data_4XS3 # _model_server_result.job_id 6QYpMF8CKu4hf9hjPhVgag _model_server_result.datetime_utc '2025-03-05 18:53:03' _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 4xs3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":501}' # _entry.id 4XS3 # _exptl.entry_id 4XS3 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 325.385 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (E)-1-benzyl-5-((1-methyl-5-oxo-2-thioxoimidazolidin-4-ylidene)methyl)pyridin-2(1H)-one _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 4XS3 _cell.length_a 82.586 _cell.length_b 82.586 _cell.length_c 306.599 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4XS3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 43 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 _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 ? 2 C N N ? 2 E N N # _chem_comp.formula 'C17 H15 N3 O2 S' _chem_comp.formula_weight 325.385 _chem_comp.id 42W _chem_comp.mon_nstd_flag . _chem_comp.name (E)-1-benzyl-5-((1-methyl-5-oxo-2-thioxoimidazolidin-4-ylidene)methyl)pyridin-2(1H)-one _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 1-benzyl-5-[(E)-(1-methyl-5-oxo-2-thioxoimidazolidin-4-ylidene)methyl]pyridin-2(1H)-one # 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 C05 C04 42W doub 1 n y C05 C06 42W sing 2 n y C04 C03 42W sing 3 n y C06 C07 42W doub 4 n y C14 C13 42W sing 5 n n C14 C16 42W doub 6 e n C03 C08 42W doub 7 n y C09 C13 42W sing 8 n n C09 C10 42W doub 9 n n C13 C12 42W doub 10 n n C16 N 42W sing 11 n n C16 C 42W sing 12 n n C10 C11 42W sing 13 n n C07 C08 42W sing 14 n y C08 C02 42W sing 15 n n N C15 42W sing 16 n n C12 N02 42W sing 17 n n C11 N02 42W sing 18 n n C11 O01 42W doub 19 n n N02 C02 42W sing 20 n n C O 42W doub 21 n n C N01 42W sing 22 n n C15 N01 42W sing 23 n n C15 S 42W doub 24 n n N01 C01 42W sing 25 n n C10 H1 42W sing 26 n n C01 H2 42W sing 27 n n C01 H3 42W sing 28 n n C01 H4 42W sing 29 n n C02 H5 42W sing 30 n n C02 H6 42W sing 31 n n C03 H7 42W sing 32 n n C04 H8 42W sing 33 n n C05 H9 42W sing 34 n n C06 H10 42W sing 35 n n C07 H11 42W sing 36 n n C09 H12 42W sing 37 n n C12 H13 42W sing 38 n n C14 H14 42W sing 39 n n N H15 42W sing 40 n n # _atom_sites.entry_id 4XS3 _atom_sites.fract_transf_matrix[1][1] 0.012109 _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] 0.012109 _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] 0.003262 _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 42W A 1 501 502 42W 42W . D 3 NAP A 1 502 2 NAP NDP . E 2 42W B 1 501 502 42W 42W . F 3 NAP B 1 502 1 NAP NDP . # 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 42W . . . C 2 -3.046 -33.863 -14.325 1 86.85 ? C10 42W 501 A 1 HETATM 2 C C13 42W . . . C 2 -1.089 -32.5 -14.118 1 98.1 ? C13 42W 501 A 1 HETATM 3 C C15 42W . . . C 2 1.795 -29.126 -14.654 1 106.51 ? C15 42W 501 A 1 HETATM 4 C C01 42W . . . C 2 4.168 -29.155 -13.949 1 83.07 ? C01 42W 501 A 1 HETATM 5 N N01 42W . . . C 2 2.86 -29.744 -14.17 1 100.58 ? N01 42W 501 A 1 HETATM 6 C C02 42W . . . C 2 -4.149 -30.409 -13.688 1 95.74 ? C02 42W 501 A 1 HETATM 7 C C03 42W . . . C 2 -4.852 -28.759 -15.474 1 85.42 ? C03 42W 501 A 1 HETATM 8 C C04 42W . . . C 2 -4.688 -27.58 -16.187 1 79.38 ? C04 42W 501 A 1 HETATM 9 C C05 42W . . . C 2 -3.621 -26.741 -15.905 1 74.12 ? C05 42W 501 A 1 HETATM 10 C C06 42W . . . C 2 -2.717 -27.081 -14.911 1 85.48 ? C06 42W 501 A 1 HETATM 11 C C07 42W . . . C 2 -2.882 -28.26 -14.199 1 96.05 ? C07 42W 501 A 1 HETATM 12 C C08 42W . . . C 2 -3.941 -29.113 -14.488 1 96.61 ? C08 42W 501 A 1 HETATM 13 N N02 42W . . . C 2 -3.24 -31.532 -13.921 1 103.45 ? N02 42W 501 A 1 HETATM 14 O O01 42W . . . C 2 -5.195 -32.834 -14.114 1 75.8 ? O01 42W 501 A 1 HETATM 15 C C09 42W . . . C 2 -1.666 -33.748 -14.326 1 89.34 ? C09 42W 501 A 1 HETATM 16 C C11 42W . . . C 2 -3.797 -32.72 -14.114 1 91.93 ? C11 42W 501 A 1 HETATM 17 C C12 42W . . . C 2 -1.915 -31.395 -13.904 1 103.57 ? C12 42W 501 A 1 HETATM 18 C C14 42W . . . C 2 0.444 -32.463 -14.125 1 93.49 ? C14 42W 501 A 1 HETATM 19 O O 42W . . . C 2 3.361 -31.996 -13.398 1 78.74 ? O 42W 501 A 1 HETATM 20 S S 42W . . . C 2 1.75 -27.376 -15.152 1 92.12 ? S 42W 501 A 1 HETATM 21 N N 42W . . . C 2 0.773 -29.968 -14.721 1 102.04 ? N 42W 501 A 1 HETATM 22 C C16 42W . . . C 2 1.194 -31.138 -14.266 1 99.01 ? C16 42W 501 A 1 HETATM 23 C C 42W . . . C 2 2.53 -30.996 -13.919 1 94.07 ? C 42W 501 A 1 # _model_server_stats.io_time_ms 38 _model_server_stats.parse_time_ms 119 _model_server_stats.create_model_time_ms 110 _model_server_stats.query_time_ms 347 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 23 #