data_84D
#

_chem_comp.id                                   84D
_chem_comp.name                                 Dibekacin
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C18 H37 N5 O8"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        "(1R,2S,3S,4R,6S)-4,6-diamino-3-[(3-amino-3-deoxy-alpha-D-glucopyranosyl)oxy]-2-hydroxycyclohexyl 2,6-diamino-2,3,4,6-tetradeoxy-alpha-D-erythro-hexopyranoside"
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2016-12-23
_chem_comp.pdbx_modified_date                   2021-03-13
_chem_comp.pdbx_ambiguous_flag                  N
_chem_comp.pdbx_release_status                  REL
_chem_comp.pdbx_replaced_by                     ?
_chem_comp.pdbx_replaces                        ?
_chem_comp.formula_weight                       451.515
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    84D
_chem_comp.pdbx_model_coordinates_details       ?
_chem_comp.pdbx_model_coordinates_missing_flag  N
_chem_comp.pdbx_ideal_coordinates_details       Corina
_chem_comp.pdbx_ideal_coordinates_missing_flag  N
_chem_comp.pdbx_model_coordinates_db_code       5U7Y
_chem_comp.pdbx_subcomponent_list               ?
_chem_comp.pdbx_processing_site                 RCSB
#   #
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.alt_atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.charge
_chem_comp_atom.pdbx_align
_chem_comp_atom.pdbx_aromatic_flag
_chem_comp_atom.pdbx_leaving_atom_flag
_chem_comp_atom.pdbx_stereo_config
_chem_comp_atom.model_Cartn_x
_chem_comp_atom.model_Cartn_y
_chem_comp_atom.model_Cartn_z
_chem_comp_atom.pdbx_model_Cartn_x_ideal
_chem_comp_atom.pdbx_model_Cartn_y_ideal
_chem_comp_atom.pdbx_model_Cartn_z_ideal
_chem_comp_atom.pdbx_component_atom_id
_chem_comp_atom.pdbx_component_comp_id
_chem_comp_atom.pdbx_ordinal
84D  C1   C1   C  0  1  N  N  N  30.997  -3.229  64.129   4.963  -1.356   1.736  C1   84D   1  
84D  C2   C2   C  0  1  N  N  R  31.359  -1.756  63.998   3.632  -2.055   1.445  C2   84D   2  
84D  C3   C3   C  0  1  N  N  R  32.315  -1.663  62.822   2.824  -1.207   0.460  C3   84D   3  
84D  O3   O1   O  0  1  N  N  N  37.067   0.183  61.426  -2.202   0.919   0.567  O3   84D   4  
84D  C4   C4   C  0  1  N  N  S  31.461  -3.585  61.683   4.819  -0.317  -0.529  C4   84D   5  
84D  O4   O2   O  0  1  N  N  N  35.781   1.829  60.542  -3.010   0.084  -1.457  O4   84D   6  
84D  C5   C5   C  0  1  N  N  N  30.849  -3.815  60.318   5.532  -0.137  -1.871  C5   84D   7  
84D  O5   O3   O  0  1  N  N  N  33.971   3.274  61.315  -1.418  -1.925  -2.727  O5   84D   8  
84D  C6   C6   C  0  1  N  N  R  34.663  -2.444  62.428   1.546   0.818   0.343  C6   84D   9  
84D  O6   O4   O  0  1  N  N  N  38.072   4.522  61.497  -4.297  -2.962   0.121  O6   84D  10  
84D  C7   C7   C  0  1  N  N  S  35.609  -3.369  63.201   1.794   2.311   0.569  C7   84D  11  
84D  O7   O5   O  0  1  N  N  N  38.739   0.269  59.047  -4.791   1.697   1.310  O7   84D  12  
84D  C8   C8   C  0  1  N  N  N  37.017  -3.337  62.606   0.744   3.123  -0.191  C8   84D  13  
84D  C9   C9   C  0  1  N  N  R  37.556  -1.913  62.507  -0.651   2.755   0.318  C9   84D  14  
84D  C10  C10  C  0  1  N  N  S  36.580  -1.137  61.651  -0.899   1.262   0.092  C10  84D  15  
84D  C11  C11  C  0  1  N  N  S  35.236  -1.033  62.339   0.151   0.450   0.852  C11  84D  16  
84D  C12  C12  C  0  1  N  N  S  36.675   0.781  60.222  -3.231   1.039  -0.417  C12  84D  17  
84D  C13  C13  C  0  1  N  N  R  37.897   1.331  59.502  -4.593   0.779   0.232  C13  84D  18  
84D  C14  C14  C  0  1  N  N  S  38.562   2.323  60.469  -4.628  -0.655   0.768  C14  84D  19  
84D  N1   N1   N  0  1  N  N  N  39.894   2.786  60.067  -5.957  -0.938   1.326  N1   84D  20  
84D  C15  C15  C  0  1  N  N  S  37.567   3.478  60.668  -4.338  -1.625  -0.381  C15  84D  21  
84D  C16  C16  C  0  1  N  N  R  36.342   2.881  61.352  -2.986  -1.272  -1.007  C16  84D  22  
84D  C17  C17  C  0  1  N  N  N  35.239   3.887  61.548  -2.716  -2.199  -2.194  C17  84D  23  
84D  N2   N2   N  0  1  N  N  N  38.909  -1.854  61.937  -1.660   3.535  -0.411  N2   84D  24  
84D  N3   N3   N  0  1  N  N  N  35.102  -4.747  63.280   3.134   2.664   0.080  N3   84D  25  
84D  O2   O6   O  0  1  N  N  N  34.419  -0.100  61.635  -0.080  -0.944   0.641  O2   84D  26  
84D  O1   O7   O  0  1  N  N  N  33.432  -2.467  63.170   2.528   0.060   1.052  O1   84D  27  
84D  N4   N4   N  0  1  N  N  N  32.004  -1.289  65.233   2.876  -2.210   2.695  N4   84D  28  
84D  O    O8   O  0  1  N  N  N  31.685  -2.167  61.667   3.585  -1.009  -0.733  O    84D  29  
84D  C    C18  C  0  1  N  N  N  30.581  -3.958  62.849   5.710  -1.130   0.418  C    84D  30  
84D  N    N5   N  0  1  N  N  N  31.811  -3.783  59.210   4.733   0.741  -2.736  N    84D  31  
84D  H1   H1   H  0  1  N  N  N  30.161  -3.303  64.840   4.774  -0.396   2.217  H1   84D  32  
84D  H2   H2   H  0  1  N  N  N  31.874  -3.751  64.538   5.567  -1.980   2.395  H2   84D  33  
84D  H3   H3   H  0  1  N  N  N  30.453  -1.167  63.790   3.823  -3.036   1.011  H3   84D  34  
84D  H4   H4   H  0  1  N  N  N  32.618  -0.615  62.680   1.893  -1.720   0.216  H4   84D  35  
84D  H5   H5   H  0  1  N  N  N  32.416  -4.127  61.753   4.619   0.660  -0.090  H5   84D  36  
84D  H6   H6   H  0  1  N  N  N  30.096  -3.033  60.142   6.512   0.311  -1.705  H6   84D  37  
84D  H7   H7   H  0  1  N  N  N  30.361  -4.801  60.321   5.653  -1.108  -2.351  H7   84D  38  
84D  H8   H8   H  0  1  N  N  N  33.281   3.915  61.441  -1.179  -2.477  -3.484  H8   84D  39  
84D  H9   H9   H  0  1  N  N  N  34.512  -2.842  61.414   1.615   0.596  -0.722  H9   84D  40  
84D  H10  H10  H  0  1  N  N  N  37.416   5.204  61.583  -4.117  -3.631  -0.554  H10  84D  41  
84D  H11  H11  H  0  1  N  N  N  35.681  -2.976  64.226   1.726   2.534   1.634  H11  84D  42  
84D  H12  H12  H  0  1  N  N  N  39.495   0.633  58.601  -4.775   2.626   1.043  H12  84D  43  
84D  H13  H13  H  0  1  N  N  N  36.988  -3.778  61.599   0.920   4.187  -0.030  H13  84D  44  
84D  H14  H14  H  0  1  N  N  N  37.688  -3.928  63.246   0.812   2.901  -1.256  H14  84D  45  
84D  H15  H15  H  0  1  N  N  N  37.568  -1.473  63.515  -0.720   2.978   1.383  H15  84D  46  
84D  H16  H16  H  0  1  N  N  N  36.450  -1.661  60.693  -0.831   1.040  -0.973  H16  84D  47  
84D  H17  H17  H  0  1  N  N  N  35.403  -0.669  63.363   0.083   0.673   1.917  H17  84D  48  
84D  H18  H18  H  0  1  N  N  N  36.181   0.045  59.570  -3.215   2.045  -0.838  H18  84D  49  
84D  H19  H19  H  0  1  N  N  N  37.543   1.903  58.632  -5.381   0.912  -0.509  H19  84D  50  
84D  H20  H20  H  0  1  N  N  N  38.660   1.812  61.438  -3.873  -0.773   1.545  H20  84D  51  
84D  H21  H21  H  0  1  N  N  N  40.246   3.424  60.752  -6.175  -0.306   2.082  H21  84D  52  
84D  H22  H22  H  0  1  N  N  N  40.511   2.002  59.993  -6.666  -0.902   0.609  H22  84D  53  
84D  H24  H24  H  0  1  N  N  N  37.275   3.873  59.684  -5.121  -1.542  -1.135  H24  84D  54  
84D  H25  H25  H  0  1  N  N  N  36.642   2.481  62.332  -2.198  -1.395  -0.264  H25  84D  55  
84D  H26  H26  H  0  1  N  N  N  35.376   4.720  60.842  -3.468  -2.030  -2.965  H26  84D  56  
84D  H27  H27  H  0  1  N  N  N  35.274   4.270  62.579  -2.761  -3.236  -1.863  H27  84D  57  
84D  H28  H28  H  0  1  N  N  N  39.538  -2.372  62.516  -1.518   4.525  -0.278  H28  84D  58  
84D  H29  H29  H  0  1  N  N  N  38.901  -2.248  61.018  -1.660   3.299  -1.392  H29  84D  59  
84D  H31  H31  H  0  1  N  N  N  35.750  -5.312  63.791   3.280   3.662   0.117  H31  84D  60  
84D  H32  H32  H  0  1  N  N  N  34.217  -4.750  63.746   3.848   2.175   0.598  H32  84D  61  
84D  H34  H34  H  0  1  N  N  N  33.574  -0.032  62.064  -0.903  -1.270   1.031  H34  84D  62  
84D  H35  H35  H  0  1  N  N  N  31.358  -1.358  65.994   3.391  -2.763   3.363  H35  84D  63  
84D  H36  H36  H  0  1  N  N  N  32.806  -1.854  65.424   2.629  -1.312   3.082  H36  84D  64  
84D  H38  H38  H  0  1  N  N  N  29.541  -3.692  62.610   6.633  -0.583   0.609  H38  84D  65  
84D  H39  H39  H  0  1  N  N  N  30.653  -5.043  63.017   5.943  -2.092  -0.038  H39  84D  66  
84D  H40  H40  H  0  1  N  N  N  31.332  -3.942  58.347   4.552   1.626  -2.285  H40  84D  67  
84D  H41  H41  H  0  1  N  N  N  32.258  -2.889  59.183   5.182   0.876  -3.629  H41  84D  68  
#   #
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_aromatic_flag
_chem_comp_bond.pdbx_stereo_config
_chem_comp_bond.pdbx_ordinal
84D  O7   C13  SING  N  N   1  
84D  N    C5   SING  N  N   2  
84D  C13  C12  SING  N  N   3  
84D  C13  C14  SING  N  N   4  
84D  N1   C14  SING  N  N   5  
84D  C12  O4   SING  N  N   6  
84D  C12  O3   SING  N  N   7  
84D  C5   C4   SING  N  N   8  
84D  C14  C15  SING  N  N   9  
84D  O4   C16  SING  N  N  10  
84D  C15  C16  SING  N  N  11  
84D  C15  O6   SING  N  N  12  
84D  O5   C17  SING  N  N  13  
84D  C16  C17  SING  N  N  14  
84D  O3   C10  SING  N  N  15  
84D  O2   C11  SING  N  N  16  
84D  C10  C11  SING  N  N  17  
84D  C10  C9   SING  N  N  18  
84D  O    C4   SING  N  N  19  
84D  O    C3   SING  N  N  20  
84D  C4   C    SING  N  N  21  
84D  N2   C9   SING  N  N  22  
84D  C11  C6   SING  N  N  23  
84D  C6   O1   SING  N  N  24  
84D  C6   C7   SING  N  N  25  
84D  C9   C8   SING  N  N  26  
84D  C8   C7   SING  N  N  27  
84D  C3   O1   SING  N  N  28  
84D  C3   C2   SING  N  N  29  
84D  C    C1   SING  N  N  30  
84D  C7   N3   SING  N  N  31  
84D  C2   C1   SING  N  N  32  
84D  C2   N4   SING  N  N  33  
84D  C1   H1   SING  N  N  34  
84D  C1   H2   SING  N  N  35  
84D  C2   H3   SING  N  N  36  
84D  C3   H4   SING  N  N  37  
84D  C4   H5   SING  N  N  38  
84D  C5   H6   SING  N  N  39  
84D  C5   H7   SING  N  N  40  
84D  O5   H8   SING  N  N  41  
84D  C6   H9   SING  N  N  42  
84D  O6   H10  SING  N  N  43  
84D  C7   H11  SING  N  N  44  
84D  O7   H12  SING  N  N  45  
84D  C8   H13  SING  N  N  46  
84D  C8   H14  SING  N  N  47  
84D  C9   H15  SING  N  N  48  
84D  C10  H16  SING  N  N  49  
84D  C11  H17  SING  N  N  50  
84D  C12  H18  SING  N  N  51  
84D  C13  H19  SING  N  N  52  
84D  C14  H20  SING  N  N  53  
84D  N1   H21  SING  N  N  54  
84D  N1   H22  SING  N  N  55  
84D  C15  H24  SING  N  N  56  
84D  C16  H25  SING  N  N  57  
84D  C17  H26  SING  N  N  58  
84D  C17  H27  SING  N  N  59  
84D  N2   H28  SING  N  N  60  
84D  N2   H29  SING  N  N  61  
84D  N3   H31  SING  N  N  62  
84D  N3   H32  SING  N  N  63  
84D  O2   H34  SING  N  N  64  
84D  N4   H35  SING  N  N  65  
84D  N4   H36  SING  N  N  66  
84D  C    H38  SING  N  N  67  
84D  C    H39  SING  N  N  68  
84D  N    H40  SING  N  N  69  
84D  N    H41  SING  N  N  70  
#   #
loop_
_pdbx_chem_comp_descriptor.comp_id
_pdbx_chem_comp_descriptor.type
_pdbx_chem_comp_descriptor.program
_pdbx_chem_comp_descriptor.program_version
_pdbx_chem_comp_descriptor.descriptor
84D  SMILES            ACDLabs               12.01  "C3C(N)C(OC2C(N)CC(C(OC1OC(C(O)C(C1O)N)CO)C2O)N)OC(C3)CN"  
84D  InChI             InChI                 1.03   "InChI=1S/C18H37N5O8/c19-4-6-1-2-7(20)17(28-6)30-15-8(21)3-9(22)16(14(15)27)31-18-13(26)11(23)12(25)10(5-24)29-18/h6-18,24-27H,1-5,19-23H2/t6-,7+,8-,9+,10+,11-,12+,13+,14-,15+,16-,17+,18+/m0/s1"  
84D  InChIKey          InChI                 1.03   JJCQSGDBDPYCEO-XVZSLQNASA-N  
84D  SMILES_CANONICAL  CACTVS                3.385  "NC[C@@H]1CC[C@@H](N)[C@H](O1)O[C@@H]2[C@@H](N)C[C@@H](N)[C@H](O[C@H]3O[C@H](CO)[C@@H](O)[C@H](N)[C@H]3O)[C@H]2O"  
84D  SMILES            CACTVS                3.385  "NC[CH]1CC[CH](N)[CH](O1)O[CH]2[CH](N)C[CH](N)[CH](O[CH]3O[CH](CO)[CH](O)[CH](N)[CH]3O)[CH]2O"  
84D  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.6  "C1C[C@H]([C@H](O[C@@H]1CN)O[C@@H]2[C@H](C[C@H]([C@@H]([C@H]2O)O[C@@H]3[C@@H]([C@H]([C@@H]([C@H](O3)CO)O)N)O)N)N)N"  
84D  SMILES            "OpenEye OEToolkits"  2.0.6  "C1CC(C(OC1CN)OC2C(CC(C(C2O)OC3C(C(C(C(O3)CO)O)N)O)N)N)N"  
#   #
loop_
_pdbx_chem_comp_identifier.comp_id
_pdbx_chem_comp_identifier.type
_pdbx_chem_comp_identifier.program
_pdbx_chem_comp_identifier.program_version
_pdbx_chem_comp_identifier.identifier
84D  "SYSTEMATIC NAME"  ACDLabs               12.01  "(1R,2S,3S,4R,6S)-4,6-diamino-3-[(3-amino-3-deoxy-alpha-D-glucopyranosyl)oxy]-2-hydroxycyclohexyl 2,6-diamino-2,3,4,6-tetradeoxy-alpha-D-erythro-hexopyranoside"  
84D  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  2.0.6  "(2~{S},3~{R},4~{S},5~{S},6~{R})-2-[(1~{S},2~{S},3~{R},4~{S},6~{R})-3-[(2~{R},3~{R},6~{S})-6-(aminomethyl)-3-azanyl-oxan-2-yl]oxy-4,6-bis(azanyl)-2-oxidanyl-cyclohexyl]oxy-4-azanyl-6-(hydroxymethyl)oxane-3,5-diol"  
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
84D  "Create component"  2016-12-23  RCSB  
84D  "Initial release"   2018-04-11  RCSB  
84D  "Modify synonyms"   2021-03-13  RCSB  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     84D
_pdbx_chem_comp_synonyms.name        "(1R,2S,3S,4R,6S)-4,6-diamino-3-[(3-amino-3-deoxy-alpha-D-glucopyranosyl)oxy]-2-hydroxycyclohexyl 2,6-diamino-2,3,4,6-tetradeoxy-alpha-D-erythro-hexopyranoside"
_pdbx_chem_comp_synonyms.provenance  PDB
_pdbx_chem_comp_synonyms.type        ?
##
