data_3LD6 # _model_server_result.job_id kQPS-jW3mRQW6bmkJ4uZwg _model_server_result.datetime_utc '2024-11-23 13:38:29' _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 3ld6 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":602}' # _entry.id 3LD6 # _exptl.entry_id 3LD6 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 531.431 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1-acetyl-4-(4-{[(2R,4S)-2-(2,4-dichlorophenyl)-2-(1H-imidazol-1-ylmethyl)-1,3-dioxolan-4-yl]methoxy}phenyl)piperazine _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 90 _cell.angle_gamma 90 _cell.entry_id 3LD6 _cell.length_a 145.726 _cell.length_b 145.726 _cell.length_c 110.341 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3LD6 _symmetry.cell_setting ? _symmetry.Int_Tables_number 90 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 4 21 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? dimeric 2 author_defined_assembly 1 PISA dimeric 2 software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G,H,I,J 1 1 A,C,E,F,I 2 1 B,D,G,H,J 2 2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 4_555 y+1/2,-x+1/2,z 0 1 0 -1 0 0 0 0 1 72.863 72.863 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 F N N ? 4 H N N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 2 1 7 GLC GLC C1 O1 . O4 HO4 . sing 2 ? 2 2 1 GLC GLC C1 O1 . O4 HO4 . sing 3 ? 2 3 2 GLC GLC C1 O1 . O4 HO4 . sing 4 ? 2 4 3 GLC GLC C1 O1 . O4 HO4 . sing 5 ? 2 5 4 GLC GLC C1 O1 . O4 HO4 . sing 6 ? 2 6 5 GLC GLC C1 O1 . O4 HO4 . sing 7 ? 2 7 6 GLC GLC C1 O1 . O4 HO4 . sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 2 n C GLC 1 C 1 GLC B 603 BCD 2 n C GLC 2 C 2 GLC B 603 BCD 2 n C GLC 3 C 3 GLC B 603 BCD 2 n C GLC 4 C 4 GLC B 603 BCD 2 n C GLC 5 C 5 GLC B 603 BCD 2 n C GLC 6 C 6 GLC B 603 BCD 2 n C GLC 7 C 7 GLC B 603 BCD 2 n D GLC 1 D 1 GLC A 603 BCD 2 n D GLC 2 D 2 GLC A 603 BCD 2 n D GLC 3 D 3 GLC A 603 BCD 2 n D GLC 4 D 4 GLC A 603 BCD 2 n D GLC 5 D 5 GLC A 603 BCD 2 n D GLC 6 D 6 GLC A 603 BCD 2 n D GLC 7 D 7 GLC A 603 BCD # 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 covale ? covale1 C O4 GLC . C GLC 1 1_555 C C1 GLC . C GLC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.42 sing covale ? covale2 C C1 GLC . C GLC 1 1_555 C O4 GLC . C GLC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 sing covale ? covale3 C O4 GLC . C GLC 2 1_555 C C1 GLC . C GLC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.426 sing covale ? covale4 C O4 GLC . C GLC 3 1_555 C C1 GLC . C GLC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 sing covale ? covale5 C O4 GLC . C GLC 4 1_555 C C1 GLC . C GLC 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.428 sing covale ? covale6 C O4 GLC . C GLC 5 1_555 C C1 GLC . C GLC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.422 sing covale ? covale7 C O4 GLC . C GLC 6 1_555 C C1 GLC . C GLC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 sing covale ? covale8 D O4 GLC . D GLC 1 1_555 D C1 GLC . D GLC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 sing covale ? covale9 D C1 GLC . D GLC 1 1_555 D O4 GLC . D GLC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 sing covale ? covale10 D O4 GLC . D GLC 2 1_555 D C1 GLC . D GLC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.429 sing covale ? covale11 D O4 GLC . D GLC 3 1_555 D C1 GLC . D GLC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.415 sing covale ? covale12 D O4 GLC . D GLC 4 1_555 D C1 GLC . D GLC 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.426 sing covale ? covale13 D O4 GLC . D GLC 5 1_555 D C1 GLC . D GLC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.427 sing covale ? covale14 D O4 GLC . D GLC 6 1_555 D C1 GLC . D GLC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 sing metalc ? metalc1 A SG CYS 401 A CYS 449 1_555 E FE HEM . A HEM 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.351 ? metalc ? metalc2 E FE HEM . A HEM 601 1_555 F N2 KKK . A KKK 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.405 ? metalc ? metalc3 B SG CYS 401 B CYS 449 1_555 G FE HEM . B HEM 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.397 ? metalc ? metalc4 G FE HEM . B HEM 601 1_555 H N2 KKK . B KKK 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.233 ? # _chem_comp.formula 'C26 H28 Cl2 N4 O4' _chem_comp.formula_weight 531.431 _chem_comp.id KKK _chem_comp.mon_nstd_flag . _chem_comp.name 1-acetyl-4-(4-{[(2R,4S)-2-(2,4-dichlorophenyl)-2-(1H-imidazol-1-ylmethyl)-1,3-dioxolan-4-yl]methoxy}phenyl)piperazine _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 N2 C1 KKK doub 279 n y C1 N1 KKK sing 280 n y C1 H1 KKK sing 281 n n C3 N1 KKK sing 282 n y N1 C4 KKK sing 283 n n C5 O1 KKK sing 284 n n O1 C6 KKK sing 285 n n CL1 C11 KKK sing 286 n n C2 N2 KKK sing 287 n y C2 C3 KKK doub 288 n y C2 H2 KKK sing 289 n n C5 O2 KKK sing 290 n n O2 C7 KKK sing 291 n n C9 CL2 KKK sing 292 n n C3 H3 KKK sing 293 n n C18 N3 KKK sing 294 n n N3 C21 KKK sing 295 n n N3 C24 KKK sing 296 n n C14 O3 KKK sing 297 n n O3 C15 KKK sing 298 n n C5 C4 KKK sing 299 n n C4 H4 KKK sing 300 n n C4 H4A KKK sing 301 n n C22 N4 KKK sing 302 n n C23 N4 KKK sing 303 n n N4 C25 KKK sing 304 n n C25 O4 KKK doub 305 n n C8 C5 KKK sing 306 n n C7 C6 KKK sing 307 n n C6 C14 KKK sing 308 n n C6 H6 KKK sing 309 n n C7 H7 KKK sing 310 n n C7 H7A KKK sing 311 n n C9 C8 KKK doub 312 n y C13 C8 KKK sing 313 n y C10 C9 KKK sing 314 n y C11 C10 KKK doub 315 n y C10 H10 KKK sing 316 n n C11 C12 KKK sing 317 n y C12 C13 KKK doub 318 n y C12 H12 KKK sing 319 n n C13 H13 KKK sing 320 n n C14 H14 KKK sing 321 n n C14 H14A KKK sing 322 n n C15 C16 KKK doub 323 n y C15 C20 KKK sing 324 n y C16 C17 KKK sing 325 n y C16 H16 KKK sing 326 n n C17 C18 KKK doub 327 n y C17 H17 KKK sing 328 n n C19 C18 KKK sing 329 n y C20 C19 KKK doub 330 n y C19 H19 KKK sing 331 n n C20 H20 KKK sing 332 n n C21 C22 KKK sing 333 n n C21 H21 KKK sing 334 n n C21 H21A KKK sing 335 n n C22 H22 KKK sing 336 n n C22 H22A KKK sing 337 n n C24 C23 KKK sing 338 n n C23 H23 KKK sing 339 n n C23 H23A KKK sing 340 n n C24 H24 KKK sing 341 n n C24 H24A KKK sing 342 n n C25 C26 KKK sing 343 n n C26 H26 KKK sing 344 n n C26 H26A KKK sing 345 n n C26 H26B KKK sing 346 n n # _atom_sites.entry_id 3LD6 _atom_sites.fract_transf_matrix[1][1] 0.006862 _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] 0.006862 _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] 0.009063 _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 E 3 HEM A 1 601 601 HEM HEM . F 4 KKK A 1 602 602 KKK KKK . G 3 HEM B 1 601 601 HEM HEM . H 4 KKK B 1 602 602 KKK KKK . I 5 HOH A 1 1 1 HOH HOH . I 5 HOH A 2 2 2 HOH HOH . I 5 HOH A 3 3 3 HOH HOH . I 5 HOH A 4 5 5 HOH HOH . I 5 HOH A 5 6 6 HOH HOH . I 5 HOH A 6 7 7 HOH HOH . I 5 HOH A 7 8 8 HOH HOH . I 5 HOH A 8 12 12 HOH HOH . I 5 HOH A 9 13 13 HOH HOH . I 5 HOH A 10 14 14 HOH HOH . I 5 HOH A 11 15 15 HOH HOH . I 5 HOH A 12 18 18 HOH HOH . I 5 HOH A 13 20 20 HOH HOH . I 5 HOH A 14 21 21 HOH HOH . I 5 HOH A 15 23 23 HOH HOH . I 5 HOH A 16 24 24 HOH HOH . I 5 HOH A 17 25 25 HOH HOH . I 5 HOH A 18 26 26 HOH HOH . I 5 HOH A 19 27 27 HOH HOH . I 5 HOH A 20 30 30 HOH HOH . I 5 HOH A 21 31 31 HOH HOH . I 5 HOH A 22 34 34 HOH HOH . I 5 HOH A 23 35 35 HOH HOH . I 5 HOH A 24 36 36 HOH HOH . I 5 HOH A 25 37 37 HOH HOH . I 5 HOH A 26 38 38 HOH HOH . J 5 HOH B 1 4 4 HOH HOH . J 5 HOH B 2 9 9 HOH HOH . J 5 HOH B 3 10 10 HOH HOH . J 5 HOH B 4 11 11 HOH HOH . J 5 HOH B 5 16 16 HOH HOH . J 5 HOH B 6 17 17 HOH HOH . J 5 HOH B 7 19 19 HOH HOH . J 5 HOH B 8 22 22 HOH HOH . J 5 HOH B 9 28 28 HOH HOH . J 5 HOH B 10 29 29 HOH HOH . J 5 HOH B 11 32 32 HOH HOH . J 5 HOH B 12 33 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 C1 KKK . . . F 4 39.125 3.902 -3.773 1 41.99 ? C1 KKK 602 A 1 HETATM 2 N N1 KKK . . . F 4 40.312 3.701 -3.155 1 42.86 ? N1 KKK 602 A 1 HETATM 3 O O1 KKK . . . F 4 40.94 6.661 -1.237 1 46.65 ? O1 KKK 602 A 1 HETATM 4 CL CL1 KKK . . . F 4 42.624 7.583 -7.639 1 51.1 ? CL1 KKK 602 A 1 HETATM 5 C C2 KKK . . . F 4 40.165 2.423 -4.89 1 41.18 ? C2 KKK 602 A 1 HETATM 6 N N2 KKK . . . F 4 39.045 3.143 -4.815 1 39.48 ? N2 KKK 602 A 1 HETATM 7 O O2 KKK . . . F 4 42.801 5.35 -1.364 1 48.98 ? O2 KKK 602 A 1 HETATM 8 CL CL2 KKK . . . F 4 43.862 4.181 -3.617 1 51.95 ? CL2 KKK 602 A 1 HETATM 9 C C3 KKK . . . F 4 40.968 2.742 -3.854 1 42.02 ? C3 KKK 602 A 1 HETATM 10 N N3 KKK . . . F 4 43.457 4.177 6.861 1 55.19 ? N3 KKK 602 A 1 HETATM 11 O O3 KKK . . . F 4 41.96 5.338 1.575 1 50.23 ? O3 KKK 602 A 1 HETATM 12 C C4 KKK . . . F 4 40.757 4.339 -1.918 1 45.61 ? C4 KKK 602 A 1 HETATM 13 N N4 KKK . . . F 4 43.979 3.675 9.49 1 57.3 ? N4 KKK 602 A 1 HETATM 14 O O4 KKK . . . F 4 42.917 3.565 11.448 1 57.96 ? O4 KKK 602 A 1 HETATM 15 C C5 KKK . . . F 4 41.563 5.629 -2.001 1 47.33 ? C5 KKK 602 A 1 HETATM 16 C C6 KKK . . . F 4 41.73 6.982 -0.105 1 47.49 ? C6 KKK 602 A 1 HETATM 17 C C7 KKK . . . F 4 43.051 6.277 -0.31 1 48.76 ? C7 KKK 602 A 1 HETATM 18 C C8 KKK . . . F 4 41.821 6.101 -3.397 1 48.84 ? C8 KKK 602 A 1 HETATM 19 C C9 KKK . . . F 4 42.821 5.53 -4.184 1 50.89 ? C9 KKK 602 A 1 HETATM 20 C C10 KKK . . . F 4 43.047 5.983 -5.477 1 50.78 ? C10 KKK 602 A 1 HETATM 21 C C11 KKK . . . F 4 42.288 7.025 -5.973 1 50.64 ? C11 KKK 602 A 1 HETATM 22 C C12 KKK . . . F 4 41.288 7.605 -5.197 1 50.2 ? C12 KKK 602 A 1 HETATM 23 C C13 KKK . . . F 4 41.053 7.141 -3.906 1 49.41 ? C13 KKK 602 A 1 HETATM 24 C C14 KKK . . . F 4 41.086 6.357 1.113 1 49.5 ? C14 KKK 602 A 1 HETATM 25 C C15 KKK . . . F 4 42.292 5.094 2.887 1 51.53 ? C15 KKK 602 A 1 HETATM 26 C C16 KKK . . . F 4 43.635 4.978 3.223 1 52.23 ? C16 KKK 602 A 1 HETATM 27 C C17 KKK . . . F 4 44.013 4.686 4.532 1 53.3 ? C17 KKK 602 A 1 HETATM 28 C C18 KKK . . . F 4 43.055 4.516 5.533 1 54.24 ? C18 KKK 602 A 1 HETATM 29 C C19 KKK . . . F 4 41.705 4.602 5.175 1 53.54 ? C19 KKK 602 A 1 HETATM 30 C C20 KKK . . . F 4 41.323 4.9 3.865 1 51.98 ? C20 KKK 602 A 1 HETATM 31 C C21 KKK . . . F 4 44.472 5.013 7.53 1 56.09 ? C21 KKK 602 A 1 HETATM 32 C C22 KKK . . . F 4 45.089 4.162 8.654 1 56.7 ? C22 KKK 602 A 1 HETATM 33 C C23 KKK . . . F 4 42.931 2.914 8.808 1 56.07 ? C23 KKK 602 A 1 HETATM 34 C C24 KKK . . . F 4 42.348 3.895 7.794 1 55.62 ? C24 KKK 602 A 1 HETATM 35 C C25 KKK . . . F 4 43.867 3.962 10.792 1 57.76 ? C25 KKK 602 A 1 HETATM 36 C C26 KKK . . . F 4 44.967 4.77 11.43 1 58.05 ? C26 KKK 602 A 1 # _model_server_stats.io_time_ms 58 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 29 _model_server_stats.query_time_ms 216 _model_server_stats.encode_time_ms 11 _model_server_stats.element_count 36 #