NP-MRD: Showing NP-Card for Sibiromycin (NP0021499)

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Record Information

Version

2.0

Created at

2021-01-06 06:46:50 UTC

Updated at

2021-07-15 17:36:31 UTC

NP-MRD ID

NP0021499

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Sibiromycin

Provided By

NPAtlas

Description

Sibiromycin belongs to the class of organic compounds known as aminoglycosides. These are molecules or a portion of a molecule composed of amino-modified sugars. Sibiromycin is a secondary metabolite. Secondary metabolites are metabolically or physiologically non-essential metabolites that may serve a role as defense or signalling molecules. In some cases they are simply molecules that arise from the incomplete metabolism of other secondary metabolites. Sibiromycin is found in Streptosporangium sibiricum. Sibiromycin was first documented in 1969 (PMID: 4907802). Based on a literature review a small amount of articles have been published on sibiromycin (PMID: 1119795) (PMID: 18983) (PMID: 20544978) (PMID: 21111423).

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652306242105163D          

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M  END

     RDKit          3D

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M  END


  Mrv1652306242105163D          

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   -0.4993   -1.1214   -2.0737 C   0  0  0  0  0  0  0  0  0  0  0  0
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    6.0958   -0.0149   -0.1001 C   0  0  1  0  0  0  0  0  0  0  0  0
    9.2478    1.1518    3.6293 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -3.7347    0.7866   -2.3249 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4959    0.6291   -2.2901 H   0  0  0  0  0  0  0  0  0  0  0  0
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    0.4249   -2.1909   -4.2648 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1971   -1.4575   -3.0684 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2233   -1.5501   -1.9943 H   0  0  0  0  0  0  0  0  0  0  0  0
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    6.6009   -1.0031   -0.1577 H   0  0  0  0  0  0  0  0  0  0  0  0
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 23 13  1  0  0  0  0
  1 35  1  0  0  0  0
  1 36  1  0  0  0  0
  1 37  1  0  0  0  0
  2 38  1  0  0  0  0
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 34 67  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0021499

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]OC1=C2N([H])[C@]([H])(O[H])[C@@]3([H])N(C([H])=C(\C([H])=C(/[H])C([H])([H])[H])C3([H])[H])C(=O)C2=C([H])C(O[C@]2([H])O[C@@]([H])(C([H])([H])[H])[C@]([H])(N([H])C([H])([H])[H])[C@](O[H])(C([H])([H])[H])[C@@]2([H])O[H])=C1C([H])([H])[H]

> <INCHI_IDENTIFIER>
InChI=1S/C24H33N3O7/c1-6-7-13-8-15-21(30)26-17-14(22(31)27(15)10-13)9-16(11(2)18(17)28)34-23-20(29)24(4,32)19(25-5)12(3)33-23/h6-7,9-10,12,15,19-21,23,25-26,28-30,32H,8H2,1-5H3/b7-6+/t12-,15-,19-,20-,21+,23-,24+/m0/s1

> <INCHI_KEY>
RAGFPHFDFVNLCG-INYQBOQCSA-N

> <FORMULA>
C24H33N3O7

> <MOLECULAR_WEIGHT>
475.542

> <EXACT_MASS>
475.231850415

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
67

> <JCHEM_AVERAGE_POLARIZABILITY>
51.07991754158459

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(7S,8R)-13-{[(2S,3R,4R,5S,6S)-3,4-dihydroxy-4,6-dimethyl-5-(methylamino)oxan-2-yl]oxy}-8,11-dihydroxy-12-methyl-5-[(1E)-prop-1-en-1-yl]-3,9-diazatricyclo[8.4.0.0^{3,7}]tetradeca-1(14),4,10,12-tetraen-2-one

> <ALOGPS_LOGP>
1.21

> <JCHEM_LOGP>
0.9674679926774941

> <ALOGPS_LOGS>
-2.13

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
12.038710022348516

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.798500785783244

> <JCHEM_PKA_STRONGEST_BASIC>
9.00969916063099

> <JCHEM_POLAR_SURFACE_AREA>
143.75000000000003

> <JCHEM_REFRACTIVITY>
126.7634

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
3.54e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(7S,8R)-13-{[(2S,3R,4R,5S,6S)-3,4-dihydroxy-4,6-dimethyl-5-(methylamino)oxan-2-yl]oxy}-8,11-dihydroxy-12-methyl-5-[(1E)-prop-1-en-1-yl]-3,9-diazatricyclo[8.4.0.0^{3,7}]tetradeca-1(14),4,10,12-tetraen-2-one

> <JCHEM_VEBER_RULE>
0

$$$$

     RDKit          3D

 67 70  0  0  0  0  0  0  0  0999 V2000
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  3 39  1  0
  5 40  1  0
 10 41  1  0
 13 42  1  1
 15 43  1  6
 16 44  1  0
 16 45  1  0
 16 46  1  0
 17 47  1  1
 18 48  1  0
 19 49  1  0
 19 50  1  0
 19 51  1  0
 21 52  1  0
 21 53  1  0
 21 54  1  0
 22 55  1  0
 23 56  1  6
 24 57  1  0
 26 58  1  0
 26 59  1  0
 26 60  1  0
 28 61  1  0
 30 62  1  0
 31 63  1  6
 32 64  1  0
 33 65  1  6
 34 66  1  0
 34 67  1  0
M  END

HEADER    PROTEIN                                 24-JUN-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-JUN-21         0                                  
HETATM    1  C   UNK     0       9.549   0.954   2.585  0.00  0.00           C+0
HETATM    2  C   UNK     0       8.379   0.642   1.724  0.00  0.00           C+0
HETATM    3  C   UNK     0       7.130   0.760   2.163  0.00  0.00           C+0
HETATM    4  C   UNK     0       6.000   0.447   1.298  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.730   0.532   1.638  0.00  0.00           C+0
HETATM    6  N   UNK     0       3.880   0.162   0.581  0.00  0.00           N+0
HETATM    7  C   UNK     0       2.454   0.038   0.692  0.00  0.00           C+0
HETATM    8  O   UNK     0       1.941   0.343   1.795  0.00  0.00           O+0
HETATM    9  C   UNK     0       1.528  -0.412  -0.355  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.190  -0.193  -0.025  0.00  0.00           C+0
HETATM   11  C   UNK     0      -0.853  -0.533  -0.856  0.00  0.00           C+0
HETATM   12  O   UNK     0      -2.186  -0.347  -0.594  0.00  0.00           O+0
HETATM   13  C   UNK     0      -2.782   0.204   0.541  0.00  0.00           C+0
HETATM   14  O   UNK     0      -3.603  -0.622   1.220  0.00  0.00           O+0
HETATM   15  C   UNK     0      -4.931  -0.429   1.312  0.00  0.00           C+0
HETATM   16  C   UNK     0      -5.236  -0.197   2.807  0.00  0.00           C+0
HETATM   17  C   UNK     0      -5.572   0.670   0.554  0.00  0.00           C+0
HETATM   18  N   UNK     0      -6.815   0.217  -0.048  0.00  0.00           N+0
HETATM   19  C   UNK     0      -7.780  -0.176   0.958  0.00  0.00           C+0
HETATM   20  C   UNK     0      -4.679   1.330  -0.470  0.00  0.00           C+0
HETATM   21  C   UNK     0      -4.569   0.483  -1.694  0.00  0.00           C+0
HETATM   22  O   UNK     0      -5.264   2.545  -0.825  0.00  0.00           O+0
HETATM   23  C   UNK     0      -3.376   1.588   0.235  0.00  0.00           C+0
HETATM   24  O   UNK     0      -3.627   2.221   1.430  0.00  0.00           O+0
HETATM   25  C   UNK     0      -0.499  -1.121  -2.074  0.00  0.00           C+0
HETATM   26  C   UNK     0      -1.593  -1.503  -2.995  0.00  0.00           C+0
HETATM   27  C   UNK     0       0.812  -1.350  -2.428  0.00  0.00           C+0
HETATM   28  O   UNK     0       1.174  -1.935  -3.637  0.00  0.00           O+0
HETATM   29  C   UNK     0       1.842  -0.994  -1.563  0.00  0.00           C+0
HETATM   30  N   UNK     0       3.147  -1.284  -2.043  0.00  0.00           N+0
HETATM   31  C   UNK     0       4.394  -1.367  -1.291  0.00  0.00           C+0
HETATM   32  O   UNK     0       4.376  -2.397  -0.367  0.00  0.00           O+0
HETATM   33  C   UNK     0       4.679  -0.060  -0.589  0.00  0.00           C+0
HETATM   34  C   UNK     0       6.096  -0.015  -0.100  0.00  0.00           C+0
HETATM   35  H   UNK     0       9.248   1.152   3.629  0.00  0.00           H+0
HETATM   36  H   UNK     0      10.060   1.875   2.226  0.00  0.00           H+0
HETATM   37  H   UNK     0      10.279   0.105   2.609  0.00  0.00           H+0
HETATM   38  H   UNK     0       8.602   0.308   0.706  0.00  0.00           H+0
HETATM   39  H   UNK     0       6.999   1.095   3.182  0.00  0.00           H+0
HETATM   40  H   UNK     0       4.399   0.856   2.632  0.00  0.00           H+0
HETATM   41  H   UNK     0       0.001   0.263   0.926  0.00  0.00           H+0
HETATM   42  H   UNK     0      -1.934   0.461   1.255  0.00  0.00           H+0
HETATM   43  H   UNK     0      -5.514  -1.383   1.095  0.00  0.00           H+0
HETATM   44  H   UNK     0      -4.337  -0.380   3.433  0.00  0.00           H+0
HETATM   45  H   UNK     0      -6.108  -0.776   3.137  0.00  0.00           H+0
HETATM   46  H   UNK     0      -5.482   0.875   2.937  0.00  0.00           H+0
HETATM   47  H   UNK     0      -5.873   1.483   1.272  0.00  0.00           H+0
HETATM   48  H   UNK     0      -7.250   0.908  -0.666  0.00  0.00           H+0
HETATM   49  H   UNK     0      -7.666   0.486   1.838  0.00  0.00           H+0
HETATM   50  H   UNK     0      -7.590  -1.220   1.307  0.00  0.00           H+0
HETATM   51  H   UNK     0      -8.805  -0.066   0.542  0.00  0.00           H+0
HETATM   52  H   UNK     0      -3.735   0.787  -2.325  0.00  0.00           H+0
HETATM   53  H   UNK     0      -5.496   0.629  -2.290  0.00  0.00           H+0
HETATM   54  H   UNK     0      -4.504  -0.595  -1.487  0.00  0.00           H+0
HETATM   55  H   UNK     0      -4.811   3.276  -0.361  0.00  0.00           H+0
HETATM   56  H   UNK     0      -2.629   2.118  -0.377  0.00  0.00           H+0
HETATM   57  H   UNK     0      -2.861   2.234   2.048  0.00  0.00           H+0
HETATM   58  H   UNK     0      -1.420  -2.496  -3.477  0.00  0.00           H+0
HETATM   59  H   UNK     0      -2.554  -1.630  -2.419  0.00  0.00           H+0
HETATM   60  H   UNK     0      -1.728  -0.689  -3.720  0.00  0.00           H+0
HETATM   61  H   UNK     0       0.425  -2.191  -4.265  0.00  0.00           H+0
HETATM   62  H   UNK     0       3.197  -1.458  -3.068  0.00  0.00           H+0
HETATM   63  H   UNK     0       5.223  -1.550  -1.994  0.00  0.00           H+0
HETATM   64  H   UNK     0       5.063  -3.082  -0.517  0.00  0.00           H+0
HETATM   65  H   UNK     0       4.551   0.737  -1.355  0.00  0.00           H+0
HETATM   66  H   UNK     0       6.714   0.670  -0.729  0.00  0.00           H+0
HETATM   67  H   UNK     0       6.601  -1.003  -0.158  0.00  0.00           H+0
CONECT    1    2   35   36   37                                             
CONECT    2    1    3   38                                                  
CONECT    3    2    4   39                                                  
CONECT    4    3    5   34                                                  
CONECT    5    4    6   40                                                  
CONECT    6    5    7   33                                                  
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10   29                                                  
CONECT   10    9   11   41                                                  
CONECT   11   10   12   25                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14   23   42                                             
CONECT   14   13   15                                                       
CONECT   15   14   16   17   43                                             
CONECT   16   15   44   45   46                                             
CONECT   17   15   18   20   47                                             
CONECT   18   17   19   48                                                  
CONECT   19   18   49   50   51                                             
CONECT   20   17   21   22   23                                             
CONECT   21   20   52   53   54                                             
CONECT   22   20   55                                                       
CONECT   23   20   24   13   56                                             
CONECT   24   23   57                                                       
CONECT   25   11   26   27                                                  
CONECT   26   25   58   59   60                                             
CONECT   27   25   28   29                                                  
CONECT   28   27   61                                                       
CONECT   29   27   30    9                                                  
CONECT   30   29   31   62                                                  
CONECT   31   30   32   33   63                                             
CONECT   32   31   64                                                       
CONECT   33   31   34    6   65                                             
CONECT   34   33    4   66   67                                             
CONECT   35    1                                                            
CONECT   36    1                                                            
CONECT   37    1                                                            
CONECT   38    2                                                            
CONECT   39    3                                                            
CONECT   40    5                                                            
CONECT   41   10                                                            
CONECT   42   13                                                            
CONECT   43   15                                                            
CONECT   44   16                                                            
CONECT   45   16                                                            
CONECT   46   16                                                            
CONECT   47   17                                                            
CONECT   48   18                                                            
CONECT   49   19                                                            
CONECT   50   19                                                            
CONECT   51   19                                                            
CONECT   52   21                                                            
CONECT   53   21                                                            
CONECT   54   21                                                            
CONECT   55   22                                                            
CONECT   56   23                                                            
CONECT   57   24                                                            
CONECT   58   26                                                            
CONECT   59   26                                                            
CONECT   60   26                                                            
CONECT   61   28                                                            
CONECT   62   30                                                            
CONECT   63   31                                                            
CONECT   64   32                                                            
CONECT   65   33                                                            
CONECT   66   34                                                            
CONECT   67   34                                                            
MASTER        0    0    0    0    0    0    0    0   67    0  140    0
END

RDKit          3D

67 70  0  0  0  0  0  0  0  0999 V2000
    9.5489    0.9540    2.5849 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.3788    0.6417    1.7241 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1295    0.7600    2.1634 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0001    0.4472    1.2981 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7301    0.5321    1.6377 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8799    0.1618    0.5814 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.4545    0.0378    0.6924 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9407    0.3433    1.7947 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5277   -0.4117   -0.3553 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1896   -0.1928   -0.0251 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8526   -0.5332   -0.8563 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1863   -0.3465   -0.5936 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7823    0.2043    0.5412 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.6027   -0.6221    1.2197 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9310   -0.4285    1.3122 C   0  0  1  0  0  0  0  0  0  0  0  0
   -5.2358   -0.1969    2.8074 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5721    0.6702    0.5540 C   0  0  2  0  0  0  0  0  0  0  0  0
   -6.8154    0.2174   -0.0479 N   0  0  0  0  0  0  0  0  0  0  0  0
   -7.7797   -0.1756    0.9584 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6789    1.3296   -0.4702 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.5691    0.4825   -1.6942 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2643    2.5446   -0.8248 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3760    1.5880    0.2354 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.6273    2.2214    1.4302 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4993   -1.1214   -2.0737 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5933   -1.5034   -2.9947 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8120   -1.3504   -2.4282 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1743   -1.9347   -3.6371 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8421   -0.9935   -1.5626 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1465   -1.2839   -2.0430 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.3938   -1.3672   -1.2908 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.3763   -2.3973   -0.3674 O   0  0  0  0  0  0  0  0  0  0  0  0
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    6.0958   -0.0149   -0.1001 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.2478    1.1518    3.6293 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.0605    1.8751    2.2262 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.2791    0.1047    2.6091 H   0  0  0  0  0  0  0  0  0  0  0  0
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    6.9991    1.0953    3.1822 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3988    0.8555    2.6318 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0011    0.2630    0.9263 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9339    0.4608    1.2549 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -7.6656    0.4857    1.8380 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.5900   -1.2196    1.3073 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.8048   -0.0664    0.5424 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7347    0.7866   -2.3249 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4959    0.6291   -2.2901 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5042   -0.5952   -1.4868 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8109    3.2765   -0.3614 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -2.8605    2.2342    2.0482 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4195   -2.4962   -3.4771 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5538   -1.6298   -2.4187 H   0  0  0  0  0  0  0  0  0  0  0  0
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    0.4249   -2.1909   -4.2648 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1971   -1.4575   -3.0684 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2233   -1.5501   -1.9943 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0625   -3.0817   -0.5165 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5507    0.7370   -1.3554 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.7137    0.6696   -0.7292 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.6009   -1.0031   -0.1577 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  7  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 15 17  1  0
 17 18  1  0
 18 19  1  0
 17 20  1  0
 20 21  1  0
 20 22  1  6
 20 23  1  0
 23 24  1  0
 11 25  2  0
 25 26  1  0
 25 27  1  0
 27 28  1  0
 27 29  2  0
 29 30  1  0
 30 31  1  0
 31 32  1  0
 31 33  1  0
 33 34  1  0
 34  4  1  0
 33  6  1  0
 29  9  1  0
 23 13  1  0
  1 35  1  0
  1 36  1  0
  1 37  1  0
  2 38  1  0
  3 39  1  0
  5 40  1  0
 10 41  1  0
 13 42  1  1
 15 43  1  6
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 16 45  1  0
 16 46  1  0
 17 47  1  1
 18 48  1  0
 19 49  1  0
 19 50  1  0
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 21 52  1  0
 21 53  1  0
 21 54  1  0
 22 55  1  0
 23 56  1  6
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 26 59  1  0
 26 60  1  0
 28 61  1  0
 30 62  1  0
 31 63  1  6
 32 64  1  0
 33 65  1  6
 34 66  1  0
 34 67  1  0
M  END

View in JSmol View NMR Assignments

Synonyms

Value	Source
Sybiromycin	ChEBI

Chemical Formula

C₂₄H₃₃N₃O₇

Average Mass

475.5420 Da

Monoisotopic Mass

475.23185 Da

IUPAC Name

(7S,8R)-13-{[(2S,3R,4R,5S,6S)-3,4-dihydroxy-4,6-dimethyl-5-(methylamino)oxan-2-yl]oxy}-8,11-dihydroxy-12-methyl-5-[(1E)-prop-1-en-1-yl]-3,9-diazatricyclo[8.4.0.0^{3,7}]tetradeca-1(14),4,10,12-tetraen-2-one

Traditional Name

CAS Registry Number

Not Available

SMILES

CN[C@H]1[C@H](C)O[C@@H](OC2=C(C)C(O)=C3N[C@H](O)[C@@H]4CC(\C=C\C)=CN4C(=O)C3=C2)[C@H](O)[C@]1(C)O

InChI Identifier

InChI=1S/C24H33N3O7/c1-6-7-13-8-15-21(30)26-17-14(22(31)27(15)10-13)9-16(11(2)18(17)28)34-23-20(29)24(4,32)19(25-5)12(3)33-23/h6-7,9-10,12,15,19-21,23,25-26,28-30,32H,8H2,1-5H3/b7-6+/t12-,15-,19-,20-,21+,23-,24+/m0/s1

InChI Key

RAGFPHFDFVNLCG-INYQBOQCSA-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
Streptosporangium sibiricum	NPAtlas	4907802

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as aminoglycosides. These are molecules or a portion of a molecule composed of amino-modified sugars.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Aminoglycosides

Alternative Parents

Substituents

Aminoglycoside core
1,4-benzodiazepine
Benzodiazepine
Secondary aliphatic/aromatic amine
1-hydroxy-4-unsubstituted benzenoid
Oxane
Monosaccharide
Benzenoid
Vinylogous amide
Tertiary carboxylic acid amide
Tertiary alcohol
Pyrroline
Lactam
Secondary alcohol
1,2-aminoalcohol
1,2-diol
Carboxamide group
Amino acid or derivatives
Acetal
Alkanolamine
Oxacycle
Azacycle
Carboxylic acid derivative
Secondary aliphatic amine
Organoheterocyclic compound
Secondary amine
Organic nitrogen compound
Alcohol
Organopnictogen compound
Amine
Organic oxide
Hydrocarbon derivative
Organonitrogen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Physical Properties

State

Not Available

Experimental Properties

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

Predicted Properties

Property	Value	Source
logP	1.21	ALOGPS
logP	0.97	ChemAxon
logS	-2.1	ALOGPS
pKa (Strongest Acidic)	9.8	ChemAxon
pKa (Strongest Basic)	9.01	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	143.75 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	126.76 m³·mol⁻¹	ChemAxon
Polarizability	51.08 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

NPAtlas ID

NPA001741

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00018852

Chemspider ID

4941925

KEGG Compound ID

Not Available

BioCyc ID

CPD-18442

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

6437361

PDB ID

Not Available

ChEBI ID

90941

Good Scents ID

Not Available

References

General References

Gauze GF, Preobrazhenskaia TP, Ivanitskaia LP, Sveshnikova MA: [Production of the antibiotic sibiromycin by the Streptosporangium sibiricum sp. nov. culture]. Antibiotiki. 1969 Nov;14(11):963-9. [PubMed:4907802 ]
Shepelevtseva NG: [Effect of the antibiotic sibiromycin on the bioelectrical activity of the heart and the serum transaminase activity in dogs]. Antibiotiki. 1975 Feb;20(2):145-50. [PubMed:1119795 ]
Koz'mian LI, Dudnik IuV, Shepelevtseva NG: [Role of the functional groups of the sibiromycin molecule in DNA binding]. Antibiotiki. 1977 Jul;22(7):602-6. [PubMed:18983 ]
Gerratana B: Biosynthesis, synthesis, and biological activities of pyrrolobenzodiazepines. Med Res Rev. 2012 Mar;32(2):254-93. doi: 10.1002/med.20212. Epub 2010 Jun 13. [PubMed:20544978 ]
Sulc M, Fadrhoncova I, Jelinkova M, Chudomelova M, Felsberg J, Olsovska J: Determination of sibiromycin and its natural derivatives using new analytical and structural approaches. J Chromatogr A. 2011 Jan 7;1218(1):83-91. doi: 10.1016/j.chroma.2010.10.110. Epub 2010 Nov 3. [PubMed:21111423 ]

Showing NP-Card for Sibiromycin (NP0021499)

MOL for NP0021499 (Sibiromycin)

3D MOL for NP0021499 (Sibiromycin)

3D SDF for NP0021499 (Sibiromycin)

3D-SDF for NP0021499 (Sibiromycin)

PDB for NP0021499 (Sibiromycin)

3D PDB for NP0021499 (Sibiromycin)

SMILES for NP0021499 (Sibiromycin)

INCHI for NP0021499 (Sibiromycin)

Structure for NP0021499 (Sibiromycin)

3D Structure for NP0021499 (Sibiromycin)