data_5VQS # _model_server_result.job_id wV5-mxBM8XqqsPFcMUVfJA _model_server_result.datetime_utc '2025-01-10 11:55:06' _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 5vqs # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":601}' # _entry.id 5VQS # _exptl.entry_id 5VQS _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 107.64 _cell.angle_gamma 90 _cell.entry_id 5VQS _cell.length_a 222.849 _cell.length_b 67.966 _cell.length_c 103.67 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5VQS _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 5VQS _atom_sites.fract_transf_matrix[1][1] 0.004487 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001427 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014713 _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] 0.010122 _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 92 HOH HOH . E 5 HOH A 2 702 67 HOH HOH . E 5 HOH A 3 703 52 HOH HOH . E 5 HOH A 4 704 137 HOH HOH . E 5 HOH A 5 705 54 HOH HOH . E 5 HOH A 6 706 142 HOH HOH . E 5 HOH A 7 707 103 HOH HOH . E 5 HOH A 8 708 3 HOH HOH . E 5 HOH A 9 709 18 HOH HOH . E 5 HOH A 10 710 114 HOH HOH . E 5 HOH A 11 711 194 HOH HOH . E 5 HOH A 12 712 26 HOH HOH . E 5 HOH A 13 713 117 HOH HOH . E 5 HOH A 14 714 120 HOH HOH . E 5 HOH A 15 715 11 HOH HOH . E 5 HOH A 16 716 23 HOH HOH . E 5 HOH A 17 717 77 HOH HOH . E 5 HOH A 18 718 7 HOH HOH . E 5 HOH A 19 719 174 HOH HOH . E 5 HOH A 20 720 56 HOH HOH . E 5 HOH A 21 721 145 HOH HOH . E 5 HOH A 22 722 4 HOH HOH . E 5 HOH A 23 723 17 HOH HOH . E 5 HOH A 24 724 51 HOH HOH . E 5 HOH A 25 725 32 HOH HOH . E 5 HOH A 26 726 138 HOH HOH . E 5 HOH A 27 727 27 HOH HOH . E 5 HOH A 28 728 106 HOH HOH . E 5 HOH A 29 729 34 HOH HOH . E 5 HOH A 30 730 44 HOH HOH . E 5 HOH A 31 731 29 HOH HOH . E 5 HOH A 32 732 102 HOH HOH . E 5 HOH A 33 733 37 HOH HOH . E 5 HOH A 34 734 118 HOH HOH . E 5 HOH A 35 735 108 HOH HOH . E 5 HOH A 36 736 176 HOH HOH . E 5 HOH A 37 737 128 HOH HOH . E 5 HOH A 38 738 33 HOH HOH . E 5 HOH A 39 739 30 HOH HOH . E 5 HOH A 40 740 48 HOH HOH . E 5 HOH A 41 741 24 HOH HOH . E 5 HOH A 42 742 72 HOH HOH . E 5 HOH A 43 743 99 HOH HOH . E 5 HOH A 44 744 94 HOH HOH . E 5 HOH A 45 745 45 HOH HOH . E 5 HOH A 46 746 19 HOH HOH . E 5 HOH A 47 747 50 HOH HOH . E 5 HOH A 48 748 124 HOH HOH . E 5 HOH A 49 749 6 HOH HOH . E 5 HOH A 50 750 104 HOH HOH . E 5 HOH A 51 751 74 HOH HOH . E 5 HOH A 52 752 5 HOH HOH . E 5 HOH A 53 753 123 HOH HOH . E 5 HOH A 54 754 107 HOH HOH . E 5 HOH A 55 755 101 HOH HOH . E 5 HOH A 56 756 69 HOH HOH . E 5 HOH A 57 757 110 HOH HOH . E 5 HOH A 58 758 81 HOH HOH . E 5 HOH A 59 759 165 HOH HOH . E 5 HOH A 60 760 172 HOH HOH . E 5 HOH A 61 761 38 HOH HOH . E 5 HOH A 62 762 85 HOH HOH . E 5 HOH A 63 763 180 HOH HOH . E 5 HOH A 64 764 83 HOH HOH . E 5 HOH A 65 765 171 HOH HOH . E 5 HOH A 66 766 97 HOH HOH . E 5 HOH A 67 767 175 HOH HOH . E 5 HOH A 68 768 88 HOH HOH . E 5 HOH A 69 769 53 HOH HOH . E 5 HOH A 70 770 151 HOH HOH . E 5 HOH A 71 771 122 HOH HOH . E 5 HOH A 72 772 190 HOH HOH . E 5 HOH A 73 773 163 HOH HOH . E 5 HOH A 74 774 191 HOH HOH . E 5 HOH A 75 775 153 HOH HOH . E 5 HOH A 76 776 184 HOH HOH . E 5 HOH A 77 777 35 HOH HOH . E 5 HOH A 78 778 169 HOH HOH . E 5 HOH A 79 779 15 HOH HOH . E 5 HOH A 80 780 161 HOH HOH . E 5 HOH A 81 781 134 HOH HOH . E 5 HOH A 82 782 160 HOH HOH . E 5 HOH A 83 783 187 HOH HOH . E 5 HOH A 84 784 146 HOH HOH . E 5 HOH A 85 785 162 HOH HOH . E 5 HOH A 86 786 183 HOH HOH . E 5 HOH A 87 787 13 HOH HOH . E 5 HOH A 88 788 91 HOH HOH . E 5 HOH A 89 789 193 HOH HOH . E 5 HOH A 90 790 149 HOH HOH . E 5 HOH A 91 791 189 HOH HOH . E 5 HOH A 92 792 143 HOH HOH . E 5 HOH A 93 793 87 HOH HOH . F 5 HOH B 1 501 22 HOH HOH . F 5 HOH B 2 502 158 HOH HOH . F 5 HOH B 3 503 136 HOH HOH . F 5 HOH B 4 504 46 HOH HOH . F 5 HOH B 5 505 21 HOH HOH . F 5 HOH B 6 506 70 HOH HOH . F 5 HOH B 7 507 55 HOH HOH . F 5 HOH B 8 508 40 HOH HOH . F 5 HOH B 9 509 185 HOH HOH . F 5 HOH B 10 510 16 HOH HOH . F 5 HOH B 11 511 93 HOH HOH . F 5 HOH B 12 512 121 HOH HOH . F 5 HOH B 13 513 12 HOH HOH . F 5 HOH B 14 514 31 HOH HOH . F 5 HOH B 15 515 65 HOH HOH . F 5 HOH B 16 516 14 HOH HOH . F 5 HOH B 17 517 113 HOH HOH . F 5 HOH B 18 518 195 HOH HOH . F 5 HOH B 19 519 181 HOH HOH . F 5 HOH B 20 520 36 HOH HOH . F 5 HOH B 21 521 8 HOH HOH . F 5 HOH B 22 522 126 HOH HOH . F 5 HOH B 23 523 43 HOH HOH . F 5 HOH B 24 524 119 HOH HOH . F 5 HOH B 25 525 47 HOH HOH . F 5 HOH B 26 526 105 HOH HOH . F 5 HOH B 27 527 86 HOH HOH . F 5 HOH B 28 528 186 HOH HOH . F 5 HOH B 29 529 2 HOH HOH . F 5 HOH B 30 530 28 HOH HOH . F 5 HOH B 31 531 131 HOH HOH . F 5 HOH B 32 532 177 HOH HOH . F 5 HOH B 33 533 82 HOH HOH . F 5 HOH B 34 534 95 HOH HOH . F 5 HOH B 35 535 192 HOH HOH . F 5 HOH B 36 536 135 HOH HOH . F 5 HOH B 37 537 188 HOH HOH . F 5 HOH B 38 538 90 HOH HOH . F 5 HOH B 39 539 100 HOH HOH . F 5 HOH B 40 540 89 HOH HOH . F 5 HOH B 41 541 25 HOH HOH . F 5 HOH B 42 542 41 HOH HOH . F 5 HOH B 43 543 178 HOH HOH . F 5 HOH B 44 544 96 HOH HOH . F 5 HOH B 45 545 10 HOH HOH . F 5 HOH B 46 546 167 HOH HOH . F 5 HOH B 47 547 155 HOH HOH . F 5 HOH B 48 548 140 HOH HOH . F 5 HOH B 49 549 80 HOH HOH . F 5 HOH B 50 550 164 HOH HOH . F 5 HOH B 51 551 179 HOH HOH . F 5 HOH B 52 552 109 HOH HOH . F 5 HOH B 53 553 116 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 3 460.294 3.27 117.777 1 42.78 ? C1 9KD 601 A 1 HETATM 2 C C2 9KD . . . C 3 460.551 2.723 119.058 1 40.32 ? C2 9KD 601 A 1 HETATM 3 C C4 9KD . . . C 3 462.831 3.608 118.949 1 42.78 ? C4 9KD 601 A 1 HETATM 4 O O5 9KD . . . C 3 458.456 5.222 124.535 1 53.82 ? O5 9KD 601 A 1 HETATM 5 C C7 9KD . . . C 3 458.478 1.547 119.08 1 43.97 ? C7 9KD 601 A 1 HETATM 6 C C9 9KD . . . C 3 458.795 -1.502 120.055 1 38.63 ? C9 9KD 601 A 1 HETATM 7 C C11 9KD . . . C 3 459.611 -1.035 122.716 1 40.12 ? C11 9KD 601 A 1 HETATM 8 C C13 9KD . . . C 3 461.968 3.118 122.02 1 41.26 ? C13 9KD 601 A 1 HETATM 9 C C14 9KD . . . C 3 462.691 2.71 123.16 1 41.56 ? C14 9KD 601 A 1 HETATM 10 C C15 9KD . . . C 3 462.591 3.435 124.368 1 44.03 ? C15 9KD 601 A 1 HETATM 11 C C16 9KD . . . C 3 461.752 4.582 124.437 1 43.28 ? C16 9KD 601 A 1 HETATM 12 C C17 9KD . . . C 3 461.025 4.996 123.289 1 45.59 ? C17 9KD 601 A 1 HETATM 13 C C19 9KD . . . C 3 463.322 3.025 125.508 1 42.01 ? C19 9KD 601 A 1 HETATM 14 C C21 9KD . . . C 3 462.4 4.874 126.784 1 49.08 ? C21 9KD 601 A 1 HETATM 15 C C22 9KD . . . C 3 461.668 5.294 125.658 1 43.6 ? C22 9KD 601 A 1 HETATM 16 C C23 9KD . . . C 3 463.983 3.311 127.879 1 43.97 ? C23 9KD 601 A 1 HETATM 17 C C24 9KD . . . C 3 463.585 1.483 123.067 1 44.3 ? C24 9KD 601 A 1 HETATM 18 C C25 9KD . . . C 3 458.981 6.188 123.985 1 55.45 ? C25 9KD 601 A 1 HETATM 19 C C26 9KD . . . C 3 458.368 7.5 123.912 1 49.88 ? C26 9KD 601 A 1 HETATM 20 C C27 9KD . . . C 3 457.162 7.677 124.478 1 51.24 ? C27 9KD 601 A 1 HETATM 21 C C3 9KD . . . C 3 461.825 2.905 119.64 1 40.06 ? C3 9KD 601 A 1 HETATM 22 C C5 9KD . . . C 3 462.568 4.15 117.677 1 43.05 ? C5 9KD 601 A 1 HETATM 23 C C6 9KD . . . C 3 461.298 3.98 117.093 1 44.54 ? C6 9KD 601 A 1 HETATM 24 O O1 9KD . . . C 3 462.1 2.375 120.873 1 41.01 ? O1 9KD 601 A 1 HETATM 25 O O2 9KD . . . C 3 459.618 2.019 119.784 1 43.99 ? O2 9KD 601 A 1 HETATM 26 C C8 9KD . . . C 3 457.656 0.666 120.028 1 38.66 ? C8 9KD 601 A 1 HETATM 27 N N1 9KD . . . C 3 458.45 -0.311 120.735 1 43.38 ? N1 9KD 601 A 1 HETATM 28 N N2 9KD . . . C 3 459.554 -2.427 120.758 1 37.46 ? N2 9KD 601 A 1 HETATM 29 C C10 9KD . . . C 3 460 -2.282 122.068 1 44.23 ? C10 9KD 601 A 1 HETATM 30 C C12 9KD . . . C 3 458.87 -0.124 122.042 1 42.55 ? C12 9KD 601 A 1 HETATM 31 C C18 9KD . . . C 3 461.135 4.254 122.09 1 43.57 ? C18 9KD 601 A 1 HETATM 32 C C20 9KD . . . C 3 463.228 3.74 126.713 1 44.84 ? C20 9KD 601 A 1 HETATM 33 O O3 9KD . . . C 3 458.46 -1.741 118.897 1 39.45 ? O3 9KD 601 A 1 HETATM 34 O O4 9KD . . . C 3 460.667 -3.171 122.589 1 47.87 ? O4 9KD 601 A 1 HETATM 35 N N3 9KD . . . C 3 460.181 6.142 123.38 1 50.38 ? N3 9KD 601 A 1 HETATM 36 N N4 9KD . . . C 3 464.582 2.97 128.806 1 50.1 ? N4 9KD 601 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 60 _model_server_stats.query_time_ms 312 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 36 #