data_4YKT # _model_server_result.job_id smUAuKfl9W8hmNdl4b3kww _model_server_result.datetime_utc '2024-10-28 02:30:37' _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 4ykt # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 4YKT # _exptl.entry_id 4YKT _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 448.88 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1-(5-chloro-2,4-dihydroxyphenyl)-5-({[dihydroxy(pyridin-3-yl)-lambda~4~-sulfanyl]amino}methyl)-1,3-dihydro-2H-benzimidazol-2-one _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 4YKT _cell.length_a 64.932 _cell.length_b 89.063 _cell.length_c 99.45 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4YKT _symmetry.cell_setting ? _symmetry.Int_Tables_number 23 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 2 2 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _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 B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C19 H17 Cl N4 O5 S' _chem_comp.formula_weight 448.88 _chem_comp.id 4EQ _chem_comp.mon_nstd_flag . _chem_comp.name 1-(5-chloro-2,4-dihydroxyphenyl)-5-({[dihydroxy(pyridin-3-yl)-lambda~4~-sulfanyl]amino}methyl)-1,3-dihydro-2H-benzimidazol-2-one _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 O5 S 4EQ sing 1 n n S O4 4EQ sing 2 n n S C12 4EQ sing 3 n n S N3 4EQ sing 4 n n C12 C16 4EQ doub 5 n y C12 C13 4EQ sing 6 n y C16 N4 4EQ sing 7 n y N4 C15 4EQ doub 8 n y C15 C14 4EQ sing 9 n y C14 C13 4EQ doub 10 n y N3 C11 4EQ sing 11 n n C11 C10 4EQ sing 12 n n C10 C9 4EQ doub 13 n y C10 C17 4EQ sing 14 n y C9 C8 4EQ sing 15 n y C17 C18 4EQ doub 16 n y C18 C19 4EQ sing 17 n y C19 C8 4EQ doub 18 n y C19 N1 4EQ sing 19 n n C8 N2 4EQ sing 20 n n N2 C7 4EQ sing 21 n n C7 O3 4EQ doub 22 n n C7 N1 4EQ sing 23 n n N1 C4 4EQ sing 24 n n C4 C5 4EQ doub 25 n y C4 C3 4EQ sing 26 n y C5 C6 4EQ sing 27 n y C6 CL 4EQ sing 28 n n C6 C1 4EQ doub 29 n y C3 O2 4EQ sing 30 n n C3 C2 4EQ doub 31 n y C2 C1 4EQ sing 32 n y C1 O1 4EQ sing 33 n n O5 H16 4EQ sing 34 n n O4 H17 4EQ sing 35 n n C16 H13 4EQ sing 36 n n C15 H12 4EQ sing 37 n n C14 H11 4EQ sing 38 n n C13 H10 4EQ sing 39 n n N3 H9 4EQ sing 40 n n C11 H7 4EQ sing 41 n n C11 H8 4EQ sing 42 n n C9 H6 4EQ sing 43 n n C17 H14 4EQ sing 44 n n C18 H15 4EQ sing 45 n n N2 H5 4EQ sing 46 n n C5 H4 4EQ sing 47 n n O2 H3 4EQ sing 48 n n C2 H2 4EQ sing 49 n n O1 H1 4EQ sing 50 n n # _atom_sites.entry_id 4YKT _atom_sites.fract_transf_matrix[1][1] 0.015401 _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] 0.011228 _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] 0.010055 _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 4EQ A 1 301 1 4EQ UNL . C 3 HOH A 1 401 75 HOH HOH . C 3 HOH A 2 402 7 HOH HOH . C 3 HOH A 3 403 126 HOH HOH . C 3 HOH A 4 404 26 HOH HOH . C 3 HOH A 5 405 179 HOH HOH . C 3 HOH A 6 406 25 HOH HOH . C 3 HOH A 7 407 180 HOH HOH . C 3 HOH A 8 408 185 HOH HOH . C 3 HOH A 9 409 181 HOH HOH . C 3 HOH A 10 410 31 HOH HOH . C 3 HOH A 11 411 190 HOH HOH . C 3 HOH A 12 412 169 HOH HOH . C 3 HOH A 13 413 37 HOH HOH . C 3 HOH A 14 414 87 HOH HOH . C 3 HOH A 15 415 141 HOH HOH . C 3 HOH A 16 416 182 HOH HOH . C 3 HOH A 17 417 21 HOH HOH . C 3 HOH A 18 418 110 HOH HOH . C 3 HOH A 19 419 159 HOH HOH . C 3 HOH A 20 420 35 HOH HOH . C 3 HOH A 21 421 58 HOH HOH . C 3 HOH A 22 422 29 HOH HOH . C 3 HOH A 23 423 33 HOH HOH . C 3 HOH A 24 424 56 HOH HOH . C 3 HOH A 25 425 165 HOH HOH . C 3 HOH A 26 426 188 HOH HOH . C 3 HOH A 27 427 88 HOH HOH . C 3 HOH A 28 428 4 HOH HOH . C 3 HOH A 29 429 13 HOH HOH . C 3 HOH A 30 430 32 HOH HOH . C 3 HOH A 31 431 121 HOH HOH . C 3 HOH A 32 432 10 HOH HOH . C 3 HOH A 33 433 23 HOH HOH . C 3 HOH A 34 434 11 HOH HOH . C 3 HOH A 35 435 19 HOH HOH . C 3 HOH A 36 436 175 HOH HOH . C 3 HOH A 37 437 41 HOH HOH . C 3 HOH A 38 438 16 HOH HOH . C 3 HOH A 39 439 43 HOH HOH . C 3 HOH A 40 440 120 HOH HOH . C 3 HOH A 41 441 22 HOH HOH . C 3 HOH A 42 442 123 HOH HOH . C 3 HOH A 43 443 94 HOH HOH . C 3 HOH A 44 444 122 HOH HOH . C 3 HOH A 45 445 60 HOH HOH . C 3 HOH A 46 446 92 HOH HOH . C 3 HOH A 47 447 183 HOH HOH . C 3 HOH A 48 448 39 HOH HOH . C 3 HOH A 49 449 125 HOH HOH . C 3 HOH A 50 450 86 HOH HOH . C 3 HOH A 51 451 55 HOH HOH . C 3 HOH A 52 452 95 HOH HOH . C 3 HOH A 53 453 189 HOH HOH . C 3 HOH A 54 454 176 HOH HOH . C 3 HOH A 55 455 155 HOH HOH . C 3 HOH A 56 456 49 HOH HOH . C 3 HOH A 57 457 117 HOH HOH . C 3 HOH A 58 458 107 HOH HOH . C 3 HOH A 59 459 187 HOH HOH . C 3 HOH A 60 460 144 HOH HOH . C 3 HOH A 61 461 44 HOH HOH . C 3 HOH A 62 462 8 HOH HOH . C 3 HOH A 63 463 73 HOH HOH . C 3 HOH A 64 464 127 HOH HOH . C 3 HOH A 65 465 51 HOH HOH . C 3 HOH A 66 466 111 HOH HOH . C 3 HOH A 67 467 34 HOH HOH . C 3 HOH A 68 468 103 HOH HOH . C 3 HOH A 69 469 76 HOH HOH . C 3 HOH A 70 470 40 HOH HOH . C 3 HOH A 71 471 12 HOH HOH . C 3 HOH A 72 472 5 HOH HOH . C 3 HOH A 73 473 62 HOH HOH . C 3 HOH A 74 474 59 HOH HOH . C 3 HOH A 75 475 171 HOH HOH . C 3 HOH A 76 476 149 HOH HOH . C 3 HOH A 77 477 9 HOH HOH . C 3 HOH A 78 478 99 HOH HOH . C 3 HOH A 79 479 152 HOH HOH . C 3 HOH A 80 480 30 HOH HOH . C 3 HOH A 81 481 53 HOH HOH . C 3 HOH A 82 482 128 HOH HOH . C 3 HOH A 83 483 118 HOH HOH . C 3 HOH A 84 484 14 HOH HOH . C 3 HOH A 85 485 89 HOH HOH . C 3 HOH A 86 486 168 HOH HOH . C 3 HOH A 87 487 2 HOH HOH . C 3 HOH A 88 488 137 HOH HOH . C 3 HOH A 89 489 6 HOH HOH . C 3 HOH A 90 490 66 HOH HOH . C 3 HOH A 91 491 61 HOH HOH . C 3 HOH A 92 492 97 HOH HOH . C 3 HOH A 93 493 20 HOH HOH . C 3 HOH A 94 494 24 HOH HOH . C 3 HOH A 95 495 38 HOH HOH . C 3 HOH A 96 496 148 HOH HOH . C 3 HOH A 97 497 17 HOH HOH . C 3 HOH A 98 498 42 HOH HOH . C 3 HOH A 99 499 70 HOH HOH . C 3 HOH A 100 500 146 HOH HOH . C 3 HOH A 101 501 158 HOH HOH . C 3 HOH A 102 502 54 HOH HOH . C 3 HOH A 103 503 151 HOH HOH . C 3 HOH A 104 504 69 HOH HOH . C 3 HOH A 105 505 50 HOH HOH . C 3 HOH A 106 506 136 HOH HOH . C 3 HOH A 107 507 52 HOH HOH . C 3 HOH A 108 508 139 HOH HOH . C 3 HOH A 109 509 45 HOH HOH . C 3 HOH A 110 510 79 HOH HOH . C 3 HOH A 111 511 64 HOH HOH . C 3 HOH A 112 512 177 HOH HOH . C 3 HOH A 113 513 18 HOH HOH . C 3 HOH A 114 514 85 HOH HOH . C 3 HOH A 115 515 47 HOH HOH . C 3 HOH A 116 516 65 HOH HOH . C 3 HOH A 117 517 90 HOH HOH . C 3 HOH A 118 518 109 HOH HOH . C 3 HOH A 119 519 74 HOH HOH . C 3 HOH A 120 520 93 HOH HOH . C 3 HOH A 121 521 161 HOH HOH . C 3 HOH A 122 522 77 HOH HOH . C 3 HOH A 123 523 15 HOH HOH . C 3 HOH A 124 524 1 HOH HOH . C 3 HOH A 125 525 98 HOH HOH . C 3 HOH A 126 526 36 HOH HOH . C 3 HOH A 127 527 112 HOH HOH . C 3 HOH A 128 528 67 HOH HOH . C 3 HOH A 129 529 140 HOH HOH . C 3 HOH A 130 530 27 HOH HOH . C 3 HOH A 131 531 138 HOH HOH . C 3 HOH A 132 532 72 HOH HOH . C 3 HOH A 133 533 124 HOH HOH . C 3 HOH A 134 534 150 HOH HOH . C 3 HOH A 135 535 100 HOH HOH . C 3 HOH A 136 536 104 HOH HOH . C 3 HOH A 137 537 184 HOH HOH . C 3 HOH A 138 538 119 HOH HOH . C 3 HOH A 139 539 28 HOH HOH . C 3 HOH A 140 540 174 HOH HOH . C 3 HOH A 141 541 81 HOH HOH . C 3 HOH A 142 542 130 HOH HOH . C 3 HOH A 143 543 3 HOH HOH . C 3 HOH A 144 544 68 HOH HOH . C 3 HOH A 145 545 147 HOH HOH . C 3 HOH A 146 546 186 HOH HOH . C 3 HOH A 147 547 114 HOH HOH . C 3 HOH A 148 548 133 HOH HOH . C 3 HOH A 149 549 57 HOH HOH . C 3 HOH A 150 550 63 HOH HOH . C 3 HOH A 151 551 113 HOH HOH . C 3 HOH A 152 552 163 HOH HOH . C 3 HOH A 153 553 91 HOH HOH . C 3 HOH A 154 554 102 HOH HOH . C 3 HOH A 155 555 46 HOH HOH . C 3 HOH A 156 556 106 HOH HOH . C 3 HOH A 157 557 143 HOH HOH . C 3 HOH A 158 558 145 HOH HOH . C 3 HOH A 159 559 116 HOH HOH . C 3 HOH A 160 560 115 HOH HOH . C 3 HOH A 161 561 82 HOH HOH . C 3 HOH A 162 562 157 HOH HOH . C 3 HOH A 163 563 131 HOH HOH . C 3 HOH A 164 564 154 HOH HOH . C 3 HOH A 165 565 129 HOH HOH . C 3 HOH A 166 566 48 HOH HOH . C 3 HOH A 167 567 71 HOH HOH . C 3 HOH A 168 568 135 HOH HOH . C 3 HOH A 169 569 80 HOH HOH . C 3 HOH A 170 570 84 HOH HOH . C 3 HOH A 171 571 134 HOH HOH . C 3 HOH A 172 572 142 HOH HOH . C 3 HOH A 173 573 105 HOH HOH . C 3 HOH A 174 574 96 HOH HOH . C 3 HOH A 175 575 101 HOH HOH . C 3 HOH A 176 576 108 HOH HOH . C 3 HOH A 177 577 172 HOH HOH . C 3 HOH A 178 578 178 HOH HOH . C 3 HOH A 179 579 160 HOH HOH . C 3 HOH A 180 580 78 HOH HOH . C 3 HOH A 181 581 166 HOH HOH . C 3 HOH A 182 582 153 HOH HOH . C 3 HOH A 183 583 170 HOH HOH . C 3 HOH A 184 584 167 HOH HOH . C 3 HOH A 185 585 132 HOH HOH . C 3 HOH A 186 586 83 HOH HOH . C 3 HOH A 187 587 162 HOH HOH . C 3 HOH A 188 588 173 HOH HOH . C 3 HOH A 189 589 156 HOH HOH . C 3 HOH A 190 590 164 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 O O5 4EQ . . . B 2 -1.68 -41.58 -30.214 1 51.81 ? O5 4EQ 301 A 1 HETATM 2 S S 4EQ . . . B 2 -1.194 -41.909 -28.909 1 49.07 ? S 4EQ 301 A 1 HETATM 3 O O4 4EQ . . . B 2 -0.269 -42.99 -28.746 1 47.57 ? O4 4EQ 301 A 1 HETATM 4 C C12 4EQ . . . B 2 -2.592 -42.221 -27.881 1 47.52 ? C12 4EQ 301 A 1 HETATM 5 C C16 4EQ . . . B 2 -2.679 -43.314 -27.048 1 45.86 ? C16 4EQ 301 A 1 HETATM 6 N N4 4EQ . . . B 2 -3.732 -43.587 -26.27 1 45.15 ? N4 4EQ 301 A 1 HETATM 7 C C15 4EQ . . . B 2 -4.751 -42.725 -26.304 1 47.91 ? C15 4EQ 301 A 1 HETATM 8 C C14 4EQ . . . B 2 -4.758 -41.594 -27.094 1 49.48 ? C14 4EQ 301 A 1 HETATM 9 C C13 4EQ . . . B 2 -3.664 -41.339 -27.905 1 48.9 ? C13 4EQ 301 A 1 HETATM 10 N N3 4EQ . . . B 2 -0.467 -40.588 -28.332 1 41.47 ? N3 4EQ 301 A 1 HETATM 11 C C11 4EQ . . . B 2 0.359 -40.642 -27.111 1 37.57 ? C11 4EQ 301 A 1 HETATM 12 C C10 4EQ . . . B 2 0.913 -39.292 -26.722 1 34.07 ? C10 4EQ 301 A 1 HETATM 13 C C9 4EQ . . . B 2 1.466 -38.475 -27.703 1 29.87 ? C9 4EQ 301 A 1 HETATM 14 C C17 4EQ . . . B 2 0.72 -38.772 -25.442 1 30.59 ? C17 4EQ 301 A 1 HETATM 15 C C18 4EQ . . . B 2 1.006 -37.446 -25.152 1 28.82 ? C18 4EQ 301 A 1 HETATM 16 C C19 4EQ . . . B 2 1.505 -36.637 -26.169 1 27.04 ? C19 4EQ 301 A 1 HETATM 17 C C8 4EQ . . . B 2 1.747 -37.139 -27.446 1 28.62 ? C8 4EQ 301 A 1 HETATM 18 N N2 4EQ . . . B 2 2.215 -36.095 -28.226 1 25.87 ? N2 4EQ 301 A 1 HETATM 19 C C7 4EQ . . . B 2 2.284 -34.949 -27.49 1 26.56 ? C7 4EQ 301 A 1 HETATM 20 O O3 4EQ . . . B 2 2.655 -33.843 -27.864 1 25.13 ? O3 4EQ 301 A 1 HETATM 21 N N1 4EQ . . . B 2 1.839 -35.283 -26.187 1 26.63 ? N1 4EQ 301 A 1 HETATM 22 C C4 4EQ . . . B 2 1.741 -34.365 -25.087 1 24.98 ? C4 4EQ 301 A 1 HETATM 23 C C5 4EQ . . . B 2 0.47 -34.085 -24.607 1 25.01 ? C5 4EQ 301 A 1 HETATM 24 C C6 4EQ . . . B 2 0.338 -33.249 -23.519 1 27.04 ? C6 4EQ 301 A 1 HETATM 25 CL CL 4EQ . . . B 2 -1.257 -32.75 -23.034 1 32.05 ? CL 4EQ 301 A 1 HETATM 26 C C3 4EQ . . . B 2 2.871 -33.805 -24.494 1 23.96 ? C3 4EQ 301 A 1 HETATM 27 O O2 4EQ . . . B 2 4.117 -34.122 -24.935 1 25.68 ? O2 4EQ 301 A 1 HETATM 28 C C2 4EQ . . . B 2 2.718 -32.983 -23.392 1 25.55 ? C2 4EQ 301 A 1 HETATM 29 C C1 4EQ . . . B 2 1.454 -32.702 -22.881 1 24.91 ? C1 4EQ 301 A 1 HETATM 30 O O1 4EQ . . . B 2 1.308 -32.091 -21.681 1 25.42 ? O1 4EQ 301 A 1 HETATM 31 H H13 4EQ . . . B 2 -1.872 -44.042 -26.972 0 45.83 ? H13 4EQ 301 A 1 HETATM 32 H H12 4EQ . . . B 2 -5.59 -42.968 -25.656 0 47.96 ? H12 4EQ 301 A 1 HETATM 33 H H11 4EQ . . . B 2 -5.603 -40.907 -27.072 0 49.79 ? H11 4EQ 301 A 1 HETATM 34 H H10 4EQ . . . B 2 -3.646 -40.461 -28.547 0 49.09 ? H10 4EQ 301 A 1 HETATM 35 H H9 4EQ . . . B 2 -0.561 -39.669 -28.75 0 41.57 ? H9 4EQ 301 A 1 HETATM 36 H H7 4EQ . . . B 2 -0.194 -41.094 -26.289 0 37.59 ? H7 4EQ 301 A 1 HETATM 37 H H8 4EQ . . . B 2 1.198 -41.319 -27.262 0 37.59 ? H8 4EQ 301 A 1 HETATM 38 H H6 4EQ . . . B 2 1.661 -38.874 -28.696 0 29.99 ? H6 4EQ 301 A 1 HETATM 39 H H14 4EQ . . . B 2 0.347 -39.409 -24.642 0 30.49 ? H14 4EQ 301 A 1 HETATM 40 H H15 4EQ . . . B 2 0.844 -37.046 -24.152 0 28.49 ? H15 4EQ 301 A 1 HETATM 41 H H5 4EQ . . . B 2 2.443 -36.164 -29.211 0 25.81 ? H5 4EQ 301 A 1 HETATM 42 H H4 4EQ . . . B 2 -0.417 -34.497 -25.087 0 24.72 ? H4 4EQ 301 A 1 HETATM 43 H H3 4EQ . . . B 2 4.233 -33.785 -25.861 0 25.55 ? H3 4EQ 301 A 1 HETATM 44 H H2 4EQ . . . B 2 3.588 -32.535 -22.914 0 25.29 ? H2 4EQ 301 A 1 HETATM 45 H H1 4EQ . . . B 2 2.111 -31.552 -21.454 0 25.25 ? H1 4EQ 301 A 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 333 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 45 #