data_8SZ3 # _model_server_result.job_id 5myb8qYBZoPMBszEl9btgg _model_server_result.datetime_utc '2025-01-09 21:43:04' _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 8sz3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":401}' # _entry.id 8SZ3 # _exptl.entry_id 8SZ3 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 445.353 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description N-[(1S)-1-(5-bromopyridin-2-yl)ethyl]-3-[(2R)-3,3-dimethylbutan-2-yl]-2-oxo-2,3-dihydro-1H-benzimidazole-5-carboxamide _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 102.58 _cell.angle_gamma 90 _cell.entry_id 8SZ3 _cell.length_a 82.375 _cell.length_b 76.405 _cell.length_c 128.019 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8SZ3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall 'C 2y' _symmetry.space_group_name_H-M 'C 1 2 1' # _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 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,G,H,K 1 1 B,E,F,I,J,L 1 2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_556 -x,y,-z+1 -1 0 0 0 1 0 0 0 -1 -27.882867 0 124.945629 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 G N N ? 3 I N N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 2 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 NAG _pdbx_entity_branch_link.comp_id_2 NAG _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 2 n C NAG 1 C 1 NAG A 400 NAG 2 n C NAG 2 C 2 NAG A 401 NAG 2 n D NAG 1 D 1 NAG A 402 NAG 2 n D NAG 2 D 2 NAG A 403 NAG 2 n E NAG 1 E 1 NAG B 401 NAG 2 n E NAG 2 E 2 NAG B 402 NAG 2 n F NAG 1 F 1 NAG B 404 NAG 2 n F NAG 2 F 2 NAG B 405 NAG # 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 disulf ? disulf1 A SG CYS 96 A CYS 96 1_555 A SG CYS 125 A CYS 125 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf2 A SG CYS 138 A CYS 138 1_555 A SG CYS 235 A CYS 235 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf3 A SG CYS 367 A CYS 367 1_555 A SG CYS 397 A CYS 397 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf4 B SG CYS 96 B CYS 96 1_555 B SG CYS 125 B CYS 125 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf5 B SG CYS 138 B CYS 138 1_555 B SG CYS 235 B CYS 235 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf6 B SG CYS 367 B CYS 367 1_555 B SG CYS 397 B CYS 397 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? covale ? covale1 A ND2 ASN 127 A ASN 127 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale2 A ND2 ASN 219 A ASN 219 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale3 B ND2 ASN 127 B ASN 127 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale4 B ND2 ASN 219 B ASN 219 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale5 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale6 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale7 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.428 ? covale ? covale8 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? # _chem_comp.formula 'C21 H25 Br N4 O2' _chem_comp.formula_weight 445.353 _chem_comp.id X18 _chem_comp.mon_nstd_flag . _chem_comp.name N-[(1S)-1-(5-bromopyridin-2-yl)ethyl]-3-[(2R)-3,3-dimethylbutan-2-yl]-2-oxo-2,3-dihydro-1H-benzimidazole-5-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 C21 C20 X18 sing 415 n n C22 C20 X18 sing 416 n n C23 C20 X18 sing 417 n n C20 C18 X18 sing 418 n n C18 C19 X18 sing 419 n n C18 N17 X18 sing 420 n n N17 C24 X18 sing 421 n n N17 C16 X18 sing 422 n n O25 C24 X18 doub 423 n n C15 C16 X18 doub 424 n y C15 C02 X18 sing 425 n y C06 C05 X18 sing 426 n n C24 N26 X18 sing 427 n n C16 C27 X18 sing 428 n y O14 C03 X18 doub 429 n n C05 N04 X18 sing 430 n n C05 C07 X18 sing 431 n n C03 N04 X18 sing 432 n n C03 C02 X18 sing 433 n n C02 C01 X18 doub 434 n y C13 C07 X18 doub 435 n y C13 C12 X18 sing 436 n y C27 N26 X18 sing 437 n n C27 C28 X18 doub 438 n y C07 N08 X18 sing 439 n y C12 C10 X18 doub 440 n y C01 C28 X18 sing 441 n y N08 C09 X18 doub 442 n y C10 C09 X18 sing 443 n y C10 BR11 X18 sing 444 n n C13 H1 X18 sing 445 n n C15 H2 X18 sing 446 n n C21 H3 X18 sing 447 n n C21 H4 X18 sing 448 n n C21 H5 X18 sing 449 n n C22 H6 X18 sing 450 n n C22 H7 X18 sing 451 n n C22 H8 X18 sing 452 n n C28 H9 X18 sing 453 n n C01 H10 X18 sing 454 n n C05 H11 X18 sing 455 n n C06 H12 X18 sing 456 n n C06 H13 X18 sing 457 n n C06 H14 X18 sing 458 n n C09 H15 X18 sing 459 n n C12 H16 X18 sing 460 n n C18 H17 X18 sing 461 n n C19 H18 X18 sing 462 n n C19 H19 X18 sing 463 n n C19 H20 X18 sing 464 n n C23 H21 X18 sing 465 n n C23 H22 X18 sing 466 n n C23 H23 X18 sing 467 n n N04 H24 X18 sing 468 n n N26 H25 X18 sing 469 n n # _atom_sites.entry_id 8SZ3 _atom_sites.fract_transf_matrix[1][1] 0.01214 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002709 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013088 _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] 0.008003 _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 G 3 X18 A 1 401 500 X18 LIG . H 4 EDO A 1 402 1 EDO EDO . I 3 X18 B 1 401 500 X18 LIG . J 4 EDO B 1 402 2 EDO EDO . K 5 HOH A 1 501 51 HOH HOH . K 5 HOH A 2 502 59 HOH HOH . K 5 HOH A 3 503 44 HOH HOH . K 5 HOH A 4 504 15 HOH HOH . K 5 HOH A 5 505 43 HOH HOH . K 5 HOH A 6 506 38 HOH HOH . K 5 HOH A 7 507 4 HOH HOH . K 5 HOH A 8 508 30 HOH HOH . K 5 HOH A 9 509 8 HOH HOH . K 5 HOH A 10 510 25 HOH HOH . K 5 HOH A 11 511 31 HOH HOH . K 5 HOH A 12 512 1 HOH HOH . K 5 HOH A 13 513 5 HOH HOH . K 5 HOH A 14 514 21 HOH HOH . K 5 HOH A 15 515 27 HOH HOH . K 5 HOH A 16 516 39 HOH HOH . K 5 HOH A 17 517 14 HOH HOH . K 5 HOH A 18 518 45 HOH HOH . K 5 HOH A 19 519 29 HOH HOH . K 5 HOH A 20 520 13 HOH HOH . K 5 HOH A 21 521 7 HOH HOH . K 5 HOH A 22 522 57 HOH HOH . K 5 HOH A 23 523 46 HOH HOH . K 5 HOH A 24 524 24 HOH HOH . K 5 HOH A 25 525 58 HOH HOH . K 5 HOH A 26 526 52 HOH HOH . K 5 HOH A 27 527 63 HOH HOH . K 5 HOH A 28 528 47 HOH HOH . K 5 HOH A 29 529 33 HOH HOH . K 5 HOH A 30 530 65 HOH HOH . K 5 HOH A 31 531 61 HOH HOH . L 5 HOH B 1 501 11 HOH HOH . L 5 HOH B 2 502 26 HOH HOH . L 5 HOH B 3 503 22 HOH HOH . L 5 HOH B 4 504 55 HOH HOH . L 5 HOH B 5 505 23 HOH HOH . L 5 HOH B 6 506 2 HOH HOH . L 5 HOH B 7 507 12 HOH HOH . L 5 HOH B 8 508 28 HOH HOH . L 5 HOH B 9 509 42 HOH HOH . L 5 HOH B 10 510 17 HOH HOH . L 5 HOH B 11 511 54 HOH HOH . L 5 HOH B 12 512 16 HOH HOH . L 5 HOH B 13 513 20 HOH HOH . L 5 HOH B 14 514 3 HOH HOH . L 5 HOH B 15 515 37 HOH HOH . L 5 HOH B 16 516 60 HOH HOH . L 5 HOH B 17 517 48 HOH HOH . L 5 HOH B 18 518 66 HOH HOH . L 5 HOH B 19 519 35 HOH HOH . L 5 HOH B 20 520 18 HOH HOH . L 5 HOH B 21 521 9 HOH HOH . L 5 HOH B 22 522 49 HOH HOH . L 5 HOH B 23 523 6 HOH HOH . L 5 HOH B 24 524 19 HOH HOH . L 5 HOH B 25 525 32 HOH HOH . L 5 HOH B 26 526 10 HOH HOH . L 5 HOH B 27 527 50 HOH HOH . L 5 HOH B 28 528 40 HOH HOH . L 5 HOH B 29 529 64 HOH HOH . L 5 HOH B 30 530 41 HOH HOH . L 5 HOH B 31 531 67 HOH HOH . L 5 HOH B 32 532 56 HOH HOH . L 5 HOH B 33 533 34 HOH HOH . L 5 HOH B 34 534 62 HOH HOH . L 5 HOH B 35 535 53 HOH HOH . L 5 HOH B 36 536 36 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 C10 X18 . . . I 3 -16.188 13.864 105.42 1 39.93 ? C10 X18 401 B 1 HETATM 2 C C13 X18 . . . I 3 -16.295 11.543 104.829 1 34.31 ? C13 X18 401 B 1 HETATM 3 C C15 X18 . . . I 3 -12.316 7.948 102.145 1 24.76 ? C15 X18 401 B 1 HETATM 4 C C20 X18 . . . I 3 -10.349 6.353 99.186 1 28.86 ? C20 X18 401 B 1 HETATM 5 C C21 X18 . . . I 3 -11.642 7.169 99.008 1 23.08 ? C21 X18 401 B 1 HETATM 6 C C22 X18 . . . I 3 -10.679 4.875 99.018 1 25.38 ? C22 X18 401 B 1 HETATM 7 C C24 X18 . . . I 3 -10.191 4.856 102.372 1 26.5 ? C24 X18 401 B 1 HETATM 8 C C28 X18 . . . I 3 -13.156 6.246 104.215 1 29.27 ? C28 X18 401 B 1 HETATM 9 C C01 X18 . . . I 3 -13.845 7.461 103.979 1 24.43 ? C01 X18 401 B 1 HETATM 10 C C02 X18 . . . I 3 -13.417 8.317 102.947 1 29.25 ? C02 X18 401 B 1 HETATM 11 C C03 X18 . . . I 3 -14.146 9.654 102.637 1 32.76 ? C03 X18 401 B 1 HETATM 12 C C05 X18 . . . I 3 -16.379 10.924 102.384 1 34.89 ? C05 X18 401 B 1 HETATM 13 C C06 X18 . . . I 3 -17.841 10.552 102.142 1 30.41 ? C06 X18 401 B 1 HETATM 14 C C07 X18 . . . I 3 -16.307 11.95 103.508 1 36.31 ? C07 X18 401 B 1 HETATM 15 C C09 X18 . . . I 3 -16.207 14.198 104.08 1 38.28 ? C09 X18 401 B 1 HETATM 16 C C12 X18 . . . I 3 -16.233 12.528 105.81 1 37.24 ? C12 X18 401 B 1 HETATM 17 C C16 X18 . . . I 3 -11.619 6.728 102.37 1 25.38 ? C16 X18 401 B 1 HETATM 18 C C18 X18 . . . I 3 -9.657 6.6 100.564 1 25.65 ? C18 X18 401 B 1 HETATM 19 C C19 X18 . . . I 3 -9.3 8.064 100.735 1 23.34 ? C19 X18 401 B 1 HETATM 20 C C23 X18 . . . I 3 -9.395 6.779 98.075 1 23.23 ? C23 X18 401 B 1 HETATM 21 C C27 X18 . . . I 3 -12.042 5.883 103.405 1 26.78 ? C27 X18 401 B 1 HETATM 22 N N04 X18 . . . I 3 -15.632 9.701 102.692 1 31.76 ? N04 X18 401 B 1 HETATM 23 N N08 X18 . . . I 3 -16.267 13.236 103.175 1 38.24 ? N08 X18 401 B 1 HETATM 24 N N17 X18 . . . I 3 -10.448 6.098 101.696 1 26.58 ? N17 X18 401 B 1 HETATM 25 N N26 X18 . . . I 3 -11.157 4.7 103.422 1 26.6 ? N26 X18 401 B 1 HETATM 26 O O14 X18 . . . I 3 -13.529 10.615 102.346 1 34.26 ? O14 X18 401 B 1 HETATM 27 O O25 X18 . . . I 3 -9.33 4.089 102.107 1 27.23 ? O25 X18 401 B 1 HETATM 28 BR BR11 X18 . . . I 3 -16.104 15.273 106.756 1 58.81 ? BR11 X18 401 B 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 342 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 28 #