NP-MRD: Showing NP-Card for Rhodopeptin C4 (NP0003087)

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Record Information

Version

1.0

Created at

2020-12-09 00:10:57 UTC

Updated at

2021-07-15 16:45:28 UTC

NP-MRD ID

NP0003087

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Rhodopeptin C4

Provided By

NPAtlas

Description

(3S,6S,13R)-6-(3-aminopropyl)-13-(9-methylundecyl)-3-(propan-2-yl)-1,4,7,10-tetraazacyclotrideca-1,4,7,10-tetraene-2,5,8,11-tetrol belongs to the class of organic compounds known as cyclic peptides. Cyclic peptides are compounds containing a cyclic moiety bearing a peptide backbone. Rhodopeptin C4 is found in Rhodococcus. It was first documented in 1999 (PMID: 10580383). Based on a literature review very few articles have been published on (3S,6S,13R)-6-(3-aminopropyl)-13-(9-methylundecyl)-3-(propan-2-yl)-1,4,7,10-tetraazacyclotrideca-1,4,7,10-tetraene-2,5,8,11-tetrol.

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652307012117063D          

 87 87  0  0  0  0            999 V2000
    9.3677    2.0574    0.4880 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.1653    1.8165    1.3737 C   0  0  2  0  0  0  0  0  0  0  0  0
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    8.4037   -0.6111    1.1180 C   0  0  0  0  0  0  0  0  0  0  0  0
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    6.2152   -0.5485   -0.9035 C   0  0  1  0  0  0  0  0  0  0  0  0
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  3  4  1  0  0  0  0
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M  END

     RDKit          3D

 87 87  0  0  0  0  0  0  0  0999 V2000
    9.3677    2.0574    0.4880 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.1653    1.8165    1.3737 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.4589    0.5363    0.9783 C   0  0  2  0  0  0  0  0  0  0  0  0
    8.4037   -0.6111    1.1180 C   0  0  0  0  0  0  0  0  0  0  0  0
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    0.8999    0.5996   -0.3580 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1298    0.1192   -1.8905 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0685   -1.3935    0.7272 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5510   -2.9016   -0.8433 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1182   -2.4074   -0.2199 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4000   -2.1487   -3.4626 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5022    0.5572   -2.1899 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7038   -0.2795   -3.1362 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5628   -0.1935   -0.1666 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2086    1.7381   -0.3439 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1268    2.1559    0.4383 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8208    3.3636    0.3335 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7878    3.0531   -2.1955 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3435    3.5580   -1.5323 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.6415    1.9433   -3.2883 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7001    0.6950   -2.3875 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.7253    1.8548   -0.7742 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.5762    0.2212   -1.3877 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9501   -0.0776    3.1186 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5445    0.2149    3.5385 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5044   -2.0867    1.7589 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3974   -2.9386    1.9506 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8566   -1.5516    2.9460 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7220   -2.9952    3.6782 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8019   -1.0930    4.5148 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9082   -2.0672    3.5007 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5004   -2.8761    4.3045 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8592    0.7278   -0.5319 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  3  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  2  0
 15 17  1  0
 17 18  1  0
 18 19  1  0
 19 20  2  0
 19 21  1  0
 21 22  1  0
 22 23  1  0
 23 24  1  0
 24 25  1  0
 25 26  1  0
 22 27  1  0
 27 28  2  0
 27 29  1  0
 29 30  1  0
 30 31  1  0
 31 32  1  0
 31 33  1  0
 30 34  1  0
 34 35  2  0
 34 36  1  0
 36 13  1  0
  1 37  1  0
  1 38  1  0
  1 39  1  0
  2 40  1  0
  2 41  1  0
  3 42  1  1
  4 43  1  0
  4 44  1  0
  4 45  1  0
  5 46  1  0
  5 47  1  0
  6 48  1  0
  6 49  1  0
  7 50  1  0
  7 51  1  0
  8 52  1  0
  8 53  1  0
  9 54  1  0
  9 55  1  0
 10 56  1  0
 10 57  1  0
 11 58  1  0
 11 59  1  0
 12 60  1  0
 12 61  1  0
 13 62  1  1
 14 63  1  0
 14 64  1  0
 17 65  1  0
 18 66  1  0
 18 67  1  0
 21 68  1  0
 22 69  1  6
 23 70  1  0
 23 71  1  0
 24 72  1  0
 24 73  1  0
 25 74  1  0
 25 75  1  0
 26 76  1  0
 26 77  1  0
 29 78  1  0
 30 79  1  1
 31 80  1  6
 32 81  1  0
 32 82  1  0
 32 83  1  0
 33 84  1  0
 33 85  1  0
 33 86  1  0
 36 87  1  0
M  END


  Mrv1652307012117063D          

 87 87  0  0  0  0            999 V2000
    9.3677    2.0574    0.4880 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.1653    1.8165    1.3737 C   0  0  2  0  0  0  0  0  0  0  0  0
    7.4589    0.5363    0.9783 C   0  0  2  0  0  0  0  0  0  0  0  0
    8.4037   -0.6111    1.1180 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9379    0.6960   -0.4335 C   0  0  1  0  0  0  0  0  0  0  0  0
    6.2152   -0.5485   -0.9035 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.0383   -0.8893   -0.0458 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.9915    0.1706    0.0091 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.3923    0.5105   -1.3209 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.7270   -0.6569   -1.9898 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.5988   -1.2505   -1.1913 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.5059   -0.2669   -0.9228 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.6409   -0.9176   -0.1153 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.2725   -2.0420   -0.8654 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.7203   -1.7362   -2.2347 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7942   -1.6938   -3.1297 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0231   -1.4872   -2.6943 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9452   -0.4618   -2.2980 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.7712   -0.8280   -1.1227 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7712   -2.0272   -0.7634 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5603    0.0954   -0.3828 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1513    1.3630    0.1119 C   0  0  1  0  0  0  0  0  0  0  0  0
   -6.2037    2.4026   -0.1584 C   0  0  1  0  0  0  0  0  0  0  0  0
   -6.6135    2.6916   -1.5269 C   0  0  2  0  0  0  0  0  0  0  0  0
   -7.2895    1.5906   -2.2831 C   0  0  1  0  0  0  0  0  0  0  0  0
   -8.5117    1.2253   -1.5642 N   0  0  2  0  0  0  0  0  0  0  0  0
   -4.8559    1.3568    1.5956 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2069    2.4698    2.1723 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3050    0.4060    2.3913 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9327   -0.1187    2.5109 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.9826   -1.5957    2.6128 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.6846   -2.3022    2.8035 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8608   -1.9406    3.8248 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0366    0.5008    1.5337 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6377    1.6866    1.9425 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5368    0.1222    0.3085 N   0  0  0  0  0  0  0  0  0  0  0  0
    9.9508    1.1268    0.4028 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.9931    2.8256    0.9775 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.0657    2.3661   -0.5419 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.4830    2.6817    1.3835 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.5689    1.6363    2.4046 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.6347    0.3958    1.7113 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.9425   -1.4521    1.6750 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.7935   -0.9601    0.1478 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.2932   -0.3057    1.7218 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.3346    1.6057   -0.5119 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.8214    0.8179   -1.0951 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9199   -0.3879   -1.9478 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.9363   -1.3841   -0.8519 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6163   -1.8432   -0.4184 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3877   -1.0781    0.9905 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4517    1.1161    0.4006 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2197   -0.1084    0.7335 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1773    0.8843   -1.9862 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6670    1.3222   -1.1721 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4588   -1.3984   -2.3209 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2584   -0.2507   -2.9340 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0726   -1.5134   -0.1887 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3111   -2.2115   -1.6095 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8999    0.5996   -0.3580 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1298    0.1192   -1.8905 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0685   -1.3935    0.7272 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5510   -2.9016   -0.8433 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1182   -2.4074   -0.2199 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4000   -2.1487   -3.4626 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5022    0.5572   -2.1899 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7038   -0.2795   -3.1362 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5628   -0.1935   -0.1666 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2086    1.7381   -0.3439 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1268    2.1559    0.4383 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8208    3.3636    0.3335 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7878    3.0531   -2.1955 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3435    3.5580   -1.5323 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.6415    1.9433   -3.2883 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7001    0.6950   -2.3875 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.7253    1.8548   -0.7742 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.5762    0.2212   -1.3877 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9501   -0.0776    3.1186 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5445    0.2149    3.5385 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5044   -2.0867    1.7589 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3974   -2.9386    1.9506 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8566   -1.5516    2.9460 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7220   -2.9952    3.6782 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8019   -1.0930    4.5148 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9082   -2.0672    3.5007 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5004   -2.8761    4.3045 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8592    0.7278   -0.5319 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
  3  5  1  0  0  0  0
  5  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  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
 15 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  2  0  0  0  0
 19 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  1  0  0  0  0
 24 25  1  0  0  0  0
 25 26  1  0  0  0  0
 22 27  1  0  0  0  0
 27 28  2  0  0  0  0
 27 29  1  0  0  0  0
 29 30  1  0  0  0  0
 30 31  1  0  0  0  0
 31 32  1  0  0  0  0
 31 33  1  0  0  0  0
 30 34  1  0  0  0  0
 34 35  2  0  0  0  0
 34 36  1  0  0  0  0
 36 13  1  0  0  0  0
  1 37  1  0  0  0  0
  1 38  1  0  0  0  0
  1 39  1  0  0  0  0
  2 40  1  0  0  0  0
  2 41  1  0  0  0  0
  3 42  1  1  0  0  0
  4 43  1  0  0  0  0
  4 44  1  0  0  0  0
  4 45  1  0  0  0  0
  5 46  1  0  0  0  0
  5 47  1  0  0  0  0
  6 48  1  0  0  0  0
  6 49  1  0  0  0  0
  7 50  1  0  0  0  0
  7 51  1  0  0  0  0
  8 52  1  0  0  0  0
  8 53  1  0  0  0  0
  9 54  1  0  0  0  0
  9 55  1  0  0  0  0
 10 56  1  0  0  0  0
 10 57  1  0  0  0  0
 11 58  1  0  0  0  0
 11 59  1  0  0  0  0
 12 60  1  0  0  0  0
 12 61  1  0  0  0  0
 13 62  1  1  0  0  0
 14 63  1  0  0  0  0
 14 64  1  0  0  0  0
 17 65  1  0  0  0  0
 18 66  1  0  0  0  0
 18 67  1  0  0  0  0
 21 68  1  0  0  0  0
 22 69  1  6  0  0  0
 23 70  1  0  0  0  0
 23 71  1  0  0  0  0
 24 72  1  0  0  0  0
 24 73  1  0  0  0  0
 25 74  1  0  0  0  0
 25 75  1  0  0  0  0
 26 76  1  0  0  0  0
 26 77  1  0  0  0  0
 29 78  1  0  0  0  0
 30 79  1  1  0  0  0
 31 80  1  6  0  0  0
 32 81  1  0  0  0  0
 32 82  1  0  0  0  0
 32 83  1  0  0  0  0
 33 84  1  0  0  0  0
 33 85  1  0  0  0  0
 33 86  1  0  0  0  0
 36 87  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0003087

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C27H51N5O4/c1-5-20(4)13-10-8-6-7-9-11-14-21-17-23(33)29-18-24(34)31-22(15-12-16-28)26(35)32-25(19(2)3)27(36)30-21/h19-22,25H,5-18,28H2,1-4H3,(H,29,33)(H,30,36)(H,31,34)(H,32,35)/t20-,21+,22-,25-/m0/s1

> <INCHI_KEY>
SQSJOUYJBHDMLJ-AVRPPCKLSA-N

> <FORMULA>
C27H51N5O4

> <MOLECULAR_WEIGHT>
509.736

> <EXACT_MASS>
509.394105142

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
87

> <JCHEM_AVERAGE_POLARIZABILITY>
58.774862416524186

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3S,6S,13R)-6-(3-aminopropyl)-13-[(9S)-9-methylundecyl]-3-(propan-2-yl)-1,4,7,10-tetraazacyclotridecane-2,5,8,11-tetrone

> <ALOGPS_LOGP>
3.20

> <JCHEM_LOGP>
2.310379915732072

> <ALOGPS_LOGS>
-4.81

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
11.957279106392413

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.080452405997235

> <JCHEM_PKA_STRONGEST_BASIC>
9.580075028044902

> <JCHEM_POLAR_SURFACE_AREA>
142.42

> <JCHEM_REFRACTIVITY>
141.5084

> <JCHEM_ROTATABLE_BOND_COUNT>
14

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
7.84e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(3S,6S,13R)-6-(3-aminopropyl)-3-isopropyl-13-[(9S)-9-methylundecyl]-1,4,7,10-tetraazacyclotridecane-2,5,8,11-tetrone

> <JCHEM_VEBER_RULE>
0

$$$$

     RDKit          3D

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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       9.368   2.057   0.488  0.00  0.00           C+0
HETATM    2  C   UNK     0       8.165   1.817   1.374  0.00  0.00           C+0
HETATM    3  C   UNK     0       7.459   0.536   0.978  0.00  0.00           C+0
HETATM    4  C   UNK     0       8.404  -0.611   1.118  0.00  0.00           C+0
HETATM    5  C   UNK     0       6.938   0.696  -0.434  0.00  0.00           C+0
HETATM    6  C   UNK     0       6.215  -0.549  -0.904  0.00  0.00           C+0
HETATM    7  C   UNK     0       5.038  -0.889  -0.046  0.00  0.00           C+0
HETATM    8  C   UNK     0       3.991   0.171   0.009  0.00  0.00           C+0
HETATM    9  C   UNK     0       3.392   0.510  -1.321  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.727  -0.657  -1.990  0.00  0.00           C+0
HETATM   11  C   UNK     0       1.599  -1.250  -1.191  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.506  -0.267  -0.923  0.00  0.00           C+0
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HETATM   85  H   UNK     0      -4.908  -2.067   3.501  0.00  0.00           H+0
HETATM   86  H   UNK     0      -3.500  -2.876   4.305  0.00  0.00           H+0
HETATM   87  H   UNK     0      -1.859   0.728  -0.532  0.00  0.00           H+0
CONECT    1    2   37   38   39                                             
CONECT    2    1    3   40   41                                             
CONECT    3    2    4    5   42                                             
CONECT    4    3   43   44   45                                             
CONECT    5    3    6   46   47                                             
CONECT    6    5    7   48   49                                             
CONECT    7    6    8   50   51                                             
CONECT    8    7    9   52   53                                             
CONECT    9    8   10   54   55                                             
CONECT   10    9   11   56   57                                             
CONECT   11   10   12   58   59                                             
CONECT   12   11   13   60   61                                             
CONECT   13   12   14   36   62                                             
CONECT   14   13   15   63   64                                             
CONECT   15   14   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15   18   65                                                  
CONECT   18   17   19   66   67                                             
CONECT   19   18   20   21                                                  
CONECT   20   19                                                            
CONECT   21   19   22   68                                                  
CONECT   22   21   23   27   69                                             
CONECT   23   22   24   70   71                                             
CONECT   24   23   25   72   73                                             
CONECT   25   24   26   74   75                                             
CONECT   26   25   76   77                                                  
CONECT   27   22   28   29                                                  
CONECT   28   27                                                            
CONECT   29   27   30   78                                                  
CONECT   30   29   31   34   79                                             
CONECT   31   30   32   33   80                                             
CONECT   32   31   81   82   83                                             
CONECT   33   31   84   85   86                                             
CONECT   34   30   35   36                                                  
CONECT   35   34                                                            
CONECT   36   34   13   87                                                  
CONECT   37    1                                                            
CONECT   38    1                                                            
CONECT   39    1                                                            
CONECT   40    2                                                            
CONECT   41    2                                                            
CONECT   42    3                                                            
CONECT   43    4                                                            
CONECT   44    4                                                            
CONECT   45    4                                                            
CONECT   46    5                                                            
CONECT   47    5                                                            
CONECT   48    6                                                            
CONECT   49    6                                                            
CONECT   50    7                                                            
CONECT   51    7                                                            
CONECT   52    8                                                            
CONECT   53    8                                                            
CONECT   54    9                                                            
CONECT   55    9                                                            
CONECT   56   10                                                            
CONECT   57   10                                                            
CONECT   58   11                                                            
CONECT   59   11                                                            
CONECT   60   12                                                            
CONECT   61   12                                                            
CONECT   62   13                                                            
CONECT   63   14                                                            
CONECT   64   14                                                            
CONECT   65   17                                                            
CONECT   66   18                                                            
CONECT   67   18                                                            
CONECT   68   21                                                            
CONECT   69   22                                                            
CONECT   70   23                                                            
CONECT   71   23                                                            
CONECT   72   24                                                            
CONECT   73   24                                                            
CONECT   74   25                                                            
CONECT   75   25                                                            
CONECT   76   26                                                            
CONECT   77   26                                                            
CONECT   78   29                                                            
CONECT   79   30                                                            
CONECT   80   31                                                            
CONECT   81   32                                                            
CONECT   82   32                                                            
CONECT   83   32                                                            
CONECT   84   33                                                            
CONECT   85   33                                                            
CONECT   86   33                                                            
CONECT   87   36                                                            
MASTER        0    0    0    0    0    0    0    0   87    0  174    0
END

RDKit          3D

87 87  0  0  0  0  0  0  0  0999 V2000
    9.3677    2.0574    0.4880 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.1653    1.8165    1.3737 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.4589    0.5363    0.9783 C   0  0  2  0  0  0  0  0  0  0  0  0
    8.4037   -0.6111    1.1180 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9379    0.6960   -0.4335 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2152   -0.5485   -0.9035 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0383   -0.8893   -0.0458 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9915    0.1706    0.0091 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3923    0.5105   -1.3209 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7270   -0.6569   -1.9898 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5988   -1.2505   -1.1913 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5059   -0.2669   -0.9228 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6409   -0.9176   -0.1153 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.2725   -2.0420   -0.8654 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7203   -1.7362   -2.2347 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7942   -1.6938   -3.1297 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0231   -1.4872   -2.6943 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9452   -0.4618   -2.2980 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7712   -0.8280   -1.1227 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7712   -2.0272   -0.7634 O   0  0  0  0  0  0  0  0  0  0  0  0
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    2.2584   -0.2507   -2.9340 H   0  0  0  0  0  0  0  0  0  0  0  0
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    1.3111   -2.2115   -1.6095 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8999    0.5996   -0.3580 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1298    0.1192   -1.8905 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0685   -1.3935    0.7272 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5510   -2.9016   -0.8433 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1182   -2.4074   -0.2199 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4000   -2.1487   -3.4626 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5022    0.5572   -2.1899 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -6.5628   -0.1935   -0.1666 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2086    1.7381   -0.3439 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1268    2.1559    0.4383 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8208    3.3636    0.3335 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
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 33 86  1  0
 36 87  1  0
M  END

View in JSmol View NMR Assignments

Synonyms

Not Available

Chemical Formula

C₂₇H₅₁N₅O₄

Average Mass

509.7360 Da

Monoisotopic Mass

509.39411 Da

IUPAC Name

(3S,6S,13R)-6-(3-aminopropyl)-13-[(9S)-9-methylundecyl]-3-(propan-2-yl)-1,4,7,10-tetraazacyclotridecane-2,5,8,11-tetrone

Traditional Name

(3S,6S,13R)-6-(3-aminopropyl)-3-isopropyl-13-[(9S)-9-methylundecyl]-1,4,7,10-tetraazacyclotridecane-2,5,8,11-tetrone

CAS Registry Number

Not Available

SMILES

CCC(C)CCCCCCCC[C@@H]1CC(=O)NCC(=O)N[C@@H](CCCN)C(=O)N[C@@H](C(C)C)C(=O)N1

InChI Identifier

InChI=1S/C27H51N5O4/c1-5-20(4)13-10-8-6-7-9-11-14-21-17-23(33)29-18-24(34)31-22(15-12-16-28)26(35)32-25(19(2)3)27(36)30-21/h19-22,25H,5-18,28H2,1-4H3,(H,29,33)(H,30,36)(H,31,34)(H,32,35)/t20?,21-,22+,25+/m1/s1

InChI Key

SQSJOUYJBHDMLJ-AVRPPCKLSA-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
Rhodococcus	NPAtlas	10580383

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
Cyclic carboximidic acid
Azacycle
Organoheterocyclic compound
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Polyol
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Hydrocarbon derivative
Primary amine
Organooxygen compound
Organonitrogen compound
Primary aliphatic amine
Amine
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic 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	3.2	ALOGPS
logP	2.31	ChemAxon
logS	-4.8	ALOGPS
pKa (Strongest Acidic)	11.08	ChemAxon
pKa (Strongest Basic)	9.58	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	142.42 Å²	ChemAxon
Rotatable Bond Count	14	ChemAxon
Refractivity	141.51 m³·mol⁻¹	ChemAxon
Polarizability	58.77 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

NPAtlas ID

NPA010393

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

78437494

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

139585972

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Chiba H, Agematu H, Dobashi K, Yoshioka T: Rhodopeptins, novel cyclic tetrapeptides with antifungal activities from Rhodococcus sp. II. Structure elucidation. J Antibiot (Tokyo). 1999 Aug;52(8):700-9. doi: 10.7164/antibiotics.52.700. [PubMed:10580383 ]

Showing NP-Card for Rhodopeptin C4 (NP0003087)

MOL for NP0003087 (Rhodopeptin C4)

3D MOL for NP0003087 (Rhodopeptin C4)

3D SDF for NP0003087 (Rhodopeptin C4)

3D-SDF for NP0003087 (Rhodopeptin C4)

PDB for NP0003087 (Rhodopeptin C4)

3D PDB for NP0003087 (Rhodopeptin C4)

SMILES for NP0003087 (Rhodopeptin C4)

INCHI for NP0003087 (Rhodopeptin C4)

Structure for NP0003087 (Rhodopeptin C4)

3D Structure for NP0003087 (Rhodopeptin C4)