data_8U6T # _model_server_result.job_id 5_isK6pOXE7TSahsUK9x9Q _model_server_result.datetime_utc '2024-11-22 06:28:54' _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 8u6t # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":601}' # _entry.id 8U6T # _exptl.entry_id 8U6T _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 477.511 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 5-(2-{2-[2-oxo-3-(prop-2-enoyl)-2,3-dihydro-1H-benzimidazol-1-yl]ethoxy}phenoxy)naphthalene-2-carbonitrile _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 108.1 _cell.angle_gamma 90 _cell.entry_id 8U6T _cell.length_a 222.153 _cell.length_b 67.265 _cell.length_c 103.259 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8U6T _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _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,D,E,F,G,H,I,J _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 # 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 covale ? covale1 A NZ LYS 104 A LYS 102 1_555 C C1 VO8 . A VO8 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.488 ? metalc ? metalc1 A OD1 ASP 445 A ASP 443 1_555 G MG MG . A MG 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.613 ? metalc ? metalc2 A OE2 GLU 480 A GLU 478 1_555 G MG MG . A MG 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.524 ? metalc ? metalc3 A OD1 ASP 500 A ASP 498 1_555 G MG MG . A MG 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.466 ? metalc ? metalc4 A OD2 ASP 500 A ASP 498 1_555 G MG MG . A MG 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.712 ? metalc ? metalc5 B OE1 GLN 23 B GLN 23 1_555 H MG MG . B MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.557 ? metalc ? metalc6 B O THR 58 B THR 58 1_555 H MG MG . B MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.645 ? metalc ? metalc7 B O THR 131 B THR 131 1_555 H MG MG . B MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.998 ? # _chem_comp.formula 'C29 H23 N3 O4' _chem_comp.formula_weight 477.511 _chem_comp.id VO8 _chem_comp.mon_nstd_flag . _chem_comp.name 5-(2-{2-[2-oxo-3-(prop-2-enoyl)-2,3-dihydro-1H-benzimidazol-1-yl]ethoxy}phenoxy)naphthalene-2-carbonitrile _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 C9 C8 VO8 doub 380 n y C9 C10 VO8 sing 381 n y C8 C7 VO8 sing 382 n y C10 C11 VO8 doub 383 n y C1 C2 VO8 sing 384 n n O2 C4 VO8 doub 385 n n C6 O3 VO8 sing 386 n n C6 C5 VO8 sing 387 n n C7 O3 VO8 sing 388 n n C7 C12 VO8 doub 389 n y C2 C3 VO8 sing 390 n n C11 C12 VO8 sing 391 n y C4 N2 VO8 sing 392 n n C4 N1 VO8 sing 393 n n C5 N2 VO8 sing 394 n n C12 O4 VO8 sing 395 n n N2 C24 VO8 sing 396 n n C3 N1 VO8 sing 397 n n C3 O1 VO8 doub 398 n n N1 C29 VO8 sing 399 n n O4 C13 VO8 sing 400 n n C24 C29 VO8 doub 401 n y C24 C25 VO8 sing 402 n y C29 C28 VO8 sing 403 n y C14 C13 VO8 doub 404 n y C14 C15 VO8 sing 405 n y C13 C23 VO8 sing 406 n y C25 C26 VO8 doub 407 n y C15 C16 VO8 doub 408 n y C28 C27 VO8 doub 409 n y C23 C22 VO8 doub 410 n y C23 C17 VO8 sing 411 n y C26 C27 VO8 sing 412 n y C22 C21 VO8 sing 413 n y C16 C17 VO8 sing 414 n y C17 C18 VO8 doub 415 n y C21 C19 VO8 doub 416 n y C18 C19 VO8 sing 417 n y C19 C20 VO8 sing 418 n n C20 N3 VO8 trip 419 n n C10 H10 VO8 sing 420 n n C1 H22 VO8 sing 421 n n C1 H1 VO8 sing 422 n n C2 H3 VO8 sing 423 n n C5 H5 VO8 sing 424 n n C5 H4 VO8 sing 425 n n C6 H7 VO8 sing 426 n n C6 H6 VO8 sing 427 n n C8 H8 VO8 sing 428 n n C9 H9 VO8 sing 429 n n C11 H11 VO8 sing 430 n n C14 H12 VO8 sing 431 n n C15 H13 VO8 sing 432 n n C16 H14 VO8 sing 433 n n C18 H15 VO8 sing 434 n n C21 H16 VO8 sing 435 n n C22 H17 VO8 sing 436 n n C25 H18 VO8 sing 437 n n C26 H19 VO8 sing 438 n n C27 H20 VO8 sing 439 n n C28 H21 VO8 sing 440 n n C1 H2 VO8 sing 441 n n C2 H23 VO8 sing 442 n n # _atom_sites.entry_id 8U6T _atom_sites.fract_transf_matrix[1][1] 0.004501 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001471 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014867 _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] 0.010189 _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 VO8 A 1 601 601 VO8 J58 . D 4 PO4 A 1 602 1 PO4 PO4 . E 4 PO4 A 1 603 2 PO4 PO4 . F 4 PO4 A 1 604 3 PO4 PO4 . G 5 MG A 1 605 1 MG MG . H 5 MG B 1 501 2 MG MG . I 6 HOH A 1 701 6 HOH HOH . I 6 HOH A 2 702 7 HOH HOH . I 6 HOH A 3 703 23 HOH HOH . I 6 HOH A 4 704 11 HOH HOH . I 6 HOH A 5 705 21 HOH HOH . I 6 HOH A 6 706 19 HOH HOH . I 6 HOH A 7 707 27 HOH HOH . I 6 HOH A 8 708 40 HOH HOH . I 6 HOH A 9 709 25 HOH HOH . I 6 HOH A 10 710 4 HOH HOH . I 6 HOH A 11 711 24 HOH HOH . I 6 HOH A 12 712 28 HOH HOH . I 6 HOH A 13 713 3 HOH HOH . I 6 HOH A 14 714 29 HOH HOH . I 6 HOH A 15 715 33 HOH HOH . I 6 HOH A 16 716 2 HOH HOH . I 6 HOH A 17 717 8 HOH HOH . I 6 HOH A 18 718 20 HOH HOH . I 6 HOH A 19 719 26 HOH HOH . I 6 HOH A 20 720 5 HOH HOH . J 6 HOH B 1 601 31 HOH HOH . J 6 HOH B 2 602 22 HOH HOH . J 6 HOH B 3 603 13 HOH HOH . J 6 HOH B 4 604 36 HOH HOH . J 6 HOH B 5 605 30 HOH HOH . J 6 HOH B 6 606 38 HOH HOH . J 6 HOH B 7 607 15 HOH HOH . J 6 HOH B 8 608 35 HOH HOH . J 6 HOH B 9 609 34 HOH HOH . J 6 HOH B 10 610 1 HOH HOH . J 6 HOH B 11 611 10 HOH HOH . J 6 HOH B 12 612 14 HOH HOH . J 6 HOH B 13 613 12 HOH HOH . J 6 HOH B 14 614 39 HOH HOH . J 6 HOH B 15 615 9 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 C10 VO8 . . . C 3 48.029 5.307 18.71 1 0.5 ? C10 VO8 601 A 1 HETATM 2 C C1 VO8 . . . C 3 44.017 -2.553 19.137 1 0.5 ? C1 VO8 601 A 1 HETATM 3 C C2 VO8 . . . C 3 45.007 -2.844 19.937 1 0.5 ? C2 VO8 601 A 1 HETATM 4 C C3 VO8 . . . C 3 45.351 -2.106 21.004 1 0.5 ? C3 VO8 601 A 1 HETATM 5 O O1 VO8 . . . C 3 46.166 -2.554 21.788 1 0.5 ? O1 VO8 601 A 1 HETATM 6 N N1 VO8 . . . C 3 44.842 -0.831 21.238 1 0.5 ? N1 VO8 601 A 1 HETATM 7 C C4 VO8 . . . C 3 43.998 -0.137 20.376 1 0.5 ? C4 VO8 601 A 1 HETATM 8 O O2 VO8 . . . C 3 43.558 -0.514 19.294 1 0.5 ? O2 VO8 601 A 1 HETATM 9 N N2 VO8 . . . C 3 43.746 1.072 20.985 1 0.5 ? N2 VO8 601 A 1 HETATM 10 C C5 VO8 . . . C 3 42.897 2.095 20.38 1 0.5 ? C5 VO8 601 A 1 HETATM 11 C C6 VO8 . . . C 3 43.676 2.967 19.461 1 0.5 ? C6 VO8 601 A 1 HETATM 12 O O3 VO8 . . . C 3 44.534 3.758 20.267 1 0.5 ? O3 VO8 601 A 1 HETATM 13 C C7 VO8 . . . C 3 45.654 4.271 19.68 1 0.5 ? C7 VO8 601 A 1 HETATM 14 C C8 VO8 . . . C 3 45.767 4.626 18.346 1 0.5 ? C8 VO8 601 A 1 HETATM 15 C C9 VO8 . . . C 3 46.962 5.144 17.866 1 0.5 ? C9 VO8 601 A 1 HETATM 16 C C11 VO8 . . . C 3 47.92 4.956 20.048 1 0.5 ? C11 VO8 601 A 1 HETATM 17 C C12 VO8 . . . C 3 46.746 4.435 20.525 1 0.5 ? C12 VO8 601 A 1 HETATM 18 O O4 VO8 . . . C 3 46.619 4.09 21.863 1 0.5 ? O4 VO8 601 A 1 HETATM 19 C C13 VO8 . . . C 3 46.496 5.125 22.765 1 0.5 ? C13 VO8 601 A 1 HETATM 20 C C14 VO8 . . . C 3 45.876 6.291 22.465 1 0.5 ? C14 VO8 601 A 1 HETATM 21 C C15 VO8 . . . C 3 45.79 7.308 23.426 1 0.5 ? C15 VO8 601 A 1 HETATM 22 C C16 VO8 . . . C 3 46.323 7.145 24.664 1 0.5 ? C16 VO8 601 A 1 HETATM 23 C C17 VO8 . . . C 3 46.979 5.944 25.01 1 0.5 ? C17 VO8 601 A 1 HETATM 24 C C18 VO8 . . . C 3 47.547 5.736 26.285 1 0.5 ? C18 VO8 601 A 1 HETATM 25 C C19 VO8 . . . C 3 48.179 4.552 26.591 1 0.5 ? C19 VO8 601 A 1 HETATM 26 C C20 VO8 . . . C 3 48.762 4.357 27.891 1 0.5 ? C20 VO8 601 A 1 HETATM 27 N N3 VO8 . . . C 3 49.264 4.225 28.912 1 0.5 ? N3 VO8 601 A 1 HETATM 28 C C21 VO8 . . . C 3 48.261 3.546 25.623 1 0.5 ? C21 VO8 601 A 1 HETATM 29 C C22 VO8 . . . C 3 47.726 3.716 24.381 1 0.5 ? C22 VO8 601 A 1 HETATM 30 C C23 VO8 . . . C 3 47.067 4.917 24.042 1 0.5 ? C23 VO8 601 A 1 HETATM 31 C C24 VO8 . . . C 3 44.411 1.165 22.192 1 0.5 ? C24 VO8 601 A 1 HETATM 32 C C25 VO8 . . . C 3 44.454 2.177 23.128 1 0.5 ? C25 VO8 601 A 1 HETATM 33 C C26 VO8 . . . C 3 45.224 1.944 24.257 1 0.5 ? C26 VO8 601 A 1 HETATM 34 C C27 VO8 . . . C 3 45.917 0.76 24.432 1 0.5 ? C27 VO8 601 A 1 HETATM 35 C C28 VO8 . . . C 3 45.871 -0.256 23.492 1 0.5 ? C28 VO8 601 A 1 HETATM 36 C C29 VO8 . . . C 3 45.104 -0.027 22.369 1 0.5 ? C29 VO8 601 A 1 HETATM 37 H H10 VO8 . . . C 3 48.96 5.71 18.335 1 0.5 ? H10 VO8 601 A 1 HETATM 38 H H1 VO8 . . . C 3 44.211 -2.353 18.091 1 0.5 ? H1 VO8 601 A 1 HETATM 39 H H5 VO8 . . . C 3 42.098 1.606 19.826 1 0.5 ? H5 VO8 601 A 1 HETATM 40 H H4 VO8 . . . C 3 42.462 2.702 21.172 1 0.5 ? H4 VO8 601 A 1 HETATM 41 H H7 VO8 . . . C 3 44.261 2.354 18.778 1 0.5 ? H7 VO8 601 A 1 HETATM 42 H H6 VO8 . . . C 3 43.002 3.603 18.89 1 0.5 ? H6 VO8 601 A 1 HETATM 43 H H8 VO8 . . . C 3 44.925 4.497 17.68 1 0.5 ? H8 VO8 601 A 1 HETATM 44 H H9 VO8 . . . C 3 47.047 5.418 16.823 1 0.5 ? H9 VO8 601 A 1 HETATM 45 H H11 VO8 . . . C 3 48.763 5.084 20.714 1 0.5 ? H11 VO8 601 A 1 HETATM 46 H H12 VO8 . . . C 3 45.441 6.442 21.486 1 0.5 ? H12 VO8 601 A 1 HETATM 47 H H13 VO8 . . . C 3 45.288 8.232 23.175 1 0.5 ? H13 VO8 601 A 1 HETATM 48 H H14 VO8 . . . C 3 46.246 7.941 25.392 1 0.5 ? H14 VO8 601 A 1 HETATM 49 H H15 VO8 . . . C 3 47.483 6.52 27.028 1 0.5 ? H15 VO8 601 A 1 HETATM 50 H H16 VO8 . . . C 3 48.76 2.616 25.86 1 0.5 ? H16 VO8 601 A 1 HETATM 51 H H17 VO8 . . . C 3 47.801 2.918 23.655 1 0.5 ? H17 VO8 601 A 1 HETATM 52 H H18 VO8 . . . C 3 43.914 3.104 22.99 1 0.5 ? H18 VO8 601 A 1 HETATM 53 H H19 VO8 . . . C 3 45.288 2.711 25.017 1 0.5 ? H19 VO8 601 A 1 HETATM 54 H H20 VO8 . . . C 3 46.507 0.622 25.328 1 0.5 ? H20 VO8 601 A 1 HETATM 55 H H21 VO8 . . . C 3 46.414 -1.18 23.634 1 0.5 ? H21 VO8 601 A 1 HETATM 56 H H2 VO8 . . . C 3 43.007 -2.51 19.518 1 0.5 ? H2 VO8 601 A 1 HETATM 57 H H23 VO8 . . . C 3 45.592 -3.732 19.742 1 0.5 ? H23 VO8 601 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 27 _model_server_stats.create_model_time_ms 20 _model_server_stats.query_time_ms 626 _model_server_stats.encode_time_ms 14 _model_server_stats.element_count 57 #