NP-MRD: Showing NP-Card for Apicidin D2 (NP0004035)

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Record Information

Version

1.0

Created at

2020-12-09 01:32:48 UTC

Updated at

2021-07-15 16:48:03 UTC

NP-MRD ID

NP0004035

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Apicidin D2

Provided By

NPAtlas

Description

Apicidin D2 is found in Fusarium sp., Fusarium sp.ATCC74289 and Fusarium sp.ATCC74322. It was first documented in 2002 (PMID: 11856024). Based on a literature review very few articles have been published on (3S,6S,9S,15aR)-9-(butan-2-yl)-1,4,7-trihydroxy-3-[(6S)-6-hydroxyoctyl]-6-[(1-methoxy-1H-indol-3-yl)methyl]-3H,6H,9H,10H,12H,13H,14H,15H,15aH-pyrido[1,2-a]1,4,7,10-tetraazacyclododecan-10-one.

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652307012117503D          

 96 99  0  0  0  0            999 V2000
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   -4.1202   -3.0188   -0.4447 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1992   -1.5325    0.2414 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.9820   -1.5057   -1.1593 N   0  0  0  0  0  0  0  0  0  0  0  0
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M  END

     RDKit          3D

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M  END


  Mrv1652307012117503D          

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 27 72  1  0  0  0  0
 27 73  1  0  0  0  0
 28 74  1  0  0  0  0
 28 75  1  0  0  0  0
 29 76  1  0  0  0  0
 29 77  1  0  0  0  0
 30 78  1  0  0  0  0
 30 79  1  0  0  0  0
 31 80  1  6  0  0  0
 32 81  1  0  0  0  0
 33 82  1  0  0  0  0
 33 83  1  0  0  0  0
 34 84  1  0  0  0  0
 34 85  1  0  0  0  0
 34 86  1  0  0  0  0
 35 87  1  0  0  0  0
 38 88  1  6  0  0  0
 39 89  1  0  0  0  0
 39 90  1  0  0  0  0
 40 91  1  0  0  0  0
 40 92  1  0  0  0  0
 41 93  1  0  0  0  0
 41 94  1  0  0  0  0
 42 95  1  0  0  0  0
 42 96  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0004035

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]O[C@@]([H])(C([H])([H])C([H])([H])[H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])[C@]1([H])N([H])C(=O)[C@]2([H])N(C(=O)[C@@]([H])(N([H])C(=O)[C@@]([H])(N([H])C1=O)C([H])([H])C1=C([H])N(OC([H])([H])[H])C3=C([H])C([H])=C([H])C([H])=C13)[C@@]([H])(C([H])([H])[H])C([H])([H])C([H])([H])[H])C([H])([H])C([H])([H])C([H])([H])C2([H])[H]

> <INCHI_IDENTIFIER>
InChI=1S/C34H51N5O6/c1-5-22(3)30-34(44)38-19-13-12-18-29(38)33(43)35-26(16-9-7-8-14-24(40)6-2)31(41)36-27(32(42)37-30)20-23-21-39(45-4)28-17-11-10-15-25(23)28/h10-11,15,17,21-22,24,26-27,29-30,40H,5-9,12-14,16,18-20H2,1-4H3,(H,35,43)(H,36,41)(H,37,42)/t22-,24-,26-,27-,29+,30-/m0/s1

> <INCHI_KEY>
XSKZVBPNWYDMNT-YWHDRAQFSA-N

> <FORMULA>
C34H51N5O6

> <MOLECULAR_WEIGHT>
625.811

> <EXACT_MASS>
625.383934382

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
96

> <JCHEM_AVERAGE_POLARIZABILITY>
69.99858551078853

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3S,6S,9S,15aR)-9-[(2S)-butan-2-yl]-3-[(6S)-6-hydroxyoctyl]-6-[(1-methoxy-1H-indol-3-yl)methyl]-tetradecahydro-1H-pyrido[1,2-a]1,4,7,10-tetraazacyclododecane-1,4,7,10-tetrone

> <ALOGPS_LOGP>
3.47

> <JCHEM_LOGP>
3.1671820363333327

> <ALOGPS_LOGS>
-4.60

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
11.425047641619322

> <JCHEM_PKA_STRONGEST_ACIDIC>
10.86284973745052

> <JCHEM_PKA_STRONGEST_BASIC>
-1.3601939811928885

> <JCHEM_POLAR_SURFACE_AREA>
142.00000000000003

> <JCHEM_REFRACTIVITY>
172.23890000000006

> <JCHEM_ROTATABLE_BOND_COUNT>
12

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.59e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(3S,6S,9S,15aR)-9-[(2S)-butan-2-yl]-3-[(6S)-6-hydroxyoctyl]-6-[(1-methoxyindol-3-yl)methyl]-decahydro-2H-pyrido[1,2-a]1,4,7,10-tetraazacyclododecane-1,4,7,10-tetrone

> <JCHEM_VEBER_RULE>
0

$$$$

     RDKit          3D

 96 99  0  0  0  0  0  0  0  0999 V2000
   -5.6567   -1.9847    1.8248 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -4.1202   -3.0188   -0.4447 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -1.9820   -1.5057   -1.1593 N   0  0  0  0  0  0  0  0  0  0  0  0
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  1  2  1  0
  2  3  1  0
  3  4  1  0
  3  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  7  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  2  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 13 16  1  0
 16 17  2  0
 17 18  1  0
 18 19  2  0
 19 20  1  0
 20 21  2  0
  9 22  1  0
 22 23  1  0
 23 24  2  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
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 31 32  1  0
 31 33  1  0
 33 34  1  0
 25 35  1  0
 35 36  1  0
 36 37  2  0
 36 38  1  0
 38 39  1  0
 39 40  1  0
 40 41  1  0
 41 42  1  0
 42 43  1  0
 43 44  1  0
 44 45  2  0
 44  5  1  0
 21 11  1  0
 43 38  1  0
 21 16  1  0
  1 46  1  0
  1 47  1  0
  1 48  1  0
  2 49  1  0
  2 50  1  0
  3 51  1  6
  4 52  1  0
  4 53  1  0
  4 54  1  0
  5 55  1  1
  6 56  1  0
  9 57  1  1
 10 58  1  0
 10 59  1  0
 12 60  1  0
 15 61  1  0
 15 62  1  0
 15 63  1  0
 17 64  1  0
 18 65  1  0
 19 66  1  0
 20 67  1  0
 22 68  1  0
 25 69  1  1
 26 70  1  0
 26 71  1  0
 27 72  1  0
 27 73  1  0
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 28 75  1  0
 29 76  1  0
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 30 78  1  0
 30 79  1  0
 31 80  1  6
 32 81  1  0
 33 82  1  0
 33 83  1  0
 34 84  1  0
 34 85  1  0
 34 86  1  0
 35 87  1  0
 38 88  1  6
 39 89  1  0
 39 90  1  0
 40 91  1  0
 40 92  1  0
 41 93  1  0
 41 94  1  0
 42 95  1  0
 42 96  1  0
M  END

HEADER    PROTEIN                                 01-JUL-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   01-JUL-21         0                                  
HETATM    1  C   UNK     0      -5.657  -1.985   1.825  0.00  0.00           C+0
HETATM    2  C   UNK     0      -4.122  -1.951   1.832  0.00  0.00           C+0
HETATM    3  C   UNK     0      -3.690  -1.874   0.411  0.00  0.00           C+0
HETATM    4  C   UNK     0      -4.120  -3.019  -0.445  0.00  0.00           C+0
HETATM    5  C   UNK     0      -2.199  -1.533   0.241  0.00  0.00           C+0
HETATM    6  N   UNK     0      -1.982  -1.506  -1.159  0.00  0.00           N+0
HETATM    7  C   UNK     0      -1.929  -0.240  -1.802  0.00  0.00           C+0
HETATM    8  O   UNK     0      -1.683  -0.239  -3.044  0.00  0.00           O+0
HETATM    9  C   UNK     0      -2.138   1.038  -1.126  0.00  0.00           C+0
HETATM   10  C   UNK     0      -2.856   1.939  -2.155  0.00  0.00           C+0
HETATM   11  C   UNK     0      -3.106   3.268  -1.538  0.00  0.00           C+0
HETATM   12  C   UNK     0      -2.434   4.454  -1.754  0.00  0.00           C+0
HETATM   13  N   UNK     0      -2.938   5.444  -1.022  0.00  0.00           N+0
HETATM   14  O   UNK     0      -2.539   6.773  -0.961  0.00  0.00           O+0
HETATM   15  C   UNK     0      -2.736   7.514  -2.174  0.00  0.00           C+0
HETATM   16  C   UNK     0      -3.958   4.919  -0.308  0.00  0.00           C+0
HETATM   17  C   UNK     0      -4.815   5.507   0.603  0.00  0.00           C+0
HETATM   18  C   UNK     0      -5.785   4.722   1.196  0.00  0.00           C+0
HETATM   19  C   UNK     0      -5.904   3.385   0.892  0.00  0.00           C+0
HETATM   20  C   UNK     0      -5.042   2.801  -0.022  0.00  0.00           C+0
HETATM   21  C   UNK     0      -4.085   3.573  -0.608  0.00  0.00           C+0
HETATM   22  N   UNK     0      -0.926   1.734  -0.764  0.00  0.00           N+0
HETATM   23  C   UNK     0       0.381   1.312  -0.701  0.00  0.00           C+0
HETATM   24  O   UNK     0       1.261   1.844  -1.473  0.00  0.00           O+0
HETATM   25  C   UNK     0       0.998   0.242   0.202  0.00  0.00           C+0
HETATM   26  C   UNK     0       2.003   0.963   1.043  0.00  0.00           C+0
HETATM   27  C   UNK     0       2.807   0.258   2.035  0.00  0.00           C+0
HETATM   28  C   UNK     0       3.807  -0.684   1.443  0.00  0.00           C+0
HETATM   29  C   UNK     0       4.844   0.069   0.598  0.00  0.00           C+0
HETATM   30  C   UNK     0       5.782  -0.944   0.035  0.00  0.00           C+0
HETATM   31  C   UNK     0       6.864  -0.344  -0.822  0.00  0.00           C+0
HETATM   32  O   UNK     0       6.363   0.353  -1.918  0.00  0.00           O+0
HETATM   33  C   UNK     0       7.816   0.514  -0.006  0.00  0.00           C+0
HETATM   34  C   UNK     0       8.880   1.092  -0.907  0.00  0.00           C+0
HETATM   35  N   UNK     0       1.567  -0.781  -0.618  0.00  0.00           N+0
HETATM   36  C   UNK     0       1.073  -2.061  -0.951  0.00  0.00           C+0
HETATM   37  O   UNK     0       0.838  -2.137  -2.243  0.00  0.00           O+0
HETATM   38  C   UNK     0       0.786  -3.255  -0.218  0.00  0.00           C+0
HETATM   39  C   UNK     0       2.018  -3.786   0.559  0.00  0.00           C+0
HETATM   40  C   UNK     0       1.760  -5.242   0.834  0.00  0.00           C+0
HETATM   41  C   UNK     0       0.580  -5.257   1.821  0.00  0.00           C+0
HETATM   42  C   UNK     0      -0.609  -4.796   1.017  0.00  0.00           C+0
HETATM   43  N   UNK     0      -0.396  -3.397   0.578  0.00  0.00           N+0
HETATM   44  C   UNK     0      -1.348  -2.478   1.012  0.00  0.00           C+0
HETATM   45  O   UNK     0      -1.580  -2.377   2.286  0.00  0.00           O+0
HETATM   46  H   UNK     0      -6.058  -1.554   2.767  0.00  0.00           H+0
HETATM   47  H   UNK     0      -6.015  -3.021   1.668  0.00  0.00           H+0
HETATM   48  H   UNK     0      -5.984  -1.375   0.961  0.00  0.00           H+0
HETATM   49  H   UNK     0      -3.793  -1.085   2.401  0.00  0.00           H+0
HETATM   50  H   UNK     0      -3.817  -2.938   2.251  0.00  0.00           H+0
HETATM   51  H   UNK     0      -4.207  -0.963  -0.026  0.00  0.00           H+0
HETATM   52  H   UNK     0      -3.369  -3.834  -0.374  0.00  0.00           H+0
HETATM   53  H   UNK     0      -4.207  -2.705  -1.521  0.00  0.00           H+0
HETATM   54  H   UNK     0      -5.122  -3.325  -0.137  0.00  0.00           H+0
HETATM   55  H   UNK     0      -2.096  -0.542   0.738  0.00  0.00           H+0
HETATM   56  H   UNK     0      -1.868  -2.387  -1.680  0.00  0.00           H+0
HETATM   57  H   UNK     0      -2.870   1.007  -0.277  0.00  0.00           H+0
HETATM   58  H   UNK     0      -3.784   1.452  -2.498  0.00  0.00           H+0
HETATM   59  H   UNK     0      -2.175   2.034  -3.010  0.00  0.00           H+0
HETATM   60  H   UNK     0      -1.599   4.553  -2.438  0.00  0.00           H+0
HETATM   61  H   UNK     0      -2.648   6.837  -3.056  0.00  0.00           H+0
HETATM   62  H   UNK     0      -1.972   8.298  -2.275  0.00  0.00           H+0
HETATM   63  H   UNK     0      -3.749   7.933  -2.191  0.00  0.00           H+0
HETATM   64  H   UNK     0      -4.717   6.552   0.836  0.00  0.00           H+0
HETATM   65  H   UNK     0      -6.454   5.174   1.906  0.00  0.00           H+0
HETATM   66  H   UNK     0      -6.691   2.801   1.389  0.00  0.00           H+0
HETATM   67  H   UNK     0      -5.190   1.740  -0.217  0.00  0.00           H+0
HETATM   68  H   UNK     0      -1.106   2.765  -0.518  0.00  0.00           H+0
HETATM   69  H   UNK     0       0.233  -0.136   0.910  0.00  0.00           H+0
HETATM   70  H   UNK     0       1.396   1.776   1.588  0.00  0.00           H+0
HETATM   71  H   UNK     0       2.640   1.607   0.347  0.00  0.00           H+0
HETATM   72  H   UNK     0       2.140  -0.379   2.686  0.00  0.00           H+0
HETATM   73  H   UNK     0       3.372   0.962   2.726  0.00  0.00           H+0
HETATM   74  H   UNK     0       3.369  -1.439   0.799  0.00  0.00           H+0
HETATM   75  H   UNK     0       4.353  -1.256   2.244  0.00  0.00           H+0
HETATM   76  H   UNK     0       5.420   0.757   1.270  0.00  0.00           H+0
HETATM   77  H   UNK     0       4.346   0.621  -0.179  0.00  0.00           H+0
HETATM   78  H   UNK     0       5.266  -1.707  -0.581  0.00  0.00           H+0
HETATM   79  H   UNK     0       6.320  -1.504   0.854  0.00  0.00           H+0
HETATM   80  H   UNK     0       7.475  -1.205  -1.206  0.00  0.00           H+0
HETATM   81  H   UNK     0       6.774   0.020  -2.765  0.00  0.00           H+0
HETATM   82  H   UNK     0       8.300  -0.124   0.758  0.00  0.00           H+0
HETATM   83  H   UNK     0       7.295   1.367   0.466  0.00  0.00           H+0
HETATM   84  H   UNK     0       8.465   1.372  -1.895  0.00  0.00           H+0
HETATM   85  H   UNK     0       9.409   1.940  -0.426  0.00  0.00           H+0
HETATM   86  H   UNK     0       9.641   0.307  -1.089  0.00  0.00           H+0
HETATM   87  H   UNK     0       2.507  -0.459  -1.058  0.00  0.00           H+0
HETATM   88  H   UNK     0       0.693  -4.134  -0.987  0.00  0.00           H+0
HETATM   89  H   UNK     0       2.046  -3.275   1.545  0.00  0.00           H+0
HETATM   90  H   UNK     0       2.880  -3.606  -0.085  0.00  0.00           H+0
HETATM   91  H   UNK     0       1.538  -5.838  -0.054  0.00  0.00           H+0
HETATM   92  H   UNK     0       2.659  -5.619   1.399  0.00  0.00           H+0
HETATM   93  H   UNK     0       0.839  -4.597   2.649  0.00  0.00           H+0
HETATM   94  H   UNK     0       0.385  -6.291   2.145  0.00  0.00           H+0
HETATM   95  H   UNK     0      -1.556  -5.017   1.459  0.00  0.00           H+0
HETATM   96  H   UNK     0      -0.566  -5.393   0.057  0.00  0.00           H+0
CONECT    1    2   46   47   48                                             
CONECT    2    1    3   49   50                                             
CONECT    3    2    4    5   51                                             
CONECT    4    3   52   53   54                                             
CONECT    5    3    6   44   55                                             
CONECT    6    5    7   56                                                  
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10   22   57                                             
CONECT   10    9   11   58   59                                             
CONECT   11   10   12   21                                                  
CONECT   12   11   13   60                                                  
CONECT   13   12   14   16                                                  
CONECT   14   13   15                                                       
CONECT   15   14   61   62   63                                             
CONECT   16   13   17   21                                                  
CONECT   17   16   18   64                                                  
CONECT   18   17   19   65                                                  
CONECT   19   18   20   66                                                  
CONECT   20   19   21   67                                                  
CONECT   21   20   11   16                                                  
CONECT   22    9   23   68                                                  
CONECT   23   22   24   25                                                  
CONECT   24   23                                                            
CONECT   25   23   26   35   69                                             
CONECT   26   25   27   70   71                                             
CONECT   27   26   28   72   73                                             
CONECT   28   27   29   74   75                                             
CONECT   29   28   30   76   77                                             
CONECT   30   29   31   78   79                                             
CONECT   31   30   32   33   80                                             
CONECT   32   31   81                                                       
CONECT   33   31   34   82   83                                             
CONECT   34   33   84   85   86                                             
CONECT   35   25   36   87                                                  
CONECT   36   35   37   38                                                  
CONECT   37   36                                                            
CONECT   38   36   39   43   88                                             
CONECT   39   38   40   89   90                                             
CONECT   40   39   41   91   92                                             
CONECT   41   40   42   93   94                                             
CONECT   42   41   43   95   96                                             
CONECT   43   42   44   38                                                  
CONECT   44   43   45    5                                                  
CONECT   45   44                                                            
CONECT   46    1                                                            
CONECT   47    1                                                            
CONECT   48    1                                                            
CONECT   49    2                                                            
CONECT   50    2                                                            
CONECT   51    3                                                            
CONECT   52    4                                                            
CONECT   53    4                                                            
CONECT   54    4                                                            
CONECT   55    5                                                            
CONECT   56    6                                                            
CONECT   57    9                                                            
CONECT   58   10                                                            
CONECT   59   10                                                            
CONECT   60   12                                                            
CONECT   61   15                                                            
CONECT   62   15                                                            
CONECT   63   15                                                            
CONECT   64   17                                                            
CONECT   65   18                                                            
CONECT   66   19                                                            
CONECT   67   20                                                            
CONECT   68   22                                                            
CONECT   69   25                                                            
CONECT   70   26                                                            
CONECT   71   26                                                            
CONECT   72   27                                                            
CONECT   73   27                                                            
CONECT   74   28                                                            
CONECT   75   28                                                            
CONECT   76   29                                                            
CONECT   77   29                                                            
CONECT   78   30                                                            
CONECT   79   30                                                            
CONECT   80   31                                                            
CONECT   81   32                                                            
CONECT   82   33                                                            
CONECT   83   33                                                            
CONECT   84   34                                                            
CONECT   85   34                                                            
CONECT   86   34                                                            
CONECT   87   35                                                            
CONECT   88   38                                                            
CONECT   89   39                                                            
CONECT   90   39                                                            
CONECT   91   40                                                            
CONECT   92   40                                                            
CONECT   93   41                                                            
CONECT   94   41                                                            
CONECT   95   42                                                            
CONECT   96   42                                                            
MASTER        0    0    0    0    0    0    0    0   96    0  198    0
END

RDKit          3D

96 99  0  0  0  0  0  0  0  0999 V2000
   -5.6567   -1.9847    1.8248 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1219   -1.9508    1.8320 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6899   -1.8738    0.4105 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.1202   -3.0188   -0.4447 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1992   -1.5325    0.2414 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.9820   -1.5057   -1.1593 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9291   -0.2400   -1.8017 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6832   -0.2387   -3.0436 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1379    1.0376   -1.1259 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.8559    1.9387   -2.1550 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1058    3.2676   -1.5383 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4343    4.4539   -1.7535 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9377    5.4437   -1.0224 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5386    6.7731   -0.9607 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7358    7.5137   -2.1739 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9579    4.9189   -0.3082 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8146    5.5071    0.6032 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7851    4.7223    1.1959 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9041    3.3848    0.8922 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0423    2.8006   -0.0224 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0845    3.5729   -0.6079 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9256    1.7339   -0.7644 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.3809    1.3122   -0.7009 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2610    1.8439   -1.4730 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9980    0.2420    0.2024 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.0028    0.9630    1.0429 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8073    0.2576    2.0348 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8070   -0.6837    1.4432 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8443    0.0690    0.5978 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7825   -0.9442    0.0351 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8638   -0.3435   -0.8216 C   0  0  1  0  0  0  0  0  0  0  0  0
    6.3627    0.3527   -1.9175 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.8155    0.5141   -0.0059 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.8797    1.0920   -0.9073 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5671   -0.7810   -0.6175 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.0732   -2.0606   -0.9512 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8377   -2.1367   -2.2428 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7862   -3.2547   -0.2182 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.0175   -3.7858    0.5592 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7599   -5.2424    0.8341 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5799   -5.2573    1.8207 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6093   -4.7959    1.0170 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3960   -3.3965    0.5783 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3476   -2.4777    1.0123 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5803   -2.3773    2.2864 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0575   -1.5535    2.7671 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0147   -3.0211    1.6681 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9839   -1.3748    0.9610 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7926   -1.0853    2.4015 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8167   -2.9375    2.2511 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2068   -0.9626   -0.0260 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3691   -3.8343   -0.3744 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2065   -2.7050   -1.5207 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1225   -3.3250   -0.1373 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0964   -0.5419    0.7382 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8679   -2.3872   -1.6801 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8700    1.0068   -0.2773 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7838    1.4518   -2.4985 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1748    2.0341   -3.0095 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5988    4.5529   -2.4384 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6479    6.8373   -3.0564 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9719    8.2979   -2.2751 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7494    7.9333   -2.1914 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7167    6.5524    0.8364 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4539    5.1742    1.9055 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6914    2.8005    1.3885 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1904    1.7395   -0.2174 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1063    2.7653   -0.5182 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2329   -0.1356    0.9101 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3964    1.7756    1.5878 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6403    1.6066    0.3474 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1401   -0.3790    2.6863 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3718    0.9621    2.7263 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3687   -1.4390    0.7990 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3527   -1.2559    2.2435 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4205    0.7565    1.2702 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3465    0.6213   -0.1789 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2659   -1.7073   -0.5811 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.3201   -1.5040    0.8542 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.4749   -1.2047   -1.2063 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.7739    0.0197   -2.7649 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.2997   -0.1243    0.7579 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.2945    1.3673    0.4661 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.4653    1.3720   -1.8954 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.4088    1.9403   -0.4263 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.6406    0.3070   -1.0891 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5073   -0.4592   -1.0576 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6928   -4.1336   -0.9868 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0462   -3.2745    1.5447 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8800   -3.6063   -0.0854 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5378   -5.8382   -0.0537 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6589   -5.6191    1.3988 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8390   -4.5972    2.6489 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3845   -6.2910    2.1454 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5562   -5.0172    1.4594 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5657   -5.3933    0.0566 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  3  5  1  0
  5  6  1  0
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M  END

View in JSmol View NMR Assignments

Synonyms

Not Available

Chemical Formula

C₃₄H₅₁N₅O₆

Average Mass

625.8110 Da

Monoisotopic Mass

625.38393 Da

IUPAC Name

(3S,6S,9S,15aR)-9-[(2S)-butan-2-yl]-3-[(6S)-6-hydroxyoctyl]-6-[(1-methoxy-1H-indol-3-yl)methyl]-tetradecahydro-1H-pyrido[1,2-a]1,4,7,10-tetraazacyclododecane-1,4,7,10-tetrone

Traditional Name

(3S,6S,9S,15aR)-9-[(2S)-butan-2-yl]-3-[(6S)-6-hydroxyoctyl]-6-[(1-methoxyindol-3-yl)methyl]-decahydro-2H-pyrido[1,2-a]1,4,7,10-tetraazacyclododecane-1,4,7,10-tetrone

CAS Registry Number

Not Available

SMILES

CC[C@H](O)CCCCC[C@@H]1NC(=O)[C@H]2CCCCN2C(=O)[C@@H](NC(=O)[C@H](CC2=CN(OC)C3=CC=CC=C23)NC1=O)C(C)CC

InChI Identifier

InChI=1S/C34H51N5O6/c1-5-22(3)30-34(44)38-19-13-12-18-29(38)33(43)35-26(16-9-7-8-14-24(40)6-2)31(41)36-27(32(42)37-30)20-23-21-39(45-4)28-17-11-10-15-25(23)28/h10-11,15,17,21-22,24,26-27,29-30,40H,5-9,12-14,16,18-20H2,1-4H3,(H,35,43)(H,36,41)(H,37,42)/t22?,24-,26-,27-,29+,30-/m0/s1

InChI Key

XSKZVBPNWYDMNT-YWHDRAQFSA-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
Fusarium sp.	NPAtlas	11856024
Fusarium sp.ATCC74289	Fungi	KNApSAcK
Fusarium sp.ATCC74322	Fungi	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	3.47	ALOGPS
logP	3.17	ChemAxon
logS	-4.6	ALOGPS
pKa (Strongest Acidic)	10.86	ChemAxon
pKa (Strongest Basic)	-1.4	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	142 Å²	ChemAxon
Rotatable Bond Count	12	ChemAxon
Refractivity	172.24 m³·mol⁻¹	ChemAxon
Polarizability	70 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

External Links

NPAtlas ID

NPA016250

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

9192781

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

11017597

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Singh SB, Zink DL, Liesch JM, Mosley RT, Dombrowski AW, Bills GF, Darkin-Rattray SJ, Schmatz DM, Goetz MA: Structure and chemistry of apicidins, a class of novel cyclic tetrapeptides without a terminal alpha-keto epoxide as inhibitors of histone deacetylase with potent antiprotozoal activities. J Org Chem. 2002 Feb 8;67(3):815-25. doi: 10.1021/jo016088w. [PubMed:11856024 ]

Showing NP-Card for Apicidin D2 (NP0004035)

MOL for NP0004035 (Apicidin D2)

3D MOL for NP0004035 (Apicidin D2)

3D SDF for NP0004035 (Apicidin D2)

3D-SDF for NP0004035 (Apicidin D2)

PDB for NP0004035 (Apicidin D2)

3D PDB for NP0004035 (Apicidin D2)

SMILES for NP0004035 (Apicidin D2)

INCHI for NP0004035 (Apicidin D2)

Structure for NP0004035 (Apicidin D2)

3D Structure for NP0004035 (Apicidin D2)