NP-MRD: Showing NP-Card for ribostamycin (NP0330240)

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Record Information

Version

1.0

Created at

2022-09-12 15:24:03 UTC

Updated at

2022-09-12 15:24:03 UTC

NP-MRD ID

NP0330240

Secondary Accession Numbers

None

Natural Product Identification

Common Name

ribostamycin

Description

Xylostasin belongs to the class of organic compounds known as 4,5-disubstituted 2-deoxystreptamines. These are 2-deoxystreptamine aminoglycosides that are glycosidically linked to a pyranose of furanose unit at the C4- and C5-positions. ribostamycin is found in Streptomyces fradiae. Xylostasin is a very strong basic compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1533004171519122D          

 31 33  0  0  0  0            999 V2000
   -2.8579   -1.6500    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -1.6500    0.0000 C   0  0  0  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  0  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
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   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
    0.7145    2.0625    0.0000 N   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
    2.1434    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4760   -1.7224    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7309   -2.5070    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2460   -3.1745    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5815   -3.9282    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5559   -2.5070    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0408   -3.1745    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8109   -1.7224    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5955   -1.4675    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -2.4750    0.0000 C   0  0  0  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
   -0.7145   -3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -2.4750    0.0000 C   0  0  0  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
  1  2  1  0  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
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  8 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 11 13  1  0  0  0  0
 13 14  1  0  0  0  0
 13 15  1  0  0  0  0
  7 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 19 22  1  0  0  0  0
 22 23  1  0  0  0  0
 22 24  1  0  0  0  0
 17 24  1  0  0  0  0
 24 25  1  0  0  0  0
  5 26  1  0  0  0  0
 26 27  1  0  0  0  0
 26 28  1  0  0  0  0
 28 29  1  0  0  0  0
 28 30  1  0  0  0  0
  3 30  1  0  0  0  0
 30 31  1  0  0  0  0
M  END

     RDKit          3D

 65 67  0  0  0  0  0  0  0  0999 V2000
   -1.9889   -0.7906    2.7232 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8757   -2.1317    2.2097 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0470   -2.2101    0.7160 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.1073   -1.4658    0.0601 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5624   -0.3458   -0.5824 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.5043    0.2025   -1.2817 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2208    1.4948   -1.0676 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.1255    2.4089   -2.2160 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.2594    2.4499   -3.0990 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0433    3.8337   -1.6774 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2231    3.9459   -0.7535 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.1343    5.2359   -0.0922 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1554    2.8988    0.3554 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.0790    3.0349    1.0292 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1336    1.5549   -0.3421 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.2954    0.5259    0.5470 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3668   -0.2645    0.1736 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.9954   -1.5778    0.0522 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1324   -2.3657    0.1226 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.7630   -3.6033    0.9228 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7422   -4.3179    0.3297 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1931   -1.5842    0.8214 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.6722   -2.2335    1.9680 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4693   -0.3013    1.1955 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.9924   -0.4622    2.4906 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6222   -0.6843   -1.6372 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.4533    0.5039   -1.8406 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5590   -1.7573   -1.1280 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.8446   -1.5362   -1.5795 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4699   -1.8262    0.3834 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.2941   -2.8205    0.8978 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6014   -0.8198    3.7100 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0162   -0.5609    2.8634 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6461   -2.7427    2.7271 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8911   -2.5714    2.5346 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9209   -3.2974    0.4511 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0600    0.3857    0.0921 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9467    1.9131   -0.3196 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8310    2.2092   -2.7755 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9399    2.8360   -4.0160 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0047    3.1124   -2.7657 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8610    4.0905   -1.0864 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1948    4.5562   -2.5017 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1894    3.8712   -1.2536 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5270    5.9513   -0.7404 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7648    5.2094    0.7397 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0105    3.0439    1.0112 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0937    3.4920    1.8812 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8901    1.5341   -1.1626 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8288    0.1461   -0.7706 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4176   -2.6563   -0.8966 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5434   -3.3375    1.9733 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6593   -4.2500    0.9328 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6111   -5.1411    0.8464 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0151   -1.3608    0.1045 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6305   -2.3902    1.8243 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1512    0.5702    1.1233 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5079   -1.1032    3.0030 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1653   -0.9269   -2.6058 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3168    0.4629   -1.2554 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7241    0.5623   -2.8653 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1875   -2.7289   -1.5143 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4008   -1.3365   -0.7701 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6933   -0.8528    0.8400 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7890   -3.6810    0.9405 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
  8  9  1  0
  8 10  1  0
 10 11  1  0
 11 12  1  0
 11 13  1  0
 13 14  1  0
 13 15  1  0
 15 16  1  0
 16 17  1  0
 17 18  1  0
 18 19  1  0
 19 20  1  0
 20 21  1  0
 19 22  1  0
 22 23  1  0
 22 24  1  0
 24 25  1  0
  5 26  1  0
 26 27  1  0
 26 28  1  0
 28 29  1  0
 28 30  1  0
 30 31  1  0
 30  3  1  0
 15  7  1  0
 24 17  1  0
  1 32  1  0
  1 33  1  0
  2 34  1  0
  2 35  1  0
  3 36  1  6
  5 37  1  1
  7 38  1  1
  8 39  1  6
  9 40  1  0
  9 41  1  0
 10 42  1  0
 10 43  1  0
 11 44  1  6
 12 45  1  0
 12 46  1  0
 13 47  1  1
 14 48  1  0
 15 49  1  6
 17 50  1  6
 19 51  1  6
 20 52  1  0
 20 53  1  0
 21 54  1  0
 22 55  1  6
 23 56  1  0
 24 57  1  1
 25 58  1  0
 26 59  1  6
 27 60  1  0
 27 61  1  0
 28 62  1  6
 29 63  1  0
 30 64  1  1
 31 65  1  0
M  END


  Mrv1533004171519122D          

 31 33  0  0  0  0            999 V2000
   -2.8579   -1.6500    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -1.6500    0.0000 C   0  0  0  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  0  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
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   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
    0.7145    2.0625    0.0000 N   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
    2.1434    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4760   -1.7224    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7309   -2.5070    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2460   -3.1745    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5815   -3.9282    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5559   -2.5070    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0408   -3.1745    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8109   -1.7224    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5955   -1.4675    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -2.4750    0.0000 C   0  0  0  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
   -0.7145   -3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -2.4750    0.0000 C   0  0  0  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
  1  2  1  0  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
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  8 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 11 13  1  0  0  0  0
 13 14  1  0  0  0  0
 13 15  1  0  0  0  0
  7 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 19 22  1  0  0  0  0
 22 23  1  0  0  0  0
 22 24  1  0  0  0  0
 17 24  1  0  0  0  0
 24 25  1  0  0  0  0
  5 26  1  0  0  0  0
 26 27  1  0  0  0  0
 26 28  1  0  0  0  0
 28 29  1  0  0  0  0
 28 30  1  0  0  0  0
  3 30  1  0  0  0  0
 30 31  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0330240

> <DATABASE_NAME>
NP-MRD

> <SMILES>
NCC1OC(OC2C(N)CC(N)C(O)C2OC2OC(CO)C(O)C2O)C(N)C(O)C1O

> <INCHI_IDENTIFIER>
InChI=1S/C17H34N4O10/c18-2-6-10(24)12(26)8(21)16(28-6)30-14-5(20)1-4(19)9(23)15(14)31-17-13(27)11(25)7(3-22)29-17/h4-17,22-27H,1-3,18-21H2

> <INCHI_KEY>
NSKGQURZWSPSBC-UHFFFAOYSA-N

> <FORMULA>
C17H34N4O10

> <MOLECULAR_WEIGHT>
454.477

> <EXACT_MASS>
454.227493311

> <JCHEM_ACCEPTOR_COUNT>
14

> <JCHEM_ATOM_COUNT>
65

> <JCHEM_AVERAGE_POLARIZABILITY>
44.597587896539245

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
10

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
5-amino-2-(aminomethyl)-6-[(4,6-diamino-2-{[3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy}-3-hydroxycyclohexyl)oxy]oxane-3,4-diol

> <ALOGPS_LOGP>
-2.92

> <JCHEM_LOGP>
-6.430578507000001

> <ALOGPS_LOGS>
-0.71

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
4

> <JCHEM_PKA>
12.973624259648087

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.1938657158369

> <JCHEM_PKA_STRONGEST_BASIC>
9.931338624305102

> <JCHEM_POLAR_SURFACE_AREA>
262.38

> <JCHEM_REFRACTIVITY>
100.17200000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
8.87e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
ribostamycin

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 17-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-APR-15         0                                  
HETATM    1  N   UNK     0      -5.335  -3.080   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0      -4.001  -2.310   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -2.667  -3.080   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      -1.334  -2.310   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       0.000  -3.080   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       1.334  -2.310   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0      -1.334  -0.770   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM   12  N   UNK     0       1.334   3.850   0.000  0.00  0.00           N+0
HETATM   13  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       4.001   2.310   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       4.001  -0.770   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       2.755  -3.215   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       3.231  -4.680   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       2.326  -5.926   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       2.952  -7.333   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0       4.771  -4.680   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0       5.676  -5.926   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0       5.247  -3.215   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0       6.712  -2.739   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0       0.000  -4.620   0.000  0.00  0.00           C+0
HETATM   27  N   UNK     0       1.334  -5.390   0.000  0.00  0.00           N+0
HETATM   28  C   UNK     0      -1.334  -5.390   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0      -1.334  -6.930   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0      -2.667  -4.620   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0      -4.001  -5.390   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   30                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6   26                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8   15                                                  
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11                                                       
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13    7   16                                                  
CONECT   16   15   17                                                       
CONECT   17   16   18   24                                                  
CONECT   18   17   19                                                       
CONECT   19   18   20   22                                                  
CONECT   20   19   21                                                       
CONECT   21   20                                                            
CONECT   22   19   23   24                                                  
CONECT   23   22                                                            
CONECT   24   22   17   25                                                  
CONECT   25   24                                                            
CONECT   26    5   27   28                                                  
CONECT   27   26                                                            
CONECT   28   26   29   30                                                  
CONECT   29   28                                                            
CONECT   30   28    3   31                                                  
CONECT   31   30                                                            
MASTER        0    0    0    0    0    0    0    0   31    0   66    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₇H₃₄N₄O₁₀

Average Mass

454.4770 Da

Monoisotopic Mass

454.22749 Da

IUPAC Name

5-amino-2-(aminomethyl)-6-[(4,6-diamino-2-{[3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy}-3-hydroxycyclohexyl)oxy]oxane-3,4-diol

Traditional Name

ribostamycin

CAS Registry Number

Not Available

SMILES

NCC1OC(OC2C(N)CC(N)C(O)C2OC2OC(CO)C(O)C2O)C(N)C(O)C1O

InChI Identifier

InChI=1S/C17H34N4O10/c18-2-6-10(24)12(26)8(21)16(28-6)30-14-5(20)1-4(19)9(23)15(14)31-17-13(27)11(25)7(3-22)29-17/h4-17,22-27H,1-3,18-21H2

InChI Key

NSKGQURZWSPSBC-UHFFFAOYSA-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 fradiae	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as 4,5-disubstituted 2-deoxystreptamines. These are 2-deoxystreptamine aminoglycosides that are glycosidically linked to a pyranose of furanose unit at the C4- and C5-positions.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

4,5-disubstituted 2-deoxystreptamines

Alternative Parents

Substituents

4,5-disubstituted 2-deoxystreptamine
Glycosyl compound
O-glycosyl compound
Aminocyclitol or derivatives
Cyclohexanol
Cyclohexylamine
Cyclitol or derivatives
Monosaccharide
Oxane
Tetrahydrofuran
Cyclic alcohol
Secondary alcohol
1,2-aminoalcohol
Organoheterocyclic compound
Acetal
Oxacycle
Primary alcohol
Hydrocarbon derivative
Organopnictogen compound
Primary aliphatic amine
Organonitrogen compound
Organic nitrogen compound
Amine
Primary amine
Alcohol
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic 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	-2.9	ALOGPS
logP	-6.4	ChemAxon
logS	-0.71	ALOGPS
pKa (Strongest Acidic)	12.19	ChemAxon
pKa (Strongest Basic)	9.93	ChemAxon
Physiological Charge	4	ChemAxon
Hydrogen Acceptor Count	14	ChemAxon
Hydrogen Donor Count	10	ChemAxon
Polar Surface Area	262.38 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	100.17 m³·mol⁻¹	ChemAxon
Polarizability	44.6 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

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

5066

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for ribostamycin (NP0330240)

MOL for NP0330240 (ribostamycin)

3D MOL for NP0330240 (ribostamycin)

3D SDF for NP0330240 (ribostamycin)

3D-SDF for NP0330240 (ribostamycin)

PDB for NP0330240 (ribostamycin)

3D PDB for NP0330240 (ribostamycin)

SMILES for NP0330240 (ribostamycin)

INCHI for NP0330240 (ribostamycin)

Structure for NP0330240 (ribostamycin)

3D Structure for NP0330240 (ribostamycin)