NP-MRD: Showing NP-Card for micronomicin (NP0146307)

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Record Information

Version

2.0

Created at

2022-09-02 01:40:55 UTC

Updated at

2022-09-02 01:40:55 UTC

NP-MRD ID

NP0146307

Secondary Accession Numbers

None

Natural Product Identification

Common Name

micronomicin

Description

Micronomicin, also known as sagamicin or MCR, belongs to the class of organic compounds known as aminocyclitol glycosides. These are organic compounds containing an amicocyclitol moiety glycosidically linked to a carbohydrate moiety. There are two major classes of aminoglycosides containing a 2-streptamine core. They are called 4,5- and 4,6-disubstituted 2-deoxystreptamines. Micronomicin is a very strong basic compound (based on its pKa). Micronomicin (INN) is an aminoglycoside antibiotic for use on the eye.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652306231722392D          

 32 34  0  0  1  0            999 V2000
    4.4710   -0.6055    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -1.2375    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.7158   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158   -2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -2.8875    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.2868   -2.4750    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.2868   -1.6500    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.5724   -1.2375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158   -4.1250    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    6.4302   -3.7125    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    7.1447   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1447   -4.9500    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    6.4302   -5.3625    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.7158   -4.9500    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.0013   -5.3625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302   -6.1875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158   -6.6000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.7158   -7.4250    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.0013   -7.8375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -7.4250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -6.6000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.0013   -6.1875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -6.1875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -5.3625    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302   -7.8375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    7.8592   -5.3625    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302   -2.8875    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.5316   -0.6055    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  6  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  2  7  1  0  0  0  0
  7  8  1  1  0  0  0
  8  9  1  0  0  0  0
  6 10  1  6  0  0  0
  5 11  1  6  0  0  0
 12 11  1  1  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 12 17  1  0  0  0  0
 17 18  1  6  0  0  0
 16 19  1  1  0  0  0
 20 19  1  6  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  1  0  0  0  0
 24 25  1  0  0  0  0
 20 25  1  0  0  0  0
 24 26  1  1  0  0  0
 26 27  1  0  0  0  0
 27 28  1  0  0  0  0
 21 29  1  6  0  0  0
 15 30  1  6  0  0  0
 13 31  1  6  0  0  0
  2 32  1  1  0  0  0
M  END

     RDKit          3D

 73 75  0  0  0  0  0  0  0  0999 V2000
   -6.3996   -1.5725    4.0602 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3756   -2.1713    3.2481 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4886   -1.2125    2.6500 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1510   -0.3644    1.5967 C   0  0  2  0  0  0  0  0  0  0  0  0
   -5.8036   -1.1902    0.5173 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2634   -0.8206   -0.8418 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7473   -0.8475   -0.8401 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.3062   -0.3945   -2.1579 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2721    0.0216    0.2761 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.4948    1.0450   -0.1917 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2071    1.0753    0.3279 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.0952    2.3579    1.1852 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.0963    2.2833    2.2035 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.2849    2.3322    1.7698 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3383    2.4368    0.6856 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.6152    2.4849    1.3743 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2391    1.2850   -0.2762 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.9760    1.4812   -1.4345 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8911    0.4926   -1.6932 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.6735   -0.1704   -2.8885 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7413   -0.9675   -3.2674 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7004   -1.2551   -2.1561 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.8958   -1.9778   -2.7946 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1338   -2.1721   -1.2414 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.2297   -0.0721   -1.4278 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.2855   -0.2997    0.0243 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.1716   -1.3588    0.3927 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2783    1.0887   -1.6146 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.5906    1.8803   -2.7079 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2175    1.1998   -0.7588 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.3105    0.2251   -1.7499 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3268    0.5724    1.0121 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9402   -0.7441    3.5976 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9296   -1.2469    5.0308 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1479   -2.3633    4.2947 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7324   -2.8848    2.5826 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0528   -0.6041    3.4637 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6572   -1.7946    2.2004 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9559    0.2069    2.1058 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9181   -0.9996    0.4628 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6997   -2.2695    0.6343 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5776    0.2444   -1.0217 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6342   -1.5013   -1.6191 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3888   -1.9093   -0.7472 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8643   -0.8161   -2.9162 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2578    0.6521   -2.1999 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6154   -0.5934    0.9495 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9788    0.2682    1.0198 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2087    3.2646    0.5585 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9701    2.7838    1.9799 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1986    1.3335    2.5765 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3830    1.3531    2.3228 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4650    3.1732    2.4747 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1386    3.3891    0.1490 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5527    2.0037    2.2809 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7837    3.5141    1.5849 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5262    0.3558    0.2424 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8364   -0.2681   -0.8854 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2484   -0.6293   -4.1950 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2795   -1.9640   -3.5436 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6693   -2.3302   -3.8126 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1969   -2.8509   -2.1661 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.7728   -1.3055   -2.8683 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4573   -3.0877   -1.4028 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2383    0.2477   -1.7819 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6335    0.6109    0.4307 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6004   -2.2951    0.5672 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.9587   -1.4541   -0.3719 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.6814   -1.1059    1.3688 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2913    1.7701   -0.7310 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9441    1.6924   -3.4259 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3902    2.1805   -1.2945 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0282    0.5588   -2.6409 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 12 14  1  0
 14 15  1  0
 15 16  1  0
 15 17  1  0
 17 18  1  0
 18 19  1  0
 19 20  1  0
 20 21  1  0
 21 22  1  0
 22 23  1  0
 22 24  1  1
 22 25  1  0
 25 26  1  0
 26 27  1  0
 25 28  1  0
 28 29  1  0
 17 30  1  0
 30 31  1  0
  9 32  1  0
 32  4  1  0
 30 11  1  0
 28 19  1  0
  1 33  1  0
  1 34  1  0
  1 35  1  0
  2 36  1  0
  3 37  1  0
  3 38  1  0
  4 39  1  1
  5 40  1  0
  5 41  1  0
  6 42  1  0
  6 43  1  0
  7 44  1  1
  8 45  1  0
  8 46  1  0
  9 47  1  1
 11 48  1  1
 12 49  1  6
 13 50  1  0
 13 51  1  0
 14 52  1  0
 14 53  1  0
 15 54  1  6
 16 55  1  0
 16 56  1  0
 17 57  1  1
 19 58  1  1
 21 59  1  0
 21 60  1  0
 23 61  1  0
 23 62  1  0
 23 63  1  0
 24 64  1  0
 25 65  1  6
 26 66  1  0
 27 67  1  0
 27 68  1  0
 27 69  1  0
 28 70  1  1
 29 71  1  0
 30 72  1  6
 31 73  1  0
M  END


  Mrv1652306231722392D          

 32 34  0  0  1  0            999 V2000
    4.4710   -0.6055    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -1.2375    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.7158   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158   -2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -2.8875    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.2868   -2.4750    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.2868   -1.6500    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.5724   -1.2375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158   -4.1250    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    6.4302   -3.7125    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    7.1447   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1447   -4.9500    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    6.4302   -5.3625    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.7158   -4.9500    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.0013   -5.3625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302   -6.1875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158   -6.6000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.7158   -7.4250    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.0013   -7.8375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -7.4250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -6.6000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.0013   -6.1875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -6.1875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -5.3625    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302   -7.8375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    7.8592   -5.3625    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302   -2.8875    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.5316   -0.6055    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  6  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  2  7  1  0  0  0  0
  7  8  1  1  0  0  0
  8  9  1  0  0  0  0
  6 10  1  6  0  0  0
  5 11  1  6  0  0  0
 12 11  1  1  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 12 17  1  0  0  0  0
 17 18  1  6  0  0  0
 16 19  1  1  0  0  0
 20 19  1  6  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  1  0  0  0  0
 24 25  1  0  0  0  0
 20 25  1  0  0  0  0
 24 26  1  1  0  0  0
 26 27  1  0  0  0  0
 27 28  1  0  0  0  0
 21 29  1  6  0  0  0
 15 30  1  6  0  0  0
 13 31  1  6  0  0  0
  2 32  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0146307

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CNC[C@@H]1CC[C@@H](N)[C@@H](O[C@@H]2[C@@H](N)C[C@@H](N)[C@H](O[C@H]3OC[C@](C)(O)[C@H](NC)[C@H]3O)[C@H]2O)O1

> <INCHI_IDENTIFIER>
InChI=1S/C20H41N5O7/c1-20(28)8-29-19(14(27)17(20)25-3)32-16-12(23)6-11(22)15(13(16)26)31-18-10(21)5-4-9(30-18)7-24-2/h9-19,24-28H,4-8,21-23H2,1-3H3/t9-,10+,11-,12+,13-,14+,15+,16-,17+,18+,19+,20-/m0/s1

> <INCHI_KEY>
DNYGXMICFMACRA-XHEDQWPISA-N

> <FORMULA>
C20H41N5O7

> <MOLECULAR_WEIGHT>
463.576

> <EXACT_MASS>
463.30059868

> <JCHEM_ACCEPTOR_COUNT>
12

> <JCHEM_ATOM_COUNT>
73

> <JCHEM_AVERAGE_POLARIZABILITY>
49.66129412670688

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
8

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3R,4R,5R)-2-{[(1S,2S,3R,4S,6R)-4,6-diamino-3-{[(2R,3R,6S)-3-amino-6-[(methylamino)methyl]oxan-2-yl]oxy}-2-hydroxycyclohexyl]oxy}-5-methyl-4-(methylamino)oxane-3,5-diol

> <ALOGPS_LOGP>
-1.84

> <JCHEM_LOGP>
-3.5537305539999995

> <ALOGPS_LOGS>
-1.42

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
5

> <JCHEM_PKA>
13.159314888955901

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.548824540405306

> <JCHEM_PKA_STRONGEST_BASIC>
10.062735189141732

> <JCHEM_POLAR_SURFACE_AREA>
199.73000000000002

> <JCHEM_REFRACTIVITY>
113.60189999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.75e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2R,3R,4R,5R)-2-{[(1S,2S,3R,4S,6R)-4,6-diamino-3-{[(2R,3R,6S)-3-amino-6-[(methylamino)methyl]oxan-2-yl]oxy}-2-hydroxycyclohexyl]oxy}-5-methyl-4-(methylamino)oxane-3,5-diol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 23-JUN-17   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-JUN-17         0                                  
HETATM    1  C   UNK     0       8.346  -1.130   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       9.336  -2.310   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      10.669  -3.080   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      10.669  -4.620   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       9.336  -5.390   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       8.002  -4.620   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       8.002  -3.080   0.000  0.00  0.00           C+0
HETATM    8  N   UNK     0       6.668  -2.310   0.000  0.00  0.00           N+0
HETATM    9  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       6.668  -5.390   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       9.336  -6.930   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0      10.669  -7.700   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      12.003  -6.930   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      13.337  -7.700   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      13.337  -9.240   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      12.003 -10.010   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      10.669  -9.240   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       9.336 -10.010   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0      12.003 -11.550   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0      10.669 -12.320   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      10.669 -13.860   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       9.336 -14.630   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       8.002 -13.860   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       8.002 -12.320   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0       9.336 -11.550   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0       6.668 -11.550   0.000  0.00  0.00           C+0
HETATM   27  N   UNK     0       6.668 -10.010   0.000  0.00  0.00           N+0
HETATM   28  C   UNK     0       8.002  -9.240   0.000  0.00  0.00           C+0
HETATM   29  N   UNK     0      12.003 -14.630   0.000  0.00  0.00           N+0
HETATM   30  N   UNK     0      14.670 -10.010   0.000  0.00  0.00           N+0
HETATM   31  N   UNK     0      12.003  -5.390   0.000  0.00  0.00           N+0
HETATM   32  O   UNK     0      10.326  -1.130   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    7   32                                             
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6   11                                                  
CONECT    6    5    7   10                                                  
CONECT    7    6    2    8                                                  
CONECT    8    7    9                                                       
CONECT    9    8                                                            
CONECT   10    6                                                            
CONECT   11    5   12                                                       
CONECT   12   11   13   17                                                  
CONECT   13   12   14   31                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16   30                                                  
CONECT   16   15   17   19                                                  
CONECT   17   16   12   18                                                  
CONECT   18   17                                                            
CONECT   19   16   20                                                       
CONECT   20   19   21   25                                                  
CONECT   21   20   22   29                                                  
CONECT   22   21   23                                                       
CONECT   23   22   24                                                       
CONECT   24   23   25   26                                                  
CONECT   25   24   20                                                       
CONECT   26   24   27                                                       
CONECT   27   26   28                                                       
CONECT   28   27                                                            
CONECT   29   21                                                            
CONECT   30   15                                                            
CONECT   31   13                                                            
CONECT   32    2                                                            
MASTER        0    0    0    0    0    0    0    0   32    0   68    0
END

View in JSmol

Synonyms

Value	Source
Sagamicin	Kegg
MCR	Kegg
MICRONOMICIN sulfATE	ChEMBL
MICRONOMICIN sulfuric acid	Generator
MICRONOMICIN sulphate	Generator
MICRONOMICIN sulphuric acid	Generator
6'-N-Methylgentamicin C	MeSH
Gentamicin C2b	MeSH
XK-62-2	MeSH

Chemical Formula

C₂₀H₄₁N₅O₇

Average Mass

463.5760 Da

Monoisotopic Mass

463.30060 Da

IUPAC Name

(2R,3R,4R,5R)-2-{[(1S,2S,3R,4S,6R)-4,6-diamino-3-{[(2R,3R,6S)-3-amino-6-[(methylamino)methyl]oxan-2-yl]oxy}-2-hydroxycyclohexyl]oxy}-5-methyl-4-(methylamino)oxane-3,5-diol

Traditional Name

(2R,3R,4R,5R)-2-{[(1S,2S,3R,4S,6R)-4,6-diamino-3-{[(2R,3R,6S)-3-amino-6-[(methylamino)methyl]oxan-2-yl]oxy}-2-hydroxycyclohexyl]oxy}-5-methyl-4-(methylamino)oxane-3,5-diol

CAS Registry Number

Not Available

SMILES

CNC[C@@H]1CC[C@@H](N)[C@@H](O[C@@H]2[C@@H](N)C[C@@H](N)[C@H](O[C@H]3OC[C@](C)(O)[C@H](NC)[C@H]3O)[C@H]2O)O1

InChI Identifier

InChI=1S/C20H41N5O7/c1-20(28)8-29-19(14(27)17(20)25-3)32-16-12(23)6-11(22)15(13(16)26)31-18-10(21)5-4-9(30-18)7-24-2/h9-19,24-28H,4-8,21-23H2,1-3H3/t9-,10+,11-,12+,13-,14+,15+,16-,17+,18+,19+,20-/m0/s1

InChI Key

DNYGXMICFMACRA-XHEDQWPISA-N

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Not Available

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as aminocyclitol glycosides. These are organic compounds containing an amicocyclitol moiety glycosidically linked to a carbohydrate moiety. There are two major classes of aminoglycosides containing a 2-streptamine core. They are called 4,5- and 4,6-disubstituted 2-deoxystreptamines.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Aminocyclitol glycosides

Alternative Parents

Substituents

Amino cyclitol glycoside
2-deoxystreptamine aminoglycoside
Glycosyl compound
O-glycosyl compound
Aminocyclitol or derivatives
Cyclohexanol
Cyclohexylamine
Cyclitol or derivatives
Monosaccharide
Oxane
Tertiary alcohol
Cyclic alcohol
Secondary alcohol
1,2-aminoalcohol
Secondary amine
Acetal
Organoheterocyclic compound
Secondary aliphatic amine
Oxacycle
Alcohol
Hydrocarbon derivative
Primary aliphatic amine
Organopnictogen compound
Organic nitrogen compound
Amine
Primary amine
Organonitrogen compound
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

aminoglycoside (CHEBI:81283 )

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	-1.8	ALOGPS
logP	-3.6	ChemAxon
logS	-1.4	ALOGPS
pKa (Strongest Acidic)	12.55	ChemAxon
pKa (Strongest Basic)	10.06	ChemAxon
Physiological Charge	5	ChemAxon
Hydrogen Acceptor Count	12	ChemAxon
Hydrogen Donor Count	8	ChemAxon
Polar Surface Area	199.73 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	113.6 m³·mol⁻¹	ChemAxon
Polarizability	49.66 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

External Links

HMDB ID

Not Available

DrugBank ID

DB13274

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00018016

Chemspider ID

Not Available

KEGG Compound ID

C17706

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Micronomicin

METLIN ID

Not Available

PubChem Compound

3037206

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for micronomicin (NP0146307)

MOL for NP0146307 (micronomicin)

3D MOL for NP0146307 (micronomicin)

3D SDF for NP0146307 (micronomicin)

3D-SDF for NP0146307 (micronomicin)

PDB for NP0146307 (micronomicin)

3D PDB for NP0146307 (micronomicin)

SMILES for NP0146307 (micronomicin)

INCHI for NP0146307 (micronomicin)

Structure for NP0146307 (micronomicin)

3D Structure for NP0146307 (micronomicin)