data_CK0 # _chem_comp.id CK0 _chem_comp.name "(2S,3R,4S,5S,6R)-2-[(1S,2S,3R,4S,6R)-3-[(2R,3R,4R,5S,6R)-6-(aminomethyl)-3-azanyl-4,5-bis(oxidanyl)oxan-2-yl]oxy-4,6-bis(azanyl)-2-oxidanyl-cyclohexyl]oxy-6-(hydroxymethyl)oxane-3,4,5-triol" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C18 H36 N4 O11" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms '3"-deamino-3"-hydroxykanamycin B' _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2019-04-25 _chem_comp.pdbx_modified_date 2021-03-01 _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 484.499 _chem_comp.one_letter_code ? _chem_comp.three_letter_code CK0 _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 6JW8 _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBJ # # 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 CK0 C4 C1 C 0 1 N N S 47.993 3.457 1.105 -4.817 1.666 0.370 C4 CK0 1 CK0 C5 C2 C 0 1 N N R 49.018 3.720 -0.050 -3.480 1.324 1.032 C5 CK0 2 CK0 C6 C3 C 0 1 N N N 50.187 2.755 -0.164 -3.274 2.216 2.258 C6 CK0 3 CK0 C3 C4 C 0 1 N N S 46.818 4.418 0.828 -5.045 0.729 -0.820 C3 CK0 4 CK0 O2 O1 O 0 1 N N N 45.236 5.077 -0.932 -5.134 -1.606 -1.444 O2 CK0 5 CK0 C2 C5 C 0 1 N N R 46.243 4.175 -0.608 -4.994 -0.721 -0.331 C2 CK0 6 CK0 O3 O2 O 0 1 N N N 45.724 4.275 1.712 -6.325 0.994 -1.398 O3 CK0 7 CK0 O4 O3 O 0 1 N N N 48.627 3.694 2.424 -4.791 3.020 -0.087 O4 CK0 8 CK0 O6 O4 O 0 1 N N N 49.531 1.487 -0.136 -1.977 1.977 2.808 O6 CK0 9 CK0 O5 O5 O 0 1 N N N 48.443 3.451 -1.336 -3.488 -0.047 1.436 O5 CK0 10 CK0 C1 C6 C 0 1 N N S 47.330 4.252 -1.696 -3.650 -0.973 0.357 C1 CK0 11 CK0 O1 O6 O 0 1 N N N 47.761 5.593 -1.828 -2.591 -0.795 -0.586 O1 CK0 12 CK0 CBG C7 C 0 1 N N S 48.128 5.953 -3.110 -1.324 -1.277 -0.135 CBG CK0 13 CK0 CBA C8 C 0 1 N N S 49.575 6.462 -2.991 -0.207 -0.436 -0.757 CBA CK0 14 CK0 OAK O7 O 0 1 N N N 50.446 5.439 -2.532 -0.365 0.930 -0.365 OAK CK0 15 CK0 CAT C9 C 0 1 N N R 47.194 7.061 -3.610 -1.155 -2.739 -0.554 CAT CK0 16 CK0 NAC N1 N 0 1 N N N 45.740 6.700 -3.570 -2.227 -3.546 0.044 NAC CK0 17 CK0 CAN C10 C 0 1 N N N 47.620 7.375 -4.992 0.202 -3.254 -0.070 CAN CK0 18 CK0 CAS C11 C 0 1 N N S 48.929 8.074 -4.906 1.319 -2.413 -0.692 CAS CK0 19 CK0 NAB N2 N 0 1 N N N 49.256 8.611 -6.221 2.622 -2.908 -0.228 NAB CK0 20 CK0 CBF C12 C 0 1 N N R 49.981 6.995 -4.403 1.150 -0.951 -0.273 CBF CK0 21 CK0 OAQ O8 O 0 1 N N N 51.268 7.548 -4.282 2.193 -0.166 -0.854 OAQ CK0 22 CK0 CBD C13 C 0 1 N N R 52.443 6.671 -4.424 2.502 1.022 -0.122 CBD CK0 23 CK0 OAO O9 O 0 1 N N N 52.478 6.213 -5.800 3.188 0.674 1.082 OAO CK0 24 CK0 CBB C14 C 0 1 N N R 52.507 7.429 -6.660 4.404 -0.046 0.873 CBB CK0 25 CK0 CAL C15 C 0 1 N N N 52.235 7.027 -8.093 5.034 -0.387 2.226 CAL CK0 26 CK0 NAA N3 N 0 1 N N N 53.222 5.965 -8.373 4.156 -1.312 2.955 NAA CK0 27 CK0 CAX C16 C 0 1 N N S 53.849 8.168 -6.430 5.374 0.817 0.062 CAX CK0 28 CK0 OAH O10 O 0 1 N N N 54.071 9.307 -7.246 6.569 0.077 -0.197 OAH CK0 29 CK0 CAV C17 C 0 1 N N R 53.718 8.721 -5.073 4.714 1.204 -1.264 CAV CK0 30 CK0 OAF O11 O 0 1 N N N 54.807 9.588 -4.857 5.583 2.070 -1.996 OAF CK0 31 CK0 CAU C18 C 0 1 N N R 53.654 7.560 -4.082 3.396 1.928 -0.974 CAU CK0 32 CK0 NAD N4 N 0 1 N N N 53.472 8.115 -2.752 2.717 2.238 -2.239 NAD CK0 33 CK0 H1 H1 H 0 1 N N N 47.637 2.418 1.038 -5.624 1.541 1.092 H1 CK0 34 CK0 H2 H2 H 0 1 N N N 49.387 4.754 0.015 -2.670 1.489 0.322 H2 CK0 35 CK0 H3 H3 H 0 1 N N N 50.880 2.865 0.683 -3.357 3.262 1.964 H3 CK0 36 CK0 H4 H4 H 0 1 N N N 50.735 2.901 -1.107 -4.034 1.987 3.005 H4 CK0 37 CK0 H5 H5 H 0 1 N N N 47.201 5.449 0.869 -4.268 0.891 -1.566 H5 CK0 38 CK0 H6 H6 H 0 1 N N N 44.555 5.043 -0.270 -5.110 -2.543 -1.207 H6 CK0 39 CK0 H7 H7 H 0 1 N N N 45.835 3.154 -0.624 -5.805 -0.896 0.377 H7 CK0 40 CK0 H8 H8 H 0 1 N N N 46.018 4.413 2.605 -6.536 0.435 -2.159 H8 CK0 41 CK0 H9 H9 H 0 1 N N N 47.994 3.531 3.114 -5.607 3.305 -0.520 H9 CK0 42 CK0 H10 H10 H 0 1 N N N 50.177 0.794 -0.202 -1.777 2.510 3.590 H10 CK0 43 CK0 H11 H11 H 0 1 N N N 46.900 3.897 -2.644 -3.625 -1.991 0.745 H11 CK0 44 CK0 H12 H12 H 0 1 N N N 48.093 5.099 -3.802 -1.273 -1.202 0.952 H12 CK0 45 CK0 H13 H13 H 0 1 N N N 49.588 7.309 -2.290 -0.258 -0.510 -1.843 H13 CK0 46 CK0 H14 H14 H 0 1 N N N 50.165 5.144 -1.674 -1.156 1.353 -0.726 H14 CK0 47 CK0 H15 H15 H 0 1 N N N 47.351 7.950 -2.981 -1.206 -2.813 -1.640 H15 CK0 48 CK0 H16 H16 H 0 1 N N N 45.473 6.492 -2.629 -2.137 -4.516 -0.219 H16 CK0 49 CK0 H17 H17 H 0 1 N N N 45.196 7.468 -3.908 -2.241 -3.443 1.047 H17 CK0 50 CK0 H19 H19 H 0 1 N N N 46.877 8.026 -5.476 0.253 -3.180 1.016 H19 CK0 51 CK0 H20 H20 H 0 1 N N N 47.727 6.447 -5.572 0.323 -4.296 -0.369 H20 CK0 52 CK0 H21 H21 H 0 1 N N N 48.874 8.884 -4.164 1.268 -2.488 -1.779 H21 CK0 53 CK0 H22 H22 H 0 1 N N N 50.136 9.085 -6.179 2.760 -3.870 -0.500 H22 CK0 54 CK0 H23 H23 H 0 1 N N N 49.312 7.863 -6.882 3.372 -2.325 -0.567 H23 CK0 55 CK0 H25 H25 H 0 1 N N N 49.981 6.153 -5.111 1.201 -0.877 0.813 H25 CK0 56 CK0 H26 H26 H 0 1 N N N 52.389 5.825 -3.723 1.580 1.548 0.123 H26 CK0 57 CK0 H27 H27 H 0 1 N N N 51.698 8.101 -6.336 4.193 -0.966 0.328 H27 CK0 58 CK0 H28 H28 H 0 1 N N N 52.380 7.881 -8.771 6.004 -0.857 2.067 H28 CK0 59 CK0 H29 H29 H 0 1 N N N 51.210 6.643 -8.201 5.162 0.526 2.807 H29 CK0 60 CK0 H30 H30 H 0 1 N N N 53.107 5.642 -9.312 3.968 -2.139 2.408 H30 CK0 61 CK0 H31 H31 H 0 1 N N N 54.146 6.330 -8.257 4.549 -1.553 3.852 H31 CK0 62 CK0 H33 H33 H 0 1 N N N 54.684 7.455 -6.487 5.618 1.718 0.625 H33 CK0 63 CK0 H34 H34 H 0 1 N N N 54.914 9.690 -7.033 7.230 0.564 -0.708 H34 CK0 64 CK0 H35 H35 H 0 1 N N N 52.775 9.283 -5.006 4.517 0.306 -1.849 H35 CK0 65 CK0 H36 H36 H 0 1 N N N 54.748 9.961 -3.985 6.441 1.678 -2.209 H36 CK0 66 CK0 H37 H37 H 0 1 N N N 54.579 6.967 -4.139 3.599 2.852 -0.432 H37 CK0 67 CK0 H38 H38 H 0 1 N N N 53.427 7.372 -2.084 1.841 2.712 -2.073 H38 CK0 68 CK0 H39 H39 H 0 1 N N N 54.242 8.714 -2.533 3.312 2.782 -2.845 H39 CK0 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 CK0 NAA CAL SING N N 1 CK0 CAL CBB SING N N 2 CK0 OAH CAX SING N N 3 CK0 CBB CAX SING N N 4 CK0 CBB OAO SING N N 5 CK0 CAX CAV SING N N 6 CK0 NAB CAS SING N N 7 CK0 OAO CBD SING N N 8 CK0 CAV OAF SING N N 9 CK0 CAV CAU SING N N 10 CK0 CAN CAS SING N N 11 CK0 CAN CAT SING N N 12 CK0 CAS CBF SING N N 13 CK0 CBD OAQ SING N N 14 CK0 CBD CAU SING N N 15 CK0 CBF OAQ SING N N 16 CK0 CBF CBA SING N N 17 CK0 CAU NAD SING N N 18 CK0 CAT NAC SING N N 19 CK0 CAT CBG SING N N 20 CK0 CBG CBA SING N N 21 CK0 CBG O1 SING N N 22 CK0 CBA OAK SING N N 23 CK0 O1 C1 SING N N 24 CK0 C1 O5 SING N N 25 CK0 C1 C2 SING N N 26 CK0 O5 C5 SING N N 27 CK0 O2 C2 SING N N 28 CK0 C2 C3 SING N N 29 CK0 C6 O6 SING N N 30 CK0 C6 C5 SING N N 31 CK0 C5 C4 SING N N 32 CK0 C3 C4 SING N N 33 CK0 C3 O3 SING N N 34 CK0 C4 O4 SING N N 35 CK0 C4 H1 SING N N 36 CK0 C5 H2 SING N N 37 CK0 C6 H3 SING N N 38 CK0 C6 H4 SING N N 39 CK0 C3 H5 SING N N 40 CK0 O2 H6 SING N N 41 CK0 C2 H7 SING N N 42 CK0 O3 H8 SING N N 43 CK0 O4 H9 SING N N 44 CK0 O6 H10 SING N N 45 CK0 C1 H11 SING N N 46 CK0 CBG H12 SING N N 47 CK0 CBA H13 SING N N 48 CK0 OAK H14 SING N N 49 CK0 CAT H15 SING N N 50 CK0 NAC H16 SING N N 51 CK0 NAC H17 SING N N 52 CK0 CAN H19 SING N N 53 CK0 CAN H20 SING N N 54 CK0 CAS H21 SING N N 55 CK0 NAB H22 SING N N 56 CK0 NAB H23 SING N N 57 CK0 CBF H25 SING N N 58 CK0 CBD H26 SING N N 59 CK0 CBB H27 SING N N 60 CK0 CAL H28 SING N N 61 CK0 CAL H29 SING N N 62 CK0 NAA H30 SING N N 63 CK0 NAA H31 SING N N 64 CK0 CAX H33 SING N N 65 CK0 OAH H34 SING N N 66 CK0 CAV H35 SING N N 67 CK0 OAF H36 SING N N 68 CK0 CAU H37 SING N N 69 CK0 NAD H38 SING N N 70 CK0 NAD H39 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 CK0 InChI InChI 1.03 "InChI=1S/C18H36N4O11/c19-2-6-9(24)11(26)8(22)17(30-6)32-15-4(20)1-5(21)16(14(15)29)33-18-13(28)12(27)10(25)7(3-23)31-18/h4-18,23-29H,1-3,19-22H2/t4-,5+,6+,7+,8+,9+,10+,11+,12-,13+,14-,15+,16-,17+,18+/m0/s1" CK0 InChIKey InChI 1.03 MOWMHIINUAQFMU-DNBVWFFRSA-N CK0 SMILES_CANONICAL CACTVS 3.385 "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](O)[C@H]3O)[C@H]2O)[C@H](N)[C@@H](O)[C@@H]1O" CK0 SMILES CACTVS 3.385 "NC[CH]1O[CH](O[CH]2[CH](N)C[CH](N)[CH](O[CH]3O[CH](CO)[CH](O)[CH](O)[CH]3O)[CH]2O)[CH](N)[CH](O)[CH]1O" CK0 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "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)O)O)O)O[C@@H]3[C@@H]([C@H]([C@@H]([C@H](O3)CN)O)O)N)N" CK0 SMILES "OpenEye OEToolkits" 2.0.6 "C1C(C(C(C(C1N)OC2C(C(C(C(O2)CO)O)O)O)O)OC3C(C(C(C(O3)CN)O)O)N)N" # _pdbx_chem_comp_identifier.comp_id CK0 _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 2.0.6 _pdbx_chem_comp_identifier.identifier "(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},4~{R},5~{S},6~{R})-6-(aminomethyl)-3-azanyl-4,5-bis(oxidanyl)oxan-2-yl]oxy-4,6-bis(azanyl)-2-oxidanyl-cyclohexyl]oxy-6-(hydroxymethyl)oxane-3,4,5-triol" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site CK0 "Create component" 2019-04-25 PDBJ CK0 "Initial release" 2020-04-15 RCSB CK0 "Modify synonyms" 2021-03-01 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id CK0 _pdbx_chem_comp_synonyms.name '3"-deamino-3"-hydroxykanamycin B' _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##