data_7Y28 # _model_server_result.job_id SKJ93X272fJ9Xt4t7qE5JA _model_server_result.datetime_utc '2025-07-05 13:22:33' _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 7y28 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":2601}' # _entry.id 7Y28 # _exptl.entry_id 7Y28 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 367.417 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1-[6-(3-fluorophenyl)benzimidazol-1-yl]-3-[(2R,3S)-3-oxidanylpiperidin-2-yl]propan-2-one _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 108.72 _cell.angle_gamma 90 _cell.entry_id 7Y28 _cell.length_a 71.563 _cell.length_b 92.38 _cell.length_c 86.059 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7Y28 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 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,K,L,M,N _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 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 OE1 GLN 222 A GLN 1237 1_555 G MG MG . A MG 2605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.572 ? metalc ? metalc2 A SG CYS 433 A CYS 1448 1_555 E ZN ZN . A ZN 2603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.272 ? metalc ? metalc3 A SG CYS 438 A CYS 1453 1_555 E ZN ZN . A ZN 2603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.384 ? metalc ? metalc4 A SG CYS 480 A CYS 1495 1_555 E ZN ZN . A ZN 2603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.366 ? metalc ? metalc5 A SG CYS 482 A CYS 1497 1_555 E ZN ZN . A ZN 2603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.38 ? metalc ? metalc6 D O1G ATP . A ATP 2602 1_555 F MG MG . A MG 2604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.377 ? metalc ? metalc7 D O2B ATP . A ATP 2602 1_555 F MG MG . A MG 2604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.448 ? metalc ? metalc8 D O2G ATP . A ATP 2602 1_555 G MG MG . A MG 2605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.526 ? metalc ? metalc9 D O1B ATP . A ATP 2602 1_555 G MG MG . A MG 2605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.356 ? metalc ? metalc10 B SG CYS 433 B CYS 1448 1_555 J ZN ZN . B ZN 2603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.249 ? metalc ? metalc11 B SG CYS 438 B CYS 1453 1_555 J ZN ZN . B ZN 2603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.433 ? metalc ? metalc12 I O3G ATP . B ATP 2602 1_555 K MG MG . B MG 2604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.815 ? metalc ? metalc13 I O1B ATP . B ATP 2602 1_555 K MG MG . B MG 2604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.671 ? metalc ? metalc14 I O2B ATP . B ATP 2602 1_555 L MG MG . B MG 2605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.591 ? # _chem_comp.formula 'C21 H22 F N3 O2' _chem_comp.formula_weight 367.417 _chem_comp.id F96 _chem_comp.mon_nstd_flag . _chem_comp.name 1-[6-(3-fluorophenyl)benzimidazol-1-yl]-3-[(2R,3S)-3-oxidanylpiperidin-2-yl]propan-2-one _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 C16 C15 F96 doub 132 n y C16 C17 F96 sing 133 n y F C17 F96 sing 134 n n C15 C14 F96 sing 135 n y C17 C18 F96 doub 136 n y C14 C13 F96 doub 137 n y C18 C13 F96 sing 138 n y C13 C12 F96 sing 139 n n C12 C11 F96 doub 140 n y C12 C19 F96 sing 141 n y C11 C10 F96 sing 142 n y C19 C20 F96 doub 143 n y C10 C9 F96 doub 144 n y C20 C9 F96 sing 145 n y C20 N1 F96 sing 146 n y C9 N2 F96 sing 147 n y C7 N1 F96 sing 148 n n C7 C F96 sing 149 n n N C3 F96 sing 150 n n N C2 F96 sing 151 n n N1 C8 F96 sing 152 n y C3 C4 F96 sing 153 n n C O F96 doub 154 n n C C1 F96 sing 155 n n C1 C2 F96 sing 156 n n C2 C6 F96 sing 157 n n N2 C8 F96 doub 158 n y C4 C5 F96 sing 159 n n C6 C5 F96 sing 160 n n C6 O1 F96 sing 161 n n C11 H1 F96 sing 162 n n C7 H2 F96 sing 163 n n C7 H3 F96 sing 164 n n C6 H4 F96 sing 165 n n C5 H5 F96 sing 166 n n C5 H6 F96 sing 167 n n C4 H7 F96 sing 168 n n C4 H8 F96 sing 169 n n C3 H9 F96 sing 170 n n C3 H10 F96 sing 171 n n C2 H11 F96 sing 172 n n C10 H12 F96 sing 173 n n C8 H13 F96 sing 174 n n N H14 F96 sing 175 n n C1 H16 F96 sing 176 n n C1 H17 F96 sing 177 n n C14 H18 F96 sing 178 n n C15 H19 F96 sing 179 n n C16 H20 F96 sing 180 n n C18 H21 F96 sing 181 n n C19 H22 F96 sing 182 n n O1 H23 F96 sing 183 n n # _atom_sites.entry_id 7Y28 _atom_sites.fract_transf_matrix[1][1] 0.013974 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004735 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010825 _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] 0.012269 _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 F96 A 1 2601 2601 F96 DW5 . D 3 ATP A 1 2602 2602 ATP ATP . E 4 ZN A 1 2603 2603 ZN ZN . F 5 MG A 1 2604 2604 MG MG . G 5 MG A 1 2605 2605 MG MG . H 2 F96 B 1 2601 2601 F96 DW5 . I 3 ATP B 1 2602 2602 ATP ATP . J 4 ZN B 1 2603 2603 ZN ZN . K 5 MG B 1 2604 2604 MG MG . L 5 MG B 1 2605 2605 MG MG . M 6 HOH A 1 2701 72 HOH HOH . M 6 HOH A 2 2702 71 HOH HOH . M 6 HOH A 3 2703 132 HOH HOH . M 6 HOH A 4 2704 60 HOH HOH . M 6 HOH A 5 2705 62 HOH HOH . M 6 HOH A 6 2706 120 HOH HOH . M 6 HOH A 7 2707 17 HOH HOH . M 6 HOH A 8 2708 41 HOH HOH . M 6 HOH A 9 2709 84 HOH HOH . M 6 HOH A 10 2710 117 HOH HOH . M 6 HOH A 11 2711 65 HOH HOH . M 6 HOH A 12 2712 32 HOH HOH . M 6 HOH A 13 2713 14 HOH HOH . M 6 HOH A 14 2714 92 HOH HOH . M 6 HOH A 15 2715 68 HOH HOH . M 6 HOH A 16 2716 12 HOH HOH . M 6 HOH A 17 2717 91 HOH HOH . M 6 HOH A 18 2718 125 HOH HOH . M 6 HOH A 19 2719 26 HOH HOH . M 6 HOH A 20 2720 78 HOH HOH . M 6 HOH A 21 2721 7 HOH HOH . M 6 HOH A 22 2722 5 HOH HOH . M 6 HOH A 23 2723 1 HOH HOH . M 6 HOH A 24 2724 97 HOH HOH . M 6 HOH A 25 2725 18 HOH HOH . M 6 HOH A 26 2726 63 HOH HOH . M 6 HOH A 27 2727 15 HOH HOH . M 6 HOH A 28 2728 50 HOH HOH . M 6 HOH A 29 2729 69 HOH HOH . M 6 HOH A 30 2730 109 HOH HOH . M 6 HOH A 31 2731 112 HOH HOH . M 6 HOH A 32 2732 57 HOH HOH . M 6 HOH A 33 2733 105 HOH HOH . M 6 HOH A 34 2734 45 HOH HOH . M 6 HOH A 35 2735 93 HOH HOH . M 6 HOH A 36 2736 47 HOH HOH . M 6 HOH A 37 2737 129 HOH HOH . M 6 HOH A 38 2738 22 HOH HOH . M 6 HOH A 39 2739 44 HOH HOH . M 6 HOH A 40 2740 29 HOH HOH . M 6 HOH A 41 2741 53 HOH HOH . M 6 HOH A 42 2742 16 HOH HOH . M 6 HOH A 43 2743 28 HOH HOH . M 6 HOH A 44 2744 23 HOH HOH . M 6 HOH A 45 2745 21 HOH HOH . M 6 HOH A 46 2746 27 HOH HOH . M 6 HOH A 47 2747 38 HOH HOH . M 6 HOH A 48 2748 4 HOH HOH . M 6 HOH A 49 2749 123 HOH HOH . M 6 HOH A 50 2750 89 HOH HOH . M 6 HOH A 51 2751 13 HOH HOH . M 6 HOH A 52 2752 2 HOH HOH . M 6 HOH A 53 2753 9 HOH HOH . M 6 HOH A 54 2754 86 HOH HOH . M 6 HOH A 55 2755 25 HOH HOH . M 6 HOH A 56 2756 43 HOH HOH . M 6 HOH A 57 2757 110 HOH HOH . M 6 HOH A 58 2758 83 HOH HOH . M 6 HOH A 59 2759 37 HOH HOH . M 6 HOH A 60 2760 107 HOH HOH . M 6 HOH A 61 2761 111 HOH HOH . M 6 HOH A 62 2762 130 HOH HOH . M 6 HOH A 63 2763 88 HOH HOH . M 6 HOH A 64 2764 61 HOH HOH . M 6 HOH A 65 2765 75 HOH HOH . M 6 HOH A 66 2766 133 HOH HOH . M 6 HOH A 67 2767 118 HOH HOH . M 6 HOH A 68 2768 58 HOH HOH . M 6 HOH A 69 2769 113 HOH HOH . M 6 HOH A 70 2770 46 HOH HOH . M 6 HOH A 71 2771 119 HOH HOH . M 6 HOH A 72 2772 70 HOH HOH . M 6 HOH A 73 2773 56 HOH HOH . M 6 HOH A 74 2774 122 HOH HOH . M 6 HOH A 75 2775 116 HOH HOH . M 6 HOH A 76 2776 128 HOH HOH . M 6 HOH A 77 2777 90 HOH HOH . N 6 HOH B 1 2701 104 HOH HOH . N 6 HOH B 2 2702 115 HOH HOH . N 6 HOH B 3 2703 102 HOH HOH . N 6 HOH B 4 2704 76 HOH HOH . N 6 HOH B 5 2705 54 HOH HOH . N 6 HOH B 6 2706 6 HOH HOH . N 6 HOH B 7 2707 8 HOH HOH . N 6 HOH B 8 2708 67 HOH HOH . N 6 HOH B 9 2709 96 HOH HOH . N 6 HOH B 10 2710 10 HOH HOH . N 6 HOH B 11 2711 31 HOH HOH . N 6 HOH B 12 2712 131 HOH HOH . N 6 HOH B 13 2713 42 HOH HOH . N 6 HOH B 14 2714 94 HOH HOH . N 6 HOH B 15 2715 55 HOH HOH . N 6 HOH B 16 2716 106 HOH HOH . N 6 HOH B 17 2717 36 HOH HOH . N 6 HOH B 18 2718 59 HOH HOH . N 6 HOH B 19 2719 11 HOH HOH . N 6 HOH B 20 2720 35 HOH HOH . N 6 HOH B 21 2721 3 HOH HOH . N 6 HOH B 22 2722 48 HOH HOH . N 6 HOH B 23 2723 66 HOH HOH . N 6 HOH B 24 2724 73 HOH HOH . N 6 HOH B 25 2725 85 HOH HOH . N 6 HOH B 26 2726 52 HOH HOH . N 6 HOH B 27 2727 49 HOH HOH . N 6 HOH B 28 2728 64 HOH HOH . N 6 HOH B 29 2729 20 HOH HOH . N 6 HOH B 30 2730 33 HOH HOH . N 6 HOH B 31 2731 34 HOH HOH . N 6 HOH B 32 2732 126 HOH HOH . N 6 HOH B 33 2733 51 HOH HOH . N 6 HOH B 34 2734 87 HOH HOH . N 6 HOH B 35 2735 81 HOH HOH . N 6 HOH B 36 2736 80 HOH HOH . N 6 HOH B 37 2737 103 HOH HOH . N 6 HOH B 38 2738 99 HOH HOH . N 6 HOH B 39 2739 74 HOH HOH . N 6 HOH B 40 2740 39 HOH HOH . N 6 HOH B 41 2741 100 HOH HOH . N 6 HOH B 42 2742 98 HOH HOH . N 6 HOH B 43 2743 124 HOH HOH . N 6 HOH B 44 2744 19 HOH HOH . N 6 HOH B 45 2745 134 HOH HOH . N 6 HOH B 46 2746 79 HOH HOH . N 6 HOH B 47 2747 95 HOH HOH . N 6 HOH B 48 2748 24 HOH HOH . N 6 HOH B 49 2749 77 HOH HOH . N 6 HOH B 50 2750 121 HOH HOH . N 6 HOH B 51 2751 108 HOH HOH . N 6 HOH B 52 2752 101 HOH HOH . N 6 HOH B 53 2753 30 HOH HOH . N 6 HOH B 54 2754 40 HOH HOH . N 6 HOH B 55 2755 127 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 C11 F96 . . . C 2 16.975 19.924 182.312 1 30.82 ? C11 F96 2601 A 1 HETATM 2 C C12 F96 . . . C 2 15.952 19.247 181.631 1 32.58 ? C12 F96 2601 A 1 HETATM 3 C C7 F96 . . . C 2 13.444 16.711 184.49 1 36.18 ? C7 F96 2601 A 1 HETATM 4 C C6 F96 . . . C 2 14.123 12.855 186.849 1 24.78 ? C6 F96 2601 A 1 HETATM 5 C C5 F96 . . . C 2 14.383 11.41 187.22 1 28.04 ? C5 F96 2601 A 1 HETATM 6 C C4 F96 . . . C 2 14.843 10.585 186.021 1 34.34 ? C4 F96 2601 A 1 HETATM 7 C C3 F96 . . . C 2 13.963 10.774 184.815 1 31.61 ? C3 F96 2601 A 1 HETATM 8 C C2 F96 . . . C 2 13.236 12.938 185.587 1 24.77 ? C2 F96 2601 A 1 HETATM 9 N N1 F96 . . . C 2 14.51 17.697 184.721 1 34.59 ? N1 F96 2601 A 1 HETATM 10 C C10 F96 . . . C 2 17.123 19.835 183.687 1 37.25 ? C10 F96 2601 A 1 HETATM 11 C C9 F96 . . . C 2 16.218 19.052 184.419 1 39.85 ? C9 F96 2601 A 1 HETATM 12 C C8 F96 . . . C 2 15.081 18.027 185.902 1 28.55 ? C8 F96 2601 A 1 HETATM 13 C C13 F96 . . . C 2 15.851 19.318 180.156 1 32.56 ? C13 F96 2601 A 1 HETATM 14 N N F96 . . . C 2 13.843 12.199 184.488 1 28.81 ? N F96 2601 A 1 HETATM 15 C C F96 . . . C 2 13.863 15.313 184.901 1 33.8 ? C F96 2601 A 1 HETATM 16 O O F96 . . . C 2 15.03 14.995 184.961 1 43.89 ? O F96 2601 A 1 HETATM 17 C C1 F96 . . . C 2 12.766 14.343 185.231 1 30.24 ? C1 F96 2601 A 1 HETATM 18 C C14 F96 . . . C 2 15.576 18.188 179.387 1 40.51 ? C14 F96 2601 A 1 HETATM 19 C C15 F96 . . . C 2 15.567 18.255 178.002 1 39.64 ? C15 F96 2601 A 1 HETATM 20 C C16 F96 . . . C 2 15.823 19.452 177.354 1 25.08 ? C16 F96 2601 A 1 HETATM 21 C C17 F96 . . . C 2 16.056 20.555 178.132 1 36.4 ? C17 F96 2601 A 1 HETATM 22 C C18 F96 . . . C 2 16.089 20.52 179.499 1 31.7 ? C18 F96 2601 A 1 HETATM 23 C C19 F96 . . . C 2 15.053 18.459 182.362 1 36.01 ? C19 F96 2601 A 1 HETATM 24 C C20 F96 . . . C 2 15.208 18.37 183.723 1 33.97 ? C20 F96 2601 A 1 HETATM 25 F F F96 . . . C 2 16.194 21.766 177.525 1 39.17 ? F F96 2601 A 1 HETATM 26 N N2 F96 . . . C 2 16.114 18.833 185.784 1 39.1 ? N2 F96 2601 A 1 HETATM 27 O O1 F96 . . . C 2 13.457 13.532 187.913 1 26.25 ? O1 F96 2601 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 247 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #