data_6BN7
#
_model_server_result.job_id            7HPAQJlpAx7sxq7rW7PIGg 
_model_server_result.datetime_utc      '2024-10-18 17:20:45' 
_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          6bn7 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":502}' 
#
_entry.id    6BN7 
#
_exptl.entry_id    6BN7 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              885.384 
_entity.id                          5 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'methyl {(6S)-4-(4-chlorophenyl)-2-[(8-{[({2-[(3S)-2,6-dioxopiperidin-3-yl]-1,3-dioxo-2,3-dihydro-1H-isoindol-4-yl}oxy)acetyl]amino}octyl)carbamoyl]-3,9-dimethyl-6H-thieno[3,2-f][1,2,4]triazolo[4,3-a][1,4]diazepin-6-yl}acetate' 
_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         120 
_cell.entry_id            6BN7 
_cell.length_a            115.571 
_cell.length_b            115.571 
_cell.length_c            596.315 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6BN7 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        179 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 65 2 2' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    trimeric 
_pdbx_struct_assembly.oligomeric_count      3 
_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                      5 
_struct_asym.id                             E 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    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 B SG CYS 344 B CYS 323 1_555 D ZN ZN . B ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.339 ? 
metalc ? metalc2 B SG CYS 347 B CYS 326 1_555 D ZN ZN . B ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.429 ? 
metalc ? metalc3 B SG CYS 412 B CYS 391 1_555 D ZN ZN . B ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.302 ? 
metalc ? metalc4 B SG CYS 415 B CYS 394 1_555 D ZN ZN . B ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.408 ? 
#
_chem_comp.formula           'C43 H45 Cl N8 O9 S' 
_chem_comp.formula_weight    885.384 
_chem_comp.id                RN3 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'methyl {(6S)-4-(4-chlorophenyl)-2-[(8-{[({2-[(3S)-2,6-dioxopiperidin-3-yl]-1,3-dioxo-2,3-dihydro-1H-isoindol-4-yl}oxy)acetyl]amino}octyl)carbamoyl]-3,9-dimethyl-6H-thieno[3,2-f][1,2,4]triazolo[4,3-a][1,4]diazepin-6-yl}acetate' 
_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
O4 C37 RN3 doub 275 n n 
C36 C37 RN3 sing 276 n n 
C36 C35 RN3 sing 277 n n 
C37 N6 RN3 sing 278 n n 
O5 C33 RN3 doub 279 n n 
N6 C38 RN3 sing 280 n n 
C34 C38 RN3 sing 281 n n 
C34 C35 RN3 sing 282 n n 
C34 N5 RN3 sing 283 n n 
C38 O3 RN3 doub 284 n n 
C33 N5 RN3 sing 285 n n 
C33 C32 RN3 sing 286 n n 
N5 C40 RN3 sing 287 n n 
C32 C31 RN3 doub 288 n y 
C32 C39 RN3 sing 289 n y 
C31 C30 RN3 sing 290 n y 
C40 C39 RN3 sing 291 n n 
C40 O6 RN3 doub 292 n n 
CL C11 RN3 sing 293 n n 
C39 C28 RN3 doub 294 n y 
C30 C29 RN3 doub 295 n y 
C6 O RN3 sing 296 n n 
C12 C11 RN3 doub 297 n y 
C12 C13 RN3 sing 298 n y 
C11 C10 RN3 sing 299 n y 
C28 C29 RN3 sing 300 n y 
C28 O2 RN3 sing 301 n n 
C13 C8 RN3 doub 302 n y 
O C5 RN3 sing 303 n n 
O1 C5 RN3 doub 304 n n 
C10 C9 RN3 doub 305 n y 
O2 C27 RN3 sing 306 n n 
C5 C4 RN3 sing 307 n n 
C8 C9 RN3 sing 308 n y 
C8 C7 RN3 sing 309 n n 
C42 C41 RN3 sing 310 n n 
N2 C7 RN3 doub 311 n n 
N2 C3 RN3 sing 312 n n 
C27 C26 RN3 sing 313 n n 
C7 C14 RN3 sing 314 n n 
C4 C3 RN3 sing 315 n n 
C26 N4 RN3 sing 316 n n 
C26 O7 RN3 doub 317 n n 
C41 C14 RN3 sing 318 n y 
C41 C16 RN3 doub 319 n y 
C3 C2 RN3 sing 320 n n 
C14 C15 RN3 doub 321 n y 
N4 C25 RN3 sing 322 n n 
N3 C18 RN3 sing 323 n n 
N3 C17 RN3 sing 324 n n 
C18 C19 RN3 sing 325 n n 
C20 C21 RN3 sing 326 n n 
C20 C19 RN3 sing 327 n n 
C16 C17 RN3 sing 328 n n 
C16 S RN3 sing 329 n y 
C21 C22 RN3 sing 330 n n 
C2 N1 RN3 doub 331 n y 
C2 N7 RN3 sing 332 n y 
C17 O8 RN3 doub 333 n n 
C25 C24 RN3 sing 334 n n 
C15 N7 RN3 sing 335 n n 
C15 S RN3 sing 336 n y 
C23 C24 RN3 sing 337 n n 
C23 C22 RN3 sing 338 n n 
N1 N RN3 sing 339 n y 
N7 C1 RN3 sing 340 n y 
C1 N RN3 doub 341 n y 
C1 C RN3 sing 342 n n 
C H1 RN3 sing 343 n n 
C H2 RN3 sing 344 n n 
C H3 RN3 sing 345 n n 
C10 H4 RN3 sing 346 n n 
C12 H5 RN3 sing 347 n n 
C13 H6 RN3 sing 348 n n 
C18 H7 RN3 sing 349 n n 
C18 H8 RN3 sing 350 n n 
C19 H9 RN3 sing 351 n n 
C19 H10 RN3 sing 352 n n 
C20 H11 RN3 sing 353 n n 
C20 H12 RN3 sing 354 n n 
C21 H13 RN3 sing 355 n n 
C21 H14 RN3 sing 356 n n 
C22 H15 RN3 sing 357 n n 
C22 H16 RN3 sing 358 n n 
C23 H17 RN3 sing 359 n n 
C23 H18 RN3 sing 360 n n 
C24 H19 RN3 sing 361 n n 
C24 H20 RN3 sing 362 n n 
C25 H21 RN3 sing 363 n n 
C25 H22 RN3 sing 364 n n 
C27 H23 RN3 sing 365 n n 
C27 H24 RN3 sing 366 n n 
C29 H25 RN3 sing 367 n n 
C3 H26 RN3 sing 368 n n 
C30 H27 RN3 sing 369 n n 
C31 H28 RN3 sing 370 n n 
C34 H29 RN3 sing 371 n n 
C35 H30 RN3 sing 372 n n 
C35 H31 RN3 sing 373 n n 
C36 H32 RN3 sing 374 n n 
C36 H33 RN3 sing 375 n n 
C4 H34 RN3 sing 376 n n 
C4 H35 RN3 sing 377 n n 
C42 H36 RN3 sing 378 n n 
C42 H37 RN3 sing 379 n n 
C42 H38 RN3 sing 380 n n 
C6 H39 RN3 sing 381 n n 
C6 H40 RN3 sing 382 n n 
C6 H41 RN3 sing 383 n n 
C9 H42 RN3 sing 384 n n 
N3 H43 RN3 sing 385 n n 
N4 H44 RN3 sing 386 n n 
N6 H45 RN3 sing 387 n n 
#
_atom_sites.entry_id                     6BN7 
_atom_sites.fract_transf_matrix[1][1]    0.008653 
_atom_sites.fract_transf_matrix[1][2]    0.004996 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.009991 
_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]    0.001677 
_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 4 ZN B 1 501 1437 ZN ZN . 
E 5 RN3 B 1 502 1 RN3 RN3 . 
#
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 RN3 . . . E 5 73.831 33.753 58.131 1 193.91 ? N RN3 502 B 1 
HETATM 2 C C RN3 . . . E 5 72.693 35.697 59.186 1 187.36 ? C RN3 502 B 1 
HETATM 3 O O RN3 . . . E 5 71.989 32.209 52.278 1 196.65 ? O RN3 502 B 1 
HETATM 4 C C1 RN3 . . . E 5 72.915 34.686 58.122 1 186.58 ? C1 RN3 502 B 1 
HETATM 5 C C10 RN3 . . . E 5 72.558 38.705 52.552 1 147.96 ? C10 RN3 502 B 1 
HETATM 6 C C11 RN3 . . . E 5 72.91 38.34 51.272 1 163.79 ? C11 RN3 502 B 1 
HETATM 7 C C12 RN3 . . . E 5 72.947 37.018 50.889 1 166.96 ? C12 RN3 502 B 1 
HETATM 8 C C13 RN3 . . . E 5 72.623 36.039 51.811 1 152.82 ? C13 RN3 502 B 1 
HETATM 9 C C14 RN3 . . . E 5 70.969 35.686 55.155 1 179.58 ? C14 RN3 502 B 1 
HETATM 10 C C15 RN3 . . . E 5 71.106 35.34 56.48 1 183.57 ? C15 RN3 502 B 1 
HETATM 11 C C16 RN3 . . . E 5 69.062 36.655 56.081 1 165.26 ? C16 RN3 502 B 1 
HETATM 12 C C17 RN3 . . . E 5 67.784 37.375 56.35 1 172.33 ? C17 RN3 502 B 1 
HETATM 13 C C18 RN3 . . . E 5 65.446 37.44 55.637 1 159.73 ? C18 RN3 502 B 1 
HETATM 14 C C19 RN3 . . . E 5 65.06 38.644 56.474 1 161.65 ? C19 RN3 502 B 1 
HETATM 15 C C2 RN3 . . . E 5 72.712 33.529 56.268 1 182.55 ? C2 RN3 502 B 1 
HETATM 16 C C20 RN3 . . . E 5 64.466 39.779 55.656 1 163.88 ? C20 RN3 502 B 1 
HETATM 17 C C21 RN3 . . . E 5 64.883 41.162 56.129 1 163.37 ? C21 RN3 502 B 1 
HETATM 18 C C22 RN3 . . . E 5 63.986 41.739 57.212 1 158.4 ? C22 RN3 502 B 1 
HETATM 19 C C23 RN3 . . . E 5 63.47 43.136 56.905 1 155.31 ? C23 RN3 502 B 1 
HETATM 20 C C24 RN3 . . . E 5 64.512 44.229 57.078 1 156.53 ? C24 RN3 502 B 1 
HETATM 21 C C25 RN3 . . . E 5 64.116 45.542 56.431 1 157.08 ? C25 RN3 502 B 1 
HETATM 22 C C26 RN3 . . . E 5 65.364 46.958 54.87 1 185.58 ? C26 RN3 502 B 1 
HETATM 23 C C27 RN3 . . . E 5 66.578 46.943 53.973 1 178.18 ? C27 RN3 502 B 1 
HETATM 24 C C28 RN3 . . . E 5 66.292 46.377 51.671 1 151.3 ? C28 RN3 502 B 1 
HETATM 25 C C29 RN3 . . . E 5 66.708 45.074 51.899 1 135.09 ? C29 RN3 502 B 1 
HETATM 26 C C3 RN3 . . . E 5 72.127 33.137 54.929 1 177.37 ? C3 RN3 502 B 1 
HETATM 27 C C30 RN3 . . . E 5 66.739 44.167 50.849 1 141.45 ? C30 RN3 502 B 1 
HETATM 28 C C31 RN3 . . . E 5 66.358 44.551 49.573 1 146.04 ? C31 RN3 502 B 1 
HETATM 29 C C32 RN3 . . . E 5 65.943 45.863 49.358 1 138.85 ? C32 RN3 502 B 1 
HETATM 30 C C33 RN3 . . . E 5 65.488 46.534 48.115 1 122.45 ? C33 RN3 502 B 1 
HETATM 31 C C34 RN3 . . . E 5 64.709 48.874 47.552 1 136.68 ? C34 RN3 502 B 1 
HETATM 32 C C35 RN3 . . . E 5 63.212 49.095 47.723 1 133.04 ? C35 RN3 502 B 1 
HETATM 33 C C36 RN3 . . . E 5 62.76 50.202 46.778 1 136.23 ? C36 RN3 502 B 1 
HETATM 34 C C37 RN3 . . . E 5 63.573 51.455 46.895 1 141.87 ? C37 RN3 502 B 1 
HETATM 35 C C38 RN3 . . . E 5 65.491 50.162 47.715 1 141.33 ? C38 RN3 502 B 1 
HETATM 36 C C39 RN3 . . . E 5 65.904 46.78 50.385 1 152.2 ? C39 RN3 502 B 1 
HETATM 37 C C4 RN3 . . . E 5 72.684 31.784 54.47 1 174.01 ? C4 RN3 502 B 1 
HETATM 38 C C40 RN3 . . . E 5 65.424 48.074 49.842 1 144.03 ? C40 RN3 502 B 1 
HETATM 39 C C41 RN3 . . . E 5 69.776 36.453 54.921 1 159.35 ? C41 RN3 502 B 1 
HETATM 40 C C42 RN3 . . . E 5 69.354 36.973 53.578 1 151.47 ? C42 RN3 502 B 1 
HETATM 41 C C5 RN3 . . . E 5 73.015 31.779 53.004 1 181.11 ? C5 RN3 502 B 1 
HETATM 42 C C6 RN3 . . . E 5 72.07 31.964 50.854 1 206.55 ? C6 RN3 502 B 1 
HETATM 43 C C7 RN3 . . . E 5 71.917 35.33 54.094 1 178.62 ? C7 RN3 502 B 1 
HETATM 44 C C8 RN3 . . . E 5 72.263 36.377 53.112 1 156.14 ? C8 RN3 502 B 1 
HETATM 45 C C9 RN3 . . . E 5 72.235 37.721 53.469 1 149.11 ? C9 RN3 502 B 1 
HETATM 46 N N1 RN3 . . . E 5 73.707 33.017 56.958 1 192.13 ? N1 RN3 502 B 1 
HETATM 47 N N2 RN3 . . . E 5 72.471 34.182 53.954 1 183.01 ? N2 RN3 502 B 1 
HETATM 48 N N3 RN3 . . . E 5 66.877 37.394 55.371 1 172 ? N3 RN3 502 B 1 
HETATM 49 N N4 RN3 . . . E 5 64.835 45.778 55.187 1 164.38 ? N4 RN3 502 B 1 
HETATM 50 N N5 RN3 . . . E 5 65.194 47.855 48.479 1 122.81 ? N5 RN3 502 B 1 
HETATM 51 N N6 RN3 . . . E 5 64.856 51.326 47.362 1 142.37 ? N6 RN3 502 B 1 
HETATM 52 N N7 RN3 . . . E 5 72.174 34.593 56.963 1 183.46 ? N7 RN3 502 B 1 
HETATM 53 O O1 RN3 . . . E 5 74.065 31.435 52.534 1 176.96 ? O1 RN3 502 B 1 
HETATM 54 O O2 RN3 . . . E 5 66.232 47.334 52.648 1 154.91 ? O2 RN3 502 B 1 
HETATM 55 O O3 RN3 . . . E 5 66.642 50.164 48.145 1 144.2 ? O3 RN3 502 B 1 
HETATM 56 O O4 RN3 . . . E 5 63.131 52.56 46.592 1 158.33 ? O4 RN3 502 B 1 
HETATM 57 O O5 RN3 . . . E 5 65.376 46.079 46.992 1 136.82 ? O5 RN3 502 B 1 
HETATM 58 O O6 RN3 . . . E 5 65.249 49.132 50.417 1 158.03 ? O6 RN3 502 B 1 
HETATM 59 O O7 RN3 . . . E 5 64.914 48.029 55.27 1 193.14 ? O7 RN3 502 B 1 
HETATM 60 O O8 RN3 . . . E 5 67.604 37.919 57.438 1 165.03 ? O8 RN3 502 B 1 
HETATM 61 S S RN3 . . . E 5 69.812 35.928 57.465 1 182.23 ? S RN3 502 B 1 
HETATM 62 CL CL RN3 . . . E 5 73.317 39.576 50.114 1 183.6 ? CL RN3 502 B 1 
#
_model_server_stats.io_time_ms              114 
_model_server_stats.parse_time_ms           13 
_model_server_stats.create_model_time_ms    12 
_model_server_stats.query_time_ms           260 
_model_server_stats.encode_time_ms          13 
_model_server_stats.element_count           62 
#