data_YKO # _chem_comp.id YKO _chem_comp.name "7-[(1~{S})-1-[2-(aminomethyl)-6-oxidanylidene-5-oxa-7-azaspiro[3.4]octan-7-yl]ethyl]-3-(5-fluoranyl-6-oxidanylidene-1~{H}-pyridin-3-yl)-1~{H}-indole-2-carboxylic acid" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C23 H23 F 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 454.451 _chem_comp.one_letter_code ? _chem_comp.three_letter_code YKO _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 8PGX _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 YKO C12 C1 C 0 1 N N N N N N -20.164 -12.806 6.034 -6.196 -0.793 -0.609 C12 YKO 1 YKO C26 C2 C 0 1 N N N N N N -27.680 -12.734 15.777 4.004 -1.922 -0.477 C26 YKO 2 YKO C27 C3 C 0 1 N N N N N N -28.791 -13.640 15.216 5.487 -2.016 -0.876 C27 YKO 3 YKO C24 C4 C 0 1 N N N N N N -25.452 -13.417 14.883 3.514 0.178 0.963 C24 YKO 4 YKO C30 C5 C 0 1 N N N N N N -27.847 -14.101 14.145 5.725 -0.768 -0.006 C30 YKO 5 YKO C10 C6 C 0 1 N N N N N N -21.536 -13.313 7.872 -4.692 0.260 0.858 C10 YKO 6 YKO C14 C7 C 0 1 N N N N N N -19.770 -11.651 6.731 -5.132 -1.212 -1.431 C14 YKO 7 YKO C01 C8 C 0 1 N N N N N N -22.709 -12.435 15.798 2.683 3.708 1.095 C01 YKO 8 YKO C02 C9 C 0 1 N N S N N N -23.220 -12.065 14.418 2.032 2.324 1.129 C02 YKO 9 YKO C03 C10 C 0 1 Y N N N N N -22.631 -12.861 13.303 0.669 2.394 0.489 C03 YKO 10 YKO C04 C11 C 0 1 Y N N N N N -22.336 -14.230 13.352 0.329 3.475 -0.292 C04 YKO 11 YKO C05 C12 C 0 1 Y N N N N N -21.774 -14.900 12.251 -0.923 3.553 -0.888 C05 YKO 12 YKO C06 C13 C 0 1 Y N N N N N -21.480 -14.279 11.080 -1.839 2.556 -0.707 C06 YKO 13 YKO C07 C14 C 0 1 Y N N N N N -21.793 -12.886 10.961 -1.516 1.450 0.082 C07 YKO 14 YKO C08 C15 C 0 1 Y N N N N N -21.653 -11.949 9.904 -2.246 0.237 0.471 C08 YKO 15 YKO C09 C16 C 0 1 N N N N N N -21.149 -12.182 8.604 -3.624 -0.130 0.081 C09 YKO 16 YKO C16 C17 C 0 1 N N N N N N -20.220 -11.305 7.978 -3.854 -0.886 -1.093 C16 YKO 17 YKO C17 C18 C 0 1 Y N N N N N -22.139 -10.762 10.471 -1.389 -0.495 1.276 C17 YKO 18 YKO C18 C19 C 0 1 N N N N N N -22.302 -9.423 9.798 -1.698 -1.784 1.894 C18 YKO 19 YKO C22 C20 C 0 1 Y N N N N N -22.345 -12.251 12.062 -0.247 1.363 0.684 C22 YKO 20 YKO C25 C21 C 0 1 N N N N N N -26.841 -13.042 14.581 4.249 -0.433 -0.235 C25 YKO 21 YKO C28 C22 C 0 1 N N N N N N -29.325 -14.752 16.047 6.185 -3.272 -0.348 C28 YKO 22 YKO C32 C23 C 0 1 N N N N N N -25.462 -11.491 13.533 3.173 1.449 -0.912 C32 YKO 23 YKO F15 F1 F 0 1 N N N N N N -18.816 -10.823 6.172 -5.377 -1.933 -2.547 F15 YKO 24 YKO N11 N1 N 0 1 N N N N N N -21.101 -13.519 6.635 -5.957 -0.075 0.504 N11 YKO 25 YKO N21 N2 N 0 1 Y N N N N N -22.500 -10.930 11.740 -0.195 0.190 1.400 N21 YKO 26 YKO N23 N3 N 0 1 N N N N N N -24.707 -12.227 14.414 2.869 1.373 0.392 N23 YKO 27 YKO N29 N4 N 0 1 N N N N N N -30.510 -14.307 16.712 7.554 -3.331 -0.878 N29 YKO 28 YKO O13 O1 O 0 1 N N N N N N -19.780 -13.123 4.882 -7.344 -1.079 -0.910 O13 YKO 29 YKO O19 O2 O 0 1 N N N N N N -22.275 -8.363 10.522 -0.776 -2.403 2.661 O19 YKO 30 YKO O20 O3 O 0 1 N N N N N N -22.678 -9.457 8.632 -2.786 -2.299 1.717 O20 YKO 31 YKO O31 O4 O 0 1 N N N N N N -26.741 -11.998 13.597 3.959 0.451 -1.343 O31 YKO 32 YKO O33 O5 O 0 1 N N N N N N -25.142 -10.580 12.851 2.773 2.339 -1.636 O33 YKO 33 YKO H262 H1 H 0 0 N N N N N N -27.253 -13.082 16.729 3.316 -2.124 -1.298 H262 YKO 34 YKO H261 H2 H 0 0 N N N N N N -27.964 -11.675 15.868 3.758 -2.477 0.429 H261 YKO 35 YKO H271 H3 H 0 0 N N N N N N -29.605 -13.034 14.791 5.665 -1.849 -1.938 H271 YKO 36 YKO H241 H4 H 0 0 N N N N N N -25.152 -14.320 14.331 2.767 -0.515 1.349 H241 YKO 37 YKO H242 H5 H 0 0 N N N N N N -25.307 -13.581 15.961 4.220 0.456 1.746 H242 YKO 38 YKO H302 H6 H 0 0 N N N N N N -28.227 -13.966 13.122 5.965 -0.999 1.032 H302 YKO 39 YKO H301 H7 H 0 0 N N N N N N -27.494 -15.135 14.271 6.411 -0.048 -0.450 H301 YKO 40 YKO H101 H8 H 0 0 N N N N N N -22.203 -14.032 8.324 -4.521 0.836 1.755 H101 YKO 41 YKO H013 H9 H 0 0 N N N N N N -23.196 -11.800 16.552 2.061 4.416 1.644 H013 YKO 42 YKO H012 H10 H 0 0 N N N N N N -22.940 -13.491 16.003 3.669 3.657 1.558 H012 YKO 43 YKO H011 H11 H 0 0 N N N N N N -21.620 -12.283 15.839 2.783 4.038 0.061 H011 YKO 44 YKO H021 H12 H 0 0 N N N N N N -22.989 -11.004 14.244 1.932 1.994 2.163 H021 YKO 45 YKO H041 H13 H 0 0 N N N N N N -22.545 -14.783 14.256 1.043 4.271 -0.444 H041 YKO 46 YKO H051 H14 H 0 0 N N N N N N -21.567 -15.956 12.341 -1.174 4.408 -1.498 H051 YKO 47 YKO H061 H15 H 0 0 N N N N N N -21.024 -14.819 10.263 -2.811 2.623 -1.173 H061 YKO 48 YKO H161 H16 H 0 0 N N N N N N -19.883 -10.403 8.466 -3.027 -1.199 -1.713 H161 YKO 49 YKO H281 H17 H 0 0 N N N N N N -29.564 -15.612 15.404 6.218 -3.238 0.741 H281 YKO 50 YKO H282 H18 H 0 0 N N N N N N -28.573 -15.050 16.793 5.633 -4.155 -0.669 H282 YKO 51 YKO H111 H19 H 0 0 N N N N N N -21.513 -14.270 6.119 -6.700 0.206 1.061 H111 YKO 52 YKO H211 H20 H 0 0 N N N N N N -22.829 -10.213 12.354 0.570 -0.114 1.914 H211 YKO 53 YKO H291 H21 H 0 0 N N N N N N -30.876 -15.049 17.274 8.035 -4.152 -0.544 H291 YKO 54 YKO H1 H22 H 0 1 N N N N N N -30.291 -13.525 17.295 7.553 -3.297 -1.887 H1 YKO 55 YKO H2 H24 H 0 1 N N N N N N -22.589 -7.624 10.014 -1.071 -3.248 3.026 H2 YKO 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 YKO O13 C12 DOUB N N 1 YKO C12 N11 SING N N 2 YKO C12 C14 SING N N 3 YKO F15 C14 SING N N 4 YKO N11 C10 SING N N 5 YKO C14 C16 DOUB N N 6 YKO C10 C09 DOUB N N 7 YKO C16 C09 SING N N 8 YKO C09 C08 SING N N 9 YKO O20 C18 DOUB N N 10 YKO C18 C17 SING N N 11 YKO C18 O19 SING N N 12 YKO C08 C17 DOUB Y N 13 YKO C08 C07 SING Y N 14 YKO C17 N21 SING Y N 15 YKO C07 C06 DOUB Y N 16 YKO C07 C22 SING Y N 17 YKO C06 C05 SING Y N 18 YKO N21 C22 SING Y N 19 YKO C22 C03 DOUB Y N 20 YKO C05 C04 DOUB Y N 21 YKO O33 C32 DOUB N N 22 YKO C03 C04 SING Y N 23 YKO C03 C02 SING N N 24 YKO C32 O31 SING N N 25 YKO C32 N23 SING N N 26 YKO O31 C25 SING N N 27 YKO C30 C25 SING N N 28 YKO C30 C27 SING N N 29 YKO N23 C02 SING N N 30 YKO N23 C24 SING N N 31 YKO C02 C01 SING N N 32 YKO C25 C24 SING N N 33 YKO C25 C26 SING N N 34 YKO C27 C26 SING N N 35 YKO C27 C28 SING N N 36 YKO C28 N29 SING N N 37 YKO C26 H262 SING N N 38 YKO C26 H261 SING N N 39 YKO C27 H271 SING N N 40 YKO C24 H241 SING N N 41 YKO C24 H242 SING N N 42 YKO C30 H302 SING N N 43 YKO C30 H301 SING N N 44 YKO C10 H101 SING N N 45 YKO C01 H013 SING N N 46 YKO C01 H012 SING N N 47 YKO C01 H011 SING N N 48 YKO C02 H021 SING N N 49 YKO C04 H041 SING N N 50 YKO C05 H051 SING N N 51 YKO C06 H061 SING N N 52 YKO C16 H161 SING N N 53 YKO C28 H281 SING N N 54 YKO C28 H282 SING N N 55 YKO N11 H111 SING N N 56 YKO N21 H211 SING N N 57 YKO N29 H291 SING N N 58 YKO N29 H1 SING N N 59 YKO O19 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 YKO InChI InChI 1.06 "InChI=1S/C23H23FN4O5/c1-11(28-10-23(33-22(28)32)6-12(7-23)8-25)14-3-2-4-15-17(19(21(30)31)27-18(14)15)13-5-16(24)20(29)26-9-13/h2-5,9,11-12,27H,6-8,10,25H2,1H3,(H,26,29)(H,30,31)/t11-,12-,23-/m0/s1" YKO InChIKey InChI 1.06 PWIXGVSRGNKFLQ-RSPIHXBNSA-N YKO SMILES_CANONICAL CACTVS 3.385 "C[C@H](N1C[C@@]2(C[C@H](CN)C2)OC1=O)c3cccc4c3[nH]c(C(O)=O)c4C5=CNC(=O)C(=C5)F" YKO SMILES CACTVS 3.385 "C[CH](N1C[C]2(C[CH](CN)C2)OC1=O)c3cccc4c3[nH]c(C(O)=O)c4C5=CNC(=O)C(=C5)F" YKO SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C[C@@H](c1cccc2c1[nH]c(c2C3=CNC(=O)C(=C3)F)C(=O)O)N4CC5(CC(C5)CN)OC4=O" YKO SMILES "OpenEye OEToolkits" 2.0.7 "CC(c1cccc2c1[nH]c(c2C3=CNC(=O)C(=C3)F)C(=O)O)N4CC5(CC(C5)CN)OC4=O" # _pdbx_chem_comp_identifier.comp_id YKO _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-fluoranyl-6-oxidanylidene-1~{H}-pyridin-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 YKO "Create component" 2023-06-19 PDBE YKO "Initial release" 2024-07-10 RCSB #