data_8BLB # _model_server_result.job_id ZU317CkuuU9jsizkMROF7w _model_server_result.datetime_utc '2024-11-04 23:13:04' _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 8blb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"W","auth_seq_id":502}' # _entry.id 8BLB # _exptl.entry_id 8BLB _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 298.446 _entity.id 4 _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 8BLB _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8BLB _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 PISA _pdbx_struct_assembly.oligomeric_details pentameric _pdbx_struct_assembly.oligomeric_count 5 _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,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y _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 ? 4 Q N N ? 4 S N N ? 4 U N N ? 4 W N N ? 4 Y N N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 2 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 NAG _pdbx_entity_branch_link.comp_id_2 NAG _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order 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 509 NAG 2 n F NAG 2 F 2 NAG A 510 NAG 2 n G NAG 1 G 1 NAG A 511 NAG 2 n G NAG 2 G 2 NAG A 512 NAG 2 n H NAG 1 H 1 NAG B 509 NAG 2 n H NAG 2 H 2 NAG B 510 NAG 2 n I NAG 1 I 1 NAG B 511 NAG 2 n I NAG 2 I 2 NAG B 512 NAG 2 n J NAG 1 J 1 NAG C 509 NAG 2 n J NAG 2 J 2 NAG C 510 NAG 2 n K NAG 1 K 1 NAG C 511 NAG 2 n K NAG 2 K 2 NAG C 512 NAG 2 n L NAG 1 L 1 NAG D 509 NAG 2 n L NAG 2 L 2 NAG D 510 NAG 2 n M NAG 1 M 1 NAG D 511 NAG 2 n M NAG 2 M 2 NAG D 512 NAG 2 n N NAG 1 N 1 NAG E 509 NAG 2 n N NAG 2 N 2 NAG E 510 NAG 2 n O NAG 1 O 1 NAG E 511 NAG 2 n O NAG 2 O 2 NAG E 512 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 disulf ? disulf1 A SG CYS 129 A CYS 157 1_555 A SG CYS 143 A CYS 171 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf2 B SG CYS 129 B CYS 157 1_555 B SG CYS 143 B CYS 171 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf3 C SG CYS 129 C CYS 157 1_555 C SG CYS 143 C CYS 171 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf4 D SG CYS 129 D CYS 157 1_555 D SG CYS 143 D CYS 171 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf5 E SG CYS 129 E CYS 157 1_555 E SG CYS 143 E CYS 171 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? covale ? covale1 A ND2 ASN 76 A ASN 104 1_555 P C1 NAG . A NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale2 A ND2 ASN 142 A ASN 170 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale3 A ND2 ASN 158 A ASN 186 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale4 B ND2 ASN 76 B ASN 104 1_555 R C1 NAG . B NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale5 B ND2 ASN 142 B ASN 170 1_555 I C1 NAG . I NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale6 B ND2 ASN 158 B ASN 186 1_555 H C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale7 C ND2 ASN 76 C ASN 104 1_555 T C1 NAG . C NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale8 C ND2 ASN 142 C ASN 170 1_555 K C1 NAG . K NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale9 C ND2 ASN 158 C ASN 186 1_555 J C1 NAG . J NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale10 D ND2 ASN 76 D ASN 104 1_555 V C1 NAG . D NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale11 D ND2 ASN 142 D ASN 170 1_555 M C1 NAG . M NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale12 D ND2 ASN 158 D ASN 186 1_555 L C1 NAG . L NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale13 E ND2 ASN 76 E ASN 104 1_555 X C1 NAG . E NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale14 E ND2 ASN 142 E ASN 170 1_555 O C1 NAG . O NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale15 E ND2 ASN 158 E ASN 186 1_555 N C1 NAG . N NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale16 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale17 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale18 H O4 NAG . H NAG 1 1_555 H C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale19 I O4 NAG . I NAG 1 1_555 I C1 NAG . I NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale20 J O4 NAG . J NAG 1 1_555 J C1 NAG . J NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale21 K O4 NAG . K NAG 1 1_555 K C1 NAG . K NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale22 L O4 NAG . L NAG 1 1_555 L C1 NAG . L NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale23 M O4 NAG . M NAG 1 1_555 M C1 NAG . M NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale24 N O4 NAG . N NAG 1 1_555 N C1 NAG . N NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale25 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 404 n n C21 C19 VTX doub 405 n y C21 C02 VTX sing 406 n y C01 C02 VTX sing 407 n n C19 C05 VTX sing 408 n y C02 C03 VTX doub 409 n y C05 S06 VTX sing 410 n n C05 C04 VTX doub 411 n y C03 C04 VTX sing 412 n y S06 C07 VTX sing 413 n n C08 C09 VTX doub 414 n y C08 C07 VTX sing 415 n y C09 C10 VTX sing 416 n y C18 C17 VTX sing 417 n n C18 N13 VTX sing 418 n n C07 C12 VTX doub 419 n y C10 C11 VTX doub 420 n y C17 N16 VTX sing 421 n n C12 C11 VTX sing 422 n y C12 N13 VTX sing 423 n n N13 C14 VTX sing 424 n n N16 C15 VTX sing 425 n n C14 C15 VTX sing 426 n n C01 H1 VTX sing 427 n n C01 H2 VTX sing 428 n n C01 H3 VTX sing 429 n n C03 H4 VTX sing 430 n n C04 H5 VTX sing 431 n n C08 H6 VTX sing 432 n n C09 H7 VTX sing 433 n n C10 H8 VTX sing 434 n n C11 H9 VTX sing 435 n n C14 H10 VTX sing 436 n n C14 H11 VTX sing 437 n n C15 H12 VTX sing 438 n n C15 H13 VTX sing 439 n n C17 H14 VTX sing 440 n n C17 H15 VTX sing 441 n n C18 H16 VTX sing 442 n n C18 H17 VTX sing 443 n n C20 H18 VTX sing 444 n n C20 H19 VTX sing 445 n n C20 H20 VTX sing 446 n n C21 H21 VTX sing 447 n n N16 H22 VTX sing 448 n n # _atom_sites.entry_id 8BLB _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 3 NAG A 1 501 508 NAG NAG . Q 4 VTX A 1 502 1102 VTX VTX . R 3 NAG B 1 501 508 NAG NAG . S 4 VTX B 1 502 1102 VTX VTX . T 3 NAG C 1 501 508 NAG NAG . U 4 VTX C 1 502 1102 VTX VTX . V 3 NAG D 1 501 508 NAG NAG . W 4 VTX D 1 502 1102 VTX VTX . X 3 NAG E 1 501 508 NAG NAG . Y 4 VTX E 1 502 1102 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 . . . W 4 160.725 174.607 107.733 1 53.02 ? C01 VTX 502 D 1 HETATM 2 C C02 VTX . . . W 4 159.379 173.934 107.472 1 49.58 ? C02 VTX 502 D 1 HETATM 3 C C03 VTX . . . W 4 158.875 173.881 106.203 1 47.13 ? C03 VTX 502 D 1 HETATM 4 C C04 VTX . . . W 4 157.643 173.264 105.963 1 47.21 ? C04 VTX 502 D 1 HETATM 5 C C05 VTX . . . W 4 156.912 172.694 107.034 1 47.84 ? C05 VTX 502 D 1 HETATM 6 C C07 VTX . . . W 4 155.561 170.123 106.404 1 44.48 ? C07 VTX 502 D 1 HETATM 7 C C08 VTX . . . W 4 156.821 169.572 106.569 1 43.3 ? C08 VTX 502 D 1 HETATM 8 C C09 VTX . . . W 4 157.038 168.248 106.307 1 42.92 ? C09 VTX 502 D 1 HETATM 9 C C10 VTX . . . W 4 156.011 167.449 105.881 1 44.92 ? C10 VTX 502 D 1 HETATM 10 C C11 VTX . . . W 4 154.741 167.974 105.709 1 41.92 ? C11 VTX 502 D 1 HETATM 11 C C12 VTX . . . W 4 154.488 169.329 105.968 1 42.62 ? C12 VTX 502 D 1 HETATM 12 C C14 VTX . . . W 4 152.878 170.698 104.652 1 46.32 ? C14 VTX 502 D 1 HETATM 13 C C15 VTX . . . W 4 151.465 171.25 104.463 1 47.47 ? C15 VTX 502 D 1 HETATM 14 C C17 VTX . . . W 4 150.681 169.935 106.344 1 49.68 ? C17 VTX 502 D 1 HETATM 15 C C18 VTX . . . W 4 152.065 169.313 106.509 1 51.6 ? C18 VTX 502 D 1 HETATM 16 C C19 VTX . . . W 4 157.473 172.777 108.317 1 49.94 ? C19 VTX 502 D 1 HETATM 17 C C20 VTX . . . W 4 156.735 172.184 109.515 1 51.84 ? C20 VTX 502 D 1 HETATM 18 C C21 VTX . . . W 4 158.685 173.392 108.501 1 51.72 ? C21 VTX 502 D 1 HETATM 19 N N13 VTX . . . W 4 153.158 169.885 105.791 1 46.1 ? N13 VTX 502 D 1 HETATM 20 N N16 VTX . . . W 4 150.424 170.328 104.949 1 49.06 ? N16 VTX 502 D 1 HETATM 21 S S06 VTX . . . W 4 155.307 171.886 106.762 1 63.05 ? S06 VTX 502 D 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 25 _model_server_stats.query_time_ms 270 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 21 #