1-3,5-6H3,(H2,33,40)(H,34,41)(H,35,37)/b19-18-

InChI Key

NODOLTRBPIFGCQ-HNENSFHCSA-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
Micromonospora sp.	NPAtlas	8557602
Micromonospora sp. No. R385-2	Bacteria	KNApSAcK

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	4.75	ALOGPS
logP	3.54	ChemAxon
logS	-5.5	ALOGPS
pKa (Strongest Acidic)	10.66	ChemAxon
pKa (Strongest Basic)	-0.57	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	168.13 Å²	ChemAxon
Rotatable Bond Count	15	ChemAxon
Refractivity	165.46 m³·mol⁻¹	ChemAxon
Polarizability	67.78 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

NPAtlas ID

NPA019491

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00016159

Chemspider ID

78444600

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

101689637

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

McBrien KD, Berry RL, Lowe SE, Neddermann KM, Bursuker I, Huang S, Klohr SE, Leet JE: Rakicidins, new cytotoxic lipopeptides from Micromonospora sp. fermentation, isolation and characterization. J Antibiot (Tokyo). 1995 Dec;48(12):1446-52. doi: 10.7164/antibiotics.48.1446. [PubMed:8557602 ]
Poulsen TB: Total Synthesis of Natural Products Containing Enamine or Enol Ether Derivatives. Acc Chem Res. 2021 Apr 20;54(8):1830-1842. doi: 10.1021/acs.accounts.0c00851. Epub 2021 Mar 4. [PubMed:33660974 ]
Chen J, Li J, Wu L, Geng Y, Yu J, Chong C, Wang M, Gao Y, Bai C, Ding Y, Chen Y, Zhang Q: Syntheses and anti-pancreatic cancer activities of rakicidin A analogues. Eur J Med Chem. 2018 May 10;151:601-627. doi: 10.1016/j.ejmech.2018.03.078. Epub 2018 Mar 29. [PubMed:29656202 ]
Sang F, Ding Y, Wang J, Sun B, Sun J, Geng Y, Zhang Z, Ding K, Wu LL, Liu JW, Bai C, Yang G, Zhang Q, Li LY, Chen Y: Structure-Activity Relationship Study of Rakicidins: Overcoming Chronic Myeloid Leukemia Resistance to Imatinib with 4-Methylester-Rakicidin A. J Med Chem. 2016 Feb 11;59(3):1184-96. doi: 10.1021/acs.jmedchem.5b01841. Epub 2016 Jan 27. [PubMed:26814890 ]
Tsakos M, Clement LL, Schaffert ES, Olsen FN, Rupiani S, Djurhuus R, Yu W, Jacobsen KM, Villadsen NL, Poulsen TB: Total Synthesis and Biological Evaluation of Rakicidin A and Discovery of a Simplified Bioactive Analogue. Angew Chem Int Ed Engl. 2016 Jan 18;55(3):1030-5. doi: 10.1002/anie.201509926. Epub 2015 Dec 4. [PubMed:26637117 ]

Showing NP-Card for Rakicidin A (NP0023048)

MOL for NP0023048 (Rakicidin A)

3D MOL for NP0023048 (Rakicidin A)

3D SDF for NP0023048 (Rakicidin A)

3D-SDF for NP0023048 (Rakicidin A)

PDB for NP0023048 (Rakicidin A)

3D PDB for NP0023048 (Rakicidin A)

SMILES for NP0023048 (Rakicidin A)

INCHI for NP0023048 (Rakicidin A)

Structure for NP0023048 (Rakicidin A)

3D Structure for NP0023048 (Rakicidin A)