data_5ZXF
#
_model_server_result.job_id            IdjXzUE6X6tJxGdRbl_W4Q 
_model_server_result.datetime_utc      '2025-01-25 14:18:35' 
_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          5zxf 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":101}' 
#
_entry.id    5ZXF 
#
_exptl.entry_id    5ZXF 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              581.49 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            4-({(4S,5R)-4,5-bis(4-chlorophenyl)-2-[4-methoxy-2-(propan-2-yloxy)phenyl]-4,5-dihydro-1H-imidazol-1-yl}carbonyl)piperazin-2-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            5ZXF 
_cell.length_a            42.575 
_cell.length_b            43.222 
_cell.length_c            53.853 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5ZXF 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_pdbx_struct_assembly.details               author_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C 
_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                      2 
_struct_asym.id                             B 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    N 
#
_chem_comp.formula           'C30 H30 Cl2 N4 O4' 
_chem_comp.formula_weight    581.49 
_chem_comp.id                NUT 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              4-({(4S,5R)-4,5-bis(4-chlorophenyl)-2-[4-methoxy-2-(propan-2-yloxy)phenyl]-4,5-dihydro-1H-imidazol-1-yl}carbonyl)piperazin-2-one 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     'Nutlin 3a' 
#
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
O2 C28 NUT doub 237 n n 
C28 C29 NUT sing 238 n n 
C28 N3 NUT sing 239 n n 
C29 N2 NUT sing 240 n n 
O3 C25 NUT doub 241 n n 
N3 C27 NUT sing 242 n n 
C25 N2 NUT sing 243 n n 
C25 N1 NUT sing 244 n n 
N2 C26 NUT sing 245 n n 
C27 C26 NUT sing 246 n n 
C11 C18 NUT sing 247 n n 
C11 N NUT sing 248 n n 
C11 C12 NUT sing 249 n n 
C3 C2 NUT doub 250 n y 
C3 C9 NUT sing 251 n y 
N1 C18 NUT sing 252 n n 
N1 C10 NUT sing 253 n n 
C2 C1 NUT sing 254 n y 
C17 C12 NUT doub 255 n y 
C17 C16 NUT sing 256 n y 
C18 C19 NUT sing 257 n n 
C10 N NUT doub 258 n n 
C10 C9 NUT sing 259 n n 
C9 C5 NUT doub 260 n y 
C O NUT sing 261 n n 
C12 C13 NUT sing 262 n y 
C1 O NUT sing 263 n n 
C1 C4 NUT doub 264 n y 
C16 C15 NUT doub 265 n y 
C5 C4 NUT sing 266 n y 
C5 O1 NUT sing 267 n n 
C8 C6 NUT sing 268 n n 
O1 C6 NUT sing 269 n n 
C19 C24 NUT doub 270 n y 
C19 C20 NUT sing 271 n y 
C24 C23 NUT sing 272 n y 
C13 C14 NUT doub 273 n y 
C15 C14 NUT sing 274 n y 
C15 CL NUT sing 275 n n 
C6 C7 NUT sing 276 n n 
C20 C21 NUT doub 277 n y 
C23 C22 NUT doub 278 n y 
C21 C22 NUT sing 279 n y 
C22 CL1 NUT sing 280 n n 
C29 H1 NUT sing 281 n n 
C29 H2 NUT sing 282 n n 
N3 H3 NUT sing 283 n n 
C27 H4 NUT sing 284 n n 
C27 H5 NUT sing 285 n n 
C26 H6 NUT sing 286 n n 
C26 H7 NUT sing 287 n n 
C3 H9 NUT sing 288 n n 
C2 H10 NUT sing 289 n n 
C6 H11 NUT sing 290 n n 
C8 H12 NUT sing 291 n n 
C8 H13 NUT sing 292 n n 
C8 H14 NUT sing 293 n n 
C7 H15 NUT sing 294 n n 
C7 H16 NUT sing 295 n n 
C7 H17 NUT sing 296 n n 
C4 H18 NUT sing 297 n n 
C H19 NUT sing 298 n n 
C H20 NUT sing 299 n n 
C H21 NUT sing 300 n n 
C18 H22 NUT sing 301 n n 
C24 H23 NUT sing 302 n n 
C23 H24 NUT sing 303 n n 
C21 H25 NUT sing 304 n n 
C20 H26 NUT sing 305 n n 
C11 H27 NUT sing 306 n n 
C17 H30 NUT sing 307 n n 
C16 H31 NUT sing 308 n n 
C14 H32 NUT sing 309 n n 
C13 H33 NUT sing 310 n n 
#
_atom_sites.entry_id                     5ZXF 
_atom_sites.fract_transf_matrix[1][1]    0.023488 
_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]    0.023136 
_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]    0.018569 
_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
B 2 NUT A 1 101 101 NUT NUT . 
C 3 HOH A 1 201 34 HOH HOH . 
C 3 HOH A 2 202 6 HOH HOH . 
C 3 HOH A 3 203 5 HOH HOH . 
C 3 HOH A 4 204 29 HOH HOH . 
C 3 HOH A 5 205 10 HOH HOH . 
C 3 HOH A 6 206 17 HOH HOH . 
C 3 HOH A 7 207 25 HOH HOH . 
C 3 HOH A 8 208 8 HOH HOH . 
C 3 HOH A 9 209 1 HOH HOH . 
C 3 HOH A 10 210 12 HOH HOH . 
C 3 HOH A 11 211 33 HOH HOH . 
C 3 HOH A 12 212 36 HOH HOH . 
C 3 HOH A 13 213 2 HOH HOH . 
C 3 HOH A 14 214 11 HOH HOH . 
C 3 HOH A 15 215 19 HOH HOH . 
C 3 HOH A 16 216 31 HOH HOH . 
C 3 HOH A 17 217 20 HOH HOH . 
C 3 HOH A 18 218 13 HOH HOH . 
C 3 HOH A 19 219 24 HOH HOH . 
C 3 HOH A 20 220 26 HOH HOH . 
C 3 HOH A 21 221 27 HOH HOH . 
C 3 HOH A 22 222 30 HOH HOH . 
C 3 HOH A 23 223 4 HOH HOH . 
C 3 HOH A 24 224 15 HOH HOH . 
C 3 HOH A 25 225 35 HOH HOH . 
C 3 HOH A 26 226 9 HOH HOH . 
C 3 HOH A 27 227 28 HOH HOH . 
C 3 HOH A 28 228 7 HOH HOH . 
C 3 HOH A 29 229 18 HOH HOH . 
C 3 HOH A 30 230 3 HOH HOH . 
C 3 HOH A 31 231 32 HOH HOH . 
C 3 HOH A 32 232 23 HOH HOH . 
C 3 HOH A 33 233 22 HOH HOH . 
C 3 HOH A 34 234 14 HOH HOH . 
C 3 HOH A 35 235 16 HOH HOH . 
C 3 HOH A 36 236 21 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 O O3 NUT . . . B 2 8.012 -20.288 -8.203 1 18.93 ? O3 NUT 101 A 1 
HETATM 2 C C25 NUT . . . B 2 8.212 -21.072 -7.312 1 18.02 ? C25 NUT 101 A 1 
HETATM 3 N N2 NUT . . . B 2 8.723 -22.279 -7.603 1 21.95 ? N2 NUT 101 A 1 
HETATM 4 C C29 NUT . . . B 2 9.303 -22.476 -8.933 1 21.9 ? C29 NUT 101 A 1 
HETATM 5 C C28 NUT . . . B 2 10.27 -23.6 -9.032 1 24.81 ? C28 NUT 101 A 1 
HETATM 6 O O2 NUT . . . B 2 10.889 -23.771 -10.112 1 28.7 ? O2 NUT 101 A 1 
HETATM 7 N N3 NUT . . . B 2 10.427 -24.384 -8.002 1 24.93 ? N3 NUT 101 A 1 
HETATM 8 C C27 NUT . . . B 2 9.675 -24.404 -6.757 1 24.76 ? C27 NUT 101 A 1 
HETATM 9 C C26 NUT . . . B 2 8.442 -23.527 -6.863 1 24.35 ? C26 NUT 101 A 1 
HETATM 10 N N1 NUT . . . B 2 7.89 -20.682 -6.037 1 19.01 ? N1 NUT 101 A 1 
HETATM 11 C C10 NUT . . . B 2 8.375 -21.047 -4.743 1 18.68 ? C10 NUT 101 A 1 
HETATM 12 C C9 NUT . . . B 2 9.664 -21.724 -4.507 1 20.34 ? C9 NUT 101 A 1 
HETATM 13 C C3 NUT . . . B 2 9.704 -22.78 -3.6 1 25.26 ? C3 NUT 101 A 1 
HETATM 14 C C2 NUT . . . B 2 10.893 -23.445 -3.358 1 26.38 ? C2 NUT 101 A 1 
HETATM 15 C C5 NUT . . . B 2 10.841 -21.302 -5.116 1 18.71 ? C5 NUT 101 A 1 
HETATM 16 O O1 NUT . . . B 2 10.744 -20.237 -5.936 1 18.02 ? O1 NUT 101 A 1 
HETATM 17 C C6 NUT . . . B 2 11.845 -19.87 -6.772 1 17.24 ? C6 NUT 101 A 1 
HETATM 18 C C8 NUT . . . B 2 12.76 -18.979 -5.965 1 18.36 ? C8 NUT 101 A 1 
HETATM 19 C C7 NUT . . . B 2 11.317 -19.148 -7.975 1 17.62 ? C7 NUT 101 A 1 
HETATM 20 C C4 NUT . . . B 2 12.054 -21.945 -4.841 1 22.9 ? C4 NUT 101 A 1 
HETATM 21 C C1 NUT . . . B 2 12.064 -23.013 -3.966 1 25.3 ? C1 NUT 101 A 1 
HETATM 22 O O NUT . . . B 2 13.306 -23.577 -3.765 1 27.7 ? O NUT 101 A 1 
HETATM 23 C C NUT . . . B 2 13.414 -24.606 -2.779 1 32.26 ? C NUT 101 A 1 
HETATM 24 C C18 NUT . . . B 2 6.781 -19.721 -5.837 1 17.94 ? C18 NUT 101 A 1 
HETATM 25 C C19 NUT . . . B 2 7.13 -18.255 -5.934 1 15.77 ? C19 NUT 101 A 1 
HETATM 26 C C24 NUT . . . B 2 8.412 -17.81 -5.647 1 17.01 ? C24 NUT 101 A 1 
HETATM 27 C C23 NUT . . . B 2 8.712 -16.452 -5.666 1 15.33 ? C23 NUT 101 A 1 
HETATM 28 C C22 NUT . . . B 2 7.73 -15.553 -5.997 1 15.56 ? C22 NUT 101 A 1 
HETATM 29 CL CL1 NUT . . . B 2 8.078 -13.852 -5.945 1 17.46 ? CL1 NUT 101 A 1 
HETATM 30 C C21 NUT . . . B 2 6.45 -15.975 -6.275 1 16.92 ? C21 NUT 101 A 1 
HETATM 31 C C20 NUT . . . B 2 6.165 -17.32 -6.277 1 17.03 ? C20 NUT 101 A 1 
HETATM 32 C C11 NUT . . . B 2 6.37 -20.194 -4.41 1 20 ? C11 NUT 101 A 1 
HETATM 33 N N NUT . . . B 2 7.607 -20.698 -3.789 1 20.29 ? N NUT 101 A 1 
HETATM 34 C C12 NUT . . . B 2 5.727 -19.103 -3.593 1 18.08 ? C12 NUT 101 A 1 
HETATM 35 C C17 NUT . . . B 2 6.486 -18.268 -2.794 1 20.31 ? C17 NUT 101 A 1 
HETATM 36 C C16 NUT . . . B 2 5.903 -17.249 -2.072 1 19.9 ? C16 NUT 101 A 1 
HETATM 37 C C15 NUT . . . B 2 4.54 -17.065 -2.136 1 20.79 ? C15 NUT 101 A 1 
HETATM 38 CL CL NUT . . . B 2 3.805 -15.746 -1.252 1 24.4 ? CL NUT 101 A 1 
HETATM 39 C C14 NUT . . . B 2 3.754 -17.904 -2.911 1 20.94 ? C14 NUT 101 A 1 
HETATM 40 C C13 NUT . . . B 2 4.352 -18.893 -3.656 1 22.48 ? C13 NUT 101 A 1 
#
_model_server_stats.io_time_ms              22 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           351 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           40 
#