data_3WS8 # _model_server_result.job_id 0ZEKfIcKBgMKggQ7VgtQlw _model_server_result.datetime_utc '2024-11-22 09:27:56' _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 3ws8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":803}' # _entry.id 3WS8 # _exptl.entry_id 3WS8 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 367.446 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 8-methyl-6-[2-(5-methyl-1-phenyl-1H-benzimidazol-2-yl)ethyl]imidazo[1,5-a]pyrimidine _entity.pdbx_number_of_molecules 2 _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 3WS8 _cell.length_a 49.31 _cell.length_b 81.107 _cell.length_c 160.47 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3WS8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,I 1 1 B,F,G,H,J 2 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 E N N ? 4 H N N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order metalc ? metalc1 A NE2 HIS 85 A HIS 529 1_555 C ZN ZN . A ZN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.369 ? metalc ? metalc2 A NE2 HIS 119 A HIS 563 1_555 C ZN ZN . A ZN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.16 ? metalc ? metalc3 A OD2 ASP 120 A ASP 564 1_555 C ZN ZN . A ZN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? metalc ? metalc4 A OD1 ASP 120 A ASP 564 1_555 D MG MG . A MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.99 ? metalc ? metalc5 A OD1 ASP 230 A ASP 674 1_555 C ZN ZN . A ZN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.127 ? metalc ? metalc6 C ZN ZN . A ZN 801 1_555 I O HOH . A HOH 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.413 ? metalc ? metalc7 D MG MG . A MG 802 1_555 I O HOH . A HOH 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.841 ? metalc ? metalc8 D MG MG . A MG 802 1_555 I O HOH . A HOH 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? metalc ? metalc9 D MG MG . A MG 802 1_555 I O HOH . A HOH 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.085 ? metalc ? metalc10 D MG MG . A MG 802 1_555 I O HOH . A HOH 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.151 ? metalc ? metalc11 D MG MG . A MG 802 1_555 I O HOH . A HOH 905 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.101 ? metalc ? metalc12 B NE2 HIS 85 B HIS 529 1_555 F ZN ZN . B ZN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.413 ? metalc ? metalc13 B NE2 HIS 119 B HIS 563 1_555 F ZN ZN . B ZN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.951 ? metalc ? metalc14 B OD2 ASP 120 B ASP 564 1_555 F ZN ZN . B ZN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.228 ? metalc ? metalc15 B OD1 ASP 120 B ASP 564 1_555 G MG MG . B MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.104 ? metalc ? metalc16 B OD1 ASP 230 B ASP 674 1_555 F ZN ZN . B ZN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.21 ? metalc ? metalc17 G MG MG . B MG 802 1_555 J O HOH . B HOH 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.144 ? metalc ? metalc18 G MG MG . B MG 802 1_555 J O HOH . B HOH 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.148 ? metalc ? metalc19 G MG MG . B MG 802 1_555 J O HOH . B HOH 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.728 ? metalc ? metalc20 G MG MG . B MG 802 1_555 J O HOH . B HOH 906 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.408 ? # _chem_comp.formula 'C23 H21 N5' _chem_comp.formula_weight 367.446 _chem_comp.id X4C _chem_comp.mon_nstd_flag . _chem_comp.name 8-methyl-6-[2-(5-methyl-1-phenyl-1H-benzimidazol-2-yl)ethyl]imidazo[1,5-a]pyrimidine _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 C17 C15 X4C doub 376 n y C17 C16 X4C sing 377 n y C15 C10 X4C sing 378 n y C20 C16 X4C sing 379 n n C26 C25 X4C doub 380 n y C26 C27 X4C sing 381 n y C25 C24 X4C sing 382 n y C16 C12 X4C doub 383 n y C27 C18 X4C doub 384 n y C24 C23 X4C doub 385 n y C10 N5 X4C sing 386 n y C10 C8 X4C doub 387 n y C18 C23 X4C sing 388 n y C18 N5 X4C sing 389 n n C12 C8 X4C sing 390 n y N5 C1 X4C sing 391 n y C8 N4 X4C sing 392 n y C1 N4 X4C doub 393 n y C1 C11 X4C sing 394 n n C11 C13 X4C sing 395 n n C21 C14 X4C doub 396 n y C21 C22 X4C sing 397 n y C14 N6 X4C sing 398 n y C13 C2 X4C sing 399 n n N6 C2 X4C sing 400 n y N6 C7 X4C sing 401 n y C22 N19 X4C doub 402 n y C2 N3 X4C doub 403 n y C7 N19 X4C sing 404 n y C7 C9 X4C doub 405 n y N3 C9 X4C sing 406 n y C9 C28 X4C sing 407 n n C25 H1 X4C sing 408 n n C24 H2 X4C sing 409 n n C26 H3 X4C sing 410 n n C17 H4 X4C sing 411 n n C15 H5 X4C sing 412 n n C23 H6 X4C sing 413 n n C27 H7 X4C sing 414 n n C12 H8 X4C sing 415 n n C21 H9 X4C sing 416 n n C14 H10 X4C sing 417 n n C22 H11 X4C sing 418 n n C20 H12 X4C sing 419 n n C20 H13 X4C sing 420 n n C20 H14 X4C sing 421 n n C28 H15 X4C sing 422 n n C28 H16 X4C sing 423 n n C28 H17 X4C sing 424 n n C11 H18 X4C sing 425 n n C11 H19 X4C sing 426 n n C13 H20 X4C sing 427 n n C13 H21 X4C sing 428 n n # _atom_sites.entry_id 3WS8 _atom_sites.fract_transf_matrix[1][1] 0.02028 _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] 0.012329 _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] 0.006232 _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 2 ZN A 1 801 1 ZN ZN . D 3 MG A 1 802 2 MG MG . E 4 X4C A 1 803 1 X4C X4C . F 2 ZN B 1 801 1 ZN ZN . G 3 MG B 1 802 2 MG MG . H 4 X4C B 1 803 1 X4C X4C . I 5 HOH A 1 901 1 HOH HOH . I 5 HOH A 2 902 2 HOH HOH . I 5 HOH A 3 903 3 HOH HOH . I 5 HOH A 4 904 4 HOH HOH . I 5 HOH A 5 905 5 HOH HOH . I 5 HOH A 6 906 6 HOH HOH . I 5 HOH A 7 907 7 HOH HOH . I 5 HOH A 8 908 16 HOH HOH . I 5 HOH A 9 909 17 HOH HOH . J 5 HOH B 1 901 8 HOH HOH . J 5 HOH B 2 902 9 HOH HOH . J 5 HOH B 3 903 10 HOH HOH . J 5 HOH B 4 904 11 HOH HOH . J 5 HOH B 5 905 12 HOH HOH . J 5 HOH B 6 906 13 HOH HOH . J 5 HOH B 7 907 14 HOH HOH . J 5 HOH B 8 908 15 HOH HOH . J 5 HOH B 9 909 18 HOH HOH . J 5 HOH B 10 910 19 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 C25 X4C . . . E 4 17.793 7.941 55.807 1 37.09 ? C25 X4C 803 A 1 HETATM 2 C C24 X4C . . . E 4 18.94 8.562 56.258 1 38.72 ? C24 X4C 803 A 1 HETATM 3 C C26 X4C . . . E 4 17.719 6.558 55.798 1 38.4 ? C26 X4C 803 A 1 HETATM 4 C C17 X4C . . . E 4 23.98 6.234 55.016 1 49.67 ? C17 X4C 803 A 1 HETATM 5 C C15 X4C . . . E 4 22.629 6.355 55.274 1 46.05 ? C15 X4C 803 A 1 HETATM 6 C C23 X4C . . . E 4 20.002 7.797 56.693 1 38.73 ? C23 X4C 803 A 1 HETATM 7 C C27 X4C . . . E 4 18.789 5.784 56.212 1 40.51 ? C27 X4C 803 A 1 HETATM 8 C C12 X4C . . . E 4 24.469 4.981 57.014 1 42.37 ? C12 X4C 803 A 1 HETATM 9 C C16 X4C . . . E 4 24.867 5.574 55.843 1 43.87 ? C16 X4C 803 A 1 HETATM 10 C C8 X4C . . . E 4 23.127 5.09 57.295 1 41.67 ? C8 X4C 803 A 1 HETATM 11 C C10 X4C . . . E 4 22.253 5.748 56.453 1 46.29 ? C10 X4C 803 A 1 HETATM 12 C C18 X4C . . . E 4 19.924 6.418 56.66 1 40.3 ? C18 X4C 803 A 1 HETATM 13 C C9 X4C . . . E 4 18.529 3.265 63.046 1 42.73 ? C9 X4C 803 A 1 HETATM 14 C C7 X4C . . . E 4 17.688 2.714 62.107 1 40.86 ? C7 X4C 803 A 1 HETATM 15 C C1 X4C . . . E 4 21.205 4.963 58.216 1 41.1 ? C1 X4C 803 A 1 HETATM 16 C C2 X4C . . . E 4 19.58 3.37 61.187 1 41.47 ? C2 X4C 803 A 1 HETATM 17 C C21 X4C . . . E 4 16.658 1.78 59.705 1 42.83 ? C21 X4C 803 A 1 HETATM 18 C C14 X4C . . . E 4 17.878 2.324 59.728 1 41.29 ? C14 X4C 803 A 1 HETATM 19 C C22 X4C . . . E 4 15.983 1.732 61.027 1 39.1 ? C22 X4C 803 A 1 HETATM 20 C C20 X4C . . . E 4 26.295 5.508 55.458 1 44.65 ? C20 X4C 803 A 1 HETATM 21 C C28 X4C . . . E 4 18.335 3.452 64.487 1 43.14 ? C28 X4C 803 A 1 HETATM 22 C C11 X4C . . . E 4 20.114 4.655 59.16 1 40.97 ? C11 X4C 803 A 1 HETATM 23 C C13 X4C . . . E 4 20.582 3.616 60.158 1 39.09 ? C13 X4C 803 A 1 HETATM 24 N N4 X4C . . . E 4 22.463 4.612 58.374 1 41.11 ? N4 X4C 803 A 1 HETATM 25 N N3 X4C . . . E 4 19.699 3.674 62.461 1 45.92 ? N3 X4C 803 A 1 HETATM 26 N N19 X4C . . . E 4 16.453 2.165 62.156 1 41.57 ? N19 X4C 803 A 1 HETATM 27 N N5 X4C . . . E 4 21.026 5.655 57.052 1 42.83 ? N5 X4C 803 A 1 HETATM 28 N N6 X4C . . . E 4 18.373 2.78 60.923 1 42.85 ? N6 X4C 803 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 288 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 28 #