data_YRC
# 
_chem_comp.id                                    YRC 
_chem_comp.name                                  "7-[(1~{S})-1-[2-(aminomethyl)-6-oxidanylidene-5-oxa-7-azaspiro[3.4]octan-7-yl]ethyl]-3-(1-oxidanylidene-2,3-dihydroisoindol-5-yl)-1~{H}-indole-2-carboxylic acid" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C26 H26 N4 O5" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-06-20 
_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                        474.508 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     YRC 
_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        8PGS 
_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 
YRC C11  C1  C 0 1 Y N N N N N -21.254 -12.132 8.451  3.175  0.221  -0.226 C11  YRC 1  
YRC C13  C2  C 0 1 Y N N N N N -19.782 -11.278 6.728  5.506  0.800  -0.322 C13  YRC 2  
YRC C15  C3  C 0 1 N N N N N N -19.750 -12.617 4.668  7.105  -0.929 0.842  C15  YRC 3  
YRC C18  C4  C 0 1 N N N N N N -21.122 -14.311 5.117  5.461  -2.370 1.513  C18  YRC 4  
YRC C19  C5  C 0 1 Y N N N N N -21.114 -13.345 6.379  4.796  -1.228 0.786  C19  YRC 5  
YRC C23  C6  C 0 1 Y N N N N N -21.878 -14.896 12.120 0.296  3.656  1.084  C23  YRC 6  
YRC C24  C7  C 0 1 Y N N N N N -22.422 -14.218 13.264 -0.966 3.547  0.515  C24  YRC 7  
YRC C26  C8  C 0 1 N N N N N N -25.579 -13.421 14.838 -3.990 0.164  -0.904 C26  YRC 8  
YRC C01  C9  C 0 1 N N N N N N -22.695 -12.390 15.721 -3.369 3.739  -0.793 C01  YRC 9  
YRC C02  C10 C 0 1 N N S N N N -23.231 -12.041 14.408 -2.641 2.402  -0.945 C02  YRC 10 
YRC C03  C11 C 0 1 Y N N N N N -22.686 -12.868 13.209 -1.266 2.507  -0.336 C03  YRC 11 
YRC C04  C12 C 0 1 Y N N N N N -22.421 -12.227 12.017 -0.296 1.553  -0.634 C04  YRC 12 
YRC C06  C13 C 0 1 Y N N N N N -22.212 -10.738 10.446 0.930  -0.186 -1.387 C06  YRC 13 
YRC C07  C14 C 0 1 N N N N N N -22.412 -9.324  9.771  1.295  -1.409 -2.110 C07  YRC 14 
YRC C10  C15 C 0 1 Y N N N N N -21.782 -11.895 9.884  1.768  0.534  -0.552 C10  YRC 15 
YRC C12  C16 C 0 1 Y N N N N N -20.265 -11.170 7.927  4.195  1.089  -0.624 C12  YRC 16 
YRC C14  C17 C 0 1 Y N N N N N -20.152 -12.341 5.911  5.821  -0.365 0.384  C14  YRC 17 
YRC C20  C18 C 0 1 Y N N N N N -21.658 -13.224 7.726  3.488  -0.942 0.486  C20  YRC 18 
YRC C21  C19 C 0 1 Y N N N N N -21.901 -12.845 10.876 0.982  1.669  -0.055 C21  YRC 19 
YRC C22  C20 C 0 1 Y N N N N N -21.576 -14.273 10.943 1.263  2.733  0.806  C22  YRC 20 
YRC C27  C21 C 0 1 N N N N N N -26.924 -13.144 14.541 -4.654 -0.575 0.263  C27  YRC 21 
YRC C28  C22 C 0 1 N N N N N N -27.885 -14.050 14.125 -6.111 -0.980 0.047  C28  YRC 22 
YRC C29  C23 C 0 1 N N N N N N -28.845 -13.520 15.166 -5.776 -2.271 0.815  C29  YRC 23 
YRC C30  C24 C 0 1 N N N N N N -29.709 -14.454 16.161 -6.416 -3.524 0.214  C30  YRC 24 
YRC C32  C25 C 0 1 N N N N N N -27.764 -12.826 15.717 -4.313 -2.059 0.385  C32  YRC 25 
YRC C34  C26 C 0 1 N N N N N N -25.637 -11.499 13.534 -3.669 1.314  1.052  C34  YRC 26 
YRC N05  N1  N 0 1 Y N N N N N -22.568 -10.914 11.674 -0.301 0.431  -1.429 N05  YRC 27 
YRC N17  N2  N 0 1 N N N N N N -20.306 -13.789 4.091  6.900  -2.088 1.491  N17  YRC 28 
YRC N25  N3  N 0 1 N N N N N N -24.773 -12.236 14.374 -3.399 1.352  -0.261 N25  YRC 29 
YRC N31  N4  N 0 1 N N N N N N -30.668 -15.412 15.324 -6.138 -4.679 1.080  N31  YRC 30 
YRC O08  O1  O 0 1 N N N N N N -22.835 -9.328  8.576  2.415  -1.869 -2.001 O08  YRC 31 
YRC O09  O2  O 0 1 N N N N N N -22.338 -8.337  10.488 0.387  -2.023 -2.897 O09  YRC 32 
YRC O16  O3  O 0 1 N N N N N N -18.932 -11.948 4.014  8.193  -0.419 0.657  O16  YRC 33 
YRC O33  O4  O 0 1 N N N N N N -26.857 -11.929 13.521 -4.383 0.242  1.427  O33  YRC 34 
YRC O35  O5  O 0 1 N N N N N N -25.206 -10.534 12.806 -3.302 2.171  1.831  O35  YRC 35 
YRC H131 H1  H 0 0 N N N N N N -19.087 -10.537 6.361  6.293  1.473  -0.631 H131 YRC 36 
YRC H182 H2  H 0 0 N N N N N N -20.742 -15.299 5.415  5.105  -2.417 2.542  H182 YRC 37 
YRC H181 H3  H 0 0 N N N N N N -22.152 -14.412 4.745  5.254  -3.310 1.002  H181 YRC 38 
YRC H231 H4  H 0 0 N N N N N N -21.698 -15.958 12.195 0.516  4.480  1.746  H231 YRC 39 
YRC H241 H5  H 0 0 N N N N N N -22.625 -14.769 14.170 -1.721 4.285  0.744  H241 YRC 40 
YRC H262 H6  H 0 0 N N N N N N -25.453 -13.563 15.921 -3.216 -0.452 -1.359 H262 YRC 41 
YRC H261 H7  H 0 0 N N N N N N -25.255 -14.329 14.309 -4.734 0.458  -1.645 H261 YRC 42 
YRC H011 H8  H 0 0 N N N N N N -23.149 -11.744 16.487 -2.805 4.520  -1.302 H011 YRC 43 
YRC H013 H9  H 0 0 N N N N N N -22.927 -13.442 15.944 -4.364 3.663  -1.234 H013 YRC 44 
YRC H012 H10 H 0 0 N N N N N N -21.604 -12.247 15.721 -3.459 3.986  0.264  H012 YRC 45 
YRC H021 H11 H 0 0 N N N N N N -23.022 -10.980 14.207 -2.551 2.155  -2.003 H021 YRC 46 
YRC H121 H12 H 0 0 N N N N N N -19.936 -10.357 8.557  3.954  1.989  -1.170 H121 YRC 47 
YRC H201 H13 H 0 0 N N N N N N -22.342 -13.955 8.131  2.701  -1.612 0.798  H201 YRC 48 
YRC H221 H14 H 0 0 N N N N N N -21.126 -14.799 10.114 2.243  2.824  1.251  H221 YRC 49 
YRC H282 H15 H 0 0 N N N N N N -28.222 -13.902 13.088 -6.825 -0.337 0.562  H282 YRC 50 
YRC H281 H16 H 0 0 N N N N N N -27.602 -15.103 14.272 -6.368 -1.147 -0.999 H281 YRC 51 
YRC H291 H17 H 0 0 N N N N N N -29.541 -12.820 14.681 -5.932 -2.191 1.891  H291 YRC 52 
YRC H301 H18 H 0 0 N N N N N N -29.026 -15.065 16.770 -7.493 -3.380 0.135  H301 YRC 53 
YRC H302 H19 H 0 0 N N N N N N -30.317 -13.817 16.820 -6.000 -3.705 -0.777 H302 YRC 54 
YRC H322 H20 H 0 0 N N N N N N -27.392 -13.257 16.659 -4.064 -2.531 -0.566 H322 YRC 55 
YRC H321 H21 H 0 0 N N N N N N -27.949 -11.750 15.854 -3.590 -2.279 1.171  H321 YRC 56 
YRC H051 H22 H 0 0 N N N N N N -22.902 -10.195 12.284 -1.061 0.119  -1.944 H051 YRC 57 
YRC H171 H23 H 0 0 N N N N N N -20.155 -14.158 3.174  7.591  -2.645 1.884  H171 YRC 58 
YRC H312 H24 H 0 0 N N N N N N -31.197 -15.985 15.950 -6.457 -4.509 2.022  H312 YRC 59 
YRC H1   H25 H 0 1 N N N N N N -31.291 -14.859 14.771 -6.550 -5.519 0.704  H1   YRC 60 
YRC H2   H27 H 0 1 N N N N N N -22.646 -7.575  10.012 0.674  -2.826 -3.354 H2   YRC 61 
# 
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 
YRC C11 C10  SING N N 1  
YRC C11 C12  DOUB Y N 2  
YRC C11 C20  SING Y N 3  
YRC C13 C12  SING Y N 4  
YRC C13 C14  DOUB Y N 5  
YRC C15 C14  SING N N 6  
YRC C15 N17  SING N N 7  
YRC C15 O16  DOUB N N 8  
YRC C18 C19  SING N N 9  
YRC C18 N17  SING N N 10 
YRC C19 C14  SING Y N 11 
YRC C19 C20  DOUB Y N 12 
YRC C23 C24  DOUB Y N 13 
YRC C23 C22  SING Y N 14 
YRC C24 C03  SING Y N 15 
YRC C26 C27  SING N N 16 
YRC C26 N25  SING N N 17 
YRC C01 C02  SING N N 18 
YRC C02 C03  SING N N 19 
YRC C02 N25  SING N N 20 
YRC C03 C04  DOUB Y N 21 
YRC C04 C21  SING Y N 22 
YRC C04 N05  SING Y N 23 
YRC C06 C07  SING N N 24 
YRC C06 C10  DOUB Y N 25 
YRC C06 N05  SING Y N 26 
YRC C07 O08  DOUB N N 27 
YRC C07 O09  SING N N 28 
YRC C10 C21  SING Y N 29 
YRC C21 C22  DOUB Y N 30 
YRC C27 C28  SING N N 31 
YRC C27 C32  SING N N 32 
YRC C27 O33  SING N N 33 
YRC C28 C29  SING N N 34 
YRC C29 C30  SING N N 35 
YRC C29 C32  SING N N 36 
YRC C30 N31  SING N N 37 
YRC C34 N25  SING N N 38 
YRC C34 O33  SING N N 39 
YRC C34 O35  DOUB N N 40 
YRC C13 H131 SING N N 41 
YRC C18 H182 SING N N 42 
YRC C18 H181 SING N N 43 
YRC C23 H231 SING N N 44 
YRC C24 H241 SING N N 45 
YRC C26 H262 SING N N 46 
YRC C26 H261 SING N N 47 
YRC C01 H011 SING N N 48 
YRC C01 H013 SING N N 49 
YRC C01 H012 SING N N 50 
YRC C02 H021 SING N N 51 
YRC C12 H121 SING N N 52 
YRC C20 H201 SING N N 53 
YRC C22 H221 SING N N 54 
YRC C28 H282 SING N N 55 
YRC C28 H281 SING N N 56 
YRC C29 H291 SING N N 57 
YRC C30 H301 SING N N 58 
YRC C30 H302 SING N N 59 
YRC C32 H322 SING N N 60 
YRC C32 H321 SING N N 61 
YRC N05 H051 SING N N 62 
YRC N17 H171 SING N N 63 
YRC N31 H312 SING N N 64 
YRC N31 H1   SING N N 65 
YRC O09 H2   SING N N 66 
# 
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 
YRC InChI            InChI                1.06  "InChI=1S/C26H26N4O5/c1-13(30-12-26(35-25(30)34)8-14(9-26)10-27)17-3-2-4-19-20(22(24(32)33)29-21(17)19)15-5-6-18-16(7-15)11-28-23(18)31/h2-7,13-14,29H,8-12,27H2,1H3,(H,28,31)(H,32,33)/t13-,14-,26-/m0/s1" 
YRC InChIKey         InChI                1.06  KZULCUQDDHEBJP-SYMLIENRSA-N                                                                                                                                                                                 
YRC SMILES_CANONICAL CACTVS               3.385 "C[C@H](N1C[C@]2(C[C@@H](CN)C2)OC1=O)c3cccc4c3[nH]c(C(O)=O)c4c5ccc6C(=O)NCc6c5"                                                                                                                             
YRC SMILES           CACTVS               3.385 "C[CH](N1C[C]2(C[CH](CN)C2)OC1=O)c3cccc4c3[nH]c(C(O)=O)c4c5ccc6C(=O)NCc6c5"                                                                                                                                 
YRC SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C[C@@H](c1cccc2c1[nH]c(c2c3ccc4c(c3)CNC4=O)C(=O)O)N5CC6(CC(C6)CN)OC5=O"                                                                                                                                    
YRC SMILES           "OpenEye OEToolkits" 2.0.7 "CC(c1cccc2c1[nH]c(c2c3ccc4c(c3)CNC4=O)C(=O)O)N5CC6(CC(C6)CN)OC5=O"                                                                                                                                         
# 
_pdbx_chem_comp_identifier.comp_id           YRC 
_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-(1-oxidanylidene-2,3-dihydroisoindol-5-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 
YRC "Create component" 2023-06-20 PDBE 
YRC "Initial release"  2024-07-10 RCSB 
# 
