data_4XS3
#
_model_server_result.job_id            Km8F5D6BOyQ--rRtBSnlBA 
_model_server_result.datetime_utc      '2025-03-05 19:07:00' 
_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          4xs3 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","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 . . . E 2 1.245 -41.483 18.273 1 111.63 ? C10 42W 501 B 1 
HETATM 2 C C13 42W . . . E 2 3.577 -41.144 17.889 1 114.75 ? C13 42W 501 B 1 
HETATM 3 C C15 42W . . . E 2 7.655 -42.516 17.979 1 104.86 ? C15 42W 501 B 1 
HETATM 4 C C01 42W . . . E 2 9.5 -41.482 16.706 1 100.59 ? C01 42W 501 B 1 
HETATM 5 N N01 42W . . . E 2 8.167 -41.523 17.276 1 108.78 ? N01 42W 501 B 1 
HETATM 6 C C02 42W . . . E 2 2.615 -44.449 16.527 1 114.83 ? C02 42W 501 B 1 
HETATM 7 C C03 42W . . . E 2 1.345 -46.339 17.646 1 109.71 ? C03 42W 501 B 1 
HETATM 8 C C04 42W . . . E 2 1.257 -47.41 18.524 1 89.43 ? C04 42W 501 B 1 
HETATM 9 C C05 42W . . . E 2 2.367 -47.786 19.26 1 76.81 ? C05 42W 501 B 1 
HETATM 10 C C06 42W . . . E 2 3.553 -47.084 19.122 1 82.26 ? C06 42W 501 B 1 
HETATM 11 C C07 42W . . . E 2 3.642 -46.012 18.245 1 95.88 ? C07 42W 501 B 1 
HETATM 12 C C08 42W . . . E 2 2.531 -45.629 17.507 1 112.3 ? C08 42W 501 B 1 
HETATM 13 N N02 42W . . . E 2 2.532 -43.146 17.182 1 119.31 ? N02 42W 501 B 1 
HETATM 14 O O01 42W . . . E 2 0.23 -43.522 17.533 1 131.34 ? O01 42W 501 B 1 
HETATM 15 C C09 42W . . . E 2 2.369 -40.679 18.392 1 110.24 ? C09 42W 501 B 1 
HETATM 16 C C11 42W . . . E 2 1.371 -42.716 17.652 1 121.48 ? C11 42W 501 B 1 
HETATM 17 C C12 42W . . . E 2 3.617 -42.392 17.277 1 113.74 ? C12 42W 501 B 1 
HETATM 18 C C14 42W . . . E 2 4.82 -40.254 18.021 1 104.96 ? C14 42W 501 B 1 
HETATM 19 O O 42W . . . E 2 7.401 -39.348 16.512 1 85.94 ? O 42W 501 B 1 
HETATM 20 S S 42W . . . E 2 8.515 -44.062 18.39 1 98.4 ? S 42W 501 B 1 
HETATM 21 N N 42W . . . E 2 6.423 -42.221 18.341 1 104.07 ? N 42W 501 B 1 
HETATM 22 C C16 42W . . . E 2 6.134 -41.022 17.86 1 104.46 ? C16 42W 501 B 1 
HETATM 23 C C 42W . . . E 2 7.257 -40.571 17.178 1 101.26 ? C 42W 501 B 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           286 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           23 
#