data_5VQX # _model_server_result.job_id ZMu317TSgslzoj1ZHPMmOg _model_server_result.datetime_utc '2025-01-10 07:23:02' _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 5vqx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":601}' # _entry.id 5VQX # _exptl.entry_id 5VQX _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 484.503 _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-methylacetamide _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 99.3 _cell.angle_gamma 90 _cell.entry_id 5VQX _cell.length_a 162.3 _cell.length_b 73.53 _cell.length_c 108.67 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5VQX _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,G _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 C26 _struct_conn.ptnr2_label_comp_id 9HY _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id 9HY _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 1.83 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C27 H24 N4 O5' _chem_comp.formula_weight 484.503 _chem_comp.id 9HY _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-methylacetamide _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 9HY doub 1 n n C8 C7 9HY sing 2 n n C8 N1 9HY sing 3 n n C9 N1 9HY sing 4 n n C9 N2 9HY sing 5 n n C7 O2 9HY sing 6 n n N1 C12 9HY sing 7 n n N2 C10 9HY sing 8 n n C12 C11 9HY doub 9 n n O2 C2 9HY sing 10 n n C10 C11 9HY sing 11 n n C10 O4 9HY doub 12 n n C1 C2 9HY doub 13 n y C1 C6 9HY sing 14 n y C2 C3 9HY sing 15 n y C6 C5 9HY doub 16 n y C3 O1 9HY sing 17 n n C3 C4 9HY doub 18 n y O1 C13 9HY sing 19 n n C5 C4 9HY sing 20 n y C13 C18 9HY doub 21 n y C13 C14 9HY sing 22 n y C18 C17 9HY sing 23 n y C24 C14 9HY sing 24 n n C27 N3 9HY sing 25 n n C14 C15 9HY doub 26 n y C17 N3 9HY sing 27 n n C17 C16 9HY doub 28 n y N3 C25 9HY sing 29 n n C25 O5 9HY doub 30 n n C25 C26 9HY sing 31 n n C15 C16 9HY sing 32 n y C15 C19 9HY sing 33 n y C16 C22 9HY sing 34 n y C19 C20 9HY doub 35 n y C22 C21 9HY doub 36 n y C20 C21 9HY sing 37 n y C20 C23 9HY sing 38 n n C23 N4 9HY trip 39 n n C26 H1 9HY sing 40 n n C26 H2 9HY sing 41 n n C26 H3 9HY sing 42 n n C27 H4 9HY sing 43 n n C27 H5 9HY sing 44 n n C27 H6 9HY sing 45 n n C24 H7 9HY sing 46 n n C24 H8 9HY sing 47 n n C24 H9 9HY sing 48 n n C22 H10 9HY sing 49 n n C21 H11 9HY sing 50 n n C1 H12 9HY sing 51 n n C7 H13 9HY sing 52 n n C7 H14 9HY sing 53 n n C6 H15 9HY sing 54 n n C5 H16 9HY sing 55 n n C4 H17 9HY sing 56 n n C8 H18 9HY sing 57 n n C8 H19 9HY sing 58 n n C11 H20 9HY sing 59 n n C12 H21 9HY sing 60 n n N2 H22 9HY sing 61 n n C19 H23 9HY sing 62 n n C18 H24 9HY sing 63 n n # _atom_sites.entry_id 5VQX _atom_sites.fract_transf_matrix[1][1] 0.006161 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001009 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.0136 _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] 0.009325 _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 9HY A 1 601 1 9HY 686 . D 4 SO4 A 1 602 1 SO4 SO4 . E 4 SO4 A 1 603 2 SO4 SO4 . F 5 HOH A 1 701 4 HOH HOH . F 5 HOH A 2 702 91 HOH HOH . F 5 HOH A 3 703 36 HOH HOH . F 5 HOH A 4 704 88 HOH HOH . F 5 HOH A 5 705 40 HOH HOH . F 5 HOH A 6 706 109 HOH HOH . F 5 HOH A 7 707 83 HOH HOH . F 5 HOH A 8 708 87 HOH HOH . F 5 HOH A 9 709 6 HOH HOH . F 5 HOH A 10 710 69 HOH HOH . F 5 HOH A 11 711 28 HOH HOH . F 5 HOH A 12 712 85 HOH HOH . F 5 HOH A 13 713 52 HOH HOH . F 5 HOH A 14 714 119 HOH HOH . F 5 HOH A 15 715 17 HOH HOH . F 5 HOH A 16 716 43 HOH HOH . F 5 HOH A 17 717 27 HOH HOH . F 5 HOH A 18 718 89 HOH HOH . F 5 HOH A 19 719 103 HOH HOH . F 5 HOH A 20 720 101 HOH HOH . F 5 HOH A 21 721 8 HOH HOH . F 5 HOH A 22 722 51 HOH HOH . F 5 HOH A 23 723 78 HOH HOH . F 5 HOH A 24 724 24 HOH HOH . F 5 HOH A 25 725 63 HOH HOH . F 5 HOH A 26 726 70 HOH HOH . F 5 HOH A 27 727 102 HOH HOH . F 5 HOH A 28 728 141 HOH HOH . F 5 HOH A 29 729 54 HOH HOH . F 5 HOH A 30 730 53 HOH HOH . F 5 HOH A 31 731 26 HOH HOH . F 5 HOH A 32 732 107 HOH HOH . F 5 HOH A 33 733 60 HOH HOH . F 5 HOH A 34 734 42 HOH HOH . F 5 HOH A 35 735 118 HOH HOH . F 5 HOH A 36 736 15 HOH HOH . F 5 HOH A 37 737 84 HOH HOH . F 5 HOH A 38 738 73 HOH HOH . F 5 HOH A 39 739 72 HOH HOH . F 5 HOH A 40 740 32 HOH HOH . F 5 HOH A 41 741 62 HOH HOH . F 5 HOH A 42 742 94 HOH HOH . F 5 HOH A 43 743 86 HOH HOH . F 5 HOH A 44 744 80 HOH HOH . F 5 HOH A 45 745 50 HOH HOH . F 5 HOH A 46 746 5 HOH HOH . F 5 HOH A 47 747 66 HOH HOH . F 5 HOH A 48 748 143 HOH HOH . F 5 HOH A 49 749 116 HOH HOH . F 5 HOH A 50 750 131 HOH HOH . F 5 HOH A 51 751 25 HOH HOH . F 5 HOH A 52 752 92 HOH HOH . F 5 HOH A 53 753 46 HOH HOH . F 5 HOH A 54 754 99 HOH HOH . F 5 HOH A 55 755 114 HOH HOH . F 5 HOH A 56 756 59 HOH HOH . F 5 HOH A 57 757 3 HOH HOH . F 5 HOH A 58 758 57 HOH HOH . F 5 HOH A 59 759 41 HOH HOH . F 5 HOH A 60 760 82 HOH HOH . F 5 HOH A 61 761 44 HOH HOH . F 5 HOH A 62 762 148 HOH HOH . F 5 HOH A 63 763 35 HOH HOH . F 5 HOH A 64 764 56 HOH HOH . F 5 HOH A 65 765 150 HOH HOH . F 5 HOH A 66 766 95 HOH HOH . F 5 HOH A 67 767 104 HOH HOH . F 5 HOH A 68 768 48 HOH HOH . F 5 HOH A 69 769 98 HOH HOH . F 5 HOH A 70 770 151 HOH HOH . F 5 HOH A 71 771 123 HOH HOH . F 5 HOH A 72 772 93 HOH HOH . F 5 HOH A 73 773 120 HOH HOH . F 5 HOH A 74 774 144 HOH HOH . F 5 HOH A 75 775 38 HOH HOH . F 5 HOH A 76 776 13 HOH HOH . F 5 HOH A 77 777 140 HOH HOH . F 5 HOH A 78 778 23 HOH HOH . F 5 HOH A 79 779 75 HOH HOH . F 5 HOH A 80 780 136 HOH HOH . F 5 HOH A 81 781 125 HOH HOH . F 5 HOH A 82 782 34 HOH HOH . F 5 HOH A 83 783 76 HOH HOH . F 5 HOH A 84 784 96 HOH HOH . F 5 HOH A 85 785 130 HOH HOH . F 5 HOH A 86 786 129 HOH HOH . F 5 HOH A 87 787 149 HOH HOH . F 5 HOH A 88 788 110 HOH HOH . F 5 HOH A 89 789 10 HOH HOH . F 5 HOH A 90 790 132 HOH HOH . F 5 HOH A 91 791 105 HOH HOH . F 5 HOH A 92 792 128 HOH HOH . F 5 HOH A 93 793 112 HOH HOH . F 5 HOH A 94 794 9 HOH HOH . F 5 HOH A 95 795 64 HOH HOH . F 5 HOH A 96 796 126 HOH HOH . F 5 HOH A 97 797 147 HOH HOH . F 5 HOH A 98 798 61 HOH HOH . F 5 HOH A 99 799 67 HOH HOH . G 5 HOH B 1 501 97 HOH HOH . G 5 HOH B 2 502 142 HOH HOH . G 5 HOH B 3 503 138 HOH HOH . G 5 HOH B 4 504 55 HOH HOH . G 5 HOH B 5 505 47 HOH HOH . G 5 HOH B 6 506 18 HOH HOH . G 5 HOH B 7 507 33 HOH HOH . G 5 HOH B 8 508 21 HOH HOH . G 5 HOH B 9 509 122 HOH HOH . G 5 HOH B 10 510 1 HOH HOH . G 5 HOH B 11 511 127 HOH HOH . G 5 HOH B 12 512 45 HOH HOH . G 5 HOH B 13 513 135 HOH HOH . G 5 HOH B 14 514 11 HOH HOH . G 5 HOH B 15 515 20 HOH HOH . G 5 HOH B 16 516 30 HOH HOH . G 5 HOH B 17 517 81 HOH HOH . G 5 HOH B 18 518 74 HOH HOH . G 5 HOH B 19 519 115 HOH HOH . G 5 HOH B 20 520 19 HOH HOH . G 5 HOH B 21 521 29 HOH HOH . G 5 HOH B 22 522 71 HOH HOH . G 5 HOH B 23 523 7 HOH HOH . G 5 HOH B 24 524 39 HOH HOH . G 5 HOH B 25 525 12 HOH HOH . G 5 HOH B 26 526 37 HOH HOH . G 5 HOH B 27 527 108 HOH HOH . G 5 HOH B 28 528 2 HOH HOH . G 5 HOH B 29 529 16 HOH HOH . G 5 HOH B 30 530 133 HOH HOH . G 5 HOH B 31 531 146 HOH HOH . G 5 HOH B 32 532 134 HOH HOH . G 5 HOH B 33 533 90 HOH HOH . G 5 HOH B 34 534 139 HOH HOH . G 5 HOH B 35 535 111 HOH HOH . G 5 HOH B 36 536 49 HOH HOH . G 5 HOH B 37 537 77 HOH HOH . G 5 HOH B 38 538 100 HOH HOH . G 5 HOH B 39 539 79 HOH HOH . G 5 HOH B 40 540 113 HOH HOH . G 5 HOH B 41 541 14 HOH HOH . G 5 HOH B 42 542 106 HOH HOH . G 5 HOH B 43 543 145 HOH HOH . G 5 HOH B 44 544 68 HOH HOH . G 5 HOH B 45 545 65 HOH HOH . G 5 HOH B 46 546 117 HOH HOH . G 5 HOH B 47 547 22 HOH HOH . G 5 HOH B 48 548 124 HOH HOH . G 5 HOH B 49 549 121 HOH HOH . G 5 HOH B 50 550 58 HOH HOH . G 5 HOH B 51 551 31 HOH HOH . G 5 HOH B 52 552 137 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 C26 9HY . . . C 3 -30.229 -37.802 40.333 1 55.58 ? C26 9HY 601 A 1 HETATM 2 C C25 9HY . . . C 3 -31.537 -37.201 39.812 1 52.84 ? C25 9HY 601 A 1 HETATM 3 C C27 9HY . . . C 3 -33.764 -37.298 38.807 1 56.56 ? C27 9HY 601 A 1 HETATM 4 N N4 9HY . . . C 3 -35.953 -43.617 43.358 1 58.06 ? N4 9HY 601 A 1 HETATM 5 C C24 9HY . . . C 3 -32.278 -43.701 38.61 1 47.98 ? C24 9HY 601 A 1 HETATM 6 C C22 9HY . . . C 3 -34.028 -39.737 41.109 1 51.01 ? C22 9HY 601 A 1 HETATM 7 C C21 9HY . . . C 3 -34.732 -40.602 41.965 1 49.9 ? C21 9HY 601 A 1 HETATM 8 N N3 9HY . . . C 3 -32.545 -37.956 39.293 1 56.99 ? N3 9HY 601 A 1 HETATM 9 C C23 9HY . . . C 3 -35.378 -42.897 42.658 1 51.9 ? C23 9HY 601 A 1 HETATM 10 C C20 9HY . . . C 3 -34.654 -41.994 41.778 1 48.13 ? C20 9HY 601 A 1 HETATM 11 C C1 9HY . . . C 3 -27.636 -41.646 35.324 1 40.83 ? C1 9HY 601 A 1 HETATM 12 C C2 9HY . . . C 3 -29.024 -41.83 35.532 1 43.01 ? C2 9HY 601 A 1 HETATM 13 C C7 9HY . . . C 3 -29.497 -42.437 33.245 1 42.05 ? C7 9HY 601 A 1 HETATM 14 C C6 9HY . . . C 3 -26.802 -41.337 36.416 1 40.52 ? C6 9HY 601 A 1 HETATM 15 C C5 9HY . . . C 3 -27.346 -41.211 37.709 1 45.23 ? C5 9HY 601 A 1 HETATM 16 C C4 9HY . . . C 3 -28.727 -41.392 37.917 1 40.94 ? C4 9HY 601 A 1 HETATM 17 C C3 9HY . . . C 3 -29.562 -41.698 36.823 1 46.35 ? C3 9HY 601 A 1 HETATM 18 C C8 9HY . . . C 3 -30.603 -43.266 32.575 1 43.47 ? C8 9HY 601 A 1 HETATM 19 C C9 9HY . . . C 3 -30.08 -45.595 33.112 1 38.75 ? C9 9HY 601 A 1 HETATM 20 C C10 9HY . . . C 3 -31.371 -46.821 34.827 1 41.67 ? C10 9HY 601 A 1 HETATM 21 C C11 9HY . . . C 3 -32.16 -45.612 35.022 1 38.93 ? C11 9HY 601 A 1 HETATM 22 C C12 9HY . . . C 3 -31.893 -44.505 34.291 1 43.38 ? C12 9HY 601 A 1 HETATM 23 C C13 9HY . . . C 3 -31.656 -41.334 37.958 1 44.59 ? C13 9HY 601 A 1 HETATM 24 O O2 9HY . . . C 3 -29.938 -42.132 34.553 1 47.58 ? O2 9HY 601 A 1 HETATM 25 O O1 9HY . . . C 3 -30.915 -41.894 36.946 1 41.44 ? O1 9HY 601 A 1 HETATM 26 N N1 9HY . . . C 3 -30.883 -44.456 33.345 1 43.49 ? N1 9HY 601 A 1 HETATM 27 C C14 9HY . . . C 3 -32.369 -42.193 38.819 1 44.32 ? C14 9HY 601 A 1 HETATM 28 N N2 9HY . . . C 3 -30.37 -46.721 33.867 1 40.17 ? N2 9HY 601 A 1 HETATM 29 C C15 9HY . . . C 3 -33.155 -41.65 39.864 1 44.65 ? C15 9HY 601 A 1 HETATM 30 C C19 9HY . . . C 3 -33.869 -42.512 40.733 1 44.2 ? C19 9HY 601 A 1 HETATM 31 O O5 9HY . . . C 3 -31.634 -35.976 39.881 1 58.41 ? O5 9HY 601 A 1 HETATM 32 C C16 9HY . . . C 3 -33.232 -40.241 40.048 1 46.23 ? C16 9HY 601 A 1 HETATM 33 C C17 9HY . . . C 3 -32.508 -39.379 39.175 1 47.87 ? C17 9HY 601 A 1 HETATM 34 C C18 9HY . . . C 3 -31.739 -39.938 38.133 1 51.97 ? C18 9HY 601 A 1 HETATM 35 O O4 9HY . . . C 3 -31.531 -47.875 35.433 1 50.41 ? O4 9HY 601 A 1 HETATM 36 O O3 9HY . . . C 3 -29.163 -45.637 32.295 1 40.94 ? O3 9HY 601 A 1 # _model_server_stats.io_time_ms 103 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 440 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 36 #