data_7KP8 # _model_server_result.job_id 6tUhUNCCs_yLtY_sNJELDA _model_server_result.datetime_utc '2024-10-19 11:36:41' _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 7kp8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":201}' # _entry.id 7KP8 # _exptl.entry_id 7KP8 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 449.496 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1-{[2-(difluoromethoxy)phenyl]methyl}-2-methyl-6-[6-(piperazin-1-yl)pyridin-3-yl]-1H-benzimidazole _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 7KP8 _cell.length_a 133.577 _cell.length_b 133.577 _cell.length_c 141.445 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7KP8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details pentameric _pdbx_struct_assembly.oligomeric_count 5 _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 _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 F _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 60 A CYS 69 1_555 A SG CYS 91 A CYS 100 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? disulf ? disulf2 B SG CYS 60 B CYS 69 1_555 B SG CYS 91 B CYS 100 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf3 C SG CYS 60 C CYS 69 1_555 C SG CYS 91 C CYS 100 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? disulf ? disulf4 D SG CYS 2 E CYS 15 1_555 D SG CYS 16 E CYS 29 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? disulf ? disulf5 D SG CYS 17 E CYS 30 1_555 D SG CYS 30 E CYS 43 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.973 ? disulf ? disulf6 D SG CYS 20 E CYS 33 1_555 D SG CYS 39 E CYS 52 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.003 ? disulf ? disulf7 D SG CYS 42 E CYS 55 1_555 D SG CYS 57 E CYS 70 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? disulf ? disulf8 D SG CYS 60 E CYS 73 1_555 D SG CYS 75 E CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? disulf ? disulf9 D SG CYS 63 E CYS 76 1_555 D SG CYS 83 E CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? disulf ? disulf10 D SG CYS 85 E CYS 98 1_555 D SG CYS 101 E CYS 114 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf11 D SG CYS 104 E CYS 117 1_555 D SG CYS 116 E CYS 129 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? disulf ? disulf12 D SG CYS 107 E CYS 120 1_555 D SG CYS 124 E CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.015 ? disulf ? disulf13 E SG CYS 2 F CYS 15 1_555 E SG CYS 16 F CYS 29 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf14 E SG CYS 17 F CYS 30 1_555 E SG CYS 30 F CYS 43 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.961 ? disulf ? disulf15 E SG CYS 20 F CYS 33 1_555 E SG CYS 39 F CYS 52 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.983 ? disulf ? disulf16 E SG CYS 42 F CYS 55 1_555 E SG CYS 57 F CYS 70 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? disulf ? disulf17 E SG CYS 60 F CYS 73 1_555 E SG CYS 75 F CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf18 E SG CYS 63 F CYS 76 1_555 E SG CYS 83 F CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? disulf ? disulf19 E SG CYS 85 F CYS 98 1_555 E SG CYS 101 F CYS 114 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf20 E SG CYS 104 F CYS 117 1_555 E SG CYS 116 F CYS 129 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? disulf ? disulf21 E SG CYS 107 F CYS 120 1_555 E SG CYS 124 F CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.013 ? # _chem_comp.formula 'C25 H25 F2 N5 O' _chem_comp.formula_weight 449.496 _chem_comp.id A7G _chem_comp.mon_nstd_flag . _chem_comp.name 1-{[2-(difluoromethoxy)phenyl]methyl}-2-methyl-6-[6-(piperazin-1-yl)pyridin-3-yl]-1H-benzimidazole _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 C1 C2 A7G sing 1 n n N1 C2 A7G doub 2 n y N1 C3 A7G sing 3 n y C2 N2 A7G sing 4 n y C3 C4 A7G doub 5 n y C3 C8 A7G sing 6 n y N2 C9 A7G sing 7 n n N2 C8 A7G sing 8 n y C4 C5 A7G sing 9 n y C9 C10 A7G sing 10 n n C8 C7 A7G doub 11 n y C11 C10 A7G doub 12 n y C11 C12 A7G sing 13 n y C5 C6 A7G doub 14 n y C10 C15 A7G sing 15 n y C7 C6 A7G sing 16 n y C6 C17 A7G sing 17 n n C12 C13 A7G doub 18 n y C15 O A7G sing 19 n n C15 C14 A7G doub 20 n y F1 C16 A7G sing 21 n n O C16 A7G sing 22 n n C16 F2 A7G sing 23 n n C13 C14 A7G sing 24 n y C17 C18 A7G doub 25 n y C17 C21 A7G sing 26 n y C18 C19 A7G sing 27 n y C21 N3 A7G doub 28 n y C19 C20 A7G doub 29 n y N3 C20 A7G sing 30 n y C20 N4 A7G sing 31 n n N4 C25 A7G sing 32 n n N4 C22 A7G sing 33 n n C25 C24 A7G sing 34 n n C22 C23 A7G sing 35 n n C24 N5 A7G sing 36 n n C23 N5 A7G sing 37 n n C16 H1 A7G sing 38 n n C14 H2 A7G sing 39 n n C13 H3 A7G sing 40 n n C12 H4 A7G sing 41 n n C11 H5 A7G sing 42 n n C9 H6 A7G sing 43 n n C9 H7 A7G sing 44 n n C1 H8 A7G sing 45 n n C1 H9 A7G sing 46 n n C1 H10 A7G sing 47 n n C7 H11 A7G sing 48 n n C5 H12 A7G sing 49 n n C4 H13 A7G sing 50 n n C21 H14 A7G sing 51 n n C19 H15 A7G sing 52 n n C18 H16 A7G sing 53 n n C25 H17 A7G sing 54 n n C25 H18 A7G sing 55 n n C24 H19 A7G sing 56 n n C24 H20 A7G sing 57 n n N5 H21 A7G sing 58 n n C23 H23 A7G sing 59 n n C23 H24 A7G sing 60 n n C22 H25 A7G sing 61 n n C22 H26 A7G sing 62 n n # _atom_sites.entry_id 7KP8 _atom_sites.fract_transf_matrix[1][1] 0.007486 _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] 0.007486 _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] 0.00707 _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 F 3 A7G C 1 201 1 A7G 433 . G 4 HOH A 1 201 1 HOH HOH . H 4 HOH B 1 201 3 HOH HOH . I 4 HOH F 1 201 4 HOH HOH . I 4 HOH F 2 202 2 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 F F2 A7G . . . F 3 -29.333 17.417 0.778 1 51.33 ? F2 A7G 201 C 1 HETATM 2 C C16 A7G . . . F 3 -29.526 17.514 -0.562 1 54.19 ? C16 A7G 201 C 1 HETATM 3 F F1 A7G . . . F 3 -29.664 16.276 -1.141 1 63.29 ? F1 A7G 201 C 1 HETATM 4 O O A7G . . . F 3 -28.408 18.14 -1.099 1 53.6 ? O A7G 201 C 1 HETATM 5 C C15 A7G . . . F 3 -28.428 19.479 -1.296 1 51.68 ? C15 A7G 201 C 1 HETATM 6 C C14 A7G . . . F 3 -28.839 20.321 -0.258 1 46.9 ? C14 A7G 201 C 1 HETATM 7 C C13 A7G . . . F 3 -28.852 21.675 -0.46 1 47.8 ? C13 A7G 201 C 1 HETATM 8 C C12 A7G . . . F 3 -28.447 22.199 -1.703 1 52.92 ? C12 A7G 201 C 1 HETATM 9 C C11 A7G . . . F 3 -28.027 21.352 -2.745 1 48.99 ? C11 A7G 201 C 1 HETATM 10 C C10 A7G . . . F 3 -28.009 19.995 -2.532 1 50.21 ? C10 A7G 201 C 1 HETATM 11 C C9 A7G . . . F 3 -27.57 19.059 -3.626 1 49.85 ? C9 A7G 201 C 1 HETATM 12 N N2 A7G . . . F 3 -26.233 19.373 -4.101 1 51.33 ? N2 A7G 201 C 1 HETATM 13 C C2 A7G . . . F 3 -25.952 19.916 -5.291 1 56.58 ? C2 A7G 201 C 1 HETATM 14 C C1 A7G . . . F 3 -26.954 20.255 -6.347 1 56.8 ? C1 A7G 201 C 1 HETATM 15 C C8 A7G . . . F 3 -25.084 19.211 -3.44 1 52.72 ? C8 A7G 201 C 1 HETATM 16 C C3 A7G . . . F 3 -24.064 19.694 -4.258 1 55 ? C3 A7G 201 C 1 HETATM 17 N N1 A7G . . . F 3 -24.615 20.117 -5.388 1 56.33 ? N1 A7G 201 C 1 HETATM 18 C C7 A7G . . . F 3 -24.787 18.718 -2.175 1 54.41 ? C7 A7G 201 C 1 HETATM 19 C C6 A7G . . . F 3 -23.45 18.662 -1.737 1 57.34 ? C6 A7G 201 C 1 HETATM 20 C C5 A7G . . . F 3 -22.445 19.189 -2.571 1 59.18 ? C5 A7G 201 C 1 HETATM 21 C C4 A7G . . . F 3 -22.759 19.68 -3.836 1 56.93 ? C4 A7G 201 C 1 HETATM 22 C C17 A7G . . . F 3 -23.107 18.269 -0.424 1 61.07 ? C17 A7G 201 C 1 HETATM 23 C C21 A7G . . . F 3 -24.057 17.996 0.543 1 66.86 ? C21 A7G 201 C 1 HETATM 24 N N3 A7G . . . F 3 -23.682 17.652 1.793 1 70 ? N3 A7G 201 C 1 HETATM 25 C C20 A7G . . . F 3 -22.39 17.554 2.157 1 71.77 ? C20 A7G 201 C 1 HETATM 26 C C19 A7G . . . F 3 -21.417 17.825 1.222 1 72.46 ? C19 A7G 201 C 1 HETATM 27 C C18 A7G . . . F 3 -21.781 18.173 -0.074 1 69.03 ? C18 A7G 201 C 1 HETATM 28 N N4 A7G . . . F 3 -22.033 17.223 3.506 1 78.26 ? N4 A7G 201 C 1 HETATM 29 C C25 A7G . . . F 3 -20.69 17.542 4.024 1 80.41 ? C25 A7G 201 C 1 HETATM 30 C C24 A7G . . . F 3 -20.122 16.271 4.643 1 82.05 ? C24 A7G 201 C 1 HETATM 31 N N5 A7G . . . F 3 -21.068 15.65 5.529 1 82.96 ? N5 A7G 201 C 1 HETATM 32 C C23 A7G . . . F 3 -22.439 15.449 5.11 1 83.63 ? C23 A7G 201 C 1 HETATM 33 C C22 A7G . . . F 3 -23.039 16.68 4.427 1 80.05 ? C22 A7G 201 C 1 # _model_server_stats.io_time_ms 72 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 299 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 33 #