data_3LC5 # _model_server_result.job_id U7QOO-lB3u4j5MnZAAJKyg _model_server_result.datetime_utc '2025-09-01 07:56:21' _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 3lc5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1}' # _entry.id 3LC5 # _exptl.entry_id 3LC5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 428.506 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1-{4-[(R)-phenyl(3-phenyl-1,2,4-oxadiazol-5-yl)methoxy]-1-benzothiophen-2-yl}methanediamine _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 3LC5 _cell.length_a 43.12 _cell.length_b 65.738 _cell.length_c 93.985 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3LC5 _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 dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 # 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 26 A CYS 42 1_555 A SG CYS 42 A CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf2 A SG CYS 109 A CYS 122 1_555 B SG CYS 47 B CYS 132 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? disulf ? disulf3 A SG CYS 156 A CYS 168 1_555 A SG CYS 170 A CYS 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.008 ? disulf ? disulf4 A SG CYS 181 A CYS 191 1_555 A SG CYS 209 A CYS 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf5 B SG CYS 3 B CYS 88 1_555 B SG CYS 14 B CYS 99 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? disulf ? disulf6 B SG CYS 10 B CYS 95 1_555 B SG CYS 24 B CYS 109 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf7 B SG CYS 26 B CYS 111 1_555 B SG CYS 39 B CYS 124 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? metalc ? metalc1 A OE1 GLU 55 A GLU 70 1_555 C CA CA . A CA 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.336 ? metalc ? metalc2 A O ASN 57 A ASN 72 1_555 C CA CA . A CA 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.551 ? metalc ? metalc3 A O GLU 60 A GLU 75 1_555 C CA CA . A CA 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.441 ? metalc ? metalc4 A OE1 GLU 62 A GLU 77 1_555 C CA CA . A CA 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.14 ? metalc ? metalc5 A OE2 GLU 65 A GLU 80 1_555 C CA CA . A CA 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.368 ? metalc ? metalc6 E O HOH . A HOH 246 1_555 C CA CA . A CA 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.25 ? # _chem_comp.formula 'C24 H20 N4 O2 S' _chem_comp.formula_weight 428.506 _chem_comp.id IZX _chem_comp.mon_nstd_flag . _chem_comp.name 1-{4-[(R)-phenyl(3-phenyl-1,2,4-oxadiazol-5-yl)methoxy]-1-benzothiophen-2-yl}methanediamine _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 C3 C1 IZX doub 173 n y C1 C7 IZX sing 174 n y C1 C2 IZX sing 175 n y C4 C2 IZX doub 176 n y C2 S9 IZX sing 177 n y O13 C3 IZX sing 178 n n C5 C3 IZX sing 179 n y C6 C4 IZX sing 180 n y C4 H4 IZX sing 181 n n C5 C6 IZX doub 182 n y C5 H5 IZX sing 183 n n C6 H6 IZX sing 184 n n C7 C8 IZX doub 185 n y C7 H7 IZX sing 186 n n C8 C10 IZX sing 187 n n C8 S9 IZX sing 188 n y N11 C10 IZX sing 189 n n C10 N12 IZX sing 190 n n N11 HN1C IZX sing 191 n n N12 HN12 IZX sing 192 n n N12 HN1A IZX sing 193 n n C14 O13 IZX sing 194 n n C21 C14 IZX sing 195 n n C15 C14 IZX sing 196 n n C14 H14 IZX sing 197 n n C16 C15 IZX doub 198 n y C15 C17 IZX sing 199 n y C18 C16 IZX sing 200 n y C16 H16 IZX sing 201 n n C19 C17 IZX doub 202 n y C17 H17 IZX sing 203 n n C18 C20 IZX doub 204 n y C18 H18 IZX sing 205 n n C20 C19 IZX sing 206 n y C19 H19 IZX sing 207 n n C20 H20 IZX sing 208 n n O22 C21 IZX sing 209 n y N24 C21 IZX doub 210 n y N23 O22 IZX sing 211 n y N23 C25 IZX doub 212 n y C25 N24 IZX sing 213 n y C26 C25 IZX sing 214 n y C28 C26 IZX doub 215 n y C26 C27 IZX sing 216 n y C29 C27 IZX doub 217 n y C27 H27 IZX sing 218 n n C30 C28 IZX sing 219 n y C28 H28 IZX sing 220 n n C31 C29 IZX sing 221 n y C29 H29 IZX sing 222 n n C30 C31 IZX doub 223 n y C30 H30 IZX sing 224 n n C31 H31 IZX sing 225 n n C10 H10 IZX sing 226 n n N11 HN1D IZX sing 227 n n # _atom_sites.entry_id 3LC5 _atom_sites.fract_transf_matrix[1][1] 0.023191 _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] 0.015212 _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] 0.01064 _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 C 3 CA A 1 500 500 CA CA . D 4 IZX A 1 1 1 IZX IZX . E 5 HOH A 1 2 2 HOH HOH . E 5 HOH A 2 3 3 HOH HOH . E 5 HOH A 3 4 4 HOH HOH . E 5 HOH A 4 5 5 HOH HOH . E 5 HOH A 5 6 6 HOH HOH . E 5 HOH A 6 7 7 HOH HOH . E 5 HOH A 7 8 8 HOH HOH . E 5 HOH A 8 9 9 HOH HOH . E 5 HOH A 9 10 10 HOH HOH . E 5 HOH A 10 11 11 HOH HOH . E 5 HOH A 11 12 12 HOH HOH . E 5 HOH A 12 13 13 HOH HOH . E 5 HOH A 13 246 1 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 IZX . . . D 4 -13.408 -6.431 6.851 1 23.37 ? C1 IZX 1 A 1 HETATM 2 C C2 IZX . . . D 4 -13.067 -5.632 7.928 1 20.45 ? C2 IZX 1 A 1 HETATM 3 C C3 IZX . . . D 4 -13.707 -5.864 5.619 1 21 ? C3 IZX 1 A 1 HETATM 4 C C4 IZX . . . D 4 -13.013 -4.258 7.826 1 21.2 ? C4 IZX 1 A 1 HETATM 5 C C5 IZX . . . D 4 -13.657 -4.466 5.505 1 20.01 ? C5 IZX 1 A 1 HETATM 6 C C6 IZX . . . D 4 -13.311 -3.669 6.595 1 20.22 ? C6 IZX 1 A 1 HETATM 7 C C7 IZX . . . D 4 -13.399 -7.784 7.174 1 21.06 ? C7 IZX 1 A 1 HETATM 8 C C8 IZX . . . D 4 -13.049 -7.979 8.502 1 20.64 ? C8 IZX 1 A 1 HETATM 9 S S9 IZX . . . D 4 -12.781 -6.552 9.2 1 20.91 ? S9 IZX 1 A 1 HETATM 10 C C10 IZX . . . D 4 -12.941 -9.269 9.194 1 22.19 ? C10 IZX 1 A 1 HETATM 11 N N11 IZX . . . D 4 -13.305 -10.386 8.63 1 24.74 ? N11 IZX 1 A 1 HETATM 12 N N12 IZX . . . D 4 -12.441 -9.284 10.477 1 26.72 ? N12 IZX 1 A 1 HETATM 13 O O13 IZX . . . D 4 -14.032 -6.714 4.596 1 20.25 ? O13 IZX 1 A 1 HETATM 14 C C14 IZX . . . D 4 -14.262 -6.451 3.212 1 24.81 ? C14 IZX 1 A 1 HETATM 15 C C15 IZX . . . D 4 -15.744 -6.589 2.915 1 22.82 ? C15 IZX 1 A 1 HETATM 16 C C16 IZX . . . D 4 -16.419 -5.624 2.177 1 20.98 ? C16 IZX 1 A 1 HETATM 17 C C17 IZX . . . D 4 -16.435 -7.669 3.444 1 24.94 ? C17 IZX 1 A 1 HETATM 18 C C18 IZX . . . D 4 -17.776 -5.759 1.946 1 23.14 ? C18 IZX 1 A 1 HETATM 19 C C19 IZX . . . D 4 -17.792 -7.807 3.212 1 23.69 ? C19 IZX 1 A 1 HETATM 20 C C20 IZX . . . D 4 -18.458 -6.852 2.468 1 25.36 ? C20 IZX 1 A 1 HETATM 21 C C21 IZX . . . D 4 -13.347 -7.386 2.445 1 30.37 ? C21 IZX 1 A 1 HETATM 22 O O22 IZX . . . D 4 -13.599 -8.461 1.912 1 32.38 ? O22 IZX 1 A 1 HETATM 23 N N23 IZX . . . D 4 -12.571 -8.928 1.396 1 33.08 ? N23 IZX 1 A 1 HETATM 24 N N24 IZX . . . D 4 -12.057 -7.07 2.324 1 35.25 ? N24 IZX 1 A 1 HETATM 25 C C25 IZX . . . D 4 -11.557 -8.077 1.634 1 34.19 ? C25 IZX 1 A 1 HETATM 26 C C26 IZX . . . D 4 -10.135 -8.171 1.234 1 33.92 ? C26 IZX 1 A 1 HETATM 27 C C27 IZX . . . D 4 -9.182 -7.319 1.804 1 34.88 ? C27 IZX 1 A 1 HETATM 28 C C28 IZX . . . D 4 -9.742 -9.098 0.28 1 36.16 ? C28 IZX 1 A 1 HETATM 29 C C29 IZX . . . D 4 -7.845 -7.395 1.425 1 32.8 ? C29 IZX 1 A 1 HETATM 30 C C30 IZX . . . D 4 -8.405 -9.172 -0.094 1 35.32 ? C30 IZX 1 A 1 HETATM 31 C C31 IZX . . . D 4 -7.459 -8.325 0.472 1 34.41 ? C31 IZX 1 A 1 # _model_server_stats.io_time_ms 24 _model_server_stats.parse_time_ms 5 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 328 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 31 #