NP-MRD: Showing NP-Card for n-[(3s,6s,12r,15s,16r,19s,22s)-3-benzyl-12-ethyl-14,21-dihydroxy-4,16-dimethyl-2,5,11,18,24-pentaoxo-19-phenyl-17-oxa-1,4,10,13,20-pentaazatricyclo[20.4.0.0⁶,¹⁰]hexacosa-13,20-dien-15-yl]-3-hydroxypyridine-2-carboximidic acid (NP0250932)

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Record Information

Version

2.0

Created at

2022-09-07 13:56:45 UTC

Updated at

2022-09-07 13:56:45 UTC

NP-MRD ID

NP0250932

Secondary Accession Numbers

None

Natural Product Identification

Common Name

n-[(3s,6s,12r,15s,16r,19s,22s)-3-benzyl-12-ethyl-14,21-dihydroxy-4,16-dimethyl-2,5,11,18,24-pentaoxo-19-phenyl-17-oxa-1,4,10,13,20-pentaazatricyclo[20.4.0.0⁶,¹⁰]hexacosa-13,20-dien-15-yl]-3-hydroxypyridine-2-carboximidic acid

Description

Virginiamycin S1 belongs to the class of organic compounds known as cyclic depsipeptides. These are natural or synthetic compounds having sequences of amino and hydroxy carboxylic acid residues (usually α-amino and α-hydroxy acids) connected in a ring. The residues are commonly but not necessarily regularly alternating. n-[(3s,6s,12r,15s,16r,19s,22s)-3-benzyl-12-ethyl-14,21-dihydroxy-4,16-dimethyl-2,5,11,18,24-pentaoxo-19-phenyl-17-oxa-1,4,10,13,20-pentaazatricyclo[20.4.0.0⁶,¹⁰]hexacosa-13,20-dien-15-yl]-3-hydroxypyridine-2-carboximidic acid is found in Streptomyces virginiae. n-[(3s,6s,12r,15s,16r,19s,22s)-3-benzyl-12-ethyl-14,21-dihydroxy-4,16-dimethyl-2,5,11,18,24-pentaoxo-19-phenyl-17-oxa-1,4,10,13,20-pentaazatricyclo[20.4.0.0⁶,¹⁰]hexacosa-13,20-dien-15-yl]-3-hydroxypyridine-2-carboximidic acid was first documented in 1986 (PMID: 3097264). Virginiamycin S1 is a moderately basic compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309272007292D          

 60 65  0  0  0  0            999 V2000
   13.8116  -14.8417    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   13.8243  -15.6700    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   14.5322  -14.4168    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.1059  -14.4337    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.5404  -16.0735    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.1141  -16.0835    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.3923  -14.8517    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.2541  -15.6600    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   14.5393  -16.9019    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.3912  -15.6800    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.9700  -16.0599    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   11.6775  -16.0902    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.8047  -12.3706    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.9791  -16.8884    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.6760  -15.6387    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.5148  -11.9459    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.0816  -11.9662    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.2691  -17.3054    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.6945  -17.2918    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.3919  -16.0465    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.6668  -14.8180    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.5020  -11.1210    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.0724  -11.1380    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.2749  -18.1302    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.7039  -18.1168    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.1056  -15.6252    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   13.7825  -10.7174    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.9944  -18.5414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.2504  -14.8226    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.5245  -13.5919    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   13.8101  -13.1795    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.2371  -13.1761    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   15.2333  -12.3512    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.9534  -13.5852    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.6659  -13.1695    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   15.9573  -14.4101    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.0784  -11.9000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.4110  -12.3850    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.4909  -13.1695    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   17.7458  -12.3850    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.9758  -13.8369    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.8241  -16.0307    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   18.0977  -14.8002    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.5345  -15.6113    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.8320  -16.8557    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   18.1216  -17.2750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.1297  -18.0998    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.4033  -16.8692    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.4152  -18.5124    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   17.4152  -19.3374    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.1297  -19.7499    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.8438  -19.3374    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.8438  -18.5124    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.5585  -18.1000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   20.2528  -16.0168    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   19.5265  -14.7864    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   18.9436  -13.8904    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   17.6013  -14.5720    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   19.3569  -13.1764    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   20.1819  -13.1773    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  4  1  0  0  0  0
  2  5  1  6  0  0  0
  2  6  1  0  0  0  0
  4  7  1  0  0  0  0
  5  8  1  0  0  0  0
  5  9  2  0  0  0  0
  6 10  1  0  0  0  0
  8 11  1  0  0  0  0
 10 12  2  0  0  0  0
 11 14  1  6  0  0  0
 11 15  1  0  0  0  0
 13 16  2  0  0  0  0
 13 17  1  0  0  0  0
 14 18  2  0  0  0  0
 14 19  1  0  0  0  0
 15 20  1  0  0  0  0
 15 21  2  0  0  0  0
 16 22  1  0  0  0  0
 17 23  2  0  0  0  0
 18 24  1  0  0  0  0
 19 25  2  0  0  0  0
 20 26  1  0  0  0  0
 22 27  2  0  0  0  0
 24 28  2  0  0  0  0
  7 10  1  0  0  0  0
 23 27  1  0  0  0  0
 25 28  1  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  3 29  2  0  0  0  0
  3 30  1  0  0  0  0
 30 31  1  6  0  0  0
 31 13  1  0  0  0  0
 30 32  1  0  0  0  0
 32 33  1  0  0  0  0
 32 34  1  0  0  0  0
 35 34  1  6  0  0  0
 34 36  2  0  0  0  0
 37 38  1  0  0  0  0
 39 40  1  0  0  0  0
 37 40  1  0  0  0  0
 38 35  1  0  0  0  0
 35 39  1  0  0  0  0
 39 41  1  0  0  0  0
 26 42  1  0  0  0  0
 26 43  1  6  0  0  0
 42 44  1  0  0  0  0
 42 45  1  1  0  0  0
 45 46  1  0  0  0  0
 46 47  1  0  0  0  0
 46 48  2  0  0  0  0
 49 50  2  0  0  0  0
 50 51  1  0  0  0  0
 51 52  2  0  0  0  0
 52 53  1  0  0  0  0
 47 49  1  0  0  0  0
 47 53  2  0  0  0  0
 53 54  1  0  0  0  0
 44 55  2  0  0  0  0
 44 56  1  0  0  0  0
 41 57  1  0  0  0  0
 57 56  1  0  0  0  0
 41 58  2  0  0  0  0
 57 59  1  1  0  0  0
 59 60  1  0  0  0  0
M  END

     RDKit          3D

109114  0  0  0  0  0  0  0  0999 V2000
    1.6044   -3.3582    2.2019 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3374   -2.5041    1.1521 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3127   -2.1353    0.0859 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.8547   -1.3376   -0.9827 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.4459   -0.0710   -0.9516 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9110    0.7916   -1.7460 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5759    0.4004   -0.1513 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.7360   -0.4664   -0.4432 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.5822   -0.9666    0.5847 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3524   -0.6723    1.7693 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.7062   -1.8157    0.2319 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8892   -2.0940   -1.0996 N   0  0  0  0  0  0  0  0  0  0  0  0
    7.8882   -2.8601   -1.5328 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.8130   -3.4314   -0.6793 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.6636   -3.1772    0.6550 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6055   -2.3672    1.0998 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.5310   -2.1656    2.4390 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9860    1.8450   -0.5138 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.0063    2.0748   -1.9908 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2976    2.7302    0.2374 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2382    2.9152    0.9987 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1327    2.7781    2.2753 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9305    3.3500    0.3737 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.0524    4.8560    0.3251 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9423    5.6038    1.4635 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0620    6.9861    1.4444 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2970    7.5770    0.2285 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4098    6.8389   -0.9243 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2869    5.4733   -0.8741 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1846    2.9839    1.2088 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5361    2.9199    0.8562 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4005    3.2681    1.7365 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -2.1100    3.6727   -1.4333 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9648    4.6912   -0.7682 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6303    5.8227   -0.5004 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3421    4.2556   -0.4136 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5515    2.8025   -0.7535 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4322    1.9504   -0.3133 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6938    0.6728    0.2150 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5301    0.6222    1.1875 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1340   -0.6272   -0.2031 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.2665   -1.2931   -0.9481 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4951   -1.4947   -0.1866 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7216   -2.6001    0.6005 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9214   -2.7123    1.2677 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.8994   -1.7489    1.1689 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.6975   -0.6303    0.3865 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5034   -0.5443   -0.2623 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -2.4552   -0.6965    2.1557 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -2.0700   -3.4128    1.9162 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6849   -3.4488   -0.3774 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.6575   -4.6138   -0.5173 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7656   -5.7777   -0.8123 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6288   -5.4883    0.1667 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3863   -4.0731   -0.2230 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.8656   -3.4775   -0.4239 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7738   -4.0780   -1.1022 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2297   -3.4198    3.1034 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5149   -4.3896    1.8050 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5882   -2.9744    2.3720 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1208   -3.1788    0.7421 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8310   -1.6595    1.6174 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4739   -1.6173    0.5964 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7665   -1.8268   -1.9555 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4033    0.4666    0.9387 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9539   -0.7282   -1.4275 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.9958   -3.0521   -2.5834 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.6303   -4.0560   -1.0133 H   0  0  0  0  0  0  0  0  0  0  0  0
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    6.8830   -1.6414    2.9467 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1077    1.8137   -0.2312 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9413    2.6121   -2.2763 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1306    2.6161   -2.3980 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0658    1.0944   -2.5015 H   0  0  0  0  0  0  0  0  0  0  0  0
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    1.5988    7.3418   -1.8805 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3793    4.8888   -1.8038 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0605    2.7337    2.2166 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4616    1.7189   -0.9512 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6513    3.3224   -2.3256 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0904    3.9853   -1.6068 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6034    4.4267    0.6515 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -5.5075    2.5086   -0.2790 H   0  0  0  0  0  0  0  0  0  0  0  0
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M  END


  Mrv1652309272007292D          

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 13 16  2  0  0  0  0
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  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
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  3 30  1  0  0  0  0
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 57 59  1  1  0  0  0
 59 60  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0250932

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC[C@H]1NC(=O)[C@@H](NC(=O)C2=C(O)C=CC=N2)[C@@H](C)OC(=O)[C@@H](NC(=O)[C@@H]2CC(=O)CCN2C(=O)[C@H](CC2=CC=CC=C2)N(C)C(=O)[C@@H]2CCCN2C1=O)C1=CC=CC=C1

> <INCHI_IDENTIFIER>
InChI=1S/C43H49N7O10/c1-4-29-40(56)49-21-12-17-30(49)41(57)48(3)32(23-26-13-7-5-8-14-26)42(58)50-22-19-28(51)24-31(50)37(53)47-35(27-15-9-6-10-16-27)43(59)60-25(2)34(38(54)45-29)46-39(55)36-33(52)18-11-20-44-36/h5-11,13-16,18,20,25,29-32,34-35,52H,4,12,17,19,21-24H2,1-3H3,(H,45,54)(H,46,55)(H,47,53)/t25-,29-,30+,31+,32+,34+,35+/m1/s1

> <INCHI_KEY>
FEPMHVLSLDOMQC-IYPFLVAKSA-N

> <FORMULA>
C43H49N7O10

> <MOLECULAR_WEIGHT>
823.904

> <EXACT_MASS>
823.354090806

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_ATOM_COUNT>
109

> <JCHEM_AVERAGE_POLARIZABILITY>
83.52323527288843

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
N-[(3S,6S,12R,15S,16R,19S,22S)-3-benzyl-12-ethyl-4,16-dimethyl-2,5,11,14,18,21,24-heptaoxo-19-phenyl-17-oxa-1,4,10,13,20-pentaazatricyclo[20.4.0.0^{6,10}]hexacosan-15-yl]-3-hydroxypyridine-2-carboxamide

> <ALOGPS_LOGP>
2.25

> <JCHEM_LOGP>
1.8531505056666662

> <ALOGPS_LOGS>
-3.77

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
11.413221421039678

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.529835283668631

> <JCHEM_PKA_STRONGEST_BASIC>
1.5727269020072876

> <JCHEM_POLAR_SURFACE_AREA>
224.71999999999997

> <JCHEM_REFRACTIVITY>
213.2372000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.39e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
N-[(3S,6S,12R,15S,16R,19S,22S)-3-benzyl-12-ethyl-4,16-dimethyl-2,5,11,14,18,21,24-heptaoxo-19-phenyl-17-oxa-1,4,10,13,20-pentaazatricyclo[20.4.0.0^{6,10}]hexacosan-15-yl]-3-hydroxypyridine-2-carboxamide

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 27-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-SEP-20         0                                  
HETATM    1  N   UNK     0      25.782 -27.705   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0      25.805 -29.251   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      27.127 -26.911   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      24.464 -26.943   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      27.142 -30.004   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      24.480 -30.022   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      23.132 -27.723   0.000  0.00  0.00           C+0
HETATM    8  N   UNK     0      28.474 -29.232   0.000  0.00  0.00           N+0
HETATM    9  O   UNK     0      27.140 -31.550   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0      23.130 -29.269   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      29.811 -29.979   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      21.798 -30.035   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0      25.769 -23.092   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      29.828 -31.525   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      31.128 -29.192   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      27.094 -22.299   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      24.419 -22.337   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      28.502 -32.303   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      31.163 -32.278   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0      32.465 -29.953   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0      31.111 -27.660   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0      27.070 -20.759   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      24.402 -20.791   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      28.513 -33.843   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      31.181 -33.818   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      33.797 -29.167   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      25.727 -20.006   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      29.856 -34.611   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0      28.467 -27.669   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0      27.112 -25.371   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      25.779 -24.602   0.000  0.00  0.00           C+0
HETATM   32  N   UNK     0      28.443 -24.595   0.000  0.00  0.00           N+0
HETATM   33  C   UNK     0      28.435 -23.056   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      29.780 -25.359   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      31.110 -24.583   0.000  0.00  0.00           C+0
HETATM   36  O   UNK     0      29.787 -26.899   0.000  0.00  0.00           O+0
HETATM   37  C   UNK     0      31.880 -22.213   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0      30.634 -23.119   0.000  0.00  0.00           C+0
HETATM   39  N   UNK     0      32.650 -24.583   0.000  0.00  0.00           N+0
HETATM   40  C   UNK     0      33.125 -23.119   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0      33.555 -25.829   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0      35.138 -29.924   0.000  0.00  0.00           C+0
HETATM   43  C   UNK     0      33.782 -27.627   0.000  0.00  0.00           C+0
HETATM   44  C   UNK     0      36.464 -29.141   0.000  0.00  0.00           C+0
HETATM   45  N   UNK     0      35.153 -31.464   0.000  0.00  0.00           N+0
HETATM   46  C   UNK     0      33.827 -32.247   0.000  0.00  0.00           C+0
HETATM   47  C   UNK     0      33.842 -33.786   0.000  0.00  0.00           C+0
HETATM   48  O   UNK     0      32.486 -31.489   0.000  0.00  0.00           O+0
HETATM   49  N   UNK     0      32.508 -34.557   0.000  0.00  0.00           N+0
HETATM   50  C   UNK     0      32.508 -36.097   0.000  0.00  0.00           C+0
HETATM   51  C   UNK     0      33.842 -36.867   0.000  0.00  0.00           C+0
HETATM   52  C   UNK     0      35.175 -36.097   0.000  0.00  0.00           C+0
HETATM   53  C   UNK     0      35.175 -34.557   0.000  0.00  0.00           C+0
HETATM   54  O   UNK     0      36.509 -33.787   0.000  0.00  0.00           O+0
HETATM   55  O   UNK     0      37.805 -29.898   0.000  0.00  0.00           O+0
HETATM   56  N   UNK     0      36.450 -27.601   0.000  0.00  0.00           N+0
HETATM   57  C   UNK     0      35.361 -25.929   0.000  0.00  0.00           C+0
HETATM   58  O   UNK     0      32.856 -27.201   0.000  0.00  0.00           O+0
HETATM   59  C   UNK     0      36.133 -24.596   0.000  0.00  0.00           C+0
HETATM   60  C   UNK     0      37.673 -24.598   0.000  0.00  0.00           C+0
CONECT    1    4    2    3                                                  
CONECT    2    5    6    1                                                  
CONECT    3    1   29   30                                                  
CONECT    4    1    7                                                       
CONECT    5    2    8    9                                                  
CONECT    6    2   10                                                       
CONECT    7    4   10                                                       
CONECT    8    5   11                                                       
CONECT    9    5                                                            
CONECT   10    6   12    7                                                  
CONECT   11    8   14   15                                                  
CONECT   12   10                                                            
CONECT   13   16   17   31                                                  
CONECT   14   11   18   19                                                  
CONECT   15   11   20   21                                                  
CONECT   16   13   22                                                       
CONECT   17   13   23                                                       
CONECT   18   14   24                                                       
CONECT   19   14   25                                                       
CONECT   20   15   26                                                       
CONECT   21   15                                                            
CONECT   22   16   27                                                       
CONECT   23   17   27                                                       
CONECT   24   18   28                                                       
CONECT   25   19   28                                                       
CONECT   26   20   42   43                                                  
CONECT   27   22   23                                                       
CONECT   28   24   25                                                       
CONECT   29    3                                                            
CONECT   30    3   31   32                                                  
CONECT   31   30   13                                                       
CONECT   32   30   33   34                                                  
CONECT   33   32                                                            
CONECT   34   32   35   36                                                  
CONECT   35   34   38   39                                                  
CONECT   36   34                                                            
CONECT   37   38   40                                                       
CONECT   38   37   35                                                       
CONECT   39   40   35   41                                                  
CONECT   40   39   37                                                       
CONECT   41   39   57   58                                                  
CONECT   42   26   44   45                                                  
CONECT   43   26                                                            
CONECT   44   42   55   56                                                  
CONECT   45   42   46                                                       
CONECT   46   45   47   48                                                  
CONECT   47   46   49   53                                                  
CONECT   48   46                                                            
CONECT   49   50   47                                                       
CONECT   50   49   51                                                       
CONECT   51   50   52                                                       
CONECT   52   51   53                                                       
CONECT   53   52   47   54                                                  
CONECT   54   53                                                            
CONECT   55   44                                                            
CONECT   56   44   57                                                       
CONECT   57   41   56   59                                                  
CONECT   58   41                                                            
CONECT   59   57   60                                                       
CONECT   60   59                                                            
MASTER        0    0    0    0    0    0    0    0   60    0  130    0
END

View in JSmol

Synonyms

Value	Source
N-((3-Hydroxy-2-pyridinyl)carbonyl)-L-threonyl-D-alpha-aminobutyryl-L-prolyl-N-methyl-L-phenylalanyl-4-oxo-L-pipecoloyl-L-2-phenylglycine rho-lactone	ChEBI
N-(3-Hydroxypicolinoyl)-L-threonyl-D-alpha-aminobutyryl-L-prolyl-N-methyl-L-phenylalanyl-4-oxo-L-pipecoloyl-L-2-phenylglycine rho-lactone	ChEBI
Virginiamycin factor S	ChEBI
N-((3-Hydroxy-2-pyridinyl)carbonyl)-L-threonyl-D-a-aminobutyryl-L-prolyl-N-methyl-L-phenylalanyl-4-oxo-L-pipecoloyl-L-2-phenylglycine rho-lactone	Generator
N-((3-Hydroxy-2-pyridinyl)carbonyl)-L-threonyl-D-α-aminobutyryl-L-prolyl-N-methyl-L-phenylalanyl-4-oxo-L-pipecoloyl-L-2-phenylglycine rho-lactone	Generator
N-(3-Hydroxypicolinoyl)-L-threonyl-D-a-aminobutyryl-L-prolyl-N-methyl-L-phenylalanyl-4-oxo-L-pipecoloyl-L-2-phenylglycine rho-lactone	Generator
N-(3-Hydroxypicolinoyl)-L-threonyl-D-α-aminobutyryl-L-prolyl-N-methyl-L-phenylalanyl-4-oxo-L-pipecoloyl-L-2-phenylglycine rho-lactone	Generator
Dihydrovirginiamycin S1	MeSH
Staphylomycin S1	MeSH
Virginiamycin factor S1	MeSH
VS1	PhytoBank
Staphylomycin S	PhytoBank

Chemical Formula

C₄₃H₄₉N₇O₁₀

Average Mass

823.9040 Da

Monoisotopic Mass

823.35409 Da

IUPAC Name

N-[(3S,6S,12R,15S,16R,19S,22S)-3-benzyl-12-ethyl-4,16-dimethyl-2,5,11,14,18,21,24-heptaoxo-19-phenyl-17-oxa-1,4,10,13,20-pentaazatricyclo[20.4.0.0^{6,10}]hexacosan-15-yl]-3-hydroxypyridine-2-carboxamide

Traditional Name

CAS Registry Number

Not Available

SMILES

CC[C@H]1NC(=O)[C@@H](NC(=O)C2=C(O)C=CC=N2)[C@@H](C)OC(=O)[C@@H](NC(=O)[C@@H]2CC(=O)CCN2C(=O)[C@H](CC2=CC=CC=C2)N(C)C(=O)[C@@H]2CCCN2C1=O)C1=CC=CC=C1

InChI Identifier

InChI=1S/C43H49N7O10/c1-4-29-40(56)49-21-12-17-30(49)41(57)48(3)32(23-26-13-7-5-8-14-26)42(58)50-22-19-28(51)24-31(50)37(53)47-35(27-15-9-6-10-16-27)43(59)60-25(2)34(38(54)45-29)46-39(55)36-33(52)18-11-20-44-36/h5-11,13-16,18,20,25,29-32,34-35,52H,4,12,17,19,21-24H2,1-3H3,(H,45,54)(H,46,55)(H,47,53)/t25-,29-,30+,31+,32+,34+,35+/m1/s1

InChI Key

FEPMHVLSLDOMQC-IYPFLVAKSA-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, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, 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
Streptomyces virginiae	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as cyclic depsipeptides. These are natural or synthetic compounds having sequences of amino and hydroxy carboxylic acid residues (usually α-amino and α-hydroxy acids) connected in a ring. The residues are commonly but not necessarily regularly alternating.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Peptidomimetics

Sub Class

Depsipeptides

Direct Parent

Cyclic depsipeptides

Alternative Parents

Substituents

Cyclic depsipeptide
Macrolide lactam
Alpha-amino acid ester
Macrolactam
N-acyl-alpha amino acid or derivatives
Alpha-amino acid or derivatives
Pyridine carboxylic acid or derivatives
Pyridinecarboxamide
2-heteroaryl carboxamide
Hydroxypyridine
Piperidinone
Benzenoid
Pyridine
Monocyclic benzene moiety
Piperidine
Vinylogous acid
Tertiary carboxylic acid amide
Pyrrolidine
Heteroaromatic compound
Carboxamide group
Carboxylic acid ester
Ketone
Lactam
Lactone
Cyclic ketone
Secondary carboxylic acid amide
Oxacycle
Monocarboxylic acid or derivatives
Azacycle
Organoheterocyclic compound
Carboxylic acid derivative
Hydrocarbon derivative
Carbonyl group
Organopnictogen compound
Organic oxide
Organic oxygen compound
Organonitrogen compound
Organooxygen compound
Organic nitrogen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

macrolide antibiotic (CHEBI:46416 )
cyclodepsipeptide (CHEBI:46416 )

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	2.25	ALOGPS
logP	1.85	ChemAxon
logS	-3.8	ALOGPS
pKa (Strongest Acidic)	7.53	ChemAxon
pKa (Strongest Basic)	1.57	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	10	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	224.72 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	213.24 m³·mol⁻¹	ChemAxon
Polarizability	83.52 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

DB04805

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Virginiamycin_S1

METLIN ID

Not Available

PubChem Compound

5388936

PDB ID

Not Available

ChEBI ID

46416

Good Scents ID

Not Available

References

General References

Reed JW, Kingston DG: Biosynthesis of antibiotics of the virginiamycin family, 5. The conversion of phenylalanine to phenylglycine in the biosynthesis of virginiamycin S1. J Nat Prod. 1986 Jul-Aug;49(4):626-30. doi: 10.1021/np50046a011. [PubMed:3097264 ]
LOTUS database [Link]

Showing NP-Card for n-[(3s,6s,12r,15s,16r,19s,22s)-3-benzyl-12-ethyl-14,21-dihydroxy-4,16-dimethyl-2,5,11,18,24-pentaoxo-19-phenyl-17-oxa-1,4,10,13,20-pentaazatricyclo[20.4.0.0⁶,¹⁰]hexacosa-13,20-dien-15-yl]-3-hydroxypyridine-2-carboximidic acid (NP0250932)

MOL for NP0250932 (n-[(3s,6s,12r,15s,16r,19s,22s)-3-benzyl-12-ethyl-14,21-dihydroxy-4,16-dimethyl-2,5,11,18,24-pentaoxo-19-phenyl-17-oxa-1,4,10,13,20-pentaazatricyclo[20.4.0.0⁶,¹⁰]hexacosa-13,20-dien-15-yl]-3-hydroxypyridine-2-carboximidic acid)

3D MOL for NP0250932 (n-[(3s,6s,12r,15s,16r,19s,22s)-3-benzyl-12-ethyl-14,21-dihydroxy-4,16-dimethyl-2,5,11,18,24-pentaoxo-19-phenyl-17-oxa-1,4,10,13,20-pentaazatricyclo[20.4.0.0⁶,¹⁰]hexacosa-13,20-dien-15-yl]-3-hydroxypyridine-2-carboximidic acid)

3D SDF for NP0250932 (n-[(3s,6s,12r,15s,16r,19s,22s)-3-benzyl-12-ethyl-14,21-dihydroxy-4,16-dimethyl-2,5,11,18,24-pentaoxo-19-phenyl-17-oxa-1,4,10,13,20-pentaazatricyclo[20.4.0.0⁶,¹⁰]hexacosa-13,20-dien-15-yl]-3-hydroxypyridine-2-carboximidic acid)

3D-SDF for NP0250932 (n-[(3s,6s,12r,15s,16r,19s,22s)-3-benzyl-12-ethyl-14,21-dihydroxy-4,16-dimethyl-2,5,11,18,24-pentaoxo-19-phenyl-17-oxa-1,4,10,13,20-pentaazatricyclo[20.4.0.0⁶,¹⁰]hexacosa-13,20-dien-15-yl]-3-hydroxypyridine-2-carboximidic acid)

PDB for NP0250932 (n-[(3s,6s,12r,15s,16r,19s,22s)-3-benzyl-12-ethyl-14,21-dihydroxy-4,16-dimethyl-2,5,11,18,24-pentaoxo-19-phenyl-17-oxa-1,4,10,13,20-pentaazatricyclo[20.4.0.0⁶,¹⁰]hexacosa-13,20-dien-15-yl]-3-hydroxypyridine-2-carboximidic acid)

3D PDB for NP0250932 (n-[(3s,6s,12r,15s,16r,19s,22s)-3-benzyl-12-ethyl-14,21-dihydroxy-4,16-dimethyl-2,5,11,18,24-pentaoxo-19-phenyl-17-oxa-1,4,10,13,20-pentaazatricyclo[20.4.0.0⁶,¹⁰]hexacosa-13,20-dien-15-yl]-3-hydroxypyridine-2-carboximidic acid)

SMILES for NP0250932 (n-[(3s,6s,12r,15s,16r,19s,22s)-3-benzyl-12-ethyl-14,21-dihydroxy-4,16-dimethyl-2,5,11,18,24-pentaoxo-19-phenyl-17-oxa-1,4,10,13,20-pentaazatricyclo[20.4.0.0⁶,¹⁰]hexacosa-13,20-dien-15-yl]-3-hydroxypyridine-2-carboximidic acid)

INCHI for NP0250932 (n-[(3s,6s,12r,15s,16r,19s,22s)-3-benzyl-12-ethyl-14,21-dihydroxy-4,16-dimethyl-2,5,11,18,24-pentaoxo-19-phenyl-17-oxa-1,4,10,13,20-pentaazatricyclo[20.4.0.0⁶,¹⁰]hexacosa-13,20-dien-15-yl]-3-hydroxypyridine-2-carboximidic acid)

Structure for NP0250932 (n-[(3s,6s,12r,15s,16r,19s,22s)-3-benzyl-12-ethyl-14,21-dihydroxy-4,16-dimethyl-2,5,11,18,24-pentaoxo-19-phenyl-17-oxa-1,4,10,13,20-pentaazatricyclo[20.4.0.0⁶,¹⁰]hexacosa-13,20-dien-15-yl]-3-hydroxypyridine-2-carboximidic acid)

3D Structure for NP0250932 (n-[(3s,6s,12r,15s,16r,19s,22s)-3-benzyl-12-ethyl-14,21-dihydroxy-4,16-dimethyl-2,5,11,18,24-pentaoxo-19-phenyl-17-oxa-1,4,10,13,20-pentaazatricyclo[20.4.0.0⁶,¹⁰]hexacosa-13,20-dien-15-yl]-3-hydroxypyridine-2-carboximidic acid)