data_8S4D # _model_server_result.job_id Y6rZQ3dP5zOzqnvJGwZOOw _model_server_result.datetime_utc '2025-04-09 01:39:00' _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 8s4d # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":1201}' # _entry.id 8S4D # _exptl.entry_id 8S4D _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 455.613 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(3~{S})-5-methyl-3-[[1-pentan-3-yl-2-(thiophen-2-ylmethyl)benzimidazol-5-yl]carbonylamino]hexanoic acid' _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 8S4D _cell.length_a 65.823 _cell.length_b 153.948 _cell.length_c 111.646 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8S4D _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 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,F,G,H,I,J _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 # _struct_conn.conn_type_id disulf _struct_conn.details ? _struct_conn.id disulf1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id SG _struct_conn.ptnr1_label_comp_id CYS _struct_conn.ptnr1_label_seq_id 120 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id CYS _struct_conn.ptnr1_auth_seq_id 102 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id A _struct_conn.ptnr2_label_atom_id SG _struct_conn.ptnr2_label_comp_id CYS _struct_conn.ptnr2_label_seq_id 199 _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id CYS _struct_conn.ptnr2_auth_seq_id 181 _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 2.054 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C25 H33 N3 O3 S' _chem_comp.formula_weight 455.613 _chem_comp.id A1D5N _chem_comp.mon_nstd_flag . _chem_comp.name '(3~{S})-5-methyl-3-[[1-pentan-3-yl-2-(thiophen-2-ylmethyl)benzimidazol-5-yl]carbonylamino]hexanoic acid' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms CMF019 # 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 C31 C32 A1D5N doub 38 n y C31 C30 A1D5N sing 39 n y C32 S01 A1D5N sing 40 n y C30 C28 A1D5N doub 41 n y S01 C28 A1D5N sing 42 n y C28 C17 A1D5N sing 43 n n C17 C12 A1D5N sing 44 n n C12 N06 A1D5N doub 45 n y C12 N05 A1D5N sing 46 n y N06 C16 A1D5N sing 47 n y C22 C09 A1D5N sing 48 n n C27 C15 A1D5N sing 49 n n N05 C08 A1D5N sing 50 n n N05 C11 A1D5N sing 51 n y C16 C21 A1D5N doub 52 n y C16 C11 A1D5N sing 53 n y C09 C08 A1D5N sing 54 n n C08 C10 A1D5N sing 55 n n C26 C15 A1D5N sing 56 n n C21 C20 A1D5N sing 57 n y C11 C18 A1D5N doub 58 n y C15 C14 A1D5N sing 59 n n C20 C25 A1D5N sing 60 n n C20 C24 A1D5N doub 61 n y C18 C24 A1D5N sing 62 n y C10 C23 A1D5N sing 63 n n C25 O02 A1D5N doub 64 n n C25 N07 A1D5N sing 65 n n C14 C13 A1D5N sing 66 n n N07 C13 A1D5N sing 67 n n C13 C19 A1D5N sing 68 n n C19 C29 A1D5N sing 69 n n O04 C29 A1D5N doub 70 n n C29 O03 A1D5N sing 71 n n C08 H081 A1D5N sing 72 n n C09 H092 A1D5N sing 73 n n C09 H091 A1D5N sing 74 n n C10 H101 A1D5N sing 75 n n C10 H102 A1D5N sing 76 n n C13 H131 A1D5N sing 77 n n C14 H141 A1D5N sing 78 n n C14 H142 A1D5N sing 79 n n C15 H151 A1D5N sing 80 n n C17 H172 A1D5N sing 81 n n C17 H171 A1D5N sing 82 n n C18 H181 A1D5N sing 83 n n C19 H192 A1D5N sing 84 n n C19 H191 A1D5N sing 85 n n C21 H211 A1D5N sing 86 n n C22 H221 A1D5N sing 87 n n C22 H222 A1D5N sing 88 n n C22 H223 A1D5N sing 89 n n C23 H231 A1D5N sing 90 n n C23 H232 A1D5N sing 91 n n C23 H233 A1D5N sing 92 n n C24 H241 A1D5N sing 93 n n C26 H263 A1D5N sing 94 n n C26 H261 A1D5N sing 95 n n C26 H262 A1D5N sing 96 n n C27 H271 A1D5N sing 97 n n C27 H273 A1D5N sing 98 n n C27 H272 A1D5N sing 99 n n C30 H301 A1D5N sing 100 n n C31 H311 A1D5N sing 101 n n C32 H321 A1D5N sing 102 n n N07 H071 A1D5N sing 103 n n O03 H1 A1D5N sing 104 n n # _atom_sites.entry_id 8S4D _atom_sites.fract_transf_matrix[1][1] 0.015192 _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] 0.006496 _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] 0.008957 _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 A1D5N A 1 1201 1 A1D5N LIG . C 3 OLA A 1 1202 1 OLA OLA . D 3 OLA A 1 1203 2 OLA OLA . E 3 OLA A 1 1204 3 OLA OLA . F 3 OLA A 1 1205 4 OLA OLA . G 3 OLA A 1 1206 5 OLA OLA . H 3 OLA A 1 1207 6 OLA OLA . I 4 1PE A 1 1208 7 1PE 1PE . J 5 HOH A 1 1301 1 HOH HOH . J 5 HOH A 2 1302 8 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 C08 A1D5N . . . B 2 -3.695 -30.951 7.375 1 41.1 ? C08 A1D5N 1201 A 1 HETATM 2 C C09 A1D5N . . . B 2 -2.596 -30.293 8.224 1 41.07 ? C09 A1D5N 1201 A 1 HETATM 3 C C10 A1D5N . . . B 2 -5.112 -30.73 7.935 1 40.81 ? C10 A1D5N 1201 A 1 HETATM 4 C C11 A1D5N . . . B 2 -3.562 -29.35 5.355 1 41.74 ? C11 A1D5N 1201 A 1 HETATM 5 C C12 A1D5N . . . B 2 -3.278 -31.469 4.905 1 42.63 ? C12 A1D5N 1201 A 1 HETATM 6 C C13 A1D5N . . . B 2 -4.209 -23.64 1.871 1 47.02 ? C13 A1D5N 1201 A 1 HETATM 7 C C14 A1D5N . . . B 2 -5.613 -23.04 1.775 1 46.53 ? C14 A1D5N 1201 A 1 HETATM 8 C C15 A1D5N . . . B 2 -6.71 -24.024 1.312 1 45.97 ? C15 A1D5N 1201 A 1 HETATM 9 C C16 A1D5N . . . B 2 -3.352 -29.517 3.993 1 41.98 ? C16 A1D5N 1201 A 1 HETATM 10 C C17 A1D5N . . . B 2 -3.091 -33.011 4.974 1 43.68 ? C17 A1D5N 1201 A 1 HETATM 11 C C18 A1D5N . . . B 2 -3.784 -28.054 5.872 1 41.64 ? C18 A1D5N 1201 A 1 HETATM 12 C C19 A1D5N . . . B 2 -3.221 -22.557 2.289 1 48.56 ? C19 A1D5N 1201 A 1 HETATM 13 C C20 A1D5N . . . B 2 -3.532 -27.164 3.616 1 42.64 ? C20 A1D5N 1201 A 1 HETATM 14 C C21 A1D5N . . . B 2 -3.346 -28.431 3.105 1 42.03 ? C21 A1D5N 1201 A 1 HETATM 15 C C22 A1D5N . . . B 2 -1.208 -30.886 7.884 1 41.1 ? C22 A1D5N 1201 A 1 HETATM 16 C C23 A1D5N . . . B 2 -5.532 -31.836 8.94 1 40.67 ? C23 A1D5N 1201 A 1 HETATM 17 C C24 A1D5N . . . B 2 -3.752 -26.967 4.987 1 42.11 ? C24 A1D5N 1201 A 1 HETATM 18 C C25 A1D5N . . . B 2 -3.55 -25.982 2.569 1 44.13 ? C25 A1D5N 1201 A 1 HETATM 19 C C26 A1D5N . . . B 2 -8.07 -23.277 1.228 1 45.65 ? C26 A1D5N 1201 A 1 HETATM 20 C C27 A1D5N . . . B 2 -6.364 -24.705 -0.024 1 45.86 ? C27 A1D5N 1201 A 1 HETATM 21 C C28 A1D5N . . . B 2 -4.445 -33.658 5.241 1 45.09 ? C28 A1D5N 1201 A 1 HETATM 22 C C29 A1D5N . . . B 2 -1.743 -22.982 2.422 1 49.68 ? C29 A1D5N 1201 A 1 HETATM 23 C C30 A1D5N . . . B 2 -5 -33.9 6.499 1 45.32 ? C30 A1D5N 1201 A 1 HETATM 24 C C31 A1D5N . . . B 2 -6.287 -34.494 6.402 1 45.56 ? C31 A1D5N 1201 A 1 HETATM 25 C C32 A1D5N . . . B 2 -6.782 -34.745 5.121 1 45.92 ? C32 A1D5N 1201 A 1 HETATM 26 N N05 A1D5N . . . B 2 -3.552 -30.604 5.902 1 41.8 ? N05 A1D5N 1201 A 1 HETATM 27 N N06 A1D5N . . . B 2 -3.184 -30.829 3.747 1 42.33 ? N06 A1D5N 1201 A 1 HETATM 28 N N07 A1D5N . . . B 2 -4.22 -24.711 2.883 1 45.69 ? N07 A1D5N 1201 A 1 HETATM 29 O O02 A1D5N . . . B 2 -3.061 -26.139 1.502 1 44.2 ? O02 A1D5N 1201 A 1 HETATM 30 O O03 A1D5N . . . B 2 -1.06 -23.246 1.374 1 50.09 ? O03 A1D5N 1201 A 1 HETATM 31 O O04 A1D5N . . . B 2 -1.215 -23.051 3.582 1 49.95 -1 O04 A1D5N 1201 A 1 HETATM 32 S S01 A1D5N . . . B 2 -5.577 -34.168 4.094 1 46.28 ? S01 A1D5N 1201 A 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 382 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 32 #