data_8BDN # _model_server_result.job_id yjxjL7r2MxLxhu4oHDQu-Q _model_server_result.datetime_utc '2024-11-08 15:43:11' _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 8bdn # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"O","auth_seq_id":301}' # _entry.id 8BDN # _exptl.entry_id 8BDN _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 509.62 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (2~{R})-3-methyl-1-[(2~{S},4~{R})-2-[(5~{R})-5-methyl-5-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]-4~{H}-1,2,4-oxadiazol-3-yl]-4-oxidanyl-pyrrolidin-1-yl]-2-(3-methyl-1,2-oxazol-5-yl)butan-1-one _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 8BDN _cell.length_a 93.173 _cell.length_b 93.173 _cell.length_c 358.85 _cell.Z_PDB 32 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8BDN _symmetry.cell_setting ? _symmetry.Int_Tables_number 91 _symmetry.space_group_name_Hall 'P 4w 2c' _symmetry.space_group_name_H-M 'P 41 2 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 PISA trimeric 3 author_and_software_defined_assembly 1 PISA trimeric 3 author_and_software_defined_assembly 2 PISA trimeric 3 author_and_software_defined_assembly 3 PISA trimeric 3 author_and_software_defined_assembly 4 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,J,M,Q,R,S,Z 1 1 C,D,E,K,M,S,T,U,AA 2 1 F,G,L,N,P,V,W,BA 3 1 H,I,L,O,P,X,Y,BA 4 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 M N N ? 4 N N N ? 4 O N N ? 4 P 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 covale ? covale1 A C LEU 88 A LEU 88 1_555 A N CAS 89 A CAS 89 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.32 ? covale ? covale2 A C CAS 89 A CAS 89 1_555 A N ILE 90 A ILE 90 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale3 C C PHE 25 C PHE 76 1_555 C N CAS 26 C CAS 77 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale4 C C CAS 26 C CAS 77 1_555 C N ASN 27 C ASN 78 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale5 D C LEU 88 D LEU 88 1_555 D N CAS 89 D CAS 89 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale6 D C CAS 89 D CAS 89 1_555 D N ILE 90 D ILE 90 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale7 F C PHE 25 F PHE 76 1_555 F N CAS 26 F CAS 77 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale8 F C CAS 26 F CAS 77 1_555 F N ASN 27 F ASN 78 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale9 G C LEU 88 G LEU 88 1_555 G N CAS 89 G CAS 89 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale10 G C CAS 89 G CAS 89 1_555 G N ILE 90 G ILE 90 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale11 I C PHE 25 I PHE 76 1_555 I N CAS 26 I CAS 77 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale12 I C CAS 26 I CAS 77 1_555 I N ASN 27 I ASN 78 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale13 J C LEU 88 J LEU 88 1_555 J N CAS 89 J CAS 89 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale14 J C CAS 89 J CAS 89 1_555 J N ILE 90 J ILE 90 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale15 L C PHE 25 L PHE 76 1_555 L N CAS 26 L CAS 77 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale16 L C CAS 26 L CAS 77 1_555 L N ASN 27 L ASN 78 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? # _chem_comp.formula 'C26 H31 N5 O4 S' _chem_comp.formula_weight 509.62 _chem_comp.id QFR _chem_comp.mon_nstd_flag . _chem_comp.name (2~{R})-3-methyl-1-[(2~{S},4~{R})-2-[(5~{R})-5-methyl-5-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]-4~{H}-1,2,4-oxadiazol-3-yl]-4-oxidanyl-pyrrolidin-1-yl]-2-(3-methyl-1,2-oxazol-5-yl)butan-1-one _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 N5 C24 QFR doub 298 n y N5 C25 QFR sing 299 n y C24 S1 QFR sing 300 n y C26 C25 QFR sing 301 n n C25 C15 QFR doub 302 n y S1 C15 QFR sing 303 n y C15 C12 QFR sing 304 n n C12 C11 QFR doub 305 n y C12 C13 QFR sing 306 n y C11 C10 QFR sing 307 n y C13 C14 QFR doub 308 n y C10 C9 QFR doub 309 n y C14 C9 QFR sing 310 n y C9 C8 QFR sing 311 n n C16 C8 QFR sing 312 n n C8 N2 QFR sing 313 n n C8 O3 QFR sing 314 n n N2 C7 QFR sing 315 n n O3 N3 QFR sing 316 n n C3 C2 QFR sing 317 n n C3 C4 QFR sing 318 n n C7 N3 QFR doub 319 n n C7 C2 QFR sing 320 n n C2 N1 QFR sing 321 n n C4 O2 QFR sing 322 n n C4 C1 QFR sing 323 n n N1 C1 QFR sing 324 n n N1 C5 QFR sing 325 n n O1 C5 QFR doub 326 n n C5 C6 QFR sing 327 n n C20 C18 QFR sing 328 n n C6 C18 QFR sing 329 n n C6 C17 QFR sing 330 n n C18 C19 QFR sing 331 n n C17 C21 QFR doub 332 n y C17 O4 QFR sing 333 n y C21 C22 QFR sing 334 n y O4 N4 QFR sing 335 n y C22 N4 QFR doub 336 n y C22 C23 QFR sing 337 n n C1 H1 QFR sing 338 n n C1 H2 QFR sing 339 n n C2 H3 QFR sing 340 n n C3 H4 QFR sing 341 n n C3 H5 QFR sing 342 n n C4 H6 QFR sing 343 n n C6 H7 QFR sing 344 n n C10 H11 QFR sing 345 n n C11 H12 QFR sing 346 n n C13 H13 QFR sing 347 n n C14 H14 QFR sing 348 n n O2 H16 QFR sing 349 n n C16 H18 QFR sing 350 n n C16 H19 QFR sing 351 n n C16 H20 QFR sing 352 n n C18 H21 QFR sing 353 n n C19 H22 QFR sing 354 n n C19 H23 QFR sing 355 n n C19 H24 QFR sing 356 n n C20 H25 QFR sing 357 n n C20 H26 QFR sing 358 n n C20 H27 QFR sing 359 n n C21 H28 QFR sing 360 n n C23 H29 QFR sing 361 n n C23 H30 QFR sing 362 n n C23 H31 QFR sing 363 n n N2 H8 QFR sing 364 n n C24 H9 QFR sing 365 n n C26 H10 QFR sing 366 n n C26 H15 QFR sing 367 n n C26 H17 QFR sing 368 n n # _atom_sites.entry_id 8BDN _atom_sites.fract_transf_matrix[1][1] 0.010733 _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] 0.010733 _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] 0.002787 _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 M 4 QFR C 1 301 301 QFR UNL . N 4 QFR F 1 301 301 QFR UNL . O 4 QFR I 1 301 301 QFR UNL . P 4 QFR L 1 301 301 QFR UNL . Q 5 HOH A 1 201 26 HOH HOH . Q 5 HOH A 2 202 25 HOH HOH . Q 5 HOH A 3 203 4 HOH HOH . R 5 HOH B 1 201 1 HOH HOH . R 5 HOH B 2 202 38 HOH HOH . R 5 HOH B 3 203 18 HOH HOH . S 5 HOH C 1 401 10 HOH HOH . S 5 HOH C 2 402 16 HOH HOH . S 5 HOH C 3 403 19 HOH HOH . T 5 HOH D 1 201 15 HOH HOH . T 5 HOH D 2 202 7 HOH HOH . T 5 HOH D 3 203 8 HOH HOH . T 5 HOH D 4 204 30 HOH HOH . T 5 HOH D 5 205 41 HOH HOH . T 5 HOH D 6 206 32 HOH HOH . U 5 HOH E 1 201 35 HOH HOH . U 5 HOH E 2 202 5 HOH HOH . U 5 HOH E 3 203 39 HOH HOH . U 5 HOH E 4 204 36 HOH HOH . V 5 HOH F 1 401 11 HOH HOH . V 5 HOH F 2 402 13 HOH HOH . V 5 HOH F 3 403 21 HOH HOH . V 5 HOH F 4 404 2 HOH HOH . V 5 HOH F 5 405 14 HOH HOH . V 5 HOH F 6 406 40 HOH HOH . W 5 HOH G 1 201 20 HOH HOH . W 5 HOH G 2 202 22 HOH HOH . W 5 HOH G 3 203 24 HOH HOH . X 5 HOH H 1 201 3 HOH HOH . X 5 HOH H 2 202 12 HOH HOH . X 5 HOH H 3 203 37 HOH HOH . Y 5 HOH I 1 401 33 HOH HOH . Y 5 HOH I 2 402 27 HOH HOH . Y 5 HOH I 3 403 17 HOH HOH . Y 5 HOH I 4 404 6 HOH HOH . Y 5 HOH I 5 405 34 HOH HOH . Y 5 HOH I 6 406 23 HOH HOH . Z 5 HOH J 1 201 31 HOH HOH . AA 5 HOH K 1 201 28 HOH HOH . BA 5 HOH L 1 401 9 HOH HOH . BA 5 HOH L 2 402 29 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 QFR . . . O 4 -33.112 38.631 -89.534 1 59.32 ? C1 QFR 301 I 1 HETATM 2 N N1 QFR . . . O 4 -34.538 38.845 -89.253 1 61.62 ? N1 QFR 301 I 1 HETATM 3 C C2 QFR . . . O 4 -34.871 38.56 -87.853 1 57.22 ? C2 QFR 301 I 1 HETATM 4 C C3 QFR . . . O 4 -33.49 38.347 -87.226 1 54.66 ? C3 QFR 301 I 1 HETATM 5 C C4 QFR . . . O 4 -32.7 37.742 -88.372 1 52.56 ? C4 QFR 301 I 1 HETATM 6 C C5 QFR . . . O 4 -35.467 39.161 -90.171 1 55.4 ? C5 QFR 301 I 1 HETATM 7 C C6 QFR . . . O 4 -35.059 39.111 -91.638 1 59.24 ? C6 QFR 301 I 1 HETATM 8 O O1 QFR . . . O 4 -36.605 39.426 -89.842 1 58.36 ? O1 QFR 301 I 1 HETATM 9 C C7 QFR . . . O 4 -35.622 39.67 -87.19 1 53.51 ? C7 QFR 301 I 1 HETATM 10 N N2 QFR . . . O 4 -36.506 39.495 -86.186 1 56.2 ? N2 QFR 301 I 1 HETATM 11 C C8 QFR . . . O 4 -36.845 40.781 -85.607 1 54.37 ? C8 QFR 301 I 1 HETATM 12 C C9 QFR . . . O 4 -36.029 41.07 -84.357 1 55 ? C9 QFR 301 I 1 HETATM 13 C C10 QFR . . . O 4 -36.206 42.248 -83.652 1 46.24 ? C10 QFR 301 I 1 HETATM 14 C C11 QFR . . . O 4 -35.443 42.51 -82.53 1 54.77 ? C11 QFR 301 I 1 HETATM 15 C C12 QFR . . . O 4 -34.484 41.6 -82.088 1 58.21 ? C12 QFR 301 I 1 HETATM 16 C C13 QFR . . . O 4 -34.313 40.417 -82.804 1 52.87 ? C13 QFR 301 I 1 HETATM 17 C C14 QFR . . . O 4 -35.077 40.158 -83.927 1 52.72 ? C14 QFR 301 I 1 HETATM 18 C C15 QFR . . . O 4 -33.659 41.87 -80.895 1 56.05 ? C15 QFR 301 I 1 HETATM 19 O O2 QFR . . . O 4 -33.182 36.425 -88.587 1 51.89 ? O2 QFR 301 I 1 HETATM 20 N N3 QFR . . . O 4 -35.507 40.908 -87.495 1 51.99 ? N3 QFR 301 I 1 HETATM 21 O O3 QFR . . . O 4 -36.351 41.671 -86.645 1 57.2 ? O3 QFR 301 I 1 HETATM 22 C C16 QFR . . . O 4 -38.332 41.022 -85.461 1 42.94 ? C16 QFR 301 I 1 HETATM 23 C C17 QFR . . . O 4 -35.972 38.154 -92.346 1 62.03 ? C17 QFR 301 I 1 HETATM 24 C C18 QFR . . . O 4 -34.985 40.487 -92.328 1 57.32 ? C18 QFR 301 I 1 HETATM 25 C C19 QFR . . . O 4 -34.604 40.348 -93.796 1 53.4 ? C19 QFR 301 I 1 HETATM 26 C C20 QFR . . . O 4 -36.254 41.318 -92.198 1 63.26 ? C20 QFR 301 I 1 HETATM 27 C C21 QFR . . . O 4 -37.309 38.034 -92.436 1 59.58 ? C21 QFR 301 I 1 HETATM 28 C C22 QFR . . . O 4 -37.531 36.882 -93.236 1 65.93 ? C22 QFR 301 I 1 HETATM 29 N N4 QFR . . . O 4 -36.409 36.32 -93.572 1 68.82 ? N4 QFR 301 I 1 HETATM 30 O O4 QFR . . . O 4 -35.39 37.126 -92.998 1 62.02 ? O4 QFR 301 I 1 HETATM 31 C C23 QFR . . . O 4 -38.834 36.295 -93.676 1 62.45 ? C23 QFR 301 I 1 HETATM 32 S S1 QFR . . . O 4 -32.058 41.246 -80.775 1 56.81 ? S1 QFR 301 I 1 HETATM 33 C C24 QFR . . . O 4 -31.842 42.196 -79.365 1 57.37 ? C24 QFR 301 I 1 HETATM 34 N N5 QFR . . . O 4 -32.893 42.825 -78.937 1 57.46 ? N5 QFR 301 I 1 HETATM 35 C C25 QFR . . . O 4 -33.968 42.554 -79.75 1 53.18 ? C25 QFR 301 I 1 HETATM 36 C C26 QFR . . . O 4 -35.322 43.024 -79.323 1 54.91 ? C26 QFR 301 I 1 # _model_server_stats.io_time_ms 40 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 23 _model_server_stats.query_time_ms 284 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 36 #