NP-MRD: Showing NP-Card for Xenematide (NP0007754)

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Record Information

Version

2.0

Created at

2020-12-09 04:33:02 UTC

Updated at

2021-07-15 16:58:27 UTC

NP-MRD ID

NP0007754

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Xenematide

Provided By

NPAtlas

Description

2-Phenyl-N-[(2R,3S)-4,7,10-trihydroxy-6,9-bis[(1H-indol-3-yl)methyl]-2-methyl-14-oxo-1-oxa-5,8,11-triazacyclotetradeca-4,7,10-trien-3-yl]ethanimidic acid belongs to the class of organic compounds known as hybrid peptides. Hybrid peptides are compounds containing at least two different types of amino acids (alpha, beta, gamma, delta) linked to each other through a peptide bond. Xenematide is found in Xenorhabdus and Xenorhabdus nematophila. Xenematide was first documented in 2008 (PMID: 18491867). Based on a literature review very few articles have been published on 2-phenyl-N-[(2R,3S)-4,7,10-trihydroxy-6,9-bis[(1H-indol-3-yl)methyl]-2-methyl-14-oxo-1-oxa-5,8,11-triazacyclotetradeca-4,7,10-trien-3-yl]ethanimidic acid.

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652307012119533D          

 87 92  0  0  0  0            999 V2000
    3.1952   -1.3832   -1.3289 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9322   -0.6193   -0.8894 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.0495   -1.5056   -0.2825 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3416   -2.5379   -0.7907 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3063   -3.6082   -0.0791 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4037   -2.6120   -2.0572 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.1370   -1.3797   -2.4608 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.5728   -1.5167   -2.5452 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5314   -0.5746   -2.0955 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4459   -0.1357   -2.8534 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5270   -0.0290   -0.6840 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.8095   -0.3843    0.0288 C   0  0  2  0  0  0  0  0  0  0  0  0
   -5.1121   -1.7962    0.1621 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9877   -2.4904   -0.6479 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9862   -3.7527   -0.2218 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1519   -3.9307    0.8335 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8299   -5.0404    1.5966 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9409   -4.9532    2.6356 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3777   -3.7184    2.8955 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7071   -2.6182    2.1265 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5990   -2.6831    1.0739 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3522   -0.4496    0.0174 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4255    0.2556    0.7567 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9281   -0.3805    1.7805 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8695    1.6105    0.6269 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7816    2.1875   -0.7427 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.2579    3.5909   -0.6875 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9531    4.1313   -0.9967 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9514    5.4806   -0.7829 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2628    5.8454   -0.3296 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7515    7.0784    0.0245 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0492    7.1870    0.4634 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8122    6.0414    0.5300 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3161    4.7948    0.1713 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0277    4.6875   -0.2637 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4589    1.6930    1.2927 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.5559    0.8794    1.1189 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0059    0.2805    2.1747 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3444    0.5577   -0.1015 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.7527    0.3689    0.2599 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.7717    1.2168   -0.2076 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5510    2.1930   -0.9732 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.1812    0.9800    0.1995 C   0  0  2  0  0  0  0  0  0  0  0  0
    6.3268   -0.4378    0.5713 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1443   -0.7736    1.9179 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2609   -2.0698    2.3394 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5609   -3.0891    1.4571 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7417   -2.7728    0.1325 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.6184   -1.4397   -0.2823 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0435   -0.7015   -1.5266 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5301   -2.0652   -0.5185 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -3.5976    1.0936   -0.8150 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6705    0.1356   -0.4915 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7664    0.1501    1.0200 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5788   -2.0846   -1.4859 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5597   -4.5337   -0.6432 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2774   -5.9945    1.3795 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6746   -5.8295    3.2471 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6729   -3.6413    3.7155 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2683   -1.6453    2.3388 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1937   -1.5159   -0.0632 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6053    2.2404    1.1939 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6554    2.1280   -1.3743 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0271    1.6239   -1.2783 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8015    3.5891   -1.3648 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7792    6.1178   -0.9499 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0754    7.9428   -0.0592 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4334    8.1715    0.7466 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8357    6.1189    0.8756 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9328    3.9056    0.2230 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5143    2.5006    1.9843 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3808    1.4287   -0.8022 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9720   -0.4275    0.8744 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.3749    1.6179    1.0885 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.8657    1.2306   -0.6437 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9111    0.0049    2.6128 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1214   -2.3325    3.3796 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.6480   -4.1105    1.8095 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.9774   -3.5473   -0.5785 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.7709   -1.2304   -1.3353 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  4  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
  9 11  1  0  0  0  0
 11 12  1  0  0  0  0
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 14 15  1  0  0  0  0
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 11 22  1  0  0  0  0
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 21 13  1  0  0  0  0
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  1 50  1  0  0  0  0
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M  END

     RDKit          3D

 87 92  0  0  0  0  0  0  0  0999 V2000
    3.1952   -1.3832   -1.3289 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9322   -0.6193   -0.8894 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.0495   -1.5056   -0.2825 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3416   -2.5379   -0.7907 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3063   -3.6082   -0.0791 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4037   -2.6120   -2.0572 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1370   -1.3797   -2.4608 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5728   -1.5167   -2.5452 N   0  0  0  0  0  0  0  0  0  0  0  0
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   -2.9621   -2.3982   -2.9923 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -6.5788   -2.0846   -1.4859 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5597   -4.5337   -0.6432 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2774   -5.9945    1.3795 H   0  0  0  0  0  0  0  0  0  0  0  0
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    1.8015    3.5891   -1.3648 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7792    6.1178   -0.9499 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0754    7.9428   -0.0592 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4334    8.1715    0.7466 H   0  0  0  0  0  0  0  0  0  0  0  0
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    0.5143    2.5006    1.9843 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3808    1.4287   -0.8022 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9720   -0.4275    0.8744 H   0  0  0  0  0  0  0  0  0  0  0  0
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    6.8657    1.2306   -0.6437 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9111    0.0049    2.6128 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1214   -2.3325    3.3796 H   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
  4  5  2  0
  4  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  2  0
  9 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  2  0
 14 15  1  0
 15 16  1  0
 16 17  2  0
 17 18  1  0
 18 19  2  0
 19 20  1  0
 20 21  2  0
 11 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  2  0
 28 29  1  0
 29 30  1  0
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 31 32  1  0
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 40 41  1  0
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 41 43  1  0
 43 44  1  0
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 47 48  1  0
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 39  2  1  0
 49 44  1  0
 21 13  1  0
 35 27  1  0
 21 16  1  0
 35 30  1  0
  1 50  1  0
  1 51  1  0
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  2 53  1  6
  6 54  1  0
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  7 56  1  0
  7 57  1  0
  8 58  1  0
 11 59  1  6
 12 60  1  0
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 14 62  1  0
 15 63  1  0
 17 64  1  0
 18 65  1  0
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 29 73  1  0
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 40 80  1  0
 43 81  1  0
 43 82  1  0
 45 83  1  0
 46 84  1  0
 47 85  1  0
 48 86  1  0
 49 87  1  0
M  END


  Mrv1652307012119533D          

 87 92  0  0  0  0            999 V2000
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    2.0059    0.2805    2.1747 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3444    0.5577   -0.1015 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.7527    0.3689    0.2599 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.7717    1.2168   -0.2076 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5510    2.1930   -0.9732 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.1812    0.9800    0.1995 C   0  0  2  0  0  0  0  0  0  0  0  0
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    6.1443   -0.7736    1.9179 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2609   -2.0698    2.3394 C   0  0  0  0  0  0  0  0  0  0  0  0
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 25 36  1  0  0  0  0
 36 37  1  0  0  0  0
 37 38  2  0  0  0  0
 37 39  1  0  0  0  0
 39 40  1  0  0  0  0
 40 41  1  0  0  0  0
 41 42  2  0  0  0  0
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 44 45  2  0  0  0  0
 45 46  1  0  0  0  0
 46 47  2  0  0  0  0
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 48 49  2  0  0  0  0
 39  2  1  0  0  0  0
 49 44  1  0  0  0  0
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 35 27  1  0  0  0  0
 21 16  1  0  0  0  0
 35 30  1  0  0  0  0
  1 50  1  0  0  0  0
  1 51  1  0  0  0  0
  1 52  1  0  0  0  0
  2 53  1  6  0  0  0
  6 54  1  0  0  0  0
  6 55  1  0  0  0  0
  7 56  1  0  0  0  0
  7 57  1  0  0  0  0
  8 58  1  0  0  0  0
 11 59  1  6  0  0  0
 12 60  1  0  0  0  0
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 29 73  1  0  0  0  0
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 46 84  1  0  0  0  0
 47 85  1  0  0  0  0
 48 86  1  0  0  0  0
 49 87  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0007754

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]N(C(=O)C([H])([H])C1=C([H])C([H])=C([H])C([H])=C1[H])[C@]1([H])C(=O)N([H])[C@]([H])(C(=O)N([H])[C@@]([H])(C(=O)N([H])C([H])([H])C([H])([H])C(=O)O[C@]1([H])C([H])([H])[H])C([H])([H])C1=C([H])N([H])C2=C([H])C([H])=C([H])C([H])=C12)C([H])([H])C1=C([H])N([H])C2=C([H])C([H])=C([H])C([H])=C12

> <INCHI_IDENTIFIER>
InChI=1S/C37H38N6O6/c1-22-34(43-32(44)17-23-9-3-2-4-10-23)37(48)42-31(19-25-21-40-29-14-8-6-12-27(25)29)36(47)41-30(35(46)38-16-15-33(45)49-22)18-24-20-39-28-13-7-5-11-26(24)28/h2-14,20-22,30-31,34,39-40H,15-19H2,1H3,(H,38,46)(H,41,47)(H,42,48)(H,43,44)/t22-,30-,31+,34+/m1/s1

> <INCHI_KEY>
OHLKJNUNPSYJEE-RWBJUYEISA-N

> <FORMULA>
C37H38N6O6

> <MOLECULAR_WEIGHT>
662.747

> <EXACT_MASS>
662.285282968

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
87

> <JCHEM_AVERAGE_POLARIZABILITY>
69.14289469310049

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
N-[(2R,3S,6S,9R)-6,9-bis[(1H-indol-3-yl)methyl]-2-methyl-4,7,10,14-tetraoxo-1-oxa-5,8,11-triazacyclotetradecan-3-yl]-2-phenylacetamide

> <ALOGPS_LOGP>
3.39

> <JCHEM_LOGP>
2.6774795139999994

> <ALOGPS_LOGS>
-5.32

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
11.803163803830762

> <JCHEM_PKA_STRONGEST_ACIDIC>
10.888171739505221

> <JCHEM_PKA_STRONGEST_BASIC>
-2.4879137320507403

> <JCHEM_POLAR_SURFACE_AREA>
174.27999999999997

> <JCHEM_REFRACTIVITY>
180.64200000000005

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
3.20e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
N-[(2R,3S,6S,9R)-6,9-bis(1H-indol-3-ylmethyl)-2-methyl-4,7,10,14-tetraoxo-1-oxa-5,8,11-triazacyclotetradecan-3-yl]-2-phenylacetamide

> <JCHEM_VEBER_RULE>
0

$$$$

     RDKit          3D

 87 92  0  0  0  0  0  0  0  0999 V2000
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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       3.195  -1.383  -1.329  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.932  -0.619  -0.889  0.00  0.00           C+0
HETATM    3  O   UNK     0       1.050  -1.506  -0.283  0.00  0.00           O+0
HETATM    4  C   UNK     0       0.342  -2.538  -0.791  0.00  0.00           C+0
HETATM    5  O   UNK     0       0.306  -3.608  -0.079  0.00  0.00           O+0
HETATM    6  C   UNK     0      -0.404  -2.612  -2.057  0.00  0.00           C+0
HETATM    7  C   UNK     0      -1.137  -1.380  -2.461  0.00  0.00           C+0
HETATM    8  N   UNK     0      -2.573  -1.517  -2.545  0.00  0.00           N+0
HETATM    9  C   UNK     0      -3.531  -0.575  -2.095  0.00  0.00           C+0
HETATM   10  O   UNK     0      -4.446  -0.136  -2.853  0.00  0.00           O+0
HETATM   11  C   UNK     0      -3.527  -0.029  -0.684  0.00  0.00           C+0
HETATM   12  C   UNK     0      -4.809  -0.384   0.029  0.00  0.00           C+0
HETATM   13  C   UNK     0      -5.112  -1.796   0.162  0.00  0.00           C+0
HETATM   14  C   UNK     0      -5.988  -2.490  -0.648  0.00  0.00           C+0
HETATM   15  N   UNK     0      -5.986  -3.753  -0.222  0.00  0.00           N+0
HETATM   16  C   UNK     0      -5.152  -3.931   0.834  0.00  0.00           C+0
HETATM   17  C   UNK     0      -4.830  -5.040   1.597  0.00  0.00           C+0
HETATM   18  C   UNK     0      -3.941  -4.953   2.636  0.00  0.00           C+0
HETATM   19  C   UNK     0      -3.378  -3.718   2.896  0.00  0.00           C+0
HETATM   20  C   UNK     0      -3.707  -2.618   2.127  0.00  0.00           C+0
HETATM   21  C   UNK     0      -4.599  -2.683   1.074  0.00  0.00           C+0
HETATM   22  N   UNK     0      -2.352  -0.450   0.017  0.00  0.00           N+0
HETATM   23  C   UNK     0      -1.426   0.256   0.757  0.00  0.00           C+0
HETATM   24  O   UNK     0      -0.928  -0.381   1.781  0.00  0.00           O+0
HETATM   25  C   UNK     0      -0.870   1.611   0.627  0.00  0.00           C+0
HETATM   26  C   UNK     0      -0.782   2.188  -0.743  0.00  0.00           C+0
HETATM   27  C   UNK     0      -0.258   3.591  -0.688  0.00  0.00           C+0
HETATM   28  C   UNK     0       0.953   4.131  -0.997  0.00  0.00           C+0
HETATM   29  N   UNK     0       0.951   5.481  -0.783  0.00  0.00           N+0
HETATM   30  C   UNK     0      -0.263   5.845  -0.330  0.00  0.00           C+0
HETATM   31  C   UNK     0      -0.752   7.078   0.025  0.00  0.00           C+0
HETATM   32  C   UNK     0      -2.049   7.187   0.463  0.00  0.00           C+0
HETATM   33  C   UNK     0      -2.812   6.041   0.530  0.00  0.00           C+0
HETATM   34  C   UNK     0      -2.316   4.795   0.171  0.00  0.00           C+0
HETATM   35  C   UNK     0      -1.028   4.688  -0.264  0.00  0.00           C+0
HETATM   36  N   UNK     0       0.459   1.693   1.293  0.00  0.00           N+0
HETATM   37  C   UNK     0       1.556   0.879   1.119  0.00  0.00           C+0
HETATM   38  O   UNK     0       2.006   0.281   2.175  0.00  0.00           O+0
HETATM   39  C   UNK     0       2.344   0.558  -0.102  0.00  0.00           C+0
HETATM   40  N   UNK     0       3.753   0.369   0.260  0.00  0.00           N+0
HETATM   41  C   UNK     0       4.772   1.217  -0.208  0.00  0.00           C+0
HETATM   42  O   UNK     0       4.551   2.193  -0.973  0.00  0.00           O+0
HETATM   43  C   UNK     0       6.181   0.980   0.200  0.00  0.00           C+0
HETATM   44  C   UNK     0       6.327  -0.438   0.571  0.00  0.00           C+0
HETATM   45  C   UNK     0       6.144  -0.774   1.918  0.00  0.00           C+0
HETATM   46  C   UNK     0       6.261  -2.070   2.339  0.00  0.00           C+0
HETATM   47  C   UNK     0       6.561  -3.089   1.457  0.00  0.00           C+0
HETATM   48  C   UNK     0       6.742  -2.773   0.133  0.00  0.00           C+0
HETATM   49  C   UNK     0       6.618  -1.440  -0.282  0.00  0.00           C+0
HETATM   50  H   UNK     0       4.043  -0.702  -1.527  0.00  0.00           H+0
HETATM   51  H   UNK     0       3.530  -2.065  -0.519  0.00  0.00           H+0
HETATM   52  H   UNK     0       2.984  -2.019  -2.213  0.00  0.00           H+0
HETATM   53  H   UNK     0       1.532  -0.244  -1.886  0.00  0.00           H+0
HETATM   54  H   UNK     0       0.322  -2.967  -2.845  0.00  0.00           H+0
HETATM   55  H   UNK     0      -1.179  -3.437  -2.039  0.00  0.00           H+0
HETATM   56  H   UNK     0      -0.822  -1.179  -3.537  0.00  0.00           H+0
HETATM   57  H   UNK     0      -0.844  -0.475  -1.929  0.00  0.00           H+0
HETATM   58  H   UNK     0      -2.962  -2.398  -2.992  0.00  0.00           H+0
HETATM   59  H   UNK     0      -3.598   1.094  -0.815  0.00  0.00           H+0
HETATM   60  H   UNK     0      -5.670   0.136  -0.492  0.00  0.00           H+0
HETATM   61  H   UNK     0      -4.766   0.150   1.020  0.00  0.00           H+0
HETATM   62  H   UNK     0      -6.579  -2.085  -1.486  0.00  0.00           H+0
HETATM   63  H   UNK     0      -6.560  -4.534  -0.643  0.00  0.00           H+0
HETATM   64  H   UNK     0      -5.277  -5.995   1.379  0.00  0.00           H+0
HETATM   65  H   UNK     0      -3.675  -5.830   3.247  0.00  0.00           H+0
HETATM   66  H   UNK     0      -2.673  -3.641   3.716  0.00  0.00           H+0
HETATM   67  H   UNK     0      -3.268  -1.645   2.339  0.00  0.00           H+0
HETATM   68  H   UNK     0      -2.194  -1.516  -0.063  0.00  0.00           H+0
HETATM   69  H   UNK     0      -1.605   2.240   1.194  0.00  0.00           H+0
HETATM   70  H   UNK     0      -1.655   2.128  -1.374  0.00  0.00           H+0
HETATM   71  H   UNK     0       0.027   1.624  -1.278  0.00  0.00           H+0
HETATM   72  H   UNK     0       1.802   3.589  -1.365  0.00  0.00           H+0
HETATM   73  H   UNK     0       1.779   6.118  -0.950  0.00  0.00           H+0
HETATM   74  H   UNK     0      -0.075   7.943  -0.059  0.00  0.00           H+0
HETATM   75  H   UNK     0      -2.433   8.172   0.747  0.00  0.00           H+0
HETATM   76  H   UNK     0      -3.836   6.119   0.876  0.00  0.00           H+0
HETATM   77  H   UNK     0      -2.933   3.906   0.223  0.00  0.00           H+0
HETATM   78  H   UNK     0       0.514   2.501   1.984  0.00  0.00           H+0
HETATM   79  H   UNK     0       2.381   1.429  -0.802  0.00  0.00           H+0
HETATM   80  H   UNK     0       3.972  -0.428   0.874  0.00  0.00           H+0
HETATM   81  H   UNK     0       6.375   1.618   1.089  0.00  0.00           H+0
HETATM   82  H   UNK     0       6.866   1.231  -0.644  0.00  0.00           H+0
HETATM   83  H   UNK     0       5.911   0.005   2.613  0.00  0.00           H+0
HETATM   84  H   UNK     0       6.121  -2.333   3.380  0.00  0.00           H+0
HETATM   85  H   UNK     0       6.648  -4.111   1.810  0.00  0.00           H+0
HETATM   86  H   UNK     0       6.977  -3.547  -0.579  0.00  0.00           H+0
HETATM   87  H   UNK     0       6.771  -1.230  -1.335  0.00  0.00           H+0
CONECT    1    2   50   51   52                                             
CONECT    2    1    3   39   53                                             
CONECT    3    2    4                                                       
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7   54   55                                             
CONECT    7    6    8   56   57                                             
CONECT    8    7    9   58                                                  
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12   22   59                                             
CONECT   12   11   13   60   61                                             
CONECT   13   12   14   21                                                  
CONECT   14   13   15   62                                                  
CONECT   15   14   16   63                                                  
CONECT   16   15   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   13   16                                                  
CONECT   22   11   23   68                                                  
CONECT   23   22   24   25                                                  
CONECT   24   23                                                            
CONECT   25   23   26   36   69                                             
CONECT   26   25   27   70   71                                             
CONECT   27   26   28   35                                                  
CONECT   28   27   29   72                                                  
CONECT   29   28   30   73                                                  
CONECT   30   29   31   35                                                  
CONECT   31   30   32   74                                                  
CONECT   32   31   33   75                                                  
CONECT   33   32   34   76                                                  
CONECT   34   33   35   77                                                  
CONECT   35   34   27   30                                                  
CONECT   36   25   37   78                                                  
CONECT   37   36   38   39                                                  
CONECT   38   37                                                            
CONECT   39   37   40    2   79                                             
CONECT   40   39   41   80                                                  
CONECT   41   40   42   43                                                  
CONECT   42   41                                                            
CONECT   43   41   44   81   82                                             
CONECT   44   43   45   49                                                  
CONECT   45   44   46   83                                                  
CONECT   46   45   47   84                                                  
CONECT   47   46   48   85                                                  
CONECT   48   47   49   86                                                  
CONECT   49   48   44   87                                                  
CONECT   50    1                                                            
CONECT   51    1                                                            
CONECT   52    1                                                            
CONECT   53    2                                                            
CONECT   54    6                                                            
CONECT   55    6                                                            
CONECT   56    7                                                            
CONECT   57    7                                                            
CONECT   58    8                                                            
CONECT   59   11                                                            
CONECT   60   12                                                            
CONECT   61   12                                                            
CONECT   62   14                                                            
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   28                                                            
CONECT   73   29                                                            
CONECT   74   31                                                            
CONECT   75   32                                                            
CONECT   76   33                                                            
CONECT   77   34                                                            
CONECT   78   36                                                            
CONECT   79   39                                                            
CONECT   80   40                                                            
CONECT   81   43                                                            
CONECT   82   43                                                            
CONECT   83   45                                                            
CONECT   84   46                                                            
CONECT   85   47                                                            
CONECT   86   48                                                            
CONECT   87   49                                                            
MASTER        0    0    0    0    0    0    0    0   87    0  184    0
END

RDKit          3D

87 92  0  0  0  0  0  0  0  0999 V2000
    3.1952   -1.3832   -1.3289 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9322   -0.6193   -0.8894 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.0495   -1.5056   -0.2825 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -2.3522   -0.4496    0.0174 N   0  0  0  0  0  0  0  0  0  0  0  0
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   -0.2579    3.5909   -0.6875 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9531    4.1313   -0.9967 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -2.3161    4.7948    0.1713 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0277    4.6875   -0.2637 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4589    1.6930    1.2927 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.5559    0.8794    1.1189 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0059    0.2805    2.1747 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3444    0.5577   -0.1015 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.7527    0.3689    0.2599 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.7717    1.2168   -0.2076 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5510    2.1930   -0.9732 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.1812    0.9800    0.1995 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3268   -0.4378    0.5713 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1443   -0.7736    1.9179 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2609   -2.0698    2.3394 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5609   -3.0891    1.4571 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7417   -2.7728    0.1325 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.6184   -1.4397   -0.2823 C   0  0  0  0  0  0  0  0  0  0  0  0
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    0.3216   -2.9669   -2.8450 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -0.8442   -0.4752   -1.9293 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -5.6705    0.1356   -0.4915 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7664    0.1501    1.0200 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5788   -2.0846   -1.4859 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5597   -4.5337   -0.6432 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2774   -5.9945    1.3795 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6746   -5.8295    3.2471 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6729   -3.6413    3.7155 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2683   -1.6453    2.3388 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1937   -1.5159   -0.0632 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6053    2.2404    1.1939 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6554    2.1280   -1.3743 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0271    1.6239   -1.2783 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8015    3.5891   -1.3648 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7792    6.1178   -0.9499 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0754    7.9428   -0.0592 H   0  0  0  0  0  0  0  0  0  0  0  0
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    6.7709   -1.2304   -1.3353 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
  4  5  2  0
  4  6  1  0
  6  7  1  0
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 21 16  1  0
 35 30  1  0
  1 50  1  0
  1 51  1  0
  1 52  1  0
  2 53  1  6
  6 54  1  0
  6 55  1  0
  7 56  1  0
  7 57  1  0
  8 58  1  0
 11 59  1  6
 12 60  1  0
 12 61  1  0
 14 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
 28 72  1  0
 29 73  1  0
 31 74  1  0
 32 75  1  0
 33 76  1  0
 34 77  1  0
 36 78  1  0
 39 79  1  6
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 43 82  1  0
 45 83  1  0
 46 84  1  0
 47 85  1  0
 48 86  1  0
 49 87  1  0
M  END

View in JSmol View NMR Assignments

Synonyms

Value	Source
2-Phenyl-N-[(2R,3S)-4,7,10-trihydroxy-6,9-bis[(1H-indol-3-yl)methyl]-2-methyl-14-oxo-1-oxa-5,8,11-triazacyclotetradeca-4,7,10-trien-3-yl]ethanimidate	Generator

Chemical Formula

C₃₇H₃₈N₆O₆

Average Mass

662.7470 Da

Monoisotopic Mass

662.28528 Da

IUPAC Name

N-[(2R,3S,6S,9R)-6,9-bis[(1H-indol-3-yl)methyl]-2-methyl-4,7,10,14-tetraoxo-1-oxa-5,8,11-triazacyclotetradecan-3-yl]-2-phenylacetamide

Traditional Name

N-[(2R,3S,6S,9R)-6,9-bis(1H-indol-3-ylmethyl)-2-methyl-4,7,10,14-tetraoxo-1-oxa-5,8,11-triazacyclotetradecan-3-yl]-2-phenylacetamide

CAS Registry Number

Not Available

SMILES

C[C@H]1OC(=O)CCNC(=O)C(CC2=CNC3=CC=CC=C23)NC(=O)C(CC2=CNC3=CC=CC=C23)NC(=O)[C@H]1NC(=O)CC1=CC=CC=C1

InChI Identifier

InChI=1S/C37H38N6O6/c1-22-34(43-32(44)17-23-9-3-2-4-10-23)37(48)42-31(19-25-21-40-29-14-8-6-12-27(25)29)36(47)41-30(35(46)38-16-15-33(45)49-22)18-24-20-39-28-13-7-5-11-26(24)28/h2-14,20-22,30-31,34,39-40H,15-19H2,1H3,(H,38,46)(H,41,47)(H,42,48)(H,43,44)/t22-,30?,31?,34+/m1/s1

InChI Key

OHLKJNUNPSYJEE-RWBJUYEISA-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
Xenorhabdus	NPAtlas	18491867
Xenorhabdus nematophila	LOTUS Database	35616633

Species Where Detected

Species Name	Source	Reference
Xenorhabdus nematophilus	KNApSAcK Database	22123792

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as hybrid peptides. Hybrid peptides are compounds containing at least two different types of amino acids (alpha, beta, gamma, delta) linked to each other through a peptide bond.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Peptidomimetics

Sub Class

Hybrid peptides

Direct Parent

Hybrid peptides

Alternative Parents

Substituents

Cyclic hybrid peptide
Alpha-oligopeptide
N-acyl-alpha amino acid or derivatives
Macrolactam
Alpha-amino acid or derivatives
3-alkylindole
Phenylacetamide
Indole
Indole or derivatives
Monocyclic benzene moiety
Benzenoid
Substituted pyrrole
Heteroaromatic compound
Pyrrole
Secondary carboxylic acid amide
Lactam
Lactone
Carboxylic acid ester
Carboxamide group
Carboxylic acid derivative
Oxacycle
Azacycle
Organoheterocyclic compound
Monocarboxylic acid or derivatives
Hydrocarbon derivative
Organic oxide
Organic nitrogen compound
Organic oxygen compound
Carbonyl group
Organooxygen compound
Organonitrogen compound
Organopnictogen 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	3.39	ALOGPS
logP	2.68	ChemAxon
logS	-5.3	ALOGPS
pKa (Strongest Acidic)	10.89	ChemAxon
pKa (Strongest Basic)	-2.5	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	174.28 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	180.64 m³·mol⁻¹	ChemAxon
Polarizability	69.14 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

NPAtlas ID

NPA019233

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

78440487

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

24900170

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Lang G, Kalvelage T, Peters A, Wiese J, Imhoff JF: Linear and cyclic peptides from the entomopathogenic bacterium Xenorhabdus nematophilus. J Nat Prod. 2008 Jun;71(6):1074-7. doi: 10.1021/np800053n. Epub 2008 May 21. [PubMed:18491867 ]

Showing NP-Card for Xenematide (NP0007754)

MOL for NP0007754 (Xenematide)

3D MOL for NP0007754 (Xenematide)

3D SDF for NP0007754 (Xenematide)

3D-SDF for NP0007754 (Xenematide)

PDB for NP0007754 (Xenematide)

3D PDB for NP0007754 (Xenematide)

SMILES for NP0007754 (Xenematide)

INCHI for NP0007754 (Xenematide)

Structure for NP0007754 (Xenematide)

3D Structure for NP0007754 (Xenematide)