data_2YLO # _model_server_result.job_id RorFZU4WeC4jG1yTL_ITaA _model_server_result.datetime_utc '2025-07-13 19:41:01' _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 2ylo # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1922}' # _entry.id 2YLO # _exptl.entry_id 2YLO _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 404.525 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1-[2-(4-METHYLPHENOXY)ETHYL]-2-(2-PHENOXYETHYLSULFANYL)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 90 _cell.entry_id 2YLO _cell.length_a 55.32 _cell.length_b 66.5 _cell.length_c 73.12 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2YLO _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 # _struct_conn.conn_type_id covale _struct_conn.details ? _struct_conn.id covale1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id OD1 _struct_conn.ptnr1_label_comp_id ASP _struct_conn.ptnr1_label_seq_id 216 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id ASP _struct_conn.ptnr1_auth_seq_id 879 _struct_conn.ptnr1_symmetry 3_454 _struct_conn.ptnr2_label_asym_id D _struct_conn.ptnr2_label_atom_id C01 _struct_conn.ptnr2_label_comp_id YLO _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id YLO _struct_conn.ptnr2_auth_seq_id 1922 _struct_conn.ptnr2_symmetry 1_555 _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 1.761 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C24 H24 N2 O2 S' _chem_comp.formula_weight 404.525 _chem_comp.id YLO _chem_comp.mon_nstd_flag . _chem_comp.name 1-[2-(4-METHYLPHENOXY)ETHYL]-2-(2-PHENOXYETHYLSULFANYL)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 C01 C02 YLO sing 432 n n C02 C03 YLO sing 433 n y C02 C07 YLO doub 434 n y C03 C04 YLO doub 435 n y C04 C05 YLO sing 436 n y C05 C06 YLO doub 437 n y C05 O08 YLO sing 438 n n C06 C07 YLO sing 439 n y O08 C09 YLO sing 440 n n C09 C10 YLO sing 441 n n C10 N11 YLO sing 442 n n N11 C12 YLO sing 443 n y N11 C19 YLO sing 444 n y C12 C13 YLO sing 445 n y C12 C17 YLO doub 446 n y C13 C14 YLO doub 447 n y C14 C15 YLO sing 448 n y C15 C16 YLO doub 449 n y C16 C17 YLO sing 450 n y C17 N18 YLO sing 451 n y N18 C19 YLO doub 452 n y C19 S20 YLO sing 453 n n S20 C21 YLO sing 454 n n C21 C22 YLO sing 455 n n C22 O23 YLO sing 456 n n O23 C24 YLO sing 457 n n C24 C25 YLO sing 458 n y C24 C29 YLO doub 459 n y C25 C26 YLO doub 460 n y C26 C27 YLO sing 461 n y C27 C28 YLO doub 462 n y C28 C29 YLO sing 463 n y C01 H011 YLO sing 464 n n C01 H012 YLO sing 465 n n C01 H013 YLO sing 466 n n C03 H03 YLO sing 467 n n C07 H07 YLO sing 468 n n C04 H04 YLO sing 469 n n C06 H06 YLO sing 470 n n C09 H091 YLO sing 471 n n C09 H092 YLO sing 472 n n C10 H101 YLO sing 473 n n C10 H102 YLO sing 474 n n C13 H13 YLO sing 475 n n C14 H14 YLO sing 476 n n C15 H15 YLO sing 477 n n C16 H16 YLO sing 478 n n C21 H211 YLO sing 479 n n C21 H212 YLO sing 480 n n C22 H221 YLO sing 481 n n C22 H222 YLO sing 482 n n C25 H25 YLO sing 483 n n C29 H29 YLO sing 484 n n C26 H26 YLO sing 485 n n C27 H27 YLO sing 486 n n C28 H28 YLO sing 487 n n # _atom_sites.entry_id 2YLO _atom_sites.fract_transf_matrix[1][1] 0.018077 _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] 0.015038 _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] 0.013676 _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 TES A 1 1920 1920 TES TES . C 3 SO4 A 1 1921 1921 SO4 SO4 . D 4 YLO A 1 1922 1922 YLO YLO . E 5 HOH A 1 2001 2001 HOH HOH . E 5 HOH A 2 2002 2002 HOH HOH . E 5 HOH A 3 2003 2003 HOH HOH . E 5 HOH A 4 2004 2004 HOH HOH . E 5 HOH A 5 2005 2005 HOH HOH . E 5 HOH A 6 2006 2006 HOH HOH . E 5 HOH A 7 2007 2007 HOH HOH . E 5 HOH A 8 2008 2008 HOH HOH . E 5 HOH A 9 2009 2009 HOH HOH . E 5 HOH A 10 2010 2010 HOH HOH . E 5 HOH A 11 2011 2011 HOH HOH . E 5 HOH A 12 2012 2012 HOH HOH . E 5 HOH A 13 2013 2013 HOH HOH . E 5 HOH A 14 2014 2014 HOH HOH . E 5 HOH A 15 2015 2015 HOH HOH . E 5 HOH A 16 2016 2016 HOH HOH . E 5 HOH A 17 2017 2017 HOH HOH . E 5 HOH A 18 2018 2018 HOH HOH . E 5 HOH A 19 2019 2019 HOH HOH . E 5 HOH A 20 2020 2020 HOH HOH . E 5 HOH A 21 2021 2021 HOH HOH . E 5 HOH A 22 2022 2022 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 C01 YLO . . . D 4 -25.482 19.661 -27.748 1 20 ? C01 YLO 1922 A 1 HETATM 2 C C02 YLO . . . D 4 -24.4 19.3 -28.764 1 20 ? C02 YLO 1922 A 1 HETATM 3 C C03 YLO . . . D 4 -23.966 20.213 -29.731 1 20 ? C03 YLO 1922 A 1 HETATM 4 C C04 YLO . . . D 4 -22.997 19.935 -30.688 1 20 ? C04 YLO 1922 A 1 HETATM 5 C C05 YLO . . . D 4 -22.431 18.686 -30.734 1 20 ? C05 YLO 1922 A 1 HETATM 6 C C06 YLO . . . D 4 -22.86 17.759 -29.761 1 20 ? C06 YLO 1922 A 1 HETATM 7 C C07 YLO . . . D 4 -23.826 18.044 -28.787 1 20 ? C07 YLO 1922 A 1 HETATM 8 O O08 YLO . . . D 4 -21.464 18.389 -31.708 1 20 ? O08 YLO 1922 A 1 HETATM 9 C C09 YLO . . . D 4 -20.883 17.132 -31.745 1 20 ? C09 YLO 1922 A 1 HETATM 10 C C10 YLO . . . D 4 -19.504 17.147 -31.18 1 20 ? C10 YLO 1922 A 1 HETATM 11 N N11 YLO . . . D 4 -18.755 16.024 -30.594 1 20 ? N11 YLO 1922 A 1 HETATM 12 C C12 YLO . . . D 4 -18.002 16.1 -29.437 1 20 ? C12 YLO 1922 A 1 HETATM 13 C C13 YLO . . . D 4 -17.753 17.106 -28.519 1 20 ? C13 YLO 1922 A 1 HETATM 14 C C14 YLO . . . D 4 -16.952 16.933 -27.431 1 20 ? C14 YLO 1922 A 1 HETATM 15 C C15 YLO . . . D 4 -16.365 15.718 -27.216 1 20 ? C15 YLO 1922 A 1 HETATM 16 C C16 YLO . . . D 4 -16.601 14.716 -28.131 1 20 ? C16 YLO 1922 A 1 HETATM 17 C C17 YLO . . . D 4 -17.423 14.903 -29.25 1 20 ? C17 YLO 1922 A 1 HETATM 18 N N18 YLO . . . D 4 -17.803 14.075 -30.294 1 20 ? N18 YLO 1922 A 1 HETATM 19 C C19 YLO . . . D 4 -18.606 14.775 -31.092 1 20 ? C19 YLO 1922 A 1 HETATM 20 S S20 YLO . . . D 4 -19.273 14.118 -32.506 1 20 ? S20 YLO 1922 A 1 HETATM 21 C C21 YLO . . . D 4 -20.416 12.788 -32.287 1 20 ? C21 YLO 1922 A 1 HETATM 22 C C22 YLO . . . D 4 -20.347 11.8 -33.446 1 20 ? C22 YLO 1922 A 1 HETATM 23 O O23 YLO . . . D 4 -21.476 11.632 -34.244 1 20 ? O23 YLO 1922 A 1 HETATM 24 C C24 YLO . . . D 4 -21.726 12.466 -35.313 1 20 ? C24 YLO 1922 A 1 HETATM 25 C C25 YLO . . . D 4 -20.852 12.57 -36.366 1 20 ? C25 YLO 1922 A 1 HETATM 26 C C26 YLO . . . D 4 -21.124 13.4 -37.442 1 20 ? C26 YLO 1922 A 1 HETATM 27 C C27 YLO . . . D 4 -22.297 14.124 -37.463 1 20 ? C27 YLO 1922 A 1 HETATM 28 C C28 YLO . . . D 4 -23.17 14.025 -36.416 1 20 ? C28 YLO 1922 A 1 HETATM 29 C C29 YLO . . . D 4 -22.899 13.192 -35.354 1 20 ? C29 YLO 1922 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 29 _model_server_stats.query_time_ms 376 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 29 #