data_8Y9G
#
_model_server_result.job_id            WKvaW7wLwwnYGS_upIkLVA 
_model_server_result.datetime_utc      '2025-03-13 01:47:56' 
_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          8y9g 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"J","auth_seq_id":502}' 
#
_entry.id    8Y9G 
#
_exptl.entry_id    8Y9G 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              234.254 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            (3~{Z},6~{S})-3-(1~{H}-imidazol-4-ylmethylidene)-6-propan-2-yl-piperazine-2,5-dione 
_entity.pdbx_number_of_molecules    4 
_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            8Y9G 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8Y9G 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_pdbx_struct_assembly.details               author_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P 
_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    ? 
_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 F N N 
? 3 H N N 
? 3 J N N 
? 3 L N N 
#
_chem_comp.formula           'C11 H14 N4 O2' 
_chem_comp.formula_weight    234.254 
_chem_comp.id                A1LYF 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              (3~{Z},6~{S})-3-(1~{H}-imidazol-4-ylmethylidene)-6-propan-2-yl-piperazine-2,5-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
N5 C6 A1LYF sing 1 n n 
N5 C4 A1LYF sing 2 n n 
C6 C7 A1LYF sing 3 n n 
C6 C15 A1LYF sing 4 n n 
O10 C7 A1LYF doub 5 n n 
C16 C15 A1LYF sing 6 n n 
C7 N8 A1LYF sing 7 n n 
C15 C17 A1LYF sing 8 n n 
C4 O9 A1LYF doub 9 n n 
C4 C3 A1LYF sing 10 n n 
N8 C3 A1LYF sing 11 n n 
C3 C2 A1LYF doub 12 z n 
C2 C1 A1LYF sing 13 n n 
N14 C1 A1LYF sing 14 n y 
N14 C13 A1LYF doub 15 n y 
C1 C11 A1LYF doub 16 n y 
C13 N12 A1LYF sing 17 n y 
C11 N12 A1LYF sing 18 n y 
C2 H1 A1LYF sing 19 n n 
N5 H4 A1LYF sing 20 n n 
C6 H5 A1LYF sing 21 n n 
N8 H6 A1LYF sing 22 n n 
C11 H7 A1LYF sing 23 n n 
N12 H8 A1LYF sing 24 n n 
C13 H9 A1LYF sing 25 n n 
C15 H11 A1LYF sing 26 n n 
C16 H12 A1LYF sing 27 n n 
C16 H13 A1LYF sing 28 n n 
C16 H14 A1LYF sing 29 n n 
C17 H15 A1LYF sing 30 n n 
C17 H16 A1LYF sing 31 n n 
C17 H17 A1LYF sing 32 n n 
#
_atom_sites.entry_id                     8Y9G 
_atom_sites.fract_transf_matrix[1][1]    1 
_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]    1 
_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]    1 
_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
E 2 DST A 1 501 502 DST DST . 
F 3 A1LYF A 1 502 503 A1LYF LiG . 
G 2 DST B 1 501 502 DST DST . 
H 3 A1LYF B 1 502 503 A1LYF LiG . 
I 2 DST C 1 501 502 DST DST . 
J 3 A1LYF C 1 502 503 A1LYF LiG . 
K 2 DST D 1 501 502 DST DST . 
L 3 A1LYF D 1 502 503 A1LYF LiG . 
M 4 HOH A 1 601 1 HOH HOH . 
N 4 HOH B 1 601 2 HOH HOH . 
O 4 HOH C 1 601 3 HOH HOH . 
P 4 HOH D 1 601 4 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 A1LYF . . . J 3 150.603 152.148 158.899 1 20 ? C1 A1LYF 502 C 1 
HETATM 2 C C2 A1LYF . . . J 3 149.628 152.987 159.48 1 20 ? C2 A1LYF 502 C 1 
HETATM 3 C C3 A1LYF . . . J 3 148.899 152.768 160.608 1 20 ? C3 A1LYF 502 C 1 
HETATM 4 C C4 A1LYF . . . J 3 148.359 153.91 161.323 1 20 ? C4 A1LYF 502 C 1 
HETATM 5 N N5 A1LYF . . . J 3 147.263 153.67 162.06 1 20 ? N5 A1LYF 502 C 1 
HETATM 6 C C6 A1LYF . . . J 3 146.562 152.393 162.162 1 20 ? C6 A1LYF 502 C 1 
HETATM 7 C C7 A1LYF . . . J 3 147.463 151.23 161.788 1 20 ? C7 A1LYF 502 C 1 
HETATM 8 N N8 A1LYF . . . J 3 148.575 151.517 161.076 1 20 ? N8 A1LYF 502 C 1 
HETATM 9 O O9 A1LYF . . . J 3 148.864 155.016 161.235 1 20 ? O9 A1LYF 502 C 1 
HETATM 10 O O10 A1LYF . . . J 3 147.21 150.091 162.139 1 20 ? O10 A1LYF 502 C 1 
HETATM 11 C C11 A1LYF . . . J 3 151.499 152.456 157.914 1 20 ? C11 A1LYF 502 C 1 
HETATM 12 N N12 A1LYF . . . J 3 152.243 151.333 157.717 1 20 ? N12 A1LYF 502 C 1 
HETATM 13 C C13 A1LYF . . . J 3 151.794 150.403 158.553 1 20 ? C13 A1LYF 502 C 1 
HETATM 14 N N14 A1LYF . . . J 3 150.798 150.833 159.3 1 20 ? N14 A1LYF 502 C 1 
HETATM 15 C C15 A1LYF . . . J 3 145.238 152.365 161.373 1 20 ? C15 A1LYF 502 C 1 
HETATM 16 C C16 A1LYF . . . J 3 145.422 152.589 159.878 1 20 ? C16 A1LYF 502 C 1 
HETATM 17 C C17 A1LYF . . . J 3 144.21 153.318 161.94 1 20 ? C17 A1LYF 502 C 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    20 
_model_server_stats.query_time_ms           234 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           17 
#