NP-MRD: Showing NP-Card for Rakicidin B (NP0023049)

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Record Information

Version

1.0

Created at

2021-01-06 08:10:50 UTC

Updated at

2021-07-15 17:40:41 UTC

NP-MRD ID

NP0023049

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Rakicidin B

Provided By

NPAtlas

Description

Rakicidin B is found in Micromonospora sp. and Micromonospora sp. No. R385-2. It was first documented in 1995 (PMID: 8557602). Based on a literature review very few articles have been published on Rakicidin B (PMID: 25286338).

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652307042108133D          

100100  0  0  0  0            999 V2000
   -3.5808   -0.2386   -3.5052 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3667   -0.7298   -2.4922 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5938    0.0174   -2.2201 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8108   -0.3904   -1.9955 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2180   -1.7640   -1.9615 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.8019   -2.2660   -3.0211 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0981   -2.7221   -0.9163 N   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5712   -4.0304   -1.2360 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.5101   -2.5221    0.4535 C   0  0  2  0  0  0  0  0  0  0  0  0
   -6.4713   -2.4888    1.4754 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8868   -3.6061    1.7194 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0400   -1.3775    2.2241 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5464   -0.1144    1.7320 C   0  0  1  0  0  0  0  0  0  0  0  0
   -6.5092    1.0403    2.0642 C   0  0  2  0  0  0  0  0  0  0  0  0
   -7.7603    0.8520    1.4938 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -4.2056    0.1966    2.3472 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -3.0794    0.5366    1.6623 O   0  0  0  0  0  0  0  0  0  0  0  0
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    0.9998    2.4840   -0.8433 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.3550    3.1993   -0.6452 C   0  0  2  0  0  0  0  0  0  0  0  0
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    4.0753    0.7922   -1.2011 C   0  0  1  0  0  0  0  0  0  0  0  0
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    6.4091    0.6819   -0.3142 C   0  0  1  0  0  0  0  0  0  0  0  0
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    0.7998    2.0267    1.2596 H   0  0  0  0  0  0  0  0  0  0  0  0
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    4.0769   -0.3119   -1.3582 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4574    1.1931   -2.0351 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8889    1.0524   -2.3324 H   0  0  0  0  0  0  0  0  0  0  0  0
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    6.0357    0.9284    0.7068 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.3986   -0.3981   -0.5058 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.0207    1.0145   -1.6335 H   0  0  0  0  0  0  0  0  0  0  0  0
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    9.8029    1.1340    0.0932 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.5771    0.9531    1.3984 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.1480   -1.0922   -0.8243 H   0  0  0  0  0  0  0  0  0  0  0  0
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    9.9050   -2.5406    0.9518 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.8923   -1.7934    2.9220 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.6602   -1.5729    3.1004 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.6471   -0.1081    2.7962 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.2517   -0.7100   -0.4248 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.0367   -1.8696    0.7722 H   0  0  0  0  0  0  0  0  0  0  0  0
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  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
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  4  5  1  0  0  0  0
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M  END

     RDKit          3D

100100  0  0  0  0  0  0  0  0999 V2000
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M  END


  Mrv1652307042108133D          

100100  0  0  0  0            999 V2000
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  1 45  1  0  0  0  0
  1 46  1  0  0  0  0
  3 47  1  0  0  0  0
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 41 98  1  0  0  0  0
 41 99  1  0  0  0  0
 44100  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0023049

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]O[C@]([H])(C(=O)N([H])[H])[C@]1([H])N([H])C(=O)C([H])([H])N(C(=O)\C([H])=C([H])/C(=C([H])[H])N([H])C(=O)[C@@]([H])(C([H])([H])[H])[C@@]([H])(OC1=O)[C@@]([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])([H])C([H])([H])C([H])([H])C([H])([H])C([H])(C([H])([H])[H])C([H])([H])[H])C([H])([H])[H]

> <INCHI_IDENTIFIER>
InChI=1S/C33H56N4O7/c1-22(2)17-15-13-11-9-7-8-10-12-14-16-18-23(3)30-25(5)32(42)35-24(4)19-20-27(39)37(6)21-26(38)36-28(33(43)44-30)29(40)31(34)41/h19-20,22-23,25,28-30,40H,4,7-18,21H2,1-3,5-6H3,(H2,34,41)(H,35,42)(H,36,38)/b20-19-/t23-,25-,28-,29-,30-/m0/s1

> <INCHI_KEY>
AKYUFOZFLOQQQL-VXPUYCOJSA-N

> <FORMULA>
C33H56N4O7

> <MOLECULAR_WEIGHT>
620.832

> <EXACT_MASS>
620.414900159

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
100

> <JCHEM_AVERAGE_POLARIZABILITY>
69.16140605228006

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-2-[(3S,9Z,14S,15S)-7,14-dimethyl-15-[(2S)-15-methylhexadecan-2-yl]-11-methylidene-2,5,8,13-tetraoxo-1-oxa-4,7,12-triazacyclopentadec-9-en-3-yl]-2-hydroxyacetamide

> <ALOGPS_LOGP>
5.05

> <JCHEM_LOGP>
3.986646684000002

> <ALOGPS_LOGS>
-5.72

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.238852387492374

> <JCHEM_PKA_STRONGEST_ACIDIC>
10.65538558210932

> <JCHEM_PKA_STRONGEST_BASIC>
-0.5728208359309485

> <JCHEM_POLAR_SURFACE_AREA>
168.12999999999997

> <JCHEM_REFRACTIVITY>
170.0569000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
16

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.17e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S)-2-[(3S,9Z,14S,15S)-7,14-dimethyl-15-[(2S)-15-methylhexadecan-2-yl]-11-methylidene-2,5,8,13-tetraoxo-1-oxa-4,7,12-triazacyclopentadec-9-en-3-yl]-2-hydroxyacetamide

> <JCHEM_VEBER_RULE>
0

$$$$

     RDKit          3D

100100  0  0  0  0  0  0  0  0999 V2000
   -3.5808   -0.2386   -3.5052 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3667   -0.7298   -2.4922 C   0  0  0  0  0  0  0  0  0  0  0  0
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  1  2  2  0
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 40 96  1  1
 41 97  1  0
 41 98  1  0
 41 99  1  0
 44100  1  0
M  END

HEADER    PROTEIN                                 04-JUL-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-JUL-21         0                                  
HETATM    1  C   UNK     0      -3.581  -0.239  -3.505  0.00  0.00           C+0
HETATM    2  C   UNK     0      -4.367  -0.730  -2.492  0.00  0.00           C+0
HETATM    3  C   UNK     0      -5.594   0.017  -2.220  0.00  0.00           C+0
HETATM    4  C   UNK     0      -6.811  -0.390  -1.996  0.00  0.00           C+0
HETATM    5  C   UNK     0      -7.218  -1.764  -1.962  0.00  0.00           C+0
HETATM    6  O   UNK     0      -7.802  -2.266  -3.021  0.00  0.00           O+0
HETATM    7  N   UNK     0      -7.098  -2.722  -0.916  0.00  0.00           N+0
HETATM    8  C   UNK     0      -6.571  -4.030  -1.236  0.00  0.00           C+0
HETATM    9  C   UNK     0      -7.510  -2.522   0.454  0.00  0.00           C+0
HETATM   10  C   UNK     0      -6.471  -2.489   1.475  0.00  0.00           C+0
HETATM   11  O   UNK     0      -5.887  -3.606   1.719  0.00  0.00           O+0
HETATM   12  N   UNK     0      -6.040  -1.377   2.224  0.00  0.00           N+0
HETATM   13  C   UNK     0      -5.546  -0.114   1.732  0.00  0.00           C+0
HETATM   14  C   UNK     0      -6.509   1.040   2.064  0.00  0.00           C+0
HETATM   15  O   UNK     0      -7.760   0.852   1.494  0.00  0.00           O+0
HETATM   16  C   UNK     0      -5.920   2.336   1.724  0.00  0.00           C+0
HETATM   17  N   UNK     0      -6.575   3.269   0.889  0.00  0.00           N+0
HETATM   18  O   UNK     0      -4.795   2.640   2.184  0.00  0.00           O+0
HETATM   19  C   UNK     0      -4.206   0.197   2.347  0.00  0.00           C+0
HETATM   20  O   UNK     0      -4.157   0.127   3.603  0.00  0.00           O+0
HETATM   21  O   UNK     0      -3.079   0.537   1.662  0.00  0.00           O+0
HETATM   22  C   UNK     0      -2.709  -0.003   0.369  0.00  0.00           C+0
HETATM   23  C   UNK     0      -1.240   0.481   0.226  0.00  0.00           C+0
HETATM   24  C   UNK     0      -0.762   0.022  -1.115  0.00  0.00           C+0
HETATM   25  C   UNK     0      -1.130   1.927   0.449  0.00  0.00           C+0
HETATM   26  C   UNK     0       0.230   2.533   0.403  0.00  0.00           C+0
HETATM   27  C   UNK     0       1.000   2.484  -0.843  0.00  0.00           C+0
HETATM   28  C   UNK     0       2.355   3.199  -0.645  0.00  0.00           C+0
HETATM   29  C   UNK     0       3.173   2.513   0.411  0.00  0.00           C+0
HETATM   30  C   UNK     0       3.389   1.053   0.085  0.00  0.00           C+0
HETATM   31  C   UNK     0       4.075   0.792  -1.201  0.00  0.00           C+0
HETATM   32  C   UNK     0       5.464   1.310  -1.346  0.00  0.00           C+0
HETATM   33  C   UNK     0       6.409   0.682  -0.314  0.00  0.00           C+0
HETATM   34  C   UNK     0       7.770   1.239  -0.574  0.00  0.00           C+0
HETATM   35  C   UNK     0       8.829   0.682   0.360  0.00  0.00           C+0
HETATM   36  C   UNK     0       8.928  -0.825   0.222  0.00  0.00           C+0
HETATM   37  C   UNK     0       9.973  -1.434   1.110  0.00  0.00           C+0
HETATM   38  C   UNK     0       9.749  -1.189   2.567  0.00  0.00           C+0
HETATM   39  C   UNK     0      11.347  -1.010   0.645  0.00  0.00           C+0
HETATM   40  C   UNK     0      -2.834  -1.464   0.473  0.00  0.00           C+0
HETATM   41  C   UNK     0      -1.525  -2.188   0.843  0.00  0.00           C+0
HETATM   42  C   UNK     0      -3.442  -2.228  -0.604  0.00  0.00           C+0
HETATM   43  O   UNK     0      -3.579  -3.476  -0.275  0.00  0.00           O+0
HETATM   44  N   UNK     0      -3.888  -1.890  -1.880  0.00  0.00           N+0
HETATM   45  H   UNK     0      -2.672  -0.707  -3.775  0.00  0.00           H+0
HETATM   46  H   UNK     0      -3.937   0.616  -4.056  0.00  0.00           H+0
HETATM   47  H   UNK     0      -5.439   1.132  -2.198  0.00  0.00           H+0
HETATM   48  H   UNK     0      -7.620   0.411  -1.861  0.00  0.00           H+0
HETATM   49  H   UNK     0      -6.306  -4.624  -0.336  0.00  0.00           H+0
HETATM   50  H   UNK     0      -7.408  -4.551  -1.785  0.00  0.00           H+0
HETATM   51  H   UNK     0      -5.704  -4.049  -1.897  0.00  0.00           H+0
HETATM   52  H   UNK     0      -8.193  -3.412   0.662  0.00  0.00           H+0
HETATM   53  H   UNK     0      -8.242  -1.661   0.558  0.00  0.00           H+0
HETATM   54  H   UNK     0      -6.059  -1.445   3.295  0.00  0.00           H+0
HETATM   55  H   UNK     0      -5.459  -0.110   0.649  0.00  0.00           H+0
HETATM   56  H   UNK     0      -6.670   0.957   3.177  0.00  0.00           H+0
HETATM   57  H   UNK     0      -7.891   1.584   0.836  0.00  0.00           H+0
HETATM   58  H   UNK     0      -7.291   3.911   1.303  0.00  0.00           H+0
HETATM   59  H   UNK     0      -6.379   3.351  -0.135  0.00  0.00           H+0
HETATM   60  H   UNK     0      -3.282   0.536  -0.360  0.00  0.00           H+0
HETATM   61  H   UNK     0      -0.610  -0.036   0.982  0.00  0.00           H+0
HETATM   62  H   UNK     0      -1.518  -0.717  -1.551  0.00  0.00           H+0
HETATM   63  H   UNK     0      -0.775   0.832  -1.895  0.00  0.00           H+0
HETATM   64  H   UNK     0       0.198  -0.499  -1.128  0.00  0.00           H+0
HETATM   65  H   UNK     0      -1.580   2.212   1.452  0.00  0.00           H+0
HETATM   66  H   UNK     0      -1.732   2.506  -0.339  0.00  0.00           H+0
HETATM   67  H   UNK     0       0.146   3.629   0.694  0.00  0.00           H+0
HETATM   68  H   UNK     0       0.800   2.027   1.260  0.00  0.00           H+0
HETATM   69  H   UNK     0       1.233   1.468  -1.246  0.00  0.00           H+0
HETATM   70  H   UNK     0       0.465   3.029  -1.637  0.00  0.00           H+0
HETATM   71  H   UNK     0       2.088   4.212  -0.270  0.00  0.00           H+0
HETATM   72  H   UNK     0       2.875   3.286  -1.611  0.00  0.00           H+0
HETATM   73  H   UNK     0       2.670   2.587   1.379  0.00  0.00           H+0
HETATM   74  H   UNK     0       4.161   3.013   0.527  0.00  0.00           H+0
HETATM   75  H   UNK     0       4.032   0.657   0.917  0.00  0.00           H+0
HETATM   76  H   UNK     0       2.425   0.515   0.079  0.00  0.00           H+0
HETATM   77  H   UNK     0       4.077  -0.312  -1.358  0.00  0.00           H+0
HETATM   78  H   UNK     0       3.457   1.193  -2.035  0.00  0.00           H+0
HETATM   79  H   UNK     0       5.889   1.052  -2.332  0.00  0.00           H+0
HETATM   80  H   UNK     0       5.504   2.404  -1.227  0.00  0.00           H+0
HETATM   81  H   UNK     0       6.036   0.928   0.707  0.00  0.00           H+0
HETATM   82  H   UNK     0       6.399  -0.398  -0.506  0.00  0.00           H+0
HETATM   83  H   UNK     0       8.021   1.014  -1.634  0.00  0.00           H+0
HETATM   84  H   UNK     0       7.745   2.337  -0.447  0.00  0.00           H+0
HETATM   85  H   UNK     0       9.803   1.134   0.093  0.00  0.00           H+0
HETATM   86  H   UNK     0       8.577   0.953   1.398  0.00  0.00           H+0
HETATM   87  H   UNK     0       9.148  -1.092  -0.824  0.00  0.00           H+0
HETATM   88  H   UNK     0       7.933  -1.275   0.477  0.00  0.00           H+0
HETATM   89  H   UNK     0       9.905  -2.541   0.952  0.00  0.00           H+0
HETATM   90  H   UNK     0       8.892  -1.793   2.922  0.00  0.00           H+0
HETATM   91  H   UNK     0      10.660  -1.573   3.100  0.00  0.00           H+0
HETATM   92  H   UNK     0       9.647  -0.108   2.796  0.00  0.00           H+0
HETATM   93  H   UNK     0      11.252  -0.710  -0.425  0.00  0.00           H+0
HETATM   94  H   UNK     0      12.037  -1.870   0.772  0.00  0.00           H+0
HETATM   95  H   UNK     0      11.744  -0.162   1.218  0.00  0.00           H+0
HETATM   96  H   UNK     0      -3.474  -1.707   1.397  0.00  0.00           H+0
HETATM   97  H   UNK     0      -0.852  -2.319   0.005  0.00  0.00           H+0
HETATM   98  H   UNK     0      -1.097  -1.819   1.780  0.00  0.00           H+0
HETATM   99  H   UNK     0      -1.872  -3.240   1.096  0.00  0.00           H+0
HETATM  100  H   UNK     0      -3.839  -2.733  -2.585  0.00  0.00           H+0
CONECT    1    2   45   46                                                  
CONECT    2    1    3   44                                                  
CONECT    3    2    4   47                                                  
CONECT    4    3    5   48                                                  
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8    9                                                  
CONECT    8    7   49   50   51                                             
CONECT    9    7   10   52   53                                             
CONECT   10    9   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10   13   54                                                  
CONECT   13   12   14   19   55                                             
CONECT   14   13   15   16   56                                             
CONECT   15   14   57                                                       
CONECT   16   14   17   18                                                  
CONECT   17   16   58   59                                                  
CONECT   18   16                                                            
CONECT   19   13   20   21                                                  
CONECT   20   19                                                            
CONECT   21   19   22                                                       
CONECT   22   21   23   40   60                                             
CONECT   23   22   24   25   61                                             
CONECT   24   23   62   63   64                                             
CONECT   25   23   26   65   66                                             
CONECT   26   25   27   67   68                                             
CONECT   27   26   28   69   70                                             
CONECT   28   27   29   71   72                                             
CONECT   29   28   30   73   74                                             
CONECT   30   29   31   75   76                                             
CONECT   31   30   32   77   78                                             
CONECT   32   31   33   79   80                                             
CONECT   33   32   34   81   82                                             
CONECT   34   33   35   83   84                                             
CONECT   35   34   36   85   86                                             
CONECT   36   35   37   87   88                                             
CONECT   37   36   38   39   89                                             
CONECT   38   37   90   91   92                                             
CONECT   39   37   93   94   95                                             
CONECT   40   22   41   42   96                                             
CONECT   41   40   97   98   99                                             
CONECT   42   40   43   44                                                  
CONECT   43   42                                                            
CONECT   44   42    2  100                                                  
CONECT   45    1                                                            
CONECT   46    1                                                            
CONECT   47    3                                                            
CONECT   48    4                                                            
CONECT   49    8                                                            
CONECT   50    8                                                            
CONECT   51    8                                                            
CONECT   52    9                                                            
CONECT   53    9                                                            
CONECT   54   12                                                            
CONECT   55   13                                                            
CONECT   56   14                                                            
CONECT   57   15                                                            
CONECT   58   17                                                            
CONECT   59   17                                                            
CONECT   60   22                                                            
CONECT   61   23                                                            
CONECT   62   24                                                            
CONECT   63   24                                                            
CONECT   64   24                                                            
CONECT   65   25                                                            
CONECT   66   25                                                            
CONECT   67   26                                                            
CONECT   68   26                                                            
CONECT   69   27                                                            
CONECT   70   27                                                            
CONECT   71   28                                                            
CONECT   72   28                                                            
CONECT   73   29                                                            
CONECT   74   29                                                            
CONECT   75   30                                                            
CONECT   76   30                                                            
CONECT   77   31                                                            
CONECT   78   31                                                            
CONECT   79   32                                                            
CONECT   80   32                                                            
CONECT   81   33                                                            
CONECT   82   33                                                            
CONECT   83   34                                                            
CONECT   84   34                                                            
CONECT   85   35                                                            
CONECT   86   35                                                            
CONECT   87   36                                                            
CONECT   88   36                                                            
CONECT   89   37                                                            
CONECT   90   38                                                            
CONECT   91   38                                                            
CONECT   92   38                                                            
CONECT   93   39                                                            
CONECT   94   39                                                            
CONECT   95   39                                                            
CONECT   96   40                                                            
CONECT   97   41                                                            
CONECT   98   41                                                            
CONECT   99   41                                                            
CONECT  100   44                                                            
MASTER        0    0    0    0    0    0    0    0  100    0  200    0
END

RDKit          3D

100100  0  0  0  0  0  0  0  0999 V2000
   -3.5808   -0.2386   -3.5052 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3667   -0.7298   -2.4922 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5938    0.0174   -2.2201 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8108   -0.3904   -1.9955 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2180   -1.7640   -1.9615 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.8019   -2.2660   -3.0211 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0981   -2.7221   -0.9163 N   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5712   -4.0304   -1.2360 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.5101   -2.5221    0.4535 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4713   -2.4888    1.4754 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8868   -3.6061    1.7194 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0400   -1.3775    2.2241 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5464   -0.1144    1.7320 C   0  0  1  0  0  0  0  0  0  0  0  0
   -6.5092    1.0403    2.0642 C   0  0  2  0  0  0  0  0  0  0  0  0
   -7.7603    0.8520    1.4938 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9203    2.3359    1.7245 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5754    3.2687    0.8888 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7954    2.6396    2.1845 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2056    0.1966    2.3472 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1568    0.1273    3.6034 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0794    0.5366    1.6623 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7094   -0.0028    0.3694 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.2403    0.4809    0.2261 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7622    0.0217   -1.1145 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1301    1.9267    0.4485 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2302    2.5333    0.4033 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9998    2.4840   -0.8433 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3550    3.1993   -0.6452 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1729    2.5131    0.4113 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3893    1.0526    0.0852 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0753    0.7922   -1.2011 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4643    1.3104   -1.3461 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4091    0.6819   -0.3142 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.7704    1.2392   -0.5740 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.8289    0.6823    0.3596 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.9281   -0.8246    0.2223 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.9729   -1.4338    1.1096 C   0  0  2  0  0  0  0  0  0  0  0  0
    9.7495   -1.1888    2.5672 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.3473   -1.0105    0.6454 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8344   -1.4639    0.4728 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.5249   -2.1878    0.8432 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4423   -2.2275   -0.6042 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5793   -3.4763   -0.2749 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8877   -1.8896   -1.8802 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6724   -0.7068   -3.7747 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9370    0.6155   -4.0557 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4389    1.1319   -2.1984 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.6197    0.4105   -1.8614 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3063   -4.6242   -0.3358 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.4083   -4.5511   -1.7847 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7038   -4.0494   -1.8969 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.1925   -3.4118    0.6622 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.2422   -1.6610    0.5581 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0592   -1.4447    3.2950 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4592   -0.1097    0.6494 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6703    0.9570    3.1770 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.8913    1.5836    0.8359 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2910    3.9107    1.3026 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3789    3.3512   -0.1351 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2816    0.5363   -0.3599 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6101   -0.0362    0.9822 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5181   -0.7171   -1.5514 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7747    0.8315   -1.8951 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1984   -0.4986   -1.1279 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5801    2.2116    1.4517 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7321    2.5063   -0.3389 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1457    3.6291    0.6939 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7998    2.0267    1.2596 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2329    1.4684   -1.2455 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4650    3.0289   -1.6369 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0877    4.2118   -0.2697 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8752    3.2860   -1.6111 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6701    2.5865    1.3792 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1608    3.0131    0.5273 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0318    0.6567    0.9173 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4251    0.5151    0.0786 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0769   -0.3119   -1.3582 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4574    1.1931   -2.0351 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8889    1.0524   -2.3324 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5038    2.4044   -1.2272 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.0357    0.9284    0.7068 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.3986   -0.3981   -0.5058 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.0207    1.0145   -1.6335 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.7447    2.3368   -0.4467 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.8029    1.1340    0.0932 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.5771    0.9531    1.3984 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.1480   -1.0922   -0.8243 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.9327   -1.2748    0.4766 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.9050   -2.5406    0.9518 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.8923   -1.7934    2.9220 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.6602   -1.5729    3.1004 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.6471   -0.1081    2.7962 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.2517   -0.7100   -0.4248 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.0367   -1.8696    0.7722 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.7444   -0.1617    1.2178 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4740   -1.7068    1.3975 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8523   -2.3190    0.0049 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0972   -1.8187    1.7796 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8718   -3.2396    1.0963 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8389   -2.7333   -2.5848 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  5  7  1  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
 10 11  2  0
 10 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 14 16  1  0
 16 17  1  0
 16 18  2  0
 13 19  1  0
 19 20  2  0
 19 21  1  0
 21 22  1  0
 22 23  1  0
 23 24  1  0
 23 25  1  0
 25 26  1  0
 26 27  1  0
 27 28  1  0
 28 29  1  0
 29 30  1  0
 30 31  1  0
 31 32  1  0
 32 33  1  0
 33 34  1  0
 34 35  1  0
 35 36  1  0
 36 37  1  0
 37 38  1  0
 37 39  1  0
 22 40  1  0
 40 41  1  0
 40 42  1  0
 42 43  2  0
 42 44  1  0
 44  2  1  0
  1 45  1  0
  1 46  1  0
  3 47  1  0
  4 48  1  0
  8 49  1  0
  8 50  1  0
  8 51  1  0
  9 52  1  0
  9 53  1  0
 12 54  1  0
 13 55  1  6
 14 56  1  1
 15 57  1  0
 17 58  1  0
 17 59  1  0
 22 60  1  6
 23 61  1  1
 24 62  1  0
 24 63  1  0
 24 64  1  0
 25 65  1  0
 25 66  1  0
 26 67  1  0
 26 68  1  0
 27 69  1  0
 27 70  1  0
 28 71  1  0
 28 72  1  0
 29 73  1  0
 29 74  1  0
 30 75  1  0
 30 76  1  0
 31 77  1  0
 31 78  1  0
 32 79  1  0
 32 80  1  0
 33 81  1  0
 33 82  1  0
 34 83  1  0
 34 84  1  0
 35 85  1  0
 35 86  1  0
 36 87  1  0
 36 88  1  0
 37 89  1  1
 38 90  1  0
 38 91  1  0
 38 92  1  0
 39 93  1  0
 39 94  1  0
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 40 96  1  1
 41 97  1  0
 41 98  1  0
 41 99  1  0
 44100  1  0
M  END

View in JSmol View NMR Assignments

Synonyms

Value	Source
2-[(9Z)-5,13-Dihydroxy-7,14-dimethyl-15-(15-methylhexadecan-2-yl)-11-methylidene-2,8-dioxo-1-oxa-4,7,12-triazacyclopentadeca-4,9,12-trien-3-yl]-2-hydroxyethanimidate	Generator

Chemical Formula

C₃₃H₅₆N₄O₇

Average Mass

620.8320 Da

Monoisotopic Mass

620.41490 Da

IUPAC Name

(2S)-2-[(3S,9Z,14S,15S)-7,14-dimethyl-15-[(2S)-15-methylhexadecan-2-yl]-11-methylidene-2,5,8,13-tetraoxo-1-oxa-4,7,12-triazacyclopentadec-9-en-3-yl]-2-hydroxyacetamide

Traditional Name

(2S)-2-[(3S,9Z,14S,15S)-7,14-dimethyl-15-[(2S)-15-methylhexadecan-2-yl]-11-methylidene-2,5,8,13-tetraoxo-1-oxa-4,7,12-triazacyclopentadec-9-en-3-yl]-2-hydroxyacetamide

CAS Registry Number

Not Available

SMILES

CC(C)CCCCCCCCCCCCC(C)C1OC(=O)C(NC(=O)CN(C)C(=O)\C=C/C(=C)NC(=O)C1C)C(O)C(N)=O

InChI Identifier

InChI=1S/C33H56N4O7/c1-22(2)17-15-13-11-9-7-8-10-12-14-16-18-23(3)30-25(5)32(42)35-24(4)19-20-27(39)37(6)21-26(38)36-28(33(43)44-30)29(40)31(34)41/h19-20,22-23,25,28-30,40H,4,7-18,21H2,1-3,5-6H3,(H2,34,41)(H,35,42)(H,36,38)/b20-19-

InChI Key

AKYUFOZFLOQQQL-VXPUYCOJSA-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
Micromonospora sp.	NPAtlas	8557602
Micromonospora sp. No. R385-2	Bacteria	KNApSAcK

Chemical Taxonomy

Classification

Not classified

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	5.05	ALOGPS
logP	3.99	ChemAxon
logS	-5.7	ALOGPS
pKa (Strongest Acidic)	10.66	ChemAxon
pKa (Strongest Basic)	-0.57	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	168.13 Å²	ChemAxon
Rotatable Bond Count	16	ChemAxon
Refractivity	170.06 m³·mol⁻¹	ChemAxon
Polarizability	69.16 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

NPA012160

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00016160

Chemspider ID

78444576

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

101689638

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

McBrien KD, Berry RL, Lowe SE, Neddermann KM, Bursuker I, Huang S, Klohr SE, Leet JE: Rakicidins, new cytotoxic lipopeptides from Micromonospora sp. fermentation, isolation and characterization. J Antibiot (Tokyo). 1995 Dec;48(12):1446-52. doi: 10.7164/antibiotics.48.1446. [PubMed:8557602 ]
Sang F, Li D, Sun X, Cao X, Wang L, Sun J, Sun B, Wu L, Yang G, Chu X, Wang J, Dong C, Geng Y, Jiang H, Long H, Chen S, Wang G, Zhang S, Zhang Q, Chen Y: Total synthesis and determination of the absolute configuration of rakicidin A. J Am Chem Soc. 2014 Nov 5;136(44):15787-91. doi: 10.1021/ja509379j. Epub 2014 Oct 24. [PubMed:25286338 ]

Showing NP-Card for Rakicidin B (NP0023049)

MOL for NP0023049 (Rakicidin B)

3D MOL for NP0023049 (Rakicidin B)

3D SDF for NP0023049 (Rakicidin B)

3D-SDF for NP0023049 (Rakicidin B)

PDB for NP0023049 (Rakicidin B)

3D PDB for NP0023049 (Rakicidin B)

SMILES for NP0023049 (Rakicidin B)

INCHI for NP0023049 (Rakicidin B)

Structure for NP0023049 (Rakicidin B)

3D Structure for NP0023049 (Rakicidin B)