data_3M8Q # _model_server_result.job_id VGov-rtm-ogC0CY5j0NL7w _model_server_result.datetime_utc '2025-06-24 19:45:41' _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 3m8q # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":562}' # _entry.id 3M8Q # _exptl.entry_id 3M8Q _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 491.605 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 3,5-dimethyl-4-{[2-({1-[4-(methylsulfonyl)benzyl]piperidin-4-yl}amino)pyrimidin-4-yl]oxy}benzonitrile _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 90 _cell.entry_id 3M8Q _cell.length_a 118.825 _cell.length_b 153.099 _cell.length_c 154.515 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3M8Q _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # _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,D,E _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 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C26 H29 N5 O3 S' _chem_comp.formula_weight 491.605 _chem_comp.id DJZ _chem_comp.mon_nstd_flag . _chem_comp.name 3,5-dimethyl-4-{[2-({1-[4-(methylsulfonyl)benzyl]piperidin-4-yl}amino)pyrimidin-4-yl]oxy}benzonitrile _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 C2 DJZ sing 83 n n O1 C8 DJZ sing 84 n n C2 N3 DJZ doub 85 n y C2 C7 DJZ sing 86 n y N3 C6 DJZ sing 87 n y N4 C5 DJZ sing 88 n y N4 C6 DJZ doub 89 n y C5 C7 DJZ doub 90 n y C6 N17 DJZ sing 91 n n C8 C9 DJZ doub 92 n y C8 C13 DJZ sing 93 n y C9 C10 DJZ sing 94 n y C9 C15 DJZ sing 95 n n C10 C11 DJZ doub 96 n y C11 C12 DJZ sing 97 n y C11 C16 DJZ sing 98 n n C12 C13 DJZ doub 99 n y C13 C14 DJZ sing 100 n n C16 N24 DJZ trip 101 n n N17 C18 DJZ sing 102 n n C18 C19 DJZ sing 103 n n C18 C23 DJZ sing 104 n n C19 C20 DJZ sing 105 n n C20 N21 DJZ sing 106 n n N21 C22 DJZ sing 107 n n N21 C25 DJZ sing 108 n n C22 C23 DJZ sing 109 n n C25 C26 DJZ sing 110 n n C26 C27 DJZ doub 111 n y C26 C31 DJZ sing 112 n y C27 C28 DJZ sing 113 n y C28 C29 DJZ doub 114 n y C29 C30 DJZ sing 115 n y C29 S32 DJZ sing 116 n n C30 C31 DJZ doub 117 n y S32 O33 DJZ doub 118 n n S32 O34 DJZ doub 119 n n S32 C35 DJZ sing 120 n n C5 H5 DJZ sing 121 n n C7 H7 DJZ sing 122 n n C10 H10 DJZ sing 123 n n C12 H12 DJZ sing 124 n n C14 H14 DJZ sing 125 n n C14 H14A DJZ sing 126 n n C14 H14B DJZ sing 127 n n C15 H15 DJZ sing 128 n n C15 H15A DJZ sing 129 n n C15 H15B DJZ sing 130 n n N17 HN17 DJZ sing 131 n n C18 H18 DJZ sing 132 n n C19 H19 DJZ sing 133 n n C19 H19A DJZ sing 134 n n C20 H20 DJZ sing 135 n n C20 H20A DJZ sing 136 n n C22 H22 DJZ sing 137 n n C22 H22A DJZ sing 138 n n C23 H23 DJZ sing 139 n n C23 H23A DJZ sing 140 n n C25 H25 DJZ sing 141 n n C25 H25A DJZ sing 142 n n C27 H27 DJZ sing 143 n n C28 H28 DJZ sing 144 n n C30 H30 DJZ sing 145 n n C31 H31 DJZ sing 146 n n C35 H35 DJZ sing 147 n n C35 H35A DJZ sing 148 n n C35 H35B DJZ sing 149 n n # _atom_sites.entry_id 3M8Q _atom_sites.fract_transf_matrix[1][1] 0.008416 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006532 _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] 0.006472 _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 C 3 DJZ A 1 562 1 DJZ DJZ . D 4 HOH A 1 563 3 HOH HOH . D 4 HOH A 2 564 4 HOH HOH . D 4 HOH A 3 565 6 HOH HOH . D 4 HOH A 4 566 8 HOH HOH . D 4 HOH A 5 567 9 HOH HOH . D 4 HOH A 6 568 13 HOH HOH . D 4 HOH A 7 569 17 HOH HOH . D 4 HOH A 8 570 19 HOH HOH . D 4 HOH A 9 571 35 HOH HOH . D 4 HOH A 10 572 41 HOH HOH . D 4 HOH A 11 573 42 HOH HOH . D 4 HOH A 12 574 45 HOH HOH . D 4 HOH A 13 575 46 HOH HOH . D 4 HOH A 14 576 48 HOH HOH . D 4 HOH A 15 577 57 HOH HOH . D 4 HOH A 16 578 59 HOH HOH . D 4 HOH A 17 579 60 HOH HOH . D 4 HOH A 18 580 61 HOH HOH . D 4 HOH A 19 581 66 HOH HOH . D 4 HOH A 20 582 68 HOH HOH . D 4 HOH A 21 583 69 HOH HOH . D 4 HOH A 22 584 71 HOH HOH . D 4 HOH A 23 585 74 HOH HOH . D 4 HOH A 24 586 77 HOH HOH . D 4 HOH A 25 587 79 HOH HOH . D 4 HOH A 26 588 80 HOH HOH . D 4 HOH A 27 589 87 HOH HOH . D 4 HOH A 28 590 90 HOH HOH . D 4 HOH A 29 591 93 HOH HOH . D 4 HOH A 30 592 104 HOH HOH . D 4 HOH A 31 593 105 HOH HOH . D 4 HOH A 32 594 112 HOH HOH . D 4 HOH A 33 595 115 HOH HOH . D 4 HOH A 34 596 126 HOH HOH . D 4 HOH A 35 597 127 HOH HOH . D 4 HOH A 36 598 132 HOH HOH . D 4 HOH A 37 599 136 HOH HOH . D 4 HOH A 38 600 144 HOH HOH . D 4 HOH A 39 601 145 HOH HOH . D 4 HOH A 40 602 148 HOH HOH . D 4 HOH A 41 603 149 HOH HOH . E 4 HOH B 1 441 5 HOH HOH . E 4 HOH B 2 442 7 HOH HOH . E 4 HOH B 3 443 11 HOH HOH . E 4 HOH B 4 444 14 HOH HOH . E 4 HOH B 5 445 15 HOH HOH . E 4 HOH B 6 446 18 HOH HOH . E 4 HOH B 7 447 21 HOH HOH . E 4 HOH B 8 448 22 HOH HOH . E 4 HOH B 9 449 23 HOH HOH . E 4 HOH B 10 450 25 HOH HOH . E 4 HOH B 11 451 28 HOH HOH . E 4 HOH B 12 452 37 HOH HOH . E 4 HOH B 13 453 38 HOH HOH . E 4 HOH B 14 454 39 HOH HOH . E 4 HOH B 15 455 43 HOH HOH . E 4 HOH B 16 456 49 HOH HOH . E 4 HOH B 17 457 51 HOH HOH . E 4 HOH B 18 458 55 HOH HOH . E 4 HOH B 19 459 56 HOH HOH . E 4 HOH B 20 460 62 HOH HOH . E 4 HOH B 21 461 64 HOH HOH . E 4 HOH B 22 462 65 HOH HOH . E 4 HOH B 23 463 86 HOH HOH . E 4 HOH B 24 464 92 HOH HOH . E 4 HOH B 25 465 98 HOH HOH . E 4 HOH B 26 466 100 HOH HOH . E 4 HOH B 27 467 101 HOH HOH . E 4 HOH B 28 468 103 HOH HOH . E 4 HOH B 29 469 109 HOH HOH . E 4 HOH B 30 470 113 HOH HOH . E 4 HOH B 31 471 114 HOH HOH . E 4 HOH B 32 472 120 HOH HOH . E 4 HOH B 33 473 130 HOH HOH . E 4 HOH B 34 474 133 HOH HOH . E 4 HOH B 35 475 134 HOH HOH . E 4 HOH B 36 476 135 HOH HOH . E 4 HOH B 37 477 137 HOH HOH . E 4 HOH B 38 478 139 HOH HOH . E 4 HOH B 39 479 141 HOH HOH . E 4 HOH B 40 480 142 HOH HOH . E 4 HOH B 41 481 146 HOH HOH . E 4 HOH B 42 482 147 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 O O1 DJZ . . . C 3 47.064 62.601 17.141 1 52.36 ? O1 DJZ 562 A 1 HETATM 2 C C2 DJZ . . . C 3 47.535 62.289 15.88 1 51.06 ? C2 DJZ 562 A 1 HETATM 3 N N3 DJZ . . . C 3 48.732 62.847 15.371 1 51.02 ? N3 DJZ 562 A 1 HETATM 4 N N4 DJZ . . . C 3 48.599 61.692 13.21 1 50.9 ? N4 DJZ 562 A 1 HETATM 5 C C5 DJZ . . . C 3 47.407 61.102 13.679 1 49.84 ? C5 DJZ 562 A 1 HETATM 6 C C6 DJZ . . . C 3 49.265 62.591 14.1 1 51.62 ? C6 DJZ 562 A 1 HETATM 7 C C7 DJZ . . . C 3 46.848 61.395 15.029 1 49.61 ? C7 DJZ 562 A 1 HETATM 8 C C8 DJZ . . . C 3 47.863 63.386 18.011 1 52.97 ? C8 DJZ 562 A 1 HETATM 9 C C9 DJZ . . . C 3 47.959 64.807 17.758 1 53.56 ? C9 DJZ 562 A 1 HETATM 10 C C10 DJZ . . . C 3 48.79 65.628 18.613 1 54.94 ? C10 DJZ 562 A 1 HETATM 11 C C11 DJZ . . . C 3 49.499 65.031 19.734 1 54.78 ? C11 DJZ 562 A 1 HETATM 12 C C12 DJZ . . . C 3 49.386 63.593 19.998 1 54.45 ? C12 DJZ 562 A 1 HETATM 13 C C13 DJZ . . . C 3 48.589 62.817 19.13 1 53.88 ? C13 DJZ 562 A 1 HETATM 14 C C14 DJZ . . . C 3 48.58 61.357 19.472 1 54.15 ? C14 DJZ 562 A 1 HETATM 15 C C15 DJZ . . . C 3 47.211 65.532 16.607 1 52.12 ? C15 DJZ 562 A 1 HETATM 16 C C16 DJZ . . . C 3 50.282 65.928 20.533 1 54.27 ? C16 DJZ 562 A 1 HETATM 17 N N17 DJZ . . . C 3 50.431 63.204 13.716 1 53.39 ? N17 DJZ 562 A 1 HETATM 18 C C18 DJZ . . . C 3 51.32 63.775 14.675 1 56.2 ? C18 DJZ 562 A 1 HETATM 19 C C19 DJZ . . . C 3 52.738 63.68 14.119 1 57.41 ? C19 DJZ 562 A 1 HETATM 20 C C20 DJZ . . . C 3 53.563 64.498 15.063 1 60.37 ? C20 DJZ 562 A 1 HETATM 21 N N21 DJZ . . . C 3 53.19 65.911 15.024 1 62.1 ? N21 DJZ 562 A 1 HETATM 22 C C22 DJZ . . . C 3 51.877 66.028 15.7 1 60.65 ? C22 DJZ 562 A 1 HETATM 23 C C23 DJZ . . . C 3 50.788 65.254 14.893 1 58.59 ? C23 DJZ 562 A 1 HETATM 24 N N24 DJZ . . . C 3 50.904 66.641 21.168 1 54.55 ? N24 DJZ 562 A 1 HETATM 25 C C25 DJZ . . . C 3 54.234 66.674 15.709 1 65.23 ? C25 DJZ 562 A 1 HETATM 26 C C26 DJZ . . . C 3 54.039 68.193 15.518 1 67.94 ? C26 DJZ 562 A 1 HETATM 27 C C27 DJZ . . . C 3 54.523 69.039 16.567 1 68.4 ? C27 DJZ 562 A 1 HETATM 28 C C28 DJZ . . . C 3 54.323 70.436 16.376 1 70.01 ? C28 DJZ 562 A 1 HETATM 29 C C29 DJZ . . . C 3 53.667 71.065 15.21 1 70.67 ? C29 DJZ 562 A 1 HETATM 30 C C30 DJZ . . . C 3 53.177 70.184 14.128 1 69.45 ? C30 DJZ 562 A 1 HETATM 31 C C31 DJZ . . . C 3 53.366 68.785 14.287 1 68.9 ? C31 DJZ 562 A 1 HETATM 32 S S32 DJZ . . . C 3 53.477 72.901 15.124 1 71.23 ? S32 DJZ 562 A 1 HETATM 33 O O33 DJZ . . . C 3 54.246 73.098 13.917 1 73.54 ? O33 DJZ 562 A 1 HETATM 34 O O34 DJZ . . . C 3 52.044 73.155 14.905 1 69.31 ? O34 DJZ 562 A 1 HETATM 35 C C35 DJZ . . . C 3 54.474 73.498 16.537 1 70.48 ? C35 DJZ 562 A 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 23 _model_server_stats.create_model_time_ms 104 _model_server_stats.query_time_ms 288 _model_server_stats.encode_time_ms 38 _model_server_stats.element_count 35 #