data_YRK # _chem_comp.id YRK _chem_comp.name "7-[(1~{S})-1-[2-(aminomethyl)-6-oxidanylidene-5-oxa-7-azaspiro[3.4]octan-7-yl]ethyl]-3-(5-methoxy-6-oxidanyl-pyridin-3-yl)-1~{H}-indole-2-carboxylic acid" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C24 H26 N4 O6" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2023-06-20 _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 466.486 _chem_comp.one_letter_code ? _chem_comp.three_letter_code YRK _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 8PGW _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 YRK C12 C1 C 0 1 Y N N N N N -22.309 -12.204 12.104 0.014 -1.587 0.592 C12 YRK 1 YRK C13 C2 C 0 1 Y N N N N N -22.529 -12.839 13.335 -0.946 -2.552 0.293 C13 YRK 2 YRK C27 C3 C 0 1 Y N N N N N -22.226 -14.193 13.453 -0.645 -3.569 -0.586 C27 YRK 3 YRK C29 C4 C 0 1 Y N N N N N -21.470 -14.235 11.155 1.565 -2.710 -0.902 C29 YRK 4 YRK C31 C5 C 0 1 Y N N N N N -20.155 -11.539 8.073 4.501 -1.036 0.496 C31 YRK 5 YRK C30 C6 C 0 1 Y N N N N N -21.781 -12.875 11.020 1.282 -1.670 -0.013 C30 YRK 6 YRK C14 C7 C 0 1 N N S N N N -23.119 -12.062 14.521 -2.310 -2.483 0.930 C14 YRK 7 YRK C15 C8 C 0 1 N N N N N N -22.580 -12.550 15.850 -3.018 -3.829 0.764 C15 YRK 8 YRK C01 C9 C 0 1 N N N N N N -22.970 -15.180 6.203 4.320 3.283 -1.888 C01 YRK 9 YRK C03 C10 C 0 1 Y N N N N N -21.213 -13.645 6.703 5.064 1.275 -0.854 C03 YRK 10 YRK C04 C11 C 0 1 Y N N N N N -21.716 -13.345 7.964 3.742 0.997 -0.550 C04 YRK 11 YRK C05 C12 C 0 1 Y N N N N N -21.180 -12.268 8.670 3.454 -0.187 0.142 C05 YRK 12 YRK C06 C13 C 0 1 Y N N N N N -21.667 -11.964 9.951 2.059 -0.531 0.491 C06 YRK 13 YRK C07 C14 C 0 1 Y N N N N N -22.149 -10.764 10.495 1.227 0.158 1.357 C07 YRK 14 YRK C08 C15 C 0 1 N N N N N N -22.340 -9.409 9.845 1.584 1.371 2.095 C08 YRK 15 YRK C17 C16 C 0 1 N N N N N N -25.353 -13.301 14.970 -3.697 -0.269 0.959 C17 YRK 16 YRK C18 C17 C 0 1 N N N N N N -26.777 -12.971 14.643 -4.396 0.485 -0.177 C18 YRK 17 YRK C19 C18 C 0 1 N N N N N N -27.671 -14.117 14.311 -5.856 0.860 0.079 C19 YRK 18 YRK C20 C19 C 0 1 N N N N N N -28.701 -13.532 15.244 -5.558 2.174 -0.667 C20 YRK 19 YRK C21 C20 C 0 1 N N N N N N -29.257 -14.474 16.238 -6.205 3.403 -0.025 C21 YRK 20 YRK C23 C21 C 0 1 N N N N N N -27.640 -12.662 15.834 -4.083 1.978 -0.272 C23 YRK 21 YRK C25 C22 C 0 1 N N N N N N -25.435 -11.422 13.627 -3.394 -1.372 -1.025 C25 YRK 22 YRK C28 C23 C 0 1 Y N N N N N -21.693 -14.887 12.365 0.608 -3.645 -1.179 C28 YRK 23 YRK C33 C24 C 0 1 Y N N N N N -20.196 -12.868 6.188 6.056 0.379 -0.456 C33 YRK 24 YRK N11 N1 N 0 1 Y N N N N N -22.520 -10.946 11.745 0.003 -0.479 1.406 N11 YRK 25 YRK N16 N2 N 0 1 N N N N N N -24.560 -12.257 14.412 -3.099 -1.433 0.282 N16 YRK 26 YRK N22 N3 N 0 1 N N N N N N -30.429 -15.124 15.678 -5.964 4.580 -0.870 N22 YRK 27 YRK N32 N4 N 0 1 Y N N N N N -19.698 -11.850 6.865 5.747 -0.733 0.191 N32 YRK 28 YRK O02 O1 O 0 1 N N N N N N -21.687 -14.706 5.916 5.392 2.412 -1.524 O02 YRK 29 YRK O09 O2 O 0 1 N N N N N N -22.744 -9.378 8.654 2.694 1.854 1.970 O09 YRK 30 YRK O10 O3 O 0 1 N N N N N N -22.220 -8.365 10.536 0.683 1.954 2.912 O10 YRK 31 YRK O24 O4 O 0 1 N N N N N N -26.772 -11.915 13.709 -4.136 -0.300 -1.364 O24 YRK 32 YRK O26 O5 O 0 1 N N N N N N -25.077 -10.491 12.988 -3.027 -2.206 -1.829 O26 YRK 33 YRK O34 O6 O 0 1 N N N N N N -19.710 -13.190 4.914 7.354 0.642 -0.751 O34 YRK 34 YRK H271 H1 H 0 0 N N N N N N -22.403 -14.707 14.386 -1.391 -4.315 -0.815 H271 YRK 35 YRK H291 H2 H 0 0 N N N N N N -21.056 -14.779 10.318 2.537 -2.775 -1.368 H291 YRK 36 YRK H311 H3 H 0 0 N N N N N N -19.722 -10.703 8.603 4.290 -1.951 1.029 H311 YRK 37 YRK H141 H4 H 0 0 N N N N N N -22.876 -10.996 14.403 -2.204 -2.257 1.991 H141 YRK 38 YRK H152 H5 H 0 0 N N N N N N -23.030 -11.965 16.666 -2.431 -4.611 1.246 H152 YRK 39 YRK H153 H6 H 0 0 N N N N N N -22.831 -13.613 15.979 -4.005 -3.779 1.224 H153 YRK 40 YRK H151 H7 H 0 0 N N N N N N -21.487 -12.426 15.870 -3.124 -4.056 -0.297 H151 YRK 41 YRK H013 H8 H 0 0 N N N N N N -23.218 -16.005 5.519 4.718 4.150 -2.415 H013 YRK 42 YRK H011 H9 H 0 0 N N N N N N -23.003 -15.542 7.241 3.624 2.752 -2.537 H011 YRK 43 YRK H012 H10 H 0 0 N N N N N N -23.699 -14.366 6.075 3.799 3.613 -0.989 H012 YRK 44 YRK H041 H11 H 0 0 N N N N N N -22.511 -13.938 8.391 2.952 1.673 -0.845 H041 YRK 45 YRK H172 H12 H 0 0 N N N N N N -25.075 -14.268 14.526 -2.923 0.352 1.413 H172 YRK 46 YRK H171 H13 H 0 0 N N N N N N -25.213 -13.344 16.060 -4.419 -0.590 1.710 H171 YRK 47 YRK H192 H14 H 0 0 N N N N N N -27.984 -14.160 13.257 -6.569 0.217 -0.436 H192 YRK 48 YRK H191 H15 H 0 0 N N N N N N -27.284 -15.100 14.619 -6.093 1.000 1.133 H191 YRK 49 YRK H201 H16 H 0 0 N N N N N N -29.475 -12.959 14.713 -5.733 2.115 -1.741 H201 YRK 50 YRK H212 H17 H 0 0 N N N N N N -28.501 -15.232 16.489 -7.278 3.239 0.072 H212 YRK 51 YRK H211 H18 H 0 0 N N N N N N -29.541 -13.924 17.147 -5.772 3.568 0.961 H211 YRK 52 YRK H231 H19 H 0 0 N N N N N N -27.238 -13.022 16.792 -3.822 2.432 0.684 H231 YRK 53 YRK H232 H20 H 0 0 N N N N N N -27.921 -11.603 15.929 -3.380 2.227 -1.067 H232 YRK 54 YRK H281 H21 H 0 0 N N N N N N -21.452 -15.935 12.462 0.828 -4.449 -1.867 H281 YRK 55 YRK H111 H22 H 0 0 N N N N N N -22.905 -10.238 12.337 -0.753 -0.191 1.942 H111 YRK 56 YRK H222 H23 H 0 0 N N N N N N -30.809 -15.762 16.348 -6.300 4.426 -1.809 H222 YRK 57 YRK H1 H24 H 0 1 N N N N N N -31.116 -14.434 15.449 -6.383 5.406 -0.467 H1 YRK 58 YRK H2 H26 H 0 1 N N N N N N -22.476 -7.611 10.018 1.010 2.748 3.356 H2 YRK 59 YRK H341 H27 H 0 0 N N N N N N -19.021 -12.581 4.674 7.816 1.153 -0.071 H341 YRK 60 # 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 YRK O34 C33 SING N N 1 YRK O02 C01 SING N N 2 YRK O02 C03 SING N N 3 YRK C33 C03 DOUB Y N 4 YRK C33 N32 SING Y N 5 YRK C03 C04 SING Y N 6 YRK N32 C31 DOUB Y N 7 YRK C04 C05 DOUB Y N 8 YRK C31 C05 SING Y N 9 YRK O09 C08 DOUB N N 10 YRK C05 C06 SING N N 11 YRK C08 C07 SING N N 12 YRK C08 O10 SING N N 13 YRK C06 C07 DOUB Y N 14 YRK C06 C30 SING Y N 15 YRK C07 N11 SING Y N 16 YRK C30 C29 DOUB Y N 17 YRK C30 C12 SING Y N 18 YRK C29 C28 SING Y N 19 YRK N11 C12 SING Y N 20 YRK C12 C13 DOUB Y N 21 YRK C28 C27 DOUB Y N 22 YRK O26 C25 DOUB N N 23 YRK C13 C27 SING Y N 24 YRK C13 C14 SING N N 25 YRK C25 O24 SING N N 26 YRK C25 N16 SING N N 27 YRK O24 C18 SING N N 28 YRK C19 C18 SING N N 29 YRK C19 C20 SING N N 30 YRK N16 C14 SING N N 31 YRK N16 C17 SING N N 32 YRK C14 C15 SING N N 33 YRK C18 C17 SING N N 34 YRK C18 C23 SING N N 35 YRK C20 C23 SING N N 36 YRK C20 C21 SING N N 37 YRK N22 C21 SING N N 38 YRK C27 H271 SING N N 39 YRK C29 H291 SING N N 40 YRK C31 H311 SING N N 41 YRK C14 H141 SING N N 42 YRK C15 H152 SING N N 43 YRK C15 H153 SING N N 44 YRK C15 H151 SING N N 45 YRK C01 H013 SING N N 46 YRK C01 H011 SING N N 47 YRK C01 H012 SING N N 48 YRK C04 H041 SING N N 49 YRK C17 H172 SING N N 50 YRK C17 H171 SING N N 51 YRK C19 H192 SING N N 52 YRK C19 H191 SING N N 53 YRK C20 H201 SING N N 54 YRK C21 H212 SING N N 55 YRK C21 H211 SING N N 56 YRK C23 H231 SING N N 57 YRK C23 H232 SING N N 58 YRK C28 H281 SING N N 59 YRK N11 H111 SING N N 60 YRK N22 H222 SING N N 61 YRK N22 H1 SING N N 62 YRK O10 H2 SING N N 63 YRK O34 H341 SING N N 64 # 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 YRK InChI InChI 1.06 "InChI=1S/C24H26N4O6/c1-12(28-11-24(34-23(28)32)7-13(8-24)9-25)15-4-3-5-16-18(20(22(30)31)27-19(15)16)14-6-17(33-2)21(29)26-10-14/h3-6,10,12-13,27H,7-9,11,25H2,1-2H3,(H,26,29)(H,30,31)/t12-,13-,24-/m0/s1" YRK InChIKey InChI 1.06 GPHDBHLNQMSHHX-ORPWPGRKSA-N YRK SMILES_CANONICAL CACTVS 3.385 "COc1cc(cnc1O)c2c([nH]c3c(cccc23)[C@H](C)N4C[C@]5(C[C@@H](CN)C5)OC4=O)C(O)=O" YRK SMILES CACTVS 3.385 "COc1cc(cnc1O)c2c([nH]c3c(cccc23)[CH](C)N4C[C]5(C[CH](CN)C5)OC4=O)C(O)=O" YRK SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C[C@@H](c1cccc2c1[nH]c(c2c3cc(c(nc3)O)OC)C(=O)O)N4CC5(CC(C5)CN)OC4=O" YRK SMILES "OpenEye OEToolkits" 2.0.7 "CC(c1cccc2c1[nH]c(c2c3cc(c(nc3)O)OC)C(=O)O)N4CC5(CC(C5)CN)OC4=O" # _pdbx_chem_comp_identifier.comp_id YRK _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-methoxy-6-oxidanyl-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 YRK "Create component" 2023-06-20 PDBE YRK "Initial release" 2024-07-10 RCSB #