data_8FYY # _model_server_result.job_id mQDrKA9_-CkChQ2Uugoj6A _model_server_result.datetime_utc '2024-10-26 02:26:34' _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 8fyy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1101}' # _entry.id 8FYY # _exptl.entry_id 8FYY _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 424.455 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-(4-{[2-(1H-benzimidazol-2-yl)ethyl]carbamoyl}phenyl)-1H-benzimidazole-7-carboxamide _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 8FYY _cell.length_a 92.732 _cell.length_b 92.732 _cell.length_c 136.359 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8FYY _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61 2 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F _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 # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 2 _pdbx_entity_branch_link.entity_branch_list_num_1 1 _pdbx_entity_branch_link.entity_branch_list_num_2 2 _pdbx_entity_branch_link.comp_id_1 GLC _pdbx_entity_branch_link.comp_id_2 FRU _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O2 _pdbx_entity_branch_link.leaving_atom_id_2 HO2 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 2 n B GLC 1 B 1 GLC A 1201 SUC 2 n B FRU 2 B 2 FRU A 1201 SUC # 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 104 A CYS 845 1_555 A SG CYS 104 A CYS 845 7_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? covale ? covale1 B C1 GLC . B GLC 1 1_555 B O2 FRU . B FRU 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.418 ? # _chem_comp.formula 'C24 H20 N6 O2' _chem_comp.formula_weight 424.455 _chem_comp.id YH0 _chem_comp.mon_nstd_flag . _chem_comp.name 2-(4-{[2-(1H-benzimidazol-2-yl)ethyl]carbamoyl}phenyl)-1H-benzimidazole-7-carboxamide _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 C22 C21 YH0 doub 449 n y C22 C23 YH0 sing 450 n y C21 C20 YH0 sing 451 n y C23 C18 YH0 doub 452 n y C20 C19 YH0 doub 453 n y C18 C19 YH0 sing 454 n y C18 N4 YH0 sing 455 n y C19 N5 YH0 sing 456 n y N4 C17 YH0 sing 457 n y N5 C17 YH0 doub 458 n y C17 C16 YH0 sing 459 n n C16 C15 YH0 sing 460 n n C15 N3 YH0 sing 461 n n O1 C14 YH0 doub 462 n n N3 C14 YH0 sing 463 n n C14 C11 YH0 sing 464 n n C11 C12 YH0 doub 465 n y C11 C10 YH0 sing 466 n y C12 C13 YH0 sing 467 n y C10 C9 YH0 doub 468 n y C13 C8 YH0 doub 469 n y C9 C8 YH0 sing 470 n y C8 C3 YH0 sing 471 n n C3 N1 YH0 sing 472 n y C3 N2 YH0 doub 473 n y N1 C2 YH0 sing 474 n y N2 C4 YH0 sing 475 n y N C YH0 sing 476 n n C2 C4 YH0 doub 477 n y C2 C1 YH0 sing 478 n y C4 C5 YH0 sing 479 n y C C1 YH0 sing 480 n n C O YH0 doub 481 n n C1 C7 YH0 doub 482 n y C5 C6 YH0 doub 483 n y C7 C6 YH0 sing 484 n y N1 H1 YH0 sing 485 n n C7 H2 YH0 sing 486 n n C9 H4 YH0 sing 487 n n C5 H5 YH0 sing 488 n n C6 H6 YH0 sing 489 n n N3 H7 YH0 sing 490 n n N4 H8 YH0 sing 491 n n N H9 YH0 sing 492 n n N H10 YH0 sing 493 n n C10 H11 YH0 sing 494 n n C12 H12 YH0 sing 495 n n C13 H13 YH0 sing 496 n n C15 H14 YH0 sing 497 n n C15 H15 YH0 sing 498 n n C16 H16 YH0 sing 499 n n C16 H17 YH0 sing 500 n n C20 H18 YH0 sing 501 n n C21 H19 YH0 sing 502 n n C22 H20 YH0 sing 503 n n C23 H21 YH0 sing 504 n n # _atom_sites.entry_id 8FYY _atom_sites.fract_transf_matrix[1][1] 0.010784 _atom_sites.fract_transf_matrix[1][2] 0.006226 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012452 _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] 0.007334 _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 YH0 A 1 1101 1101 YH0 XXX . D 4 DMS A 1 1102 1301 DMS DMS . E 5 PEG A 1 1103 1401 PEG PGE . F 6 HOH A 1 1201 9 HOH HOH . F 6 HOH A 2 1202 18 HOH HOH . F 6 HOH A 3 1203 17 HOH HOH . F 6 HOH A 4 1204 11 HOH HOH . F 6 HOH A 5 1205 13 HOH HOH . F 6 HOH A 6 1206 2 HOH HOH . F 6 HOH A 7 1207 7 HOH HOH . F 6 HOH A 8 1208 5 HOH HOH . F 6 HOH A 9 1209 1 HOH HOH . F 6 HOH A 10 1210 6 HOH HOH . F 6 HOH A 11 1211 16 HOH HOH . F 6 HOH A 12 1212 8 HOH HOH . F 6 HOH A 13 1213 10 HOH HOH . F 6 HOH A 14 1214 3 HOH HOH . F 6 HOH A 15 1215 12 HOH HOH . F 6 HOH A 16 1216 15 HOH HOH . F 6 HOH A 17 1217 4 HOH HOH . F 6 HOH A 18 1218 14 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 N N1 YH0 . . . C 3 -3.593 38.699 10.789 1 28.06 ? N1 YH0 1101 A 1 HETATM 2 C C7 YH0 . . . C 3 -1.847 36.305 8.506 1 30.2 ? C7 YH0 1101 A 1 HETATM 3 C C8 YH0 . . . C 3 -5.696 39.251 11.978 1 37.68 ? C8 YH0 1101 A 1 HETATM 4 N N2 YH0 . . . C 3 -5.308 37.295 10.48 1 29.64 ? N2 YH0 1101 A 1 HETATM 5 C C9 YH0 . . . C 3 -5.371 40.581 12.214 1 28.74 ? C9 YH0 1101 A 1 HETATM 6 O O1 YH0 . . . C 3 -7.234 42.257 15.663 1 36.69 ? O1 YH0 1101 A 1 HETATM 7 C C1 YH0 . . . C 3 -1.964 37.438 9.314 1 27.83 ? C1 YH0 1101 A 1 HETATM 8 C C5 YH0 . . . C 3 -4.141 35.668 8.931 1 30.34 ? C5 YH0 1101 A 1 HETATM 9 C C6 YH0 . . . C 3 -2.917 35.436 8.318 1 28.94 ? C6 YH0 1101 A 1 HETATM 10 N N3 YH0 . . . C 3 -9.204 41.561 14.844 1 37.73 ? N3 YH0 1101 A 1 HETATM 11 C C4 YH0 . . . C 3 -4.255 36.792 9.738 1 31.79 ? C4 YH0 1101 A 1 HETATM 12 C C3 YH0 . . . C 3 -4.861 38.429 11.085 1 37.68 ? C3 YH0 1101 A 1 HETATM 13 C C2 YH0 . . . C 3 -3.196 37.674 9.939 1 29.93 ? C2 YH0 1101 A 1 HETATM 14 N N4 YH0 . . . C 3 -12.735 43.655 14.435 1 60.32 ? N4 YH0 1101 A 1 HETATM 15 N N YH0 . . . C 3 -0.913 39.399 10.265 1 25.85 ? N YH0 1101 A 1 HETATM 16 C C YH0 . . . C 3 -0.786 38.347 9.464 1 27.62 ? C YH0 1101 A 1 HETATM 17 O O YH0 . . . C 3 0.259 38.104 8.847 1 31.01 ? O YH0 1101 A 1 HETATM 18 C C10 YH0 . . . C 3 -6.097 41.336 13.117 1 41.08 ? C10 YH0 1101 A 1 HETATM 19 C C11 YH0 . . . C 3 -7.168 40.782 13.807 1 38.95 ? C11 YH0 1101 A 1 HETATM 20 C C12 YH0 . . . C 3 -7.512 39.459 13.549 1 37.56 ? C12 YH0 1101 A 1 HETATM 21 C C13 YH0 . . . C 3 -6.786 38.704 12.646 1 36.99 ? C13 YH0 1101 A 1 HETATM 22 C C14 YH0 . . . C 3 -7.87 41.596 14.846 1 41.39 ? C14 YH0 1101 A 1 HETATM 23 C C15 YH0 . . . C 3 -9.992 42.26 15.85 1 47.83 ? C15 YH0 1101 A 1 HETATM 24 C C16 YH0 . . . C 3 -10.427 43.633 15.382 1 48.33 ? C16 YH0 1101 A 1 HETATM 25 C C17 YH0 . . . C 3 -11.428 43.549 14.281 1 49.79 ? C17 YH0 1101 A 1 HETATM 26 C C18 YH0 . . . C 3 -13.267 43.442 13.163 1 62.7 ? C18 YH0 1101 A 1 HETATM 27 C C19 YH0 . . . C 3 -12.231 43.217 12.259 1 59.37 ? C19 YH0 1101 A 1 HETATM 28 C C20 YH0 . . . C 3 -12.474 42.95 10.918 1 70.32 ? C20 YH0 1101 A 1 HETATM 29 C C21 YH0 . . . C 3 -13.795 42.902 10.494 1 73.15 ? C21 YH0 1101 A 1 HETATM 30 C C22 YH0 . . . C 3 -14.839 43.121 11.387 1 73.77 ? C22 YH0 1101 A 1 HETATM 31 C C23 YH0 . . . C 3 -14.588 43.396 12.725 1 67.55 ? C23 YH0 1101 A 1 HETATM 32 N N5 YH0 . . . C 3 -11.067 43.296 13.001 1 60.81 ? N5 YH0 1101 A 1 # _model_server_stats.io_time_ms 62 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 255 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 32 #