data_5DY4 # _model_server_result.job_id IGN-byKePJV9Xjnqjhrj4A _model_server_result.datetime_utc '2025-06-26 23:25:51' _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 5dy4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":402}' # _entry.id 5DY4 # _exptl.entry_id 5DY4 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 499.446 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description N-{5-[(7-bromonaphthalen-1-yl)methyl]-1,3-thiazol-2-yl}-2-[(4,6-dimethylpyrimidin-2-yl)sulfanyl]acetamide _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 114.91 _cell.angle_gamma 90 _cell.entry_id 5DY4 _cell.length_a 84.303 _cell.length_b 55.432 _cell.length_c 96.176 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5DY4 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 1 2 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E 1 1,2 A,B,C,D,E 2 1 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 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 # 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 A SG CYS 143 A CYS 195 1_555 B ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.3 ? metalc ? metalc2 A SG CYS 148 A CYS 200 1_555 B ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.28 ? metalc ? metalc3 A SG CYS 169 A CYS 221 1_555 B ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.289 ? metalc ? metalc4 A SG CYS 172 A CYS 224 1_555 B ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.319 ? # _chem_comp.formula 'C22 H19 Br N4 O S2' _chem_comp.formula_weight 499.446 _chem_comp.id 5GN _chem_comp.mon_nstd_flag . _chem_comp.name N-{5-[(7-bromonaphthalen-1-yl)methyl]-1,3-thiazol-2-yl}-2-[(4,6-dimethylpyrimidin-2-yl)sulfanyl]acetamide _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 BR C12 5GN sing 1 n n S1 C16 5GN sing 2 n n S1 C15 5GN sing 3 n n N3 C16 5GN doub 4 n y N3 C20 5GN sing 5 n y C21 C20 5GN sing 6 n n C16 N2 5GN sing 7 n y C15 C 5GN sing 8 n n C20 C19 5GN doub 9 n y C12 C13 5GN doub 10 n y C12 C11 5GN sing 11 n y C13 C14 5GN sing 12 n y O C 5GN doub 13 n n C N 5GN sing 14 n n C11 C10 5GN doub 15 n y N2 C17 5GN doub 16 n y C19 C17 5GN sing 17 n y N C1 5GN sing 18 n n C14 C9 5GN doub 19 n y S C1 5GN sing 20 n y S C3 5GN sing 21 n y C17 C18 5GN sing 22 n n C1 N1 5GN doub 23 n y C10 C9 5GN sing 24 n y C10 C5 5GN sing 25 n y C9 C8 5GN sing 26 n y N1 C2 5GN sing 27 n y C3 C4 5GN sing 28 n n C3 C2 5GN doub 29 n y C4 C5 5GN sing 30 n n C5 C6 5GN doub 31 n y C8 C7 5GN doub 32 n y C6 C7 5GN sing 33 n y C11 H1 5GN sing 34 n n C6 H2 5GN sing 35 n n C8 H3 5GN sing 36 n n C4 H4 5GN sing 37 n n C4 H5 5GN sing 38 n n C7 H6 5GN sing 39 n n C2 H7 5GN sing 40 n n C13 H8 5GN sing 41 n n C14 H9 5GN sing 42 n n N H10 5GN sing 43 n n C15 H11 5GN sing 44 n n C15 H12 5GN sing 45 n n C21 H13 5GN sing 46 n n C21 H14 5GN sing 47 n n C21 H15 5GN sing 48 n n C19 H16 5GN sing 49 n n C18 H17 5GN sing 50 n n C18 H18 5GN sing 51 n n C18 H19 5GN sing 52 n n # _atom_sites.entry_id 5DY4 _atom_sites.fract_transf_matrix[1][1] 0.011862 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.005509 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01804 _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] 0.011464 _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 B 2 ZN A 1 401 400 ZN ZN . C 3 5GN A 1 402 1 5GN 229 . D 4 NAD A 1 403 2 NAD NAD . E 5 HOH A 1 501 143 HOH HOH . E 5 HOH A 2 502 31 HOH HOH . E 5 HOH A 3 503 130 HOH HOH . E 5 HOH A 4 504 65 HOH HOH . E 5 HOH A 5 505 17 HOH HOH . E 5 HOH A 6 506 52 HOH HOH . E 5 HOH A 7 507 10 HOH HOH . E 5 HOH A 8 508 20 HOH HOH . E 5 HOH A 9 509 82 HOH HOH . E 5 HOH A 10 510 165 HOH HOH . E 5 HOH A 11 511 180 HOH HOH . E 5 HOH A 12 512 28 HOH HOH . E 5 HOH A 13 513 171 HOH HOH . E 5 HOH A 14 514 64 HOH HOH . E 5 HOH A 15 515 45 HOH HOH . E 5 HOH A 16 516 183 HOH HOH . E 5 HOH A 17 517 123 HOH HOH . E 5 HOH A 18 518 44 HOH HOH . E 5 HOH A 19 519 93 HOH HOH . E 5 HOH A 20 520 72 HOH HOH . E 5 HOH A 21 521 146 HOH HOH . E 5 HOH A 22 522 162 HOH HOH . E 5 HOH A 23 523 94 HOH HOH . E 5 HOH A 24 524 29 HOH HOH . E 5 HOH A 25 525 109 HOH HOH . E 5 HOH A 26 526 53 HOH HOH . E 5 HOH A 27 527 9 HOH HOH . E 5 HOH A 28 528 19 HOH HOH . E 5 HOH A 29 529 66 HOH HOH . E 5 HOH A 30 530 23 HOH HOH . E 5 HOH A 31 531 164 HOH HOH . E 5 HOH A 32 532 170 HOH HOH . E 5 HOH A 33 533 128 HOH HOH . E 5 HOH A 34 534 27 HOH HOH . E 5 HOH A 35 535 35 HOH HOH . E 5 HOH A 36 536 98 HOH HOH . E 5 HOH A 37 537 4 HOH HOH . E 5 HOH A 38 538 47 HOH HOH . E 5 HOH A 39 539 150 HOH HOH . E 5 HOH A 40 540 158 HOH HOH . E 5 HOH A 41 541 43 HOH HOH . E 5 HOH A 42 542 34 HOH HOH . E 5 HOH A 43 543 63 HOH HOH . E 5 HOH A 44 544 116 HOH HOH . E 5 HOH A 45 545 80 HOH HOH . E 5 HOH A 46 546 62 HOH HOH . E 5 HOH A 47 547 141 HOH HOH . E 5 HOH A 48 548 16 HOH HOH . E 5 HOH A 49 549 69 HOH HOH . E 5 HOH A 50 550 120 HOH HOH . E 5 HOH A 51 551 32 HOH HOH . E 5 HOH A 52 552 1 HOH HOH . E 5 HOH A 53 553 8 HOH HOH . E 5 HOH A 54 554 172 HOH HOH . E 5 HOH A 55 555 173 HOH HOH . E 5 HOH A 56 556 30 HOH HOH . E 5 HOH A 57 557 67 HOH HOH . E 5 HOH A 58 558 41 HOH HOH . E 5 HOH A 59 559 161 HOH HOH . E 5 HOH A 60 560 7 HOH HOH . E 5 HOH A 61 561 6 HOH HOH . E 5 HOH A 62 562 26 HOH HOH . E 5 HOH A 63 563 60 HOH HOH . E 5 HOH A 64 564 22 HOH HOH . E 5 HOH A 65 565 104 HOH HOH . E 5 HOH A 66 566 74 HOH HOH . E 5 HOH A 67 567 36 HOH HOH . E 5 HOH A 68 568 42 HOH HOH . E 5 HOH A 69 569 58 HOH HOH . E 5 HOH A 70 570 33 HOH HOH . E 5 HOH A 71 571 151 HOH HOH . E 5 HOH A 72 572 103 HOH HOH . E 5 HOH A 73 573 136 HOH HOH . E 5 HOH A 74 574 156 HOH HOH . E 5 HOH A 75 575 111 HOH HOH . E 5 HOH A 76 576 21 HOH HOH . E 5 HOH A 77 577 149 HOH HOH . E 5 HOH A 78 578 86 HOH HOH . E 5 HOH A 79 579 71 HOH HOH . E 5 HOH A 80 580 122 HOH HOH . E 5 HOH A 81 581 11 HOH HOH . E 5 HOH A 82 582 48 HOH HOH . E 5 HOH A 83 583 125 HOH HOH . E 5 HOH A 84 584 115 HOH HOH . E 5 HOH A 85 585 126 HOH HOH . E 5 HOH A 86 586 25 HOH HOH . E 5 HOH A 87 587 78 HOH HOH . E 5 HOH A 88 588 84 HOH HOH . E 5 HOH A 89 589 154 HOH HOH . E 5 HOH A 90 590 114 HOH HOH . E 5 HOH A 91 591 24 HOH HOH . E 5 HOH A 92 592 110 HOH HOH . E 5 HOH A 93 593 51 HOH HOH . E 5 HOH A 94 594 75 HOH HOH . E 5 HOH A 95 595 124 HOH HOH . E 5 HOH A 96 596 119 HOH HOH . E 5 HOH A 97 597 2 HOH HOH . E 5 HOH A 98 598 148 HOH HOH . E 5 HOH A 99 599 97 HOH HOH . E 5 HOH A 100 600 113 HOH HOH . E 5 HOH A 101 601 40 HOH HOH . E 5 HOH A 102 602 163 HOH HOH . E 5 HOH A 103 603 179 HOH HOH . E 5 HOH A 104 604 12 HOH HOH . E 5 HOH A 105 605 37 HOH HOH . E 5 HOH A 106 606 73 HOH HOH . E 5 HOH A 107 607 59 HOH HOH . E 5 HOH A 108 608 15 HOH HOH . E 5 HOH A 109 609 18 HOH HOH . E 5 HOH A 110 610 79 HOH HOH . E 5 HOH A 111 611 166 HOH HOH . E 5 HOH A 112 612 105 HOH HOH . E 5 HOH A 113 613 85 HOH HOH . E 5 HOH A 114 614 77 HOH HOH . E 5 HOH A 115 615 49 HOH HOH . E 5 HOH A 116 616 138 HOH HOH . E 5 HOH A 117 617 81 HOH HOH . E 5 HOH A 118 618 177 HOH HOH . E 5 HOH A 119 619 76 HOH HOH . E 5 HOH A 120 620 13 HOH HOH . E 5 HOH A 121 621 88 HOH HOH . E 5 HOH A 122 622 178 HOH HOH . E 5 HOH A 123 623 14 HOH HOH . E 5 HOH A 124 624 50 HOH HOH . E 5 HOH A 125 625 70 HOH HOH . E 5 HOH A 126 626 134 HOH HOH . E 5 HOH A 127 627 174 HOH HOH . E 5 HOH A 128 628 107 HOH HOH . E 5 HOH A 129 629 57 HOH HOH . E 5 HOH A 130 630 54 HOH HOH . E 5 HOH A 131 631 91 HOH HOH . E 5 HOH A 132 632 167 HOH HOH . E 5 HOH A 133 633 142 HOH HOH . E 5 HOH A 134 634 147 HOH HOH . E 5 HOH A 135 635 92 HOH HOH . E 5 HOH A 136 636 38 HOH HOH . E 5 HOH A 137 637 160 HOH HOH . E 5 HOH A 138 638 153 HOH HOH . E 5 HOH A 139 639 135 HOH HOH . E 5 HOH A 140 640 46 HOH HOH . E 5 HOH A 141 641 96 HOH HOH . E 5 HOH A 142 642 39 HOH HOH . E 5 HOH A 143 643 99 HOH HOH . E 5 HOH A 144 644 5 HOH HOH . E 5 HOH A 145 645 108 HOH HOH . E 5 HOH A 146 646 117 HOH HOH . E 5 HOH A 147 647 131 HOH HOH . E 5 HOH A 148 648 95 HOH HOH . E 5 HOH A 149 649 112 HOH HOH . E 5 HOH A 150 650 137 HOH HOH . E 5 HOH A 151 651 168 HOH HOH . E 5 HOH A 152 652 3 HOH HOH . E 5 HOH A 153 653 132 HOH HOH . E 5 HOH A 154 654 139 HOH HOH . E 5 HOH A 155 655 182 HOH HOH . E 5 HOH A 156 656 152 HOH HOH . E 5 HOH A 157 657 176 HOH HOH . E 5 HOH A 158 658 68 HOH HOH . E 5 HOH A 159 659 145 HOH HOH . E 5 HOH A 160 660 90 HOH HOH . E 5 HOH A 161 661 155 HOH HOH . E 5 HOH A 162 662 181 HOH HOH . E 5 HOH A 163 663 118 HOH HOH . E 5 HOH A 164 664 159 HOH HOH . E 5 HOH A 165 665 55 HOH HOH . E 5 HOH A 166 666 144 HOH HOH . E 5 HOH A 167 667 175 HOH HOH . E 5 HOH A 168 668 83 HOH HOH . E 5 HOH A 169 669 133 HOH HOH . E 5 HOH A 170 670 61 HOH HOH . E 5 HOH A 171 671 129 HOH HOH . E 5 HOH A 172 672 87 HOH HOH . E 5 HOH A 173 673 169 HOH HOH . E 5 HOH A 174 674 56 HOH HOH . E 5 HOH A 175 675 140 HOH HOH . E 5 HOH A 176 676 121 HOH HOH . E 5 HOH A 177 677 101 HOH HOH . E 5 HOH A 178 678 89 HOH HOH . E 5 HOH A 179 679 106 HOH HOH . E 5 HOH A 180 680 100 HOH HOH . E 5 HOH A 181 681 102 HOH HOH . E 5 HOH A 182 682 127 HOH HOH . E 5 HOH A 183 683 157 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 C11 5GN . . . C 3 -13.431 -26.99 12.434 1 25.33 ? C11 5GN 402 A 1 HETATM 2 C C6 5GN . . . C 3 -13.204 -26.821 16.161 1 27.38 ? C6 5GN 402 A 1 HETATM 3 C C8 5GN . . . C 3 -11.829 -28.61 15.386 1 27.59 ? C8 5GN 402 A 1 HETATM 4 C C3 5GN . . . C 3 -15.973 -25.851 14.291 1 28.37 ? C3 5GN 402 A 1 HETATM 5 N N2 5GN . . . C 3 -21.493 -28.015 12.582 1 27.3 ? N2 5GN 402 A 1 HETATM 6 C C10 5GN . . . C 3 -13.099 -27.269 13.787 1 27.46 ? C10 5GN 402 A 1 HETATM 7 C C4 5GN . . . C 3 -14.601 -25.374 14.669 1 27.78 ? C4 5GN 402 A 1 HETATM 8 C C1 5GN . . . C 3 -18.203 -26.174 13.416 1 28.34 ? C1 5GN 402 A 1 HETATM 9 C C7 5GN . . . C 3 -12.332 -27.866 16.407 1 26.95 ? C7 5GN 402 A 1 HETATM 10 N N3 5GN . . . C 3 -22.218 -29.201 10.63 1 26.28 ? N3 5GN 402 A 1 HETATM 11 C C9 5GN . . . C 3 -12.198 -28.34 14.05 1 27.12 ? C9 5GN 402 A 1 HETATM 12 N N1 5GN . . . C 3 -17.888 -27.157 14.209 1 28.74 ? N1 5GN 402 A 1 HETATM 13 C C2 5GN . . . C 3 -16.624 -26.959 14.698 1 29.2 ? C2 5GN 402 A 1 HETATM 14 C C5 5GN . . . C 3 -13.606 -26.499 14.888 1 26.87 ? C5 5GN 402 A 1 HETATM 15 BR BR 5GN . . . C 3 -13.269 -27.266 9.628 1 29.05 ? BR 5GN 402 A 1 HETATM 16 C C12 5GN . . . C 3 -12.89 -27.737 11.431 1 25.79 ? C12 5GN 402 A 1 HETATM 17 C C13 5GN . . . C 3 -12.029 -28.787 11.678 1 27.96 ? C13 5GN 402 A 1 HETATM 18 C C14 5GN . . . C 3 -11.684 -29.085 12.963 1 26.34 ? C14 5GN 402 A 1 HETATM 19 S S 5GN . . . C 3 -16.983 -24.979 13.197 1 28.23 ? S 5GN 402 A 1 HETATM 20 N N 5GN . . . C 3 -19.477 -26.084 12.905 1 30.2 ? N 5GN 402 A 1 HETATM 21 C C 5GN . . . C 3 -19.883 -25.132 12.017 1 30.38 ? C 5GN 402 A 1 HETATM 22 O O 5GN . . . C 3 -19.25 -24.107 11.777 1 31.16 ? O 5GN 402 A 1 HETATM 23 C C15 5GN . . . C 3 -21.217 -25.423 11.364 1 30.19 ? C15 5GN 402 A 1 HETATM 24 S S1 5GN . . . C 3 -21.421 -26.796 10.198 1 29.59 ? S1 5GN 402 A 1 HETATM 25 C C16 5GN . . . C 3 -21.698 -28.151 11.272 1 26.79 ? C16 5GN 402 A 1 HETATM 26 C C20 5GN . . . C 3 -22.559 -30.244 11.405 1 27.25 ? C20 5GN 402 A 1 HETATM 27 C C21 5GN . . . C 3 -23.158 -31.43 10.711 1 27.67 ? C21 5GN 402 A 1 HETATM 28 C C19 5GN . . . C 3 -22.351 -30.218 12.772 1 26.83 ? C19 5GN 402 A 1 HETATM 29 C C17 5GN . . . C 3 -21.799 -29.084 13.331 1 26.51 ? C17 5GN 402 A 1 HETATM 30 C C18 5GN . . . C 3 -21.431 -29.008 14.781 1 27.71 ? C18 5GN 402 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 257 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 30 #