data_5KVT # _model_server_result.job_id 1RR7zJfhPpB4piALdwhluQ _model_server_result.datetime_utc '2025-02-05 06:47:06' _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 5kvt # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":801}' # _entry.id 5KVT # _exptl.entry_id 5KVT _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 560.637 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description Entrectinib _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 90 _cell.angle_gamma 120 _cell.entry_id 5KVT _cell.length_a 75.9 _cell.length_b 75.9 _cell.length_c 111.74 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5KVT _symmetry.cell_setting ? _symmetry.Int_Tables_number 172 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 64' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # _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 'C31 H34 F2 N6 O2' _chem_comp.formula_weight 560.637 _chem_comp.id YMX _chem_comp.mon_nstd_flag . _chem_comp.name Entrectinib _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 C1 C2 YMX doub 389 n y C1 C41 YMX sing 390 n y C2 N3 YMX sing 391 n y C2 C29 YMX sing 392 n y N3 N4 YMX sing 393 n y N4 C5 YMX doub 394 n y C5 N6 YMX sing 395 n n C5 C29 YMX sing 396 n y N6 C7 YMX sing 397 n n C7 O8 YMX doub 398 n n C7 C9 YMX sing 399 n n C9 C10 YMX doub 400 n y C9 C21 YMX sing 401 n y C10 C11 YMX sing 402 n y C11 C12 YMX doub 403 n y C12 N13 YMX sing 404 n n C12 C20 YMX sing 405 n y N13 C14 YMX sing 406 n n N13 C19 YMX sing 407 n n C14 C15 YMX sing 408 n n C15 N16 YMX sing 409 n n N16 C17 YMX sing 410 n n N16 C18 YMX sing 411 n n C18 C19 YMX sing 412 n n C20 C21 YMX doub 413 n y C21 N22 YMX sing 414 n n N22 C23 YMX sing 415 n n C23 C24 YMX sing 416 n n C23 C28 YMX sing 417 n n C24 C25 YMX sing 418 n n C25 O26 YMX sing 419 n n O26 C27 YMX sing 420 n n C27 C28 YMX sing 421 n n C29 C30 YMX doub 422 n y C30 C31 YMX sing 423 n y C31 C32 YMX sing 424 n n C31 C41 YMX doub 425 n y C32 C33 YMX sing 426 n n C33 C34 YMX doub 427 n y C33 C40 YMX sing 428 n y C34 C35 YMX sing 429 n y C35 F36 YMX sing 430 n n C35 C37 YMX doub 431 n y C37 C38 YMX sing 432 n y C38 F39 YMX sing 433 n n C38 C40 YMX doub 434 n y C1 H1 YMX sing 435 n n C10 H10 YMX sing 436 n n C11 H11 YMX sing 437 n n C14 H14 YMX sing 438 n n C14 H14A YMX sing 439 n n C15 H15 YMX sing 440 n n C15 H15A YMX sing 441 n n C17 H17 YMX sing 442 n n C17 H17A YMX sing 443 n n C17 H17B YMX sing 444 n n C18 H18 YMX sing 445 n n C18 H18A YMX sing 446 n n C19 H19 YMX sing 447 n n C19 H19A YMX sing 448 n n C20 H20 YMX sing 449 n n N22 HN22 YMX sing 450 n n C23 H23 YMX sing 451 n n C24 H24 YMX sing 452 n n C24 H24A YMX sing 453 n n C25 H25 YMX sing 454 n n C25 H25A YMX sing 455 n n C27 H27 YMX sing 456 n n C27 H27A YMX sing 457 n n C28 H28 YMX sing 458 n n C28 H28A YMX sing 459 n n C30 H30 YMX sing 460 n n C32 H32 YMX sing 461 n n C32 H32A YMX sing 462 n n C34 H34 YMX sing 463 n n C37 H37 YMX sing 464 n n C40 H40 YMX sing 465 n n C41 H41 YMX sing 466 n n N6 H6 YMX sing 467 n n N3 H3 YMX sing 468 n n # _atom_sites.entry_id 5KVT _atom_sites.fract_transf_matrix[1][1] 0.013175 _atom_sites.fract_transf_matrix[1][2] 0.007607 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.015213 _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] 0.008949 _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 YMX A 1 801 999 YMX LIG . C 3 GOL A 1 802 1 GOL GOL . D 4 HOH A 1 901 8 HOH HOH . D 4 HOH A 2 902 7 HOH HOH . D 4 HOH A 3 903 2 HOH HOH . D 4 HOH A 4 904 4 HOH HOH . D 4 HOH A 5 905 3 HOH HOH . D 4 HOH A 6 906 5 HOH HOH . D 4 HOH A 7 907 6 HOH HOH . D 4 HOH A 8 908 9 HOH HOH . D 4 HOH A 9 909 1 HOH HOH . D 4 HOH A 10 910 11 HOH HOH . D 4 HOH A 11 911 10 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 YMX . . . B 2 32.26 -35.053 0.842 1 41.5 ? C1 YMX 801 A 1 HETATM 2 C C2 YMX . . . B 2 31.427 -35.122 1.957 1 44.9 ? C2 YMX 801 A 1 HETATM 3 N N3 YMX . . . B 2 31.637 -35.587 3.205 1 46.96 ? N3 YMX 801 A 1 HETATM 4 N N4 YMX . . . B 2 30.527 -35.405 3.966 1 51.88 ? N4 YMX 801 A 1 HETATM 5 C C5 YMX . . . B 2 29.599 -34.872 3.19 1 46.66 ? C5 YMX 801 A 1 HETATM 6 N N6 YMX . . . B 2 28.368 -34.556 3.737 1 41.92 ? N6 YMX 801 A 1 HETATM 7 C C7 YMX . . . B 2 27.132 -34.69 3.2 1 49.16 ? C7 YMX 801 A 1 HETATM 8 O O8 YMX . . . B 2 26.928 -35.221 2.097 1 49.6 ? O8 YMX 801 A 1 HETATM 9 C C9 YMX . . . B 2 26.002 -34.119 4.008 1 53 ? C9 YMX 801 A 1 HETATM 10 C C10 YMX . . . B 2 26.085 -34.098 5.407 1 54.03 ? C10 YMX 801 A 1 HETATM 11 C C11 YMX . . . B 2 25.055 -33.567 6.175 1 56.7 ? C11 YMX 801 A 1 HETATM 12 C C12 YMX . . . B 2 23.929 -33.055 5.555 1 60.74 ? C12 YMX 801 A 1 HETATM 13 N N13 YMX . . . B 2 22.865 -32.519 6.34 1 72.17 ? N13 YMX 801 A 1 HETATM 14 C C14 YMX . . . B 2 22.502 -33.026 7.664 1 76.74 ? C14 YMX 801 A 1 HETATM 15 C C15 YMX . . . B 2 22.392 -31.88 8.657 1 81.63 ? C15 YMX 801 A 1 HETATM 16 N N16 YMX . . . B 2 21.434 -30.88 8.189 1 76.67 ? N16 YMX 801 A 1 HETATM 17 C C17 YMX . . . B 2 21.276 -29.806 9.175 1 82.15 ? C17 YMX 801 A 1 HETATM 18 C C18 YMX . . . B 2 21.889 -30.341 6.911 1 76.16 ? C18 YMX 801 A 1 HETATM 19 C C19 YMX . . . B 2 21.998 -31.441 5.868 1 76.74 ? C19 YMX 801 A 1 HETATM 20 C C20 YMX . . . B 2 23.832 -33.081 4.159 1 58.48 ? C20 YMX 801 A 1 HETATM 21 C C21 YMX . . . B 2 24.858 -33.591 3.375 1 54.68 ? C21 YMX 801 A 1 HETATM 22 N N22 YMX . . . B 2 24.753 -33.617 2.012 1 58.35 ? N22 YMX 801 A 1 HETATM 23 C C23 YMX . . . B 2 24.064 -32.659 1.165 1 57.16 ? C23 YMX 801 A 1 HETATM 24 C C24 YMX . . . B 2 24.263 -33.056 -0.295 1 62.93 ? C24 YMX 801 A 1 HETATM 25 C C25 YMX . . . B 2 23.748 -31.978 -1.215 1 71.04 ? C25 YMX 801 A 1 HETATM 26 O O26 YMX . . . B 2 24.303 -30.699 -0.915 1 68.59 ? O26 YMX 801 A 1 HETATM 27 C C27 YMX . . . B 2 23.976 -30.299 0.413 1 62.55 ? C27 YMX 801 A 1 HETATM 28 C C28 YMX . . . B 2 24.576 -31.245 1.413 1 62.06 ? C28 YMX 801 A 1 HETATM 29 C C29 YMX . . . B 2 30.108 -34.643 1.924 1 48.46 ? C29 YMX 801 A 1 HETATM 30 C C30 YMX . . . B 2 29.613 -34.087 0.739 1 45.13 ? C30 YMX 801 A 1 HETATM 31 C C31 YMX . . . B 2 30.425 -34.042 -0.389 1 38.47 ? C31 YMX 801 A 1 HETATM 32 C C32 YMX . . . B 2 29.934 -33.368 -1.653 1 40.69 ? C32 YMX 801 A 1 HETATM 33 C C33 YMX . . . B 2 29.721 -31.895 -1.364 1 37.85 ? C33 YMX 801 A 1 HETATM 34 C C34 YMX . . . B 2 30.799 -31.081 -1.089 1 37.62 ? C34 YMX 801 A 1 HETATM 35 C C35 YMX . . . B 2 30.587 -29.766 -0.745 1 40.8 ? C35 YMX 801 A 1 HETATM 36 F F36 YMX . . . B 2 31.664 -28.97 -0.493 1 44.3 ? F36 YMX 801 A 1 HETATM 37 C C37 YMX . . . B 2 29.332 -29.221 -0.634 1 37.62 ? C37 YMX 801 A 1 HETATM 38 C C38 YMX . . . B 2 28.281 -30.059 -0.891 1 39.49 ? C38 YMX 801 A 1 HETATM 39 F F39 YMX . . . B 2 27.02 -29.569 -0.791 1 47.89 ? F39 YMX 801 A 1 HETATM 40 C C40 YMX . . . B 2 28.449 -31.384 -1.228 1 35.98 ? C40 YMX 801 A 1 HETATM 41 C C41 YMX . . . B 2 31.752 -34.498 -0.306 1 45.69 ? C41 YMX 801 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 334 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 41 #