data_5YKF # _model_server_result.job_id 9mXAyjItur_y_fr0Q8vF0w _model_server_result.datetime_utc '2024-12-23 18:16:38' _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 5ykf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"S","auth_seq_id":2001}' # _entry.id 5YKF # _exptl.entry_id 5YKF _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 494.004 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 5-chloro-N-(2-{4-[(cyclohexylcarbamoyl)sulfamoyl]phenyl}ethyl)-2-methoxybenzamide _entity.pdbx_number_of_molecules 4 _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 5YKF _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5YKF _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details octameric _pdbx_struct_assembly.oligomeric_count 8 _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,G,H,I,J,K,L,M,N,O,P,Q,R,S,T _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 ? 4 K N N ? 4 N N N ? 4 Q N N ? 4 S 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 disulf ? disulf1 A SG CYS 110 A CYS 110 1_555 A SG CYS 142 A CYS 142 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf2 C SG CYS 110 C CYS 110 1_555 C SG CYS 142 C CYS 142 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf3 E SG CYS 110 E CYS 110 1_555 E SG CYS 142 E CYS 142 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf4 G SG CYS 110 G CYS 110 1_555 G SG CYS 142 G CYS 142 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? # _chem_comp.formula 'C23 H28 Cl N3 O5 S' _chem_comp.formula_weight 494.004 _chem_comp.id GBM _chem_comp.mon_nstd_flag . _chem_comp.name 5-chloro-N-(2-{4-[(cyclohexylcarbamoyl)sulfamoyl]phenyl}ethyl)-2-methoxybenzamide _chem_comp.type non-polymer _chem_comp.pdbx_synonyms Glibenclamide;Glyburide # 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 C31 GBM sing 132 n n C31 C29 GBM doub 133 n y C31 C32 GBM sing 134 n y C29 C27 GBM sing 135 n y C32 C30 GBM doub 136 n y O6 C26 GBM doub 137 n n C27 C26 GBM sing 138 n n C27 C28 GBM doub 139 n y C30 C28 GBM sing 140 n y C26 N10 GBM sing 141 n n C28 O7 GBM sing 142 n n O3 C17 GBM doub 143 n n N10 C25 GBM sing 144 n n C23 C21 GBM doub 145 n y C23 C19 GBM sing 146 n y O7 C33 GBM sing 147 n n C21 C18 GBM sing 148 n y C25 C20 GBM sing 149 n n N9 C17 GBM sing 150 n n N9 S2 GBM sing 151 n n C17 N8 GBM sing 152 n n C20 C19 GBM sing 153 n n C19 C24 GBM doub 154 n y O5 S2 GBM doub 155 n n C18 S2 GBM sing 156 n n C18 C22 GBM doub 157 n y C14 C12 GBM sing 158 n n C14 C16 GBM sing 159 n n C13 C11 GBM sing 160 n n C13 C15 GBM sing 161 n n S2 O4 GBM doub 162 n n C12 C11 GBM sing 163 n n N8 C11 GBM sing 164 n n C15 C16 GBM sing 165 n n C24 C22 GBM sing 166 n y N8 H1 GBM sing 167 n n N9 H2 GBM sing 168 n n N10 H3 GBM sing 169 n n C11 H4 GBM sing 170 n n C12 H5 GBM sing 171 n n C12 H6 GBM sing 172 n n C13 H7 GBM sing 173 n n C13 H8 GBM sing 174 n n C14 H9 GBM sing 175 n n C14 H10 GBM sing 176 n n C15 H11 GBM sing 177 n n C15 H12 GBM sing 178 n n C16 H13 GBM sing 179 n n C16 H14 GBM sing 180 n n C20 H15 GBM sing 181 n n C20 H16 GBM sing 182 n n C21 H17 GBM sing 183 n n C22 H18 GBM sing 184 n n C23 H19 GBM sing 185 n n C24 H20 GBM sing 186 n n C25 H21 GBM sing 187 n n C25 H22 GBM sing 188 n n C29 H23 GBM sing 189 n n C30 H24 GBM sing 190 n n C32 H25 GBM sing 191 n n C33 H26 GBM sing 192 n n C33 H27 GBM sing 193 n n C33 H28 GBM sing 194 n n # _atom_sites.entry_id 5YKF _atom_sites.fract_transf_matrix[1][1] 0.003038 _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] 0.003038 _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] 0.003038 _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 I 3 AGS A 1 401 401 AGS AGS . J 3 AGS A 1 402 401 AGS AGS . K 4 GBM B 1 2001 2001 GBM GBM . L 3 AGS B 1 2002 2501 AGS AGS . M 3 AGS C 1 401 401 AGS AGS . N 4 GBM D 1 2001 2001 GBM GBM . O 3 AGS D 1 2002 2501 AGS AGS . P 3 AGS E 1 401 401 AGS AGS . Q 4 GBM F 1 2001 2001 GBM GBM . R 3 AGS F 1 2002 2501 AGS AGS . S 4 GBM H 1 2001 2001 GBM GBM . T 3 AGS H 1 2002 2501 AGS AGS . # 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 O O3 GBM . . . S 4 216.491 131.093 178.44 1 90.52 ? O3 GBM 2001 H 1 HETATM 2 O O4 GBM . . . S 4 217.274 129.341 180.433 1 86.59 ? O4 GBM 2001 H 1 HETATM 3 O O5 GBM . . . S 4 218.656 127.664 179.61 1 96.56 ? O5 GBM 2001 H 1 HETATM 4 O O6 GBM . . . S 4 222.161 129.695 182.679 1 107.93 ? O6 GBM 2001 H 1 HETATM 5 CL CL1 GBM . . . S 4 224.738 132.069 187.947 1 139.31 ? CL1 GBM 2001 H 1 HETATM 6 S S2 GBM . . . S 4 218.293 129.049 179.459 1 92.62 ? S2 GBM 2001 H 1 HETATM 7 O O7 GBM . . . S 4 221.09 128.479 184.859 1 114.47 ? O7 GBM 2001 H 1 HETATM 8 N N8 GBM . . . S 4 216.742 130.557 176.319 1 94.3 ? N8 GBM 2001 H 1 HETATM 9 N N9 GBM . . . S 4 217.748 129.3 177.96 1 92.05 ? N9 GBM 2001 H 1 HETATM 10 N N10 GBM . . . S 4 223.565 131.43 182.837 1 104.37 ? N10 GBM 2001 H 1 HETATM 11 C C11 GBM . . . S 4 217.434 129.87 175.254 1 91.65 ? C11 GBM 2001 H 1 HETATM 12 C C12 GBM . . . S 4 218.75 130.586 174.993 1 89.08 ? C12 GBM 2001 H 1 HETATM 13 C C13 GBM . . . S 4 216.556 129.929 174.013 1 93.33 ? C13 GBM 2001 H 1 HETATM 14 C C14 GBM . . . S 4 219.458 130.026 173.769 1 85.31 ? C14 GBM 2001 H 1 HETATM 15 C C15 GBM . . . S 4 217.267 129.401 172.775 1 92.2 ? C15 GBM 2001 H 1 HETATM 16 C C16 GBM . . . S 4 218.566 130.157 172.543 1 85.93 ? C16 GBM 2001 H 1 HETATM 17 C C17 GBM . . . S 4 216.98 130.341 177.611 1 92.19 ? C17 GBM 2001 H 1 HETATM 18 C C18 GBM . . . S 4 219.581 129.957 179.759 1 96.44 ? C18 GBM 2001 H 1 HETATM 19 C C19 GBM . . . S 4 221.798 131.544 180.309 1 95.04 ? C19 GBM 2001 H 1 HETATM 20 C C20 GBM . . . S 4 222.992 132.407 180.635 1 101.6 ? C20 GBM 2001 H 1 HETATM 21 C C21 GBM . . . S 4 220.753 129.804 179.022 1 97.39 ? C21 GBM 2001 H 1 HETATM 22 C C22 GBM . . . S 4 219.528 130.903 180.777 1 95.31 ? C22 GBM 2001 H 1 HETATM 23 C C23 GBM . . . S 4 221.863 130.596 179.296 1 95.19 ? C23 GBM 2001 H 1 HETATM 24 C C24 GBM . . . S 4 220.634 131.693 181.051 1 94.45 ? C24 GBM 2001 H 1 HETATM 25 C C25 GBM . . . S 4 223.029 132.593 182.149 1 103.57 ? C25 GBM 2001 H 1 HETATM 26 C C26 GBM . . . S 4 222.81 130.464 183.365 1 107.07 ? C26 GBM 2001 H 1 HETATM 27 C C27 GBM . . . S 4 222.8 130.307 184.856 1 113.54 ? C27 GBM 2001 H 1 HETATM 28 C C28 GBM . . . S 4 221.934 129.312 185.548 1 116.32 ? C28 GBM 2001 H 1 HETATM 29 C C29 GBM . . . S 4 223.632 131.118 185.613 1 115.5 ? C29 GBM 2001 H 1 HETATM 30 C C30 GBM . . . S 4 221.991 129.231 186.933 1 117.51 ? C30 GBM 2001 H 1 HETATM 31 C C31 GBM . . . S 4 223.651 131 186.997 1 120.22 ? C31 GBM 2001 H 1 HETATM 32 C C32 GBM . . . S 4 222.841 130.071 187.646 1 131.44 ? C32 GBM 2001 H 1 HETATM 33 C C33 GBM . . . S 4 221.462 127.127 184.591 1 115.15 ? C33 GBM 2001 H 1 # _model_server_stats.io_time_ms 25 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 69 _model_server_stats.query_time_ms 302 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 33 #