data_7Y1W # _model_server_result.job_id Ufl2l77fbTmckSRUM2GHXA _model_server_result.datetime_utc '2025-07-31 18:33:17' _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 7y1w # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":1602}' # _entry.id 7Y1W # _exptl.entry_id 7Y1W _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 328.237 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (2R,3S)-2-[3-[4,5-bis(chloranyl)benzimidazol-1-yl]propyl]piperidin-3-ol _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 108.77 _cell.angle_gamma 90 _cell.entry_id 7Y1W _cell.length_a 71.556 _cell.length_b 92.147 _cell.length_c 86.728 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7Y1W _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 _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 ? 3 D N N ? 3 I 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 223 A GLN 1237 1_555 G MG MG . A MG 1605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.466 ? metalc ? metalc2 A SG CYS 434 A CYS 1448 1_555 C ZN ZN . A ZN 1601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.325 ? metalc ? metalc3 A SG CYS 439 A CYS 1453 1_555 C ZN ZN . A ZN 1601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.308 ? metalc ? metalc4 A SG CYS 481 A CYS 1495 1_555 C ZN ZN . A ZN 1601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.343 ? metalc ? metalc5 E O3G ATP . A ATP 1603 1_555 F MG MG . A MG 1604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.956 ? metalc ? metalc6 E O2B ATP . A ATP 1603 1_555 F MG MG . A MG 1604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.321 ? metalc ? metalc7 E O2G ATP . A ATP 1603 1_555 G MG MG . A MG 1605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.19 ? metalc ? metalc8 B SG CYS 434 B CYS 1448 1_555 H ZN ZN . B ZN 1601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.269 ? metalc ? metalc9 B SG CYS 439 B CYS 1453 1_555 H ZN ZN . B ZN 1601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.337 ? metalc ? metalc10 B SG CYS 481 B CYS 1495 1_555 H ZN ZN . B ZN 1601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.264 ? # _chem_comp.formula 'C15 H19 Cl2 N3 O' _chem_comp.formula_weight 328.237 _chem_comp.id F9O _chem_comp.mon_nstd_flag . _chem_comp.name (2R,3S)-2-[3-[4,5-bis(chloranyl)benzimidazol-1-yl]propyl]piperidin-3-ol _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 CL1 C13 F9O sing 132 n n C12 C13 F9O doub 133 n y C12 C11 F9O sing 134 n y C13 C14 F9O sing 135 n y C11 C10 F9O doub 136 n y C14 CL F9O sing 137 n n C14 C9 F9O doub 138 n y C10 C9 F9O sing 139 n y C10 N1 F9O sing 140 n y C9 N2 F9O sing 141 n y N C3 F9O sing 142 n n N C4 F9O sing 143 n n N1 C7 F9O sing 144 n n N1 C8 F9O sing 145 n y C3 C2 F9O sing 146 n n C7 C6 F9O sing 147 n n C5 C4 F9O sing 148 n n C5 C6 F9O sing 149 n n N2 C8 F9O doub 150 n y C4 C F9O sing 151 n n C2 C1 F9O sing 152 n n C C1 F9O sing 153 n n C O F9O sing 154 n n C4 H1 F9O sing 155 n n C5 H2 F9O sing 156 n n C5 H3 F9O sing 157 n n C6 H4 F9O sing 158 n n C6 H5 F9O sing 159 n n C3 H6 F9O sing 160 n n C3 H7 F9O sing 161 n n C2 H8 F9O sing 162 n n C2 H9 F9O sing 163 n n C1 H10 F9O sing 164 n n C1 H11 F9O sing 165 n n N H12 F9O sing 166 n n C H14 F9O sing 167 n n O H15 F9O sing 168 n n C11 H16 F9O sing 169 n n C12 H17 F9O sing 170 n n C7 H18 F9O sing 171 n n C7 H19 F9O sing 172 n n C8 H20 F9O sing 173 n n # _atom_sites.entry_id 7Y1W _atom_sites.fract_transf_matrix[1][1] 0.013975 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004749 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010852 _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] 0.012178 _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 ZN A 1 1601 2604 ZN ZN . D 3 F9O A 1 1602 1 F9O DWN . E 4 ATP A 1 1603 1 ATP ATP . F 5 MG A 1 1604 1 MG MG . G 5 MG A 1 1605 3 MG MG . H 2 ZN B 1 1601 2604 ZN ZN . I 3 F9O B 1 1602 2 F9O DWN . J 6 HOH A 1 1701 11 HOH HOH . J 6 HOH A 2 1702 8 HOH HOH . J 6 HOH A 3 1703 6 HOH HOH . J 6 HOH A 4 1704 22 HOH HOH . J 6 HOH A 5 1705 16 HOH HOH . J 6 HOH A 6 1706 32 HOH HOH . J 6 HOH A 7 1707 14 HOH HOH . J 6 HOH A 8 1708 12 HOH HOH . J 6 HOH A 9 1709 2 HOH HOH . J 6 HOH A 10 1710 35 HOH HOH . J 6 HOH A 11 1711 25 HOH HOH . J 6 HOH A 12 1712 4 HOH HOH . J 6 HOH A 13 1713 7 HOH HOH . J 6 HOH A 14 1714 28 HOH HOH . J 6 HOH A 15 1715 34 HOH HOH . J 6 HOH A 16 1716 13 HOH HOH . J 6 HOH A 17 1717 15 HOH HOH . J 6 HOH A 18 1718 19 HOH HOH . J 6 HOH A 19 1719 3 HOH HOH . J 6 HOH A 20 1720 20 HOH HOH . J 6 HOH A 21 1721 10 HOH HOH . J 6 HOH A 22 1722 24 HOH HOH . J 6 HOH A 23 1723 23 HOH HOH . J 6 HOH A 24 1724 1 HOH HOH . J 6 HOH A 25 1725 37 HOH HOH . J 6 HOH A 26 1726 36 HOH HOH . J 6 HOH A 27 1727 21 HOH HOH . K 6 HOH B 1 1701 29 HOH HOH . K 6 HOH B 2 1702 5 HOH HOH . K 6 HOH B 3 1703 31 HOH HOH . K 6 HOH B 4 1704 27 HOH HOH . K 6 HOH B 5 1705 18 HOH HOH . K 6 HOH B 6 1706 30 HOH HOH . K 6 HOH B 7 1707 26 HOH HOH . K 6 HOH B 8 1708 17 HOH HOH . K 6 HOH B 9 1709 9 HOH HOH . K 6 HOH B 10 1710 33 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 C4 F9O . . . I 3 71.866 5.749 95.165 1 42.8 ? C4 F9O 1602 B 1 HETATM 2 C C5 F9O . . . I 3 71.828 6.143 93.694 1 45.31 ? C5 F9O 1602 B 1 HETATM 3 C C6 F9O . . . I 3 71.962 7.644 93.553 1 52.66 ? C6 F9O 1602 B 1 HETATM 4 C C3 F9O . . . I 3 71.566 6.502 97.462 1 47.89 ? C3 F9O 1602 B 1 HETATM 5 C C2 F9O . . . I 3 70.49 5.49 97.695 1 43.13 ? C2 F9O 1602 B 1 HETATM 6 C C1 F9O . . . I 3 70.707 4.265 96.814 1 41.66 ? C1 F9O 1602 B 1 HETATM 7 N N F9O . . . I 3 71.63 6.898 96.05 1 42.95 ? N F9O 1602 B 1 HETATM 8 C C F9O . . . I 3 70.822 4.658 95.352 1 41.6 ? C F9O 1602 B 1 HETATM 9 O O F9O . . . I 3 71.184 3.526 94.561 1 45.37 ? O F9O 1602 B 1 HETATM 10 C C10 F9O . . . I 3 70.795 9.648 91.167 1 76.63 ? C10 F9O 1602 B 1 HETATM 11 C C11 F9O . . . I 3 71.226 10.828 91.77 1 78.99 ? C11 F9O 1602 B 1 HETATM 12 C C12 F9O . . . I 3 70.586 12.005 91.43 1 87.5 ? C12 F9O 1602 B 1 HETATM 13 C C13 F9O . . . I 3 69.549 11.991 90.514 1 89.73 ? C13 F9O 1602 B 1 HETATM 14 C C14 F9O . . . I 3 69.137 10.803 89.922 1 86.63 ? C14 F9O 1602 B 1 HETATM 15 C C7 F9O . . . I 3 72.363 7.891 92.116 1 61.93 ? C7 F9O 1602 B 1 HETATM 16 C C8 F9O . . . I 3 70.455 7.603 90.468 1 68.99 ? C8 F9O 1602 B 1 HETATM 17 C C9 F9O . . . I 3 69.756 9.598 90.247 1 78.75 ? C9 F9O 1602 B 1 HETATM 18 N N1 F9O . . . I 3 71.249 8.346 91.298 1 68.42 ? N1 F9O 1602 B 1 HETATM 19 N N2 F9O . . . I 3 69.552 8.289 89.815 1 74.69 ? N2 F9O 1602 B 1 HETATM 20 CL CL F9O . . . I 3 67.868 10.812 88.758 0.68 91.69 ? CL F9O 1602 B 1 HETATM 21 CL CL1 F9O . . . I 3 68.766 13.487 90.116 0.84 102.06 ? CL1 F9O 1602 B 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 334 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 21 #