data_TOY # _chem_comp.id TOY _chem_comp.name TOBRAMYCIN _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAD _chem_comp.formula "C18 H37 N5 O9" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "4-AMINO-2-[4,6-DIAMINO-3-(3-AMINO-6-AMINOMETHYL-5-HYDROXY-TETRAHYDRO-PYRAN-2-YLOXY)-2-HYDROXY-CYCLOHEXYLOXY]-6-HYDROXYMETHYL-TETRAHYDRO-PYRAN-3,5-DIOL" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2002-04-09 _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 467.514 _chem_comp.one_letter_code ? _chem_comp.three_letter_code TOY _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details ? _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 1LC4 _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site EBI # # 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 TOY C11 C11 C 0 1 N N R 11.840 -7.108 5.575 -1.142 -0.196 -2.574 C11 TOY 1 TOY O11 O11 O 0 1 N N N 13.055 -7.680 5.183 0.028 -0.989 -2.371 O11 TOY 2 TOY C21 C21 C 0 1 N N R 10.692 -7.628 4.673 -2.181 -1.012 -3.346 C21 TOY 3 TOY N21 N21 N 0 1 N N N 10.573 -9.108 4.690 -2.551 -2.200 -2.565 N21 TOY 4 TOY C31 C31 C 0 1 N N N 10.848 -7.107 3.231 -1.580 -1.445 -4.688 C31 TOY 5 TOY C41 C41 C 0 1 N N S 10.940 -5.573 3.252 -1.058 -0.200 -5.414 C41 TOY 6 TOY O41 O41 O 0 1 N N N 11.078 -5.083 1.923 -0.362 -0.593 -6.598 O41 TOY 7 TOY C51 C51 C 0 1 N N R 12.136 -5.142 4.130 -0.102 0.554 -4.486 C51 TOY 8 TOY O51 O51 O 0 1 N N N 11.964 -5.655 5.484 -0.799 0.973 -3.315 O51 TOY 9 TOY C61 C61 C 0 1 N N N 12.296 -3.629 4.239 0.451 1.780 -5.215 C61 TOY 10 TOY N61 N61 N 0 1 N N N 12.888 -3.046 3.011 1.371 2.503 -4.326 N61 TOY 11 TOY C12 C12 C 0 1 N N R 16.671 -8.899 7.111 2.642 -0.465 0.915 C12 TOY 12 TOY N12 N12 N 0 1 N N N 17.844 -8.943 8.018 3.431 0.201 1.959 N12 TOY 13 TOY C22 C22 C 0 1 N N N 16.702 -7.619 6.265 3.100 0.022 -0.460 C22 TOY 14 TOY C32 C32 C 0 1 N N S 15.481 -7.595 5.314 2.277 -0.671 -1.547 C32 TOY 15 TOY N32 N32 N 0 1 N N N 15.602 -6.428 4.401 2.717 -0.203 -2.868 N32 TOY 16 TOY C42 C42 C 0 1 N N R 14.164 -7.620 6.118 0.796 -0.341 -1.356 C42 TOY 17 TOY C52 C52 C 0 1 N N S 14.122 -8.865 7.052 0.338 -0.829 0.019 C52 TOY 18 TOY O52 O52 O 0 1 N N N 12.973 -8.788 7.881 -1.045 -0.520 0.198 O52 TOY 19 TOY C62 C62 C 0 1 N N S 15.384 -8.933 7.949 1.160 -0.134 1.107 C62 TOY 20 TOY O62 O62 O 0 1 N N N 15.356 -10.153 8.726 0.732 -0.590 2.392 O62 TOY 21 TOY C13 C13 C 0 1 N N S 15.424 -10.045 10.116 0.951 0.485 3.306 C13 TOY 22 TOY C23 C23 C 0 1 N N R 15.972 -11.354 10.714 0.886 -0.043 4.740 C23 TOY 23 TOY O23 O23 O 0 1 N N N 17.273 -11.609 10.210 1.910 -1.021 4.936 O23 TOY 24 TOY C33 C33 C 0 1 N N S 15.035 -12.506 10.356 -0.484 -0.683 4.976 C33 TOY 25 TOY N33 N33 N 0 1 N N N 15.568 -13.807 10.829 -0.621 -1.059 6.389 N33 TOY 26 TOY C43 C43 C 0 1 N N S 13.653 -12.229 10.970 -1.569 0.334 4.607 C43 TOY 27 TOY O43 O43 O 0 1 N N N 12.748 -13.280 10.641 -2.854 -0.286 4.677 O43 TOY 28 TOY C53 C53 C 0 1 N N R 13.107 -10.869 10.470 -1.320 0.835 3.183 C53 TOY 29 TOY O53 O53 O 0 1 N N N 14.090 -9.783 10.648 -0.050 1.482 3.114 O53 TOY 30 TOY C63 C63 C 0 1 N N N 11.851 -10.453 11.213 -2.418 1.828 2.795 C63 TOY 31 TOY O63 O63 O 0 1 N N N 12.112 -10.225 12.594 -2.245 2.221 1.432 O63 TOY 32 TOY H11 H11 H 0 1 N N N 11.598 -7.392 6.626 -1.554 0.094 -1.608 H11 TOY 33 TOY H21 H21 H 0 1 N N N 9.743 -7.226 5.099 -3.067 -0.402 -3.523 H21 TOY 34 TOY HN21 1HN2 H 0 0 N N N 10.475 -9.456 5.644 -3.234 -2.704 -3.111 HN21 TOY 35 TOY HN22 2HN2 H 0 0 N N N 9.817 -9.450 4.096 -1.729 -2.784 -2.518 HN22 TOY 36 TOY H311 1H31 H 0 0 N N N 10.036 -7.472 2.560 -0.758 -2.139 -4.514 H311 TOY 37 TOY H312 2H31 H 0 0 N N N 11.712 -7.575 2.704 -2.347 -1.926 -5.294 H312 TOY 38 TOY H41 H41 H 0 1 N N N 10.008 -5.142 3.688 -1.895 0.444 -5.680 H41 TOY 39 TOY H41O OH41 H 0 0 N N N 11.135 -4.135 1.936 -0.997 -1.071 -7.150 H41O TOY 40 TOY H51 H51 H 0 1 N N N 13.043 -5.558 3.633 0.720 -0.101 -4.203 H51 TOY 41 TOY H611 1H61 H 0 0 N N N 12.882 -3.348 5.145 -0.370 2.436 -5.499 H611 TOY 42 TOY H612 2H61 H 0 0 N N N 11.329 -3.137 4.496 0.986 1.460 -6.109 H612 TOY 43 TOY HN61 1HN6 H 0 0 N N N 12.352 -3.303 2.183 1.710 3.299 -4.846 HN61 TOY 44 TOY HN62 2HN6 H 0 0 N N N 12.995 -2.034 3.084 0.814 2.867 -3.568 HN62 TOY 45 TOY H12 H12 H 0 1 N N N 16.701 -9.780 6.429 2.785 -1.543 0.984 H12 TOY 46 TOY HN11 1HN1 H 0 0 N N N 17.910 -8.105 8.597 4.396 -0.043 1.794 HN11 TOY 47 TOY HN12 2HN1 H 0 0 N N N 17.823 -9.794 8.580 3.352 1.193 1.794 HN12 TOY 48 TOY H221 1H22 H 0 0 N N N 17.665 -7.501 5.716 4.155 -0.212 -0.596 H221 TOY 49 TOY H222 2H22 H 0 0 N N N 16.763 -6.700 6.894 2.956 1.101 -0.529 H222 TOY 50 TOY H32 H32 H 0 1 N N N 15.461 -8.512 4.680 2.421 -1.750 -1.478 H32 TOY 51 TOY HN1 1HN H 0 1 N N N 16.488 -6.420 3.896 3.723 -0.277 -2.882 HN1 TOY 52 TOY HN2 2HN H 0 1 N N N 14.797 -6.412 3.774 2.368 -0.867 -3.542 HN2 TOY 53 TOY H42 H42 H 0 1 N N N 14.094 -6.702 6.747 0.653 0.737 -1.425 H42 TOY 54 TOY H52 H52 H 0 1 N N N 14.086 -9.780 6.416 0.481 -1.907 0.088 H52 TOY 55 TOY H52O OH52 H 0 0 N N N 12.947 -9.548 8.451 -1.325 -0.955 1.015 H52O TOY 56 TOY H62 H62 H 0 1 N N N 15.379 -8.043 8.621 1.017 0.943 1.037 H62 TOY 57 TOY H13 H13 H 0 1 N N N 16.105 -9.205 10.389 1.934 0.921 3.124 H13 TOY 58 TOY H23 H23 H 0 1 N N N 16.031 -11.259 11.823 1.029 0.779 5.440 H23 TOY 59 TOY H23O OH23 H 0 0 N N N 17.611 -12.416 10.579 2.754 -0.577 4.778 H23O TOY 60 TOY H33 H33 H 0 1 N N N 14.949 -12.573 9.246 -0.587 -1.570 4.350 H33 TOY 61 TOY HN31 1HN3 H 0 0 N N N 15.769 -13.787 11.829 0.110 -1.726 6.584 HN31 TOY 62 TOY HN32 2HN3 H 0 0 N N N 14.942 -14.576 10.590 -0.411 -0.233 6.930 HN32 TOY 63 TOY H43 H43 H 0 1 N N N 13.756 -12.183 12.079 -1.532 1.174 5.301 H43 TOY 64 TOY H43O OH43 H 0 0 N N N 11.894 -13.109 11.020 -3.504 0.386 4.432 H43O TOY 65 TOY H53 H53 H 0 1 N N N 12.885 -11.022 9.388 -1.335 -0.008 2.494 H53 TOY 66 TOY H631 1H63 H 0 0 N N N 11.029 -11.193 11.070 -3.393 1.356 2.916 H631 TOY 67 TOY H632 2H63 H 0 0 N N N 11.371 -9.566 10.737 -2.357 2.707 3.437 H632 TOY 68 TOY H63O OH63 H 0 0 N N N 11.326 -9.965 13.059 -2.905 2.903 1.252 H63O TOY 69 # # 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 TOY C11 O11 SING N N 1 TOY C11 C21 SING N N 2 TOY C11 O51 SING N N 3 TOY C11 H11 SING N N 4 TOY O11 C42 SING N N 5 TOY C21 N21 SING N N 6 TOY C21 C31 SING N N 7 TOY C21 H21 SING N N 8 TOY N21 HN21 SING N N 9 TOY N21 HN22 SING N N 10 TOY C31 C41 SING N N 11 TOY C31 H311 SING N N 12 TOY C31 H312 SING N N 13 TOY C41 O41 SING N N 14 TOY C41 C51 SING N N 15 TOY C41 H41 SING N N 16 TOY O41 H41O SING N N 17 TOY C51 O51 SING N N 18 TOY C51 C61 SING N N 19 TOY C51 H51 SING N N 20 TOY C61 N61 SING N N 21 TOY C61 H611 SING N N 22 TOY C61 H612 SING N N 23 TOY N61 HN61 SING N N 24 TOY N61 HN62 SING N N 25 TOY C12 N12 SING N N 26 TOY C12 C22 SING N N 27 TOY C12 C62 SING N N 28 TOY C12 H12 SING N N 29 TOY N12 HN11 SING N N 30 TOY N12 HN12 SING N N 31 TOY C22 C32 SING N N 32 TOY C22 H221 SING N N 33 TOY C22 H222 SING N N 34 TOY C32 N32 SING N N 35 TOY C32 C42 SING N N 36 TOY C32 H32 SING N N 37 TOY N32 HN1 SING N N 38 TOY N32 HN2 SING N N 39 TOY C42 C52 SING N N 40 TOY C42 H42 SING N N 41 TOY C52 O52 SING N N 42 TOY C52 C62 SING N N 43 TOY C52 H52 SING N N 44 TOY O52 H52O SING N N 45 TOY C62 O62 SING N N 46 TOY C62 H62 SING N N 47 TOY O62 C13 SING N N 48 TOY C13 C23 SING N N 49 TOY C13 O53 SING N N 50 TOY C13 H13 SING N N 51 TOY C23 O23 SING N N 52 TOY C23 C33 SING N N 53 TOY C23 H23 SING N N 54 TOY O23 H23O SING N N 55 TOY C33 N33 SING N N 56 TOY C33 C43 SING N N 57 TOY C33 H33 SING N N 58 TOY N33 HN31 SING N N 59 TOY N33 HN32 SING N N 60 TOY C43 O43 SING N N 61 TOY C43 C53 SING N N 62 TOY C43 H43 SING N N 63 TOY O43 H43O SING N N 64 TOY C53 O53 SING N N 65 TOY C53 C63 SING N N 66 TOY C53 H53 SING N N 67 TOY C63 O63 SING N N 68 TOY C63 H631 SING N N 69 TOY C63 H632 SING N N 70 TOY O63 H63O SING N N 71 # # 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 TOY SMILES ACDLabs 10.04 "O(C2C(O)C(OC1OC(CN)C(O)CC1N)C(N)CC2N)C3OC(C(O)C(N)C3O)CO" TOY 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[C@@H]1O" TOY 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)C[CH]1O" TOY 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[C@@H]([C@H](O3)CN)O)N)N" TOY SMILES "OpenEye OEToolkits" 1.5.0 "C1C(C(C(C(C1N)OC2C(C(C(C(O2)CO)O)N)O)O)OC3C(CC(C(O3)CN)O)N)N" TOY InChI InChI 1.03 "InChI=1S/C18H37N5O9/c19-3-9-8(25)2-7(22)17(29-9)31-15-5(20)1-6(21)16(14(15)28)32-18-13(27)11(23)12(26)10(4-24)30-18/h5-18,24-28H,1-4,19-23H2/t5-,6+,7+,8-,9+,10+,11-,12+,13+,14-,15+,16-,17+,18+/m0/s1" TOY InChIKey InChI 1.03 NLVFBUXFDBBNBW-PBSUHMDJSA-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 TOY "SYSTEMATIC NAME" ACDLabs 10.04 "(1S,2S,3R,4S,6R)-4,6-diamino-3-[(2,6-diamino-2,3,6-trideoxy-alpha-D-ribo-hexopyranosyl)oxy]-2-hydroxycyclohexyl 3-amino-3-deoxy-alpha-D-glucopyranoside" TOY "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(2S,3R,4S,5S,6R)-4-amino-2-[(1S,2S,3R,4S,6R)-4,6-diamino-3-[(2R,3R,5S,6R)-3-amino-6-(aminomethyl)-5-hydroxy-oxan-2-yl]oxy-2-hydroxy-cyclohexyl]oxy-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 TOY "Create component" 2002-04-09 EBI TOY "Modify descriptor" 2011-06-04 RCSB TOY "Modify synonyms" 2021-03-13 RCSB # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id TOY _pdbx_chem_comp_synonyms.name "4-AMINO-2-[4,6-DIAMINO-3-(3-AMINO-6-AMINOMETHYL-5-HYDROXY-TETRAHYDRO-PYRAN-2-YLOXY)-2-HYDROXY-CYCLOHEXYLOXY]-6-HYDROXYMETHYL-TETRAHYDRO-PYRAN-3,5-DIOL" _pdbx_chem_comp_synonyms.provenance PDB _pdbx_chem_comp_synonyms.type ? ##