data_7KP9 # _model_server_result.job_id v6tRBefAwsVHnDQIsL-eOQ _model_server_result.datetime_utc '2024-11-16 08:44:13' _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 7kp9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":201}' # _entry.id 7KP9 # _exptl.entry_id 7KP9 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 449.496 _entity.id 2 _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 7KP9 _cell.length_a 54.52 _cell.length_b 81.96 _cell.length_c 93.24 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7KP9 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 _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 2 _struct_asym.id D _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 70 A CYS 69 1_555 A SG CYS 102 A CYS 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? disulf ? disulf2 B SG CYS 70 B CYS 69 1_555 B SG CYS 102 B CYS 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? disulf ? disulf3 C SG CYS 70 C CYS 69 1_555 C SG CYS 102 C CYS 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? # _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 7KP9 _atom_sites.fract_transf_matrix[1][1] 0.018342 _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] 0.012201 _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] 0.010725 _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 D 2 A7G C 1 201 1 A7G 433 . E 3 HOH A 1 201 87 HOH HOH . E 3 HOH A 2 202 136 HOH HOH . E 3 HOH A 3 203 33 HOH HOH . E 3 HOH A 4 204 160 HOH HOH . E 3 HOH A 5 205 142 HOH HOH . E 3 HOH A 6 206 157 HOH HOH . E 3 HOH A 7 207 100 HOH HOH . E 3 HOH A 8 208 154 HOH HOH . E 3 HOH A 9 209 62 HOH HOH . E 3 HOH A 10 210 86 HOH HOH . E 3 HOH A 11 211 45 HOH HOH . E 3 HOH A 12 212 109 HOH HOH . E 3 HOH A 13 213 5 HOH HOH . E 3 HOH A 14 214 158 HOH HOH . E 3 HOH A 15 215 30 HOH HOH . E 3 HOH A 16 216 64 HOH HOH . E 3 HOH A 17 217 153 HOH HOH . E 3 HOH A 18 218 99 HOH HOH . E 3 HOH A 19 219 121 HOH HOH . E 3 HOH A 20 220 59 HOH HOH . E 3 HOH A 21 221 16 HOH HOH . E 3 HOH A 22 222 112 HOH HOH . E 3 HOH A 23 223 17 HOH HOH . E 3 HOH A 24 224 156 HOH HOH . E 3 HOH A 25 225 82 HOH HOH . E 3 HOH A 26 226 72 HOH HOH . E 3 HOH A 27 227 126 HOH HOH . E 3 HOH A 28 228 76 HOH HOH . E 3 HOH A 29 229 140 HOH HOH . E 3 HOH A 30 230 25 HOH HOH . E 3 HOH A 31 231 34 HOH HOH . E 3 HOH A 32 232 14 HOH HOH . E 3 HOH A 33 233 65 HOH HOH . E 3 HOH A 34 234 31 HOH HOH . E 3 HOH A 35 235 37 HOH HOH . E 3 HOH A 36 236 57 HOH HOH . E 3 HOH A 37 237 91 HOH HOH . E 3 HOH A 38 238 53 HOH HOH . E 3 HOH A 39 239 95 HOH HOH . E 3 HOH A 40 240 90 HOH HOH . E 3 HOH A 41 241 103 HOH HOH . E 3 HOH A 42 242 174 HOH HOH . E 3 HOH A 43 243 39 HOH HOH . E 3 HOH A 44 244 101 HOH HOH . E 3 HOH A 45 245 152 HOH HOH . E 3 HOH A 46 246 143 HOH HOH . E 3 HOH A 47 247 108 HOH HOH . E 3 HOH A 48 248 50 HOH HOH . E 3 HOH A 49 249 23 HOH HOH . E 3 HOH A 50 250 1 HOH HOH . E 3 HOH A 51 251 170 HOH HOH . E 3 HOH A 52 252 8 HOH HOH . E 3 HOH A 53 253 77 HOH HOH . E 3 HOH A 54 254 10 HOH HOH . E 3 HOH A 55 255 19 HOH HOH . E 3 HOH A 56 256 173 HOH HOH . E 3 HOH A 57 257 122 HOH HOH . E 3 HOH A 58 258 38 HOH HOH . E 3 HOH A 59 259 155 HOH HOH . E 3 HOH A 60 260 27 HOH HOH . E 3 HOH A 61 261 47 HOH HOH . E 3 HOH A 62 262 3 HOH HOH . E 3 HOH A 63 263 150 HOH HOH . E 3 HOH A 64 264 6 HOH HOH . E 3 HOH A 65 265 48 HOH HOH . E 3 HOH A 66 266 49 HOH HOH . E 3 HOH A 67 267 138 HOH HOH . E 3 HOH A 68 268 60 HOH HOH . E 3 HOH A 69 269 132 HOH HOH . E 3 HOH A 70 270 2 HOH HOH . E 3 HOH A 71 271 32 HOH HOH . E 3 HOH A 72 272 15 HOH HOH . E 3 HOH A 73 273 63 HOH HOH . E 3 HOH A 74 274 180 HOH HOH . E 3 HOH A 75 275 56 HOH HOH . E 3 HOH A 76 276 146 HOH HOH . E 3 HOH A 77 277 151 HOH HOH . E 3 HOH A 78 278 159 HOH HOH . E 3 HOH A 79 279 172 HOH HOH . E 3 HOH A 80 280 161 HOH HOH . E 3 HOH A 81 281 111 HOH HOH . E 3 HOH A 82 282 40 HOH HOH . E 3 HOH A 83 283 171 HOH HOH . F 3 HOH B 1 201 176 HOH HOH . F 3 HOH B 2 202 175 HOH HOH . F 3 HOH B 3 203 80 HOH HOH . F 3 HOH B 4 204 164 HOH HOH . F 3 HOH B 5 205 135 HOH HOH . F 3 HOH B 6 206 44 HOH HOH . F 3 HOH B 7 207 81 HOH HOH . F 3 HOH B 8 208 127 HOH HOH . F 3 HOH B 9 209 55 HOH HOH . F 3 HOH B 10 210 9 HOH HOH . F 3 HOH B 11 211 113 HOH HOH . F 3 HOH B 12 212 79 HOH HOH . F 3 HOH B 13 213 104 HOH HOH . F 3 HOH B 14 214 22 HOH HOH . F 3 HOH B 15 215 147 HOH HOH . F 3 HOH B 16 216 102 HOH HOH . F 3 HOH B 17 217 130 HOH HOH . F 3 HOH B 18 218 131 HOH HOH . F 3 HOH B 19 219 94 HOH HOH . F 3 HOH B 20 220 36 HOH HOH . F 3 HOH B 21 221 116 HOH HOH . F 3 HOH B 22 222 51 HOH HOH . F 3 HOH B 23 223 58 HOH HOH . F 3 HOH B 24 224 92 HOH HOH . F 3 HOH B 25 225 178 HOH HOH . F 3 HOH B 26 226 18 HOH HOH . F 3 HOH B 27 227 12 HOH HOH . F 3 HOH B 28 228 20 HOH HOH . F 3 HOH B 29 229 97 HOH HOH . F 3 HOH B 30 230 21 HOH HOH . F 3 HOH B 31 231 70 HOH HOH . F 3 HOH B 32 232 7 HOH HOH . F 3 HOH B 33 233 13 HOH HOH . F 3 HOH B 34 234 78 HOH HOH . F 3 HOH B 35 235 46 HOH HOH . F 3 HOH B 36 236 35 HOH HOH . F 3 HOH B 37 237 163 HOH HOH . F 3 HOH B 38 238 105 HOH HOH . F 3 HOH B 39 239 133 HOH HOH . F 3 HOH B 40 240 139 HOH HOH . F 3 HOH B 41 241 43 HOH HOH . F 3 HOH B 42 242 124 HOH HOH . F 3 HOH B 43 243 75 HOH HOH . F 3 HOH B 44 244 117 HOH HOH . F 3 HOH B 45 245 120 HOH HOH . F 3 HOH B 46 246 125 HOH HOH . F 3 HOH B 47 247 110 HOH HOH . F 3 HOH B 48 248 115 HOH HOH . F 3 HOH B 49 249 61 HOH HOH . F 3 HOH B 50 250 179 HOH HOH . F 3 HOH B 51 251 26 HOH HOH . F 3 HOH B 52 252 88 HOH HOH . F 3 HOH B 53 253 114 HOH HOH . F 3 HOH B 54 254 71 HOH HOH . F 3 HOH B 55 255 68 HOH HOH . F 3 HOH B 56 256 54 HOH HOH . F 3 HOH B 57 257 67 HOH HOH . F 3 HOH B 58 258 162 HOH HOH . G 3 HOH C 1 301 83 HOH HOH . G 3 HOH C 2 302 107 HOH HOH . G 3 HOH C 3 303 177 HOH HOH . G 3 HOH C 4 304 93 HOH HOH . G 3 HOH C 5 305 24 HOH HOH . G 3 HOH C 6 306 141 HOH HOH . G 3 HOH C 7 307 98 HOH HOH . G 3 HOH C 8 308 148 HOH HOH . G 3 HOH C 9 309 128 HOH HOH . G 3 HOH C 10 310 119 HOH HOH . G 3 HOH C 11 311 167 HOH HOH . G 3 HOH C 12 312 42 HOH HOH . G 3 HOH C 13 313 4 HOH HOH . G 3 HOH C 14 314 96 HOH HOH . G 3 HOH C 15 315 74 HOH HOH . G 3 HOH C 16 316 66 HOH HOH . G 3 HOH C 17 317 168 HOH HOH . G 3 HOH C 18 318 69 HOH HOH . G 3 HOH C 19 319 52 HOH HOH . G 3 HOH C 20 320 166 HOH HOH . G 3 HOH C 21 321 165 HOH HOH . G 3 HOH C 22 322 11 HOH HOH . G 3 HOH C 23 323 84 HOH HOH . G 3 HOH C 24 324 28 HOH HOH . G 3 HOH C 25 325 129 HOH HOH . G 3 HOH C 26 326 134 HOH HOH . G 3 HOH C 27 327 123 HOH HOH . G 3 HOH C 28 328 29 HOH HOH . G 3 HOH C 29 329 169 HOH HOH . G 3 HOH C 30 330 85 HOH HOH . G 3 HOH C 31 331 149 HOH HOH . G 3 HOH C 32 332 41 HOH HOH . G 3 HOH C 33 333 118 HOH HOH . G 3 HOH C 34 334 106 HOH HOH . G 3 HOH C 35 335 89 HOH HOH . G 3 HOH C 36 336 144 HOH HOH . G 3 HOH C 37 337 145 HOH HOH . G 3 HOH C 38 338 137 HOH HOH . G 3 HOH C 39 339 73 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 . . . D 2 -10.89 -1.945 23.482 1 36.23 ? F2 A7G 201 C 1 HETATM 2 C C16 A7G . . . D 2 -11.647 -0.944 23.042 1 28.22 ? C16 A7G 201 C 1 HETATM 3 F F1 A7G . . . D 2 -11.088 0.266 23.386 1 28.6 ? F1 A7G 201 C 1 HETATM 4 O O A7G . . . D 2 -11.749 -1.014 21.63 1 25.95 ? O A7G 201 C 1 HETATM 5 C C15 A7G . . . D 2 -11.318 -2.051 20.827 1 21.43 ? C15 A7G 201 C 1 HETATM 6 C C14 A7G . . . D 2 -11.146 -3.366 21.285 1 21.61 ? C14 A7G 201 C 1 HETATM 7 C C13 A7G . . . D 2 -10.763 -4.368 20.375 1 19.4 ? C13 A7G 201 C 1 HETATM 8 C C12 A7G . . . D 2 -10.57 -4.045 19.059 1 19.56 ? C12 A7G 201 C 1 HETATM 9 C C11 A7G . . . D 2 -10.774 -2.727 18.613 1 19.14 ? C11 A7G 201 C 1 HETATM 10 C C10 A7G . . . D 2 -11.135 -1.753 19.504 1 18.97 ? C10 A7G 201 C 1 HETATM 11 C C9 A7G . . . D 2 -11.353 -0.331 19.07 1 17.94 ? C9 A7G 201 C 1 HETATM 12 N N2 A7G . . . D 2 -12.354 -0.222 18.012 1 16.92 ? N2 A7G 201 C 1 HETATM 13 C C2 A7G . . . D 2 -12.113 0.294 16.802 1 17.7 ? C2 A7G 201 C 1 HETATM 14 C C1 A7G . . . D 2 -10.789 0.845 16.326 1 18.34 ? C1 A7G 201 C 1 HETATM 15 C C8 A7G . . . D 2 -13.639 -0.561 18.08 1 16.63 ? C8 A7G 201 C 1 HETATM 16 C C3 A7G . . . D 2 -14.215 -0.236 16.844 1 16.16 ? C3 A7G 201 C 1 HETATM 17 N N1 A7G . . . D 2 -13.243 0.262 16.072 1 17.05 ? N1 A7G 201 C 1 HETATM 18 C C7 A7G . . . D 2 -14.412 -1.173 19.08 1 16.19 ? C7 A7G 201 C 1 HETATM 19 C C6 A7G . . . D 2 -15.78 -1.423 18.837 1 17.59 ? C6 A7G 201 C 1 HETATM 20 C C5 A7G . . . D 2 -16.351 -1.068 17.579 1 16.27 ? C5 A7G 201 C 1 HETATM 21 C C4 A7G . . . D 2 -15.55 -0.516 16.58 1 15.19 ? C4 A7G 201 C 1 HETATM 22 C C17 A7G . . . D 2 -16.602 -2.002 19.818 1 18.82 ? C17 A7G 201 C 1 HETATM 23 C C21 A7G . . . D 2 -17.943 -1.638 19.873 1 21.88 ? C21 A7G 201 C 1 HETATM 24 N N3 A7G . . . D 2 -18.761 -2.164 20.794 1 23.14 ? N3 A7G 201 C 1 HETATM 25 C C20 A7G . . . D 2 -18.302 -3.08 21.683 1 24.36 ? C20 A7G 201 C 1 HETATM 26 C C19 A7G . . . D 2 -16.95 -3.475 21.665 1 21.52 ? C19 A7G 201 C 1 HETATM 27 C C18 A7G . . . D 2 -16.111 -2.937 20.719 1 19.13 ? C18 A7G 201 C 1 HETATM 28 N N4 A7G . . . D 2 -19.194 -3.568 22.648 1 26.33 ? N4 A7G 201 C 1 HETATM 29 C C25 A7G . . . D 2 -18.825 -4.583 23.581 1 27.94 ? C25 A7G 201 C 1 HETATM 30 C C24 A7G . . . D 2 -19.427 -5.825 22.934 0.6 28.34 ? C24 A7G 201 C 1 HETATM 31 N N5 A7G . . . D 2 -20.873 -5.731 22.811 0.6 30.41 ? N5 A7G 201 C 1 HETATM 32 C C23 A7G . . . D 2 -21.303 -4.48 22.148 0.6 31.37 ? C23 A7G 201 C 1 HETATM 33 C C22 A7G . . . D 2 -20.578 -3.209 22.613 1 29.87 ? C22 A7G 201 C 1 # _model_server_stats.io_time_ms 65 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 301 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 33 #