data_84G # _chem_comp.id 84G _chem_comp.name Arbekacin _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C22 H44 N6 O10" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms (2S)-4-amino-N-{(1R,2S,3S,4R,5S)-5-amino-2-[(3-amino-3-deoxy-alpha-D-glucopyranosyl)oxy]-4-[(2,6-diamino-2,3,4,6-tetradeoxy-alpha-D-erythro-hexopyranosyl)oxy]-3-hydroxycyclohexyl}-2-hydroxybutanamide _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 552.619 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 84G _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 5U8B _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.pdbx_backbone_atom_flag _chem_comp_atom.pdbx_n_terminal_atom_flag _chem_comp_atom.pdbx_c_terminal_atom_flag _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 84G C1 C1 C 0 1 N N N N N N 36.402 -3.228 18.417 -4.536 3.418 -0.705 C1 84G 1 84G C2 C2 C 0 1 N N S N N N 37.617 -3.352 17.508 -4.646 2.494 0.510 C2 84G 2 84G C3 C3 C 0 1 N N N N N N 37.410 -4.535 16.494 -3.267 2.192 1.037 C3 84G 3 84G C4 C4 C 0 1 N N R N N N 37.485 -5.349 14.195 -1.055 1.199 0.795 C4 84G 4 84G C5 C5 C 0 1 N N N N N N 36.008 -5.718 14.072 -0.128 2.383 0.510 C5 84G 5 84G O1 O1 O 0 1 N N N N N N 37.075 -5.638 16.916 -2.942 2.576 2.141 O1 84G 6 84G O2 O2 O 0 1 N N N N N N 36.313 -9.325 13.159 3.125 0.536 0.856 O2 84G 7 84G O3 O3 O 0 1 N N N N N N 36.373 -10.902 14.903 4.451 0.889 -1.031 O3 84G 8 84G O4 O4 O 0 1 N N N N N N 38.885 -8.894 14.282 1.400 -1.531 -0.001 O4 84G 9 84G O5 O5 O 0 1 N N N N N N 39.725 -6.183 14.085 -1.375 -1.159 0.374 O5 84G 10 84G O O6 O 0 1 N N N N N N 37.833 -2.103 16.874 -5.415 3.137 1.529 O 84G 11 84G C C6 C 0 1 N N N N N N 36.617 -3.825 19.796 -5.924 3.625 -1.315 C 84G 12 84G N N1 N 0 1 N N N N N N 36.211 -2.876 20.875 -5.818 4.511 -2.482 N 84G 13 84G N1 N2 N 0 1 N N N N N N 37.614 -4.290 15.192 -2.395 1.493 0.283 N1 84G 14 84G C15 C7 C 0 1 N N S N N N 38.412 -6.528 14.565 -0.509 -0.053 0.107 C15 84G 15 84G C16 C8 C 0 1 N N S N N N 40.411 -5.161 14.762 -1.980 -1.718 -0.794 C16 84G 16 84G C21 C9 C 0 1 N N R N N N 41.857 -5.083 14.278 -3.173 -2.586 -0.384 C21 84G 17 84G O9 O7 O 0 1 N N N N N N 41.917 -4.739 12.900 -4.103 -1.799 0.362 O9 84G 18 84G C20 C10 C 0 1 N N S N N N 42.568 -6.408 14.550 -2.675 -3.747 0.483 C20 84G 19 84G N5 N3 N 0 1 N N N N N N 43.973 -6.361 14.131 -3.802 -4.628 0.818 N5 84G 20 84G C19 C11 C 0 1 N N S N N N 42.477 -6.688 16.046 -1.621 -4.538 -0.299 C19 84G 21 84G O8 O8 O 0 1 N N N N N N 43.026 -7.965 16.323 -1.097 -5.580 0.527 O8 84G 22 84G C17 C12 C 0 1 N N R N N N 41.012 -6.712 16.469 -0.489 -3.594 -0.712 C17 84G 23 84G C18 C13 C 0 1 N N N N N N 40.841 -6.899 17.963 0.539 -4.364 -1.544 C18 84G 24 84G O7 O9 O 0 1 N N N N N N 40.621 -5.649 18.616 1.701 -3.554 -1.734 O7 84G 25 84G O6 O10 O 0 1 N N N N N N 40.382 -5.460 16.137 -1.024 -2.521 -1.489 O6 84G 26 84G C14 C14 C 0 1 N N S N N N 38.094 -7.812 13.802 0.891 -0.361 0.642 C14 84G 27 84G C7 C15 C 0 1 N N R N N N 36.608 -8.123 13.897 1.817 0.823 0.356 C7 84G 28 84G C6 C16 C 0 1 N N S N N N 35.802 -6.990 13.260 1.272 2.075 1.045 C6 84G 29 84G N2 N4 N 0 1 N N N N N N 34.368 -7.286 13.149 2.161 3.212 0.770 N2 84G 30 84G C8 C17 C 0 1 N N R N N N 36.832 -10.558 13.614 3.987 -0.088 -0.097 C8 84G 31 84G C13 C18 C 0 1 N N R N N N 36.386 -11.596 12.585 5.185 -0.708 0.627 C13 84G 32 84G N4 N5 N 0 1 N N N N N N 36.521 -11.019 11.243 4.708 -1.670 1.630 N4 84G 33 84G C12 C19 C 0 1 N N N N N N 34.978 -12.154 12.751 5.983 0.400 1.320 C12 84G 34 84G C11 C20 C 0 1 N N N N N N 34.570 -12.341 14.200 6.408 1.437 0.276 C11 84G 35 84G C9 C21 C 0 1 N N S N N N 34.958 -11.126 15.000 5.163 1.975 -0.434 C9 84G 36 84G C10 C22 C 0 1 N N N N N N 34.729 -11.296 16.486 5.584 2.967 -1.520 C10 84G 37 84G N3 N6 N 0 1 N N N N N N 34.972 -10.064 17.213 4.388 3.571 -2.122 N3 84G 38 84G H1 H1 H 0 1 N N N N N N 36.161 -2.161 18.533 -4.128 4.380 -0.394 H1 84G 39 84G H2 H2 H 0 1 N N N N N N 35.556 -3.746 17.941 -3.877 2.966 -1.446 H2 84G 40 84G H3 H3 H 0 1 N N N N N N 38.487 -3.601 18.133 -5.135 1.565 0.218 H3 84G 41 84G H4 H4 H 0 1 N N N N N N 37.816 -4.958 13.222 -1.106 1.030 1.871 H4 84G 42 84G H5 H5 H 0 1 N N N N N N 35.476 -4.892 13.578 -0.077 2.553 -0.566 H5 84G 43 84G H6 H6 H 0 1 N N N N N N 35.595 -5.870 15.080 -0.517 3.275 1.000 H6 84G 44 84G H7 H7 H 0 1 N N N N N N 39.805 -8.670 14.210 2.247 -1.837 0.353 H7 84G 45 84G H8 H8 H 0 1 N N N N N N 37.951 -1.429 17.533 -5.038 3.972 1.838 H8 84G 46 84G H9 H9 H 0 1 N N N N N N 36.018 -4.744 19.885 -6.331 2.663 -1.625 H9 84G 47 84G H10 H10 H 0 1 N N N N N N 37.683 -4.069 19.917 -6.583 4.077 -0.574 H10 84G 48 84G H11 H11 H 0 1 N N N N N N 36.365 -3.300 21.768 -5.162 4.146 -3.155 H11 84G 49 84G H12 H12 H 0 1 N N N N N N 36.754 -2.039 20.805 -6.722 4.664 -2.903 H12 84G 50 84G H14 H14 H 0 1 N N N N N N 37.859 -3.366 14.898 -2.656 1.186 -0.600 H14 84G 51 84G H15 H15 H 0 1 N N N N N N 38.400 -6.704 15.651 -0.458 0.116 -0.969 H15 84G 52 84G H16 H16 H 0 1 N N N N N N 39.927 -4.191 14.575 -2.323 -0.914 -1.446 H16 84G 53 84G H17 H17 H 0 1 N N N N N N 42.365 -4.304 14.865 -3.660 -2.980 -1.276 H17 84G 54 84G H18 H18 H 0 1 N N N N N N 41.469 -3.913 12.759 -4.460 -1.044 -0.127 H18 84G 55 84G H19 H19 H 0 1 N N N N N N 42.046 -7.209 14.006 -2.232 -3.355 1.398 H19 84G 56 84G H20 H20 H 0 1 N N N N N N 44.408 -7.241 14.322 -4.514 -4.127 1.328 H20 84G 57 84G H21 H21 H 0 1 N N N N N N 44.022 -6.171 13.150 -4.185 -5.057 -0.011 H21 84G 58 84G H23 H23 H 0 1 N N N N N N 43.007 -5.900 16.601 -2.077 -4.972 -1.188 H23 84G 59 84G H24 H24 H 0 1 N N N N N N 42.969 -8.139 17.255 -0.423 -6.122 0.095 H24 84G 60 84G H25 H25 H 0 1 N N N N N N 40.506 -7.537 15.946 -0.007 -3.192 0.180 H25 84G 61 84G H26 H26 H 0 1 N N N N N N 39.978 -7.557 18.146 0.816 -5.280 -1.023 H26 84G 62 84G H27 H27 H 0 1 N N N N N N 41.750 -7.363 18.373 0.107 -4.613 -2.514 H27 84G 63 84G H28 H28 H 0 1 N N N N N N 40.517 -5.793 19.549 2.396 -3.979 -2.255 H28 84G 64 84G H29 H29 H 0 1 N N N N N N 38.332 -7.638 12.742 0.839 -0.530 1.717 H29 84G 65 84G H30 H30 H 0 1 N N N N N N 36.319 -8.232 14.953 1.869 0.993 -0.719 H30 84G 66 84G H31 H31 H 0 1 N N N N N N 36.204 -6.816 12.251 1.220 1.906 2.120 H31 84G 67 84G H32 H32 H 0 1 N N N N N N 33.899 -6.510 12.727 1.735 4.081 1.055 H32 84G 68 84G H33 H33 H 0 1 N N N N N N 34.239 -8.101 12.584 3.057 3.085 1.216 H33 84G 69 84G H35 H35 H 0 1 N N N N N N 37.931 -10.521 13.609 3.440 -0.867 -0.628 H35 84G 70 84G H36 H36 H 0 1 N N N N N N 37.082 -12.445 12.659 5.823 -1.219 -0.094 H36 84G 71 84G H37 H37 H 0 1 N N N N N N 37.444 -10.651 11.129 5.481 -2.089 2.125 H37 84G 72 84G H38 H38 H 0 1 N N N N N N 36.358 -11.728 10.557 4.062 -1.234 2.270 H38 84G 73 84G H40 H40 H 0 1 N N N N N N 34.270 -11.459 12.276 5.361 0.879 2.077 H40 84G 74 84G H41 H41 H 0 1 N N N N N N 34.928 -13.130 12.246 6.868 -0.027 1.791 H41 84G 75 84G H42 H42 H 0 1 N N N N N N 33.481 -12.483 14.257 6.929 2.258 0.770 H42 84G 76 84G H43 H43 H 0 1 N N N N N N 35.078 -13.226 14.611 7.071 0.970 -0.452 H43 84G 77 84G H44 H44 H 0 1 N N N N N N 34.400 -10.250 14.638 4.521 2.477 0.288 H44 84G 78 84G H45 H45 H 0 1 N N N N N N 33.687 -11.608 16.652 6.203 3.748 -1.079 H45 84G 79 84G H46 H46 H 0 1 N N N N N N 35.409 -12.073 16.865 6.154 2.444 -2.289 H46 84G 80 84G H47 H47 H 0 1 N N N N N N 34.811 -10.215 18.188 3.810 4.007 -1.419 H47 84G 81 84G H48 H48 H 0 1 N N N N N N 35.919 -9.775 17.072 4.640 4.231 -2.843 H48 84G 82 # 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 84G N4 C13 SING N N 1 84G C13 C12 SING N N 2 84G C13 C8 SING N N 3 84G C12 C11 SING N N 4 84G O9 C21 SING N N 5 84G N2 C6 SING N N 6 84G O2 C8 SING N N 7 84G O2 C7 SING N N 8 84G C6 C7 SING N N 9 84G C6 C5 SING N N 10 84G C8 O3 SING N N 11 84G C14 C7 SING N N 12 84G C14 O4 SING N N 13 84G C14 C15 SING N N 14 84G C5 C4 SING N N 15 84G O5 C15 SING N N 16 84G O5 C16 SING N N 17 84G N5 C20 SING N N 18 84G C4 C15 SING N N 19 84G C4 N1 SING N N 20 84G C11 C9 SING N N 21 84G C21 C20 SING N N 22 84G C21 C16 SING N N 23 84G C20 C19 SING N N 24 84G C16 O6 SING N N 25 84G O3 C9 SING N N 26 84G C9 C10 SING N N 27 84G N1 C3 SING N N 28 84G C19 O8 SING N N 29 84G C19 C17 SING N N 30 84G O6 C17 SING N N 31 84G C17 C18 SING N N 32 84G C10 N3 SING N N 33 84G C3 O1 DOUB N N 34 84G C3 C2 SING N N 35 84G O C2 SING N N 36 84G C2 C1 SING N N 37 84G C18 O7 SING N N 38 84G C1 C SING N N 39 84G C N SING N N 40 84G C1 H1 SING N N 41 84G C1 H2 SING N N 42 84G C2 H3 SING N N 43 84G C4 H4 SING N N 44 84G C5 H5 SING N N 45 84G C5 H6 SING N N 46 84G O4 H7 SING N N 47 84G O H8 SING N N 48 84G C H9 SING N N 49 84G C H10 SING N N 50 84G N H11 SING N N 51 84G N H12 SING N N 52 84G N1 H14 SING N N 53 84G C15 H15 SING N N 54 84G C16 H16 SING N N 55 84G C21 H17 SING N N 56 84G O9 H18 SING N N 57 84G C20 H19 SING N N 58 84G N5 H20 SING N N 59 84G N5 H21 SING N N 60 84G C19 H23 SING N N 61 84G O8 H24 SING N N 62 84G C17 H25 SING N N 63 84G C18 H26 SING N N 64 84G C18 H27 SING N N 65 84G O7 H28 SING N N 66 84G C14 H29 SING N N 67 84G C7 H30 SING N N 68 84G C6 H31 SING N N 69 84G N2 H32 SING N N 70 84G N2 H33 SING N N 71 84G C8 H35 SING N N 72 84G C13 H36 SING N N 73 84G N4 H37 SING N N 74 84G N4 H38 SING N N 75 84G C12 H40 SING N N 76 84G C12 H41 SING N N 77 84G C11 H42 SING N N 78 84G C11 H43 SING N N 79 84G C9 H44 SING N N 80 84G C10 H45 SING N N 81 84G C10 H46 SING N N 82 84G N3 H47 SING N N 83 84G N3 H48 SING N N 84 # 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 84G SMILES ACDLabs 12.01 C(CN)C(C(=O)NC3C(OC1OC(C(C(C1O)N)O)CO)C(O)C(OC2OC(CCC2N)CN)C(C3)N)O 84G InChI InChI 1.03 InChI=1S/C22H44N6O10/c23-4-3-12(30)20(34)28-11-5-10(26)18(37-21-9(25)2-1-8(6-24)35-21)17(33)19(11)38-22-16(32)14(27)15(31)13(7-29)36-22/h8-19,21-22,29-33H,1-7,23-27H2,(H,28,34)/t8-,9+,10-,11+,12-,13+,14-,15+,16+,17-,18+,19-,21+,22+/m0/s1 84G InChIKey InChI 1.03 MKKYBZZTJQGVCD-XTCKQBCOSA-N 84G SMILES_CANONICAL CACTVS 3.385 NCC[C@H](O)C(=O)N[C@@H]1C[C@H](N)[C@@H](O[C@H]2O[C@H](CN)CC[C@H]2N)[C@H](O)[C@H]1O[C@H]3O[C@H](CO)[C@@H](O)[C@H](N)[C@H]3O 84G SMILES CACTVS 3.385 NCC[CH](O)C(=O)N[CH]1C[CH](N)[CH](O[CH]2O[CH](CN)CC[CH]2N)[CH](O)[CH]1O[CH]3O[CH](CO)[CH](O)[CH](N)[CH]3O 84G 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)NC(=O)[C@H](CCN)O)N)N 84G SMILES "OpenEye OEToolkits" 2.0.6 C1CC(C(OC1CN)OC2C(CC(C(C2O)OC3C(C(C(C(O3)CO)O)N)O)NC(=O)C(CCN)O)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 84G "SYSTEMATIC NAME" ACDLabs 12.01 (2S)-4-amino-N-{(1R,2S,3S,4R,5S)-5-amino-2-[(3-amino-3-deoxy-alpha-D-glucopyranosyl)oxy]-4-[(2,6-diamino-2,3,4,6-tetradeoxy-alpha-D-erythro-hexopyranosyl)oxy]-3-hydroxycyclohexyl}-2-hydroxybutanamide 84G "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 (2~{S})-~{N}-[(1~{R},2~{S},3~{S},4~{R},5~{S})-4-[(2~{R},3~{R},6~{S})-6-(aminomethyl)-3-azanyl-oxan-2-yl]oxy-5-azanyl-2-[(2~{S},3~{R},4~{S},5~{S},6~{R})-4-azanyl-6-(hydroxymethyl)-3,5-bis(oxidanyl)oxan-2-yl]oxy-3-oxidanyl-cyclohexyl]-4-azanyl-2-oxidanyl-butanamide # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site 84G 'Create component' 2016-12-23 RCSB 84G 'Initial release' 2018-04-11 RCSB 84G 'Modify synonyms' 2021-03-13 RCSB # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id 84G _pdbx_chem_comp_synonyms.name (2S)-4-amino-N-{(1R,2S,3S,4R,5S)-5-amino-2-[(3-amino-3-deoxy-alpha-D-glucopyranosyl)oxy]-4-[(2,6-diamino-2,3,4,6-tetradeoxy-alpha-D-erythro-hexopyranosyl)oxy]-3-hydroxycyclohexyl}-2-hydroxybutanamide _pdbx_chem_comp_synonyms.provenance PDB _pdbx_chem_comp_synonyms.type ? # _pdbe_chem_comp_drugbank_details.comp_id 84G _pdbe_chem_comp_drugbank_details.drugbank_id DB06696 _pdbe_chem_comp_drugbank_details.type 'small molecule' _pdbe_chem_comp_drugbank_details.name Arbekacin _pdbe_chem_comp_drugbank_details.description 'An semisynthetic aminoglycoside antibiotic. Often used for treatment of multi-resistant bacterial infection such as methicillin-resistant _Staphylococcus aureus_ (MRSA).' _pdbe_chem_comp_drugbank_details.cas_number 51025-85-5 _pdbe_chem_comp_drugbank_details.mechanism_of_action 'Arbekacin irreversibly binds bacterial 30S and 16S ribosomal subunits inhibiting protein synthesis. Arbekacin binds to 4 nucleotides of the 16S subunit and 1 amino acid of protein S12 to interfere with the decoding site around nucleotide 1400 in the 16S subunit. Interference with the decoding site interferes with its interaction with the wobble base of tRNA. This hindered interaction causes mRNA to be misread and the incorrect amino acids are inserted into protein. These error filled proteins are not able to function or may even be toxic.' # loop_ _pdbe_chem_comp_synonyms.comp_id _pdbe_chem_comp_synonyms.name _pdbe_chem_comp_synonyms.provenance _pdbe_chem_comp_synonyms.type 84G '(2S)-4-amino-N-{(1R,2S,3S,4R,5S)-5-amino-2-[(3-amino-3-deoxy-alpha-D-glucopyranosyl)oxy]-4-[(2,6-diamino-2,3,4,6-tetradeoxy-alpha-D-erythro-hexopyranosyl)oxy]-3-hydroxycyclohexyl}-2-hydroxybutanamide' wwPDB ? 84G ABK DrugBank ? 84G Arbekacin DrugBank ? 84G Arbekacinum DrugBank ? 84G Haberacin DrugBank ? # _pdbe_chem_comp_drugbank_classification.comp_id 84G _pdbe_chem_comp_drugbank_classification.drugbank_id DB06696 _pdbe_chem_comp_drugbank_classification.parent '4,6-disubstituted 2-deoxystreptamines' _pdbe_chem_comp_drugbank_classification.kingdom 'Organic compounds' _pdbe_chem_comp_drugbank_classification.class 'Organooxygen compounds' _pdbe_chem_comp_drugbank_classification.superclass 'Organic oxygen compounds' _pdbe_chem_comp_drugbank_classification.description 'This compound belongs to the class of organic compounds known as 4,6-disubstituted 2-deoxystreptamines. These are 2-deoxystreptamine aminoglycosides that a glycosidically linked to a pyranose of furanose unit at the C4- and C6-positions.' # _pdbe_chem_comp_drugbank_targets.comp_id 84G _pdbe_chem_comp_drugbank_targets.drugbank_id DB06696 _pdbe_chem_comp_drugbank_targets.name '30S ribosomal protein S12' _pdbe_chem_comp_drugbank_targets.organism 'Escherichia coli (strain K12)' _pdbe_chem_comp_drugbank_targets.uniprot_id P0A7S3 _pdbe_chem_comp_drugbank_targets.pharmacologically_active yes _pdbe_chem_comp_drugbank_targets.ordinal 1 # loop_ _software.name _software.version _software.description rdkit 2023.09.6 'Core functionality.' pdbeccdutils 0.8.6 'Wrapper to provide 2D templates and molecular fragments.' # loop_ _pdbe_chem_comp_atom_depiction.comp_id _pdbe_chem_comp_atom_depiction.atom_id _pdbe_chem_comp_atom_depiction.element _pdbe_chem_comp_atom_depiction.model_Cartn_x _pdbe_chem_comp_atom_depiction.model_Cartn_y _pdbe_chem_comp_atom_depiction.pdbx_ordinal 84G C1 C 16.796 -1.168 1 84G C2 C 15.497 -1.918 2 84G C3 C 14.198 -1.168 3 84G C4 C 11.600 -1.168 4 84G C5 C 11.600 0.332 5 84G O1 O 14.198 0.332 6 84G O2 O 7.702 1.082 7 84G O3 O 7.702 3.680 8 84G O4 O 7.702 -1.918 9 84G O5 O 10.301 -3.418 10 84G O O 15.497 -3.418 11 84G C C 18.095 -1.918 12 84G N N 19.394 -1.168 13 84G N1 N 12.899 -1.918 14 84G C15 C 10.301 -1.918 15 84G C16 C 9.002 -4.168 16 84G C21 C 9.002 -5.668 17 84G O9 O 10.301 -6.418 18 84G C20 C 7.702 -6.418 19 84G N5 N 7.702 -7.918 20 84G C19 C 6.404 -5.668 21 84G O8 O 5.104 -6.418 22 84G C17 C 6.404 -4.168 23 84G C18 C 5.104 -3.418 24 84G O7 O 3.805 -4.168 25 84G O6 O 7.702 -3.418 26 84G C14 C 9.002 -1.168 27 84G C7 C 9.002 0.332 28 84G C6 C 10.301 1.082 29 84G N2 N 11.051 2.381 30 84G C8 C 6.952 2.381 31 84G C13 C 5.452 2.381 32 84G N4 N 4.702 1.082 33 84G C12 C 4.702 3.680 34 84G C11 C 5.452 4.979 35 84G C9 C 6.952 4.979 36 84G C10 C 7.702 6.278 37 84G N3 N 6.952 7.577 38 # loop_ _pdbe_chem_comp_bond_depiction.comp_id _pdbe_chem_comp_bond_depiction.atom_id_1 _pdbe_chem_comp_bond_depiction.atom_id_2 _pdbe_chem_comp_bond_depiction.value_order _pdbe_chem_comp_bond_depiction.bond_dir _pdbe_chem_comp_bond_depiction.pdbx_ordinal 84G C13 N4 SINGLE BEGINDASH 1 84G C13 C12 SINGLE NONE 2 84G C13 C8 SINGLE NONE 3 84G C12 C11 SINGLE NONE 4 84G C21 O9 SINGLE BEGINDASH 5 84G C6 N2 SINGLE BEGINWEDGE 6 84G C8 O2 SINGLE BEGINDASH 7 84G C7 O2 SINGLE BEGINDASH 8 84G C6 C7 SINGLE NONE 9 84G C6 C5 SINGLE NONE 10 84G C8 O3 SINGLE NONE 11 84G C14 C7 SINGLE NONE 12 84G C14 O4 SINGLE BEGINWEDGE 13 84G C14 C15 SINGLE NONE 14 84G C5 C4 SINGLE NONE 15 84G C15 O5 SINGLE BEGINDASH 16 84G C16 O5 SINGLE BEGINDASH 17 84G C20 N5 SINGLE BEGINWEDGE 18 84G C4 C15 SINGLE NONE 19 84G C4 N1 SINGLE BEGINWEDGE 20 84G C11 C9 SINGLE NONE 21 84G C21 C20 SINGLE NONE 22 84G C21 C16 SINGLE NONE 23 84G C20 C19 SINGLE NONE 24 84G C16 O6 SINGLE NONE 25 84G O3 C9 SINGLE NONE 26 84G C9 C10 SINGLE BEGINWEDGE 27 84G N1 C3 SINGLE NONE 28 84G C19 O8 SINGLE BEGINDASH 29 84G C19 C17 SINGLE NONE 30 84G O6 C17 SINGLE NONE 31 84G C17 C18 SINGLE BEGINWEDGE 32 84G C10 N3 SINGLE NONE 33 84G C3 O1 DOUBLE NONE 34 84G C3 C2 SINGLE NONE 35 84G C2 O SINGLE BEGINDASH 36 84G C2 C1 SINGLE NONE 37 84G C18 O7 SINGLE NONE 38 84G C1 C SINGLE NONE 39 84G C N SINGLE NONE 40 # loop_ _pdbe_chem_comp_substructure.comp_id _pdbe_chem_comp_substructure.substructure_name _pdbe_chem_comp_substructure.id _pdbe_chem_comp_substructure.substructure_type _pdbe_chem_comp_substructure.substructure_smiles _pdbe_chem_comp_substructure.substructure_inchis _pdbe_chem_comp_substructure.substructure_inchikeys 84G MurckoScaffold S1 scaffold 'C1CC[C@@H](O[C@@H]2CCC[C@H](O[C@@H]3CCCCO3)C2)OC1' InChI=1S/C16H28O4/c1-3-10-17-15(8-1)19-13-6-5-7-14(12-13)20-16-9-2-4-11-18-16/h13-16H,1-12H2/t13-,14+,15-,16-/m1/s1 UOYDWHSPHHJHEM-QKPAOTATSA-N 84G amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N 84G cyclohexane F2 fragment C1CCCCC1 InChI=1S/C6H12/c1-2-4-6-5-3-1/h1-6H2 XDTMQSROBMDMFD-UHFFFAOYSA-N 84G pyranose F3 fragment OC1CCCCO1 InChI=1S/C5H10O2/c6-5-3-1-2-4-7-5/h5-6H,1-4H2 CELWCAITJAEQNL-UHFFFAOYSA-N 84G Z2856434893 F4 fragment CC(O)CNC1CCCCC1 InChI=1S/C9H19NO/c1-8(11)7-10-9-5-3-2-4-6-9/h8-11H,2-7H2,1H3 HFHPBMVMXFZJNO-UHFFFAOYSA-N # loop_ _pdbe_chem_comp_substructure_mapping.comp_id _pdbe_chem_comp_substructure_mapping.atom_id _pdbe_chem_comp_substructure_mapping.substructure_id _pdbe_chem_comp_substructure_mapping.substructure_ordinal 84G C4 S1 1 84G C5 S1 1 84G O2 S1 1 84G O3 S1 1 84G O5 S1 1 84G C15 S1 1 84G C16 S1 1 84G C21 S1 1 84G C20 S1 1 84G C19 S1 1 84G C17 S1 1 84G O6 S1 1 84G C14 S1 1 84G C7 S1 1 84G C6 S1 1 84G C8 S1 1 84G C13 S1 1 84G C12 S1 1 84G C11 S1 1 84G C9 S1 1 84G N1 F1 1 84G C3 F1 1 84G O1 F1 1 84G C2 F1 1 84G C4 F2 1 84G C5 F2 1 84G C6 F2 1 84G C7 F2 1 84G C14 F2 1 84G C15 F2 1 84G C19 F3 1 84G C17 F3 1 84G O6 F3 1 84G C16 F3 1 84G C21 F3 1 84G C20 F3 1 84G O5 F3 1 84G C11 F3 2 84G C9 F3 2 84G O3 F3 2 84G C8 F3 2 84G C13 F3 2 84G C12 F3 2 84G O2 F3 2 84G C1 F4 1 84G C2 F4 1 84G O F4 1 84G C3 F4 1 84G N1 F4 1 84G C4 F4 1 84G C5 F4 1 84G C6 F4 1 84G C7 F4 1 84G C14 F4 1 84G C15 F4 1 # _pdbe_chem_comp_rdkit_properties.comp_id 84G _pdbe_chem_comp_rdkit_properties.exactmw 552.312 _pdbe_chem_comp_rdkit_properties.amw 552.626 _pdbe_chem_comp_rdkit_properties.lipinskiHBA 16 _pdbe_chem_comp_rdkit_properties.lipinskiHBD 16 _pdbe_chem_comp_rdkit_properties.NumRotatableBonds 20 _pdbe_chem_comp_rdkit_properties.NumHBD 11 _pdbe_chem_comp_rdkit_properties.NumHBA 15 _pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 38 _pdbe_chem_comp_rdkit_properties.NumAtoms 82 _pdbe_chem_comp_rdkit_properties.NumHeteroatoms 16 _pdbe_chem_comp_rdkit_properties.NumAmideBonds 1 _pdbe_chem_comp_rdkit_properties.FractionCSP3 0.955 _pdbe_chem_comp_rdkit_properties.NumRings 3 _pdbe_chem_comp_rdkit_properties.NumAromaticRings 0 _pdbe_chem_comp_rdkit_properties.NumAliphaticRings 3 _pdbe_chem_comp_rdkit_properties.NumSaturatedRings 3 _pdbe_chem_comp_rdkit_properties.NumHeterocycles 2 _pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0 _pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 2 _pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 2 _pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0 _pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0 _pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 14 _pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0 _pdbe_chem_comp_rdkit_properties.labuteASA 283.112 _pdbe_chem_comp_rdkit_properties.tpsa 297.270 _pdbe_chem_comp_rdkit_properties.CrippenClogP -6.399 _pdbe_chem_comp_rdkit_properties.CrippenMR 130.615 _pdbe_chem_comp_rdkit_properties.chi0v 17.766 _pdbe_chem_comp_rdkit_properties.chi1v 9.173 _pdbe_chem_comp_rdkit_properties.chi2v 3.939 _pdbe_chem_comp_rdkit_properties.chi3v 3.939 _pdbe_chem_comp_rdkit_properties.chi4v 2.334 _pdbe_chem_comp_rdkit_properties.chi0n 61.766 _pdbe_chem_comp_rdkit_properties.chi1n 30.134 _pdbe_chem_comp_rdkit_properties.chi2n 3.939 _pdbe_chem_comp_rdkit_properties.chi3n 3.939 _pdbe_chem_comp_rdkit_properties.chi4n 2.334 _pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.090 _pdbe_chem_comp_rdkit_properties.kappa1 6.924 _pdbe_chem_comp_rdkit_properties.kappa2 14.000 _pdbe_chem_comp_rdkit_properties.kappa3 7.154 _pdbe_chem_comp_rdkit_properties.Phi 2.551 # loop_ _pdbe_chem_comp_external_mappings.comp_id _pdbe_chem_comp_external_mappings.source _pdbe_chem_comp_external_mappings.resource _pdbe_chem_comp_external_mappings.resource_id 84G UniChem ChEMBL CHEMBL426926 84G UniChem DrugBank DB06696 84G UniChem 'Guide to Pharmacology' 7345 84G UniChem 'PubChem DOTF' 12012746 84G UniChem ChEBI 37922 84G UniChem ZINC ZINC000009575047 84G UniChem fdasrs G7V6SLI20L 84G UniChem SureChEMBL SCHEMBL18413 84G UniChem HMDB HMDB0015642 84G UniChem 'PubChem TPHARMA' 15012131 84G UniChem ACTor 51025-85-5 84G UniChem ACTor 52444-06-1 84G UniChem DrugCentral 235 84G UniChem ChemicalBook CB7347991 84G UniChem ClinicalTrials ARBEKACIN 84G UniChem ClinicalTrials 'ARBEKACIN SULFATE' 84G UniChem ClinicalTrials ME-1100 84G UniChem ClinicalTrials ME1100 84G UniChem rxnorm ARBEKACIN 84G UniChem rxnorm 'ARBEKACIN SULFATE' 84G UniChem 'Probes And Drugs' PD009288 84G UniChem 'EPA CompTox Dashboard' DTXSID8048319 84G UniChem PubChem 68682 84G UniChem Nikkaji J33.173B # loop_ _pdbe_chem_comp_rdkit_conformer.comp_id _pdbe_chem_comp_rdkit_conformer.atom_id _pdbe_chem_comp_rdkit_conformer.Cartn_x_rdkit _pdbe_chem_comp_rdkit_conformer.Cartn_y_rdkit _pdbe_chem_comp_rdkit_conformer.Cartn_z_rdkit _pdbe_chem_comp_rdkit_conformer.rdkit_method _pdbe_chem_comp_rdkit_conformer.rdkit_ordinal 84G C1 -4.761 3.957 -1.239 ETKDGv3 1 84G C2 -3.274 3.916 -1.640 ETKDGv3 2 84G C3 -2.394 3.535 -0.476 ETKDGv3 3 84G C4 -0.795 1.887 0.625 ETKDGv3 4 84G C5 0.520 2.660 0.328 ETKDGv3 5 84G O1 -2.176 4.388 0.427 ETKDGv3 6 84G O2 3.119 0.755 0.971 ETKDGv3 7 84G O3 4.493 0.614 -0.892 ETKDGv3 8 84G O4 0.980 -1.349 1.442 ETKDGv3 9 84G O5 -1.550 -0.205 1.583 ETKDGv3 10 84G O -3.074 3.037 -2.717 ETKDGv3 11 84G C -5.290 2.601 -0.744 ETKDGv3 12 84G N -6.732 2.646 -0.511 ETKDGv3 13 84G N1 -1.821 2.219 -0.374 ETKDGv3 14 84G C15 -0.578 0.345 0.703 ETKDGv3 15 84G C16 -2.061 -1.447 1.121 ETKDGv3 16 84G C21 -3.320 -1.216 0.243 ETKDGv3 17 84G O9 -4.053 -0.102 0.686 ETKDGv3 18 84G C20 -4.235 -2.471 0.196 ETKDGv3 19 84G N5 -4.862 -2.588 -1.123 ETKDGv3 20 84G C19 -3.415 -3.738 0.519 ETKDGv3 21 84G O8 -4.217 -4.894 0.497 ETKDGv3 22 84G C17 -2.712 -3.578 1.904 ETKDGv3 23 84G C18 -1.458 -4.458 2.006 ETKDGv3 24 84G O7 -0.902 -4.342 3.287 ETKDGv3 25 84G O6 -2.405 -2.229 2.250 ETKDGv3 26 84G C14 0.838 0.033 1.233 ETKDGv3 27 84G C7 1.923 0.524 0.238 ETKDGv3 28 84G C6 1.522 1.837 -0.501 ETKDGv3 29 84G N2 0.958 1.537 -1.822 ETKDGv3 30 84G C8 4.223 0.079 0.398 ETKDGv3 31 84G C13 5.438 0.253 1.326 ETKDGv3 32 84G N4 5.676 1.672 1.612 ETKDGv3 33 84G C12 6.671 -0.425 0.705 ETKDGv3 34 84G C11 6.867 -0.008 -0.756 ETKDGv3 35 84G C9 5.547 -0.070 -1.557 ETKDGv3 36 84G C10 5.138 -1.500 -1.984 ETKDGv3 37 84G N3 5.948 -1.957 -3.110 ETKDGv3 38 84G H1 -5.356 4.284 -2.120 ETKDGv3 39 84G H2 -4.905 4.719 -0.441 ETKDGv3 40 84G H3 -2.975 4.944 -1.954 ETKDGv3 41 84G H4 -1.160 2.229 1.620 ETKDGv3 42 84G H5 0.315 3.623 -0.187 ETKDGv3 43 84G H6 1.006 2.927 1.293 ETKDGv3 44 84G H7 1.779 -1.471 2.019 ETKDGv3 45 84G H8 -3.452 3.478 -3.523 ETKDGv3 46 84G H9 -5.071 1.806 -1.490 ETKDGv3 47 84G H10 -4.786 2.335 0.209 ETKDGv3 48 84G H11 -6.940 3.407 0.176 ETKDGv3 49 84G H12 -7.212 2.887 -1.408 ETKDGv3 50 84G H14 -2.164 1.478 -1.025 ETKDGv3 51 84G H15 -0.652 -0.068 -0.332 ETKDGv3 52 84G H16 -1.296 -2.000 0.521 ETKDGv3 53 84G H17 -2.960 -0.993 -0.785 ETKDGv3 54 84G H18 -4.289 -0.256 1.639 ETKDGv3 55 84G H19 -5.034 -2.373 0.968 ETKDGv3 56 84G H20 -5.410 -1.715 -1.302 ETKDGv3 57 84G H21 -5.564 -3.362 -1.091 ETKDGv3 58 84G H23 -2.644 -3.852 -0.276 ETKDGv3 59 84G H24 -4.956 -4.763 1.147 ETKDGv3 60 84G H25 -3.420 -3.939 2.682 ETKDGv3 61 84G H26 -1.736 -5.519 1.818 ETKDGv3 62 84G H27 -0.708 -4.150 1.245 ETKDGv3 63 84G H28 -0.097 -4.923 3.291 ETKDGv3 64 84G H29 0.957 0.562 2.209 ETKDGv3 65 84G H30 2.034 -0.282 -0.531 ETKDGv3 66 84G H31 2.433 2.462 -0.648 ETKDGv3 67 84G H32 0.719 2.440 -2.294 ETKDGv3 68 84G H33 1.707 1.100 -2.407 ETKDGv3 69 84G H35 3.988 -1.010 0.349 ETKDGv3 70 84G H36 5.213 -0.259 2.289 ETKDGv3 71 84G H37 5.920 2.182 0.733 ETKDGv3 72 84G H38 6.491 1.754 2.263 ETKDGv3 73 84G H40 6.542 -1.528 0.754 ETKDGv3 74 84G H41 7.583 -0.177 1.290 ETKDGv3 75 84G H42 7.643 -0.649 -1.223 ETKDGv3 76 84G H43 7.255 1.033 -0.785 ETKDGv3 77 84G H44 5.729 0.494 -2.498 ETKDGv3 78 84G H45 5.233 -2.219 -1.141 ETKDGv3 79 84G H46 4.071 -1.482 -2.297 ETKDGv3 80 84G H47 5.505 -2.825 -3.490 ETKDGv3 81 84G H48 6.886 -2.245 -2.749 ETKDGv3 82 #