data_5VQV # _model_server_result.job_id emis34UukAgRWXrzs21RhA _model_server_result.datetime_utc '2025-01-10 12:14:25' _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 5vqv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":601}' # _entry.id 5VQV # _exptl.entry_id 5VQV _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 498.53 _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)-N-methylpropanamide _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 99.42 _cell.angle_gamma 90 _cell.entry_id 5VQV _cell.length_a 162.51 _cell.length_b 73.54 _cell.length_c 109.23 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5VQV _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 # _struct_conn.conn_type_id covale _struct_conn.details ? _struct_conn.id covale1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id SG _struct_conn.ptnr1_label_comp_id CYS _struct_conn.ptnr1_label_seq_id 183 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id CYS _struct_conn.ptnr1_auth_seq_id 181 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id C _struct_conn.ptnr2_label_atom_id C28 _struct_conn.ptnr2_label_comp_id 9J1 _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id 9J1 _struct_conn.ptnr2_auth_seq_id 601 _struct_conn.ptnr2_symmetry 1_555 _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 1.821 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C28 H26 N4 O5' _chem_comp.formula_weight 498.53 _chem_comp.id 9J1 _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)-N-methylpropanamide _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 O3 C9 9J1 doub 1 n n C8 C7 9J1 sing 2 n n C8 N1 9J1 sing 3 n n C9 N1 9J1 sing 4 n n C9 N2 9J1 sing 5 n n C7 O2 9J1 sing 6 n n N1 C12 9J1 sing 7 n n N2 C10 9J1 sing 8 n n C12 C11 9J1 doub 9 n n O2 C2 9J1 sing 10 n n C10 C11 9J1 sing 11 n n C10 O4 9J1 doub 12 n n C1 C2 9J1 doub 13 n y C1 C6 9J1 sing 14 n y C2 C3 9J1 sing 15 n y C6 C5 9J1 doub 16 n y C3 O1 9J1 sing 17 n n C3 C4 9J1 doub 18 n y O1 C13 9J1 sing 19 n n C5 C4 9J1 sing 20 n y C13 C18 9J1 doub 21 n y C13 C14 9J1 sing 22 n y C18 C17 9J1 sing 23 n y C27 N3 9J1 sing 24 n n C24 C14 9J1 sing 25 n n C14 C15 9J1 doub 26 n y C17 N3 9J1 sing 27 n n C17 C16 9J1 doub 28 n y N3 C25 9J1 sing 29 n n C25 O5 9J1 doub 30 n n C25 C26 9J1 sing 31 n n C15 C16 9J1 sing 32 n y C15 C19 9J1 sing 33 n y C16 C22 9J1 sing 34 n y C26 C28 9J1 sing 35 n n C19 C20 9J1 doub 36 n y C22 C21 9J1 doub 37 n y C20 C21 9J1 sing 38 n y C20 C23 9J1 sing 39 n n C23 N4 9J1 trip 40 n n N2 H1 9J1 sing 41 n n C4 H2 9J1 sing 42 n n C6 H3 9J1 sing 43 n n C7 H4 9J1 sing 44 n n C7 H5 9J1 sing 45 n n C1 H6 9J1 sing 46 n n C5 H7 9J1 sing 47 n n C8 H8 9J1 sing 48 n n C8 H9 9J1 sing 49 n n C11 H10 9J1 sing 50 n n C12 H11 9J1 sing 51 n n C18 H12 9J1 sing 52 n n C19 H13 9J1 sing 53 n n C21 H14 9J1 sing 54 n n C22 H15 9J1 sing 55 n n C24 H16 9J1 sing 56 n n C24 H17 9J1 sing 57 n n C24 H18 9J1 sing 58 n n C26 H19 9J1 sing 59 n n C26 H20 9J1 sing 60 n n C27 H21 9J1 sing 61 n n C27 H22 9J1 sing 62 n n C27 H23 9J1 sing 63 n n C28 H24 9J1 sing 64 n n C28 H25 9J1 sing 65 n n C28 H26 9J1 sing 66 n n # _atom_sites.entry_id 5VQV _atom_sites.fract_transf_matrix[1][1] 0.006153 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001021 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013598 _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] 0.00928 _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 9J1 A 1 601 1 9J1 684 . D 4 SO4 A 1 602 1 SO4 SO4 . E 5 HOH A 1 701 2 HOH HOH . E 5 HOH A 2 702 42 HOH HOH . E 5 HOH A 3 703 67 HOH HOH . E 5 HOH A 4 704 92 HOH HOH . E 5 HOH A 5 705 13 HOH HOH . E 5 HOH A 6 706 82 HOH HOH . E 5 HOH A 7 707 84 HOH HOH . E 5 HOH A 8 708 94 HOH HOH . E 5 HOH A 9 709 17 HOH HOH . E 5 HOH A 10 710 24 HOH HOH . E 5 HOH A 11 711 56 HOH HOH . E 5 HOH A 12 712 16 HOH HOH . E 5 HOH A 13 713 33 HOH HOH . E 5 HOH A 14 714 57 HOH HOH . E 5 HOH A 15 715 86 HOH HOH . E 5 HOH A 16 716 20 HOH HOH . E 5 HOH A 17 717 77 HOH HOH . E 5 HOH A 18 718 34 HOH HOH . E 5 HOH A 19 719 14 HOH HOH . E 5 HOH A 20 720 51 HOH HOH . E 5 HOH A 21 721 90 HOH HOH . E 5 HOH A 22 722 8 HOH HOH . E 5 HOH A 23 723 65 HOH HOH . E 5 HOH A 24 724 18 HOH HOH . E 5 HOH A 25 725 19 HOH HOH . E 5 HOH A 26 726 30 HOH HOH . E 5 HOH A 27 727 78 HOH HOH . E 5 HOH A 28 728 54 HOH HOH . E 5 HOH A 29 729 79 HOH HOH . E 5 HOH A 30 730 38 HOH HOH . E 5 HOH A 31 731 27 HOH HOH . E 5 HOH A 32 732 7 HOH HOH . E 5 HOH A 33 733 87 HOH HOH . E 5 HOH A 34 734 52 HOH HOH . E 5 HOH A 35 735 91 HOH HOH . E 5 HOH A 36 736 81 HOH HOH . E 5 HOH A 37 737 73 HOH HOH . E 5 HOH A 38 738 23 HOH HOH . E 5 HOH A 39 739 50 HOH HOH . E 5 HOH A 40 740 4 HOH HOH . E 5 HOH A 41 741 29 HOH HOH . E 5 HOH A 42 742 64 HOH HOH . E 5 HOH A 43 743 88 HOH HOH . E 5 HOH A 44 744 39 HOH HOH . E 5 HOH A 45 745 43 HOH HOH . E 5 HOH A 46 746 59 HOH HOH . E 5 HOH A 47 747 22 HOH HOH . E 5 HOH A 48 748 25 HOH HOH . E 5 HOH A 49 749 74 HOH HOH . E 5 HOH A 50 750 15 HOH HOH . E 5 HOH A 51 751 32 HOH HOH . E 5 HOH A 52 752 89 HOH HOH . E 5 HOH A 53 753 83 HOH HOH . E 5 HOH A 54 754 26 HOH HOH . E 5 HOH A 55 755 85 HOH HOH . E 5 HOH A 56 756 41 HOH HOH . E 5 HOH A 57 757 71 HOH HOH . F 5 HOH B 1 501 70 HOH HOH . F 5 HOH B 2 502 47 HOH HOH . F 5 HOH B 3 503 49 HOH HOH . F 5 HOH B 4 504 55 HOH HOH . F 5 HOH B 5 505 12 HOH HOH . F 5 HOH B 6 506 9 HOH HOH . F 5 HOH B 7 507 31 HOH HOH . F 5 HOH B 8 508 45 HOH HOH . F 5 HOH B 9 509 68 HOH HOH . F 5 HOH B 10 510 58 HOH HOH . F 5 HOH B 11 511 66 HOH HOH . F 5 HOH B 12 512 60 HOH HOH . F 5 HOH B 13 513 80 HOH HOH . F 5 HOH B 14 514 28 HOH HOH . F 5 HOH B 15 515 1 HOH HOH . F 5 HOH B 16 516 36 HOH HOH . F 5 HOH B 17 517 48 HOH HOH . F 5 HOH B 18 518 6 HOH HOH . F 5 HOH B 19 519 5 HOH HOH . F 5 HOH B 20 520 72 HOH HOH . F 5 HOH B 21 521 10 HOH HOH . F 5 HOH B 22 522 37 HOH HOH . F 5 HOH B 23 523 63 HOH HOH . F 5 HOH B 24 524 3 HOH HOH . F 5 HOH B 25 525 75 HOH HOH . F 5 HOH B 26 526 62 HOH HOH . F 5 HOH B 27 527 40 HOH HOH . F 5 HOH B 28 528 46 HOH HOH . F 5 HOH B 29 529 21 HOH HOH . F 5 HOH B 30 530 44 HOH HOH . F 5 HOH B 31 531 11 HOH HOH . F 5 HOH B 32 532 61 HOH HOH . F 5 HOH B 33 533 93 HOH HOH . F 5 HOH B 34 534 69 HOH HOH . F 5 HOH B 35 535 35 HOH HOH . F 5 HOH B 36 536 53 HOH HOH . F 5 HOH B 37 537 76 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 N N1 9J1 . . . C 3 844.93 -33.355 141.216 1 47.24 ? N1 9J1 601 A 1 HETATM 2 C C2 9J1 . . . C 3 846.747 -30.728 143.427 1 46.11 ? C2 9J1 601 A 1 HETATM 3 N N2 9J1 . . . C 3 845.349 -35.638 141.757 1 42.51 ? N2 9J1 601 A 1 HETATM 4 N N3 9J1 . . . C 3 843 -27.041 147.024 1 56.94 ? N3 9J1 601 A 1 HETATM 5 C C4 9J1 . . . C 3 847.005 -30.397 145.835 1 46.37 ? C4 9J1 601 A 1 HETATM 6 N N4 9J1 . . . C 3 839.847 -32.663 151.34 1 55.09 ? N4 9J1 601 A 1 HETATM 7 C C6 9J1 . . . C 3 848.935 -30.163 144.363 1 46.01 ? C6 9J1 601 A 1 HETATM 8 C C7 9J1 . . . C 3 846.348 -31.35 141.131 1 46.68 ? C7 9J1 601 A 1 HETATM 9 C C9 9J1 . . . C 3 845.686 -34.527 140.995 1 47.33 ? C9 9J1 601 A 1 HETATM 10 C C1 9J1 . . . C 3 848.127 -30.459 143.25 1 41.29 ? C1 9J1 601 A 1 HETATM 11 C C3 9J1 . . . C 3 846.196 -30.688 144.722 1 43.86 ? C3 9J1 601 A 1 HETATM 12 C C5 9J1 . . . C 3 848.376 -30.132 145.654 1 49.11 ? C5 9J1 601 A 1 HETATM 13 O O1 9J1 . . . C 3 844.86 -30.959 144.864 1 49.43 ? O1 9J1 601 A 1 HETATM 14 O O2 9J1 . . . C 3 845.86 -31.027 142.417 1 47.64 ? O2 9J1 601 A 1 HETATM 15 C C8 9J1 . . . C 3 845.274 -32.195 140.434 1 48.62 ? C8 9J1 601 A 1 HETATM 16 C C10 9J1 . . . C 3 844.338 -35.692 142.71 1 46.45 ? C10 9J1 601 A 1 HETATM 17 C C11 9J1 . . . C 3 843.597 -34.451 142.891 1 44.25 ? C11 9J1 601 A 1 HETATM 18 C C12 9J1 . . . C 3 843.911 -33.359 142.157 1 48.22 ? C12 9J1 601 A 1 HETATM 19 C C13 9J1 . . . C 3 844.08 -30.411 145.852 1 50.47 ? C13 9J1 601 A 1 HETATM 20 C C14 9J1 . . . C 3 843.406 -31.271 146.745 1 45.48 ? C14 9J1 601 A 1 HETATM 21 C C15 9J1 . . . C 3 842.58 -30.733 147.764 1 44.98 ? C15 9J1 601 A 1 HETATM 22 C C16 9J1 . . . C 3 842.424 -29.323 147.885 1 47.25 ? C16 9J1 601 A 1 HETATM 23 C C17 9J1 . . . C 3 843.105 -28.464 146.977 1 48.91 ? C17 9J1 601 A 1 HETATM 24 C C18 9J1 . . . C 3 843.918 -29.018 145.967 1 52.38 ? C18 9J1 601 A 1 HETATM 25 C C19 9J1 . . . C 3 841.904 -31.59 148.667 1 47.52 ? C19 9J1 601 A 1 HETATM 26 C C20 9J1 . . . C 3 841.083 -31.066 149.684 1 49.7 ? C20 9J1 601 A 1 HETATM 27 C C21 9J1 . . . C 3 840.931 -29.673 149.806 1 50.59 ? C21 9J1 601 A 1 HETATM 28 C C22 9J1 . . . C 3 841.595 -28.809 148.914 1 54 ? C22 9J1 601 A 1 HETATM 29 O O3 9J1 . . . C 3 846.604 -34.597 140.178 1 46.83 ? O3 9J1 601 A 1 HETATM 30 O O4 9J1 . . . C 3 844.13 -36.735 143.322 1 55.38 ? O4 9J1 601 A 1 HETATM 31 C C23 9J1 . . . C 3 840.395 -31.955 150.605 1 51.93 ? C23 9J1 601 A 1 HETATM 32 C C24 9J1 . . . C 3 843.586 -32.778 146.595 1 52.51 ? C24 9J1 601 A 1 HETATM 33 C C25 9J1 . . . C 3 843.853 -26.275 147.752 1 56.3 ? C25 9J1 601 A 1 HETATM 34 O O5 9J1 . . . C 3 843.769 -25.046 147.796 1 54.88 ? O5 9J1 601 A 1 HETATM 35 C C26 9J1 . . . C 3 844.963 -26.967 148.56 1 48.19 ? C26 9J1 601 A 1 HETATM 36 C C27 9J1 . . . C 3 841.922 -26.436 146.236 1 54.85 ? C27 9J1 601 A 1 HETATM 37 C C28 9J1 . . . C 3 845.965 -25.972 149.158 1 52.9 ? C28 9J1 601 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 308 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 37 #