data_RIO # _chem_comp.id RIO _chem_comp.name RIBOSTAMYCIN _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C17 H34 N4 O10" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ;5-AMINO-2-AMINOMETHYL-6-[4,6-DIAMINO-2-(3,4-DIHYDROXY-5-HYDROXYMETHYL-TETRAHYDRO-FURAN-2-YLOXY)-3-HYDROXY-CYCLOHEXYLOXY ]-TETRAHYDRO-PYRAN-3,4-DIOL; (1R,2R,3S,4R,6S)-4,6-diamino-3-hydroxy-2-(beta-D-ribofuranosyloxy)cyclohexyl 2,6-diamino-2,6-dideoxy-alpha-D-glucopyranoside ; _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2002-07-08 _chem_comp.pdbx_modified_date 2020-06-17 _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 454.473 _chem_comp.one_letter_code ? _chem_comp.three_letter_code RIO _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 1M4G _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 RIO O1 O1 O 0 1 N N N 24.194 29.545 11.223 -2.539 2.965 -2.713 O1 RIO 1 RIO C1 C1 C 0 1 N N N 23.639 29.733 9.924 -3.088 3.041 -1.396 C1 RIO 2 RIO C2 C2 C 0 1 N N R 22.270 30.359 10.078 -3.564 1.653 -0.962 C2 RIO 3 RIO O2 O2 O 0 1 N N N 21.509 29.585 11.021 -2.437 0.773 -0.817 O2 RIO 4 RIO C3 C3 C 0 1 N N S 20.725 30.474 11.854 -2.741 -0.126 0.271 C3 RIO 5 RIO O3 O3 O 0 1 N N N 21.403 30.562 13.096 -1.543 -0.688 0.810 O3 RIO 6 RIO C4 C4 C 0 1 N N R 21.114 29.584 14.101 -0.851 -1.556 -0.090 C4 RIO 7 RIO C5 C5 C 0 1 N N S 21.571 28.179 13.689 -1.357 -2.988 0.093 C5 RIO 8 RIO O4 O4 O 0 1 N N N 22.987 28.206 13.417 -2.759 -3.037 -0.181 O4 RIO 9 RIO C6 C6 C 0 1 N N R 21.303 27.081 14.764 -0.617 -3.917 -0.871 C6 RIO 10 RIO N1 N1 N 0 1 N N N 21.626 25.763 14.126 -1.102 -5.293 -0.696 N1 RIO 11 RIO C7 C7 C 0 1 N N N 19.823 27.049 15.165 0.884 -3.865 -0.578 C7 RIO 12 RIO C8 C8 C 0 1 N N S 19.357 28.493 15.631 1.390 -2.433 -0.761 C8 RIO 13 RIO N2 N2 N 0 1 N N N 17.884 28.464 15.950 2.831 -2.382 -0.479 N2 RIO 14 RIO C9 C9 C 0 1 N N R 19.619 29.587 14.567 0.650 -1.503 0.203 C9 RIO 15 RIO O5 O5 O 0 1 N N N 19.242 30.771 15.224 1.122 -0.166 0.032 O5 RIO 16 RIO C10 C10 C 0 1 N N R 19.276 32.054 14.610 1.709 0.398 1.207 C10 RIO 17 RIO O6 O6 O 0 1 N N N 18.499 32.005 13.376 3.099 0.066 1.251 O6 RIO 18 RIO C11 C11 C 0 1 N N R 17.073 31.761 13.441 3.844 0.523 0.121 C11 RIO 19 RIO C12 C12 C 0 1 N N N 16.509 32.091 12.051 5.304 0.088 0.263 C12 RIO 20 RIO N3 N3 N 0 1 N N N 17.198 31.238 11.064 5.388 -1.376 0.189 N3 RIO 21 RIO C13 C13 C 0 1 N N S 16.388 32.628 14.526 3.771 2.051 0.047 C13 RIO 22 RIO O7 O7 O 0 1 N N N 15.072 32.122 14.687 4.468 2.507 -1.114 O7 RIO 23 RIO C14 C14 C 0 1 N N R 17.180 32.539 15.849 2.303 2.481 -0.034 C14 RIO 24 RIO O8 O8 O 0 1 N N N 16.552 33.398 16.846 2.222 3.907 -0.029 O8 RIO 25 RIO C15 C15 C 0 1 N N R 18.631 33.011 15.610 1.551 1.920 1.177 C15 RIO 26 RIO N4 N4 N 0 1 N N N 19.377 32.950 16.913 0.126 2.263 1.071 N4 RIO 27 RIO C16 C16 C 0 1 N N R 20.846 31.839 11.190 -3.433 0.789 1.313 C16 RIO 28 RIO O9 O9 O 0 1 N N N 19.857 31.990 10.220 -4.290 0.030 2.168 O9 RIO 29 RIO C17 C17 C 0 1 N N S 22.237 31.788 10.569 -4.254 1.743 0.413 C17 RIO 30 RIO O10 O10 O 0 1 N N N 22.233 32.707 9.446 -5.610 1.301 0.321 O10 RIO 31 RIO HO1 HO1 H 0 1 N N N 25.141 29.503 11.160 -2.216 3.811 -3.054 HO1 RIO 32 RIO H1 H1 H 0 1 N N N 24.288 30.395 9.332 -2.324 3.396 -0.704 H1 RIO 33 RIO H1A H1A H 0 1 N N N 23.557 28.767 9.404 -3.931 3.732 -1.393 H1A RIO 34 RIO H2 H2 H 0 1 N N N 21.859 30.367 9.058 -4.256 1.251 -1.701 H2 RIO 35 RIO H3 H3 H 0 1 N N N 19.683 30.147 11.982 -3.418 -0.914 -0.061 H3 RIO 36 RIO H4 H4 H 0 1 N N N 21.707 29.885 14.978 -1.033 -1.234 -1.116 H4 RIO 37 RIO H5 H5 H 0 1 N N N 20.980 27.912 12.801 -1.176 -3.309 1.118 H5 RIO 38 RIO HO4 HO4 H 0 1 N N N 23.129 28.212 12.478 -3.148 -3.917 -0.085 HO4 RIO 39 RIO H6 H6 H 0 1 N N N 21.909 27.286 15.659 -0.798 -3.596 -1.897 H6 RIO 40 RIO HN1 HN1 H 0 1 N N N 21.698 25.880 13.136 -0.628 -5.926 -1.321 HN1 RIO 41 RIO HN1A HN1A H 0 0 N N N 22.495 25.423 14.485 -1.004 -5.591 0.263 HN1A RIO 42 RIO H7 H7 H 0 1 N N N 19.219 26.733 14.302 1.066 -4.186 0.448 H7 RIO 43 RIO H7A H7A H 0 1 N N N 19.688 26.340 15.995 1.412 -4.527 -1.265 H7A RIO 44 RIO H8 H8 H 0 1 N N N 19.952 28.750 16.520 1.209 -2.112 -1.787 H8 RIO 45 RIO HN2 HN2 H 0 1 N N N 17.757 28.458 16.942 3.353 -2.897 -1.173 HN2 RIO 46 RIO HN2A HN2A H 0 0 N N N 17.443 29.274 15.563 3.154 -1.429 -0.417 HN2A RIO 47 RIO H9 H9 H 0 1 N N N 19.056 29.441 13.634 0.831 -1.824 1.229 H9 RIO 48 RIO H10 H10 H 0 1 N N N 20.297 32.376 14.359 1.212 -0.002 2.090 H10 RIO 49 RIO H11 H11 H 0 1 N N N 16.879 30.714 13.718 3.424 0.095 -0.789 H11 RIO 50 RIO H12 H12 H 0 1 N N N 15.427 31.893 12.028 5.894 0.527 -0.542 H12 RIO 51 RIO H12A H12A H 0 0 N N N 16.672 33.153 11.816 5.692 0.427 1.224 H12A RIO 52 RIO HN3 HN3 H 0 1 N N N 17.354 31.758 10.224 5.027 -1.716 -0.690 HN3 RIO 53 RIO HN3A HN3A H 0 0 N N N 18.076 30.938 11.438 6.335 -1.692 0.337 HN3A RIO 54 RIO H13 H13 H 0 1 N N N 16.358 33.688 14.233 4.229 2.480 0.939 H13 RIO 55 RIO HO7 HO7 H 0 1 N N N 14.887 32.009 15.612 4.462 3.467 -1.224 HO7 RIO 56 RIO H14 H14 H 0 1 N N N 17.184 31.499 16.207 1.860 2.093 -0.951 H14 RIO 57 RIO HO8 HO8 H 0 1 N N N 16.415 32.906 17.647 2.684 4.330 -0.766 HO8 RIO 58 RIO H15 H15 H 0 1 N N N 18.653 34.040 15.222 1.962 2.347 2.091 H15 RIO 59 RIO HN4 HN4 H 0 1 N N N 20.361 32.936 16.734 -0.393 1.900 1.857 HN4 RIO 60 RIO HN4A HN4A H 0 0 N N N 19.150 33.752 17.465 -0.000 3.261 0.985 HN4A RIO 61 RIO H16 H16 H 0 1 N N N 20.719 32.687 11.879 -2.695 1.341 1.896 H16 RIO 62 RIO HO9 HO9 H 0 1 N N N 19.005 32.024 10.639 -3.831 -0.645 2.687 HO9 RIO 63 RIO H17 H17 H 0 1 N N N 23.082 32.051 11.223 -4.210 2.762 0.797 H17 RIO 64 RIO HO10 HO10 H 0 0 N N N 22.232 33.601 9.768 -6.093 1.336 1.158 HO10 RIO 65 # # 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 RIO O1 C1 SING N N 1 RIO C1 C2 SING N N 2 RIO C2 O2 SING N N 3 RIO C2 C17 SING N N 4 RIO O2 C3 SING N N 5 RIO C3 O3 SING N N 6 RIO C3 C16 SING N N 7 RIO O3 C4 SING N N 8 RIO C4 C5 SING N N 9 RIO C4 C9 SING N N 10 RIO C5 O4 SING N N 11 RIO C5 C6 SING N N 12 RIO C6 N1 SING N N 13 RIO C6 C7 SING N N 14 RIO C7 C8 SING N N 15 RIO C8 N2 SING N N 16 RIO C8 C9 SING N N 17 RIO C9 O5 SING N N 18 RIO O5 C10 SING N N 19 RIO C10 O6 SING N N 20 RIO C10 C15 SING N N 21 RIO O6 C11 SING N N 22 RIO C11 C12 SING N N 23 RIO C11 C13 SING N N 24 RIO C12 N3 SING N N 25 RIO C13 O7 SING N N 26 RIO C13 C14 SING N N 27 RIO C14 O8 SING N N 28 RIO C14 C15 SING N N 29 RIO C15 N4 SING N N 30 RIO C16 O9 SING N N 31 RIO C16 C17 SING N N 32 RIO C17 O10 SING N N 33 RIO O1 HO1 SING N N 34 RIO C1 H1 SING N N 35 RIO C1 H1A SING N N 36 RIO C2 H2 SING N N 37 RIO C3 H3 SING N N 38 RIO C4 H4 SING N N 39 RIO C5 H5 SING N N 40 RIO O4 HO4 SING N N 41 RIO C6 H6 SING N N 42 RIO N1 HN1 SING N N 43 RIO N1 HN1A SING N N 44 RIO C7 H7 SING N N 45 RIO C7 H7A SING N N 46 RIO C8 H8 SING N N 47 RIO N2 HN2 SING N N 48 RIO N2 HN2A SING N N 49 RIO C9 H9 SING N N 50 RIO C10 H10 SING N N 51 RIO C11 H11 SING N N 52 RIO C12 H12 SING N N 53 RIO C12 H12A SING N N 54 RIO N3 HN3 SING N N 55 RIO N3 HN3A SING N N 56 RIO C13 H13 SING N N 57 RIO O7 HO7 SING N N 58 RIO C14 H14 SING N N 59 RIO O8 HO8 SING N N 60 RIO C15 H15 SING N N 61 RIO N4 HN4 SING N N 62 RIO N4 HN4A SING N N 63 RIO C16 H16 SING N N 64 RIO O9 HO9 SING N N 65 RIO C17 H17 SING N N 66 RIO O10 HO10 SING N N 67 # # 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 RIO SMILES ACDLabs 10.04 "O(C2C(OC1OC(CN)C(O)C(O)C1N)C(N)CC(N)C2O)C3OC(C(O)C3O)CO" RIO 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]2O[C@@H]3O[C@H](CO)[C@@H](O)[C@H]3O)[C@H](N)[C@@H](O)[C@@H]1O" RIO SMILES CACTVS 3.341 "NC[CH]1O[CH](O[CH]2[CH](N)C[CH](N)[CH](O)[CH]2O[CH]3O[CH](CO)[CH](O)[CH]3O)[CH](N)[CH](O)[CH]1O" RIO 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)CN)O)O)N)O[C@H]3[C@@H]([C@@H]([C@H](O3)CO)O)O)O)N" RIO SMILES "OpenEye OEToolkits" 1.5.0 "C1C(C(C(C(C1N)OC2C(C(C(C(O2)CN)O)O)N)OC3C(C(C(O3)CO)O)O)O)N" RIO InChI InChI 1.03 "InChI=1S/C17H34N4O10/c18-2-6-10(24)12(26)8(21)16(28-6)30-14-5(20)1-4(19)9(23)15(14)31-17-13(27)11(25)7(3-22)29-17/h4-17,22-27H,1-3,18-21H2/t4-,5+,6-,7-,8-,9+,10-,11-,12-,13-,14-,15-,16-,17+/m1/s1" RIO InChIKey InChI 1.03 NSKGQURZWSPSBC-VVPCINPTSA-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 RIO "SYSTEMATIC NAME" ACDLabs 10.04 "(1R,2R,3S,4R,6S)-4,6-diamino-3-hydroxy-2-(beta-D-ribofuranosyloxy)cyclohexyl 2,6-diamino-2,6-dideoxy-alpha-D-glucopyranoside" RIO "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(2R,3S,4R,5R,6R)-5-amino-2-(aminomethyl)-6-[(1R,2R,3S,4R,6S)-4,6-diamino-2-[(2S,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy-3-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 RIO "Create component" 2002-07-08 RCSB RIO "Modify descriptor" 2011-06-04 RCSB RIO "Modify synonyms" 2020-06-05 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 RIO "5-AMINO-2-AMINOMETHYL-6-[4,6-DIAMINO-2-(3,4-DIHYDROXY-5-HYDROXYMETHYL-TETRAHYDRO-FURAN-2-YLOXY)-3-HYDROXY-CYCLOHEXYLOXY]-TETRAHYDRO-PYRAN-3,4-DIOL" ? ? 2 RIO "(1R,2R,3S,4R,6S)-4,6-diamino-3-hydroxy-2-(beta-D-ribofuranosyloxy)cyclohexyl 2,6-diamino-2,6-dideoxy-alpha-D-glucopyranoside" ? ? ##