data_5KGD # _model_server_result.job_id 4_H7ijV4F3JTb1Gv9VReXw _model_server_result.datetime_utc '2024-12-02 14:53:42' _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 5kgd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"U","auth_seq_id":420}' # _entry.id 5KGD # _exptl.entry_id 5KGD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 195.22 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-pyridin-3-yl-1~{H}-benzimidazole _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 120 _cell.entry_id 5KGD _cell.length_a 97.585 _cell.length_b 97.585 _cell.length_c 80.962 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5KGD _symmetry.cell_setting ? _symmetry.Int_Tables_number 170 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65' # _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,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X _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 U _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C12 H9 N3' _chem_comp.formula_weight 195.22 _chem_comp.id 6SL _chem_comp.mon_nstd_flag . _chem_comp.name 2-pyridin-3-yl-1~{H}-benzimidazole _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 C10 C9 6SL doub 1 n y C10 C11 6SL sing 2 n y C9 C8 6SL sing 3 n y N1 C5 6SL sing 4 n y N1 C7 6SL doub 5 n y C6 C5 6SL doub 6 n y C6 C1 6SL sing 7 n y C11 N3 6SL doub 8 n y C5 C4 6SL sing 9 n y C8 C7 6SL sing 10 n n C8 C12 6SL doub 11 n y C7 N2 6SL sing 12 n y C1 C2 6SL doub 13 n y N3 C12 6SL sing 14 n y C4 N2 6SL sing 15 n y C4 C3 6SL doub 16 n y C2 C3 6SL sing 17 n y C1 H1 6SL sing 18 n n C2 H2 6SL sing 19 n n C3 H3 6SL sing 20 n n C9 H4 6SL sing 21 n n C10 H5 6SL sing 22 n n C11 H6 6SL sing 23 n n C12 H7 6SL sing 24 n n N2 H8 6SL sing 25 n n C6 H10 6SL sing 26 n n # _atom_sites.entry_id 5KGD _atom_sites.fract_transf_matrix[1][1] 0.010247 _atom_sites.fract_transf_matrix[1][2] 0.005916 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011833 _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] 0.012351 _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 EDO A 1 401 1 EDO EDO . C 2 EDO A 1 402 2 EDO EDO . D 2 EDO A 1 403 3 EDO EDO . E 2 EDO A 1 404 4 EDO EDO . F 2 EDO A 1 405 5 EDO EDO . G 2 EDO A 1 406 6 EDO EDO . H 2 EDO A 1 407 7 EDO EDO . I 2 EDO A 1 408 8 EDO EDO . J 2 EDO A 1 409 9 EDO EDO . K 2 EDO A 1 410 10 EDO EDO . L 2 EDO A 1 411 11 EDO EDO . M 2 EDO A 1 412 12 EDO EDO . N 2 EDO A 1 413 13 EDO EDO . O 2 EDO A 1 414 14 EDO EDO . P 2 EDO A 1 415 15 EDO EDO . Q 2 EDO A 1 416 16 EDO EDO . R 2 EDO A 1 417 17 EDO EDO . S 2 EDO A 1 418 19 EDO EDO . T 2 EDO A 1 419 20 EDO EDO . U 3 6SL A 1 420 1 6SL INH . V 4 SO4 A 1 421 1 SO4 SO4 . W 4 SO4 A 1 422 2 SO4 SO4 . X 5 HOH A 1 501 20 HOH HOH . X 5 HOH A 2 502 95 HOH HOH . X 5 HOH A 3 503 121 HOH HOH . X 5 HOH A 4 504 28 HOH HOH . X 5 HOH A 5 505 91 HOH HOH . X 5 HOH A 6 506 124 HOH HOH . X 5 HOH A 7 507 112 HOH HOH . X 5 HOH A 8 508 93 HOH HOH . X 5 HOH A 9 509 70 HOH HOH . X 5 HOH A 10 510 39 HOH HOH . X 5 HOH A 11 511 2 HOH HOH . X 5 HOH A 12 512 7 HOH HOH . X 5 HOH A 13 513 34 HOH HOH . X 5 HOH A 14 514 36 HOH HOH . X 5 HOH A 15 515 26 HOH HOH . X 5 HOH A 16 516 6 HOH HOH . X 5 HOH A 17 517 100 HOH HOH . X 5 HOH A 18 518 13 HOH HOH . X 5 HOH A 19 519 8 HOH HOH . X 5 HOH A 20 520 128 HOH HOH . X 5 HOH A 21 521 21 HOH HOH . X 5 HOH A 22 522 90 HOH HOH . X 5 HOH A 23 523 56 HOH HOH . X 5 HOH A 24 524 125 HOH HOH . X 5 HOH A 25 525 40 HOH HOH . X 5 HOH A 26 526 58 HOH HOH . X 5 HOH A 27 527 65 HOH HOH . X 5 HOH A 28 528 35 HOH HOH . X 5 HOH A 29 529 55 HOH HOH . X 5 HOH A 30 530 80 HOH HOH . X 5 HOH A 31 531 29 HOH HOH . X 5 HOH A 32 532 108 HOH HOH . X 5 HOH A 33 533 27 HOH HOH . X 5 HOH A 34 534 75 HOH HOH . X 5 HOH A 35 535 87 HOH HOH . X 5 HOH A 36 536 105 HOH HOH . X 5 HOH A 37 537 82 HOH HOH . X 5 HOH A 38 538 32 HOH HOH . X 5 HOH A 39 539 119 HOH HOH . X 5 HOH A 40 540 37 HOH HOH . X 5 HOH A 41 541 98 HOH HOH . X 5 HOH A 42 542 4 HOH HOH . X 5 HOH A 43 543 84 HOH HOH . X 5 HOH A 44 544 61 HOH HOH . X 5 HOH A 45 545 111 HOH HOH . X 5 HOH A 46 546 101 HOH HOH . X 5 HOH A 47 547 68 HOH HOH . X 5 HOH A 48 548 78 HOH HOH . X 5 HOH A 49 549 51 HOH HOH . X 5 HOH A 50 550 47 HOH HOH . X 5 HOH A 51 551 15 HOH HOH . X 5 HOH A 52 552 96 HOH HOH . X 5 HOH A 53 553 118 HOH HOH . X 5 HOH A 54 554 89 HOH HOH . X 5 HOH A 55 555 85 HOH HOH . X 5 HOH A 56 556 1 HOH HOH . X 5 HOH A 57 557 9 HOH HOH . X 5 HOH A 58 558 69 HOH HOH . X 5 HOH A 59 559 64 HOH HOH . X 5 HOH A 60 560 106 HOH HOH . X 5 HOH A 61 561 11 HOH HOH . X 5 HOH A 62 562 31 HOH HOH . X 5 HOH A 63 563 30 HOH HOH . X 5 HOH A 64 564 109 HOH HOH . X 5 HOH A 65 565 23 HOH HOH . X 5 HOH A 66 566 22 HOH HOH . X 5 HOH A 67 567 83 HOH HOH . X 5 HOH A 68 568 24 HOH HOH . X 5 HOH A 69 569 53 HOH HOH . X 5 HOH A 70 570 45 HOH HOH . X 5 HOH A 71 571 43 HOH HOH . X 5 HOH A 72 572 72 HOH HOH . X 5 HOH A 73 573 115 HOH HOH . X 5 HOH A 74 574 3 HOH HOH . X 5 HOH A 75 575 99 HOH HOH . X 5 HOH A 76 576 73 HOH HOH . X 5 HOH A 77 577 49 HOH HOH . X 5 HOH A 78 578 97 HOH HOH . X 5 HOH A 79 579 107 HOH HOH . X 5 HOH A 80 580 12 HOH HOH . X 5 HOH A 81 581 63 HOH HOH . X 5 HOH A 82 582 17 HOH HOH . X 5 HOH A 83 583 50 HOH HOH . X 5 HOH A 84 584 116 HOH HOH . X 5 HOH A 85 585 57 HOH HOH . X 5 HOH A 86 586 52 HOH HOH . X 5 HOH A 87 587 18 HOH HOH . X 5 HOH A 88 588 103 HOH HOH . X 5 HOH A 89 589 104 HOH HOH . X 5 HOH A 90 590 88 HOH HOH . X 5 HOH A 91 591 92 HOH HOH . X 5 HOH A 92 592 38 HOH HOH . X 5 HOH A 93 593 5 HOH HOH . X 5 HOH A 94 594 79 HOH HOH . X 5 HOH A 95 595 76 HOH HOH . X 5 HOH A 96 596 41 HOH HOH . X 5 HOH A 97 597 122 HOH HOH . X 5 HOH A 98 598 10 HOH HOH . X 5 HOH A 99 599 60 HOH HOH . X 5 HOH A 100 600 117 HOH HOH . X 5 HOH A 101 601 62 HOH HOH . X 5 HOH A 102 602 74 HOH HOH . X 5 HOH A 103 603 33 HOH HOH . X 5 HOH A 104 604 127 HOH HOH . X 5 HOH A 105 605 25 HOH HOH . X 5 HOH A 106 606 113 HOH HOH . X 5 HOH A 107 607 16 HOH HOH . X 5 HOH A 108 608 46 HOH HOH . X 5 HOH A 109 609 110 HOH HOH . X 5 HOH A 110 610 102 HOH HOH . X 5 HOH A 111 611 77 HOH HOH . X 5 HOH A 112 612 81 HOH HOH . X 5 HOH A 113 613 42 HOH HOH . X 5 HOH A 114 614 67 HOH HOH . X 5 HOH A 115 615 114 HOH HOH . X 5 HOH A 116 616 86 HOH HOH . X 5 HOH A 117 617 66 HOH HOH . X 5 HOH A 118 618 126 HOH HOH . X 5 HOH A 119 619 59 HOH HOH . X 5 HOH A 120 620 94 HOH HOH . X 5 HOH A 121 621 19 HOH HOH . X 5 HOH A 122 622 71 HOH HOH . X 5 HOH A 123 623 123 HOH HOH . X 5 HOH A 124 624 14 HOH HOH . X 5 HOH A 125 625 120 HOH HOH . X 5 HOH A 126 626 48 HOH HOH . X 5 HOH A 127 627 54 HOH HOH . X 5 HOH A 128 628 44 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 6SL . . . U 3 25.368 46.365 -0.219 1 38.9 ? C1 6SL 420 A 1 HETATM 2 C C2 6SL . . . U 3 25.257 46.677 1.142 1 40.66 ? C2 6SL 420 A 1 HETATM 3 C C3 6SL . . . U 3 25.583 47.947 1.615 1 36.58 ? C3 6SL 420 A 1 HETATM 4 C C7 6SL . . . U 3 26.649 50.693 -0.325 1 39.25 ? C7 6SL 420 A 1 HETATM 5 C C8 6SL . . . U 3 27.052 52.072 -0.619 1 42.43 ? C8 6SL 420 A 1 HETATM 6 C C9 6SL . . . U 3 26.988 52.576 -1.911 1 47.37 ? C9 6SL 420 A 1 HETATM 7 C C10 6SL . . . U 3 27.308 53.897 -2.146 1 49.1 ? C10 6SL 420 A 1 HETATM 8 C C11 6SL . . . U 3 27.697 54.674 -1.074 1 49.48 ? C11 6SL 420 A 1 HETATM 9 C C12 6SL . . . U 3 27.448 52.938 0.389 1 44.5 ? C12 6SL 420 A 1 HETATM 10 N N3 6SL . . . U 3 27.766 54.22 0.182 1 47.23 ? N3 6SL 420 A 1 HETATM 11 N N2 6SL . . . U 3 26.344 50.245 0.885 1 37.83 ? N2 6SL 420 A 1 HETATM 12 C C4 6SL . . . U 3 26.014 48.903 0.697 1 36.45 ? C4 6SL 420 A 1 HETATM 13 N N1 6SL . . . U 3 26.536 49.732 -1.285 1 35.63 ? N1 6SL 420 A 1 HETATM 14 C C5 6SL . . . U 3 26.132 48.572 -0.653 1 34.8 ? C5 6SL 420 A 1 HETATM 15 C C6 6SL . . . U 3 25.817 47.31 -1.134 1 37.23 ? C6 6SL 420 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 312 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 15 #