data_9BO3 # _model_server_result.job_id EuDl70wMFkLUlJfFCtuCfg _model_server_result.datetime_utc '2025-03-12 15:46:57' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 9bo3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 9BO3 # _exptl.entry_id 9BO3 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 565.379 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "(5P)-5-[(1P,3M,3'P)-3-{3-chloro-5-[(2-chlorophenyl)methoxy]-4-fluorophenyl}-2-oxo-2H-[1,3'-bipyridin]-5-yl]-1-methylpyrimidine-2,4(1H,3H)-dione" _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 101.277 _cell.angle_gamma 90 _cell.entry_id 9BO3 _cell.length_a 115.044 _cell.length_b 53.668 _cell.length_c 44.9 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9BO3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall 'C 2y' _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_556 -x,y,-z+1 -1 0 0 0 1 0 0 0 -1 -8.780307 0 44.033126 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C28 H19 Cl2 F N4 O4' _chem_comp.formula_weight 565.379 _chem_comp.id XEK _chem_comp.mon_nstd_flag . _chem_comp.name "(5P)-5-[(1P,3M,3'P)-3-{3-chloro-5-[(2-chlorophenyl)methoxy]-4-fluorophenyl}-2-oxo-2H-[1,3'-bipyridin]-5-yl]-1-methylpyrimidine-2,4(1H,3H)-dione" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag O1 C1 XEK doub 376 n n C1 C2 XEK sing 377 n n C1 N3 XEK sing 378 n n C2 C3 XEK sing 379 n n C2 C16 XEK doub 380 n n C3 C4 XEK doub 381 n y C3 C15 XEK sing 382 n y C4 C5 XEK sing 383 n y C5 CL1 XEK sing 384 n n C5 C6 XEK doub 385 n y C6 F1 XEK sing 386 n n C6 C7 XEK sing 387 n y C7 O2 XEK sing 388 n n C7 C15 XEK doub 389 n y O2 C8 XEK sing 390 n n C8 C9 XEK sing 391 n n C9 C10 XEK doub 392 n y C9 C14 XEK sing 393 n y C10 C11 XEK sing 394 n y C11 C12 XEK doub 395 n y C12 C13 XEK sing 396 n y C13 C14 XEK doub 397 n y C14 CL2 XEK sing 398 n n C16 C17 XEK sing 399 n n C17 C18 XEK sing 400 n n C17 C23 XEK doub 401 n n C18 C19 XEK sing 402 n n C18 C20 XEK doub 403 n n C19 N1 XEK sing 404 n n C19 O3 XEK doub 405 n n N1 C22 XEK sing 406 n n C20 N2 XEK sing 407 n n N2 C21 XEK sing 408 n n N2 C22 XEK sing 409 n n C22 O4 XEK doub 410 n n C23 N3 XEK sing 411 n n N3 C24 XEK sing 412 n n C24 C25 XEK doub 413 n y C24 C28 XEK sing 414 n y C25 C26 XEK sing 415 n y C26 C27 XEK doub 416 n y C27 N4 XEK sing 417 n y N4 C28 XEK doub 418 n y C4 H1 XEK sing 419 n n C8 H2 XEK sing 420 n n C8 H3 XEK sing 421 n n C10 H4 XEK sing 422 n n C11 H5 XEK sing 423 n n C12 H6 XEK sing 424 n n C13 H7 XEK sing 425 n n C15 H8 XEK sing 426 n n C21 H13 XEK sing 427 n n C21 H14 XEK sing 428 n n C21 H12 XEK sing 429 n n C25 H16 XEK sing 430 n n C27 H18 XEK sing 431 n n C16 H9 XEK sing 432 n n C20 H11 XEK sing 433 n n C23 H15 XEK sing 434 n n C26 H17 XEK sing 435 n n C28 H19 XEK sing 436 n n N1 H10 XEK sing 437 n n # _atom_sites.entry_id 9BO3 _atom_sites.fract_transf_matrix[1][1] 0.008692 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001733 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.018633 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.02271 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 XEK A 1 401 999 XEK M61 . C 3 HOH A 1 501 8 HOH HOH . C 3 HOH A 2 502 7 HOH HOH . C 3 HOH A 3 503 4 HOH HOH . C 3 HOH A 4 504 3 HOH HOH . C 3 HOH A 5 505 5 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 C C1 XEK . . . B 2 -13.362 -27.142 0.812 1 51.49 ? C1 XEK 401 A 1 HETATM 2 C C2 XEK . . . B 2 -14.125 -27.859 -0.11 1 52.48 ? C2 XEK 401 A 1 HETATM 3 C C3 XEK . . . B 2 -15.53 -27.393 -0.482 1 50.98 ? C3 XEK 401 A 1 HETATM 4 C C4 XEK . . . B 2 -16.612 -28.264 -0.376 1 51.24 ? C4 XEK 401 A 1 HETATM 5 C C5 XEK . . . B 2 -17.889 -27.833 -0.721 1 52.87 ? C5 XEK 401 A 1 HETATM 6 C C6 XEK . . . B 2 -18.085 -26.544 -1.172 1 54.54 ? C6 XEK 401 A 1 HETATM 7 C C7 XEK . . . B 2 -17.003 -25.685 -1.28 1 56.88 ? C7 XEK 401 A 1 HETATM 8 C C8 XEK . . . B 2 -17.27 -23.493 -0.648 1 59.4 ? C8 XEK 401 A 1 HETATM 9 C C9 XEK . . . B 2 -17.355 -22.094 -1.235 1 61.6 ? C9 XEK 401 A 1 HETATM 10 C C10 XEK . . . B 2 -18.599 -21.575 -1.551 1 60.6 ? C10 XEK 401 A 1 HETATM 11 C C11 XEK . . . B 2 -18.683 -20.304 -2.091 1 64.08 ? C11 XEK 401 A 1 HETATM 12 C C12 XEK . . . B 2 -17.527 -19.564 -2.314 1 61.96 ? C12 XEK 401 A 1 HETATM 13 C C13 XEK . . . B 2 -16.287 -20.092 -1.994 1 63.97 ? C13 XEK 401 A 1 HETATM 14 C C14 XEK . . . B 2 -16.194 -21.361 -1.455 1 61.87 ? C14 XEK 401 A 1 HETATM 15 C C15 XEK . . . B 2 -15.727 -26.104 -0.936 1 53.16 ? C15 XEK 401 A 1 HETATM 16 C C17 XEK . . . B 2 -12.345 -29.447 -0.393 1 57.77 ? C17 XEK 401 A 1 HETATM 17 C C21 XEK . . . B 2 -11.899 -32.07 -4.501 1 72.62 ? C21 XEK 401 A 1 HETATM 18 C C22 XEK . . . B 2 -10.853 -32.866 -2.459 1 61.56 ? C22 XEK 401 A 1 HETATM 19 C C24 XEK . . . B 2 -11.281 -26.909 2.041 1 53.82 ? C24 XEK 401 A 1 HETATM 20 C C25 XEK . . . B 2 -10.095 -26.333 1.62 1 53.5 ? C25 XEK 401 A 1 HETATM 21 C C27 XEK . . . B 2 -9.731 -25.639 3.887 1 52.38 ? C27 XEK 401 A 1 HETATM 22 C C16 XEK . . . B 2 -13.619 -29.003 -0.718 1 55.74 ? C16 XEK 401 A 1 HETATM 23 C C18 XEK . . . B 2 -11.774 -30.707 -1.066 1 59.22 ? C18 XEK 401 A 1 HETATM 24 C C19 XEK . . . B 2 -11.005 -31.689 -0.424 1 59.52 ? C19 XEK 401 A 1 HETATM 25 C C20 XEK . . . B 2 -12.042 -30.883 -2.42 1 60.78 ? C20 XEK 401 A 1 HETATM 26 C C23 XEK . . . B 2 -11.632 -28.695 0.524 1 57.08 ? C23 XEK 401 A 1 HETATM 27 C C26 XEK . . . B 2 -9.311 -25.685 2.565 1 55.01 ? C26 XEK 401 A 1 HETATM 28 C C28 XEK . . . B 2 -11.652 -26.83 3.377 1 51.22 ? C28 XEK 401 A 1 HETATM 29 F F1 XEK . . . B 2 -19.343 -26.143 -1.504 1 53.76 ? F1 XEK 401 A 1 HETATM 30 N N1 XEK . . . B 2 -10.575 -32.733 -1.154 1 64.55 ? N1 XEK 401 A 1 HETATM 31 N N2 XEK . . . B 2 -11.585 -31.938 -3.083 1 62.43 ? N2 XEK 401 A 1 HETATM 32 N N3 XEK . . . B 2 -12.135 -27.598 1.094 1 54.71 ? N3 XEK 401 A 1 HETATM 33 N N4 XEK . . . B 2 -10.877 -26.203 4.263 1 51.19 ? N4 XEK 401 A 1 HETATM 34 O O1 XEK . . . B 2 -13.794 -26.127 1.352 1 52.3 ? O1 XEK 401 A 1 HETATM 35 O O2 XEK . . . B 2 -17.181 -24.382 -1.725 1 60.23 ? O2 XEK 401 A 1 HETATM 36 O O3 XEK . . . B 2 -10.712 -31.632 0.767 1 57.28 ? O3 XEK 401 A 1 HETATM 37 O O4 XEK . . . B 2 -10.446 -33.81 -3.052 1 61.52 ? O4 XEK 401 A 1 HETATM 38 CL CL1 XEK . . . B 2 -19.315 -28.891 -0.606 1 51.42 ? CL1 XEK 401 A 1 HETATM 39 CL CL2 XEK . . . B 2 -14.587 -22.028 -1.051 1 67.53 ? CL2 XEK 401 A 1 HETATM 40 H H1 XEK . . . B 2 -16.459 -29.277 -0.024 1 61.35 ? H1 XEK 401 A 1 HETATM 41 H H2 XEK . . . B 2 -18.157 -23.705 -0.064 1 71.15 ? H2 XEK 401 A 1 HETATM 42 H H3 XEK . . . B 2 -16.392 -23.58 -0.021 1 71.15 ? H3 XEK 401 A 1 HETATM 43 H H4 XEK . . . B 2 -19.495 -22.157 -1.378 1 72.59 ? H4 XEK 401 A 1 HETATM 44 H H5 XEK . . . B 2 -19.65 -19.885 -2.341 1 76.76 ? H5 XEK 401 A 1 HETATM 45 H H6 XEK . . . B 2 -17.597 -18.571 -2.74 1 74.22 ? H6 XEK 401 A 1 HETATM 46 H H7 XEK . . . B 2 -15.39 -19.51 -2.166 1 76.63 ? H7 XEK 401 A 1 HETATM 47 H H8 XEK . . . B 2 -14.889 -25.423 -1.024 1 63.66 ? H8 XEK 401 A 1 HETATM 48 H H13 XEK . . . B 2 -12.882 -32.509 -4.614 1 87.01 ? H13 XEK 401 A 1 HETATM 49 H H14 XEK . . . B 2 -11.162 -32.706 -4.976 1 87.01 ? H14 XEK 401 A 1 HETATM 50 H H12 XEK . . . B 2 -11.885 -31.092 -4.966 1 87.01 ? H12 XEK 401 A 1 HETATM 51 H H16 XEK . . . B 2 -9.788 -26.386 0.583 1 64.06 ? H16 XEK 401 A 1 HETATM 52 H H18 XEK . . . B 2 -9.117 -25.137 4.624 1 62.72 ? H18 XEK 401 A 1 HETATM 53 H H9 XEK . . . B 2 -14.216 -29.544 -1.442 1 66.75 ? H9 XEK 401 A 1 HETATM 54 H H11 XEK . . . B 2 -12.637 -30.144 -2.943 1 72.8 ? H11 XEK 401 A 1 HETATM 55 H H15 XEK . . . B 2 -10.63 -29.009 0.789 1 68.37 ? H15 XEK 401 A 1 HETATM 56 H H17 XEK . . . B 2 -8.377 -25.22 2.273 1 65.88 ? H17 XEK 401 A 1 HETATM 57 H H19 XEK . . . B 2 -12.581 -27.282 3.703 1 61.34 ? H19 XEK 401 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 313 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 57 #