data_3LAK # _model_server_result.job_id C9-XcbDuXc7d4Ed9XSkSxg _model_server_result.datetime_utc '2025-08-05 02:43:55' _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 3lak # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":701}' # _entry.id 3LAK # _exptl.entry_id 3LAK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 421.424 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 3-({3-[(2-amino-6-fluoropyridin-4-yl)methyl]-5-(1-methylethyl)-2,6-dioxo-1,2,3,6-tetrahydropyrimidin-4-yl}carbonyl)-5-methylbenzonitrile _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 90 _cell.angle_gamma 90 _cell.entry_id 3LAK _cell.length_a 118.025 _cell.length_b 154.603 _cell.length_c 154.478 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3LAK _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # _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,H,I,J _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 2 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C22 H20 F N5 O3' _chem_comp.formula_weight 421.424 _chem_comp.id KR1 _chem_comp.mon_nstd_flag . _chem_comp.name 3-({3-[(2-amino-6-fluoropyridin-4-yl)methyl]-5-(1-methylethyl)-2,6-dioxo-1,2,3,6-tetrahydropyrimidin-4-yl}carbonyl)-5-methylbenzonitrile _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 C3 C1 KR1 sing 173 n n C1 N1 KR1 trip 174 n n C21 F1 KR1 sing 175 n n O1 C8 KR1 doub 176 n n C7 C2 KR1 doub 177 n y C3 C2 KR1 sing 178 n y C2 H2 KR1 sing 179 n n N2 C12 KR1 sing 180 n n N2 C13 KR1 sing 181 n n N2 HN2 KR1 sing 182 n n O2 C12 KR1 doub 183 n n C4 C3 KR1 doub 184 n y C13 N3 KR1 sing 185 n n N3 C9 KR1 sing 186 n n N3 C17 KR1 sing 187 n n O3 C13 KR1 doub 188 n n C5 C4 KR1 sing 189 n y C4 H4 KR1 sing 190 n n N4 C20 KR1 sing 191 n n N4 HN4 KR1 sing 192 n n N4 HN4A KR1 sing 193 n n C8 C5 KR1 sing 194 n n C5 C6 KR1 doub 195 n y C20 N5 KR1 doub 196 n y N5 C21 KR1 sing 197 n y C6 C7 KR1 sing 198 n y C6 H6 KR1 sing 199 n n C7 C10 KR1 sing 200 n n C9 C8 KR1 sing 201 n n C11 C9 KR1 doub 202 n n C10 H10 KR1 sing 203 n n C10 H10A KR1 sing 204 n n C10 H10B KR1 sing 205 n n C12 C11 KR1 sing 206 n n C11 C14 KR1 sing 207 n n C15 C14 KR1 sing 208 n n C14 C16 KR1 sing 209 n n C14 H14 KR1 sing 210 n n C15 H15 KR1 sing 211 n n C15 H15A KR1 sing 212 n n C15 H15B KR1 sing 213 n n C16 H16 KR1 sing 214 n n C16 H16A KR1 sing 215 n n C16 H16B KR1 sing 216 n n C18 C17 KR1 sing 217 n n C17 H17 KR1 sing 218 n n C17 H17A KR1 sing 219 n n C19 C18 KR1 doub 220 n y C18 C22 KR1 sing 221 n y C20 C19 KR1 sing 222 n y C19 H19 KR1 sing 223 n n C21 C22 KR1 doub 224 n y C22 H22 KR1 sing 225 n n # _atom_sites.entry_id 3LAK _atom_sites.fract_transf_matrix[1][1] 0.008473 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006468 _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] 0.006473 _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 2 KR1 A 1 701 701 KR1 KR1 . D 3 SO4 A 1 561 201 SO4 SO4 . E 3 SO4 A 1 562 202 SO4 SO4 . F 3 SO4 A 1 563 203 SO4 SO4 . G 3 SO4 A 1 564 204 SO4 SO4 . H 4 CL B 1 561 205 CL CL . I 5 HOH A 1 565 3 HOH WAT . I 5 HOH A 2 566 4 HOH WAT . I 5 HOH A 3 567 5 HOH WAT . I 5 HOH A 4 568 10 HOH WAT . I 5 HOH A 5 569 13 HOH WAT . I 5 HOH A 6 570 15 HOH WAT . I 5 HOH A 7 571 18 HOH WAT . I 5 HOH A 8 572 22 HOH WAT . I 5 HOH A 9 573 23 HOH WAT . I 5 HOH A 10 574 24 HOH WAT . I 5 HOH A 11 575 26 HOH WAT . I 5 HOH A 12 576 29 HOH WAT . I 5 HOH A 13 577 30 HOH WAT . I 5 HOH A 14 578 31 HOH WAT . I 5 HOH A 15 579 32 HOH WAT . I 5 HOH A 16 580 33 HOH WAT . I 5 HOH A 17 581 35 HOH WAT . I 5 HOH A 18 582 37 HOH WAT . I 5 HOH A 19 583 40 HOH WAT . I 5 HOH A 20 584 44 HOH WAT . I 5 HOH A 21 585 45 HOH WAT . I 5 HOH A 22 586 47 HOH WAT . I 5 HOH A 23 587 50 HOH WAT . I 5 HOH A 24 588 51 HOH WAT . I 5 HOH A 25 589 52 HOH WAT . I 5 HOH A 26 590 56 HOH WAT . I 5 HOH A 27 591 58 HOH WAT . I 5 HOH A 28 592 59 HOH WAT . I 5 HOH A 29 593 60 HOH WAT . I 5 HOH A 30 594 64 HOH WAT . I 5 HOH A 31 595 69 HOH WAT . I 5 HOH A 32 596 70 HOH WAT . I 5 HOH A 33 597 71 HOH WAT . I 5 HOH A 34 598 72 HOH WAT . I 5 HOH A 35 599 73 HOH WAT . I 5 HOH A 36 600 75 HOH WAT . I 5 HOH A 37 601 76 HOH WAT . I 5 HOH A 38 602 83 HOH WAT . I 5 HOH A 39 603 84 HOH WAT . I 5 HOH A 40 604 87 HOH WAT . I 5 HOH A 41 605 88 HOH WAT . I 5 HOH A 42 606 89 HOH WAT . I 5 HOH A 43 607 90 HOH WAT . I 5 HOH A 44 608 91 HOH WAT . I 5 HOH A 45 609 92 HOH WAT . I 5 HOH A 46 610 93 HOH WAT . I 5 HOH A 47 611 94 HOH WAT . I 5 HOH A 48 612 95 HOH WAT . I 5 HOH A 49 613 96 HOH WAT . I 5 HOH A 50 614 97 HOH WAT . I 5 HOH A 51 615 99 HOH WAT . I 5 HOH A 52 616 101 HOH WAT . I 5 HOH A 53 617 102 HOH WAT . I 5 HOH A 54 618 103 HOH WAT . I 5 HOH A 55 619 105 HOH WAT . I 5 HOH A 56 620 107 HOH WAT . I 5 HOH A 57 621 110 HOH WAT . I 5 HOH A 58 622 112 HOH WAT . I 5 HOH A 59 623 116 HOH WAT . I 5 HOH A 60 624 117 HOH WAT . I 5 HOH A 61 625 118 HOH WAT . I 5 HOH A 62 626 119 HOH WAT . I 5 HOH A 63 627 120 HOH WAT . I 5 HOH A 64 628 121 HOH WAT . I 5 HOH A 65 629 122 HOH WAT . I 5 HOH A 66 630 123 HOH WAT . I 5 HOH A 67 631 125 HOH WAT . I 5 HOH A 68 632 127 HOH WAT . I 5 HOH A 69 633 128 HOH WAT . I 5 HOH A 70 634 130 HOH WAT . I 5 HOH A 71 635 134 HOH WAT . I 5 HOH A 72 636 135 HOH WAT . I 5 HOH A 73 637 136 HOH WAT . I 5 HOH A 74 638 137 HOH WAT . I 5 HOH A 75 639 138 HOH WAT . I 5 HOH A 76 640 140 HOH WAT . I 5 HOH A 77 641 141 HOH WAT . I 5 HOH A 78 642 142 HOH WAT . I 5 HOH A 79 643 147 HOH WAT . I 5 HOH A 80 644 148 HOH WAT . I 5 HOH A 81 645 151 HOH WAT . I 5 HOH A 82 646 152 HOH WAT . I 5 HOH A 83 647 153 HOH WAT . I 5 HOH A 84 648 159 HOH WAT . I 5 HOH A 85 649 160 HOH WAT . I 5 HOH A 86 650 162 HOH WAT . I 5 HOH A 87 651 164 HOH WAT . I 5 HOH A 88 652 166 HOH WAT . I 5 HOH A 89 653 169 HOH WAT . I 5 HOH A 90 654 170 HOH WAT . I 5 HOH A 91 655 171 HOH WAT . I 5 HOH A 92 656 172 HOH WAT . I 5 HOH A 93 657 175 HOH WAT . I 5 HOH A 94 658 177 HOH WAT . I 5 HOH A 95 659 179 HOH WAT . I 5 HOH A 96 660 183 HOH WAT . I 5 HOH A 97 661 184 HOH WAT . I 5 HOH A 98 662 186 HOH WAT . I 5 HOH A 99 663 188 HOH WAT . I 5 HOH A 100 664 189 HOH WAT . I 5 HOH A 101 665 192 HOH WAT . I 5 HOH A 102 666 194 HOH WAT . I 5 HOH A 103 667 195 HOH WAT . I 5 HOH A 104 668 197 HOH WAT . I 5 HOH A 105 669 198 HOH WAT . I 5 HOH A 106 670 201 HOH WAT . I 5 HOH A 107 671 202 HOH WAT . I 5 HOH A 108 672 204 HOH WAT . I 5 HOH A 109 673 206 HOH WAT . I 5 HOH A 110 674 207 HOH WAT . J 5 HOH B 1 562 1 HOH WAT . J 5 HOH B 2 563 2 HOH WAT . J 5 HOH B 3 564 6 HOH WAT . J 5 HOH B 4 565 7 HOH WAT . J 5 HOH B 5 566 8 HOH WAT . J 5 HOH B 6 567 9 HOH WAT . J 5 HOH B 7 568 11 HOH WAT . J 5 HOH B 8 569 12 HOH WAT . J 5 HOH B 9 570 14 HOH WAT . J 5 HOH B 10 571 16 HOH WAT . J 5 HOH B 11 572 17 HOH WAT . J 5 HOH B 12 573 19 HOH WAT . J 5 HOH B 13 574 20 HOH WAT . J 5 HOH B 14 575 21 HOH WAT . J 5 HOH B 15 576 25 HOH WAT . J 5 HOH B 16 577 27 HOH WAT . J 5 HOH B 17 578 28 HOH WAT . J 5 HOH B 18 579 34 HOH WAT . J 5 HOH B 19 580 36 HOH WAT . J 5 HOH B 20 581 38 HOH WAT . J 5 HOH B 21 582 39 HOH WAT . J 5 HOH B 22 583 41 HOH WAT . J 5 HOH B 23 584 42 HOH WAT . J 5 HOH B 24 585 43 HOH WAT . J 5 HOH B 25 586 46 HOH WAT . J 5 HOH B 26 587 48 HOH WAT . J 5 HOH B 27 588 49 HOH WAT . J 5 HOH B 28 589 53 HOH WAT . J 5 HOH B 29 590 54 HOH WAT . J 5 HOH B 30 591 55 HOH WAT . J 5 HOH B 31 592 57 HOH WAT . J 5 HOH B 32 593 61 HOH WAT . J 5 HOH B 33 594 62 HOH WAT . J 5 HOH B 34 595 63 HOH WAT . J 5 HOH B 35 596 65 HOH WAT . J 5 HOH B 36 597 66 HOH WAT . J 5 HOH B 37 598 67 HOH WAT . J 5 HOH B 38 599 68 HOH WAT . J 5 HOH B 39 600 74 HOH WAT . J 5 HOH B 40 601 77 HOH WAT . J 5 HOH B 41 602 78 HOH WAT . J 5 HOH B 42 603 79 HOH WAT . J 5 HOH B 43 604 80 HOH WAT . J 5 HOH B 44 605 81 HOH WAT . J 5 HOH B 45 606 82 HOH WAT . J 5 HOH B 46 607 85 HOH WAT . J 5 HOH B 47 608 86 HOH WAT . J 5 HOH B 48 609 98 HOH WAT . J 5 HOH B 49 610 100 HOH WAT . J 5 HOH B 50 611 104 HOH WAT . J 5 HOH B 51 612 106 HOH WAT . J 5 HOH B 52 613 108 HOH WAT . J 5 HOH B 53 614 109 HOH WAT . J 5 HOH B 54 615 111 HOH WAT . J 5 HOH B 55 616 113 HOH WAT . J 5 HOH B 56 617 114 HOH WAT . J 5 HOH B 57 618 115 HOH WAT . J 5 HOH B 58 619 124 HOH WAT . J 5 HOH B 59 620 126 HOH WAT . J 5 HOH B 60 621 129 HOH WAT . J 5 HOH B 61 622 131 HOH WAT . J 5 HOH B 62 623 132 HOH WAT . J 5 HOH B 63 624 133 HOH WAT . J 5 HOH B 64 625 139 HOH WAT . J 5 HOH B 65 626 143 HOH WAT . J 5 HOH B 66 627 144 HOH WAT . J 5 HOH B 67 628 145 HOH WAT . J 5 HOH B 68 629 146 HOH WAT . J 5 HOH B 69 630 149 HOH WAT . J 5 HOH B 70 631 150 HOH WAT . J 5 HOH B 71 632 154 HOH WAT . J 5 HOH B 72 633 155 HOH WAT . J 5 HOH B 73 634 156 HOH WAT . J 5 HOH B 74 635 157 HOH WAT . J 5 HOH B 75 636 158 HOH WAT . J 5 HOH B 76 637 161 HOH WAT . J 5 HOH B 77 638 163 HOH WAT . J 5 HOH B 78 639 165 HOH WAT . J 5 HOH B 79 640 167 HOH WAT . J 5 HOH B 80 641 168 HOH WAT . J 5 HOH B 81 642 173 HOH WAT . J 5 HOH B 82 643 174 HOH WAT . J 5 HOH B 83 644 176 HOH WAT . J 5 HOH B 84 645 178 HOH WAT . J 5 HOH B 85 646 180 HOH WAT . J 5 HOH B 86 647 181 HOH WAT . J 5 HOH B 87 648 182 HOH WAT . J 5 HOH B 88 649 185 HOH WAT . J 5 HOH B 89 650 187 HOH WAT . J 5 HOH B 90 651 190 HOH WAT . J 5 HOH B 91 652 191 HOH WAT . J 5 HOH B 92 653 193 HOH WAT . J 5 HOH B 93 654 196 HOH WAT . J 5 HOH B 94 655 199 HOH WAT . J 5 HOH B 95 656 200 HOH WAT . J 5 HOH B 96 657 203 HOH WAT . J 5 HOH B 97 658 205 HOH WAT . # 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 KR1 . . . C 2 9.777 10.611 22.432 1 44.71 ? C1 KR1 701 A 1 HETATM 2 F F1 KR1 . . . C 2 4.64 7.066 17.535 1 42.05 ? F1 KR1 701 A 1 HETATM 3 N N1 KR1 . . . C 2 9.762 9.952 23.444 1 43.77 ? N1 KR1 701 A 1 HETATM 4 O O1 KR1 . . . C 2 8.966 9.94 17.35 1 48.5 ? O1 KR1 701 A 1 HETATM 5 C C2 KR1 . . . C 2 10.062 12.889 21.384 1 43.07 ? C2 KR1 701 A 1 HETATM 6 N N2 KR1 . . . C 2 8.631 13.237 13.825 1 37.84 ? N2 KR1 701 A 1 HETATM 7 O O2 KR1 . . . C 2 10.886 13.675 13.463 1 34.41 ? O2 KR1 701 A 1 HETATM 8 C C3 KR1 . . . C 2 9.776 11.46 21.244 1 44.89 ? C3 KR1 701 A 1 HETATM 9 N N3 KR1 . . . C 2 7.776 12.052 15.735 1 42.18 ? N3 KR1 701 A 1 HETATM 10 O O3 KR1 . . . C 2 6.343 12.839 14.104 1 44.8 ? O3 KR1 701 A 1 HETATM 11 C C4 KR1 . . . C 2 9.491 10.899 19.971 1 42.92 ? C4 KR1 701 A 1 HETATM 12 N N4 KR1 . . . C 2 6.393 7.635 13.142 1 40.01 ? N4 KR1 701 A 1 HETATM 13 C C5 KR1 . . . C 2 9.497 11.786 18.82 1 45.47 ? C5 KR1 701 A 1 HETATM 14 N N5 KR1 . . . C 2 5.563 7.484 15.349 1 39.79 ? N5 KR1 701 A 1 HETATM 15 C C6 KR1 . . . C 2 9.783 13.225 18.985 1 42.55 ? C6 KR1 701 A 1 HETATM 16 C C7 KR1 . . . C 2 10.068 13.754 20.251 1 43.33 ? C7 KR1 701 A 1 HETATM 17 C C8 KR1 . . . C 2 9.202 11.2 17.489 1 44.58 ? C8 KR1 701 A 1 HETATM 18 C C9 KR1 . . . C 2 9.153 11.921 16.222 1 42.34 ? C9 KR1 701 A 1 HETATM 19 C C10 KR1 . . . C 2 10.381 15.282 20.389 1 43.67 ? C10 KR1 701 A 1 HETATM 20 C C11 KR1 . . . C 2 10.278 12.431 15.529 1 38.95 ? C11 KR1 701 A 1 HETATM 21 C C12 KR1 . . . C 2 9.993 13.146 14.231 1 37.51 ? C12 KR1 701 A 1 HETATM 22 C C13 KR1 . . . C 2 7.533 12.727 14.523 1 40.3 ? C13 KR1 701 A 1 HETATM 23 C C14 KR1 . . . C 2 11.75 12.323 15.989 1 37.73 ? C14 KR1 701 A 1 HETATM 24 C C15 KR1 . . . C 2 12.653 11.579 14.909 1 35.5 ? C15 KR1 701 A 1 HETATM 25 C C16 KR1 . . . C 2 12.327 13.7 16.291 1 38.11 ? C16 KR1 701 A 1 HETATM 26 C C17 KR1 . . . C 2 6.526 11.541 16.384 1 40.65 ? C17 KR1 701 A 1 HETATM 27 C C18 KR1 . . . C 2 6.186 10.089 16.016 1 42.27 ? C18 KR1 701 A 1 HETATM 28 C C19 KR1 . . . C 2 6.496 9.554 14.654 1 41.07 ? C19 KR1 701 A 1 HETATM 29 C C20 KR1 . . . C 2 6.155 8.221 14.377 1 40.77 ? C20 KR1 701 A 1 HETATM 30 C C21 KR1 . . . C 2 5.256 7.928 16.625 1 41.39 ? C21 KR1 701 A 1 HETATM 31 C C22 KR1 . . . C 2 5.547 9.23 17.01 1 41.8 ? C22 KR1 701 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 344 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 31 #