data_5EA5 # _model_server_result.job_id YbG3dfraivS2bby--2d4Sw _model_server_result.datetime_utc '2024-10-18 02:18:20' _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 5ea5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":602}' # _entry.id 5EA5 # _exptl.entry_id 5EA5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 558.714 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-[[6-[[[2-(3-hydroxypropyl)-5-methylphenyl]amino]methyl]-2-[[3-(4-morpholinyl)propyl]amino]-1H-benzimidazol-1-yl]methyl]-6-methyl-3-pyridinol _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 5EA5 _cell.length_a 169.86 _cell.length_b 169.86 _cell.length_c 169.86 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5EA5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 213 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 3 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 1,2,3 # 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' 5_555 z,x,y 0 0 1 1 0 0 0 1 0 0 0 0 3 'crystal symmetry operation' 9_555 y,z,x 0 1 0 0 0 1 1 0 0 0 0 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 # 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 disulf ? disulf1 A SG CYS 37 F CYS 37 1_555 A SG CYS 439 F CYS 439 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? disulf ? disulf2 A SG CYS 155 F CYS 155 1_555 A SG CYS 290 F CYS 290 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf3 A SG CYS 313 F CYS 313 1_555 A SG CYS 343 F CYS 343 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf4 A SG CYS 322 F CYS 322 1_555 A SG CYS 333 F CYS 333 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? disulf ? disulf5 A SG CYS 358 F CYS 358 1_555 A SG CYS 367 F CYS 367 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? disulf ? disulf6 A SG CYS 382 F CYS 382 1_555 A SG CYS 393 F CYS 393 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf7 A SG CYS 416 F CYS 416 1_555 A SG CYS 422 F CYS 422 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? # _chem_comp.formula 'C32 H42 N6 O3' _chem_comp.formula_weight 558.714 _chem_comp.id TM3 _chem_comp.mon_nstd_flag . _chem_comp.name 2-[[6-[[[2-(3-hydroxypropyl)-5-methylphenyl]amino]methyl]-2-[[3-(4-morpholinyl)propyl]amino]-1H-benzimidazol-1-yl]methyl]-6-methyl-3-pyridinol _chem_comp.type non-polymer _chem_comp.pdbx_synonyms TMC353121 # 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 TM3 sing 353 n n C1 O6 TM3 sing 354 n n C1 H1 TM3 sing 355 n n C1 H1A TM3 sing 356 n n C2 N3 TM3 sing 357 n n C2 H2 TM3 sing 358 n n C2 H2A TM3 sing 359 n n N3 C13 TM3 sing 360 n n N3 C4 TM3 sing 361 n n C5 C4 TM3 sing 362 n n C4 H4 TM3 sing 363 n n C4 H4A TM3 sing 364 n n O6 C5 TM3 sing 365 n n C5 H5 TM3 sing 366 n n C5 H5A TM3 sing 367 n n C13 C14 TM3 sing 368 n n C13 H13 TM3 sing 369 n n C13 H13A TM3 sing 370 n n C14 C15 TM3 sing 371 n n C14 H14 TM3 sing 372 n n C14 H14A TM3 sing 373 n n C15 N16 TM3 sing 374 n n C15 H15 TM3 sing 375 n n C15 H15A TM3 sing 376 n n N16 C17 TM3 sing 377 n n N16 HN16 TM3 sing 378 n n C17 N26 TM3 sing 379 n y C17 N23 TM3 doub 380 n y N23 C24 TM3 sing 381 n y C25 C24 TM3 doub 382 n y C24 C35 TM3 sing 383 n y N26 C25 TM3 sing 384 n y C25 C32 TM3 sing 385 n y C41 N26 TM3 sing 386 n n C32 C33 TM3 doub 387 n y C32 H32 TM3 sing 388 n n C33 C34 TM3 sing 389 n y C33 C60 TM3 sing 390 n n C35 C34 TM3 doub 391 n y C34 H34 TM3 sing 392 n n C35 H35 TM3 sing 393 n n C41 C42 TM3 sing 394 n n C41 H41 TM3 sing 395 n n C41 H41A TM3 sing 396 n n C45 C42 TM3 doub 397 n y C42 N49 TM3 sing 398 n y O56 C45 TM3 sing 399 n n C45 C46 TM3 sing 400 n y C46 C47 TM3 doub 401 n y C46 H46 TM3 sing 402 n n C47 C48 TM3 sing 403 n y C47 H47 TM3 sing 404 n n N49 C48 TM3 doub 405 n y C48 C58 TM3 sing 406 n n O56 HO56 TM3 sing 407 n n C58 H58 TM3 sing 408 n n C58 H58A TM3 sing 409 n n C58 H58B TM3 sing 410 n n N61 C60 TM3 sing 411 n n C60 H60 TM3 sing 412 n n N61 C62 TM3 sing 413 n n C70 C62 TM3 doub 414 n y C62 C66 TM3 sing 415 n y C66 C67 TM3 doub 416 n y C66 H66 TM3 sing 417 n n C68 C67 TM3 sing 418 n y C67 C77 TM3 sing 419 n n C69 C68 TM3 doub 420 n y C68 H68 TM3 sing 421 n n C70 C69 TM3 sing 422 n y C69 H69 TM3 sing 423 n n C79 C70 TM3 sing 424 n n C77 H77 TM3 sing 425 n n C77 H77A TM3 sing 426 n n C77 H77B TM3 sing 427 n n C80 C79 TM3 sing 428 n n C79 H79 TM3 sing 429 n n C79 H79A TM3 sing 430 n n C80 C81 TM3 sing 431 n n C80 H80 TM3 sing 432 n n C80 H80A TM3 sing 433 n n O82 C81 TM3 sing 434 n n C81 H81 TM3 sing 435 n n C81 H81A TM3 sing 436 n n O82 HO82 TM3 sing 437 n n N61 HO83 TM3 sing 438 n n C60 HO84 TM3 sing 439 n n # _atom_sites.entry_id 5EA5 _atom_sites.fract_transf_matrix[1][1] 0.005887 _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] 0.005887 _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] 0.005887 _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 NHE F 1 601 1 NHE NHE . C 3 TM3 F 1 602 1 TM3 LIG . D 4 SO4 F 1 603 1 SO4 SO4 . E 5 TAR F 1 604 1 TAR TAR . # 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 TM3 . . . C 3 26.357 25.886 27.526 0.33 79.08 ? C1 TM3 602 F 1 HETATM 2 C C2 TM3 . . . C 3 25.006 26.212 26.922 0.33 78.62 ? C2 TM3 602 F 1 HETATM 3 N N3 TM3 . . . C 3 24.931 25.853 25.588 0.33 77.56 ? N3 TM3 602 F 1 HETATM 4 C C4 TM3 . . . C 3 25.977 26.388 24.853 0.33 78.25 ? C4 TM3 602 F 1 HETATM 5 C C5 TM3 . . . C 3 27.336 26.081 25.456 0.33 78.77 ? C5 TM3 602 F 1 HETATM 6 O O6 TM3 . . . C 3 27.404 26.43 26.794 0.33 79.34 ? O6 TM3 602 F 1 HETATM 7 C C13 TM3 . . . C 3 24.928 24.599 25.486 0.33 76.76 ? C13 TM3 602 F 1 HETATM 8 C C14 TM3 . . . C 3 23.84 24.158 24.476 0.33 73.69 ? C14 TM3 602 F 1 HETATM 9 C C15 TM3 . . . C 3 24.499 23.925 23.062 0.33 71.73 ? C15 TM3 602 F 1 HETATM 10 N N16 TM3 . . . C 3 23.637 24.526 22.033 0.33 67.67 ? N16 TM3 602 F 1 HETATM 11 C C17 TM3 . . . C 3 23.208 23.7 20.92 0.33 63.3 ? C17 TM3 602 F 1 HETATM 12 N N23 TM3 . . . C 3 23.664 23.771 19.603 0.33 61.93 ? N23 TM3 602 F 1 HETATM 13 C C24 TM3 . . . C 3 22.999 22.804 18.868 0.33 60.4 ? C24 TM3 602 F 1 HETATM 14 C C25 TM3 . . . C 3 22.148 22.157 19.752 0.33 61.5 ? C25 TM3 602 F 1 HETATM 15 N N26 TM3 . . . C 3 22.251 22.69 21.009 0.33 61.02 ? N26 TM3 602 F 1 HETATM 16 C C32 TM3 . . . C 3 21.241 21.013 19.211 0.33 62.89 ? C32 TM3 602 F 1 HETATM 17 C C33 TM3 . . . C 3 21.231 20.521 17.818 0.33 59.85 ? C33 TM3 602 F 1 HETATM 18 C C34 TM3 . . . C 3 22.14 21.203 16.844 0.33 62.39 ? C34 TM3 602 F 1 HETATM 19 C C35 TM3 . . . C 3 23.027 22.338 17.348 0.33 61.27 ? C35 TM3 602 F 1 HETATM 20 C C41 TM3 . . . C 3 21.529 22.268 22.194 0.33 60.66 ? C41 TM3 602 F 1 HETATM 21 C C42 TM3 . . . C 3 19.987 22.443 22.106 0.33 61.76 ? C42 TM3 602 F 1 HETATM 22 C C45 TM3 . . . C 3 19.288 23.434 23.007 0.33 60.72 ? C45 TM3 602 F 1 HETATM 23 C C46 TM3 . . . C 3 17.813 23.605 22.935 0.33 61.14 ? C46 TM3 602 F 1 HETATM 24 C C47 TM3 . . . C 3 17.006 22.795 21.975 0.33 60.99 ? C47 TM3 602 F 1 HETATM 25 C C48 TM3 . . . C 3 17.708 21.79 21.071 0.33 63.34 ? C48 TM3 602 F 1 HETATM 26 N N49 TM3 . . . C 3 19.179 21.637 21.165 0.33 61.26 ? N49 TM3 602 F 1 HETATM 27 O O56 TM3 . . . C 3 20.042 24.212 23.922 0.33 62.13 ? O56 TM3 602 F 1 HETATM 28 C C58 TM3 . . . C 3 16.884 20.929 20.059 0.33 61.09 ? C58 TM3 602 F 1 HETATM 29 C C60 TM3 . . . C 3 20.268 19.364 17.517 0.33 61.89 ? C60 TM3 602 F 1 HETATM 30 N N61 TM3 . . . C 3 19.574 19.006 18.751 0.33 62.22 ? N61 TM3 602 F 1 HETATM 31 C C62 TM3 . . . C 3 20.143 18.145 19.775 0.33 62.38 ? C62 TM3 602 F 1 HETATM 32 C C66 TM3 . . . C 3 20.872 18.716 20.993 0.33 63.37 ? C66 TM3 602 F 1 HETATM 33 C C67 TM3 . . . C 3 21.5 17.839 22.095 0.33 60.13 ? C67 TM3 602 F 1 HETATM 34 C C68 TM3 . . . C 3 21.355 16.314 21.953 0.33 61.45 ? C68 TM3 602 F 1 HETATM 35 C C69 TM3 . . . C 3 20.615 15.718 20.747 0.33 60.41 ? C69 TM3 602 F 1 HETATM 36 C C70 TM3 . . . C 3 20.006 16.6 19.658 0.33 59.7 ? C70 TM3 602 F 1 HETATM 37 C C77 TM3 . . . C 3 22.251 18.479 23.309 0.33 60.67 ? C77 TM3 602 F 1 HETATM 38 C C79 TM3 . . . C 3 19.28 15.978 18.481 0.33 58.32 ? C79 TM3 602 F 1 HETATM 39 C C80 TM3 . . . C 3 20.19 14.959 17.8 0.33 55.05 ? C80 TM3 602 F 1 HETATM 40 C C81 TM3 . . . C 3 19.931 14.986 16.295 0.33 52.64 ? C81 TM3 602 F 1 HETATM 41 O O82 TM3 . . . C 3 19.279 13.815 15.924 0.33 51.42 ? O82 TM3 602 F 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 296 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 41 #