data_8FC7 # _model_server_result.job_id cyHCtcjQ56OimZbcBTe6oQ _model_server_result.datetime_utc '2024-11-21 23:31:43' _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 8fc7 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"R","auth_seq_id":1001}' # _entry.id 8FC7 # _exptl.entry_id 8FC7 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 460.528 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1-({(5S,7S)-3-[5-(2-hydroxypropan-2-yl)pyrazin-2-yl]-7-methyl-2-oxo-1-oxa-3-azaspiro[4.5]decan-7-yl}methyl)-1H-benzimidazole-6-carbonitrile _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 8FC7 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8FC7 _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 octameric _pdbx_struct_assembly.oligomeric_count 8 _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 _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 ? 3 I N N ? 3 R N N ? 3 S N N ? 3 T 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 metalc ? metalc1 B OG1 THR 19 E THR 19 1_555 J MG MG . E MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.429 ? metalc ? metalc2 B O THR 37 E THR 37 1_555 J MG MG . E MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.234 ? metalc ? metalc3 J MG MG . E MG 301 1_555 K O1B GDP . E GDP 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.314 ? metalc ? metalc4 C OG1 THR 19 F THR 19 1_555 L MG MG . F MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.429 ? metalc ? metalc5 C O THR 37 F THR 37 1_555 L MG MG . F MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.234 ? metalc ? metalc6 L MG MG . F MG 301 1_555 M O1B GDP . F GDP 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.314 ? metalc ? metalc7 D OG1 THR 19 G THR 19 1_555 N MG MG . G MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.429 ? metalc ? metalc8 D O THR 37 G THR 37 1_555 N MG MG . G MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.234 ? metalc ? metalc9 N MG MG . G MG 301 1_555 O O1B GDP . G GDP 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.314 ? metalc ? metalc10 E OG1 THR 19 H THR 19 1_555 P MG MG . H MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.429 ? metalc ? metalc11 E O THR 37 H THR 37 1_555 P MG MG . H MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.234 ? metalc ? metalc12 P MG MG . H MG 301 1_555 Q O1B GDP . H GDP 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.314 ? # _chem_comp.formula 'C25 H28 N6 O3' _chem_comp.formula_weight 460.528 _chem_comp.id XPW _chem_comp.mon_nstd_flag . _chem_comp.name 1-({(5S,7S)-3-[5-(2-hydroxypropan-2-yl)pyrazin-2-yl]-7-methyl-2-oxo-1-oxa-3-azaspiro[4.5]decan-7-yl}methyl)-1H-benzimidazole-6-carbonitrile _chem_comp.type non-polymer _chem_comp.pdbx_synonyms GSK2798745 # 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 C25 C24 XPW doub 419 n y C25 C26 XPW sing 420 n y C24 C23 XPW sing 421 n y N30 C29 XPW trip 422 n n C29 C26 XPW sing 423 n n C26 C27 XPW doub 424 n y C23 N22 XPW sing 425 n y C23 C28 XPW doub 426 n y N22 C21 XPW doub 427 n y C27 C28 XPW sing 428 n y C28 N20 XPW sing 429 n y C21 N20 XPW sing 430 n y N20 C19 XPW sing 431 n n C19 C17 XPW sing 432 n n C17 C16 XPW sing 433 n n C17 C18 XPW sing 434 n n C17 C31 XPW sing 435 n n C16 C15 XPW sing 436 n n C31 C13 XPW sing 437 n n C15 C14 XPW sing 438 n n C13 C14 XPW sing 439 n n C13 C12 XPW sing 440 n n C13 O32 XPW sing 441 n n C12 N11 XPW sing 442 n n O32 C33 XPW sing 443 n n N07 C06 XPW doub 444 n y N07 C08 XPW sing 445 n y N11 C33 XPW sing 446 n n N11 C08 XPW sing 447 n n C06 C05 XPW sing 448 n y C33 O34 XPW doub 449 n n C08 C09 XPW doub 450 n y O04 C02 XPW sing 451 n n C05 C02 XPW sing 452 n n C05 N10 XPW doub 453 n y C09 N10 XPW sing 454 n y C02 C01 XPW sing 455 n n C02 C03 XPW sing 456 n n C12 H1 XPW sing 457 n n C12 H2 XPW sing 458 n n C14 H3 XPW sing 459 n n C14 H4 XPW sing 460 n n C15 H5 XPW sing 461 n n C15 H6 XPW sing 462 n n C16 H7 XPW sing 463 n n C16 H8 XPW sing 464 n n C18 H9 XPW sing 465 n n C18 H10 XPW sing 466 n n C18 H11 XPW sing 467 n n C19 H12 XPW sing 468 n n C19 H13 XPW sing 469 n n C01 H14 XPW sing 470 n n C01 H15 XPW sing 471 n n C01 H16 XPW sing 472 n n C03 H17 XPW sing 473 n n C03 H18 XPW sing 474 n n C03 H19 XPW sing 475 n n O04 H20 XPW sing 476 n n C06 H21 XPW sing 477 n n C09 H22 XPW sing 478 n n C21 H23 XPW sing 479 n n C24 H24 XPW sing 480 n n C25 H25 XPW sing 481 n n C27 H26 XPW sing 482 n n C31 H27 XPW sing 483 n n C31 H28 XPW sing 484 n n # _atom_sites.entry_id 8FC7 _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 I 3 XPW A 1 1001 1001 XPW GSK . J 4 MG E 1 301 301 MG MG . K 5 GDP E 1 302 302 GDP GDP . L 4 MG F 1 301 301 MG MG . M 5 GDP F 1 302 302 GDP GDP . N 4 MG G 1 301 301 MG MG . O 5 GDP G 1 302 302 GDP GDP . P 4 MG H 1 301 301 MG MG . Q 5 GDP H 1 302 302 GDP GDP . R 3 XPW B 1 1001 1001 XPW GSK . S 3 XPW C 1 1001 1001 XPW GSK . T 3 XPW D 1 1001 1001 XPW GSK . # 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 C12 XPW . . . R 3 163.697 113.753 156.935 1 67.16 ? C12 XPW 1001 B 1 HETATM 2 C C13 XPW . . . R 3 164.539 114.769 156.29 1 67.16 ? C13 XPW 1001 B 1 HETATM 3 C C14 XPW . . . R 3 163.878 116.143 156.44 1 67.16 ? C14 XPW 1001 B 1 HETATM 4 C C15 XPW . . . R 3 164.429 117.229 155.509 1 67.16 ? C15 XPW 1001 B 1 HETATM 5 C C16 XPW . . . R 3 164.663 116.767 154.071 1 67.16 ? C16 XPW 1001 B 1 HETATM 6 C C17 XPW . . . R 3 165.412 115.44 153.986 1 67.16 ? C17 XPW 1001 B 1 HETATM 7 C C18 XPW . . . R 3 166.841 115.667 154.477 1 67.16 ? C18 XPW 1001 B 1 HETATM 8 C C19 XPW . . . R 3 165.433 114.96 152.52 1 67.16 ? C19 XPW 1001 B 1 HETATM 9 C C23 XPW . . . R 3 166.186 111.435 152.338 1 67.16 ? C23 XPW 1001 B 1 HETATM 10 C C01 XPW . . . R 3 164.64 107.06 160.12 1 67.16 ? C01 XPW 1001 B 1 HETATM 11 C C02 XPW . . . R 3 163.383 107.685 159.52 1 67.16 ? C02 XPW 1001 B 1 HETATM 12 C C03 XPW . . . R 3 162.3 107.776 160.595 1 67.16 ? C03 XPW 1001 B 1 HETATM 13 O O04 XPW . . . R 3 162.929 106.897 158.459 1 67.16 ? O04 XPW 1001 B 1 HETATM 14 C C05 XPW . . . R 3 163.708 109.095 159.012 1 67.16 ? C05 XPW 1001 B 1 HETATM 15 C C06 XPW . . . R 3 163.83 109.328 157.65 1 67.16 ? C06 XPW 1001 B 1 HETATM 16 N N07 XPW . . . R 3 164.111 110.55 157.219 1 67.16 ? N07 XPW 1001 B 1 HETATM 17 C C08 XPW . . . R 3 164.271 111.533 158.088 1 67.16 ? C08 XPW 1001 B 1 HETATM 18 C C09 XPW . . . R 3 164.146 111.299 159.446 1 67.16 ? C09 XPW 1001 B 1 HETATM 19 N N10 XPW . . . R 3 163.866 110.079 159.879 1 67.16 ? N10 XPW 1001 B 1 HETATM 20 N N11 XPW . . . R 3 164.579 112.877 157.616 1 67.16 ? N11 XPW 1001 B 1 HETATM 21 N N20 XPW . . . R 3 165.987 113.619 152.448 1 67.16 ? N20 XPW 1001 B 1 HETATM 22 C C21 XPW . . . R 3 167.276 113.31 152.417 1 67.16 ? C21 XPW 1001 B 1 HETATM 23 N N22 XPW . . . R 3 167.424 111.997 152.352 1 67.16 ? N22 XPW 1001 B 1 HETATM 24 C C24 XPW . . . R 3 165.737 110.093 152.278 1 67.16 ? C24 XPW 1001 B 1 HETATM 25 C C25 XPW . . . R 3 164.374 109.812 152.279 1 67.16 ? C25 XPW 1001 B 1 HETATM 26 C C26 XPW . . . R 3 163.452 110.855 152.34 1 67.16 ? C26 XPW 1001 B 1 HETATM 27 C C27 XPW . . . R 3 163.888 112.174 152.399 1 67.16 ? C27 XPW 1001 B 1 HETATM 28 C C28 XPW . . . R 3 165.279 112.457 152.396 1 67.16 ? C28 XPW 1001 B 1 HETATM 29 C C29 XPW . . . R 3 161.959 110.542 152.342 1 67.16 ? C29 XPW 1001 B 1 HETATM 30 N N30 XPW . . . R 3 160.85 110.309 152.343 1 67.16 ? N30 XPW 1001 B 1 HETATM 31 C C31 XPW . . . R 3 164.75 114.355 154.838 1 67.16 ? C31 XPW 1001 B 1 HETATM 32 O O32 XPW . . . R 3 165.797 114.77 156.972 1 67.16 ? O32 XPW 1001 B 1 HETATM 33 C C33 XPW . . . R 3 165.859 113.569 157.761 1 67.16 ? C33 XPW 1001 B 1 HETATM 34 O O34 XPW . . . R 3 166.778 113.206 158.412 1 67.16 ? O34 XPW 1001 B 1 # _model_server_stats.io_time_ms 26 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 61 _model_server_stats.query_time_ms 261 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 34 #