NP-MRD: Showing NP-Card for n-[(1s,2r,3r,4s,6s)-4-amino-3-{[(2r,3r,6s)-3-amino-6-[(methylamino)methyl]oxan-2-yl]oxy}-2-hydroxy-6-methoxycyclohexyl]-2-methanimidamido-n-methylacetamide (NP0171233)

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Record Information

Version

2.0

Created at

2022-09-03 07:39:59 UTC

Updated at

2022-09-03 07:40:00 UTC

NP-MRD ID

NP0171233

Secondary Accession Numbers

None

Natural Product Identification

Common Name

n-[(1s,2r,3r,4s,6s)-4-amino-3-{[(2r,3r,6s)-3-amino-6-[(methylamino)methyl]oxan-2-yl]oxy}-2-hydroxy-6-methoxycyclohexyl]-2-methanimidamido-n-methylacetamide

Description

Istamycin A3 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. n-[(1s,2r,3r,4s,6s)-4-amino-3-{[(2r,3r,6s)-3-amino-6-[(methylamino)methyl]oxan-2-yl]oxy}-2-hydroxy-6-methoxycyclohexyl]-2-methanimidamido-n-methylacetamide is found in Streptomyces tenjimariensis. n-[(1s,2r,3r,4s,6s)-4-amino-3-{[(2r,3r,6s)-3-amino-6-[(methylamino)methyl]oxan-2-yl]oxy}-2-hydroxy-6-methoxycyclohexyl]-2-methanimidamido-n-methylacetamide was first documented in 2016 (PMID: 27778478). Based on a literature review very few articles have been published on Istamycin A3.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309032209402D          

 29 30  0  0  1  0            999 V2000
    1.4289   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -2.0625    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -0.8250    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7145   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.0000    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.1434    0.4125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    0.4125    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000    1.6500    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.0000    2.4750    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7145    2.8875    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    2.4750    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.1434    2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    1.6500    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.1434    1.2375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    1.6500    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158    1.6500    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.7145    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  4  3  1  6  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  1  0  0  0
  7  9  1  0  0  0  0
  9 10  1  1  0  0  0
 11 10  1  6  0  0  0
 11 12  1  0  0  0  0
 12 13  1  1  0  0  0
 12 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  6  0  0  0
 16 17  1  0  0  0  0
 15 18  1  0  0  0  0
 18 19  1  1  0  0  0
 19 20  1  0  0  0  0
 19 21  1  0  0  0  0
 21 22  2  0  0  0  0
 21 23  1  0  0  0  0
 23 24  1  0  0  0  0
 24 25  1  0  0  0  0
 25 26  2  0  0  0  0
 18 27  1  0  0  0  0
 11 27  1  0  0  0  0
 27 28  1  1  0  0  0
  9 29  1  0  0  0  0
  4 29  1  0  0  0  0
M  END

     RDKit          3D

 65 66  0  0  0  0  0  0  0  0999 V2000
   -8.6193    1.6542   -2.2276 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.1607    2.5722   -2.3433 N   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8947    2.6738   -2.2975 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0830    1.5422   -2.0885 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8455    1.7183   -1.3657 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1652    0.4133   -1.2651 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6664   -0.6288   -1.7649 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9262    0.2770   -0.6057 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3277    1.4723   -0.0187 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2261   -0.9925   -0.4830 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.2927   -1.3395    0.9823 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.6234   -1.6546    1.2587 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1588   -0.8458    2.2501 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4628   -2.5398    1.3354 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1267   -2.5674    0.6454 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.8841   -2.8427    1.6508 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.2077   -1.2533   -0.0456 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.4801   -1.3506   -0.4950 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4264   -0.5239    0.0233 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.3134   -1.3015    0.7623 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5240   -0.6345    0.9996 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.3663    0.5692    1.8306 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4887    1.3601    2.1702 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.1030    2.1672    1.1649 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3216   -0.5179   -0.2564 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4890    0.0647   -1.3404 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0503    0.2790   -1.0762 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.3492   -0.0346   -2.3475 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8519   -0.9699   -1.0477 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.6488    0.3387   -1.5391 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4168    3.6492   -2.4206 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3760    0.6107   -2.4490 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0272    2.1262   -0.3446 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1652    2.4411   -1.8916 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5421    1.2496    0.7045 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9543    2.1284   -0.8105 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1001    2.0560    0.5496 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8846   -1.7500   -1.0047 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0132   -0.5080    1.6444 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5512   -0.9962    3.1647 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2907    0.1955    1.9501 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1630   -1.2792    2.4919 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3368   -2.5552    2.4572 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0328   -3.4836    1.1253 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1756   -3.4042   -0.1074 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1110   -2.0294    2.2293 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6540   -3.4327    1.3249 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1441   -0.4658    0.7334 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0358    0.2018    0.7774 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0933   -1.3845    1.6402 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6758    1.2902    1.2593 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8466    0.3382    2.8167 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3596    1.9296    3.0328 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5079    2.2432    0.2351 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1780    3.2501    1.5025 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.1450    1.9012    0.9041 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2268    0.0594   -0.1116 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6398   -1.5810   -0.5200 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5882   -0.6344   -2.2259 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9038    1.0239   -1.7331 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7814    1.3664   -0.9515 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9089    0.2650   -3.1547 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0841   -1.0402   -2.3360 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8179   -1.7069   -1.8870 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0401    0.8209   -1.0370 H   0  0  0  0  0  0  0  0  0  0  0  0
 24 23  1  0
 23 22  1  0
 22 21  1  0
 21 25  1  0
 25 26  1  0
 26 27  1  0
 27 28  1  0
 27 19  1  0
 19 18  1  0
 18 17  1  0
 17 15  1  0
 15 16  1  0
 15 14  1  0
 14 11  1  0
 11 12  1  0
 12 13  1  0
 11 10  1  0
 10 29  1  0
 29 30  1  0
 10  8  1  0
  8  9  1  0
  8  6  1  0
  6  7  2  0
  6  5  1  0
  5  4  1  0
  4  3  1  0
  3  2  2  0
 19 20  1  0
 20 21  1  0
 29 17  1  0
 24 54  1  0
 24 55  1  0
 24 56  1  0
 23 53  1  0
 22 51  1  0
 22 52  1  0
 21 50  1  1
 25 57  1  0
 25 58  1  0
 26 59  1  0
 26 60  1  0
 27 61  1  1
 28 62  1  0
 28 63  1  0
 19 49  1  1
 17 48  1  1
 15 45  1  6
 16 46  1  0
 16 47  1  0
 14 43  1  0
 14 44  1  0
 11 39  1  1
 13 40  1  0
 13 41  1  0
 13 42  1  0
 10 38  1  6
 29 64  1  6
 30 65  1  0
  9 35  1  0
  9 36  1  0
  9 37  1  0
  5 33  1  0
  5 34  1  0
  4 32  1  0
  3 31  1  0
  2  1  1  0
M  END


  Mrv1652309032209402D          

 29 30  0  0  1  0            999 V2000
    1.4289   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -2.0625    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -0.8250    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7145   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.0000    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.1434    0.4125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    0.4125    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000    1.6500    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.0000    2.4750    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7145    2.8875    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    2.4750    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.1434    2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    1.6500    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.1434    1.2375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    1.6500    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158    1.6500    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.7145    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  4  3  1  6  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  1  0  0  0
  7  9  1  0  0  0  0
  9 10  1  1  0  0  0
 11 10  1  6  0  0  0
 11 12  1  0  0  0  0
 12 13  1  1  0  0  0
 12 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  6  0  0  0
 16 17  1  0  0  0  0
 15 18  1  0  0  0  0
 18 19  1  1  0  0  0
 19 20  1  0  0  0  0
 19 21  1  0  0  0  0
 21 22  2  0  0  0  0
 21 23  1  0  0  0  0
 23 24  1  0  0  0  0
 24 25  1  0  0  0  0
 25 26  2  0  0  0  0
 18 27  1  0  0  0  0
 11 27  1  0  0  0  0
 27 28  1  1  0  0  0
  9 29  1  0  0  0  0
  4 29  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0171233

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C18H36N6O5/c1-22-7-10-4-5-11(20)18(28-10)29-17-12(21)6-13(27-3)15(16(17)26)24(2)14(25)8-23-9-19/h9-13,15-18,22,26H,4-8,20-21H2,1-3H3,(H2,19,23)/t10-,11+,12-,13-,15+,16+,17+,18+/m0/s1

> <INCHI_KEY>
FBYTVIISAJWXNX-GTSDWETFSA-N

> <FORMULA>
C18H36N6O5

> <MOLECULAR_WEIGHT>
416.523

> <EXACT_MASS>
416.274718283

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_ATOM_COUNT>
65

> <JCHEM_AVERAGE_POLARIZABILITY>
43.87585311197305

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
N-[(1S,2R,3R,4S,6S)-4-amino-3-{[(2R,3R,6S)-3-amino-6-[(methylamino)methyl]oxan-2-yl]oxy}-2-hydroxy-6-methoxycyclohexyl]-2-methanimidamido-N-methylacetamide

> <ALOGPS_LOGP>
-2.08

> <JCHEM_LOGP>
-3.3640763776666676

> <ALOGPS_LOGS>
-2.37

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
4

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.449718446215392

> <JCHEM_PKA_STRONGEST_BASIC>
10.380538886742134

> <JCHEM_POLAR_SURFACE_AREA>
168.17999999999998

> <JCHEM_REFRACTIVITY>
115.9575

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.79e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
N-[(1S,2R,3R,4S,6S)-4-amino-3-{[(2R,3R,6S)-3-amino-6-[(methylamino)methyl]oxan-2-yl]oxy}-2-hydroxy-6-methoxycyclohexyl]-2-methanimidamido-N-methylacetamide

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 03-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   03-SEP-22         0                                  
HETATM    1  C   UNK     0       2.667  -4.620   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0       1.334  -3.850   0.000  0.00  0.00           N+0
HETATM    3  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.000  -1.540   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -2.667  -1.540   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -2.667   0.000   0.000  0.00  0.00           C+0
HETATM    8  N   UNK     0      -4.001   0.770   0.000  0.00  0.00           N+0
HETATM    9  C   UNK     0      -1.334   0.770   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      -1.334   2.310   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0      -0.000   3.080   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.000   4.620   0.000  0.00  0.00           C+0
HETATM   13  N   UNK     0      -1.334   5.390   0.000  0.00  0.00           N+0
HETATM   14  C   UNK     0       1.334   5.390   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       2.667   4.620   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       4.001   5.390   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       4.001   6.930   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       2.667   3.080   0.000  0.00  0.00           C+0
HETATM   19  N   UNK     0       4.001   2.310   0.000  0.00  0.00           N+0
HETATM   20  C   UNK     0       4.001   0.770   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       5.335   3.080   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0       5.335   4.620   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0       6.668   2.310   0.000  0.00  0.00           C+0
HETATM   24  N   UNK     0       8.002   3.080   0.000  0.00  0.00           N+0
HETATM   25  C   UNK     0       9.336   2.310   0.000  0.00  0.00           C+0
HETATM   26  N   UNK     0      10.669   3.080   0.000  0.00  0.00           N+0
HETATM   27  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0       1.334   0.770   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0      -0.000   0.000   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5   29                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10   29                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12   27                                                  
CONECT   12   11   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12   15                                                       
CONECT   15   14   16   18                                                  
CONECT   16   15   17                                                       
CONECT   17   16                                                            
CONECT   18   15   19   27                                                  
CONECT   19   18   20   21                                                  
CONECT   20   19                                                            
CONECT   21   19   22   23                                                  
CONECT   22   21                                                            
CONECT   23   21   24                                                       
CONECT   24   23   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25                                                            
CONECT   27   18   11   28                                                  
CONECT   28   27                                                            
CONECT   29    9    4                                                       
MASTER        0    0    0    0    0    0    0    0   29    0   60    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₈H₃₆N₆O₅

Average Mass

416.5230 Da

Monoisotopic Mass

416.27472 Da

IUPAC Name

N-[(1S,2R,3R,4S,6S)-4-amino-3-{[(2R,3R,6S)-3-amino-6-[(methylamino)methyl]oxan-2-yl]oxy}-2-hydroxy-6-methoxycyclohexyl]-2-methanimidamido-N-methylacetamide

Traditional Name

N-[(1S,2R,3R,4S,6S)-4-amino-3-{[(2R,3R,6S)-3-amino-6-[(methylamino)methyl]oxan-2-yl]oxy}-2-hydroxy-6-methoxycyclohexyl]-2-methanimidamido-N-methylacetamide

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](OC)[C@H]([C@H]2O)N(C)C(=O)CNC=N)O1

InChI Identifier

InChI=1S/C18H36N6O5/c1-22-7-10-4-5-11(20)18(28-10)29-17-12(21)6-13(27-3)15(16(17)26)24(2)14(25)8-23-9-19/h9-13,15-18,22,26H,4-8,20-21H2,1-3H3,(H2,19,23)/t10-,11+,12-,13-,15+,16+,17+,18+/m0/s1

InChI Key

FBYTVIISAJWXNX-GTSDWETFSA-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

Species Name	Source	Reference
Streptomyces tenjimariensis	LOTUS Database	35616633

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
Alpha-amino acid amide
Alpha-amino acid or derivatives
Cyclohexanol
Cyclohexylamine
Cyclitol or derivatives
Oxane
Cyclic alcohol
Tertiary carboxylic acid amide
Amino acid or derivatives
Carboxamide group
Secondary alcohol
Acetal
Formamidine
Amidine
Carboxylic acid amidine
Oxacycle
Carboxylic acid derivative
Organoheterocyclic compound
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Dialkyl ether
Secondary aliphatic amine
Secondary amine
Carboximidamide
Ether
Amine
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Carbonyl group
Organic nitrogen compound
Primary aliphatic amine
Organonitrogen compound
Alcohol
Primary amine
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

amino sugar (CHEBI:81440 )

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	-2.1	ALOGPS
logP	-3.4	ChemAxon
logS	-2.4	ALOGPS
pKa (Strongest Acidic)	13.45	ChemAxon
pKa (Strongest Basic)	10.38	ChemAxon
Physiological Charge	4	ChemAxon
Hydrogen Acceptor Count	10	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	168.18 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	115.96 m³·mol⁻¹	ChemAxon
Polarizability	43.88 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

30791527

KEGG Compound ID

C17989

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

46174027

PDB ID

Not Available

ChEBI ID

81440

Good Scents ID

Not Available

References

General References

Hoang NH, Huong NL, Kim B, Sohng JK, Yoon YJ, Park JW: Istamycin aminoglycosides profiling and their characterization in Streptomyces tenjimariensis ATCC 31603 culture using high-performance liquid chromatography with tandem mass spectrometry. J Sep Sci. 2016 Dec;39(24):4712-4722. doi: 10.1002/jssc.201600925. Epub 2016 Nov 23. [PubMed:27778478 ]
LOTUS database [Link]

Showing NP-Card for n-[(1s,2r,3r,4s,6s)-4-amino-3-{[(2r,3r,6s)-3-amino-6-[(methylamino)methyl]oxan-2-yl]oxy}-2-hydroxy-6-methoxycyclohexyl]-2-methanimidamido-n-methylacetamide (NP0171233)

MOL for NP0171233 (n-[(1s,2r,3r,4s,6s)-4-amino-3-{[(2r,3r,6s)-3-amino-6-[(methylamino)methyl]oxan-2-yl]oxy}-2-hydroxy-6-methoxycyclohexyl]-2-methanimidamido-n-methylacetamide)

3D MOL for NP0171233 (n-[(1s,2r,3r,4s,6s)-4-amino-3-{[(2r,3r,6s)-3-amino-6-[(methylamino)methyl]oxan-2-yl]oxy}-2-hydroxy-6-methoxycyclohexyl]-2-methanimidamido-n-methylacetamide)

3D SDF for NP0171233 (n-[(1s,2r,3r,4s,6s)-4-amino-3-{[(2r,3r,6s)-3-amino-6-[(methylamino)methyl]oxan-2-yl]oxy}-2-hydroxy-6-methoxycyclohexyl]-2-methanimidamido-n-methylacetamide)

3D-SDF for NP0171233 (n-[(1s,2r,3r,4s,6s)-4-amino-3-{[(2r,3r,6s)-3-amino-6-[(methylamino)methyl]oxan-2-yl]oxy}-2-hydroxy-6-methoxycyclohexyl]-2-methanimidamido-n-methylacetamide)

PDB for NP0171233 (n-[(1s,2r,3r,4s,6s)-4-amino-3-{[(2r,3r,6s)-3-amino-6-[(methylamino)methyl]oxan-2-yl]oxy}-2-hydroxy-6-methoxycyclohexyl]-2-methanimidamido-n-methylacetamide)

3D PDB for NP0171233 (n-[(1s,2r,3r,4s,6s)-4-amino-3-{[(2r,3r,6s)-3-amino-6-[(methylamino)methyl]oxan-2-yl]oxy}-2-hydroxy-6-methoxycyclohexyl]-2-methanimidamido-n-methylacetamide)

SMILES for NP0171233 (n-[(1s,2r,3r,4s,6s)-4-amino-3-{[(2r,3r,6s)-3-amino-6-[(methylamino)methyl]oxan-2-yl]oxy}-2-hydroxy-6-methoxycyclohexyl]-2-methanimidamido-n-methylacetamide)

INCHI for NP0171233 (n-[(1s,2r,3r,4s,6s)-4-amino-3-{[(2r,3r,6s)-3-amino-6-[(methylamino)methyl]oxan-2-yl]oxy}-2-hydroxy-6-methoxycyclohexyl]-2-methanimidamido-n-methylacetamide)

Structure for NP0171233 (n-[(1s,2r,3r,4s,6s)-4-amino-3-{[(2r,3r,6s)-3-amino-6-[(methylamino)methyl]oxan-2-yl]oxy}-2-hydroxy-6-methoxycyclohexyl]-2-methanimidamido-n-methylacetamide)

3D Structure for NP0171233 (n-[(1s,2r,3r,4s,6s)-4-amino-3-{[(2r,3r,6s)-3-amino-6-[(methylamino)methyl]oxan-2-yl]oxy}-2-hydroxy-6-methoxycyclohexyl]-2-methanimidamido-n-methylacetamide)