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 ? ##