data_9CS # _chem_comp.id 9CS _chem_comp.name "(1R,2S,3S,4R,6S)-4,6-DIAMINO-3-[(3-AMINO-3-DEOXY-ALPHA-D-GLUCOPYRANOSYL)OXY]-2-HYDROXYCYCLOHEXYL 2,6-DIAMINO-2,6-DIDEOXY-ALPHA-D-GLUCOPYRANOSIDE" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C18 H37 N5 O10" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "Kanamycin B; Bekanamycin" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2007-07-13 _chem_comp.pdbx_modified_date 2020-05-26 _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 483.514 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 9CS _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 ? _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 9CS C1 C1 C 0 1 N N R 9.365 13.687 -11.570 2.466 -1.029 0.093 C1 9CS 1 9CS C2 C2 C 0 1 N N R 8.713 13.162 -10.272 3.359 -1.958 0.919 C2 9CS 2 9CS C3 C3 C 0 1 N N R 8.704 11.618 -10.270 4.671 -1.236 1.244 C3 9CS 3 9CS C4 C4 C 0 1 N N S 7.982 11.076 -11.513 5.338 -0.799 -0.064 C4 9CS 4 9CS C5 C5 C 0 1 N N R 8.557 11.742 -12.770 4.368 0.084 -0.853 C5 9CS 5 9CS C6 C6 C 0 1 N N N 7.642 11.350 -13.914 5.004 0.475 -2.188 C6 9CS 6 9CS C7 C7 C 0 1 N N R 14.299 15.251 -13.019 -1.185 2.735 0.635 C7 9CS 7 9CS C8 C8 C 0 1 N N S 13.280 16.114 -12.248 -1.378 1.275 0.223 C8 9CS 8 9CS C9 C9 C 0 1 N N S 12.205 15.241 -11.551 -0.255 0.424 0.820 C9 9CS 9 9CS C10 C10 C 0 1 N N R 11.583 14.184 -12.493 1.095 0.926 0.304 C10 9CS 10 9CS C11 C11 C 0 1 N N S 12.649 13.410 -13.303 1.287 2.386 0.717 C11 9CS 11 9CS C12 C12 C 0 1 N N N 13.604 14.354 -14.042 0.165 3.237 0.119 C12 9CS 12 9CS C13 C13 C 0 1 N N S 13.688 18.146 -11.039 -3.720 1.003 -0.209 C13 9CS 13 9CS C14 C14 C 0 1 N N R 14.995 18.909 -10.771 -5.034 0.592 0.459 C14 9CS 14 9CS C15 C15 C 0 1 N N S 15.678 18.369 -9.510 -4.980 -0.900 0.800 C15 9CS 15 9CS C16 C16 C 0 1 N N S 14.738 18.401 -8.287 -4.706 -1.695 -0.480 C16 9CS 16 9CS C17 C17 C 0 1 N N R 13.314 17.876 -8.625 -3.404 -1.196 -1.112 C17 9CS 17 9CS C18 C18 C 0 1 N N N 12.283 18.255 -7.542 -3.154 -1.944 -2.423 C18 9CS 18 9CS N1 N1 N 0 1 N N N 8.428 11.257 -15.145 4.125 1.419 -2.892 N1 9CS 19 9CS N2 N2 N 0 1 N N N 12.006 12.546 -14.299 2.584 2.868 0.222 N2 9CS 20 9CS N3 N3 N 0 1 N N N 15.328 16.065 -13.670 -2.263 3.552 0.062 N3 9CS 21 9CS N4 N4 N 0 1 N N N 16.873 19.166 -9.211 -6.266 -1.320 1.373 N4 9CS 22 9CS O5 O5 O 0 1 N N N 8.594 13.199 -12.671 3.158 -0.636 -1.094 O5 9CS 23 9CS O7 O7 O 0 1 N N N 8.093 11.125 -9.086 5.541 -2.121 1.952 O7 9CS 24 9CS O8 O8 O 0 1 N N N 8.140 9.659 -11.615 6.526 -0.062 0.228 O8 9CS 25 9CS O9 O9 O 0 1 N N N 10.776 13.272 -11.705 2.143 0.131 0.862 O9 9CS 26 9CS O10 O10 O 0 1 N N N 11.167 16.068 -11.015 -0.435 -0.941 0.435 O10 9CS 27 9CS O11 O11 O 0 1 N N N 14.013 16.744 -11.218 -2.639 0.806 0.705 O11 9CS 28 9CS O12 O12 O 0 1 N N N 12.767 18.358 -9.920 -3.510 0.205 -1.375 O12 9CS 29 9CS O13 O13 O 0 1 N N N 15.857 18.788 -11.908 -5.218 1.350 1.657 O13 9CS 30 9CS O14 O14 O 0 1 N N N 15.333 17.655 -7.201 -4.581 -3.083 -0.163 O14 9CS 31 9CS O15 O15 O 0 1 N N N 11.367 17.165 -7.399 -1.897 -1.539 -2.970 O15 9CS 32 9CS N6 N6 N 0 1 N N N 9.406 13.653 -9.112 2.674 -2.315 2.168 N6 9CS 33 9CS H1 H1 H 0 1 N N N 9.372 14.787 -11.546 1.549 -1.553 -0.177 H1 9CS 34 9CS H2 H2 H 0 1 N N N 7.677 13.529 -10.235 3.573 -2.861 0.348 H2 9CS 35 9CS H3 H3 H 0 1 N N N 9.747 11.268 -10.297 4.463 -0.359 1.857 H3 9CS 36 9CS H4 H4 H 0 1 N N N 6.910 11.305 -11.422 5.591 -1.680 -0.655 H4 9CS 37 9CS H5 H5 H 0 1 N N N 9.596 11.410 -12.915 4.147 0.984 -0.278 H5 9CS 38 9CS H61 H61 H 0 1 N N N 7.178 10.376 -13.698 5.970 0.945 -2.007 H61 9CS 39 9CS H62 H62 H 0 1 N N N 6.853 12.108 -14.034 5.143 -0.417 -2.799 H62 9CS 40 9CS H7 H7 H 0 1 N N N 14.799 14.612 -12.276 -1.210 2.812 1.722 H7 9CS 41 9CS H8 H8 H 0 1 N N N 12.782 16.807 -12.943 -1.353 1.198 -0.864 H8 9CS 42 9CS H9 H9 H 0 1 N N N 12.718 14.700 -10.742 -0.280 0.501 1.907 H9 9CS 43 9CS H10 H10 H 0 1 N N N 10.956 14.707 -13.230 1.120 0.849 -0.783 H10 9CS 44 9CS H11 H11 H 0 1 N N N 13.222 12.811 -12.580 1.262 2.463 1.804 H11 9CS 45 9CS H121 H121 H 0 0 N N N 13.037 14.973 -14.753 0.190 3.161 -0.967 H121 9CS 46 9CS H122 H122 H 0 0 N N N 14.353 13.769 -14.596 0.302 4.278 0.413 H122 9CS 47 9CS H13 H13 H 0 1 N N N 13.190 18.510 -11.950 -3.769 2.055 -0.492 H13 9CS 48 9CS H14 H14 H 0 1 N N N 14.770 19.973 -10.605 -5.864 0.782 -0.222 H14 9CS 49 9CS H15 H15 H 0 1 N N N 15.953 17.322 -9.708 -4.183 -1.081 1.521 H15 9CS 50 9CS H16 H16 H 0 1 N N N 14.612 19.449 -7.977 -5.529 -1.553 -1.181 H16 9CS 51 9CS H17 H17 H 0 1 N N N 13.459 16.787 -8.683 -2.575 -1.375 -0.427 H17 9CS 52 9CS H181 H181 H 0 0 N N N 12.795 18.443 -6.586 -3.138 -3.017 -2.232 H181 9CS 53 9CS H182 H182 H 0 0 N N N 11.744 19.169 -7.833 -3.950 -1.713 -3.131 H182 9CS 54 9CS HN11 HN11 H 0 0 N N N 7.813 11.236 -15.933 4.523 1.692 -3.778 HN11 9CS 55 9CS HN12 HN12 H 0 0 N N N 9.032 12.051 -15.215 3.202 1.030 -3.015 HN12 9CS 56 9CS HN21 HN21 H 0 0 N N N 11.860 13.061 -15.143 2.687 3.859 0.384 HN21 9CS 57 9CS HN22 HN22 H 0 0 N N N 12.594 11.759 -14.487 3.344 2.352 0.638 HN22 9CS 58 9CS HN31 HN31 H 0 0 N N N 15.059 16.251 -14.615 -2.158 4.522 0.320 HN31 9CS 59 9CS HN32 HN32 H 0 0 N N N 15.431 16.929 -13.177 -2.302 3.447 -0.941 HN32 9CS 60 9CS HN41 HN41 H 0 0 N N N 17.374 19.347 -10.057 -6.473 -0.804 2.215 HN41 9CS 61 9CS HN42 HN42 H 0 0 N N N 16.600 20.033 -8.793 -7.011 -1.225 0.699 HN42 9CS 62 9CS HO7 HO7 H 0 1 N N N 8.752 11.015 -8.411 6.392 -1.728 2.190 HO7 9CS 63 9CS HO8 HO8 H 0 1 N N N 8.175 9.409 -12.531 7.185 -0.560 0.731 HO8 9CS 64 9CS HO10 HO10 H 0 0 N N N 11.348 16.251 -10.101 -1.222 -1.355 0.813 HO10 9CS 65 9CS HO13 HO13 H 0 0 N N N 15.334 18.761 -12.701 -5.256 2.306 1.517 HO13 9CS 66 9CS HO14 HO14 H 0 0 N N N 15.464 16.753 -7.470 -4.406 -3.647 -0.928 HO14 9CS 67 9CS HO15 HO15 H 0 0 N N N 11.164 16.807 -8.255 -1.673 -1.974 -3.804 HO15 9CS 68 9CS HN61 HN61 H 0 0 N N N 10.376 13.767 -9.326 1.803 -2.788 1.980 HN61 9CS 69 9CS HN62 HN62 H 0 0 N N N 9.019 14.534 -8.841 3.269 -2.875 2.760 HN62 9CS 70 # 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 9CS C1 O5 SING N N 1 9CS C1 O9 SING N N 2 9CS C1 C2 SING N N 3 9CS C1 H1 SING N N 4 9CS C2 C3 SING N N 5 9CS C2 N6 SING N N 6 9CS C2 H2 SING N N 7 9CS C3 C4 SING N N 8 9CS C3 O7 SING N N 9 9CS C3 H3 SING N N 10 9CS C4 C5 SING N N 11 9CS C4 O8 SING N N 12 9CS C4 H4 SING N N 13 9CS C5 C6 SING N N 14 9CS C5 O5 SING N N 15 9CS C5 H5 SING N N 16 9CS C6 N1 SING N N 17 9CS C6 H61 SING N N 18 9CS C6 H62 SING N N 19 9CS C7 C12 SING N N 20 9CS C7 N3 SING N N 21 9CS C7 C8 SING N N 22 9CS C7 H7 SING N N 23 9CS C8 C9 SING N N 24 9CS C8 O11 SING N N 25 9CS C8 H8 SING N N 26 9CS C9 C10 SING N N 27 9CS C9 O10 SING N N 28 9CS C9 H9 SING N N 29 9CS C10 C11 SING N N 30 9CS C10 O9 SING N N 31 9CS C10 H10 SING N N 32 9CS C11 N2 SING N N 33 9CS C11 C12 SING N N 34 9CS C11 H11 SING N N 35 9CS C12 H121 SING N N 36 9CS C12 H122 SING N N 37 9CS C13 O11 SING N N 38 9CS C13 C14 SING N N 39 9CS C13 O12 SING N N 40 9CS C13 H13 SING N N 41 9CS C14 O13 SING N N 42 9CS C14 C15 SING N N 43 9CS C14 H14 SING N N 44 9CS C15 N4 SING N N 45 9CS C15 C16 SING N N 46 9CS C15 H15 SING N N 47 9CS C16 C17 SING N N 48 9CS C16 O14 SING N N 49 9CS C16 H16 SING N N 50 9CS C17 O12 SING N N 51 9CS C17 C18 SING N N 52 9CS C17 H17 SING N N 53 9CS C18 O15 SING N N 54 9CS C18 H181 SING N N 55 9CS C18 H182 SING N N 56 9CS N1 HN11 SING N N 57 9CS N1 HN12 SING N N 58 9CS N2 HN21 SING N N 59 9CS N2 HN22 SING N N 60 9CS N3 HN31 SING N N 61 9CS N3 HN32 SING N N 62 9CS N4 HN41 SING N N 63 9CS N4 HN42 SING N N 64 9CS O7 HO7 SING N N 65 9CS O8 HO8 SING N N 66 9CS O10 HO10 SING N N 67 9CS O13 HO13 SING N N 68 9CS O14 HO14 SING N N 69 9CS O15 HO15 SING N N 70 9CS N6 HN61 SING N N 71 9CS N6 HN62 SING N N 72 # 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 9CS SMILES ACDLabs 10.04 "O(C2C(O)C(OC1OC(CN)C(O)C(O)C1N)C(N)CC2N)C3OC(C(O)C(N)C3O)CO" 9CS SMILES_CANONICAL CACTVS 3.341 "NC[C@H]1O[C@H](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)[C@H](N)[C@@H](O)[C@@H]1O" 9CS SMILES CACTVS 3.341 "NC[CH]1O[CH](O[CH]2[CH](N)C[CH](N)[CH](O[CH]3O[CH](CO)[CH](O)[CH](N)[CH]3O)[CH]2O)[CH](N)[CH](O)[CH]1O" 9CS SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1[C@@H]([C@H]([C@@H]([C@H]([C@@H]1N)O[C@@H]2[C@@H]([C@H]([C@@H]([C@H](O2)CO)O)N)O)O)O[C@@H]3[C@@H]([C@H]([C@@H]([C@H](O3)CN)O)O)N)N" 9CS SMILES "OpenEye OEToolkits" 1.5.0 "C1C(C(C(C(C1N)OC2C(C(C(C(O2)CO)O)N)O)O)OC3C(C(C(C(O3)CN)O)O)N)N" 9CS InChI InChI 1.03 "InChI=1S/C18H37N5O10/c19-2-6-11(26)12(27)9(23)17(30-6)32-15-4(20)1-5(21)16(14(15)29)33-18-13(28)8(22)10(25)7(3-24)31-18/h4-18,24-29H,1-3,19-23H2/t4-,5+,6+,7+,8-,9+,10+,11+,12+,13+,14-,15+,16-,17+,18+/m0/s1" 9CS InChIKey InChI 1.03 SKKLOUVUUNMCJE-FQSMHNGLSA-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 9CS "SYSTEMATIC NAME" ACDLabs 10.04 "(1R,2S,3S,4R,6S)-4,6-diamino-3-[(3-amino-3-deoxy-alpha-D-glucopyranosyl)oxy]-2-hydroxycyclohexyl 2,6-diamino-2,6-dideoxy-alpha-D-glucopyranoside" 9CS "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(2R,3S,4R,5R,6R)-5-amino-2-(aminomethyl)-6-[(1R,2S,3S,4R,6S)-4,6-diamino-3-[(2S,3R,4S,5S,6R)-4-amino-3,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-2-hydroxy-cyclohexyl]oxy-oxane-3,4-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 9CS "Create component" 2007-07-13 RCSB 9CS "Modify descriptor" 2011-06-04 RCSB 9CS "Modify synonyms" 2016-11-30 RCSB 9CS "Modify synonyms" 2020-05-26 PDBE # loop_ _pdbx_chem_comp_synonyms.ordinal _pdbx_chem_comp_synonyms.comp_id _pdbx_chem_comp_synonyms.name _pdbx_chem_comp_synonyms.provenance _pdbx_chem_comp_synonyms.type 1 9CS "Kanamycin B" ? ? 2 9CS Bekanamycin ? ? #