MiMeDB: Showing metabocard for streptothricin D (MMDBc0056319)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2022-06-17 20:22:43 UTC

Update Date

2025-10-07 16:09:44 UTC

Metabolite ID

MMDBc0056319

Metabolite Identification

Common Name

streptothricin D

Description

Streptothricin D is a member of the aminoglycoside antibiotic class, characterized by its unique chemical structure that includes three lysine residues. This compound is notable for its role in antimicrobial activity, particularly against highly drug-resistant pathogens such as carbapenem-resistant Enterobacterales (CRE) and Acinetobacter baumannii, as evidenced by studies demonstrating its efficacy in purifying and characterizing its components (PMID:37192172 ). The chemical analysis techniques, including RP-HPLC and ESI-MS/MS, have identified streptothricin D among other antimicrobial compounds produced by various strains, highlighting its significance in the context of antibiotic resistance (PMID:34603354 ). Additionally, spectroscopic methods like FTIR and LCMS have confirmed the structural similarities of streptothricin D to other antibiotic variants, further elucidating its chemical properties with a mass-to-charge ratio (m/z) of 758.42 (PMID:33950512 ). Streptothricin D's involvement in biosynthetic pathways contributes to its potential applications in combating resistant bacterial infections, underscoring the importance of understanding its chemistry and biological interactions.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652306172222222D          

 64 66  0  0  1  0            999 V2000
   13.5557   -4.6480    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.9833   -2.5855    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.5544    1.5395    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.8412   -5.0605    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.2689   -2.1730    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.8399    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.2702   -5.0605    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.9833   -3.4105    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.2689    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.4123   -5.0605    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.5544   -0.9355    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4110    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2840    7.5380    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8386    4.0145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.1268   -4.6480    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    9.2689   -1.3480    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    7.1255    1.5395    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.8715    6.8235    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.5531    3.6020    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   10.6978   -4.6480    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.5544   -0.1105    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6965    1.5395    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2840    6.1090    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    6.1090    6.1090    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.9820    2.7770    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.2676    2.3645    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.5531    2.7770    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    6.5215    6.8235    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9820    3.6020    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.8386    1.5395    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6965    4.8395    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.9846   -4.6480    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
   12.1268   -3.8230    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    9.9833   -0.9355    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    7.1255    2.3645    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    2.1242    1.1270    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
   10.6978   -3.8230    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    9.2689    0.3020    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.1090    7.5380    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.6965    2.3645    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.0291    5.3244    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.3640    5.3244    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.6965    4.0145    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.8386    4.8395    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0465    6.8235    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.9833   -5.0605    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.8399    0.3020    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9820    1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2676    1.5395    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.3465    6.8235    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5531    1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2676    4.0145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8386    2.3645    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.1268   -5.4730    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.5544   -1.7605    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.1255    0.7145    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4590    6.1090    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8386    3.1895    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6965    6.8235    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.9295    6.0228    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9820    1.9520    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5531    1.9520    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2676    3.1895    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6965    3.1895    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  4  1  1  0  0  0  0
  5  2  1  0  0  0  0
  6  3  1  0  0  0  0
  7  1  1  0  0  0  0
  8  2  1  0  0  0  0
  9  3  1  0  0  0  0
 15  4  1  0  0  0  0
 15 10  1  0  0  0  0
 16  5  1  0  0  0  0
 16 11  1  0  0  0  0
 17  6  1  0  0  0  0
 17 12  1  0  0  0  0
 18 13  1  0  0  0  0
 19 14  1  1  0  0  0
 20 10  1  0  0  0  0
 21 11  1  0  0  0  0
 22 12  1  0  0  0  0
 23 18  1  0  0  0  0
 24 23  1  0  0  0  0
 26 25  1  0  0  0  0
 27 19  1  0  0  0  0
 27 26  1  0  0  0  0
 28 24  1  0  0  0  0
 29 25  1  0  0  0  0
 32  7  1  0  0  0  0
 15 33  1  6  0  0  0
 16 34  1  6  0  0  0
 17 35  1  6  0  0  0
 36 30  2  0  0  0  0
 37  8  1  4  0  0  0
 37 20  2  0  0  0  0
 38  9  1  4  0  0  0
 38 21  2  0  0  0  0
 39 13  1  0  0  0  0
 39 28  2  0  0  0  0
 40 22  2  0  0  0  0
 25 40  1  6  0  0  0
 41 23  1  0  0  0  0
 41 31  2  0  0  0  0
 42 24  1  0  0  0  0
 42 31  1  0  0  0  0
 29 43  1  1  0  0  0
 43 31  1  0  0  0  0
 44 14  1  0  0  0  0
 18 45  1  6  0  0  0
 46 20  1  0  0  0  0
 47 21  1  0  0  0  0
 22 48  1  4  0  0  0
 26 49  1  6  0  0  0
 50 28  1  0  0  0  0
 51 30  1  0  0  0  0
 52 19  1  0  0  0  0
 52 29  1  0  0  0  0
 27 53  1  6  0  0  0
 53 30  1  0  0  0  0
 15 54  1  6  0  0  0
 16 55  1  6  0  0  0
 17 56  1  6  0  0  0
 18 57  1  1  0  0  0
 19 58  1  6  0  0  0
 23 59  1  1  0  0  0
 24 60  1  6  0  0  0
 25 61  1  1  0  0  0
 26 62  1  1  0  0  0
 27 63  1  6  0  0  0
 29 64  1  6  0  0  0
M  CHG  5  32   1  33   1  34   1  35   1  36   1
M  END


  Mrv1652306172222222D          

 64 66  0  0  1  0            999 V2000
   13.5557   -4.6480    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.9833   -2.5855    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.5544    1.5395    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.8412   -5.0605    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.2689   -2.1730    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.8399    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.2702   -5.0605    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.9833   -3.4105    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.2689    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.4123   -5.0605    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.5544   -0.9355    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4110    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2840    7.5380    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8386    4.0145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.1268   -4.6480    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    9.2689   -1.3480    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    7.1255    1.5395    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.8715    6.8235    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.5531    3.6020    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   10.6978   -4.6480    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.5544   -0.1105    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6965    1.5395    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2840    6.1090    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    6.1090    6.1090    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.9820    2.7770    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.2676    2.3645    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.5531    2.7770    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    6.5215    6.8235    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9820    3.6020    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.8386    1.5395    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6965    4.8395    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.9846   -4.6480    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
   12.1268   -3.8230    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    9.9833   -0.9355    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    7.1255    2.3645    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    2.1242    1.1270    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
   10.6978   -3.8230    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    9.2689    0.3020    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.1090    7.5380    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.6965    2.3645    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.0291    5.3244    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.3640    5.3244    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.6965    4.0145    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.8386    4.8395    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0465    6.8235    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.9833   -5.0605    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.8399    0.3020    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9820    1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2676    1.5395    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.3465    6.8235    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5531    1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2676    4.0145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8386    2.3645    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.1268   -5.4730    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.5544   -1.7605    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.1255    0.7145    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4590    6.1090    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8386    3.1895    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6965    6.8235    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.9295    6.0228    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9820    1.9520    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5531    1.9520    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2676    3.1895    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6965    3.1895    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  4  1  1  0  0  0  0
  5  2  1  0  0  0  0
  6  3  1  0  0  0  0
  7  1  1  0  0  0  0
  8  2  1  0  0  0  0
  9  3  1  0  0  0  0
 15  4  1  0  0  0  0
 15 10  1  0  0  0  0
 16  5  1  0  0  0  0
 16 11  1  0  0  0  0
 17  6  1  0  0  0  0
 17 12  1  0  0  0  0
 18 13  1  0  0  0  0
 19 14  1  1  0  0  0
 20 10  1  0  0  0  0
 21 11  1  0  0  0  0
 22 12  1  0  0  0  0
 23 18  1  0  0  0  0
 24 23  1  0  0  0  0
 26 25  1  0  0  0  0
 27 19  1  0  0  0  0
 27 26  1  0  0  0  0
 28 24  1  0  0  0  0
 29 25  1  0  0  0  0
 32  7  1  0  0  0  0
 15 33  1  6  0  0  0
 16 34  1  6  0  0  0
 17 35  1  6  0  0  0
 36 30  2  0  0  0  0
 37  8  1  4  0  0  0
 37 20  2  0  0  0  0
 38  9  1  4  0  0  0
 38 21  2  0  0  0  0
 39 13  1  0  0  0  0
 39 28  2  0  0  0  0
 40 22  2  0  0  0  0
 25 40  1  6  0  0  0
 41 23  1  0  0  0  0
 41 31  2  0  0  0  0
 42 24  1  0  0  0  0
 42 31  1  0  0  0  0
 29 43  1  1  0  0  0
 43 31  1  0  0  0  0
 44 14  1  0  0  0  0
 18 45  1  6  0  0  0
 46 20  1  0  0  0  0
 47 21  1  0  0  0  0
 22 48  1  4  0  0  0
 26 49  1  6  0  0  0
 50 28  1  0  0  0  0
 51 30  1  0  0  0  0
 52 19  1  0  0  0  0
 52 29  1  0  0  0  0
 27 53  1  6  0  0  0
 53 30  1  0  0  0  0
 15 54  1  6  0  0  0
 16 55  1  6  0  0  0
 17 56  1  6  0  0  0
 18 57  1  1  0  0  0
 19 58  1  6  0  0  0
 23 59  1  1  0  0  0
 24 60  1  6  0  0  0
 25 61  1  1  0  0  0
 26 62  1  1  0  0  0
 27 63  1  6  0  0  0
 29 64  1  6  0  0  0
M  CHG  5  32   1  33   1  34   1  35   1  36   1
M  END
> <DATABASE_ID>
MMDBc0056319

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@]([NH3+])(CCC[NH3+])CC(O)=NCCC[C@]([H])([NH3+])CC(O)=NCCC[C@]([H])([NH3+])CC(O)=N[C@@]1([H])[C@]([H])(NC2=N[C@@]3([H])[C@]([H])(N2)C(O)=NC[C@@]3([H])O)O[C@]([H])(CO)[C@]([H])(OC(O)=[NH2+])[C@@]1([H])O

> <INCHI_IDENTIFIER>
InChI=1S/C31H58N12O10/c32-7-1-4-15(33)10-20(46)37-8-2-5-16(34)11-21(47)38-9-3-6-17(35)12-22(48)40-25-26(49)27(53-30(36)51)19(14-44)52-29(25)43-31-41-23-18(45)13-39-28(50)24(23)42-31/h15-19,23-27,29,44-45,49H,1-14,32-35H2,(H2,36,51)(H,37,46)(H,38,47)(H,39,50)(H,40,48)(H2,41,42,43)/p+5/t15-,16-,17-,18+,19+,23+,24-,25+,26-,27-,29+/m0/s1

> <INCHI_KEY>
WUJTXMVGXDQPNN-OTQKCRDJSA-S

> <FORMULA>
C31H63N12O10

> <MOLECULAR_WEIGHT>
763.916

> <EXACT_MASS>
763.476268377

> <JCHEM_ACCEPTOR_COUNT>
17

> <JCHEM_ATOM_COUNT>
116

> <JCHEM_AVERAGE_POLARIZABILITY>
81.25382704813666

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
15

> <JCHEM_FORMAL_CHARGE>
5

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-1-{[(4S)-5-{[(2R,3R,4S,5R,6R)-2-{[(3aS,7R,7aS)-4,7-dihydroxy-3H,3aH,6H,7H,7aH-imidazo[4,5-c]pyridin-2-yl]amino}-4-hydroxy-5-[hydroxy(iminiumyl)methoxy]-6-(hydroxymethyl)oxan-3-yl]-C-hydroxycarbonimidoyl}-4-azaniumylpentyl]-C-hydroxycarbonimidoyl}-5-{[(3S)-3,6-diazaniumyl-1-hydroxyhexylidene]amino}pentan-2-aminium

> <JCHEM_LOGP>
-12.750020747956725

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
5

> <JCHEM_PKA>
3.9834994379206417

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.4083735440979344

> <JCHEM_PKA_STRONGEST_BASIC>
11.023514824771294

> <JCHEM_POLAR_SURFACE_AREA>
402.3100000000002

> <JCHEM_REFRACTIVITY>
244.44330000000008

> <JCHEM_ROTATABLE_BOND_COUNT>
22

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(2S)-1-{[(4S)-5-{[(2R,3R,4S,5R,6R)-2-{[(3aS,7R,7aS)-4,7-dihydroxy-3H,3aH,6H,7H,7aH-imidazo[4,5-c]pyridin-2-yl]amino}-4-hydroxy-5-[hydroxy(iminio)methoxy]-6-(hydroxymethyl)oxan-3-yl]-C-hydroxycarbonimidoyl}-4-ammoniopentyl]-C-hydroxycarbonimidoyl}-5-{[(3S)-3,6-diammonio-1-hydroxyhexylidene]amino}pentan-2-aminium

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 17-JUN-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-JUN-22         0                                  
HETATM    1  C   UNK     0      25.304  -8.676   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      18.636  -4.826   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      15.968   2.874   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      23.970  -9.446   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      17.302  -4.056   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      14.635   2.104   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      26.638  -9.446   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      18.636  -6.366   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      17.302   2.104   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      21.303  -9.446   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      15.968  -1.746   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      11.967   2.104   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       9.863  14.071   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       5.299   7.494   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      22.637  -8.676   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      17.302  -2.516   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      13.301   2.874   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       9.093  12.737   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       6.632   6.724   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      19.969  -8.676   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      15.968  -0.206   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      10.633   2.874   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       9.863  11.403   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      11.403  11.403   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       9.300   5.184   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       7.966   4.414   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       6.632   5.184   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      12.173  12.737   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       9.300   6.724   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       5.299   2.874   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      10.633   9.034   0.000  0.00  0.00           C+0
HETATM   32  N   UNK     0      27.971  -8.676   0.000  0.00  0.00           N+1
HETATM   33  N   UNK     0      22.637  -7.136   0.000  0.00  0.00           N+1
HETATM   34  N   UNK     0      18.636  -1.746   0.000  0.00  0.00           N+1
HETATM   35  N   UNK     0      13.301   4.414   0.000  0.00  0.00           N+1
HETATM   36  N   UNK     0       3.965   2.104   0.000  0.00  0.00           N+1
HETATM   37  N   UNK     0      19.969  -7.136   0.000  0.00  0.00           N+0
HETATM   38  N   UNK     0      17.302   0.564   0.000  0.00  0.00           N+0
HETATM   39  N   UNK     0      11.403  14.071   0.000  0.00  0.00           N+0
HETATM   40  N   UNK     0      10.633   4.414   0.000  0.00  0.00           N+0
HETATM   41  N   UNK     0       9.388   9.939   0.000  0.00  0.00           N+0
HETATM   42  N   UNK     0      11.879   9.939   0.000  0.00  0.00           N+0
HETATM   43  N   UNK     0      10.633   7.494   0.000  0.00  0.00           N+0
HETATM   44  O   UNK     0       5.299   9.034   0.000  0.00  0.00           O+0
HETATM   45  O   UNK     0       7.553  12.737   0.000  0.00  0.00           O+0
HETATM   46  O   UNK     0      18.636  -9.446   0.000  0.00  0.00           O+0
HETATM   47  O   UNK     0      14.635   0.564   0.000  0.00  0.00           O+0
HETATM   48  O   UNK     0       9.300   2.104   0.000  0.00  0.00           O+0
HETATM   49  O   UNK     0       7.966   2.874   0.000  0.00  0.00           O+0
HETATM   50  O   UNK     0      13.713  12.737   0.000  0.00  0.00           O+0
HETATM   51  O   UNK     0       6.632   2.104   0.000  0.00  0.00           O+0
HETATM   52  O   UNK     0       7.966   7.494   0.000  0.00  0.00           O+0
HETATM   53  O   UNK     0       5.299   4.414   0.000  0.00  0.00           O+0
HETATM   54  H   UNK     0      22.637 -10.216   0.000  0.00  0.00           H+0
HETATM   55  H   UNK     0      15.968  -3.286   0.000  0.00  0.00           H+0
HETATM   56  H   UNK     0      13.301   1.334   0.000  0.00  0.00           H+0
HETATM   57  H   UNK     0       8.323  11.403   0.000  0.00  0.00           H+0
HETATM   58  H   UNK     0       5.299   5.954   0.000  0.00  0.00           H+0
HETATM   59  H   UNK     0      10.633  12.737   0.000  0.00  0.00           H+0
HETATM   60  H   UNK     0      12.935  11.243   0.000  0.00  0.00           H+0
HETATM   61  H   UNK     0       9.300   3.644   0.000  0.00  0.00           H+0
HETATM   62  H   UNK     0       6.632   3.644   0.000  0.00  0.00           H+0
HETATM   63  H   UNK     0       7.966   5.954   0.000  0.00  0.00           H+0
HETATM   64  H   UNK     0      10.633   5.954   0.000  0.00  0.00           H+0
CONECT    1    4    7                                                       
CONECT    2    5    8                                                       
CONECT    3    6    9                                                       
CONECT    4    1   15                                                       
CONECT    5    2   16                                                       
CONECT    6    3   17                                                       
CONECT    7    1   32                                                       
CONECT    8    2   37                                                       
CONECT    9    3   38                                                       
CONECT   10   15   20                                                       
CONECT   11   16   21                                                       
CONECT   12   17   22                                                       
CONECT   13   18   39                                                       
CONECT   14   19   44                                                       
CONECT   15    4   10   33   54                                             
CONECT   16    5   11   34   55                                             
CONECT   17    6   12   35   56                                             
CONECT   18   13   23   45   57                                             
CONECT   19   14   27   52   58                                             
CONECT   20   10   37   46                                                  
CONECT   21   11   38   47                                                  
CONECT   22   12   40   48                                                  
CONECT   23   18   24   41   59                                             
CONECT   24   23   28   42   60                                             
CONECT   25   26   29   40   61                                             
CONECT   26   25   27   49   62                                             
CONECT   27   19   26   53   63                                             
CONECT   28   24   39   50                                                  
CONECT   29   25   43   52   64                                             
CONECT   30   36   51   53                                                  
CONECT   31   41   42   43                                                  
CONECT   32    7                                                            
CONECT   33   15                                                            
CONECT   34   16                                                            
CONECT   35   17                                                            
CONECT   36   30                                                            
CONECT   37    8   20                                                       
CONECT   38    9   21                                                       
CONECT   39   13   28                                                       
CONECT   40   22   25                                                       
CONECT   41   23   31                                                       
CONECT   42   24   31                                                       
CONECT   43   29   31                                                       
CONECT   44   14                                                            
CONECT   45   18                                                            
CONECT   46   20                                                            
CONECT   47   21                                                            
CONECT   48   22                                                            
CONECT   49   26                                                            
CONECT   50   28                                                            
CONECT   51   30                                                            
CONECT   52   19   29                                                       
CONECT   53   27   30                                                       
CONECT   54   15                                                            
CONECT   55   16                                                            
CONECT   56   17                                                            
CONECT   57   18                                                            
CONECT   58   19                                                            
CONECT   59   23                                                            
CONECT   60   24                                                            
CONECT   61   25                                                            
CONECT   62   26                                                            
CONECT   63   27                                                            
CONECT   64   29                                                            
MASTER        0    0    0    0    0    0    0    0   64    0  132    0
END

Synonyms

Value	Source
Antibiotic OP 2C penta-cation	ChEBI
Antibiotic OP 2C pentacation	ChEBI
Antibiotic OP 2C(5+)	ChEBI
Racemomycin b penta-cation	ChEBI
Racemomycin b pentacation	ChEBI
Racemomycin b(5+)	ChEBI
Streptothricin D	ChEBI
Streptothricin D penta-cation	ChEBI
Streptothricin D pentacation	ChEBI

Molecular Formula

C₃₁H₆₃N₁₂O₁₀

Average Mass

763.916

Monoisotopic Mass

763.476268377

IUPAC Name

(2S)-1-{[(4S)-5-{[(2R,3R,4S,5R,6R)-2-{[(3aS,7R,7aS)-4,7-dihydroxy-3H,3aH,6H,7H,7aH-imidazo[4,5-c]pyridin-2-yl]amino}-4-hydroxy-5-[hydroxy(iminiumyl)methoxy]-6-(hydroxymethyl)oxan-3-yl]-C-hydroxycarbonimidoyl}-4-azaniumylpentyl]-C-hydroxycarbonimidoyl}-5-{[(3S)-3,6-diazaniumyl-1-hydroxyhexylidene]amino}pentan-2-aminium

Traditional Name

(2S)-1-{[(4S)-5-{[(2R,3R,4S,5R,6R)-2-{[(3aS,7R,7aS)-4,7-dihydroxy-3H,3aH,6H,7H,7aH-imidazo[4,5-c]pyridin-2-yl]amino}-4-hydroxy-5-[hydroxy(iminio)methoxy]-6-(hydroxymethyl)oxan-3-yl]-C-hydroxycarbonimidoyl}-4-ammoniopentyl]-C-hydroxycarbonimidoyl}-5-{[(3S)-3,6-diammonio-1-hydroxyhexylidene]amino}pentan-2-aminium

CAS Registry Number

Not Available

SMILES

[H][C@]([NH3+])(CCC[NH3+])CC(O)=NCCC[C@]([H])([NH3+])CC(O)=NCCC[C@]([H])([NH3+])CC(O)=N[C@@]1([H])[C@]([H])(NC2=N[C@@]3([H])[C@]([H])(N2)C(O)=NC[C@@]3([H])O)O[C@]([H])(CO)[C@]([H])(OC(O)=[NH2+])[C@@]1([H])O

InChI Identifier

InChI=1S/C31H58N12O10/c32-7-1-4-15(33)10-20(46)37-8-2-5-16(34)11-21(47)38-9-3-6-17(35)12-22(48)40-25-26(49)27(53-30(36)51)19(14-44)52-29(25)43-31-41-23-18(45)13-39-28(50)24(23)42-31/h15-19,23-27,29,44-45,49H,1-14,32-35H2,(H2,36,51)(H,37,46)(H,38,47)(H,39,50)(H,40,48)(H2,41,42,43)/p+5/t15-,16-,17-,18+,19+,23+,24-,25+,26-,27-,29+/m0/s1

InChI Key

WUJTXMVGXDQPNN-OTQKCRDJSA-S

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as glycosylamines. Glycosylamines are compounds consisting of an amine with a beta-N-glycosidic bond to a carbohydrate, thus forming a cyclic hemiaminal ether bond (alpha-amino ether).

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Glycosylamines

Alternative Parents

Substituents

Hexose monosaccharide
Beta amino acid or derivatives
N-glycosyl compound
Alpha-amino acid or derivatives
Delta-lactam
Piperidinone
Fatty amide
Fatty acyl
Monosaccharide
N-acyl-amine
Oxane
Piperidine
Imidazolidine
Carbamic acid ester
Secondary alcohol
Secondary carboxylic acid amide
Amino acid or derivatives
Carboxamide group
Carbonic acid derivative
Lactam
Guanidine
Carboximidamide
Carboxylic acid derivative
Organoheterocyclic compound
Oxacycle
Azacycle
Primary alcohol
Primary amine
Alcohol
Primary aliphatic amine
Hydrocarbon derivative
Organic oxide
Organonitrogen compound
Carbonyl group
Organopnictogen compound
Amine
Organic nitrogen compound
Organic cation
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic compounds

External Descriptors

primary aliphatic ammonium ion (CHEBI:60829 )
guanidinium ion (CHEBI:60829 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
logP	-13	ChemAxon
pKa (Strongest Acidic)	3.41	ChemAxon
pKa (Strongest Basic)	11.02	ChemAxon
Physiological Charge	5	ChemAxon
Hydrogen Acceptor Count	17	ChemAxon
Hydrogen Donor Count	15	ChemAxon
Polar Surface Area	402.31 Å²	ChemAxon
Rotatable Bond Count	22	ChemAxon
Refractivity	244.44 m³·mol⁻¹	ChemAxon
Polarizability	81.25 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

Spectra

Spectrum Type	Description	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)	2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)	2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)	2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)	2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)	2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)	2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)	2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)	2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)	2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)	2022-08-21	View Spectrum

Chromatographic Retention Times and Retention Indices

Retention Times

Not Available

Retention Indices

Not Available

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species

Human Pathways

Pathways

Name	SMPDB/PathBank

Microbial Pathways

Pathways

Not Available

Metabolic Reactions

Reactions

This table shows at most 20 reactions. For the full list of associated reactions:

See All Associated Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Bacteria/Eubacteria	Firmicutes	1	Human feces

Exposure Sources

Other Exposures

Source Type	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

26332018

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

49852377

PDB ID

Not Available

ChEBI ID

60829

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

Not Available

General References

Bansal P, Morgat A, Axelsen KB, Muthukrishnan V, Coudert E, Aimo L, Hyka-Nouspikel N, Gasteiger E, Kerhornou A, Neto TB, Pozzato M, Blatter MC, Ignatchenko A, Redaschi N, Bridge A: Rhea, the reaction knowledgebase in 2022. Nucleic Acids Res. 2022 Jan 7;50(D1):D693-D700. doi: 10.1093/nar/gkab1016. [PubMed:34755880 ]

Showing metabocard for streptothricin D (MMDBc0056319)

MOL for #<Metabolite:0x00005615374d33f0>

3D MOL for #<Metabolite:0x00005615374d33f0>

3D SDF for #<Metabolite:0x00005615374d33f0>

3D-SDF for #<Metabolite:0x00005615374d33f0>

PDB for #<Metabolite:0x00005615374d33f0>

3D PDB for #<Metabolite:0x00005615374d33f0>

SMILES for #<Metabolite:0x00005615374d33f0>

INCHI for #<Metabolite:0x00005615374d33f0>

Structure for #<Metabolite:0x00005615374d33f0>

3D Structure for #<Metabolite:0x00005615374d33f0>