data_5VQW # _model_server_result.job_id OFBreE0LIyjU44MGCadJvA _model_server_result.datetime_utc '2025-01-10 12:18:49' _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 5vqw # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":601}' # _entry.id 5VQW # _exptl.entry_id 5VQW _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 482.487 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description N-(6-cyano-3-{2-[2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy]phenoxy}-4-methylnaphthalen-1-yl)prop-2-enamide _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 99.61 _cell.angle_gamma 90 _cell.entry_id 5VQW _cell.length_a 162.06 _cell.length_b 73.82 _cell.length_c 108.2 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5VQW _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 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 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C27 H22 N4 O5' _chem_comp.formula_weight 482.487 _chem_comp.id 9KD _chem_comp.mon_nstd_flag . _chem_comp.name N-(6-cyano-3-{2-[2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy]phenoxy}-4-methylnaphthalen-1-yl)prop-2-enamide _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 C6 C5 9KD doub 1 n y C6 C1 9KD sing 2 n y C5 C4 9KD sing 3 n y C1 C2 9KD doub 4 n y O3 C9 9KD doub 5 n n C4 C3 9KD doub 6 n y C2 C3 9KD sing 7 n y C2 O2 9KD sing 8 n n C7 O2 9KD sing 9 n n C7 C8 9KD sing 10 n n C3 O1 9KD sing 11 n n C8 N1 9KD sing 12 n n C9 N1 9KD sing 13 n n C9 N2 9KD sing 14 n n N1 C12 9KD sing 15 n n N2 C10 9KD sing 16 n n O1 C13 9KD sing 17 n n C13 C18 9KD doub 18 n y C13 C14 9KD sing 19 n y C12 C11 9KD doub 20 n n C10 O4 9KD doub 21 n n C10 C11 9KD sing 22 n n C18 C17 9KD sing 23 n y C24 C14 9KD sing 24 n n C14 C15 9KD doub 25 n y C17 N3 9KD sing 26 n n C17 C16 9KD doub 27 n y N3 C25 9KD sing 28 n n C26 C25 9KD sing 29 n n C26 C27 9KD doub 30 n n C25 O5 9KD doub 31 n n C15 C16 9KD sing 32 n y C15 C19 9KD sing 33 n y C16 C22 9KD sing 34 n y C19 C20 9KD doub 35 n y C22 C21 9KD doub 36 n y C20 C21 9KD sing 37 n y C20 C23 9KD sing 38 n n C23 N4 9KD trip 39 n n C1 H1 9KD sing 40 n n C4 H2 9KD sing 41 n n C7 H3 9KD sing 42 n n C7 H4 9KD sing 43 n n C11 H5 9KD sing 44 n n C19 H6 9KD sing 45 n n C21 H7 9KD sing 46 n n C22 H8 9KD sing 47 n n C24 H9 9KD sing 48 n n C24 H10 9KD sing 49 n n C24 H11 9KD sing 50 n n C26 H12 9KD sing 51 n n C27 H13 9KD sing 52 n n C27 H14 9KD sing 53 n n C5 H15 9KD sing 54 n n C6 H16 9KD sing 55 n n C8 H17 9KD sing 56 n n C8 H18 9KD sing 57 n n N2 H19 9KD sing 58 n n C12 H20 9KD sing 59 n n C18 H21 9KD sing 60 n n N3 H22 9KD sing 61 n n # _atom_sites.entry_id 5VQW _atom_sites.fract_transf_matrix[1][1] 0.006171 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001044 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013546 _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] 0.009374 _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 C 3 9KD A 1 601 1 9KD 685 . D 4 SO4 A 1 602 1 SO4 SO4 . E 5 HOH A 1 701 31 HOH HOH . E 5 HOH A 2 702 8 HOH HOH . E 5 HOH A 3 703 38 HOH HOH . E 5 HOH A 4 704 17 HOH HOH . E 5 HOH A 5 705 48 HOH HOH . E 5 HOH A 6 706 49 HOH HOH . E 5 HOH A 7 707 55 HOH HOH . E 5 HOH A 8 708 7 HOH HOH . E 5 HOH A 9 709 13 HOH HOH . E 5 HOH A 10 710 56 HOH HOH . E 5 HOH A 11 711 19 HOH HOH . E 5 HOH A 12 712 2 HOH HOH . E 5 HOH A 13 713 35 HOH HOH . E 5 HOH A 14 714 6 HOH HOH . E 5 HOH A 15 715 42 HOH HOH . E 5 HOH A 16 716 47 HOH HOH . E 5 HOH A 17 717 54 HOH HOH . E 5 HOH A 18 718 33 HOH HOH . E 5 HOH A 19 719 14 HOH HOH . E 5 HOH A 20 720 24 HOH HOH . E 5 HOH A 21 721 36 HOH HOH . E 5 HOH A 22 722 4 HOH HOH . E 5 HOH A 23 723 37 HOH HOH . E 5 HOH A 24 724 53 HOH HOH . E 5 HOH A 25 725 40 HOH HOH . E 5 HOH A 26 726 51 HOH HOH . E 5 HOH A 27 727 27 HOH HOH . E 5 HOH A 28 728 52 HOH HOH . E 5 HOH A 29 729 22 HOH HOH . E 5 HOH A 30 730 50 HOH HOH . E 5 HOH A 31 731 43 HOH HOH . E 5 HOH A 32 732 32 HOH HOH . E 5 HOH A 33 733 20 HOH HOH . F 5 HOH B 1 501 11 HOH HOH . F 5 HOH B 2 502 44 HOH HOH . F 5 HOH B 3 503 59 HOH HOH . F 5 HOH B 4 504 18 HOH HOH . F 5 HOH B 5 505 5 HOH HOH . F 5 HOH B 6 506 34 HOH HOH . F 5 HOH B 7 507 21 HOH HOH . F 5 HOH B 8 508 30 HOH HOH . F 5 HOH B 9 509 25 HOH HOH . F 5 HOH B 10 510 15 HOH HOH . F 5 HOH B 11 511 39 HOH HOH . F 5 HOH B 12 512 12 HOH HOH . F 5 HOH B 13 513 45 HOH HOH . F 5 HOH B 14 514 3 HOH HOH . F 5 HOH B 15 515 58 HOH HOH . F 5 HOH B 16 516 46 HOH HOH . F 5 HOH B 17 517 1 HOH HOH . F 5 HOH B 18 518 23 HOH HOH . F 5 HOH B 19 519 28 HOH HOH . F 5 HOH B 20 520 41 HOH HOH . F 5 HOH B 21 521 57 HOH HOH . F 5 HOH B 22 522 16 HOH HOH . F 5 HOH B 23 523 10 HOH HOH . F 5 HOH B 24 524 26 HOH HOH . F 5 HOH B 25 525 60 HOH HOH . F 5 HOH B 26 526 9 HOH HOH . F 5 HOH B 27 527 29 HOH HOH . F 5 HOH B 28 528 61 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 9KD . . . C 3 846.635 -25.368 141.008 1 70.28 ? C1 9KD 601 A 1 HETATM 2 C C2 9KD . . . C 3 845.601 -26.195 141.523 1 72.4 ? C2 9KD 601 A 1 HETATM 3 C C4 9KD . . . C 3 846.645 -26.107 143.719 1 63.9 ? C4 9KD 601 A 1 HETATM 4 O O5 9KD . . . C 3 844.122 -22.503 143.854 1 81.52 ? O5 9KD 601 A 1 HETATM 5 C C7 9KD . . . C 3 844.688 -26.734 139.368 1 72.28 ? C7 9KD 601 A 1 HETATM 6 C C9 9KD . . . C 3 843.83 -29.825 139.048 1 69.31 ? C9 9KD 601 A 1 HETATM 7 C C11 9KD . . . C 3 841.887 -29.853 141.097 1 76.8 ? C11 9KD 601 A 1 HETATM 8 C C13 9KD . . . C 3 843.502 -26.765 143.999 1 76.78 ? C13 9KD 601 A 1 HETATM 9 C C14 9KD . . . C 3 842.64 -27.432 144.915 1 79.72 ? C14 9KD 601 A 1 HETATM 10 C C15 9KD . . . C 3 841.58 -26.722 145.531 1 76.93 ? C15 9KD 601 A 1 HETATM 11 C C16 9KD . . . C 3 841.342 -25.344 145.264 1 76.76 ? C16 9KD 601 A 1 HETATM 12 C C17 9KD . . . C 3 842.195 -24.664 144.345 1 74.85 ? C17 9KD 601 A 1 HETATM 13 C C19 9KD . . . C 3 840.739 -27.406 146.439 1 79.77 ? C19 9KD 601 A 1 HETATM 14 C C21 9KD . . . C 3 839.42 -25.421 146.839 1 83.42 ? C21 9KD 601 A 1 HETATM 15 C C22 9KD . . . C 3 840.251 -24.717 145.93 1 82.78 ? C22 9KD 601 A 1 HETATM 16 C C23 9KD . . . C 3 838.852 -27.575 148.015 1 82.14 ? C23 9KD 601 A 1 HETATM 17 C C24 9KD . . . C 3 842.805 -28.906 145.268 1 82.13 ? C24 9KD 601 A 1 HETATM 18 C C25 9KD . . . C 3 842.91 -22.304 143.841 1 77.42 ? C25 9KD 601 A 1 HETATM 19 C C26 9KD . . . C 3 842.337 -20.989 143.593 1 80.27 ? C26 9KD 601 A 1 HETATM 20 C C27 9KD . . . C 3 843.097 -19.894 143.789 1 78.29 ? C27 9KD 601 A 1 HETATM 21 C C3 9KD . . . C 3 845.598 -26.568 142.883 1 70.65 ? C3 9KD 601 A 1 HETATM 22 C C5 9KD . . . C 3 847.673 -25.284 143.203 1 64.66 ? C5 9KD 601 A 1 HETATM 23 C C6 9KD . . . C 3 847.671 -24.913 141.846 1 70.22 ? C6 9KD 601 A 1 HETATM 24 O O1 9KD . . . C 3 844.569 -27.37 143.358 1 77.18 ? O1 9KD 601 A 1 HETATM 25 O O2 9KD . . . C 3 844.549 -26.679 140.78 1 74.34 ? O2 9KD 601 A 1 HETATM 26 C C8 9KD . . . C 3 843.457 -27.42 138.757 1 69.91 ? C8 9KD 601 A 1 HETATM 27 N N1 9KD . . . C 3 843.143 -28.653 139.435 1 72.39 ? N1 9KD 601 A 1 HETATM 28 N N2 9KD . . . C 3 843.502 -30.993 139.727 1 72.34 ? N2 9KD 601 A 1 HETATM 29 C C10 9KD . . . C 3 842.56 -31.098 140.747 1 77.14 ? C10 9KD 601 A 1 HETATM 30 C C12 9KD . . . C 3 842.2 -28.711 140.443 1 73.74 ? C12 9KD 601 A 1 HETATM 31 C C18 9KD . . . C 3 843.248 -25.399 143.743 1 70.49 ? C18 9KD 601 A 1 HETATM 32 C C20 9KD . . . C 3 839.665 -26.784 147.095 1 81.35 ? C20 9KD 601 A 1 HETATM 33 O O3 9KD . . . C 3 844.679 -29.842 138.161 1 68.98 ? O3 9KD 601 A 1 HETATM 34 O O4 9KD . . . C 3 842.355 -32.188 141.275 1 73.15 ? O4 9KD 601 A 1 HETATM 35 N N3 9KD . . . C 3 841.987 -23.269 144.057 1 79.82 ? N3 9KD 601 A 1 HETATM 36 N N4 9KD . . . C 3 838.223 -28.224 148.74 1 83.95 ? N4 9KD 601 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 313 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 36 #