data_YKZ # _chem_comp.id YKZ _chem_comp.name "7-[(1~{S})-1-[2-(aminomethyl)-6-oxidanylidene-5-oxa-7-azaspiro[3.4]octan-7-yl]ethyl]-3-(5-oxidanylpyridin-3-yl)-1~{H}-indole-2-carboxylic acid" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C23 H24 N4 O5" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2023-06-19 _chem_comp.pdbx_modified_date 2024-07-05 _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 436.460 _chem_comp.one_letter_code ? _chem_comp.three_letter_code YKZ _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 8PGT _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBE # 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.pdbx_backbone_atom_flag _chem_comp_atom.pdbx_n_terminal_atom_flag _chem_comp_atom.pdbx_c_terminal_atom_flag _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 YKZ C10 C1 C 0 1 Y N N N N N -21.715 -13.206 7.733 5.021 0.502 -0.310 C10 YKZ 1 YKZ C15 C2 C 0 1 Y N N N N N -20.457 -11.183 8.003 4.095 -1.331 0.945 C15 YKZ 2 YKZ C17 C3 C 0 1 N N N N N N -22.511 -9.399 9.808 2.000 -1.891 -1.721 C17 YKZ 3 YKZ N20 N1 N 0 1 Y N N N N N -22.662 -10.940 11.679 0.526 0.126 -1.321 N20 YKZ 4 YKZ C21 C4 C 0 1 Y N N N N N -22.452 -12.224 12.001 0.581 1.317 -0.637 C21 YKZ 5 YKZ C24 C5 C 0 1 N N N N N N -26.957 -13.051 14.561 -3.973 -0.377 0.200 C24 YKZ 6 YKZ C25 C6 C 0 1 N N N N N N -27.799 -12.654 15.753 -3.757 -1.864 0.482 C25 YKZ 7 YKZ C26 C7 C 0 1 N N N N N N -28.866 -13.596 15.232 -5.253 -1.923 0.843 C26 YKZ 8 YKZ O30 O1 O 0 1 N N N N N N -26.907 -12.025 13.572 -3.697 0.527 1.295 O30 YKZ 9 YKZ C31 C8 C 0 1 N N N N N N -25.603 -11.490 13.516 -2.882 1.501 0.863 C31 YKZ 10 YKZ O32 O2 O 0 1 N N N N N N -25.297 -10.555 12.856 -2.487 2.401 1.577 O32 YKZ 11 YKZ C01 C9 C 0 1 N N N N N N -22.675 -12.395 15.778 -2.294 3.702 -1.183 C01 YKZ 12 YKZ C02 C10 C 0 1 N N S N N N -23.302 -12.054 14.413 -1.668 2.306 -1.165 C02 YKZ 13 YKZ C03 C11 C 0 1 Y N N N N N -22.703 -12.873 13.207 -0.323 2.367 -0.489 C03 YKZ 14 YKZ C04 C12 C 0 1 Y N N N N N -22.393 -14.229 13.274 0.016 3.460 0.277 C04 YKZ 15 YKZ C05 C13 C 0 1 Y N N N N N -21.851 -14.906 12.158 1.252 3.529 0.906 C05 YKZ 16 YKZ C06 C14 C 0 1 Y N N N N N -21.588 -14.261 10.979 2.154 2.512 0.775 C06 YKZ 17 YKZ C07 C15 C 0 1 Y N N N N N -21.903 -12.881 10.878 1.832 1.393 0.003 C07 YKZ 18 YKZ C08 C16 C 0 1 Y N N N N N -21.826 -11.925 9.835 2.549 0.158 -0.337 C08 YKZ 19 YKZ C09 C17 C 0 1 Y N N N N N -21.330 -12.122 8.519 3.907 -0.228 0.105 C09 YKZ 20 YKZ C12 C18 C 0 1 Y N N N N N -20.364 -12.465 5.974 6.445 -0.878 0.863 C12 YKZ 21 YKZ C13 C19 C 0 1 Y N N N N N -19.966 -11.370 6.705 5.390 -1.650 1.330 C13 YKZ 22 YKZ C16 C20 C 0 1 Y N N N N N -22.301 -10.734 10.423 1.699 -0.579 -1.143 C16 YKZ 23 YKZ C23 C21 C 0 1 N N N N N N -25.503 -13.400 14.802 -3.194 0.191 -0.991 C23 YKZ 24 YKZ C27 C22 C 0 1 N N N N N N -29.481 -14.538 16.232 -5.958 -3.179 0.328 C27 YKZ 25 YKZ C29 C23 C 0 1 N N N N N N -27.869 -14.228 14.264 -5.445 -0.693 -0.062 C29 YKZ 26 YKZ N11 N2 N 0 1 Y N N N N N -21.231 -13.347 6.474 6.232 0.159 0.076 N11 YKZ 27 YKZ N22 N3 N 0 1 N N N N N N -24.752 -12.259 14.358 -2.543 1.389 -0.431 N22 YKZ 28 YKZ N28 N4 N 0 1 N N N N N N -30.512 -15.389 15.573 -7.341 -3.202 0.822 N28 YKZ 29 YKZ O14 O3 O 0 1 N N N N N N -19.070 -10.379 6.234 5.623 -2.716 2.141 O14 YKZ 30 YKZ O18 O4 O 0 1 N N N N N N -22.338 -8.349 10.486 1.085 -2.513 -2.494 O18 YKZ 31 YKZ O19 O5 O 0 1 N N N N N N -23.048 -9.371 8.679 3.073 -2.420 -1.504 O19 YKZ 32 YKZ H101 H1 H 0 0 N N N N N N -22.403 -13.938 8.129 4.890 1.356 -0.959 H101 YKZ 33 YKZ H151 H2 H 0 0 N N N N N N -20.160 -10.325 8.587 3.254 -1.918 1.285 H151 YKZ 34 YKZ H201 H3 H 0 0 N N N N N N -23.034 -10.245 12.294 -0.229 -0.177 -1.849 H201 YKZ 35 YKZ H252 H4 H 0 0 N N N N N N -27.375 -12.936 16.728 -3.498 -2.444 -0.404 H252 YKZ 36 YKZ H251 H5 H 0 0 N N N N N N -28.093 -11.594 15.774 -3.094 -2.058 1.324 H251 YKZ 37 YKZ H261 H6 H 0 0 N N N N N N -29.642 -13.042 14.683 -5.455 -1.727 1.896 H261 YKZ 38 YKZ H013 H7 H 0 0 N N N N N N -23.146 -11.783 16.562 -1.643 4.385 -1.730 H013 YKZ 39 YKZ H011 H8 H 0 0 N N N N N N -22.835 -13.461 15.999 -3.267 3.658 -1.672 H011 YKZ 40 YKZ H012 H9 H 0 0 N N N N N N -21.596 -12.185 15.748 -2.417 4.058 -0.160 H012 YKZ 41 YKZ H021 H10 H 0 0 N N N N N N -23.096 -10.992 14.213 -1.545 1.950 -2.188 H021 YKZ 42 YKZ H041 H11 H 0 0 N N N N N N -22.569 -14.771 14.191 -0.687 4.272 0.389 H041 YKZ 43 YKZ H051 H12 H 0 0 N N N N N N -21.638 -15.962 12.237 1.502 4.394 1.503 H051 YKZ 44 YKZ H061 H13 H 0 0 N N N N N N -21.151 -14.790 10.145 3.114 2.573 1.266 H061 YKZ 45 YKZ H121 H14 H 0 0 N N N N N N -19.969 -12.613 4.980 7.455 -1.125 1.156 H121 YKZ 46 YKZ H232 H15 H 0 0 N N N N N N -25.222 -14.293 14.224 -2.449 -0.524 -1.340 H232 YKZ 47 YKZ H231 H16 H 0 0 N N N N N N -25.325 -13.584 15.872 -3.872 0.463 -1.800 H231 YKZ 48 YKZ H271 H17 H 0 0 N N N N N N -28.696 -15.181 16.655 -5.962 -3.172 -0.762 H271 YKZ 49 YKZ H272 H18 H 0 0 N N N N N N -29.952 -13.956 17.038 -5.430 -4.064 0.683 H272 YKZ 50 YKZ H292 H19 H 0 0 N N N N N N -28.215 -14.291 13.222 -6.131 0.049 0.347 H292 YKZ 51 YKZ H291 H20 H 0 0 N N N N N N -27.477 -15.206 14.580 -5.660 -0.944 -1.101 H291 YKZ 52 YKZ H1 H21 H 0 1 N N N N N N -30.913 -16.010 16.247 -7.833 -2.361 0.560 H1 YKZ 53 YKZ H281 H22 H 0 0 N N N N N N -31.228 -14.807 15.189 -7.828 -4.023 0.495 H281 YKZ 54 YKZ H141 H24 H 0 0 N N N N N N -18.942 -9.721 6.908 5.621 -2.500 3.084 H141 YKZ 55 YKZ H2 H25 H 0 1 N N N N N N -22.671 -7.601 10.003 1.374 -3.373 -2.830 H2 YKZ 56 # 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 YKZ C12 N11 DOUB Y N 1 YKZ C12 C13 SING Y N 2 YKZ O14 C13 SING N N 3 YKZ N11 C10 SING Y N 4 YKZ C13 C15 DOUB Y N 5 YKZ C10 C09 DOUB Y N 6 YKZ C15 C09 SING Y N 7 YKZ C09 C08 SING N N 8 YKZ O19 C17 DOUB N N 9 YKZ C17 C16 SING N N 10 YKZ C17 O18 SING N N 11 YKZ C08 C16 DOUB Y N 12 YKZ C08 C07 SING Y N 13 YKZ C16 N20 SING Y N 14 YKZ C07 C06 DOUB Y N 15 YKZ C07 C21 SING Y N 16 YKZ C06 C05 SING Y N 17 YKZ N20 C21 SING Y N 18 YKZ C21 C03 DOUB Y N 19 YKZ C05 C04 DOUB Y N 20 YKZ O32 C31 DOUB N N 21 YKZ C03 C04 SING Y N 22 YKZ C03 C02 SING N N 23 YKZ C31 O30 SING N N 24 YKZ C31 N22 SING N N 25 YKZ O30 C24 SING N N 26 YKZ C29 C24 SING N N 27 YKZ C29 C26 SING N N 28 YKZ N22 C02 SING N N 29 YKZ N22 C23 SING N N 30 YKZ C02 C01 SING N N 31 YKZ C24 C23 SING N N 32 YKZ C24 C25 SING N N 33 YKZ C26 C25 SING N N 34 YKZ C26 C27 SING N N 35 YKZ N28 C27 SING N N 36 YKZ C10 H101 SING N N 37 YKZ C15 H151 SING N N 38 YKZ N20 H201 SING N N 39 YKZ C25 H252 SING N N 40 YKZ C25 H251 SING N N 41 YKZ C26 H261 SING N N 42 YKZ C01 H013 SING N N 43 YKZ C01 H011 SING N N 44 YKZ C01 H012 SING N N 45 YKZ C02 H021 SING N N 46 YKZ C04 H041 SING N N 47 YKZ C05 H051 SING N N 48 YKZ C06 H061 SING N N 49 YKZ C12 H121 SING N N 50 YKZ C23 H232 SING N N 51 YKZ C23 H231 SING N N 52 YKZ C27 H271 SING N N 53 YKZ C27 H272 SING N N 54 YKZ C29 H292 SING N N 55 YKZ C29 H291 SING N N 56 YKZ N28 H1 SING N N 57 YKZ N28 H281 SING N N 58 YKZ O14 H141 SING N N 59 YKZ O18 H2 SING N N 60 # 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 YKZ InChI InChI 1.06 "InChI=1S/C23H24N4O5/c1-12(27-11-23(32-22(27)31)6-13(7-23)8-24)16-3-2-4-17-18(14-5-15(28)10-25-9-14)20(21(29)30)26-19(16)17/h2-5,9-10,12-13,26,28H,6-8,11,24H2,1H3,(H,29,30)/t12-,13-,23-/m0/s1" YKZ InChIKey InChI 1.06 SVHSJMJSXMTRQF-XCMOZONUSA-N YKZ SMILES_CANONICAL CACTVS 3.385 "C[C@H](N1C[C@@]2(C[C@H](CN)C2)OC1=O)c3cccc4c3[nH]c(C(O)=O)c4c5cncc(O)c5" YKZ SMILES CACTVS 3.385 "C[CH](N1C[C]2(C[CH](CN)C2)OC1=O)c3cccc4c3[nH]c(C(O)=O)c4c5cncc(O)c5" YKZ SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C[C@@H](c1cccc2c1[nH]c(c2c3cc(cnc3)O)C(=O)O)N4CC5(CC(C5)CN)OC4=O" YKZ SMILES "OpenEye OEToolkits" 2.0.7 "CC(c1cccc2c1[nH]c(c2c3cc(cnc3)O)C(=O)O)N4CC5(CC(C5)CN)OC4=O" # _pdbx_chem_comp_identifier.comp_id YKZ _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 2.0.7 _pdbx_chem_comp_identifier.identifier "7-[(1~{S})-1-[2-(aminomethyl)-6-oxidanylidene-5-oxa-7-azaspiro[3.4]octan-7-yl]ethyl]-3-(5-oxidanylpyridin-3-yl)-1~{H}-indole-2-carboxylic acid" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site YKZ "Create component" 2023-06-19 PDBE YKZ "Initial release" 2024-07-10 RCSB #