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 
# 
