data_3S41 # _model_server_result.job_id b6jUf7h3B_3YE0vku1vSOg _model_server_result.datetime_utc '2024-11-23 07:28:37' _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 3s41 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":4000}' # _entry.id 3S41 # _exptl.entry_id 3S41 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 432.432 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description N,N-dimethyl-5-({2-methyl-6-[(5-methylpyrazin-2-yl)carbamoyl]-1-benzofuran-4-yl}oxy)pyrimidine-2-carboxamide _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 3S41 _cell.length_a 67.01 _cell.length_b 82.2 _cell.length_c 86.16 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3S41 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 4 _struct_asym.id D _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 O MET 242 A MET 238 1_555 C NA NA . A NA 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.35 ? metalc ? metalc2 A O VAL 245 A VAL 241 1_555 C NA NA . A NA 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.262 ? metalc ? metalc3 A O VAL 248 A VAL 244 1_555 C NA NA . A NA 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.274 ? metalc ? metalc4 A O GLY 250 A GLY 246 1_555 C NA NA . A NA 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.296 ? # _chem_comp.formula 'C22 H20 N6 O4' _chem_comp.formula_weight 432.432 _chem_comp.id S41 _chem_comp.mon_nstd_flag . _chem_comp.name N,N-dimethyl-5-({2-methyl-6-[(5-methylpyrazin-2-yl)carbamoyl]-1-benzofuran-4-yl}oxy)pyrimidine-2-carboxamide _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 C1 C2 S41 doub 301 n y C1 C6 S41 sing 302 n y C1 O7 S41 sing 303 n y C2 C3 S41 sing 304 n y C2 C9 S41 sing 305 n y C3 C4 S41 doub 306 n y C3 O12 S41 sing 307 n n C4 C5 S41 sing 308 n y C5 C6 S41 doub 309 n y C5 C11 S41 sing 310 n n O7 C8 S41 sing 311 n y C8 C9 S41 doub 312 n y C8 C10 S41 sing 313 n n C11 O13 S41 doub 314 n n C11 N14 S41 sing 315 n n O12 C15 S41 sing 316 n n N14 C26 S41 sing 317 n n C15 C16 S41 doub 318 n y C15 C20 S41 sing 319 n y C16 N17 S41 sing 320 n y N17 C18 S41 doub 321 n y C18 N19 S41 sing 322 n y C18 C21 S41 sing 323 n n N19 C20 S41 doub 324 n y C21 N22 S41 sing 325 n n C21 O23 S41 doub 326 n n N22 C24 S41 sing 327 n n N22 C25 S41 sing 328 n n C26 N27 S41 doub 329 n y C26 C31 S41 sing 330 n y N27 C28 S41 sing 331 n y C28 C29 S41 doub 332 n y C29 N30 S41 sing 333 n y C29 C32 S41 sing 334 n n N30 C31 S41 doub 335 n y C4 H4 S41 sing 336 n n C6 H6 S41 sing 337 n n C9 H9 S41 sing 338 n n C10 H10 S41 sing 339 n n C10 H10A S41 sing 340 n n C10 H10B S41 sing 341 n n N14 HN14 S41 sing 342 n n C16 H16 S41 sing 343 n n C20 H20 S41 sing 344 n n C24 H24 S41 sing 345 n n C24 H24A S41 sing 346 n n C24 H24B S41 sing 347 n n C25 H25 S41 sing 348 n n C25 H25A S41 sing 349 n n C25 H25B S41 sing 350 n n C28 H28 S41 sing 351 n n C31 H31 S41 sing 352 n n C32 H32 S41 sing 353 n n C32 H32A S41 sing 354 n n C32 H32B S41 sing 355 n n # _atom_sites.entry_id 3S41 _atom_sites.fract_transf_matrix[1][1] 0.014923 _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] 0.012165 _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] 0.011606 _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 GLC A 1 500 500 GLC GLC . C 3 NA A 1 600 600 NA NA . D 4 S41 A 1 4000 4000 S41 PFE . E 5 HOH A 1 466 1 HOH HOH . E 5 HOH A 2 467 2 HOH HOH . E 5 HOH A 3 468 3 HOH HOH . E 5 HOH A 4 469 4 HOH HOH . E 5 HOH A 5 470 5 HOH HOH . E 5 HOH A 6 471 6 HOH HOH . E 5 HOH A 7 472 7 HOH HOH . E 5 HOH A 8 473 8 HOH HOH . E 5 HOH A 9 474 9 HOH HOH . E 5 HOH A 10 475 10 HOH HOH . E 5 HOH A 11 476 11 HOH HOH . E 5 HOH A 12 477 13 HOH HOH . E 5 HOH A 13 478 14 HOH HOH . E 5 HOH A 14 479 15 HOH HOH . E 5 HOH A 15 480 16 HOH HOH . E 5 HOH A 16 481 17 HOH HOH . E 5 HOH A 17 482 18 HOH HOH . E 5 HOH A 18 483 19 HOH HOH . E 5 HOH A 19 484 20 HOH HOH . E 5 HOH A 20 485 21 HOH HOH . E 5 HOH A 21 486 22 HOH HOH . E 5 HOH A 22 487 23 HOH HOH . E 5 HOH A 23 488 24 HOH HOH . E 5 HOH A 24 489 25 HOH HOH . E 5 HOH A 25 490 26 HOH HOH . E 5 HOH A 26 491 27 HOH HOH . E 5 HOH A 27 492 28 HOH HOH . E 5 HOH A 28 493 29 HOH HOH . E 5 HOH A 29 494 30 HOH HOH . E 5 HOH A 30 495 31 HOH HOH . E 5 HOH A 31 496 32 HOH HOH . E 5 HOH A 32 497 33 HOH HOH . E 5 HOH A 33 498 34 HOH HOH . E 5 HOH A 34 499 35 HOH HOH . E 5 HOH A 35 501 36 HOH HOH . E 5 HOH A 36 502 37 HOH HOH . E 5 HOH A 37 503 38 HOH HOH . E 5 HOH A 38 504 39 HOH HOH . E 5 HOH A 39 505 40 HOH HOH . E 5 HOH A 40 506 41 HOH HOH . E 5 HOH A 41 507 42 HOH HOH . E 5 HOH A 42 508 43 HOH HOH . E 5 HOH A 43 509 44 HOH HOH . E 5 HOH A 44 510 45 HOH HOH . E 5 HOH A 45 511 46 HOH HOH . E 5 HOH A 46 512 47 HOH HOH . E 5 HOH A 47 513 48 HOH HOH . E 5 HOH A 48 514 49 HOH HOH . E 5 HOH A 49 515 50 HOH HOH . E 5 HOH A 50 516 51 HOH HOH . E 5 HOH A 51 517 52 HOH HOH . E 5 HOH A 52 518 53 HOH HOH . E 5 HOH A 53 519 54 HOH HOH . E 5 HOH A 54 520 55 HOH HOH . E 5 HOH A 55 521 56 HOH HOH . E 5 HOH A 56 522 57 HOH HOH . E 5 HOH A 57 523 58 HOH HOH . E 5 HOH A 58 524 59 HOH HOH . E 5 HOH A 59 525 60 HOH HOH . E 5 HOH A 60 526 61 HOH HOH . E 5 HOH A 61 527 62 HOH HOH . E 5 HOH A 62 528 63 HOH HOH . E 5 HOH A 63 529 64 HOH HOH . E 5 HOH A 64 530 65 HOH HOH . E 5 HOH A 65 531 66 HOH HOH . E 5 HOH A 66 532 67 HOH HOH . E 5 HOH A 67 533 68 HOH HOH . E 5 HOH A 68 534 69 HOH HOH . E 5 HOH A 69 535 70 HOH HOH . E 5 HOH A 70 536 71 HOH HOH . E 5 HOH A 71 537 72 HOH HOH . E 5 HOH A 72 538 73 HOH HOH . E 5 HOH A 73 539 74 HOH HOH . E 5 HOH A 74 540 75 HOH HOH . E 5 HOH A 75 541 76 HOH HOH . E 5 HOH A 76 542 77 HOH HOH . E 5 HOH A 77 543 78 HOH HOH . E 5 HOH A 78 544 79 HOH HOH . E 5 HOH A 79 545 80 HOH HOH . E 5 HOH A 80 546 81 HOH HOH . E 5 HOH A 81 547 82 HOH HOH . E 5 HOH A 82 548 83 HOH HOH . E 5 HOH A 83 549 84 HOH HOH . E 5 HOH A 84 550 85 HOH HOH . E 5 HOH A 85 551 86 HOH HOH . E 5 HOH A 86 552 87 HOH HOH . E 5 HOH A 87 553 88 HOH HOH . E 5 HOH A 88 554 90 HOH HOH . E 5 HOH A 89 555 91 HOH HOH . E 5 HOH A 90 556 92 HOH HOH . E 5 HOH A 91 557 93 HOH HOH . E 5 HOH A 92 558 94 HOH HOH . E 5 HOH A 93 559 95 HOH HOH . E 5 HOH A 94 560 96 HOH HOH . E 5 HOH A 95 561 97 HOH HOH . E 5 HOH A 96 562 98 HOH HOH . E 5 HOH A 97 563 99 HOH HOH . E 5 HOH A 98 564 100 HOH HOH . E 5 HOH A 99 565 101 HOH HOH . E 5 HOH A 100 566 102 HOH HOH . E 5 HOH A 101 567 103 HOH HOH . E 5 HOH A 102 568 104 HOH HOH . E 5 HOH A 103 569 105 HOH HOH . E 5 HOH A 104 570 106 HOH HOH . E 5 HOH A 105 571 107 HOH HOH . E 5 HOH A 106 572 108 HOH HOH . E 5 HOH A 107 573 109 HOH HOH . E 5 HOH A 108 574 110 HOH HOH . E 5 HOH A 109 575 111 HOH HOH . E 5 HOH A 110 576 112 HOH HOH . E 5 HOH A 111 577 113 HOH HOH . E 5 HOH A 112 578 114 HOH HOH . E 5 HOH A 113 579 115 HOH HOH . E 5 HOH A 114 580 116 HOH HOH . E 5 HOH A 115 581 117 HOH HOH . E 5 HOH A 116 582 118 HOH HOH . E 5 HOH A 117 583 119 HOH HOH . E 5 HOH A 118 584 120 HOH HOH . E 5 HOH A 119 585 121 HOH HOH . E 5 HOH A 120 586 122 HOH HOH . E 5 HOH A 121 587 123 HOH HOH . E 5 HOH A 122 588 124 HOH HOH . E 5 HOH A 123 589 125 HOH HOH . E 5 HOH A 124 590 126 HOH HOH . E 5 HOH A 125 591 127 HOH HOH . E 5 HOH A 126 592 128 HOH HOH . E 5 HOH A 127 593 129 HOH HOH . E 5 HOH A 128 594 130 HOH HOH . E 5 HOH A 129 595 131 HOH HOH . E 5 HOH A 130 596 132 HOH HOH . E 5 HOH A 131 597 133 HOH HOH . E 5 HOH A 132 598 134 HOH HOH . E 5 HOH A 133 599 135 HOH HOH . E 5 HOH A 134 601 136 HOH HOH . E 5 HOH A 135 602 137 HOH HOH . E 5 HOH A 136 603 138 HOH HOH . E 5 HOH A 137 604 139 HOH HOH . E 5 HOH A 138 605 140 HOH HOH . E 5 HOH A 139 606 141 HOH HOH . E 5 HOH A 140 607 142 HOH HOH . E 5 HOH A 141 608 143 HOH HOH . E 5 HOH A 142 609 144 HOH HOH . E 5 HOH A 143 610 145 HOH HOH . E 5 HOH A 144 611 146 HOH HOH . E 5 HOH A 145 612 147 HOH HOH . E 5 HOH A 146 613 148 HOH HOH . E 5 HOH A 147 614 149 HOH HOH . E 5 HOH A 148 615 150 HOH HOH . E 5 HOH A 149 616 151 HOH HOH . E 5 HOH A 150 617 152 HOH HOH . E 5 HOH A 151 618 153 HOH HOH . E 5 HOH A 152 619 154 HOH HOH . E 5 HOH A 153 620 155 HOH HOH . E 5 HOH A 154 621 156 HOH HOH . E 5 HOH A 155 622 157 HOH HOH . E 5 HOH A 156 623 158 HOH HOH . E 5 HOH A 157 624 159 HOH HOH . E 5 HOH A 158 625 160 HOH HOH . E 5 HOH A 159 626 161 HOH HOH . E 5 HOH A 160 627 162 HOH HOH . E 5 HOH A 161 628 163 HOH HOH . E 5 HOH A 162 629 164 HOH HOH . E 5 HOH A 163 630 165 HOH HOH . E 5 HOH A 164 631 166 HOH HOH . E 5 HOH A 165 632 167 HOH HOH . E 5 HOH A 166 633 168 HOH HOH . E 5 HOH A 167 634 169 HOH HOH . E 5 HOH A 168 635 170 HOH HOH . E 5 HOH A 169 636 171 HOH HOH . E 5 HOH A 170 637 172 HOH HOH . E 5 HOH A 171 638 173 HOH HOH . E 5 HOH A 172 639 174 HOH HOH . E 5 HOH A 173 640 175 HOH HOH . E 5 HOH A 174 641 176 HOH HOH . E 5 HOH A 175 642 177 HOH HOH . E 5 HOH A 176 643 178 HOH HOH . E 5 HOH A 177 644 179 HOH HOH . E 5 HOH A 178 645 180 HOH HOH . E 5 HOH A 179 646 181 HOH HOH . E 5 HOH A 180 647 182 HOH HOH . E 5 HOH A 181 648 183 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 S41 . . . D 4 -11.267 3.613 20.953 1 30.8 ? C1 S41 4000 A 1 HETATM 2 C C2 S41 . . . D 4 -10.829 4.283 19.781 1 29.71 ? C2 S41 4000 A 1 HETATM 3 C C3 S41 . . . D 4 -9.821 3.738 18.965 1 29.91 ? C3 S41 4000 A 1 HETATM 4 C C4 S41 . . . D 4 -9.286 2.511 19.293 1 28.94 ? C4 S41 4000 A 1 HETATM 5 C C5 S41 . . . D 4 -9.684 1.86 20.477 1 29.95 ? C5 S41 4000 A 1 HETATM 6 C C6 S41 . . . D 4 -10.692 2.392 21.293 1 30.13 ? C6 S41 4000 A 1 HETATM 7 O O7 S41 . . . D 4 -12.209 4.384 21.534 1 29.51 ? O7 S41 4000 A 1 HETATM 8 C C8 S41 . . . D 4 -12.45 5.475 20.779 1 28.92 ? C8 S41 4000 A 1 HETATM 9 C C9 S41 . . . D 4 -11.633 5.498 19.708 1 27.92 ? C9 S41 4000 A 1 HETATM 10 C C10 S41 . . . D 4 -13.464 6.542 21.112 1 27.32 ? C10 S41 4000 A 1 HETATM 11 C C11 S41 . . . D 4 -9.12 0.537 20.776 1 31.97 ? C11 S41 4000 A 1 HETATM 12 O O12 S41 . . . D 4 -9.514 4.366 17.799 1 33.29 ? O12 S41 4000 A 1 HETATM 13 O O13 S41 . . . D 4 -8.537 -0.044 19.883 1 35.9 ? O13 S41 4000 A 1 HETATM 14 N N14 S41 . . . D 4 -9.335 -0.013 21.992 1 29.3 ? N14 S41 4000 A 1 HETATM 15 C C15 S41 . . . D 4 -8.267 4.419 17.254 1 35.24 ? C15 S41 4000 A 1 HETATM 16 C C16 S41 . . . D 4 -7.092 4.38 18.025 1 34.01 ? C16 S41 4000 A 1 HETATM 17 N N17 S41 . . . D 4 -5.919 4.435 17.427 1 33.29 ? N17 S41 4000 A 1 HETATM 18 C C18 S41 . . . D 4 -5.844 4.577 16.107 1 35.77 ? C18 S41 4000 A 1 HETATM 19 N N19 S41 . . . D 4 -6.932 4.656 15.34 1 34.23 ? N19 S41 4000 A 1 HETATM 20 C C20 S41 . . . D 4 -8.138 4.591 15.869 1 34.95 ? C20 S41 4000 A 1 HETATM 21 C C21 S41 . . . D 4 -4.502 4.71 15.469 1 37.55 ? C21 S41 4000 A 1 HETATM 22 N N22 S41 . . . D 4 -3.735 3.604 15.213 1 37.86 ? N22 S41 4000 A 1 HETATM 23 O O23 S41 . . . D 4 -4.128 5.846 15.18 1 34.77 ? O23 S41 4000 A 1 HETATM 24 C C24 S41 . . . D 4 -4.22 2.256 15.546 1 36.06 ? C24 S41 4000 A 1 HETATM 25 C C25 S41 . . . D 4 -2.425 3.741 14.563 1 38.81 ? C25 S41 4000 A 1 HETATM 26 C C26 S41 . . . D 4 -8.927 -1.266 22.44 1 26.28 ? C26 S41 4000 A 1 HETATM 27 N N27 S41 . . . D 4 -9.352 -1.615 23.655 1 27.12 ? N27 S41 4000 A 1 HETATM 28 C C28 S41 . . . D 4 -9.029 -2.808 24.158 1 29.1 ? C28 S41 4000 A 1 HETATM 29 C C29 S41 . . . D 4 -8.238 -3.689 23.419 1 29.83 ? C29 S41 4000 A 1 HETATM 30 N N30 S41 . . . D 4 -7.803 -3.344 22.2 1 27.88 ? N30 S41 4000 A 1 HETATM 31 C C31 S41 . . . D 4 -8.146 -2.161 21.685 1 26.11 ? C31 S41 4000 A 1 HETATM 32 C C32 S41 . . . D 4 -7.901 -5.032 24.013 1 30.14 ? C32 S41 4000 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 408 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 32 #