data_8RDT
#
_model_server_result.job_id            J9FUeVsbmBdrGM6GUf7zwg 
_model_server_result.datetime_utc      '2024-11-26 20:06:30' 
_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          8rdt 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":202}' 
#
_entry.id    8RDT 
#
_exptl.entry_id    8RDT 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              334.324 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            (5~{S})-3-(2,3,4-trimethoxyphenyl)-1-oxa-2,9-diazaspiro[4.5]dec-2-ene-8,10-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            8RDT 
_cell.length_a            56.441 
_cell.length_b            59.488 
_cell.length_c            88.11 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8RDT 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? monomeric 1 author_defined_assembly 1 
? monomeric 1 author_defined_assembly 2 
? monomeric 1 author_defined_assembly 3 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,D,E,F,J 1 1 
B,G,H,K 2 1 
C,I,L 3 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 E N N 
? 3 H 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
metalc ? metalc1 A SG CYS 25 A CYS 24 1_555 D ZN ZN . A ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.287 ? 
metalc ? metalc2 A SG CYS 28 A CYS 27 1_555 D ZN ZN . A ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.312 ? 
metalc ? metalc3 A SG CYS 91 A CYS 90 1_555 D ZN ZN . A ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.359 ? 
metalc ? metalc4 A SG CYS 94 A CYS 93 1_555 D ZN ZN . A ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.294 ? 
metalc ? metalc5 B SG CYS 25 B CYS 24 1_555 G ZN ZN . B ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.38 ? 
metalc ? metalc6 B SG CYS 28 B CYS 27 1_555 G ZN ZN . B ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.345 ? 
metalc ? metalc7 B SG CYS 91 B CYS 90 1_555 G ZN ZN . B ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.318 ? 
metalc ? metalc8 B SG CYS 94 B CYS 93 1_555 G ZN ZN . B ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.285 ? 
metalc ? metalc9 C SG CYS 25 C CYS 24 1_555 I ZN ZN . C ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.353 ? 
metalc ? metalc10 C SG CYS 28 C CYS 27 1_555 I ZN ZN . C ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.315 ? 
metalc ? metalc11 C SG CYS 91 C CYS 90 1_555 I ZN ZN . C ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.317 ? 
metalc ? metalc12 C SG CYS 94 C CYS 93 1_555 I ZN ZN . C ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.321 ? 
#
_chem_comp.formula           'C16 H18 N2 O6' 
_chem_comp.formula_weight    334.324 
_chem_comp.id                A1HZ2 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              (5~{S})-3-(2,3,4-trimethoxyphenyl)-1-oxa-2,9-diazaspiro[4.5]dec-2-ene-8,10-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
C12 O2 A1HZ2 sing 1 n n 
O2 C11 A1HZ2 sing 2 n n 
C14 O3 A1HZ2 sing 3 n n 
C11 C10 A1HZ2 doub 4 n y 
C11 C13 A1HZ2 sing 5 n y 
C10 C9 A1HZ2 sing 6 n y 
O3 C13 A1HZ2 sing 7 n n 
C13 C15 A1HZ2 doub 8 n y 
C9 C8 A1HZ2 doub 9 n y 
C15 C8 A1HZ2 sing 10 n y 
C15 O4 A1HZ2 sing 11 n n 
C8 C7 A1HZ2 sing 12 n n 
O4 C16 A1HZ2 sing 13 n n 
C6 C7 A1HZ2 sing 14 n n 
C6 C5 A1HZ2 sing 15 n n 
C7 N2 A1HZ2 doub 16 n n 
O1 C1 A1HZ2 doub 17 n n 
C1 N1 A1HZ2 sing 18 n n 
C1 C5 A1HZ2 sing 19 n n 
N2 O5 A1HZ2 sing 20 n n 
N1 C2 A1HZ2 sing 21 n n 
C5 C4 A1HZ2 sing 22 n n 
C5 O5 A1HZ2 sing 23 n n 
O6 C2 A1HZ2 doub 24 n n 
C2 C3 A1HZ2 sing 25 n n 
C4 C3 A1HZ2 sing 26 n n 
C3 H1 A1HZ2 sing 27 n n 
C3 H2 A1HZ2 sing 28 n n 
C6 H3 A1HZ2 sing 29 n n 
C6 H4 A1HZ2 sing 30 n n 
C4 H5 A1HZ2 sing 31 n n 
C4 H6 A1HZ2 sing 32 n n 
N1 H7 A1HZ2 sing 33 n n 
C16 H10 A1HZ2 sing 34 n n 
C16 H11 A1HZ2 sing 35 n n 
C16 H12 A1HZ2 sing 36 n n 
C14 H13 A1HZ2 sing 37 n n 
C14 H14 A1HZ2 sing 38 n n 
C14 H15 A1HZ2 sing 39 n n 
C12 H16 A1HZ2 sing 40 n n 
C12 H17 A1HZ2 sing 41 n n 
C12 H18 A1HZ2 sing 42 n n 
C10 H19 A1HZ2 sing 43 n n 
C9 H20 A1HZ2 sing 44 n n 
#
_atom_sites.entry_id                     8RDT 
_atom_sites.fract_transf_matrix[1][1]    0.017718 
_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]    0.01681 
_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]    0.011349 
_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
D 2 ZN A 1 201 150 ZN ZN . 
E 3 A1HZ2 A 1 202 201 A1HZ2 069 . 
F 4 PO4 A 1 203 1 PO4 PO4 . 
G 2 ZN B 1 201 150 ZN ZN . 
H 3 A1HZ2 B 1 202 201 A1HZ2 069 . 
I 2 ZN C 1 201 150 ZN ZN . 
J 5 HOH A 1 301 23 HOH HOH . 
J 5 HOH A 2 302 29 HOH HOH . 
J 5 HOH A 3 303 33 HOH HOH . 
J 5 HOH A 4 304 55 HOH HOH . 
J 5 HOH A 5 305 19 HOH HOH . 
J 5 HOH A 6 306 22 HOH HOH . 
J 5 HOH A 7 307 26 HOH HOH . 
J 5 HOH A 8 308 51 HOH HOH . 
J 5 HOH A 9 309 10 HOH HOH . 
J 5 HOH A 10 310 32 HOH HOH . 
J 5 HOH A 11 311 48 HOH HOH . 
J 5 HOH A 12 312 59 HOH HOH . 
J 5 HOH A 13 313 39 HOH HOH . 
J 5 HOH A 14 314 34 HOH HOH . 
J 5 HOH A 15 315 6 HOH HOH . 
J 5 HOH A 16 316 58 HOH HOH . 
J 5 HOH A 17 317 53 HOH HOH . 
J 5 HOH A 18 318 31 HOH HOH . 
J 5 HOH A 19 319 5 HOH HOH . 
J 5 HOH A 20 320 3 HOH HOH . 
J 5 HOH A 21 321 63 HOH HOH . 
J 5 HOH A 22 322 57 HOH HOH . 
K 5 HOH B 1 301 15 HOH HOH . 
K 5 HOH B 2 302 7 HOH HOH . 
K 5 HOH B 3 303 20 HOH HOH . 
K 5 HOH B 4 304 61 HOH HOH . 
K 5 HOH B 5 305 56 HOH HOH . 
K 5 HOH B 6 306 67 HOH HOH . 
K 5 HOH B 7 307 14 HOH HOH . 
K 5 HOH B 8 308 21 HOH HOH . 
K 5 HOH B 9 309 12 HOH HOH . 
K 5 HOH B 10 310 28 HOH HOH . 
K 5 HOH B 11 311 45 HOH HOH . 
K 5 HOH B 12 312 60 HOH HOH . 
K 5 HOH B 13 313 40 HOH HOH . 
K 5 HOH B 14 314 54 HOH HOH . 
K 5 HOH B 15 315 38 HOH HOH . 
K 5 HOH B 16 316 36 HOH HOH . 
K 5 HOH B 17 317 65 HOH HOH . 
K 5 HOH B 18 318 44 HOH HOH . 
K 5 HOH B 19 319 35 HOH HOH . 
K 5 HOH B 20 320 37 HOH HOH . 
K 5 HOH B 21 321 62 HOH HOH . 
K 5 HOH B 22 322 13 HOH HOH . 
K 5 HOH B 23 323 47 HOH HOH . 
K 5 HOH B 24 324 1 HOH HOH . 
K 5 HOH B 25 325 8 HOH HOH . 
K 5 HOH B 26 326 17 HOH HOH . 
K 5 HOH B 27 327 52 HOH HOH . 
K 5 HOH B 28 328 18 HOH HOH . 
K 5 HOH B 29 329 69 HOH HOH . 
K 5 HOH B 30 330 68 HOH HOH . 
K 5 HOH B 31 331 49 HOH HOH . 
L 5 HOH C 1 301 42 HOH HOH . 
L 5 HOH C 2 302 66 HOH HOH . 
L 5 HOH C 3 303 41 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 C3 A1HZ2 . . . H 3 23.946 12.253 27.151 1 39.09 ? C3 A1HZ2 202 B 1 
HETATM 2 O O3 A1HZ2 . . . H 3 20.639 19.946 31.585 1 73.16 ? O3 A1HZ2 202 B 1 
HETATM 3 C C2 A1HZ2 . . . H 3 22.932 12.155 26.053 1 38.02 ? C2 A1HZ2 202 B 1 
HETATM 4 C C1 A1HZ2 . . . H 3 22.366 14.538 26.321 1 45.06 ? C1 A1HZ2 202 B 1 
HETATM 5 C C6 A1HZ2 . . . H 3 22.666 14.665 28.843 1 53.08 ? C6 A1HZ2 202 B 1 
HETATM 6 C C5 A1HZ2 . . . H 3 23.368 14.692 27.488 1 47.37 ? C5 A1HZ2 202 B 1 
HETATM 7 C C4 A1HZ2 . . . H 3 24.481 13.661 27.369 1 45.02 ? C4 A1HZ2 202 B 1 
HETATM 8 O O2 A1HZ2 . . . H 3 19.382 18.296 33.272 1 72.68 ? O2 A1HZ2 202 B 1 
HETATM 9 O O6 A1HZ2 . . . H 3 22.708 11.121 25.459 1 33.59 ? O6 A1HZ2 202 B 1 
HETATM 10 N N1 A1HZ2 . . . H 3 22.202 13.291 25.769 1 39.04 ? N1 A1HZ2 202 B 1 
HETATM 11 O O1 A1HZ2 . . . H 3 21.717 15.488 25.911 1 43.98 ? O1 A1HZ2 202 B 1 
HETATM 12 O O5 A1HZ2 . . . H 3 24.015 16.006 27.499 1 50.82 ? O5 A1HZ2 202 B 1 
HETATM 13 N N2 A1HZ2 . . . H 3 23.399 16.833 28.479 1 51.2 ? N2 A1HZ2 202 B 1 
HETATM 14 C C7 A1HZ2 . . . H 3 22.609 16.13 29.187 1 54.27 ? C7 A1HZ2 202 B 1 
HETATM 15 C C8 A1HZ2 . . . H 3 21.764 16.707 30.251 1 59.58 ? C8 A1HZ2 202 B 1 
HETATM 16 C C15 A1HZ2 . . . H 3 21.607 18.094 30.411 1 66.03 ? C15 A1HZ2 202 B 1 
HETATM 17 O O4 A1HZ2 . . . H 3 22.247 18.951 29.55 1 69.66 ? O4 A1HZ2 202 B 1 
HETATM 18 C C16 A1HZ2 . . . H 3 23.143 19.919 30.096 1 71.58 ? C16 A1HZ2 202 B 1 
HETATM 19 C C13 A1HZ2 . . . H 3 20.796 18.583 31.44 1 70.17 ? C13 A1HZ2 202 B 1 
HETATM 20 C C14 A1HZ2 . . . H 3 19.316 20.422 31.348 1 73.84 ? C14 A1HZ2 202 B 1 
HETATM 21 C C11 A1HZ2 . . . H 3 20.146 17.7 32.311 1 70.51 ? C11 A1HZ2 202 B 1 
HETATM 22 C C12 A1HZ2 . . . H 3 18.175 17.644 33.66 1 75.25 ? C12 A1HZ2 202 B 1 
HETATM 23 C C10 A1HZ2 . . . H 3 20.294 16.33 32.143 1 66.21 ? C10 A1HZ2 202 B 1 
HETATM 24 C C9 A1HZ2 . . . H 3 21.093 15.844 31.124 1 62.46 ? C9 A1HZ2 202 B 1 
#
_model_server_stats.io_time_ms              57 
_model_server_stats.parse_time_ms           66 
_model_server_stats.create_model_time_ms    70 
_model_server_stats.query_time_ms           1309 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           24 
#