NP-MRD: Showing NP-Card for SF-733 (NP0021625)

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Record Information

Version

2.0

Created at

2021-01-06 06:54:26 UTC

Updated at

2021-07-15 17:36:50 UTC

NP-MRD ID

NP0021625

Secondary Accession Numbers

None

Natural Product Identification

Common Name

SF-733

Provided By

NPAtlas

Description

Ribostamycin is also known as antibiotic SF 733 or SF-733. SF-733 is found in Streptomyces fradiae and Streptomyces ribosidificus. SF-733 was first documented in 1970 (PMID: 5423362). Based on a literature review a small amount of articles have been published on Ribostamycin (PMID: 11741285) (PMID: 1551291) (PMID: 4782052) (PMID: 4792382).

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652306242105173D          

 65 67  0  0  0  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv1652306242105173D          

 65 67  0  0  0  0            999 V2000
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   -1.0022    1.0949    0.9753 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.5041    0.6732   -0.2137 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2398   -0.4977   -0.1634 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.5889   -1.4428   -0.9386 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4892   -2.3667   -1.3914 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.3179   -2.5505   -2.9054 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.2478   -3.4940   -3.3247 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8729   -1.8610   -1.1682 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.5494   -2.5554   -0.1651 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6043   -0.4137   -0.7323 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.6006   -0.1442    0.2270 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6194   -0.0342   -2.0404 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.4166    0.1693   -2.7528 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.7782   -1.5434   -1.8059 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.5675   -2.1493   -3.0437 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2252   -1.7178   -1.3750 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.4230   -3.0477   -1.1085 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9382   -0.7037    2.3305 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9536    0.5790    1.7437 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6022   -0.7115   -0.0590 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8941   -2.1758    0.7135 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6238   -1.1601    0.5668 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8597    1.8284   -1.0538 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6032    2.4346    0.6038 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5294    0.5610    2.9720 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5957    1.2729    3.5584 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5113    2.7198    2.7118 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6249    3.5886    2.7996 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2194    2.5480    4.1790 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9817    2.0688    3.3895 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3444    4.4775    3.8678 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5483    4.6257    2.1437 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2336    3.1769    0.6327 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3571    2.4681    0.2672 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2425    0.4408    1.8387 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2955   -0.9028    0.8694 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3921   -3.3637   -0.9141 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6164   -1.5767   -3.3932 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2853   -2.7922   -3.1755 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0648   -3.0912   -3.6964 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5244   -1.8873   -2.0616 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8798   -2.8775    0.4940 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7048    0.2001   -1.6304 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3912    0.2737   -0.2351 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4632    0.1977   -2.7601 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1232    1.0152   -2.5603 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0748   -0.6592   -3.0903 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1098   -1.9151   -1.0248 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4145   -2.2571   -3.5562 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8692   -1.3384   -2.1929 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3789   -3.3219   -1.1154 H   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
 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
 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
 30 31  1  0  0  0  0
 30  3  1  0  0  0  0
 15  7  1  0  0  0  0
 24 17  1  0  0  0  0
  1 32  1  0  0  0  0
  1 33  1  0  0  0  0
  2 34  1  0  0  0  0
  2 35  1  0  0  0  0
  3 36  1  1  0  0  0
  5 37  1  6  0  0  0
  7 38  1  6  0  0  0
  8 39  1  1  0  0  0
  9 40  1  0  0  0  0
  9 41  1  0  0  0  0
 10 42  1  0  0  0  0
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 11 44  1  1  0  0  0
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 12 46  1  0  0  0  0
 13 47  1  6  0  0  0
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 15 49  1  1  0  0  0
 17 50  1  1  0  0  0
 19 51  1  1  0  0  0
 20 52  1  0  0  0  0
 20 53  1  0  0  0  0
 21 54  1  0  0  0  0
 22 55  1  6  0  0  0
 23 56  1  0  0  0  0
 24 57  1  6  0  0  0
 25 58  1  0  0  0  0
 26 59  1  6  0  0  0
 27 60  1  0  0  0  0
 27 61  1  0  0  0  0
 28 62  1  1  0  0  0
 29 63  1  0  0  0  0
 30 64  1  6  0  0  0
 31 65  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0021625

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]OC([H])([H])[C@@]1([H])O[C@@]([H])(O[C@]2([H])[C@@]([H])(O[H])[C@]([H])(N([H])[H])C([H])([H])[C@]([H])(N([H])[H])[C@@]2([H])O[C@@]2([H])O[C@]([H])(C([H])([H])N([H])[H])[C@@]([H])(O[H])[C@]([H])(O[H])[C@@]2([H])N([H])[H])[C@]([H])(O[H])[C@]1([H])O[H]

> <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/t4-,5+,6-,7-,8-,9+,10-,11-,12-,13-,14-,15-,16-,17+/m1/s1

> <INCHI_KEY>
NSKGQURZWSPSBC-VVPCINPTSA-N

> <FORMULA>
C17H34N4O10

> <MOLECULAR_WEIGHT>
454.4727

> <EXACT_MASS>
454.227493328

> <JCHEM_ACCEPTOR_COUNT>
14

> <JCHEM_ATOM_COUNT>
65

> <JCHEM_AVERAGE_POLARIZABILITY>
44.1289048297829

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
10

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3S,4R,5R,6R)-5-amino-2-(aminomethyl)-6-{[(1R,2R,3S,4R,6S)-4,6-diamino-2-{[(2S,3R,4S,5R)-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>
12.97346923745469

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.192961064467939

> <JCHEM_PKA_STRONGEST_BASIC>
9.669054121110559

> <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

$$$$

     RDKit          3D

 65 67  0  0  0  0  0  0  0  0999 V2000
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    0.8475    1.4919    2.4576 C   0  0  1  0  0  0  0  0  0  0  0  0
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    0.1038    2.6552    3.0656 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3360    2.7146    2.7573 C   0  0  1  0  0  0  0  0  0  0  0  0
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    1.6194   -0.0342   -2.0404 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.4166    0.1693   -2.7528 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.7782   -1.5434   -1.8059 C   0  0  1  0  0  0  0  0  0  0  0  0
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    3.4230   -3.0477   -1.1085 O   0  0  0  0  0  0  0  0  0  0  0  0
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    1.8597    1.8284   -1.0538 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6032    2.4346    0.6038 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5294    0.5610    2.9720 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5957    1.2729    3.5584 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5113    2.7198    2.7118 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6249    3.5886    2.7996 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2194    2.5480    4.1790 H   0  0  0  0  0  0  0  0  0  0  0  0
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    2.4632    0.1977   -2.7601 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1232    1.0152   -2.5603 H   0  0  0  0  0  0  0  0  0  0  0  0
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    1.1098   -1.9151   -1.0248 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4145   -2.2571   -3.5562 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8692   -1.3384   -2.1929 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3789   -3.3219   -1.1154 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
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 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  1
  5 37  1  6
  7 38  1  6
  8 39  1  1
  9 40  1  0
  9 41  1  0
 10 42  1  0
 10 43  1  0
 11 44  1  1
 12 45  1  0
 12 46  1  0
 13 47  1  6
 14 48  1  0
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 17 50  1  1
 19 51  1  1
 20 52  1  0
 20 53  1  0
 21 54  1  0
 22 55  1  6
 23 56  1  0
 24 57  1  6
 25 58  1  0
 26 59  1  6
 27 60  1  0
 27 61  1  0
 28 62  1  1
 29 63  1  0
 30 64  1  6
 31 65  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  N   UNK     0       4.804  -0.443   1.820  0.00  0.00           N+0
HETATM    2  C   UNK     0       4.732  -1.095   0.524  0.00  0.00           C+0
HETATM    3  C   UNK     0       3.422  -0.833  -0.167  0.00  0.00           C+0
HETATM    4  O   UNK     0       3.175   0.487  -0.404  0.00  0.00           O+0
HETATM    5  C   UNK     0       1.833   0.735  -0.797  0.00  0.00           C+0
HETATM    6  O   UNK     0       1.098   0.435   0.296  0.00  0.00           O+0
HETATM    7  C   UNK     0       0.481   1.402   0.989  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.848   1.492   2.458  0.00  0.00           C+0
HETATM    9  N   UNK     0       2.245   1.723   2.678  0.00  0.00           N+0
HETATM   10  C   UNK     0       0.104   2.655   3.066  0.00  0.00           C+0
HETATM   11  C   UNK     0      -1.336   2.715   2.757  0.00  0.00           C+0
HETATM   12  N   UNK     0      -1.796   4.090   3.009  0.00  0.00           N+0
HETATM   13  C   UNK     0      -1.693   2.424   1.322  0.00  0.00           C+0
HETATM   14  O   UNK     0      -3.062   2.352   1.213  0.00  0.00           O+0
HETATM   15  C   UNK     0      -1.002   1.095   0.975  0.00  0.00           C+0
HETATM   16  O   UNK     0      -1.504   0.673  -0.214  0.00  0.00           O+0
HETATM   17  C   UNK     0      -2.240  -0.498  -0.163  0.00  0.00           C+0
HETATM   18  O   UNK     0      -1.589  -1.443  -0.939  0.00  0.00           O+0
HETATM   19  C   UNK     0      -2.489  -2.367  -1.391  0.00  0.00           C+0
HETATM   20  C   UNK     0      -2.318  -2.551  -2.905  0.00  0.00           C+0
HETATM   21  O   UNK     0      -3.248  -3.494  -3.325  0.00  0.00           O+0
HETATM   22  C   UNK     0      -3.873  -1.861  -1.168  0.00  0.00           C+0
HETATM   23  O   UNK     0      -4.549  -2.555  -0.165  0.00  0.00           O+0
HETATM   24  C   UNK     0      -3.604  -0.414  -0.732  0.00  0.00           C+0
HETATM   25  O   UNK     0      -4.601  -0.144   0.227  0.00  0.00           O+0
HETATM   26  C   UNK     0       1.619  -0.034  -2.040  0.00  0.00           C+0
HETATM   27  N   UNK     0       0.417   0.169  -2.753  0.00  0.00           N+0
HETATM   28  C   UNK     0       1.778  -1.543  -1.806  0.00  0.00           C+0
HETATM   29  O   UNK     0       1.567  -2.149  -3.044  0.00  0.00           O+0
HETATM   30  C   UNK     0       3.225  -1.718  -1.375  0.00  0.00           C+0
HETATM   31  O   UNK     0       3.423  -3.048  -1.109  0.00  0.00           O+0
HETATM   32  H   UNK     0       3.938  -0.704   2.330  0.00  0.00           H+0
HETATM   33  H   UNK     0       4.954   0.579   1.744  0.00  0.00           H+0
HETATM   34  H   UNK     0       5.602  -0.712  -0.059  0.00  0.00           H+0
HETATM   35  H   UNK     0       4.894  -2.176   0.714  0.00  0.00           H+0
HETATM   36  H   UNK     0       2.624  -1.160   0.567  0.00  0.00           H+0
HETATM   37  H   UNK     0       1.860   1.828  -1.054  0.00  0.00           H+0
HETATM   38  H   UNK     0       0.603   2.435   0.604  0.00  0.00           H+0
HETATM   39  H   UNK     0       0.529   0.561   2.972  0.00  0.00           H+0
HETATM   40  H   UNK     0       2.596   1.273   3.558  0.00  0.00           H+0
HETATM   41  H   UNK     0       2.511   2.720   2.712  0.00  0.00           H+0
HETATM   42  H   UNK     0       0.625   3.589   2.800  0.00  0.00           H+0
HETATM   43  H   UNK     0       0.219   2.548   4.179  0.00  0.00           H+0
HETATM   44  H   UNK     0      -1.982   2.069   3.389  0.00  0.00           H+0
HETATM   45  H   UNK     0      -1.344   4.478   3.868  0.00  0.00           H+0
HETATM   46  H   UNK     0      -1.548   4.626   2.144  0.00  0.00           H+0
HETATM   47  H   UNK     0      -1.234   3.177   0.633  0.00  0.00           H+0
HETATM   48  H   UNK     0      -3.357   2.468   0.267  0.00  0.00           H+0
HETATM   49  H   UNK     0      -1.242   0.441   1.839  0.00  0.00           H+0
HETATM   50  H   UNK     0      -2.296  -0.903   0.869  0.00  0.00           H+0
HETATM   51  H   UNK     0      -2.392  -3.364  -0.914  0.00  0.00           H+0
HETATM   52  H   UNK     0      -2.616  -1.577  -3.393  0.00  0.00           H+0
HETATM   53  H   UNK     0      -1.285  -2.792  -3.176  0.00  0.00           H+0
HETATM   54  H   UNK     0      -4.065  -3.091  -3.696  0.00  0.00           H+0
HETATM   55  H   UNK     0      -4.524  -1.887  -2.062  0.00  0.00           H+0
HETATM   56  H   UNK     0      -3.880  -2.878   0.494  0.00  0.00           H+0
HETATM   57  H   UNK     0      -3.705   0.200  -1.630  0.00  0.00           H+0
HETATM   58  H   UNK     0      -5.391   0.274  -0.235  0.00  0.00           H+0
HETATM   59  H   UNK     0       2.463   0.198  -2.760  0.00  0.00           H+0
HETATM   60  H   UNK     0      -0.123   1.015  -2.560  0.00  0.00           H+0
HETATM   61  H   UNK     0      -0.075  -0.659  -3.090  0.00  0.00           H+0
HETATM   62  H   UNK     0       1.110  -1.915  -1.025  0.00  0.00           H+0
HETATM   63  H   UNK     0       2.414  -2.257  -3.556  0.00  0.00           H+0
HETATM   64  H   UNK     0       3.869  -1.338  -2.193  0.00  0.00           H+0
HETATM   65  H   UNK     0       4.379  -3.322  -1.115  0.00  0.00           H+0
CONECT    1    2   32   33                                                  
CONECT    2    1    3   34   35                                             
CONECT    3    2    4   30   36                                             
CONECT    4    3    5                                                       
CONECT    5    4    6   26   37                                             
CONECT    6    5    7                                                       
CONECT    7    6    8   15   38                                             
CONECT    8    7    9   10   39                                             
CONECT    9    8   40   41                                                  
CONECT   10    8   11   42   43                                             
CONECT   11   10   12   13   44                                             
CONECT   12   11   45   46                                                  
CONECT   13   11   14   15   47                                             
CONECT   14   13   48                                                       
CONECT   15   13   16    7   49                                             
CONECT   16   15   17                                                       
CONECT   17   16   18   24   50                                             
CONECT   18   17   19                                                       
CONECT   19   18   20   22   51                                             
CONECT   20   19   21   52   53                                             
CONECT   21   20   54                                                       
CONECT   22   19   23   24   55                                             
CONECT   23   22   56                                                       
CONECT   24   22   25   17   57                                             
CONECT   25   24   58                                                       
CONECT   26    5   27   28   59                                             
CONECT   27   26   60   61                                                  
CONECT   28   26   29   30   62                                             
CONECT   29   28   63                                                       
CONECT   30   28   31    3   64                                             
CONECT   31   30   65                                                       
CONECT   32    1                                                            
CONECT   33    1                                                            
CONECT   34    2                                                            
CONECT   35    2                                                            
CONECT   36    3                                                            
CONECT   37    5                                                            
CONECT   38    7                                                            
CONECT   39    8                                                            
CONECT   40    9                                                            
CONECT   41    9                                                            
CONECT   42   10                                                            
CONECT   43   10                                                            
CONECT   44   11                                                            
CONECT   45   12                                                            
CONECT   46   12                                                            
CONECT   47   13                                                            
CONECT   48   14                                                            
CONECT   49   15                                                            
CONECT   50   17                                                            
CONECT   51   19                                                            
CONECT   52   20                                                            
CONECT   53   20                                                            
CONECT   54   21                                                            
CONECT   55   22                                                            
CONECT   56   23                                                            
CONECT   57   24                                                            
CONECT   58   25                                                            
CONECT   59   26                                                            
CONECT   60   27                                                            
CONECT   61   27                                                            
CONECT   62   28                                                            
CONECT   63   29                                                            
CONECT   64   30                                                            
CONECT   65   31                                                            
MASTER        0    0    0    0    0    0    0    0   65    0  134    0
END

RDKit          3D

65 67  0  0  0  0  0  0  0  0999 V2000
    4.8038   -0.4425    1.8198 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.7323   -1.0951    0.5241 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4224   -0.8331   -0.1670 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.1754    0.4873   -0.4044 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8334    0.7346   -0.7970 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.0983    0.4353    0.2964 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4807    1.4021    0.9894 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.8475    1.4919    2.4576 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.2450    1.7232    2.6778 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.1038    2.6552    3.0656 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3360    2.7146    2.7573 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.7955    4.0896    3.0092 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6933    2.4235    1.3218 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.0616    2.3515    1.2130 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0022    1.0949    0.9753 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.5041    0.6732   -0.2137 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2398   -0.4977   -0.1634 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.5889   -1.4428   -0.9386 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4892   -2.3667   -1.3914 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.3179   -2.5505   -2.9054 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2478   -3.4940   -3.3247 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8729   -1.8610   -1.1682 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.5494   -2.5554   -0.1651 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6043   -0.4137   -0.7323 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.6006   -0.1442    0.2270 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6194   -0.0342   -2.0404 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.4166    0.1693   -2.7528 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.7782   -1.5434   -1.8059 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.5675   -2.1493   -3.0437 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2252   -1.7178   -1.3750 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.4230   -3.0477   -1.1085 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9382   -0.7037    2.3305 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9536    0.5790    1.7437 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6022   -0.7115   -0.0590 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8941   -2.1758    0.7135 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6238   -1.1601    0.5668 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8597    1.8284   -1.0538 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6032    2.4346    0.6038 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5294    0.5610    2.9720 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5957    1.2729    3.5584 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5113    2.7198    2.7118 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6249    3.5886    2.7996 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2194    2.5480    4.1790 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9817    2.0688    3.3895 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3444    4.4775    3.8678 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5483    4.6257    2.1437 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2336    3.1769    0.6327 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3571    2.4681    0.2672 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2425    0.4408    1.8387 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2955   -0.9028    0.8694 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3921   -3.3637   -0.9141 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6164   -1.5767   -3.3932 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2853   -2.7922   -3.1755 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0648   -3.0912   -3.6964 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5244   -1.8873   -2.0616 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8798   -2.8775    0.4940 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7048    0.2001   -1.6304 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3912    0.2737   -0.2351 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4632    0.1977   -2.7601 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1232    1.0152   -2.5603 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0748   -0.6592   -3.0903 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1098   -1.9151   -1.0248 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4145   -2.2571   -3.5562 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8692   -1.3384   -2.1929 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3789   -3.3219   -1.1154 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  1
  5 37  1  6
  7 38  1  6
  8 39  1  1
  9 40  1  0
  9 41  1  0
 10 42  1  0
 10 43  1  0
 11 44  1  1
 12 45  1  0
 12 46  1  0
 13 47  1  6
 14 48  1  0
 15 49  1  1
 17 50  1  1
 19 51  1  1
 20 52  1  0
 20 53  1  0
 21 54  1  0
 22 55  1  6
 23 56  1  0
 24 57  1  6
 25 58  1  0
 26 59  1  6
 27 60  1  0
 27 61  1  0
 28 62  1  1
 29 63  1  0
 30 64  1  6
 31 65  1  0
M  END

View in JSmol View NMR Assignments

Synonyms

Value	Source
Antibiotic SF 733	ChEBI
Ribostamicina	ChEBI
Ribostamycin a	ChEBI
Ribostamycine	ChEBI
Ribostamycinum	ChEBI
SF-733	ChEBI
Vistamycin	ChEBI
RSM	KEGG

Chemical Formula

C₁₇H₃₄N₄O₁₀

Average Mass

454.4727 Da

Monoisotopic Mass

454.22749 Da

IUPAC Name

(2R,3S,4R,5R,6R)-5-amino-2-(aminomethyl)-6-{[(1R,2R,3S,4R,6S)-4,6-diamino-2-{[(2S,3R,4S,5R)-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

NC[C@H]1O[C@H](O[C@@H]2[C@@H](N)C[C@@H](N)[C@H](O)[C@H]2O[C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O)[C@H](N)[C@@H](O)[C@@H]1O

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/t4-,5+,6-,7-,8-,9+,10-,11-,12-,13-,14-,15-,16-,17+/m1/s1

InChI Key

NSKGQURZWSPSBC-VVPCINPTSA-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 fradiae	LOTUS Database	35616633
Streptomyces ribosidificus	NPAtlas	5423362

Species Where Detected

Species Name	Source	Reference
Streptomyces ribosidificus nov. sp. SF-733	KNApSAcK Database	22123792

Chemical Taxonomy

Description

This compound belongs to the class of organic compounds known as 4,5-disubstituted 2-deoxystreptamines. These are 2-deoxystreptamine aminoglycosides that a 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

aminoglycoside antibiotic (CHEBI:45257 )
amino cyclitol glycoside (CHEBI:45257 )

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)	9.67	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	44.13 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

NPAtlas ID

NPA024702

HMDB ID

Not Available

DrugBank ID

DB03615

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

BiGG ID

Not Available

Wikipedia Link

Ribostamycin

METLIN ID

Not Available

PubChem Compound

33042

PDB ID

Not Available

ChEBI ID

45257

Good Scents ID

Not Available

References

General References

Akita E, Tsuruoka T, Ezaki N, Niida T: Studies on antibiotic SF-733. A new antibiotic. II. Chemical structure of antibiotic SF-733. J Antibiot (Tokyo). 1970 Apr;23(4):173-83. doi: 10.7164/antibiotics.23.173. [PubMed:5423362 ]
Horibe T, Nagai H, Sakakibara K, Hagiwara Y, Kikuchi M: Ribostamycin inhibits the chaperone activity of protein disulfide isomerase. Biochem Biophys Res Commun. 2001 Dec 21;289(5):967-72. doi: 10.1006/bbrc.2001.6105. [PubMed:11741285 ]
Zhou SL, Shen G, Zhong HF: Pharmacokinetics of ribostamycin in paediatric patients. Clin Pharmacokinet. 1992 Feb;22(2):144-51. doi: 10.2165/00003088-199222020-00005. [PubMed:1551291 ]
Kojima M, Inoue S, Niida T: Letter: Bioconversion of ribostamycin (SF-733). 1. Isolation and structure of 3(or 1)-N-carboxymethylribostamycin. J Antibiot (Tokyo). 1973 Apr;26(4):246-8. [PubMed:4782052 ]
Omoto S, Inouye S, Kojima M, Niida T: 13C-NMR studies on ribostamycin and its related compounds. J Antibiot (Tokyo). 1973 Dec;26(12):717-24. doi: 10.7164/antibiotics.26.717. [PubMed:4792382 ]

Showing NP-Card for SF-733 (NP0021625)

MOL for NP0021625 (SF-733)

3D MOL for NP0021625 (SF-733)

3D SDF for NP0021625 (SF-733)

3D-SDF for NP0021625 (SF-733)

PDB for NP0021625 (SF-733)

3D PDB for NP0021625 (SF-733)

SMILES for NP0021625 (SF-733)

INCHI for NP0021625 (SF-733)

Structure for NP0021625 (SF-733)

3D Structure for NP0021625 (SF-733)