NP-MRD: Showing NP-Card for gombamide A (NP0043569)

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Record Information

Version

1.0

Created at

2021-06-21 00:56:25 UTC

Updated at

2021-06-30 00:19:19 UTC

NP-MRD ID

NP0043569

Secondary Accession Numbers

None

Natural Product Identification

Common Name

gombamide A

Provided By

JEOL Database JEOL Logo

Description

NSC787890 belongs to the class of organic compounds known as oligopeptides. These are organic compounds containing a sequence of between three and ten alpha-amino acids joined by peptide bonds. gombamide A is found in Clathria gombawuiensis. It was first documented in 2013 (Woo, J. -K., et al.). Based on a literature review very few articles have been published on NSC787890.

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652306212102563D          

100105  0  0  0  0            999 V2000
   -5.8940   -5.7761    5.9827 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5332   -4.7431    5.4498 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4107   -3.3932    6.1061 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.5280   -2.6227    5.1268 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.8504   -3.2454    3.7751 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.6916   -3.2134    2.7675 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3622   -4.1904    2.0971 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0972   -1.9865    2.6046 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0319   -1.7639    1.6270 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.5690   -1.5851    0.1896 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.8069   -0.2265    0.0306 S   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7032   -0.6285   -1.7722 S   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1282    0.6700   -2.9421 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.6328    0.9900   -2.9989 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.7975   -0.2558   -3.3363 C   0  0  0  0  0  0  0  0  0  0  0  0
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    4.0997   -1.6000   -2.8921 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3447    1.8985   -4.1269 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6577    3.0609   -4.2644 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3962    3.3736   -5.4340 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -1.8892    4.3194   -0.6974 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3462    5.4485   -0.8544 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9562    3.5552    0.6444 C   0  0  2  0  0  0  0  0  0  0  0  0
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   -1.3791   -2.6417    1.6547 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -1.7481   -1.3758   -0.5001 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4807    0.3542   -3.9318 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -2.3128    1.4178   -2.0589 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -0.8863    2.7321   -1.5204 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -0.6620    5.6840    1.8554 H   0  0  0  0  0  0  0  0  0  0  0  0
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    0.7313    1.2993    2.6071 H   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


  Mrv1652306212102563D          

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M  END
> <DATABASE_ID>
NP0043569

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]OC1=C([H])C([H])=C(\C([H])=C(/[H])N([H])C(=O)[C@@]2([H])N([H])C(=O)[C@@]([H])(N([H])C(=O)[C@@]3([H])N(C(=O)[C@@]4([H])N(C(=O)[C@@]([H])(N([H])C(=O)[C@@]5([H])N([H])C(=O)C([H])([H])C5([H])[H])C([H])([H])SSC2([H])[H])C([H])([H])C([H])([H])C4([H])[H])C([H])([H])C([H])([H])C3([H])[H])C([H])([H])C2=C([H])C([H])=C([H])C([H])=C2[H])C([H])=C1[H]

> <INCHI_IDENTIFIER>
InChI=1S/C38H45N7O8S2/c46-25-12-10-23(11-13-25)16-17-39-33(48)28-21-54-55-22-29(43-34(49)26-14-15-32(47)40-26)37(52)45-19-5-9-31(45)38(53)44-18-4-8-30(44)36(51)41-27(35(50)42-28)20-24-6-2-1-3-7-24/h1-3,6-7,10-13,16-17,26-31,46H,4-5,8-9,14-15,18-22H2,(H,39,48)(H,40,47)(H,41,51)(H,42,50)(H,43,49)/b17-16+/t26-,27-,28-,29-,30-,31-/m0/s1

> <INCHI_KEY>
IMNGJUDDINZRBE-UQTWBUSUSA-N

> <FORMULA>
C38H45N7O8S2

> <MOLECULAR_WEIGHT>
791.94

> <EXACT_MASS>
791.277103785

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
100

> <JCHEM_AVERAGE_POLARIZABILITY>
80.01143134928677

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3S,9R,14R,17S,20S)-17-benzyl-N-[(E)-2-(4-hydroxyphenyl)ethenyl]-2,8,16,19-tetraoxo-9-[(2S)-5-oxopyrrolidine-2-amido]-11,12-dithia-1,7,15,18-tetraazatricyclo[18.3.0.0^{3,7}]tricosane-14-carboxamide

> <ALOGPS_LOGP>
1.47

> <JCHEM_LOGP>
-0.3650871996666657

> <ALOGPS_LOGS>
-4.11

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
10.558159433131436

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.410023725983471

> <JCHEM_PKA_STRONGEST_BASIC>
-2.191238697112944

> <JCHEM_POLAR_SURFACE_AREA>
206.35

> <JCHEM_REFRACTIVITY>
206.6097

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
6.19e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(3S,9R,14R,17S,20S)-17-benzyl-N-[(E)-2-(4-hydroxyphenyl)ethenyl]-2,8,16,19-tetraoxo-9-[(2S)-5-oxopyrrolidine-2-amido]-11,12-dithia-1,7,15,18-tetraazatricyclo[18.3.0.0^{3,7}]tricosane-14-carboxamide

> <JCHEM_VEBER_RULE>
0

$$$$

     RDKit          3D

100105  0  0  0  0  0  0  0  0999 V2000
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M  END

HEADER    PROTEIN                                 21-JUN-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   21-JUN-21         0                                  
HETATM    1  O   UNK     0      -5.894  -5.776   5.983  0.00  0.00           O+0
HETATM    2  C   UNK     0      -5.533  -4.743   5.450  0.00  0.00           C+0
HETATM    3  C   UNK     0      -5.411  -3.393   6.106  0.00  0.00           C+0
HETATM    4  C   UNK     0      -4.528  -2.623   5.127  0.00  0.00           C+0
HETATM    5  C   UNK     0      -4.850  -3.245   3.775  0.00  0.00           C+0
HETATM    6  C   UNK     0      -3.692  -3.213   2.768  0.00  0.00           C+0
HETATM    7  O   UNK     0      -3.362  -4.190   2.097  0.00  0.00           O+0
HETATM    8  N   UNK     0      -3.097  -1.986   2.605  0.00  0.00           N+0
HETATM    9  C   UNK     0      -2.032  -1.764   1.627  0.00  0.00           C+0
HETATM   10  C   UNK     0      -2.569  -1.585   0.190  0.00  0.00           C+0
HETATM   11  S   UNK     0      -3.807  -0.227   0.031  0.00  0.00           S+0
HETATM   12  S   UNK     0      -4.703  -0.629  -1.772  0.00  0.00           S+0
HETATM   13  C   UNK     0      -4.128   0.670  -2.942  0.00  0.00           C+0
HETATM   14  C   UNK     0      -2.633   0.990  -2.999  0.00  0.00           C+0
HETATM   15  C   UNK     0      -1.798  -0.256  -3.336  0.00  0.00           C+0
HETATM   16  O   UNK     0      -2.193  -1.117  -4.122  0.00  0.00           O+0
HETATM   17  N   UNK     0      -0.512  -0.227  -2.816  0.00  0.00           N+0
HETATM   18  C   UNK     0       0.444  -1.160  -3.132  0.00  0.00           C+0
HETATM   19  C   UNK     0       1.697  -1.069  -2.670  0.00  0.00           C+0
HETATM   20  C   UNK     0       2.769  -2.038  -2.942  0.00  0.00           C+0
HETATM   21  C   UNK     0       2.518  -3.397  -3.185  0.00  0.00           C+0
HETATM   22  C   UNK     0       3.571  -4.292  -3.399  0.00  0.00           C+0
HETATM   23  C   UNK     0       4.881  -3.830  -3.358  0.00  0.00           C+0
HETATM   24  O   UNK     0       5.938  -4.666  -3.559  0.00  0.00           O+0
HETATM   25  C   UNK     0       5.153  -2.493  -3.104  0.00  0.00           C+0
HETATM   26  C   UNK     0       4.100  -1.600  -2.892  0.00  0.00           C+0
HETATM   27  N   UNK     0      -2.345   1.899  -4.127  0.00  0.00           N+0
HETATM   28  C   UNK     0      -1.658   3.061  -4.264  0.00  0.00           C+0
HETATM   29  O   UNK     0      -1.396   3.374  -5.434  0.00  0.00           O+0
HETATM   30  C   UNK     0      -1.382   4.062  -3.115  0.00  0.00           C+0
HETATM   31  C   UNK     0      -0.081   4.855  -3.377  0.00  0.00           C+0
HETATM   32  C   UNK     0       1.184   4.082  -3.058  0.00  0.00           C+0
HETATM   33  C   UNK     0       1.843   4.280  -1.835  0.00  0.00           C+0
HETATM   34  C   UNK     0       3.009   3.576  -1.536  0.00  0.00           C+0
HETATM   35  C   UNK     0       3.527   2.663  -2.452  0.00  0.00           C+0
HETATM   36  C   UNK     0       2.877   2.453  -3.667  0.00  0.00           C+0
HETATM   37  C   UNK     0       1.712   3.160  -3.970  0.00  0.00           C+0
HETATM   38  N   UNK     0      -1.413   3.572  -1.748  0.00  0.00           N+0
HETATM   39  C   UNK     0      -1.889   4.319  -0.697  0.00  0.00           C+0
HETATM   40  O   UNK     0      -2.346   5.449  -0.854  0.00  0.00           O+0
HETATM   41  C   UNK     0      -1.956   3.555   0.644  0.00  0.00           C+0
HETATM   42  C   UNK     0      -2.434   4.450   1.796  0.00  0.00           C+0
HETATM   43  C   UNK     0      -1.131   4.891   2.450  0.00  0.00           C+0
HETATM   44  C   UNK     0      -0.300   3.622   2.390  0.00  0.00           C+0
HETATM   45  N   UNK     0      -0.688   2.990   1.139  0.00  0.00           N+0
HETATM   46  C   UNK     0      -0.149   1.829   0.630  0.00  0.00           C+0
HETATM   47  O   UNK     0      -0.409   1.451  -0.521  0.00  0.00           O+0
HETATM   48  C   UNK     0       0.695   0.944   1.577  0.00  0.00           C+0
HETATM   49  C   UNK     0       2.088   0.687   1.002  0.00  0.00           C+0
HETATM   50  C   UNK     0       2.302  -0.811   1.190  0.00  0.00           C+0
HETATM   51  C   UNK     0       0.910  -1.398   1.023  0.00  0.00           C+0
HETATM   52  N   UNK     0       0.039  -0.370   1.561  0.00  0.00           N+0
HETATM   53  C   UNK     0      -1.233  -0.524   2.063  0.00  0.00           C+0
HETATM   54  O   UNK     0      -1.754   0.350   2.766  0.00  0.00           O+0
HETATM   55  N   UNK     0      -5.203  -4.596   4.124  0.00  0.00           N+0
HETATM   56  H   UNK     0      -4.950  -3.474   7.093  0.00  0.00           H+0
HETATM   57  H   UNK     0      -6.406  -2.946   6.188  0.00  0.00           H+0
HETATM   58  H   UNK     0      -4.724  -1.546   5.153  0.00  0.00           H+0
HETATM   59  H   UNK     0      -3.472  -2.773   5.386  0.00  0.00           H+0
HETATM   60  H   UNK     0      -5.729  -2.778   3.316  0.00  0.00           H+0
HETATM   61  H   UNK     0      -3.404  -1.172   3.129  0.00  0.00           H+0
HETATM   62  H   UNK     0      -1.379  -2.642   1.655  0.00  0.00           H+0
HETATM   63  H   UNK     0      -3.052  -2.517  -0.125  0.00  0.00           H+0
HETATM   64  H   UNK     0      -1.748  -1.376  -0.500  0.00  0.00           H+0
HETATM   65  H   UNK     0      -4.481   0.354  -3.932  0.00  0.00           H+0
HETATM   66  H   UNK     0      -4.684   1.586  -2.708  0.00  0.00           H+0
HETATM   67  H   UNK     0      -2.313   1.418  -2.059  0.00  0.00           H+0
HETATM   68  H   UNK     0      -0.264   0.526  -2.172  0.00  0.00           H+0
HETATM   69  H   UNK     0       0.123  -1.965  -3.790  0.00  0.00           H+0
HETATM   70  H   UNK     0       1.982  -0.217  -2.061  0.00  0.00           H+0
HETATM   71  H   UNK     0       1.501  -3.782  -3.205  0.00  0.00           H+0
HETATM   72  H   UNK     0       3.348  -5.337  -3.589  0.00  0.00           H+0
HETATM   73  H   UNK     0       5.598  -5.553  -3.763  0.00  0.00           H+0
HETATM   74  H   UNK     0       6.182  -2.144  -3.074  0.00  0.00           H+0
HETATM   75  H   UNK     0       4.332  -0.556  -2.697  0.00  0.00           H+0
HETATM   76  H   UNK     0      -2.482   1.473  -5.041  0.00  0.00           H+0
HETATM   77  H   UNK     0      -2.211   4.778  -3.209  0.00  0.00           H+0
HETATM   78  H   UNK     0      -0.092   5.769  -2.768  0.00  0.00           H+0
HETATM   79  H   UNK     0      -0.029   5.205  -4.416  0.00  0.00           H+0
HETATM   80  H   UNK     0       1.454   4.997  -1.114  0.00  0.00           H+0
HETATM   81  H   UNK     0       3.523   3.751  -0.594  0.00  0.00           H+0
HETATM   82  H   UNK     0       4.444   2.126  -2.227  0.00  0.00           H+0
HETATM   83  H   UNK     0       3.282   1.748  -4.389  0.00  0.00           H+0
HETATM   84  H   UNK     0       1.231   2.997  -4.934  0.00  0.00           H+0
HETATM   85  H   UNK     0      -0.886   2.732  -1.520  0.00  0.00           H+0
HETATM   86  H   UNK     0      -2.665   2.733   0.491  0.00  0.00           H+0
HETATM   87  H   UNK     0      -3.013   3.850   2.510  0.00  0.00           H+0
HETATM   88  H   UNK     0      -3.057   5.296   1.494  0.00  0.00           H+0
HETATM   89  H   UNK     0      -1.269   5.257   3.470  0.00  0.00           H+0
HETATM   90  H   UNK     0      -0.662   5.684   1.855  0.00  0.00           H+0
HETATM   91  H   UNK     0       0.778   3.807   2.408  0.00  0.00           H+0
HETATM   92  H   UNK     0      -0.565   2.954   3.217  0.00  0.00           H+0
HETATM   93  H   UNK     0       0.731   1.299   2.607  0.00  0.00           H+0
HETATM   94  H   UNK     0       2.143   0.943  -0.061  0.00  0.00           H+0
HETATM   95  H   UNK     0       2.854   1.278   1.514  0.00  0.00           H+0
HETATM   96  H   UNK     0       3.026  -1.230   0.485  0.00  0.00           H+0
HETATM   97  H   UNK     0       2.667  -1.001   2.206  0.00  0.00           H+0
HETATM   98  H   UNK     0       0.652  -1.544  -0.029  0.00  0.00           H+0
HETATM   99  H   UNK     0       0.792  -2.344   1.557  0.00  0.00           H+0
HETATM  100  H   UNK     0      -5.194  -5.375   3.474  0.00  0.00           H+0
CONECT    1    2                                                            
CONECT    2   55    3    1                                                  
CONECT    3    2    4   56   57                                             
CONECT    4    3    5   58   59                                             
CONECT    5    6   55    4   60                                             
CONECT    6    8    5    7                                                  
CONECT    7    6                                                            
CONECT    8    9    6   61                                                  
CONECT    9    8   53   10   62                                             
CONECT   10   11    9   63   64                                             
CONECT   11   12   10                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14   65   66                                             
CONECT   14   15   27   13   67                                             
CONECT   15   17   16   14                                                  
CONECT   16   15                                                            
CONECT   17   18   15   68                                                  
CONECT   18   19   17   69                                                  
CONECT   19   18   20   70                                                  
CONECT   20   21   26   19                                                  
CONECT   21   20   22   71                                                  
CONECT   22   21   23   72                                                  
CONECT   23   22   25   24                                                  
CONECT   24   23   73                                                       
CONECT   25   23   26   74                                                  
CONECT   26   20   25   75                                                  
CONECT   27   28   14   76                                                  
CONECT   28   29   30   27                                                  
CONECT   29   28                                                            
CONECT   30   31   28   38   77                                             
CONECT   31   30   32   78   79                                             
CONECT   32   31   33   37                                                  
CONECT   33   32   34   80                                                  
CONECT   34   33   35   81                                                  
CONECT   35   34   36   82                                                  
CONECT   36   35   37   83                                                  
CONECT   37   36   32   84                                                  
CONECT   38   39   30   85                                                  
CONECT   39   41   38   40                                                  
CONECT   40   39                                                            
CONECT   41   45   39   42   86                                             
CONECT   42   43   41   87   88                                             
CONECT   43   44   42   89   90                                             
CONECT   44   45   43   91   92                                             
CONECT   45   41   46   44                                                  
CONECT   46   45   47   48                                                  
CONECT   47   46                                                            
CONECT   48   46   52   49   93                                             
CONECT   49   50   48   94   95                                             
CONECT   50   51   49   96   97                                             
CONECT   51   50   52   98   99                                             
CONECT   52   53   48   51                                                  
CONECT   53   52   54    9                                                  
CONECT   54   53                                                            
CONECT   55    5    2  100                                                  
CONECT   56    3                                                            
CONECT   57    3                                                            
CONECT   58    4                                                            
CONECT   59    4                                                            
CONECT   60    5                                                            
CONECT   61    8                                                            
CONECT   62    9                                                            
CONECT   63   10                                                            
CONECT   64   10                                                            
CONECT   65   13                                                            
CONECT   66   13                                                            
CONECT   67   14                                                            
CONECT   68   17                                                            
CONECT   69   18                                                            
CONECT   70   19                                                            
CONECT   71   21                                                            
CONECT   72   22                                                            
CONECT   73   24                                                            
CONECT   74   25                                                            
CONECT   75   26                                                            
CONECT   76   27                                                            
CONECT   77   30                                                            
CONECT   78   31                                                            
CONECT   79   31                                                            
CONECT   80   33                                                            
CONECT   81   34                                                            
CONECT   82   35                                                            
CONECT   83   36                                                            
CONECT   84   37                                                            
CONECT   85   38                                                            
CONECT   86   41                                                            
CONECT   87   42                                                            
CONECT   88   42                                                            
CONECT   89   43                                                            
CONECT   90   43                                                            
CONECT   91   44                                                            
CONECT   92   44                                                            
CONECT   93   48                                                            
CONECT   94   49                                                            
CONECT   95   49                                                            
CONECT   96   50                                                            
CONECT   97   50                                                            
CONECT   98   51                                                            
CONECT   99   51                                                            
CONECT  100   55                                                            
MASTER        0    0    0    0    0    0    0    0  100    0  210    0
END

RDKit          3D

100105  0  0  0  0  0  0  0  0999 V2000
   -5.8940   -5.7761    5.9827 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5332   -4.7431    5.4498 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4107   -3.3932    6.1061 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5280   -2.6227    5.1268 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8504   -3.2454    3.7751 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.6916   -3.2134    2.7675 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3622   -4.1904    2.0971 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0972   -1.9865    2.6046 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0319   -1.7639    1.6270 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.5690   -1.5851    0.1896 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8069   -0.2265    0.0306 S   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7032   -0.6285   -1.7722 S   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1282    0.6700   -2.9421 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6328    0.9900   -2.9989 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.7975   -0.2558   -3.3363 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1930   -1.1168   -4.1221 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5121   -0.2265   -2.8164 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.4439   -1.1603   -3.1318 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6973   -1.0691   -2.6702 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7686   -2.0385   -2.9417 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5177   -3.3970   -3.1847 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5711   -4.2923   -3.3986 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8809   -3.8299   -3.3578 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9378   -4.6661   -3.5589 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.1531   -2.4925   -3.1041 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0997   -1.6000   -2.8921 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3447    1.8985   -4.1269 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6577    3.0609   -4.2644 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3962    3.3736   -5.4340 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3820    4.0623   -3.1149 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.0809    4.8553   -3.3775 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1842    4.0824   -3.0579 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8427    4.2803   -1.8351 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0094    3.5761   -1.5356 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5266    2.6631   -2.4520 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8767    2.4531   -3.6669 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7120    3.1599   -3.9702 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4129    3.5721   -1.7482 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8892    4.3194   -0.6974 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3462    5.4485   -0.8544 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9562    3.5552    0.6444 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.4344    4.4496    1.7957 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1314    4.8910    2.4495 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3001    3.6224    2.3904 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6877    2.9896    1.1388 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1494    1.8290    0.6303 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4087    1.4509   -0.5209 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6945    0.9435    1.5765 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.0879    0.6874    1.0017 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3020   -0.8107    1.1895 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9104   -1.3979    1.0226 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0392   -0.3701    1.5608 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2330   -0.5238    2.0635 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7544    0.3496    2.7656 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2028   -4.5965    4.1238 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9497   -3.4742    7.0932 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4061   -2.9462    6.1876 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7242   -1.5464    5.1530 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4720   -2.7728    5.3861 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7288   -2.7777    3.3164 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4038   -1.1721    3.1289 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3791   -2.6417    1.6547 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0518   -2.5166   -0.1246 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7481   -1.3758   -0.5001 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4807    0.3542   -3.9318 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6843    1.5857   -2.7080 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3128    1.4178   -2.0589 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2641    0.5260   -2.1718 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1226   -1.9654   -3.7900 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9825   -0.2167   -2.0611 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5009   -3.7821   -3.2046 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3478   -5.3373   -3.5894 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5985   -5.5532   -3.7631 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1816   -2.1441   -3.0735 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3325   -0.5563   -2.6974 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4825    1.4729   -5.0409 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2106    4.7784   -3.2095 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0919    5.7692   -2.7679 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0294    5.2048   -4.4163 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4537    4.9969   -1.1144 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5225    3.7513   -0.5939 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4438    2.1259   -2.2269 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2816    1.7476   -4.3889 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2312    2.9965   -4.9336 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8863    2.7321   -1.5204 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6650    2.7328    0.4909 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0126    3.8500    2.5104 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0566    5.2961    1.4935 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2686    5.2570    3.4705 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6620    5.6840    1.8554 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7778    3.8070    2.4083 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5651    2.9542    3.2169 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7313    1.2993    2.6071 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1427    0.9430   -0.0609 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8536    1.2781    1.5143 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0256   -1.2301    0.4853 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6669   -1.0013    2.2062 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6522   -1.5438   -0.0285 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7918   -2.3435    1.5572 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1944   -5.3755    3.4742 H   0  0  0  0  0  0  0  0  0  0  0  0
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M  END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₃₈H₄₅N₇O₈S₂

Average Mass

791.9400 Da

Monoisotopic Mass

791.27710 Da

IUPAC Name

(3S,9R,14R,17S,20S)-17-benzyl-N-[(E)-2-(4-hydroxyphenyl)ethenyl]-2,8,16,19-tetraoxo-9-[(2S)-5-oxopyrrolidine-2-amido]-11,12-dithia-1,7,15,18-tetraazatricyclo[18.3.0.0^{3,7}]tricosane-14-carboxamide

Traditional Name

(3S,9R,14R,17S,20S)-17-benzyl-N-[(E)-2-(4-hydroxyphenyl)ethenyl]-2,8,16,19-tetraoxo-9-[(2S)-5-oxopyrrolidine-2-amido]-11,12-dithia-1,7,15,18-tetraazatricyclo[18.3.0.0^{3,7}]tricosane-14-carboxamide

CAS Registry Number

Not Available

SMILES

[H]OC1=C([H])C([H])=C(\C([H])=C(/[H])N([H])C(=O)[C@@]2([H])N([H])C(=O)[C@@]([H])(N([H])C(=O)[C@@]3([H])N(C(=O)[C@@]4([H])N(C(=O)[C@@]([H])(N([H])C(=O)[C@@]5([H])N([H])C(=O)C([H])([H])C5([H])[H])C([H])([H])SSC2([H])[H])C([H])([H])C([H])([H])C4([H])[H])C([H])([H])C([H])([H])C3([H])[H])C([H])([H])C2=C([H])C([H])=C([H])C([H])=C2[H])C([H])=C1[H]

InChI Identifier

InChI=1S/C38H45N7O8S2/c46-25-12-10-23(11-13-25)16-17-39-33(48)28-21-54-55-22-29(43-34(49)26-14-15-32(47)40-26)37(52)45-19-5-9-31(45)38(53)44-18-4-8-30(44)36(51)41-27(35(50)42-28)20-24-6-2-1-3-7-24/h1-3,6-7,10-13,16-17,26-31,46H,4-5,8-9,14-15,18-22H2,(H,39,48)(H,40,47)(H,41,51)(H,42,50)(H,43,49)/b17-16+/t26-,27-,28-,29-,30-,31-/m0/s1

InChI Key

IMNGJUDDINZRBE-UQTWBUSUSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, DMSO-d6, 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
Clathria gombawuiensis	JEOL database	Woo, J. -K., et al, J. Nat. Prod. 76, 1380 (2013)

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as oligopeptides. These are organic compounds containing a sequence of between three and ten alpha-amino acids joined by peptide bonds.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Oligopeptides

Alternative Parents

Substituents

Alpha-oligopeptide
Cyclic alpha peptide
Proline or derivatives
Macrolactam
N-acyl-alpha amino acid or derivatives
Alpha-amino acid amide
Alpha-amino acid or derivatives
Pyrrolidine carboxylic acid or derivatives
Styrene
Pyrrolidine-2-carboxamide
1-hydroxy-2-unsubstituted benzenoid
Phenol
Monocyclic benzene moiety
Benzenoid
2-pyrrolidone
Pyrrolidone
Tertiary carboxylic acid amide
Pyrrolidine
Organic disulfide
Lactam
Carboxamide group
Secondary carboxylic acid amide
Organoheterocyclic compound
Azacycle
Organic nitrogen compound
Organooxygen compound
Organonitrogen compound
Hydrocarbon derivative
Organic oxide
Carbonyl group
Organopnictogen compound
Organic oxygen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Physical Properties

State

Not Available

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
logP	1.47	ALOGPS
logP	-0.37	ChemAxon
logS	-4.1	ALOGPS
pKa (Strongest Acidic)	9.41	ChemAxon
pKa (Strongest Basic)	-2.2	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	206.35 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	206.61 m³·mol⁻¹	ChemAxon
Polarizability	80.01 Å³	ChemAxon
Number of Rings	6	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

29784879

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

71747152

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Woo, J. -K., et al. (2013). Woo, J. -K., et al, J. Nat. Prod. 76, 1380 (2013). J. Nat. Prod..

Showing NP-Card for gombamide A (NP0043569)

MOL for NP0043569 (gombamide A)

3D MOL for NP0043569 (gombamide A)

3D SDF for NP0043569 (gombamide A)

3D-SDF for NP0043569 (gombamide A)

PDB for NP0043569 (gombamide A)

3D PDB for NP0043569 (gombamide A)

SMILES for NP0043569 (gombamide A)

INCHI for NP0043569 (gombamide A)

Structure for NP0043569 (gombamide A)

3D Structure for NP0043569 (gombamide A)