data_4XRX
#
_model_server_result.job_id            8SIX8q1DQibuBZj0qmXPtg 
_model_server_result.datetime_utc      '2025-03-05 19:10:58' 
_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          4xrx 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":502}' 
#
_entry.id    4XRX 
#
_exptl.entry_id    4XRX 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              235.262 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            5-[(E)-(1-methyl-5-oxo-2-thioxoimidazolidin-4-ylidene)methyl]pyridin-2(1H)-one 
_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            4XRX 
_cell.length_a            82.405 
_cell.length_b            82.405 
_cell.length_c            304.301 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4XRX 
_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 
_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                      3 
_struct_asym.id                             D 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    N 
#
_chem_comp.formula           'C10 H9 N3 O2 S' 
_chem_comp.formula_weight    235.262 
_chem_comp.id                42V 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              5-[(E)-(1-methyl-5-oxo-2-thioxoimidazolidin-4-ylidene)methyl]pyridin-2(1H)-one 
_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
C N01 42V sing 1 n n 
S C03 42V doub 2 n n 
N01 C03 42V sing 3 n n 
N01 C01 42V sing 4 n n 
C03 N02 42V sing 5 n n 
C01 O01 42V doub 6 n n 
C01 C02 42V sing 7 n n 
N02 C02 42V sing 8 n n 
C07 C06 42V doub 9 n n 
C07 C08 42V sing 10 n n 
C06 C05 42V sing 11 n n 
C02 C04 42V doub 12 e n 
O C08 42V doub 13 n n 
C08 N 42V sing 14 n n 
C05 C04 42V sing 15 n n 
C05 C09 42V doub 16 n n 
N C09 42V sing 17 n n 
N H1 42V sing 18 n n 
C H2 42V sing 19 n n 
C H3 42V sing 20 n n 
C H4 42V sing 21 n n 
C04 H5 42V sing 22 n n 
C06 H7 42V sing 23 n n 
C07 H8 42V sing 24 n n 
C09 H9 42V sing 25 n n 
N02 H6 42V sing 26 n n 
#
_atom_sites.entry_id                     4XRX 
_atom_sites.fract_transf_matrix[1][1]    0.012135 
_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]    0.012135 
_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]    0.003286 
_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 NDP A 1 501 501 NDP NDP . 
D 3 42V A 1 502 1 42V UNK . 
E 2 NDP B 1 501 502 NDP 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 N N 42V . . . D 3 45.619 -9.593 -13.564 1 78.99 ? N 42V 502 A 1 
HETATM 2 C C 42V . . . D 3 37.796 -10.149 -15.142 1 81.68 ? C 42V 502 A 1 
HETATM 3 O O 42V . . . D 3 46.004 -7.272 -14.072 1 78.31 ? O 42V 502 A 1 
HETATM 4 C C01 42V . . . D 3 40.117 -10.493 -14.412 1 89.53 ? C01 42V 502 A 1 
HETATM 5 C C02 42V . . . D 3 41 -11.681 -14.093 1 90.28 ? C02 42V 502 A 1 
HETATM 6 C C03 42V . . . D 3 38.787 -12.366 -14.757 1 91.39 ? C03 42V 502 A 1 
HETATM 7 C C04 42V . . . D 3 42.417 -11.802 -13.633 1 86.4 ? C04 42V 502 A 1 
HETATM 8 C C05 42V . . . D 3 43.33 -10.595 -13.759 1 85.43 ? C05 42V 502 A 1 
HETATM 9 C C06 42V . . . D 3 42.877 -9.27 -14.184 1 82.49 ? C06 42V 502 A 1 
HETATM 10 C C07 42V . . . D 3 43.743 -8.158 -14.29 1 80.5 ? C07 42V 502 A 1 
HETATM 11 C C08 42V . . . D 3 45.151 -8.341 -13.973 1 78.68 ? C08 42V 502 A 1 
HETATM 12 C C09 42V . . . D 3 44.717 -10.704 -13.457 1 81.34 ? C09 42V 502 A 1 
HETATM 13 N N01 42V . . . D 3 38.896 -10.995 -14.773 1 89.69 ? N01 42V 502 A 1 
HETATM 14 N N02 42V . . . D 3 40.1 -12.865 -14.327 1 92.78 ? N02 42V 502 A 1 
HETATM 15 O O01 42V . . . D 3 40.43 -9.304 -14.365 1 87.34 ? O01 42V 502 A 1 
HETATM 16 S S 42V . . . D 3 37.482 -13.321 -15.125 1 89.97 ? S 42V 502 A 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    17 
_model_server_stats.query_time_ms           269 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           16 
#