NP-MRD: Showing NP-Card for Trapoxin A (NP0010952)

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Record Information

Version

2.0

Created at

2021-01-05 20:44:43 UTC

Updated at

2021-07-15 17:07:33 UTC

NP-MRD ID

NP0010952

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Trapoxin A

Provided By

NPAtlas

Description

Trapoxin A, also known as RF 1023A, belongs to the class of organic compounds known as cyclic peptides. Cyclic peptides are compounds containing a cyclic moiety bearing a peptide backbone. Trapoxin A is a secondary metabolite. Secondary metabolites are metabolically or physiologically non-essential metabolites that may serve a role as defense or signalling molecules. In some cases they are simply molecules that arise from the incomplete metabolism of other secondary metabolites. Trapoxin A is found in Helicoma and Helicoma ambiens. Trapoxin A was first documented in 1990 (PMID: 2276972). Based on a literature review very few articles have been published on trapoxin A (PMID: 1930826).

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652307012121353D          

 86 90  0  0  0  0            999 V2000
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M  END

     RDKit          3D

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    2.6533    0.1270   -1.0871 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0263    2.1680    1.1001 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9536    0.6484    1.3047 H   0  0  0  0  0  0  0  0  0  0  0  0
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    3.6797    2.9928   -0.5311 H   0  0  0  0  0  0  0  0  0  0  0  0
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    4.6042   -0.5667    0.5314 H   0  0  0  0  0  0  0  0  0  0  0  0
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    6.0814   -1.0179   -1.3525 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -3.0091   -6.3118    1.8041 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2422   -3.9804    1.8625 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  2  0
  4 12  1  0
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 14 15  1  0
 15 16  1  0
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 25 26  1  0
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 29 30  2  0
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 39 40  2  0
 40 41  1  0
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 43 44  2  0
 37  2  1  0
 44 39  1  0
 11  6  1  0
 19 14  1  0
 33 31  1  0
  3 45  1  0
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  5 48  1  0
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  8 50  1  0
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 10 52  1  0
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 15 54  1  0
 15 55  1  0
 16 56  1  0
 16 57  1  0
 17 58  1  0
 17 59  1  0
 18 60  1  0
 18 61  1  0
 19 62  1  1
 22 63  1  0
 23 64  1  6
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 36 78  1  0
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 38 80  1  0
 38 81  1  0
 40 82  1  0
 41 83  1  0
 42 84  1  0
 43 85  1  0
 44 86  1  0
M  END


  Mrv1652307012121353D          

 86 90  0  0  0  0            999 V2000
   -2.7809   -3.0652   -0.6598 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1564   -1.9936   -0.5168 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -2.8674    0.4861   -0.9784 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.3829    0.6510   -1.3217 C   0  0  2  0  0  0  0  0  0  0  0  0
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   -7.0185    0.5299    2.0078 C   0  0  0  0  0  0  0  0  0  0  0  0
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    6.2642   -2.7213    0.5155 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.2051   -1.6114    1.1901 C   0  0  2  0  0  0  0  0  0  0  0  0
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   -2.2422   -3.9804    1.8625 H   0  0  0  0  0  0  0  0  0  0  0  0
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 43 44  2  0  0  0  0
 37  2  1  0  0  0  0
 44 39  1  0  0  0  0
 11  6  1  0  0  0  0
 19 14  1  0  0  0  0
 33 31  1  0  0  0  0
  3 45  1  0  0  0  0
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  5 47  1  0  0  0  0
  5 48  1  0  0  0  0
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  8 50  1  0  0  0  0
  9 51  1  0  0  0  0
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 11 53  1  0  0  0  0
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 41 83  1  0  0  0  0
 42 84  1  0  0  0  0
 43 85  1  0  0  0  0
 44 86  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0010952

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]N1C(=O)[C@]2([H])N(C(=O)[C@@]([H])(N([H])C(=O)[C@@]([H])(N([H])C(=O)[C@]1([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C(=O)[C@@]1([H])OC1([H])[H])C([H])([H])C1=C([H])C([H])=C([H])C([H])=C1[H])C([H])([H])C1=C([H])C([H])=C([H])C([H])=C1[H])C([H])([H])C([H])([H])C([H])([H])C2([H])[H]

> <INCHI_IDENTIFIER>
InChI=1S/C34H42N4O6/c39-29(30-22-44-30)18-9-3-8-16-25-31(40)36-26(20-23-12-4-1-5-13-23)32(41)37-27(21-24-14-6-2-7-15-24)34(43)38-19-11-10-17-28(38)33(42)35-25/h1-2,4-7,12-15,25-28,30H,3,8-11,16-22H2,(H,35,42)(H,36,40)(H,37,41)/t25-,26-,27-,28+,30-/m0/s1

> <INCHI_KEY>
GXVXXETYXSPSOA-UFEOFEBPSA-N

> <FORMULA>
C34H42N4O6

> <MOLECULAR_WEIGHT>
602.732

> <EXACT_MASS>
602.310435088

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
86

> <JCHEM_AVERAGE_POLARIZABILITY>
65.47441626863029

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3S,6S,9S,15aR)-6,9-dibenzyl-3-{6-[(2S)-oxiran-2-yl]-6-oxohexyl}-tetradecahydro-1H-pyrido[1,2-a]1,4,7,10-tetraazacyclododecane-1,4,7,10-tetrone

> <ALOGPS_LOGP>
2.73

> <JCHEM_LOGP>
3.0603016033333326

> <ALOGPS_LOGS>
-4.32

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
11.360637348691082

> <JCHEM_PKA_STRONGEST_ACIDIC>
10.784488728515203

> <JCHEM_PKA_STRONGEST_BASIC>
-3.1500843861937713

> <JCHEM_POLAR_SURFACE_AREA>
137.21

> <JCHEM_REFRACTIVITY>
163.09189999999992

> <JCHEM_ROTATABLE_BOND_COUNT>
11

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.90e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(3S,6S,9S,15aR)-6,9-dibenzyl-3-{6-[(2S)-oxiran-2-yl]-6-oxohexyl}-decahydro-2H-pyrido[1,2-a]1,4,7,10-tetraazacyclododecane-1,4,7,10-tetrone

> <JCHEM_VEBER_RULE>
0

$$$$

     RDKit          3D

 86 90  0  0  0  0  0  0  0  0999 V2000
   -2.7809   -3.0652   -0.6598 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -2.8674    0.4861   -0.9784 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.3829    0.6510   -1.3217 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2645    0.6212   -0.1883 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6054    1.7485    0.5096 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4736    1.7141    1.5995 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0185    0.5299    2.0078 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6853   -0.6137    1.3157 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8214   -0.5674    0.2343 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4788    1.5836   -0.0680 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9564    1.3109    1.1246 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7719    2.7702   -0.1530 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5174    3.9587    0.4044 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1041    4.7196   -0.7341 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0259    4.7682   -1.8215 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7033    4.6651   -1.1074 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4887    3.2054   -0.5870 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.3015    2.5537   -1.6044 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2500    2.5244   -2.7723 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5849    1.9533   -1.5113 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.9241    0.8120   -0.6150 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.6610    1.4251    0.5402 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9024    2.1406    0.1605 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9518    1.3129   -0.5149 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4223    0.1601    0.3644 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4893   -0.6009   -0.4198 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9410   -1.7190    0.4379 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2642   -2.7213    0.5155 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.2051   -1.6114    1.1901 C   0  0  2  0  0  0  0  0  0  0  0  0
    8.8232   -2.7888    1.7783 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.0360   -1.9769    2.6136 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6521    0.1529   -0.1880 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3408    0.6448    0.9277 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1380   -0.7999   -0.7832 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6274   -2.1385   -0.5658 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.0740   -2.9507    0.5141 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5893   -4.3235    0.5212 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0834   -5.2601   -0.2397 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3646   -6.5653   -0.2563 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4697   -6.9916    0.4606 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1313   -6.0370    1.2179 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7081   -4.7213    1.2561 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4497   -0.7654    0.5565 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4786    0.6077   -1.9960 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5702   -0.1900   -2.0547 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4912    1.5776   -1.9623 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2262    2.7170    0.2513 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7465    2.6039    2.1550 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.6965    0.4813    2.8533 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1010   -1.5485    1.6196 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6105   -1.5258   -0.2606 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8311    4.6214    0.9748 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2500    3.6541    1.1661 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0117    4.2354   -1.0879 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3221    5.7611   -0.3719 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2173    3.9154   -2.4943 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0870    5.7433   -2.2944 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1023    4.8768   -1.8760 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6048    5.4109   -0.3379 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1650    3.4658    0.3390 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3958    2.2652   -2.0833 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6533    0.1270   -1.0871 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0263    2.1680    1.1001 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9536    0.6484    1.3047 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3116    2.6228    1.0788 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6797    2.9928   -0.5311 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8661    1.9210   -0.7212 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6448    0.8801   -1.4641 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8542    0.5514    1.2896 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6042   -0.5667    0.5314 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.3280    0.0766   -0.7015 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.0814   -1.0179   -1.3525 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.7646   -0.6589    1.0582 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.9165   -2.7004    2.0439 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.4266   -3.7784    1.5095 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6510   -0.5514   -1.7332 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4879   -2.7401   -1.5233 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0325   -2.9592    0.4332 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3495   -2.4636    1.4967 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9695   -5.0130   -0.8401 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1431   -7.3214   -0.8429 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8039   -8.0359    0.4281 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0091   -6.3118    1.8041 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2422   -3.9804    1.8625 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  2  0
  4 12  1  0
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 12 14  1  0
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 18 19  1  0
 19 20  1  0
 20 21  2  0
 20 22  1  0
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 23 34  1  0
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 36 37  1  0
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 37 79  1  6
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 44 86  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  O   UNK     0      -2.781  -3.065  -0.660  0.00  0.00           O+0
HETATM    2  C   UNK     0      -2.156  -1.994  -0.517  0.00  0.00           C+0
HETATM    3  N   UNK     0      -2.809  -0.763  -0.327  0.00  0.00           N+0
HETATM    4  C   UNK     0      -2.867   0.486  -0.978  0.00  0.00           C+0
HETATM    5  C   UNK     0      -4.383   0.651  -1.322  0.00  0.00           C+0
HETATM    6  C   UNK     0      -5.264   0.621  -0.188  0.00  0.00           C+0
HETATM    7  C   UNK     0      -5.605   1.749   0.510  0.00  0.00           C+0
HETATM    8  C   UNK     0      -6.474   1.714   1.599  0.00  0.00           C+0
HETATM    9  C   UNK     0      -7.019   0.530   2.008  0.00  0.00           C+0
HETATM   10  C   UNK     0      -6.685  -0.614   1.316  0.00  0.00           C+0
HETATM   11  C   UNK     0      -5.821  -0.567   0.234  0.00  0.00           C+0
HETATM   12  C   UNK     0      -2.479   1.584  -0.068  0.00  0.00           C+0
HETATM   13  O   UNK     0      -2.956   1.311   1.125  0.00  0.00           O+0
HETATM   14  N   UNK     0      -1.772   2.770  -0.153  0.00  0.00           N+0
HETATM   15  C   UNK     0      -2.517   3.959   0.404  0.00  0.00           C+0
HETATM   16  C   UNK     0      -3.104   4.720  -0.734  0.00  0.00           C+0
HETATM   17  C   UNK     0      -2.026   4.768  -1.821  0.00  0.00           C+0
HETATM   18  C   UNK     0      -0.703   4.665  -1.107  0.00  0.00           C+0
HETATM   19  C   UNK     0      -0.489   3.205  -0.587  0.00  0.00           C+0
HETATM   20  C   UNK     0       0.302   2.554  -1.604  0.00  0.00           C+0
HETATM   21  O   UNK     0      -0.250   2.524  -2.772  0.00  0.00           O+0
HETATM   22  N   UNK     0       1.585   1.953  -1.511  0.00  0.00           N+0
HETATM   23  C   UNK     0       1.924   0.812  -0.615  0.00  0.00           C+0
HETATM   24  C   UNK     0       2.661   1.425   0.540  0.00  0.00           C+0
HETATM   25  C   UNK     0       3.902   2.141   0.161  0.00  0.00           C+0
HETATM   26  C   UNK     0       4.952   1.313  -0.515  0.00  0.00           C+0
HETATM   27  C   UNK     0       5.422   0.160   0.364  0.00  0.00           C+0
HETATM   28  C   UNK     0       6.489  -0.601  -0.420  0.00  0.00           C+0
HETATM   29  C   UNK     0       6.941  -1.719   0.438  0.00  0.00           C+0
HETATM   30  O   UNK     0       6.264  -2.721   0.516  0.00  0.00           O+0
HETATM   31  C   UNK     0       8.205  -1.611   1.190  0.00  0.00           C+0
HETATM   32  C   UNK     0       8.823  -2.789   1.778  0.00  0.00           C+0
HETATM   33  O   UNK     0       8.036  -1.977   2.614  0.00  0.00           O+0
HETATM   34  C   UNK     0       0.652   0.153  -0.188  0.00  0.00           C+0
HETATM   35  O   UNK     0       0.341   0.645   0.928  0.00  0.00           O+0
HETATM   36  N   UNK     0      -0.138  -0.800  -0.783  0.00  0.00           N+0
HETATM   37  C   UNK     0      -0.627  -2.139  -0.566  0.00  0.00           C+0
HETATM   38  C   UNK     0      -0.074  -2.951   0.514  0.00  0.00           C+0
HETATM   39  C   UNK     0      -0.589  -4.324   0.521  0.00  0.00           C+0
HETATM   40  C   UNK     0       0.083  -5.260  -0.240  0.00  0.00           C+0
HETATM   41  C   UNK     0      -0.365  -6.565  -0.256  0.00  0.00           C+0
HETATM   42  C   UNK     0      -1.470  -6.992   0.461  0.00  0.00           C+0
HETATM   43  C   UNK     0      -2.131  -6.037   1.218  0.00  0.00           C+0
HETATM   44  C   UNK     0      -1.708  -4.721   1.256  0.00  0.00           C+0
HETATM   45  H   UNK     0      -3.450  -0.765   0.557  0.00  0.00           H+0
HETATM   46  H   UNK     0      -2.479   0.608  -1.996  0.00  0.00           H+0
HETATM   47  H   UNK     0      -4.570  -0.190  -2.055  0.00  0.00           H+0
HETATM   48  H   UNK     0      -4.491   1.578  -1.962  0.00  0.00           H+0
HETATM   49  H   UNK     0      -5.226   2.717   0.251  0.00  0.00           H+0
HETATM   50  H   UNK     0      -6.747   2.604   2.155  0.00  0.00           H+0
HETATM   51  H   UNK     0      -7.697   0.481   2.853  0.00  0.00           H+0
HETATM   52  H   UNK     0      -7.101  -1.549   1.620  0.00  0.00           H+0
HETATM   53  H   UNK     0      -5.611  -1.526  -0.261  0.00  0.00           H+0
HETATM   54  H   UNK     0      -1.831   4.621   0.975  0.00  0.00           H+0
HETATM   55  H   UNK     0      -3.250   3.654   1.166  0.00  0.00           H+0
HETATM   56  H   UNK     0      -4.012   4.235  -1.088  0.00  0.00           H+0
HETATM   57  H   UNK     0      -3.322   5.761  -0.372  0.00  0.00           H+0
HETATM   58  H   UNK     0      -2.217   3.915  -2.494  0.00  0.00           H+0
HETATM   59  H   UNK     0      -2.087   5.743  -2.294  0.00  0.00           H+0
HETATM   60  H   UNK     0       0.102   4.877  -1.876  0.00  0.00           H+0
HETATM   61  H   UNK     0      -0.605   5.411  -0.338  0.00  0.00           H+0
HETATM   62  H   UNK     0       0.165   3.466   0.339  0.00  0.00           H+0
HETATM   63  H   UNK     0       2.396   2.265  -2.083  0.00  0.00           H+0
HETATM   64  H   UNK     0       2.653   0.127  -1.087  0.00  0.00           H+0
HETATM   65  H   UNK     0       2.026   2.168   1.100  0.00  0.00           H+0
HETATM   66  H   UNK     0       2.954   0.648   1.305  0.00  0.00           H+0
HETATM   67  H   UNK     0       4.312   2.623   1.079  0.00  0.00           H+0
HETATM   68  H   UNK     0       3.680   2.993  -0.531  0.00  0.00           H+0
HETATM   69  H   UNK     0       5.866   1.921  -0.721  0.00  0.00           H+0
HETATM   70  H   UNK     0       4.645   0.880  -1.464  0.00  0.00           H+0
HETATM   71  H   UNK     0       5.854   0.551   1.290  0.00  0.00           H+0
HETATM   72  H   UNK     0       4.604  -0.567   0.531  0.00  0.00           H+0
HETATM   73  H   UNK     0       7.328   0.077  -0.702  0.00  0.00           H+0
HETATM   74  H   UNK     0       6.081  -1.018  -1.353  0.00  0.00           H+0
HETATM   75  H   UNK     0       8.765  -0.659   1.058  0.00  0.00           H+0
HETATM   76  H   UNK     0       9.916  -2.700   2.044  0.00  0.00           H+0
HETATM   77  H   UNK     0       8.427  -3.778   1.510  0.00  0.00           H+0
HETATM   78  H   UNK     0      -0.651  -0.551  -1.733  0.00  0.00           H+0
HETATM   79  H   UNK     0      -0.488  -2.740  -1.523  0.00  0.00           H+0
HETATM   80  H   UNK     0       1.032  -2.959   0.433  0.00  0.00           H+0
HETATM   81  H   UNK     0      -0.350  -2.464   1.497  0.00  0.00           H+0
HETATM   82  H   UNK     0       0.970  -5.013  -0.840  0.00  0.00           H+0
HETATM   83  H   UNK     0       0.143  -7.321  -0.843  0.00  0.00           H+0
HETATM   84  H   UNK     0      -1.804  -8.036   0.428  0.00  0.00           H+0
HETATM   85  H   UNK     0      -3.009  -6.312   1.804  0.00  0.00           H+0
HETATM   86  H   UNK     0      -2.242  -3.980   1.863  0.00  0.00           H+0
CONECT    1    2                                                            
CONECT    2    1    3   37                                                  
CONECT    3    2    4   45                                                  
CONECT    4    3    5   12   46                                             
CONECT    5    4    6   47   48                                             
CONECT    6    5    7   11                                                  
CONECT    7    6    8   49                                                  
CONECT    8    7    9   50                                                  
CONECT    9    8   10   51                                                  
CONECT   10    9   11   52                                                  
CONECT   11   10    6   53                                                  
CONECT   12    4   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12   15   19                                                  
CONECT   15   14   16   54   55                                             
CONECT   16   15   17   56   57                                             
CONECT   17   16   18   58   59                                             
CONECT   18   17   19   60   61                                             
CONECT   19   18   20   14   62                                             
CONECT   20   19   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20   23   63                                                  
CONECT   23   22   24   34   64                                             
CONECT   24   23   25   65   66                                             
CONECT   25   24   26   67   68                                             
CONECT   26   25   27   69   70                                             
CONECT   27   26   28   71   72                                             
CONECT   28   27   29   73   74                                             
CONECT   29   28   30   31                                                  
CONECT   30   29                                                            
CONECT   31   29   32   33   75                                             
CONECT   32   31   33   76   77                                             
CONECT   33   32   31                                                       
CONECT   34   23   35   36                                                  
CONECT   35   34                                                            
CONECT   36   34   37   78                                                  
CONECT   37   36   38    2   79                                             
CONECT   38   37   39   80   81                                             
CONECT   39   38   40   44                                                  
CONECT   40   39   41   82                                                  
CONECT   41   40   42   83                                                  
CONECT   42   41   43   84                                                  
CONECT   43   42   44   85                                                  
CONECT   44   43   39   86                                                  
CONECT   45    3                                                            
CONECT   46    4                                                            
CONECT   47    5                                                            
CONECT   48    5                                                            
CONECT   49    7                                                            
CONECT   50    8                                                            
CONECT   51    9                                                            
CONECT   52   10                                                            
CONECT   53   11                                                            
CONECT   54   15                                                            
CONECT   55   15                                                            
CONECT   56   16                                                            
CONECT   57   16                                                            
CONECT   58   17                                                            
CONECT   59   17                                                            
CONECT   60   18                                                            
CONECT   61   18                                                            
CONECT   62   19                                                            
CONECT   63   22                                                            
CONECT   64   23                                                            
CONECT   65   24                                                            
CONECT   66   24                                                            
CONECT   67   25                                                            
CONECT   68   25                                                            
CONECT   69   26                                                            
CONECT   70   26                                                            
CONECT   71   27                                                            
CONECT   72   27                                                            
CONECT   73   28                                                            
CONECT   74   28                                                            
CONECT   75   31                                                            
CONECT   76   32                                                            
CONECT   77   32                                                            
CONECT   78   36                                                            
CONECT   79   37                                                            
CONECT   80   38                                                            
CONECT   81   38                                                            
CONECT   82   40                                                            
CONECT   83   41                                                            
CONECT   84   42                                                            
CONECT   85   43                                                            
CONECT   86   44                                                            
MASTER        0    0    0    0    0    0    0    0   86    0  180    0
END

RDKit          3D

86 90  0  0  0  0  0  0  0  0999 V2000
   -2.7809   -3.0652   -0.6598 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1564   -1.9936   -0.5168 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8090   -0.7628   -0.3272 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8674    0.4861   -0.9784 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.3829    0.6510   -1.3217 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2645    0.6212   -0.1883 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6054    1.7485    0.5096 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4736    1.7141    1.5995 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0185    0.5299    2.0078 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6853   -0.6137    1.3157 C   0  0  0  0  0  0  0  0  0  0  0  0
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    2.0263    2.1680    1.1001 H   0  0  0  0  0  0  0  0  0  0  0  0
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 44 86  1  0
M  END

View in JSmol View NMR Assignments

Synonyms

Value	Source
Cyclo((S)-gamma-oxo-L-alpha-aminooxiraneoctanoyl-L-phenylalanyl-L-phenylalanyl-D-2-piperidinecarbonyl)	ChEBI
Cyclo((S)-phenylalanyl-(S)-phenylalanyl-(R)-pipecolinyl-(2S,9S)-2-amino-8-oxo-9,10-epoxydecanoyl)	ChEBI
RF 1023a	ChEBI
Cyclo((S)-g-oxo-L-a-aminooxiraneoctanoyl-L-phenylalanyl-L-phenylalanyl-D-2-piperidinecarbonyl)	Generator
Cyclo((S)-γ-oxo-L-α-aminooxiraneoctanoyl-L-phenylalanyl-L-phenylalanyl-D-2-piperidinecarbonyl)	Generator
Trapoxin	MeSH

Chemical Formula

C₃₄H₄₂N₄O₆

Average Mass

602.7320 Da

Monoisotopic Mass

602.31044 Da

IUPAC Name

(3S,6S,9S,15aR)-6,9-dibenzyl-3-{6-[(2S)-oxiran-2-yl]-6-oxohexyl}-tetradecahydro-1H-pyrido[1,2-a]1,4,7,10-tetraazacyclododecane-1,4,7,10-tetrone

Traditional Name

(3S,6S,9S,15aR)-6,9-dibenzyl-3-{6-[(2S)-oxiran-2-yl]-6-oxohexyl}-decahydro-2H-pyrido[1,2-a]1,4,7,10-tetraazacyclododecane-1,4,7,10-tetrone

CAS Registry Number

Not Available

SMILES

O=C(CCCCC[C@@H]1NC(=O)[C@H]2CCCCN2C(=O)[C@H](CC2=CC=CC=C2)NC(=O)[C@H](CC2=CC=CC=C2)NC1=O)[C@@H]1CO1

InChI Identifier

InChI=1S/C34H42N4O6/c39-29(30-22-44-30)18-9-3-8-16-25-31(40)36-26(20-23-12-4-1-5-13-23)32(41)37-27(21-24-14-6-2-7-15-24)34(43)38-19-11-10-17-28(38)33(42)35-25/h1-2,4-7,12-15,25-28,30H,3,8-11,16-22H2,(H,35,42)(H,36,40)(H,37,41)/t25-,26-,27-,28+,30-/m0/s1

InChI Key

GXVXXETYXSPSOA-UFEOFEBPSA-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
Helicoma	NPAtlas	2276972
Helicoma ambiens	LOTUS Database	35616633

Species Where Detected

Species Name	Source	Reference
Helicoma ambiens RF-1023	KNApSAcK Database	22123792

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as cyclic peptides. Cyclic peptides are compounds containing a cyclic moiety bearing a peptide backbone.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Cyclic peptides

Alternative Parents

Substituents

Cyclic alpha peptide
Alpha-amino acid or derivatives
Monocyclic benzene moiety
Monosaccharide
Piperidine
Benzenoid
Cyclic carboximidic acid
Tertiary carboxylic acid amide
Carboxamide group
Ketone
Lactam
Dialkyl ether
Oxirane
Ether
Oxacycle
Azacycle
Organoheterocyclic compound
Polyol
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Hydrocarbon derivative
Carbonyl group
Organopnictogen compound
Organonitrogen compound
Organooxygen compound
Organic oxide
Organic nitrogen compound
Organic oxygen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

epoxide (CHEBI:84057 )
ketone (CHEBI:84057 )
homodetic cyclic peptide (CHEBI:84057 )

Physical Properties

State

Not Available

Experimental Properties

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

Predicted Properties

Property	Value	Source
logP	2.73	ALOGPS
logP	3.06	ChemAxon
logS	-4.3	ALOGPS
pKa (Strongest Acidic)	10.78	ChemAxon
pKa (Strongest Basic)	-3.2	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	137.21 Å²	ChemAxon
Rotatable Bond Count	11	ChemAxon
Refractivity	163.09 m³·mol⁻¹	ChemAxon
Polarizability	65.47 Å³	ChemAxon
Number of Rings	5	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

NPA020686

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00017061

Chemspider ID

108725

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

121875

PDB ID

Not Available

ChEBI ID

84057

Good Scents ID

Not Available

References

General References

Itazaki H, Nagashima K, Sugita K, Yoshida H, Kawamura Y, Yasuda Y, Matsumoto K, Ishii K, Uotani N, Nakai H, et al.: Isolation and structural elucidation of new cyclotetrapeptides, trapoxins A and B, having detransformation activities as antitumor agents. J Antibiot (Tokyo). 1990 Dec;43(12):1524-32. doi: 10.7164/antibiotics.43.1524. [PubMed:2276972 ]
Nakai H, Nagashima K, Itazaki H: Structure of a new cyclotetrapeptide trapoxin A. Acta Crystallogr C. 1991 Jul 15;47 ( Pt 7):1496-9. doi: 10.1107/s0108270190012987. [PubMed:1930826 ]

Showing NP-Card for Trapoxin A (NP0010952)

MOL for NP0010952 (Trapoxin A)

3D MOL for NP0010952 (Trapoxin A)

3D SDF for NP0010952 (Trapoxin A)

3D-SDF for NP0010952 (Trapoxin A)

PDB for NP0010952 (Trapoxin A)

3D PDB for NP0010952 (Trapoxin A)

SMILES for NP0010952 (Trapoxin A)

INCHI for NP0010952 (Trapoxin A)

Structure for NP0010952 (Trapoxin A)

3D Structure for NP0010952 (Trapoxin A)