data_7ODN # _model_server_result.job_id oPl-oaDRTKF90HGmrOiNFw _model_server_result.datetime_utc '2024-11-06 01:55:51' _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 7odn # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":502}' # _entry.id 7ODN # _exptl.entry_id 7ODN _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 295.293 _entity.id 9 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'methyl N-(6-benzoyl-1H-benzimidazol-2-yl)carbamate' _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 97.23 _cell.angle_gamma 90 _cell.entry_id 7ODN _cell.length_a 73.441 _cell.length_b 91.39 _cell.length_c 82.671 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7ODN _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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,K,L,M,N,O,P,Q,R,S _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 9 _struct_asym.id J _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 D O1G GTP . A GTP 501 1_555 E MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.009 ? metalc ? metalc2 D O2B GTP . A GTP 501 1_555 E MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.186 ? metalc ? metalc3 E MG MG . A MG 502 1_555 Q O HOH . A HOH 610 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? metalc ? metalc4 E MG MG . A MG 502 1_555 Q O HOH . A HOH 627 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? metalc ? metalc5 E MG MG . A MG 502 1_555 Q O HOH . A HOH 628 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? metalc ? metalc6 E MG MG . A MG 502 1_555 Q O HOH . A HOH 638 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.088 ? # _chem_comp.formula 'C16 H13 N3 O3' _chem_comp.formula_weight 295.293 _chem_comp.id V95 _chem_comp.mon_nstd_flag . _chem_comp.name 'methyl N-(6-benzoyl-1H-benzimidazol-2-yl)carbamate' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms Mebendazole;4030 # 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 C20 C19 V95 doub 470 n y C20 C21 V95 sing 471 n y C19 C18 V95 sing 472 n y C21 C22 V95 doub 473 n y C18 C17 V95 doub 474 n y C22 C17 V95 sing 475 n y C17 C15 V95 sing 476 n n C15 O16 V95 doub 477 n n C15 C12 V95 sing 478 n n C13 C12 V95 doub 479 n y C13 C14 V95 sing 480 n y C12 C11 V95 sing 481 n y C14 C08 V95 doub 482 n y C11 C09 V95 doub 483 n y C08 C09 V95 sing 484 n y C08 N07 V95 sing 485 n y C09 N10 V95 sing 486 n y N07 C06 V95 doub 487 n y N10 C06 V95 sing 488 n y C06 N05 V95 sing 489 n n N05 C03 V95 sing 490 n n O04 C03 V95 doub 491 n n C03 O02 V95 sing 492 n n O02 C01 V95 sing 493 n n C11 H111 V95 sing 494 n n C01 H012 V95 sing 495 n n C01 H011 V95 sing 496 n n C01 H013 V95 sing 497 n n C13 H131 V95 sing 498 n n C14 H141 V95 sing 499 n n C18 H181 V95 sing 500 n n C19 H191 V95 sing 501 n n C20 H201 V95 sing 502 n n C21 H211 V95 sing 503 n n C22 H221 V95 sing 504 n n N05 H051 V95 sing 505 n n N10 H101 V95 sing 506 n n # _atom_sites.entry_id 7ODN _atom_sites.fract_transf_matrix[1][1] 0.013616 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001728 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010942 _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] 0.012193 _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 D 4 GTP A 1 501 500 GTP GTP . E 5 MG A 1 502 501 MG MG . F 6 SO4 A 1 503 502 SO4 SO4 . G 7 CL A 1 504 503 CL CL . H 6 SO4 A 1 505 501 SO4 SO4 . I 8 GDP B 1 501 500 GDP GDP . J 9 V95 B 1 502 502 V95 MBZ . K 6 SO4 B 1 503 503 SO4 SO4 . L 6 SO4 B 1 504 504 SO4 SO4 . M 7 CL B 1 505 506 CL CL . N 10 GOL F 1 201 505 GOL GOL . O 6 SO4 F 1 202 500 SO4 SO4 . P 10 GOL F 1 203 501 GOL GOL . Q 11 HOH A 1 601 4 HOH HOH . Q 11 HOH A 2 602 97 HOH HOH . Q 11 HOH A 3 603 7 HOH HOH . Q 11 HOH A 4 604 9 HOH HOH . Q 11 HOH A 5 605 99 HOH HOH . Q 11 HOH A 6 606 15 HOH HOH . Q 11 HOH A 7 607 6 HOH HOH . Q 11 HOH A 8 608 81 HOH HOH . Q 11 HOH A 9 609 20 HOH HOH . Q 11 HOH A 10 610 1 HOH HOH . Q 11 HOH A 11 611 76 HOH HOH . Q 11 HOH A 12 612 102 HOH HOH . Q 11 HOH A 13 613 31 HOH HOH . Q 11 HOH A 14 614 14 HOH HOH . Q 11 HOH A 15 615 38 HOH HOH . Q 11 HOH A 16 616 27 HOH HOH . Q 11 HOH A 17 617 12 HOH HOH . Q 11 HOH A 18 618 60 HOH HOH . Q 11 HOH A 19 619 69 HOH HOH . Q 11 HOH A 20 620 18 HOH HOH . Q 11 HOH A 21 621 70 HOH HOH . Q 11 HOH A 22 622 101 HOH HOH . Q 11 HOH A 23 623 79 HOH HOH . Q 11 HOH A 24 624 62 HOH HOH . Q 11 HOH A 25 625 41 HOH HOH . Q 11 HOH A 26 626 35 HOH HOH . Q 11 HOH A 27 627 80 HOH HOH . Q 11 HOH A 28 628 13 HOH HOH . Q 11 HOH A 29 629 55 HOH HOH . Q 11 HOH A 30 630 40 HOH HOH . Q 11 HOH A 31 631 58 HOH HOH . Q 11 HOH A 32 632 71 HOH HOH . Q 11 HOH A 33 633 21 HOH HOH . Q 11 HOH A 34 634 3 HOH HOH . Q 11 HOH A 35 635 75 HOH HOH . Q 11 HOH A 36 636 34 HOH HOH . Q 11 HOH A 37 637 106 HOH HOH . Q 11 HOH A 38 638 8 HOH HOH . Q 11 HOH A 39 639 19 HOH HOH . Q 11 HOH A 40 640 37 HOH HOH . Q 11 HOH A 41 641 25 HOH HOH . Q 11 HOH A 42 642 49 HOH HOH . Q 11 HOH A 43 643 28 HOH HOH . Q 11 HOH A 44 644 63 HOH HOH . Q 11 HOH A 45 645 64 HOH HOH . Q 11 HOH A 46 646 65 HOH HOH . Q 11 HOH A 47 647 30 HOH HOH . Q 11 HOH A 48 648 94 HOH HOH . Q 11 HOH A 49 649 107 HOH HOH . Q 11 HOH A 50 650 59 HOH HOH . Q 11 HOH A 51 651 44 HOH HOH . Q 11 HOH A 52 652 24 HOH HOH . Q 11 HOH A 53 653 50 HOH HOH . Q 11 HOH A 54 654 68 HOH HOH . Q 11 HOH A 55 655 84 HOH HOH . Q 11 HOH A 56 656 89 HOH HOH . R 11 HOH B 1 601 56 HOH HOH . R 11 HOH B 2 602 2 HOH HOH . R 11 HOH B 3 603 98 HOH HOH . R 11 HOH B 4 604 96 HOH HOH . R 11 HOH B 5 605 91 HOH HOH . R 11 HOH B 6 606 32 HOH HOH . R 11 HOH B 7 607 78 HOH HOH . R 11 HOH B 8 608 22 HOH HOH . R 11 HOH B 9 609 100 HOH HOH . R 11 HOH B 10 610 72 HOH HOH . R 11 HOH B 11 611 51 HOH HOH . R 11 HOH B 12 612 93 HOH HOH . R 11 HOH B 13 613 16 HOH HOH . R 11 HOH B 14 614 104 HOH HOH . R 11 HOH B 15 615 85 HOH HOH . R 11 HOH B 16 616 23 HOH HOH . R 11 HOH B 17 617 46 HOH HOH . R 11 HOH B 18 618 74 HOH HOH . R 11 HOH B 19 619 108 HOH HOH . R 11 HOH B 20 620 95 HOH HOH . R 11 HOH B 21 621 109 HOH HOH . R 11 HOH B 22 622 73 HOH HOH . R 11 HOH B 23 623 86 HOH HOH . R 11 HOH B 24 624 90 HOH HOH . R 11 HOH B 25 625 83 HOH HOH . S 11 HOH F 1 301 105 HOH HOH . S 11 HOH F 2 302 10 HOH HOH . S 11 HOH F 3 303 29 HOH HOH . S 11 HOH F 4 304 26 HOH HOH . S 11 HOH F 5 305 43 HOH HOH . S 11 HOH F 6 306 61 HOH HOH . S 11 HOH F 7 307 42 HOH HOH . S 11 HOH F 8 308 36 HOH HOH . S 11 HOH F 9 309 48 HOH HOH . S 11 HOH F 10 310 67 HOH HOH . S 11 HOH F 11 311 11 HOH HOH . S 11 HOH F 12 312 66 HOH HOH . S 11 HOH F 13 313 33 HOH HOH . S 11 HOH F 14 314 17 HOH HOH . S 11 HOH F 15 315 39 HOH HOH . S 11 HOH F 16 316 103 HOH HOH . S 11 HOH F 17 317 5 HOH HOH . S 11 HOH F 18 318 88 HOH HOH . S 11 HOH F 19 319 47 HOH HOH . S 11 HOH F 20 320 52 HOH HOH . S 11 HOH F 21 321 92 HOH HOH . S 11 HOH F 22 322 45 HOH HOH . S 11 HOH F 23 323 54 HOH HOH . S 11 HOH F 24 324 77 HOH HOH . S 11 HOH F 25 325 53 HOH HOH . S 11 HOH F 26 326 82 HOH HOH . S 11 HOH F 27 327 57 HOH HOH . S 11 HOH F 28 328 87 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 V95 . . . J 9 16.586 10.928 27.119 1 47.15 ? C11 V95 502 B 1 HETATM 2 C C12 V95 . . . J 9 16.317 11.565 25.912 1 45.85 ? C12 V95 502 B 1 HETATM 3 C C01 V95 . . . J 9 17.431 10.251 34.678 1 48.62 ? C01 V95 502 B 1 HETATM 4 C C03 V95 . . . J 9 16.797 11.227 32.615 1 48.56 ? C03 V95 502 B 1 HETATM 5 C C06 V95 . . . J 9 16.348 12.349 30.414 1 47.65 ? C06 V95 502 B 1 HETATM 6 C C08 V95 . . . J 9 16.034 12.939 28.335 1 47.92 ? C08 V95 502 B 1 HETATM 7 C C09 V95 . . . J 9 16.436 11.636 28.348 1 48.61 ? C09 V95 502 B 1 HETATM 8 C C13 V95 . . . J 9 15.901 12.899 25.906 1 47.43 ? C13 V95 502 B 1 HETATM 9 C C14 V95 . . . J 9 15.76 13.591 27.102 1 45.68 ? C14 V95 502 B 1 HETATM 10 C C15 V95 . . . J 9 16.476 10.791 24.6 1 47.67 ? C15 V95 502 B 1 HETATM 11 C C17 V95 . . . J 9 16.746 11.501 23.267 1 47.51 ? C17 V95 502 B 1 HETATM 12 C C18 V95 . . . J 9 16.236 10.957 22.095 1 47.53 ? C18 V95 502 B 1 HETATM 13 C C19 V95 . . . J 9 16.465 11.575 20.877 1 47.43 ? C19 V95 502 B 1 HETATM 14 C C20 V95 . . . J 9 17.211 12.742 20.824 1 49.94 ? C20 V95 502 B 1 HETATM 15 C C21 V95 . . . J 9 17.722 13.29 21.992 1 52.62 ? C21 V95 502 B 1 HETATM 16 C C22 V95 . . . J 9 17.492 12.67 23.213 1 48 ? C22 V95 502 B 1 HETATM 17 N N05 V95 . . . J 9 16.412 12.398 31.861 1 50.68 ? N05 V95 502 B 1 HETATM 18 N N07 V95 . . . J 9 15.984 13.361 29.625 1 46.94 ? N07 V95 502 B 1 HETATM 19 N N10 V95 . . . J 9 16.622 11.293 29.648 1 48.02 ? N10 V95 502 B 1 HETATM 20 O O02 V95 . . . J 9 16.822 11.311 34.009 1 50.3 ? O02 V95 502 B 1 HETATM 21 O O04 V95 . . . J 9 17.07 10.222 32.046 1 46.82 ? O04 V95 502 B 1 HETATM 22 O O16 V95 . . . J 9 16.387 9.612 24.617 1 48.83 ? O16 V95 502 B 1 HETATM 23 H H111 V95 . . . J 9 16.863 10.04 27.125 1 47.15 ? H111 V95 502 B 1 HETATM 24 H H012 V95 . . . J 9 17.778 10.562 35.529 1 48.62 ? H012 V95 502 B 1 HETATM 25 H H011 V95 . . . J 9 18.16 9.905 34.139 1 48.62 ? H011 V95 502 B 1 HETATM 26 H H013 V95 . . . J 9 16.78 9.549 34.831 1 48.62 ? H013 V95 502 B 1 HETATM 27 H H131 V95 . . . J 9 15.718 13.324 25.1 1 47.43 ? H131 V95 502 B 1 HETATM 28 H H141 V95 . . . J 9 15.487 14.48 27.095 1 45.68 ? H141 V95 502 B 1 HETATM 29 H H181 V95 . . . J 9 15.737 10.172 22.128 1 47.53 ? H181 V95 502 B 1 HETATM 30 H H191 V95 . . . J 9 16.119 11.207 20.095 1 47.43 ? H191 V95 502 B 1 HETATM 31 H H201 V95 . . . J 9 17.368 13.157 20.007 1 49.94 ? H201 V95 502 B 1 HETATM 32 H H211 V95 . . . J 9 18.22 14.074 21.956 1 52.62 ? H211 V95 502 B 1 HETATM 33 H H221 V95 . . . J 9 17.837 13.037 23.994 1 48 ? H221 V95 502 B 1 HETATM 34 H H051 V95 . . . J 9 16.22 13.129 32.273 1 50.68 ? H051 V95 502 B 1 HETATM 35 H H101 V95 . . . J 9 16.876 10.522 29.931 1 48.02 ? H101 V95 502 B 1 # _model_server_stats.io_time_ms 146 _model_server_stats.parse_time_ms 84 _model_server_stats.create_model_time_ms 53 _model_server_stats.query_time_ms 283 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 35 #