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 
# 
