data_8KCT # _model_server_result.job_id hJA6SgQ39EjQnY8a_maCmQ _model_server_result.datetime_utc '2024-11-30 19:16:02' _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 8kct # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"V","auth_seq_id":502}' # _entry.id 8KCT # _exptl.entry_id 8KCT _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 489.644 _entity.id 10 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description Nirogacestat _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 8KCT _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8KCT _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 tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 _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 # _struct_asym.details ? _struct_asym.entity_id 10 _struct_asym.id V _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 5 oligosaccharide 6 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 ? 5 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 6 2 1 NAG NAG C1 O1 . O4 HO4 . sing 3 ? 6 3 2 BMA NAG C1 O1 . O4 HO4 . sing 4 ? 6 4 3 BMA BMA C1 O1 . O3 HO3 . sing 5 ? 6 5 3 BMA BMA C1 O1 . O6 HO6 . 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 5 n E NAG 1 E 1 NAG A 1699 NAG 5 n E NAG 2 E 2 NAG A 1700 NAG 6 n F NAG 1 F 1 NAG A 1701 NAG 6 n F NAG 2 F 2 NAG A 1702 NAG 6 n F BMA 3 F 3 BMA A 1716 BMA 6 n F BMA 4 F 4 BMA A 1718 BMA 6 n F BMA 5 F 5 BMA A 1717 BMA 5 n G NAG 1 G 1 NAG A 1703 NAG 5 n G NAG 2 G 2 NAG A 1704 NAG 5 n H NAG 1 H 1 NAG A 1706 NAG 5 n H NAG 2 H 2 NAG A 1707 NAG 5 n I NAG 1 I 1 NAG A 1708 NAG 5 n I NAG 2 I 2 NAG A 1709 NAG 5 n J NAG 1 J 1 NAG A 1710 NAG 5 n J NAG 2 J 2 NAG A 1711 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 50 A CYS 50 1_555 A SG CYS 62 A CYS 62 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf2 A SG CYS 140 A CYS 140 1_555 A SG CYS 159 A CYS 159 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf3 A SG CYS 230 A CYS 230 1_555 A SG CYS 248 A CYS 248 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? disulf ? disulf4 A SG CYS 586 A CYS 586 1_555 A SG CYS 620 A CYS 620 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? covale ? covale1 A ND2 ASN 45 A ASN 45 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale2 A ND2 ASN 55 A ASN 55 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale3 A ND2 ASN 187 A ASN 187 1_555 O C1 NAG . A NAG 805 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale4 A ND2 ASN 264 A ASN 264 1_555 N C1 NAG . A NAG 804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale5 A ND2 ASN 387 A ASN 387 1_555 K C1 NAG . A NAG 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale6 A ND2 ASN 435 A ASN 435 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.428 ? covale ? covale7 A ND2 ASN 464 A ASN 464 1_555 L C1 NAG . A NAG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale8 A ND2 ASN 506 A ASN 506 1_555 M C1 NAG . A NAG 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale9 A ND2 ASN 530 A ASN 530 1_555 I C1 NAG . I NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? covale ? covale10 A ND2 ASN 562 A ASN 562 1_555 J C1 NAG . J NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale11 A ND2 ASN 573 A ASN 573 1_555 H C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.461 ? covale ? covale12 A ND2 ASN 580 A ASN 580 1_555 P C1 NAG . A NAG 806 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale13 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale14 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale15 F O4 NAG . F NAG 2 1_555 F C1 BMA . F BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale16 F O3 BMA . F BMA 3 1_555 F C1 BMA . F BMA 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale17 F O6 BMA . F BMA 3 1_555 F C1 BMA . F BMA 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? 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 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale20 I O4 NAG . I NAG 1 1_555 I C1 NAG . I NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale21 J O4 NAG . J NAG 1 1_555 J C1 NAG . J NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? # _chem_comp.formula 'C27 H41 F2 N5 O' _chem_comp.formula_weight 489.644 _chem_comp.id O6U _chem_comp.mon_nstd_flag . _chem_comp.name Nirogacestat _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 C21 C15 O6U sing 366 n n C17 C15 O6U sing 367 n n C17 N06 O6U sing 368 n n C22 C15 O6U sing 369 n n C15 N05 O6U sing 370 n n N06 C20 O6U sing 371 n n C30 C18 O6U sing 372 n n N05 C32 O6U sing 373 n y N05 C27 O6U sing 374 n y C32 N08 O6U doub 375 n y C20 C18 O6U sing 376 n n C18 C28 O6U sing 377 n n C18 C29 O6U sing 378 n n C27 C31 O6U doub 379 n y N08 C31 O6U sing 380 n y C31 N07 O6U sing 381 n n O03 C24 O6U doub 382 n n N07 C24 O6U sing 383 n n C24 C14 O6U sing 384 n n C09 C10 O6U sing 385 n n C09 N04 O6U sing 386 n n C09 C11 O6U sing 387 n n C10 C12 O6U sing 388 n n C26 C35 O6U sing 389 n n C26 C19 O6U sing 390 n n C14 N04 O6U sing 391 n n C14 C19 O6U sing 392 n n F01 C23 O6U sing 393 n n C23 C33 O6U doub 394 n y C23 C13 O6U sing 395 n y C33 C34 O6U sing 396 n y C11 C13 O6U sing 397 n n C13 C16 O6U doub 398 n y C34 F02 O6U sing 399 n n C34 C25 O6U doub 400 n y C16 C25 O6U sing 401 n y C16 C12 O6U sing 402 n n C10 H1 O6U sing 403 n n C10 H2 O6U sing 404 n n C17 H3 O6U sing 405 n n C17 H4 O6U sing 406 n n C20 H5 O6U sing 407 n n C20 H6 O6U sing 408 n n C21 H7 O6U sing 409 n n C21 H8 O6U sing 410 n n C21 H9 O6U sing 411 n n C22 H10 O6U sing 412 n n C22 H11 O6U sing 413 n n C22 H12 O6U sing 414 n n C26 H13 O6U sing 415 n n C26 H14 O6U sing 416 n n C28 H15 O6U sing 417 n n C28 H16 O6U sing 418 n n C28 H17 O6U sing 419 n n C09 H18 O6U sing 420 n n C11 H19 O6U sing 421 n n C11 H20 O6U sing 422 n n C12 H21 O6U sing 423 n n C12 H22 O6U sing 424 n n C14 H23 O6U sing 425 n n C19 H24 O6U sing 426 n n C19 H25 O6U sing 427 n n C25 H26 O6U sing 428 n n C27 H27 O6U sing 429 n n C29 H28 O6U sing 430 n n C29 H29 O6U sing 431 n n C29 H30 O6U sing 432 n n C30 H31 O6U sing 433 n n C30 H32 O6U sing 434 n n C30 H33 O6U sing 435 n n C32 H34 O6U sing 436 n n C33 H35 O6U sing 437 n n C35 H36 O6U sing 438 n n C35 H37 O6U sing 439 n n C35 H38 O6U sing 440 n n N04 H39 O6U sing 441 n n N06 H41 O6U sing 442 n n N07 H43 O6U sing 443 n n # _atom_sites.entry_id 8KCT _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 K 7 NAG A 1 801 1705 NAG NAG . L 7 NAG A 1 802 1712 NAG NAG . M 7 NAG A 1 803 1713 NAG NAG . N 7 NAG A 1 804 1714 NAG NAG . O 7 NAG A 1 805 1715 NAG NAG . P 7 NAG A 1 806 1719 NAG NAG . Q 8 CLR C 1 301 301 CLR CLR . R 8 CLR C 1 302 401 CLR CLR . S 8 CLR C 1 303 501 CLR CLR . T 9 PC1 C 1 304 601 PC1 PC1 . U 9 PC1 B 1 501 501 PC1 PC1 . V 10 O6U B 1 502 601 O6U LIG . # 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 C10 O6U . . . V 10 162.203 173.304 146.172 1 109.1 ? C10 O6U 502 B 1 HETATM 2 C C13 O6U . . . V 10 162.832 176.043 147.02 1 109.1 ? C13 O6U 502 B 1 HETATM 3 C C15 O6U . . . V 10 166.101 175.005 139.653 1 109.1 ? C15 O6U 502 B 1 HETATM 4 C C17 O6U . . . V 10 165.341 176.325 139.482 1 109.1 ? C17 O6U 502 B 1 HETATM 5 C C20 O6U . . . V 10 163.805 176.537 141.334 1 109.1 ? C20 O6U 502 B 1 HETATM 6 C C21 O6U . . . V 10 167.196 174.917 138.592 1 109.1 ? C21 O6U 502 B 1 HETATM 7 C C22 O6U . . . V 10 165.161 173.81 139.504 1 109.1 ? C22 O6U 502 B 1 HETATM 8 C C24 O6U . . . V 10 166.031 173.181 144.863 1 109.1 ? C24 O6U 502 B 1 HETATM 9 C C26 O6U . . . V 10 168.111 171.743 146.188 1 109.1 ? C26 O6U 502 B 1 HETATM 10 C C28 O6U . . . V 10 164.576 178.874 141.806 1 109.1 ? C28 O6U 502 B 1 HETATM 11 C C09 O6U . . . V 10 163.652 173.743 146.153 1 109.1 ? C09 O6U 502 B 1 HETATM 12 C C11 O6U . . . V 10 163.948 174.934 147.013 1 109.1 ? C11 O6U 502 B 1 HETATM 13 C C12 O6U . . . V 10 161.444 173.891 147.303 1 109.1 ? C12 O6U 502 B 1 HETATM 14 C C14 O6U . . . V 10 165.879 172.842 146.346 1 109.1 ? C14 O6U 502 B 1 HETATM 15 C C16 O6U . . . V 10 161.41 175.464 147.187 1 109.1 ? C16 O6U 502 B 1 HETATM 16 C C18 O6U . . . V 10 163.359 177.978 141.581 1 109.1 ? C18 O6U 502 B 1 HETATM 17 C C19 O6U . . . V 10 166.677 171.588 146.678 1 109.1 ? C19 O6U 502 B 1 HETATM 18 C C23 O6U . . . V 10 163.038 177.552 146.888 1 109.1 ? C23 O6U 502 B 1 HETATM 19 C C25 O6U . . . V 10 160.188 176.382 147.22 1 109.1 ? C25 O6U 502 B 1 HETATM 20 C C27 O6U . . . V 10 166.193 174.488 142.062 1 109.1 ? C27 O6U 502 B 1 HETATM 21 C C29 O6U . . . V 10 162.489 178.008 142.834 1 109.1 ? C29 O6U 502 B 1 HETATM 22 C C30 O6U . . . V 10 162.555 178.485 140.388 1 109.1 ? C30 O6U 502 B 1 HETATM 23 C C31 O6U . . . V 10 167.058 174.7 143.088 1 109.1 ? C31 O6U 502 B 1 HETATM 24 C C32 O6U . . . V 10 167.889 175.548 141.295 1 109.1 ? C32 O6U 502 B 1 HETATM 25 C C33 O6U . . . V 10 161.817 178.489 146.92 1 109.1 ? C33 O6U 502 B 1 HETATM 26 C C34 O6U . . . V 10 160.387 177.904 147.087 1 109.1 ? C34 O6U 502 B 1 HETATM 27 C C35 O6U . . . V 10 168.902 170.493 146.56 1 109.1 ? C35 O6U 502 B 1 HETATM 28 F F01 O6U . . . V 10 164.296 178.058 146.742 1 109.1 ? F01 O6U 502 B 1 HETATM 29 F F02 O6U . . . V 10 159.308 178.735 147.117 1 109.1 ? F02 O6U 502 B 1 HETATM 30 N N04 O6U . . . V 10 164.482 172.601 146.642 1 109.1 ? N04 O6U 502 B 1 HETATM 31 N N05 O6U . . . V 10 166.708 175.008 140.973 1 109.1 ? N05 O6U 502 B 1 HETATM 32 N N06 O6U . . . V 10 163.952 176.214 139.919 1 109.1 ? N06 O6U 502 B 1 HETATM 33 N N07 O6U . . . V 10 166.869 174.302 144.474 1 109.1 ? N07 O6U 502 B 1 HETATM 34 N N08 O6U . . . V 10 168.091 175.352 142.608 1 109.1 ? N08 O6U 502 B 1 HETATM 35 O O03 O6U . . . V 10 165.471 172.53 144.05 1 109.1 ? O03 O6U 502 B 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 21 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 323 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 35 #