data_AKN # _chem_comp.id AKN _chem_comp.name ;(2S)-N-[(1R,2S,3S,4R,5S)-4-[(2R,3R,4S,5S,6R)-6-(aminomethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-5-azanyl-2-[(2S,3R,4S,5S ,6R)-4-azanyl-6-(hydroxymethyl)-3,5-bis(oxidanyl)oxan-2-yl]oxy-3-oxidanyl-cyclohexyl]-4-azanyl-2-oxidanyl-butanamide ; _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C22 H43 N5 O13" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms AMIKACIN _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2006-02-28 _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 585.603 _chem_comp.one_letter_code ? _chem_comp.three_letter_code AKN _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 4P20 _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 AKN C1 C1 C 0 1 N N R 25.987 6.448 5.168 3.606 0.410 0.388 C1 AKN 1 AKN C3 C2 C 0 1 N N R 26.160 4.927 4.776 4.838 1.068 -0.240 C3 AKN 2 AKN C4 C3 C 0 1 N N S 26.265 4.770 3.233 5.690 -0.007 -0.921 C4 AKN 3 AKN C5 C4 C 0 1 N N S 24.921 5.332 2.611 6.064 -1.076 0.110 C5 AKN 4 AKN C7 C5 C 0 1 N N R 24.776 6.873 3.008 4.786 -1.652 0.724 C7 AKN 5 AKN C9 C6 C 0 1 N N N 23.487 7.493 2.473 5.152 -2.678 1.798 C9 AKN 6 AKN O6 O1 O 0 1 N N N 24.950 5.191 1.170 6.799 -2.121 -0.531 O6 AKN 7 AKN O2 O2 O 0 1 N N N 27.149 7.172 4.719 2.811 -0.188 -0.638 O2 AKN 8 AKN O8 O3 O 0 1 N N N 24.754 6.999 4.523 4.025 -0.595 1.314 O8 AKN 9 AKN N10 N1 N 0 1 N N N 23.020 8.627 3.330 3.929 -3.316 2.303 N10 AKN 10 AKN C11 C7 C 0 1 N N R 29.721 10.353 6.178 -1.298 -1.195 -0.758 C11 AKN 11 AKN N12 N2 N 0 1 N N N 30.099 11.587 6.780 -2.624 -1.626 -0.309 N12 AKN 12 AKN C13 C8 C 0 1 N N N 28.799 10.656 4.955 -0.285 -2.312 -0.503 C13 AKN 13 AKN C14 C9 C 0 1 N N S 28.344 9.312 4.271 1.100 -1.862 -0.972 C14 AKN 14 AKN N15 N3 N 0 1 N N N 27.464 9.623 3.100 2.073 -2.935 -0.727 N15 AKN 15 AKN C16 C10 C 0 1 N N R 27.583 8.419 5.361 1.518 -0.609 -0.200 C16 AKN 16 AKN C17 C11 C 0 1 N N S 28.569 8.145 6.568 0.504 0.509 -0.456 C17 AKN 17 AKN O18 O4 O 0 1 N N N 27.906 7.365 7.549 0.894 1.679 0.266 O18 AKN 18 AKN C19 C12 C 0 1 N N S 28.999 9.488 7.213 -0.881 0.059 0.014 C19 AKN 19 AKN O20 O5 O 0 1 N N N 29.889 9.224 8.302 -1.827 1.102 -0.225 O20 AKN 20 AKN C21 C13 C 0 1 N N S 29.709 9.688 9.581 -2.348 1.698 0.965 C21 AKN 21 AKN C22 C14 C 0 1 N N R 31.124 9.766 10.218 -3.717 2.317 0.669 C22 AKN 22 AKN O23 O6 O 0 1 N N N 31.925 10.627 9.472 -4.595 1.311 0.159 O23 AKN 23 AKN C24 C15 C 0 1 N N S 31.787 8.330 10.339 -3.551 3.428 -0.373 C24 AKN 24 AKN N25 N4 N 0 1 N N N 33.139 8.429 10.967 -4.847 4.078 -0.607 N25 AKN 25 AKN C26 C16 C 0 1 N N S 30.823 7.400 11.198 -2.548 4.459 0.152 C26 AKN 26 AKN O27 O7 O 0 1 N N N 31.375 6.089 11.341 -2.331 5.463 -0.842 O27 AKN 27 AKN C28 C17 C 0 1 N N R 29.418 7.349 10.491 -1.225 3.757 0.468 C28 AKN 28 AKN O29 O8 O 0 1 N N N 28.854 8.757 10.339 -1.454 2.716 1.419 O29 AKN 29 AKN C30 C18 C 0 1 N N N 28.436 6.491 11.284 -0.236 4.770 1.049 C30 AKN 30 AKN O31 O9 O 0 1 N N N 27.506 7.243 12.099 1.031 4.140 1.246 O31 AKN 31 AKN O32 O10 O 0 1 N N N 27.361 4.419 5.406 4.423 2.033 -1.208 O32 AKN 32 AKN O33 O11 O 0 1 N N N 26.418 3.427 2.939 6.878 0.588 -1.448 O33 AKN 33 AKN N37 N5 N 0 1 N N N 34.428 14.890 9.205 -5.865 -5.062 2.172 N37 AKN 34 AKN C35 C19 C 0 1 N N N 31.356 12.187 6.427 -3.411 -2.350 -1.129 C35 AKN 35 AKN O36 O12 O 0 1 N N N 32.236 11.509 5.782 -3.021 -2.645 -2.239 O36 AKN 36 AKN C37 C20 C 0 1 N N S 31.579 13.663 6.874 -4.775 -2.794 -0.667 C37 AKN 37 AKN C38 C21 C 0 1 N N N 32.746 13.665 7.907 -4.626 -3.770 0.501 C38 AKN 38 AKN C39 C22 C 0 1 N N N 33.341 15.037 8.216 -6.009 -4.124 1.050 C39 AKN 39 AKN O40 O13 O 0 1 N N N 30.562 14.150 7.502 -5.456 -3.440 -1.745 O40 AKN 40 AKN H1 H1 H 0 1 N N N 25.892 6.517 6.262 3.018 1.163 0.911 H1 AKN 41 AKN H2 H2 H 0 1 N N N 25.279 4.372 5.131 5.423 1.560 0.537 H2 AKN 42 AKN H3 H3 H 0 1 N N N 27.109 5.370 2.862 5.122 -0.464 -1.731 H3 AKN 43 AKN H4 H4 H 0 1 N N N 24.073 4.777 3.038 6.675 -0.628 0.894 H4 AKN 44 AKN H5 H5 H 0 1 N N N 25.641 7.421 2.606 4.194 -2.135 -0.054 H5 AKN 45 AKN H6 H6 H 0 1 N N N 23.668 7.867 1.454 5.807 -3.436 1.368 H6 AKN 46 AKN H7 H7 H 0 1 N N N 22.704 6.721 2.447 5.665 -2.177 2.619 H7 AKN 47 AKN H8 H8 H 0 1 N N N 25.036 4.273 0.943 7.623 -1.827 -0.942 H8 AKN 48 AKN H9 H9 H 0 1 N N N 22.177 9.007 2.950 3.401 -3.733 1.550 H9 AKN 49 AKN H10 H10 H 0 1 N N N 22.848 8.295 4.257 4.144 -3.999 3.014 H10 AKN 50 AKN H12 H12 H 0 1 N N N 30.610 9.813 5.820 -1.331 -0.971 -1.825 H12 AKN 51 AKN H13 H13 H 0 1 N N N 29.496 12.032 7.442 -2.936 -1.390 0.578 H13 AKN 52 AKN H14 H14 H 0 1 N N N 29.352 11.266 4.225 -0.252 -2.536 0.563 H14 AKN 53 AKN H15 H15 H 0 1 N N N 27.911 11.208 5.297 -0.582 -3.205 -1.053 H15 AKN 54 AKN H16 H16 H 0 1 N N N 29.237 8.765 3.933 1.067 -1.638 -2.038 H16 AKN 55 AKN H17 H17 H 0 1 N N N 27.174 8.771 2.665 1.727 -3.821 -1.064 H17 AKN 56 AKN H18 H18 H 0 1 N N N 26.659 10.128 3.413 2.966 -2.715 -1.140 H18 AKN 57 AKN H20 H20 H 0 1 N N N 26.714 8.982 5.732 1.550 -0.833 0.866 H20 AKN 58 AKN H21 H21 H 0 1 N N N 29.460 7.626 6.186 0.472 0.733 -1.522 H21 AKN 59 AKN H22 H22 H 0 1 N N N 28.496 7.199 8.275 1.688 2.109 -0.082 H22 AKN 60 AKN H23 H23 H 0 1 N N N 28.102 10.018 7.566 -0.848 -0.166 1.080 H23 AKN 61 AKN H24 H24 H 0 1 N N N 29.262 10.693 9.585 -2.453 0.935 1.737 H24 AKN 62 AKN H25 H25 H 0 1 N N N 31.008 10.158 11.239 -4.133 2.735 1.585 H25 AKN 63 AKN H26 H26 H 0 1 N N N 32.790 10.674 9.863 -4.742 0.573 0.766 H26 AKN 64 AKN H27 H27 H 0 1 N N N 31.877 7.901 9.330 -3.183 3.001 -1.306 H27 AKN 65 AKN H28 H28 H 0 1 N N N 33.543 7.517 11.036 -5.528 3.415 -0.947 H28 AKN 66 AKN H29 H29 H 0 1 N N N 33.726 9.011 10.405 -5.177 4.539 0.227 H29 AKN 67 AKN H31 H31 H 0 1 N N N 30.694 7.866 12.186 -2.941 4.922 1.057 H31 AKN 68 AKN H32 H32 H 0 1 N N N 30.785 5.551 11.856 -1.705 6.150 -0.576 H32 AKN 69 AKN H33 H33 H 0 1 N N N 29.550 6.908 9.492 -0.812 3.331 -0.446 H33 AKN 70 AKN H34 H34 H 0 1 N N N 27.857 5.884 10.572 -0.123 5.606 0.358 H34 AKN 71 AKN H35 H35 H 0 1 N N N 29.014 5.828 11.945 -0.611 5.137 2.005 H35 AKN 72 AKN H36 H36 H 0 1 N N N 26.931 6.643 12.559 1.709 4.725 1.613 H36 AKN 73 AKN H37 H37 H 0 1 N N N 27.291 4.518 6.348 3.874 2.742 -0.846 H37 AKN 74 AKN H38 H38 H 0 1 N N N 27.228 3.109 3.320 6.714 1.279 -2.104 H38 AKN 75 AKN H39 H39 H 0 1 N N N 34.818 15.788 9.408 -5.263 -4.681 2.886 H39 AKN 76 AKN H40 H40 H 0 1 N N N 34.063 14.488 10.045 -6.766 -5.311 2.553 H40 AKN 77 AKN H42 H42 H 0 1 N N N 31.874 14.261 5.999 -5.349 -1.925 -0.343 H42 AKN 78 AKN H43 H43 H 0 1 N N N 32.368 13.239 8.848 -4.129 -4.677 0.155 H43 AKN 79 AKN H44 H44 H 0 1 N N N 33.550 13.027 7.512 -4.029 -3.308 1.287 H44 AKN 80 AKN H45 H45 H 0 1 N N N 33.743 15.479 7.292 -6.605 -4.587 0.264 H45 AKN 81 AKN H46 H46 H 0 1 N N N 32.558 15.692 8.626 -6.505 -3.217 1.396 H46 AKN 82 AKN H47 H47 H 0 1 N N N 30.745 15.048 7.753 -5.001 -4.223 -2.084 H47 AKN 83 # # 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 AKN O6 C5 SING N N 1 AKN C9 C7 SING N N 2 AKN C9 N10 SING N N 3 AKN C5 C7 SING N N 4 AKN C5 C4 SING N N 5 AKN O33 C4 SING N N 6 AKN C7 O8 SING N N 7 AKN N15 C14 SING N N 8 AKN C4 C3 SING N N 9 AKN C14 C13 SING N N 10 AKN C14 C16 SING N N 11 AKN O8 C1 SING N N 12 AKN O2 C1 SING N N 13 AKN O2 C16 SING N N 14 AKN C3 C1 SING N N 15 AKN C3 O32 SING N N 16 AKN C13 C11 SING N N 17 AKN C16 C17 SING N N 18 AKN O36 C35 DOUB N N 19 AKN C11 N12 SING N N 20 AKN C11 C19 SING N N 21 AKN C35 N12 SING N N 22 AKN C35 C37 SING N N 23 AKN C17 C19 SING N N 24 AKN C17 O18 SING N N 25 AKN C37 O40 SING N N 26 AKN C37 C38 SING N N 27 AKN C19 O20 SING N N 28 AKN C38 C39 SING N N 29 AKN C39 N37 SING N N 30 AKN O20 C21 SING N N 31 AKN O23 C22 SING N N 32 AKN C21 C22 SING N N 33 AKN C21 O29 SING N N 34 AKN C22 C24 SING N N 35 AKN O29 C28 SING N N 36 AKN C24 N25 SING N N 37 AKN C24 C26 SING N N 38 AKN C28 C26 SING N N 39 AKN C28 C30 SING N N 40 AKN C26 O27 SING N N 41 AKN C30 O31 SING N N 42 AKN C1 H1 SING N N 43 AKN C3 H2 SING N N 44 AKN C4 H3 SING N N 45 AKN C5 H4 SING N N 46 AKN C7 H5 SING N N 47 AKN C9 H6 SING N N 48 AKN C9 H7 SING N N 49 AKN O6 H8 SING N N 50 AKN N10 H9 SING N N 51 AKN N10 H10 SING N N 52 AKN C11 H12 SING N N 53 AKN N12 H13 SING N N 54 AKN C13 H14 SING N N 55 AKN C13 H15 SING N N 56 AKN C14 H16 SING N N 57 AKN N15 H17 SING N N 58 AKN N15 H18 SING N N 59 AKN C16 H20 SING N N 60 AKN C17 H21 SING N N 61 AKN O18 H22 SING N N 62 AKN C19 H23 SING N N 63 AKN C21 H24 SING N N 64 AKN C22 H25 SING N N 65 AKN O23 H26 SING N N 66 AKN C24 H27 SING N N 67 AKN N25 H28 SING N N 68 AKN N25 H29 SING N N 69 AKN C26 H31 SING N N 70 AKN O27 H32 SING N N 71 AKN C28 H33 SING N N 72 AKN C30 H34 SING N N 73 AKN C30 H35 SING N N 74 AKN O31 H36 SING N N 75 AKN O32 H37 SING N N 76 AKN O33 H38 SING N N 77 AKN N37 H39 SING N N 78 AKN N37 H40 SING N N 79 AKN C37 H42 SING N N 80 AKN C38 H43 SING N N 81 AKN C38 H44 SING N N 82 AKN C39 H45 SING N N 83 AKN C39 H46 SING N N 84 AKN O40 H47 SING N N 85 # # 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 AKN SMILES ACDLabs 12.01 "O=C(NC3C(OC1OC(C(O)C(N)C1O)CO)C(O)C(OC2OC(CN)C(O)C(O)C2O)C(N)C3)C(O)CCN" AKN InChI InChI 1.03 "InChI=1S/C22H43N5O13/c23-2-1-8(29)20(36)27-7-3-6(25)18(39-22-16(34)15(33)13(31)9(4-24)37-22)17(35)19(7)40-21-14(32)11(26)12(30)10(5-28)38-21/h6-19,21-22,28-35H,1-5,23-26H2,(H,27,36)/t6-,7+,8-,9+,10+,11-,12+,13+,14+,15-,16+,17-,18+,19-,21+,22+/m0/s1" AKN InChIKey InChI 1.03 LKCWBDHBTVXHDL-RMDFUYIESA-N AKN 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)[C@@H](O)[C@H](O)[C@H]2O)[C@H](O)[C@H]1O[C@H]3O[C@H](CO)[C@@H](O)[C@H](N)[C@H]3O" AKN SMILES CACTVS 3.385 "NCC[CH](O)C(=O)N[CH]1C[CH](N)[CH](O[CH]2O[CH](CN)[CH](O)[CH](O)[CH]2O)[CH](O)[CH]1O[CH]3O[CH](CO)[CH](O)[CH](N)[CH]3O" AKN SMILES_CANONICAL "OpenEye OEToolkits" 1.9.2 "C1[C@@H]([C@H]([C@@H]([C@H]([C@@H]1NC(=O)[C@H](CCN)O)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)O)N" AKN SMILES "OpenEye OEToolkits" 1.9.2 "C1C(C(C(C(C1NC(=O)C(CCN)O)OC2C(C(C(C(O2)CO)O)N)O)O)OC3C(C(C(C(O3)CN)O)O)O)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 AKN "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-[(6-amino-6-deoxy-alpha-D-glucopyranosyl)oxy]-3-hydroxycyclohexyl}-2-hydroxybutanamide" AKN "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.9.2 "(2S)-N-[(1R,2S,3S,4R,5S)-4-[(2R,3R,4S,5S,6R)-6-(aminomethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-5-azanyl-2-[(2S,3R,4S,5S,6R)-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 AKN "Create component" 2006-02-28 RCSB AKN "Modify descriptor" 2011-06-04 RCSB AKN "Other modification" 2014-03-13 RCSB AKN "Modify descriptor" 2014-09-05 RCSB AKN "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id AKN _pdbx_chem_comp_synonyms.name AMIKACIN _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##