data_5YWK # _model_server_result.job_id VtE-OHoeHNUIerwFVxkYyA _model_server_result.datetime_utc '2024-10-22 06:00:53' _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 5ywk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":502}' # _entry.id 5YWK # _exptl.entry_id 5YWK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 418.442 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1,5-dimethyl-3-(2-methylphenyl)-6-(2-oxidanyl-6-oxidanylidene-cyclohexen-1-yl)carbonyl-quinazoline-2,4-dione _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 90 _cell.angle_gamma 90 _cell.entry_id 5YWK _cell.length_a 95.753 _cell.length_b 95.753 _cell.length_c 194.584 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5YWK _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 2' # _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,F,G,H _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 D N N ? 3 F N 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 401 A CYS 401 1_555 A SG CYS 416 A CYS 416 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf2 B SG CYS 401 B CYS 401 1_555 B SG CYS 416 B CYS 416 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? metalc ? metalc1 A NE2 HIS 226 A HIS 226 1_555 C CO CO . A CO 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.365 ? metalc ? metalc2 A NE2 HIS 308 A HIS 308 1_555 C CO CO . A CO 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.329 ? metalc ? metalc3 A OE1 GLU 394 A GLU 394 1_555 C CO CO . A CO 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.897 ? metalc ? metalc4 C CO CO . A CO 501 1_555 D O9 92X . A 92X 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.203 ? metalc ? metalc5 C CO CO . A CO 501 1_555 D O11 92X . A 92X 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.363 ? metalc ? metalc6 C CO CO . A CO 501 1_555 G O HOH . A HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.209 ? metalc ? metalc7 B NE2 HIS 226 B HIS 226 1_555 E CO CO . B CO 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.366 ? metalc ? metalc8 B NE2 HIS 308 B HIS 308 1_555 E CO CO . B CO 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.384 ? metalc ? metalc9 B OE2 GLU 394 B GLU 394 1_555 E CO CO . B CO 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.1 ? metalc ? metalc10 E CO CO . B CO 501 1_555 F O9 92X . B 92X 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.192 ? metalc ? metalc11 E CO CO . B CO 501 1_555 F O11 92X . B 92X 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.173 ? metalc ? metalc12 E CO CO . B CO 501 1_555 H O HOH . B HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.23 ? # _chem_comp.formula 'C24 H22 N2 O5' _chem_comp.formula_weight 418.442 _chem_comp.id 92X _chem_comp.mon_nstd_flag . _chem_comp.name 1,5-dimethyl-3-(2-methylphenyl)-6-(2-oxidanyl-6-oxidanylidene-cyclohexen-1-yl)carbonyl-quinazoline-2,4-dione _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 C1 C2 92X sing 1 n n C1 C6 92X sing 2 n n C2 C3 92X sing 3 n n C3 C4 92X sing 4 n n C6 O7 92X sing 5 n n C6 C5 92X doub 6 n n C4 C5 92X sing 7 n n C4 O9 92X doub 8 n n C31 C30 92X sing 9 n n C5 C8 92X sing 10 n n C29 C30 92X doub 11 n y C29 C28 92X sing 12 n y C17 C16 92X sing 13 n n C30 C21 92X sing 14 n y O20 C18 92X doub 15 n n C28 C27 92X doub 16 n y C8 C10 92X sing 17 n n C8 O11 92X doub 18 n n C16 C10 92X doub 19 n y C16 C15 92X sing 20 n y C18 C15 92X sing 21 n n C18 N19 92X sing 22 n n C21 N19 92X sing 23 n n C21 C26 92X doub 24 n y C27 C26 92X sing 25 n y C10 C12 92X sing 26 n y C15 C14 92X doub 27 n y N19 C22 92X sing 28 n n C12 C13 92X doub 29 n y C14 C13 92X sing 30 n y C14 N24 92X sing 31 n n C22 N24 92X sing 32 n n C22 O23 92X doub 33 n n N24 C25 92X sing 34 n n C13 H1 92X sing 35 n n C17 H2 92X sing 36 n n C17 H3 92X sing 37 n n C17 H4 92X sing 38 n n C26 H5 92X sing 39 n n C28 H6 92X sing 40 n n C1 H7 92X sing 41 n n C1 H8 92X sing 42 n n C2 H9 92X sing 43 n n C2 H10 92X sing 44 n n C3 H11 92X sing 45 n n C3 H12 92X sing 46 n n O7 H13 92X sing 47 n n C12 H14 92X sing 48 n n C25 H15 92X sing 49 n n C25 H16 92X sing 50 n n C25 H17 92X sing 51 n n C27 H18 92X sing 52 n n C29 H19 92X sing 53 n n C31 H20 92X sing 54 n n C31 H21 92X sing 55 n n C31 H22 92X sing 56 n n # _atom_sites.entry_id 5YWK _atom_sites.fract_transf_matrix[1][1] 0.010444 _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] 0.010444 _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] 0.005139 _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 2 CO A 1 501 499 CO CO . D 3 92X A 1 502 500 92X LIG . E 2 CO B 1 501 499 CO CO . F 3 92X B 1 502 500 92X LIG . G 4 HOH A 1 601 1 HOH HOH . H 4 HOH B 1 601 2 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 92X . . . F 3 6.003 -23.021 29.674 1 47.78 ? C10 92X 502 B 1 HETATM 2 C C13 92X . . . F 3 4.747 -24.325 31.202 1 49.15 ? C13 92X 502 B 1 HETATM 3 C C15 92X . . . F 3 3.58 -22.923 29.633 1 48.24 ? C15 92X 502 B 1 HETATM 4 C C17 92X . . . F 3 5.042 -21.509 27.993 1 40.63 ? C17 92X 502 B 1 HETATM 5 C C21 92X . . . F 3 -0.035 -22.439 29.17 1 65.86 ? C21 92X 502 B 1 HETATM 6 C C22 92X . . . F 3 1.244 -23.817 30.7 1 58.66 ? C22 92X 502 B 1 HETATM 7 C C26 92X . . . F 3 -0.611 -23.02 28.049 1 62.87 ? C26 92X 502 B 1 HETATM 8 C C28 92X . . . F 3 -2.454 -21.488 28.199 1 61.7 ? C28 92X 502 B 1 HETATM 9 C C1 92X . . . F 3 8.035 -23.986 25.699 1 51.49 ? C1 92X 502 B 1 HETATM 10 C C2 92X . . . F 3 9.471 -24.476 25.811 1 40.4 ? C2 92X 502 B 1 HETATM 11 C C3 92X . . . F 3 10.329 -23.464 26.559 1 38.05 ? C3 92X 502 B 1 HETATM 12 C C4 92X . . . F 3 9.566 -22.85 27.731 1 34.36 ? C4 92X 502 B 1 HETATM 13 C C5 92X . . . F 3 8.109 -23.257 28.015 1 35.17 ? C5 92X 502 B 1 HETATM 14 C C6 92X . . . F 3 7.439 -23.936 27.101 1 43.93 ? C6 92X 502 B 1 HETATM 15 O O7 92X . . . F 3 6.63 -25.006 27.512 1 54.82 ? O7 92X 502 B 1 HETATM 16 C C8 92X . . . F 3 7.356 -22.552 29.143 1 38.77 ? C8 92X 502 B 1 HETATM 17 O O9 92X . . . F 3 10.119 -22.052 28.413 1 39.11 ? O9 92X 502 B 1 HETATM 18 O O11 92X . . . F 3 7.835 -21.595 29.64 1 39.26 ? O11 92X 502 B 1 HETATM 19 C C12 92X . . . F 3 5.965 -23.917 30.71 1 49.48 ? C12 92X 502 B 1 HETATM 20 C C14 92X . . . F 3 3.562 -23.829 30.667 1 56.55 ? C14 92X 502 B 1 HETATM 21 C C16 92X . . . F 3 4.837 -22.51 29.134 1 41.67 ? C16 92X 502 B 1 HETATM 22 C C18 92X . . . F 3 2.365 -22.483 29.161 1 60.05 ? C18 92X 502 B 1 HETATM 23 N N19 92X . . . F 3 1.234 -22.926 29.687 1 65.45 ? N19 92X 502 B 1 HETATM 24 O O20 92X . . . F 3 2.238 -21.704 28.279 1 58.27 ? O20 92X 502 B 1 HETATM 25 O O23 92X . . . F 3 0.222 -24.2 31.162 1 65.75 ? O23 92X 502 B 1 HETATM 26 N N24 92X . . . F 3 2.421 -24.262 31.183 1 61.58 ? N24 92X 502 B 1 HETATM 27 C C25 92X . . . F 3 2.418 -25.221 32.28 1 54.55 ? C25 92X 502 B 1 HETATM 28 C C27 92X . . . F 3 -1.82 -22.543 27.565 1 59.8 ? C27 92X 502 B 1 HETATM 29 C C29 92X . . . F 3 -1.88 -20.905 29.319 1 55.3 ? C29 92X 502 B 1 HETATM 30 C C30 92X . . . F 3 -0.671 -21.381 29.803 1 60.7 ? C30 92X 502 B 1 HETATM 31 C C31 92X . . . F 3 -0.039 -20.736 31.037 1 61.06 ? C31 92X 502 B 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 267 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 31 #