NP-MRD: Showing NP-Card for Herbicidin E (NP0003924)

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Record Information

Version

1.0

Created at

2020-12-09 01:28:07 UTC

Updated at

2021-07-15 16:47:45 UTC

NP-MRD ID

NP0003924

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Herbicidin E

Provided By

NPAtlas

Description

Herbicidin E is found in Streptomyces. It was first documented in 1979 (PMID: 117003). Based on a literature review very few articles have been published on methyl (1S,3R,4S,5R,7R,9R,11S,12S,13S)-5-(6-amino-9H-purin-9-yl)-1,12-dihydroxy-4-methoxy-13-[(2-methylpropanoyl)oxy]-2,6,10-trioxatricyclo[7.4.0.0³,⁷]Tridecane-11-carboxylate.

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652306242117513D          

 66 70  0  0  0  0            999 V2000
   -3.3906    5.5037   -1.8462 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1274    4.1372   -1.6278 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1053    3.6940   -0.7862 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4209    4.5827   -0.2241 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8177    2.2803   -0.5477 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7685    2.1476    0.3160 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9579    1.1867    1.3086 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.4210    1.0769    1.9929 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.3019    0.7722    0.8542 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.6312    0.6541    1.0654 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0200    0.2350   -0.2242 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.4019   -0.0598   -0.3119 N   0  0  0  0  0  0  0  0  0  0  0  0
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   -3.0370    1.4823   -0.1462 C   0  0  2  0  0  0  0  0  0  0  0  0
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  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
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 37 66  1  0  0  0  0
M  END

     RDKit          3D

 66 70  0  0  0  0  0  0  0  0999 V2000
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M  END


  Mrv1652306242117513D          

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 37 66  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0003924

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]O[C@]1([H])[C@]([H])(O[C@]2([H])C([H])([H])[C@@]3([H])O[C@@]([H])(N4C([H])=NC5=C(N=C([H])N=C45)N([H])[H])[C@@]([H])(OC([H])([H])[H])[C@]3([H])O[C@]2(O[H])[C@@]1([H])OC(=O)C([H])(C([H])([H])[H])C([H])([H])[H])C(=O)OC([H])([H])[H]

> <INCHI_IDENTIFIER>
InChI=1S/C22H29N5O10/c1-8(2)20(29)36-16-12(28)14(21(30)33-4)35-10-5-9-13(37-22(10,16)31)15(32-3)19(34-9)27-7-26-11-17(23)24-6-25-18(11)27/h6-10,12-16,19,28,31H,5H2,1-4H3,(H2,23,24,25)/t9-,10-,12-,13-,14+,15+,16+,19-,22+/m1/s1

> <INCHI_KEY>
DIGRAKJXHSMXBZ-HUPRSAECSA-N

> <FORMULA>
C22H29N5O10

> <MOLECULAR_WEIGHT>
523.499

> <EXACT_MASS>
523.191442154

> <JCHEM_ACCEPTOR_COUNT>
12

> <JCHEM_ATOM_COUNT>
66

> <JCHEM_AVERAGE_POLARIZABILITY>
52.448812640777916

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
methyl (1S,3R,4S,5R,7R,9R,11S,12S,13S)-5-(6-amino-9H-purin-9-yl)-1,12-dihydroxy-4-methoxy-13-[(2-methylpropanoyl)oxy]-2,6,10-trioxatricyclo[7.4.0.0^{3,7}]tridecane-11-carboxylate

> <ALOGPS_LOGP>
0.78

> <JCHEM_LOGP>
-0.25501310633333213

> <ALOGPS_LOGS>
-2.07

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.860307502145943

> <JCHEM_PKA_STRONGEST_ACIDIC>
10.094155591810246

> <JCHEM_PKA_STRONGEST_BASIC>
3.9212111194125256

> <JCHEM_POLAR_SURFACE_AREA>
199.59999999999997

> <JCHEM_REFRACTIVITY>
120.06119999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
4.45e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
methyl (1S,3R,4S,5R,7R,9R,11S,12S,13S)-5-(6-aminopurin-9-yl)-1,12-dihydroxy-4-methoxy-13-[(2-methylpropanoyl)oxy]-2,6,10-trioxatricyclo[7.4.0.0^{3,7}]tridecane-11-carboxylate

> <JCHEM_VEBER_RULE>
0

$$$$

     RDKit          3D

 66 70  0  0  0  0  0  0  0  0999 V2000
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 33 58  1  1
 34 59  1  0
 34 60  1  0
 34 61  1  0
 35 62  1  0
 35 63  1  0
 35 64  1  0
 36 65  1  1
 37 66  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      -3.391   5.504  -1.846  0.00  0.00           C+0
HETATM    2  O   UNK     0      -3.127   4.137  -1.628  0.00  0.00           O+0
HETATM    3  C   UNK     0      -2.105   3.694  -0.786  0.00  0.00           C+0
HETATM    4  O   UNK     0      -1.421   4.583  -0.224  0.00  0.00           O+0
HETATM    5  C   UNK     0      -1.818   2.280  -0.548  0.00  0.00           C+0
HETATM    6  O   UNK     0      -0.769   2.148   0.316  0.00  0.00           O+0
HETATM    7  C   UNK     0      -0.958   1.187   1.309  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.421   1.077   1.993  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.302   0.772   0.854  0.00  0.00           C+0
HETATM   10  O   UNK     0       2.631   0.654   1.065  0.00  0.00           O+0
HETATM   11  C   UNK     0       3.020   0.235  -0.224  0.00  0.00           C+0
HETATM   12  N   UNK     0       4.402  -0.060  -0.312  0.00  0.00           N+0
HETATM   13  C   UNK     0       5.101  -0.330  -1.401  0.00  0.00           C+0
HETATM   14  N   UNK     0       6.408  -0.563  -1.084  0.00  0.00           N+0
HETATM   15  C   UNK     0       6.511  -0.431   0.233  0.00  0.00           C+0
HETATM   16  C   UNK     0       7.615  -0.563   1.050  0.00  0.00           C+0
HETATM   17  N   UNK     0       8.904  -0.887   0.549  0.00  0.00           N+0
HETATM   18  N   UNK     0       7.433  -0.372   2.367  0.00  0.00           N+0
HETATM   19  C   UNK     0       6.202  -0.060   2.869  0.00  0.00           C+0
HETATM   20  N   UNK     0       5.138   0.064   2.052  0.00  0.00           N+0
HETATM   21  C   UNK     0       5.259  -0.116   0.719  0.00  0.00           C+0
HETATM   22  C   UNK     0       2.108  -0.931  -0.506  0.00  0.00           C+0
HETATM   23  O   UNK     0       2.689  -2.156  -0.325  0.00  0.00           O+0
HETATM   24  C   UNK     0       2.688  -2.947  -1.469  0.00  0.00           C+0
HETATM   25  C   UNK     0       0.941  -0.648   0.381  0.00  0.00           C+0
HETATM   26  O   UNK     0      -0.261  -0.495  -0.284  0.00  0.00           O+0
HETATM   27  C   UNK     0      -1.262  -0.129   0.580  0.00  0.00           C+0
HETATM   28  O   UNK     0      -1.302  -1.105   1.599  0.00  0.00           O+0
HETATM   29  C   UNK     0      -2.586   0.017  -0.099  0.00  0.00           C+0
HETATM   30  O   UNK     0      -3.590  -0.808   0.437  0.00  0.00           O+0
HETATM   31  C   UNK     0      -4.274  -1.767  -0.260  0.00  0.00           C+0
HETATM   32  O   UNK     0      -4.019  -1.954  -1.454  0.00  0.00           O+0
HETATM   33  C   UNK     0      -5.321  -2.589   0.397  0.00  0.00           C+0
HETATM   34  C   UNK     0      -6.402  -1.662   0.910  0.00  0.00           C+0
HETATM   35  C   UNK     0      -5.891  -3.586  -0.586  0.00  0.00           C+0
HETATM   36  C   UNK     0      -3.037   1.482  -0.146  0.00  0.00           C+0
HETATM   37  O   UNK     0      -3.952   1.587  -1.195  0.00  0.00           O+0
HETATM   38  H   UNK     0      -3.197   6.028  -0.895  0.00  0.00           H+0
HETATM   39  H   UNK     0      -4.455   5.654  -2.143  0.00  0.00           H+0
HETATM   40  H   UNK     0      -2.704   5.919  -2.620  0.00  0.00           H+0
HETATM   41  H   UNK     0      -1.486   1.845  -1.536  0.00  0.00           H+0
HETATM   42  H   UNK     0      -1.745   1.411   2.010  0.00  0.00           H+0
HETATM   43  H   UNK     0       0.420   0.219   2.699  0.00  0.00           H+0
HETATM   44  H   UNK     0       0.576   2.045   2.487  0.00  0.00           H+0
HETATM   45  H   UNK     0       1.116   1.420  -0.039  0.00  0.00           H+0
HETATM   46  H   UNK     0       2.690   1.067  -0.901  0.00  0.00           H+0
HETATM   47  H   UNK     0       4.773  -0.383  -2.431  0.00  0.00           H+0
HETATM   48  H   UNK     0       9.792  -0.498   0.971  0.00  0.00           H+0
HETATM   49  H   UNK     0       9.060  -1.530  -0.270  0.00  0.00           H+0
HETATM   50  H   UNK     0       6.073   0.091   3.943  0.00  0.00           H+0
HETATM   51  H   UNK     0       1.767  -0.876  -1.569  0.00  0.00           H+0
HETATM   52  H   UNK     0       1.679  -3.163  -1.855  0.00  0.00           H+0
HETATM   53  H   UNK     0       3.188  -2.329  -2.272  0.00  0.00           H+0
HETATM   54  H   UNK     0       3.282  -3.853  -1.363  0.00  0.00           H+0
HETATM   55  H   UNK     0       0.872  -1.338   1.247  0.00  0.00           H+0
HETATM   56  H   UNK     0      -1.446  -2.011   1.224  0.00  0.00           H+0
HETATM   57  H   UNK     0      -2.480  -0.277  -1.170  0.00  0.00           H+0
HETATM   58  H   UNK     0      -4.839  -3.164   1.208  0.00  0.00           H+0
HETATM   59  H   UNK     0      -6.793  -2.034   1.879  0.00  0.00           H+0
HETATM   60  H   UNK     0      -6.032  -0.637   1.082  0.00  0.00           H+0
HETATM   61  H   UNK     0      -7.197  -1.592   0.141  0.00  0.00           H+0
HETATM   62  H   UNK     0      -5.575  -3.324  -1.626  0.00  0.00           H+0
HETATM   63  H   UNK     0      -5.597  -4.626  -0.346  0.00  0.00           H+0
HETATM   64  H   UNK     0      -6.998  -3.491  -0.566  0.00  0.00           H+0
HETATM   65  H   UNK     0      -3.479   1.806   0.795  0.00  0.00           H+0
HETATM   66  H   UNK     0      -4.552   2.359  -1.060  0.00  0.00           H+0
CONECT    1    2   38   39   40                                             
CONECT    2    1    3                                                       
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6   36   41                                             
CONECT    6    5    7                                                       
CONECT    7    6    8   27   42                                             
CONECT    8    7    9   43   44                                             
CONECT    9    8   10   25   45                                             
CONECT   10    9   11                                                       
CONECT   11   10   12   22   46                                             
CONECT   12   11   13   21                                                  
CONECT   13   12   14   47                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16   21                                                  
CONECT   16   15   17   18                                                  
CONECT   17   16   48   49                                                  
CONECT   18   16   19                                                       
CONECT   19   18   20   50                                                  
CONECT   20   19   21                                                       
CONECT   21   20   12   15                                                  
CONECT   22   11   23   25   51                                             
CONECT   23   22   24                                                       
CONECT   24   23   52   53   54                                             
CONECT   25   22   26    9   55                                             
CONECT   26   25   27                                                       
CONECT   27   26   28   29    7                                             
CONECT   28   27   56                                                       
CONECT   29   27   30   36   57                                             
CONECT   30   29   31                                                       
CONECT   31   30   32   33                                                  
CONECT   32   31                                                            
CONECT   33   31   34   35   58                                             
CONECT   34   33   59   60   61                                             
CONECT   35   33   62   63   64                                             
CONECT   36   29   37    5   65                                             
CONECT   37   36   66                                                       
CONECT   38    1                                                            
CONECT   39    1                                                            
CONECT   40    1                                                            
CONECT   41    5                                                            
CONECT   42    7                                                            
CONECT   43    8                                                            
CONECT   44    8                                                            
CONECT   45    9                                                            
CONECT   46   11                                                            
CONECT   47   13                                                            
CONECT   48   17                                                            
CONECT   49   17                                                            
CONECT   50   19                                                            
CONECT   51   22                                                            
CONECT   52   24                                                            
CONECT   53   24                                                            
CONECT   54   24                                                            
CONECT   55   25                                                            
CONECT   56   28                                                            
CONECT   57   29                                                            
CONECT   58   33                                                            
CONECT   59   34                                                            
CONECT   60   34                                                            
CONECT   61   34                                                            
CONECT   62   35                                                            
CONECT   63   35                                                            
CONECT   64   35                                                            
CONECT   65   36                                                            
CONECT   66   37                                                            
MASTER        0    0    0    0    0    0    0    0   66    0  140    0
END

RDKit          3D

66 70  0  0  0  0  0  0  0  0999 V2000
   -3.3906    5.5037   -1.8462 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1274    4.1372   -1.6278 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1053    3.6940   -0.7862 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4209    4.5827   -0.2241 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8177    2.2803   -0.5477 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7685    2.1476    0.3160 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9579    1.1867    1.3086 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.4210    1.0769    1.9929 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3019    0.7722    0.8542 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.6312    0.6541    1.0654 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0200    0.2350   -0.2242 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.4019   -0.0598   -0.3119 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.1005   -0.3304   -1.4013 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4077   -0.5626   -1.0836 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.5113   -0.4307    0.2333 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6151   -0.5630    1.0498 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.9036   -0.8867    0.5485 N   0  0  0  0  0  0  0  0  0  0  0  0
    7.4329   -0.3721    2.3670 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.2022   -0.0602    2.8695 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1381    0.0638    2.0524 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.2592   -0.1163    0.7194 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1084   -0.9312   -0.5057 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.6894   -2.1561   -0.3247 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6879   -2.9466   -1.4691 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9414   -0.6480    0.3809 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.2614   -0.4952   -0.2836 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2618   -0.1293    0.5797 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.3015   -1.1049    1.5991 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -3.5903   -0.8077    0.4371 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2745   -1.7672   -0.2597 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0191   -1.9537   -1.4537 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3205   -2.5893    0.3971 C   0  0  1  0  0  0  0  0  0  0  0  0
   -6.4016   -1.6621    0.9096 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8908   -3.5858   -0.5857 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0370    1.4823   -0.1462 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.9519    1.5866   -1.1951 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1973    6.0282   -0.8953 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4554    5.6537   -2.1426 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7039    5.9190   -2.6198 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4864    1.8447   -1.5360 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7454    1.4114    2.0104 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4196    0.2187    2.6988 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5755    2.0447    2.4873 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1163    1.4203   -0.0385 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6904    1.0671   -0.9008 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7729   -0.3828   -2.4312 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.7920   -0.4976    0.9706 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.0598   -1.5301   -0.2698 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.0731    0.0913    3.9431 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7672   -0.8760   -1.5693 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6792   -3.1631   -1.8552 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1877   -2.3295   -2.2718 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2818   -3.8525   -1.3635 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8719   -1.3379    1.2468 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4459   -2.0112    1.2245 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4804   -0.2766   -1.1703 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8391   -3.1636    1.2079 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7928   -2.0340    1.8791 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0320   -0.6369    1.0817 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1975   -1.5919    0.1414 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5746   -3.3238   -1.6258 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5966   -4.6259   -0.3461 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9977   -3.4913   -0.5660 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4789    1.8061    0.7950 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5520    2.3589   -1.0596 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  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  2  0
 14 15  1  0
 15 16  2  0
 16 17  1  0
 16 18  1  0
 18 19  2  0
 19 20  1  0
 20 21  2  0
 11 22  1  0
 22 23  1  0
 23 24  1  0
 22 25  1  0
 25 26  1  0
 26 27  1  0
 27 28  1  1
 27 29  1  0
 29 30  1  0
 30 31  1  0
 31 32  2  0
 31 33  1  0
 33 34  1  0
 33 35  1  0
 29 36  1  0
 36 37  1  0
 36  5  1  0
 27  7  1  0
 25  9  1  0
 21 12  1  0
 21 15  1  0
  1 38  1  0
  1 39  1  0
  1 40  1  0
  5 41  1  6
  7 42  1  1
  8 43  1  0
  8 44  1  0
  9 45  1  6
 11 46  1  6
 13 47  1  0
 17 48  1  0
 17 49  1  0
 19 50  1  0
 22 51  1  6
 24 52  1  0
 24 53  1  0
 24 54  1  0
 25 55  1  1
 28 56  1  0
 29 57  1  6
 33 58  1  1
 34 59  1  0
 34 60  1  0
 34 61  1  0
 35 62  1  0
 35 63  1  0
 35 64  1  0
 36 65  1  1
 37 66  1  0
M  END

View in JSmol View NMR Assignments

Synonyms

Value	Source
Methyl (1S,3R,4S,5R,7R,9R,11S,12S,13S)-5-(6-amino-9H-purin-9-yl)-1,12-dihydroxy-4-methoxy-13-[(2-methylpropanoyl)oxy]-2,6,10-trioxatricyclo[7.4.0.0,]tridecane-11-carboxylic acid	Generator

Chemical Formula

C₂₂H₂₉N₅O₁₀

Average Mass

523.4990 Da

Monoisotopic Mass

523.19144 Da

IUPAC Name

methyl (1S,3R,4S,5R,7R,9R,11S,12S,13S)-5-(6-amino-9H-purin-9-yl)-1,12-dihydroxy-4-methoxy-13-[(2-methylpropanoyl)oxy]-2,6,10-trioxatricyclo[7.4.0.0^{3,7}]tridecane-11-carboxylate

Traditional Name

methyl (1S,3R,4S,5R,7R,9R,11S,12S,13S)-5-(6-aminopurin-9-yl)-1,12-dihydroxy-4-methoxy-13-[(2-methylpropanoyl)oxy]-2,6,10-trioxatricyclo[7.4.0.0^{3,7}]tridecane-11-carboxylate

CAS Registry Number

Not Available

SMILES

CO[C@H]1[C@@H]2O[C@@]3(O)[C@@H](C[C@H]2O[C@H]1N1C=NC2=C1N=CN=C2N)O[C@@H]([C@@H](O)[C@@H]3OC(=O)C(C)C)C(=O)OC

InChI Identifier

InChI=1S/C22H29N5O10/c1-8(2)20(29)36-16-12(28)14(21(30)33-4)35-10-5-9-13(37-22(10,16)31)15(32-3)19(34-9)27-7-26-11-17(23)24-6-25-18(11)27/h6-10,12-16,19,28,31H,5H2,1-4H3,(H2,23,24,25)/t9-,10-,12-,13-,14+,15+,16+,19-,22+/m1/s1

InChI Key

DIGRAKJXHSMXBZ-HUPRSAECSA-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
Streptomyces	NPAtlas	117003

Species Where Detected

Species Name	Source	Reference
Streptomyces saganonensis No.4075	KNApSAcK Database	22123792

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	0.78	ALOGPS
logP	-0.26	ChemAxon
logS	-2.1	ALOGPS
pKa (Strongest Acidic)	10.09	ChemAxon
pKa (Strongest Basic)	3.92	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	12	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	199.6 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	120.06 m³·mol⁻¹	ChemAxon
Polarizability	52.45 Å³	ChemAxon
Number of Rings	5	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

External Links

NPAtlas ID

NPA021080

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

78443119

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

139589126

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Takiguchi Y, Yoshikawa H, Terahara A, Torikata A, Terao M: Herbicidins C and E, two new necleoside antibiotics. J Antibiot (Tokyo). 1979 Sep;32(9):857-61. doi: 10.7164/antibiotics.32.857. [PubMed:117003 ]

Showing NP-Card for Herbicidin E (NP0003924)

MOL for NP0003924 (Herbicidin E)

3D MOL for NP0003924 (Herbicidin E)

3D SDF for NP0003924 (Herbicidin E)

3D-SDF for NP0003924 (Herbicidin E)

PDB for NP0003924 (Herbicidin E)

3D PDB for NP0003924 (Herbicidin E)

SMILES for NP0003924 (Herbicidin E)

INCHI for NP0003924 (Herbicidin E)

Structure for NP0003924 (Herbicidin E)

3D Structure for NP0003924 (Herbicidin E)