data_8AW2 # _model_server_result.job_id NV3l1_kyKYYnBH4lVxWE6A _model_server_result.datetime_utc '2024-11-04 22:50:54' _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 8aw2 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"DA","auth_seq_id":503}' # _entry.id 8AW2 # _exptl.entry_id 8AW2 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 298.446 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description Vortioxetine _entity.pdbx_number_of_molecules 5 _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 8AW2 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8AW2 _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 pentameric _pdbx_struct_assembly.oligomeric_count 5 _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,U,V,W,X,Y,Z,AA,BA,CA,DA _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 ? _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 ? 6 R N N ? 6 U N N ? 6 X N N ? 6 AA N N ? 6 DA N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 2 oligosaccharide 3 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 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 2 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 3 2 1 NAG NAG 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 F NAG 1 F 1 NAG A 505 NAG 2 n F NAG 2 F 2 NAG A 504 NAG 2 n F BMA 3 F 3 BMA A 503 BMA 3 n G NAG 1 G 1 NAG A 506 NAG 3 n G NAG 2 G 2 NAG A 507 NAG 2 n H NAG 1 H 1 NAG B 505 NAG 2 n H NAG 2 H 2 NAG B 504 NAG 2 n H BMA 3 H 3 BMA B 503 BMA 3 n I NAG 1 I 1 NAG B 506 NAG 3 n I NAG 2 I 2 NAG B 507 NAG 2 n J NAG 1 J 1 NAG C 505 NAG 2 n J NAG 2 J 2 NAG C 504 NAG 2 n J BMA 3 J 3 BMA C 503 BMA 3 n K NAG 1 K 1 NAG C 506 NAG 3 n K NAG 2 K 2 NAG C 507 NAG 2 n L NAG 1 L 1 NAG D 505 NAG 2 n L NAG 2 L 2 NAG D 504 NAG 2 n L BMA 3 L 3 BMA D 503 BMA 3 n M NAG 1 M 1 NAG D 506 NAG 3 n M NAG 2 M 2 NAG D 507 NAG 2 n N NAG 1 N 1 NAG E 505 NAG 2 n N NAG 2 N 2 NAG E 504 NAG 2 n N BMA 3 N 3 BMA E 503 BMA 3 n O NAG 1 O 1 NAG E 506 NAG 3 n O NAG 2 O 2 NAG E 507 NAG # 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 A ND2 ASN 186 A ASN 82 1_555 P C1 NAG . A NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale2 A ND2 ASN 252 A ASN 148 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale3 A ND2 ASN 268 A ASN 164 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale4 B ND2 ASN 186 B ASN 82 1_555 S C1 NAG . B NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale5 B ND2 ASN 252 B ASN 148 1_555 I C1 NAG . I NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale6 B ND2 ASN 268 B ASN 164 1_555 H C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale7 C ND2 ASN 186 C ASN 82 1_555 V C1 NAG . C NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale8 C ND2 ASN 252 C ASN 148 1_555 K C1 NAG . K NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale9 C ND2 ASN 268 C ASN 164 1_555 J C1 NAG . J NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale10 D ND2 ASN 186 D ASN 82 1_555 Y C1 NAG . D NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale11 D ND2 ASN 252 D ASN 148 1_555 M C1 NAG . M NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale12 D ND2 ASN 268 D ASN 164 1_555 L C1 NAG . L NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale13 E ND2 ASN 186 E ASN 82 1_555 BA C1 NAG . E NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale14 E ND2 ASN 252 E ASN 148 1_555 O C1 NAG . O NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale15 E ND2 ASN 268 E ASN 164 1_555 N C1 NAG . N NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale16 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale17 F O4 NAG . F NAG 2 1_555 F C1 BMA . F BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale18 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale19 H O4 NAG . H NAG 1 1_555 H C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale20 H O4 NAG . H NAG 2 1_555 H C1 BMA . H BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale21 I O4 NAG . I NAG 1 1_555 I C1 NAG . I NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale22 J O4 NAG . J NAG 1 1_555 J C1 NAG . J NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale23 J O4 NAG . J NAG 2 1_555 J C1 BMA . J BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale24 K O4 NAG . K NAG 1 1_555 K C1 NAG . K NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale25 L O4 NAG . L NAG 1 1_555 L C1 NAG . L NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale26 L O4 NAG . L NAG 2 1_555 L C1 BMA . L BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale27 M O4 NAG . M NAG 1 1_555 M C1 NAG . M NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale28 N O4 NAG . N NAG 1 1_555 N C1 NAG . N NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale29 N O4 NAG . N NAG 2 1_555 N C1 BMA . N BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale30 O O4 NAG . O NAG 1 1_555 O C1 NAG . O NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? # _chem_comp.formula 'C18 H22 N2 S' _chem_comp.formula_weight 298.446 _chem_comp.id VTX _chem_comp.mon_nstd_flag . _chem_comp.name Vortioxetine _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 1-[2-(2,4-dimethylphenyl)sulfanylphenyl]piperazine;1-(2-((2,4-Dimethylphenyl)thio)phenyl)piperazine # 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 C20 C19 VTX sing 428 n n C21 C19 VTX doub 429 n y C21 C02 VTX sing 430 n y C01 C02 VTX sing 431 n n C19 C05 VTX sing 432 n y C02 C03 VTX doub 433 n y C05 S06 VTX sing 434 n n C05 C04 VTX doub 435 n y C03 C04 VTX sing 436 n y S06 C07 VTX sing 437 n n C08 C09 VTX doub 438 n y C08 C07 VTX sing 439 n y C09 C10 VTX sing 440 n y C18 C17 VTX sing 441 n n C18 N13 VTX sing 442 n n C07 C12 VTX doub 443 n y C10 C11 VTX doub 444 n y C17 N16 VTX sing 445 n n C12 C11 VTX sing 446 n y C12 N13 VTX sing 447 n n N13 C14 VTX sing 448 n n N16 C15 VTX sing 449 n n C14 C15 VTX sing 450 n n C01 H1 VTX sing 451 n n C01 H2 VTX sing 452 n n C01 H3 VTX sing 453 n n C03 H4 VTX sing 454 n n C04 H5 VTX sing 455 n n C08 H6 VTX sing 456 n n C09 H7 VTX sing 457 n n C10 H8 VTX sing 458 n n C11 H9 VTX sing 459 n n C14 H10 VTX sing 460 n n C14 H11 VTX sing 461 n n C15 H12 VTX sing 462 n n C15 H13 VTX sing 463 n n C17 H14 VTX sing 464 n n C17 H15 VTX sing 465 n n C18 H16 VTX sing 466 n n C18 H17 VTX sing 467 n n C20 H18 VTX sing 468 n n C20 H19 VTX sing 469 n n C20 H20 VTX sing 470 n n C21 H21 VTX sing 471 n n N16 H22 VTX sing 472 n n # _atom_sites.entry_id 8AW2 _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 P 4 NAG A 1 501 501 NAG NAG . Q 5 CL A 1 502 508 CL CL . R 6 VTX A 1 503 1101 VTX VTX . S 4 NAG B 1 501 501 NAG NAG . T 5 CL B 1 502 508 CL CL . U 6 VTX B 1 503 1101 VTX VTX . V 4 NAG C 1 501 501 NAG NAG . W 5 CL C 1 502 508 CL CL . X 6 VTX C 1 503 1101 VTX VTX . Y 4 NAG D 1 501 501 NAG NAG . Z 5 CL D 1 502 508 CL CL . AA 6 VTX D 1 503 1101 VTX VTX . BA 4 NAG E 1 501 501 NAG NAG . CA 5 CL E 1 502 508 CL CL . DA 6 VTX E 1 503 1101 VTX VTX . # 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 C01 VTX . . . DA 6 96.889 112.332 155.328 1 32.98 ? C01 VTX 503 E 1 HETATM 2 C C02 VTX . . . DA 6 97.562 113.6 155.84 1 32.98 ? C02 VTX 503 E 1 HETATM 3 C C03 VTX . . . DA 6 97.797 113.753 157.174 1 32.98 ? C03 VTX 503 E 1 HETATM 4 C C04 VTX . . . DA 6 98.413 114.913 157.646 1 32.98 ? C04 VTX 503 E 1 HETATM 5 C C05 VTX . . . DA 6 98.795 115.932 156.743 1 32.98 ? C05 VTX 503 E 1 HETATM 6 C C07 VTX . . . DA 6 101.369 117.195 157.55 1 32.98 ? C07 VTX 503 E 1 HETATM 7 C C08 VTX . . . DA 6 101.9 115.939 157.326 1 32.98 ? C08 VTX 503 E 1 HETATM 8 C C09 VTX . . . DA 6 103.235 115.711 157.494 1 32.98 ? C09 VTX 503 E 1 HETATM 9 C C10 VTX . . . DA 6 104.063 116.723 157.883 1 32.98 ? C10 VTX 503 E 1 HETATM 10 C C11 VTX . . . DA 6 103.559 117.99 158.112 1 32.98 ? C11 VTX 503 E 1 HETATM 11 C C12 VTX . . . DA 6 102.193 118.255 157.952 1 32.98 ? C12 VTX 503 E 1 HETATM 12 C C14 VTX . . . DA 6 100.925 119.858 159.378 1 32.98 ? C14 VTX 503 E 1 HETATM 13 C C15 VTX . . . DA 6 100.418 121.279 159.608 1 32.98 ? C15 VTX 503 E 1 HETATM 14 C C17 VTX . . . DA 6 101.842 122.092 157.906 1 32.98 ? C17 VTX 503 E 1 HETATM 15 C C18 VTX . . . DA 6 102.274 120.686 157.504 1 32.98 ? C18 VTX 503 E 1 HETATM 16 C C19 VTX . . . DA 6 98.529 115.724 155.385 1 32.98 ? C19 VTX 503 E 1 HETATM 17 C C20 VTX . . . DA 6 98.917 116.79 154.366 1 32.98 ? C20 VTX 503 E 1 HETATM 18 C C21 VTX . . . DA 6 97.92 114.571 154.97 1 32.98 ? C21 VTX 503 E 1 HETATM 19 N N13 VTX . . . DA 6 101.67 119.588 158.188 1 32.98 ? N13 VTX 503 E 1 HETATM 20 N N16 VTX . . . DA 6 100.448 122.048 158.359 1 32.98 ? N16 VTX 503 E 1 HETATM 21 S S06 VTX . . . DA 6 99.591 117.458 157.314 1 32.98 ? S06 VTX 503 E 1 # _model_server_stats.io_time_ms 28 _model_server_stats.parse_time_ms 22 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 256 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 21 #