data_6BOY
#
_model_server_result.job_id            IvOsTh5opaSxDd3f8H4nJQ 
_model_server_result.datetime_utc      '2024-11-24 20:16:14' 
_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          6boy 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":502}' 
#
_entry.id    6BOY 
#
_exptl.entry_id    6BOY 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              841.374 
_entity.id                          5 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            2-[(6S)-4-(4-chlorophenyl)-2,3,9-trimethyl-6H-thieno[3,2-f][1,2,4]triazolo[4,3-a][1,4]diazepin-6-yl]-N-(8-{[({2-[(3S)-2,6-dioxopiperidin-3-yl]-1,3-dioxo-2,3-dihydro-1H-isoindol-4-yl}oxy)acetyl]amino}octyl)acetamide 
_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            6BOY 
_cell.length_a            115.406 
_cell.length_b            115.406 
_cell.length_c            588.143 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6BOY 
_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 ? ? ? ? ? ? ? ? ? ? ? ? 2.307 ? 
metalc ? metalc2 B SG CYS 347 B CYS 326 1_555 D ZN ZN . B ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.347 ? 
metalc ? metalc3 B SG CYS 412 B CYS 391 1_555 D ZN ZN . B ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.397 ? 
metalc ? metalc4 B SG CYS 415 B CYS 394 1_555 D ZN ZN . B ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.27 ? 
#
_chem_comp.formula           'C42 H45 Cl N8 O7 S' 
_chem_comp.formula_weight    841.374 
_chem_comp.id                RN6 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              2-[(6S)-4-(4-chlorophenyl)-2,3,9-trimethyl-6H-thieno[3,2-f][1,2,4]triazolo[4,3-a][1,4]diazepin-6-yl]-N-(8-{[({2-[(3S)-2,6-dioxopiperidin-3-yl]-1,3-dioxo-2,3-dihydro-1H-isoindol-4-yl}oxy)acetyl]amino}octyl)acetamide 
_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 C28 RN6 doub 275 n n 
C25 C24 RN6 sing 276 n n 
C25 C26 RN6 sing 277 n n 
O1 C24 RN6 doub 278 n n 
C24 N5 RN6 sing 279 n n 
C15 C14 RN6 sing 280 n n 
C15 O RN6 sing 281 n n 
N5 C23 RN6 sing 282 n n 
C22 C23 RN6 sing 283 n n 
C22 C26 RN6 sing 284 n n 
C22 N4 RN6 sing 285 n n 
C23 O2 RN6 doub 286 n n 
C14 O5 RN6 doub 287 n n 
C14 N3 RN6 sing 288 n n 
C28 N4 RN6 sing 289 n n 
C28 C27 RN6 sing 290 n n 
N3 C13 RN6 sing 291 n n 
C13 C12 RN6 sing 292 n n 
N4 C21 RN6 sing 293 n n 
O C16 RN6 sing 294 n n 
C9 C10 RN6 sing 295 n n 
C9 C8 RN6 sing 296 n n 
C11 C10 RN6 sing 297 n n 
C11 C12 RN6 sing 298 n n 
C27 C16 RN6 doub 299 n y 
C27 C20 RN6 sing 300 n y 
C7 C8 RN6 sing 301 n n 
C7 C6 RN6 sing 302 n n 
C16 C17 RN6 sing 303 n y 
C21 C20 RN6 sing 304 n n 
C21 O3 RN6 doub 305 n n 
C6 N2 RN6 sing 306 n n 
C20 C19 RN6 doub 307 n y 
CL C33 RN6 sing 308 n n 
C17 C18 RN6 doub 309 n y 
C34 C33 RN6 doub 310 n y 
C34 C35 RN6 sing 311 n y 
C33 C32 RN6 sing 312 n y 
C19 C18 RN6 sing 313 n y 
N2 C5 RN6 sing 314 n n 
C35 C30 RN6 doub 315 n y 
O6 C5 RN6 doub 316 n n 
C5 C4 RN6 sing 317 n n 
C32 C31 RN6 doub 318 n y 
C30 C31 RN6 sing 319 n y 
C30 C29 RN6 sing 320 n n 
C41 C40 RN6 sing 321 n n 
N6 C29 RN6 doub 322 n n 
N6 C3 RN6 sing 323 n n 
C29 C36 RN6 sing 324 n n 
C4 C3 RN6 sing 325 n n 
C3 C2 RN6 sing 326 n n 
C40 C36 RN6 sing 327 n y 
C40 C38 RN6 doub 328 n y 
C36 C37 RN6 doub 329 n y 
C38 C39 RN6 sing 330 n n 
C38 S RN6 sing 331 n y 
C2 N1 RN6 doub 332 n y 
C2 N7 RN6 sing 333 n y 
C37 N7 RN6 sing 334 n n 
C37 S RN6 sing 335 n y 
N1 N RN6 sing 336 n y 
N7 C1 RN6 sing 337 n y 
C1 N RN6 doub 338 n y 
C1 C RN6 sing 339 n n 
C H1 RN6 sing 340 n n 
C H2 RN6 sing 341 n n 
C H3 RN6 sing 342 n n 
C10 H4 RN6 sing 343 n n 
C10 H5 RN6 sing 344 n n 
C11 H6 RN6 sing 345 n n 
C11 H7 RN6 sing 346 n n 
C12 H8 RN6 sing 347 n n 
C12 H9 RN6 sing 348 n n 
C13 H10 RN6 sing 349 n n 
C13 H11 RN6 sing 350 n n 
C15 H12 RN6 sing 351 n n 
C15 H13 RN6 sing 352 n n 
C17 H14 RN6 sing 353 n n 
C18 H15 RN6 sing 354 n n 
C19 H16 RN6 sing 355 n n 
C22 H17 RN6 sing 356 n n 
C25 H18 RN6 sing 357 n n 
C25 H19 RN6 sing 358 n n 
C26 H20 RN6 sing 359 n n 
C26 H21 RN6 sing 360 n n 
C3 H22 RN6 sing 361 n n 
C31 H23 RN6 sing 362 n n 
C32 H24 RN6 sing 363 n n 
C34 H25 RN6 sing 364 n n 
C35 H26 RN6 sing 365 n n 
C39 H27 RN6 sing 366 n n 
C39 H28 RN6 sing 367 n n 
C39 H29 RN6 sing 368 n n 
C4 H30 RN6 sing 369 n n 
C4 H31 RN6 sing 370 n n 
C41 H32 RN6 sing 371 n n 
C41 H33 RN6 sing 372 n n 
C41 H34 RN6 sing 373 n n 
C6 H35 RN6 sing 374 n n 
C6 H36 RN6 sing 375 n n 
C7 H37 RN6 sing 376 n n 
C7 H38 RN6 sing 377 n n 
C8 H39 RN6 sing 378 n n 
C8 H40 RN6 sing 379 n n 
C9 H41 RN6 sing 380 n n 
C9 H42 RN6 sing 381 n n 
N2 H43 RN6 sing 382 n n 
N3 H44 RN6 sing 383 n n 
N5 H45 RN6 sing 384 n n 
#
_atom_sites.entry_id                     6BOY 
_atom_sites.fract_transf_matrix[1][1]    0.008665 
_atom_sites.fract_transf_matrix[1][2]    0.005003 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.010006 
_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]    0.0017 
_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 RN6 B 1 502 1 RN6 RN6 . 
#
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 RN6 . . . E 5 76.722 32.855 57.578 1 172.21 ? N RN6 502 B 1 
HETATM 2 C C RN6 . . . E 5 75.401 34.671 58.648 1 142.48 ? C RN6 502 B 1 
HETATM 3 O O RN6 . . . E 5 68.862 41.505 48.297 1 174.37 ? O RN6 502 B 1 
HETATM 4 C C1 RN6 . . . E 5 75.728 33.706 57.568 1 157.92 ? C1 RN6 502 B 1 
HETATM 5 C C10 RN6 . . . E 5 72.92 35.237 49.023 1 143.13 ? C10 RN6 502 B 1 
HETATM 6 C C11 RN6 . . . E 5 73.147 36.73 48.815 1 126.56 ? C11 RN6 502 B 1 
HETATM 7 C C12 RN6 . . . E 5 71.963 37.638 49.142 1 145.37 ? C12 RN6 502 B 1 
HETATM 8 C C13 RN6 . . . E 5 70.911 37.676 48.05 1 133.57 ? C13 RN6 502 B 1 
HETATM 9 C C14 RN6 . . . E 5 70.77 40.108 47.714 1 171.93 ? C14 RN6 502 B 1 
HETATM 10 C C15 RN6 . . . E 5 69.867 41.256 47.326 1 187.44 ? C15 RN6 502 B 1 
HETATM 11 C C16 RN6 . . . E 5 69.147 42.392 49.3 1 125.21 ? C16 RN6 502 B 1 
HETATM 12 C C17 RN6 . . . E 5 69.671 42.002 50.523 1 127.82 ? C17 RN6 502 B 1 
HETATM 13 C C18 RN6 . . . E 5 69.876 42.945 51.515 1 126.13 ? C18 RN6 502 B 1 
HETATM 14 C C19 RN6 . . . E 5 69.562 44.274 51.295 1 116.88 ? C19 RN6 502 B 1 
HETATM 15 C C2 RN6 . . . E 5 75.69 32.603 55.668 1 137.4 ? C2 RN6 502 B 1 
HETATM 16 C C20 RN6 . . . E 5 69.042 44.653 50.061 1 116.59 ? C20 RN6 502 B 1 
HETATM 17 C C21 RN6 . . . E 5 68.613 45.99 49.585 1 109.77 ? C21 RN6 502 B 1 
HETATM 18 C C22 RN6 . . . E 5 67.593 46.861 47.437 1 118.04 ? C22 RN6 502 B 1 
HETATM 19 C C23 RN6 . . . E 5 68.393 48.148 47.516 1 128.07 ? C23 RN6 502 B 1 
HETATM 20 C C24 RN6 . . . E 5 66.364 49.478 47.151 1 110.91 ? C24 RN6 502 B 1 
HETATM 21 C C25 RN6 . . . E 5 65.553 48.223 47.048 1 110.53 ? C25 RN6 502 B 1 
HETATM 22 C C26 RN6 . . . E 5 66.14 47.072 47.851 1 123.68 ? C26 RN6 502 B 1 
HETATM 23 C C27 RN6 . . . E 5 68.832 43.738 49.044 1 137.45 ? C27 RN6 502 B 1 
HETATM 24 C C28 RN6 . . . E 5 68.272 44.464 47.874 1 132.6 ? C28 RN6 502 B 1 
HETATM 25 C C29 RN6 . . . E 5 74.833 34.433 53.601 1 161.62 ? C29 RN6 502 B 1 
HETATM 26 C C3 RN6 . . . E 5 75.276 32.218 54.265 1 123.83 ? C3 RN6 502 B 1 
HETATM 27 C C30 RN6 . . . E 5 75.153 35.602 52.755 1 135.36 ? C30 RN6 502 B 1 
HETATM 28 C C31 RN6 . . . E 5 74.893 36.899 53.186 1 149.4 ? C31 RN6 502 B 1 
HETATM 29 C C32 RN6 . . . E 5 75.223 37.986 52.397 1 161.24 ? C32 RN6 502 B 1 
HETATM 30 C C33 RN6 . . . E 5 75.817 37.772 51.173 1 144.84 ? C33 RN6 502 B 1 
HETATM 31 C C34 RN6 . . . E 5 76.089 36.5 50.722 1 137.64 ? C34 RN6 502 B 1 
HETATM 32 C C35 RN6 . . . E 5 75.754 35.418 51.515 1 133.35 ? C35 RN6 502 B 1 
HETATM 33 C C36 RN6 . . . E 5 73.718 34.567 54.571 1 187.61 ? C36 RN6 502 B 1 
HETATM 34 C C37 RN6 . . . E 5 73.874 34.204 55.889 1 166.25 ? C37 RN6 502 B 1 
HETATM 35 C C38 RN6 . . . E 5 71.605 35.064 55.422 1 131.65 ? C38 RN6 502 B 1 
HETATM 36 C C39 RN6 . . . E 5 70.179 35.499 55.575 1 161.16 ? C39 RN6 502 B 1 
HETATM 37 C C4 RN6 . . . E 5 75.905 30.925 53.732 1 130.65 ? C4 RN6 502 B 1 
HETATM 38 C C40 RN6 . . . E 5 72.382 35.05 54.306 1 138.24 ? C40 RN6 502 B 1 
HETATM 39 C C41 RN6 . . . E 5 71.861 35.441 52.955 1 130.87 ? C41 RN6 502 B 1 
HETATM 40 C C5 RN6 . . . E 5 75.375 30.601 52.352 1 156.17 ? C5 RN6 502 B 1 
HETATM 41 C C6 RN6 . . . E 5 75.62 30.986 49.948 1 145.54 ? C6 RN6 502 B 1 
HETATM 42 C C7 RN6 . . . E 5 75.488 32.269 49.15 1 115.57 ? C7 RN6 502 B 1 
HETATM 43 C C8 RN6 . . . E 5 74.215 33.054 49.43 1 133.75 ? C8 RN6 502 B 1 
HETATM 44 C C9 RN6 . . . E 5 74.134 34.38 48.684 1 117.43 ? C9 RN6 502 B 1 
HETATM 45 N N1 RN6 . . . E 5 76.7 32.152 56.376 1 168.12 ? N1 RN6 502 B 1 
HETATM 46 N N2 RN6 . . . E 5 75.972 31.228 51.34 1 176.45 ? N2 RN6 502 B 1 
HETATM 47 N N3 RN6 . . . E 5 70.186 38.939 47.984 1 163.61 ? N3 RN6 502 B 1 
HETATM 48 N N4 RN6 . . . E 5 68.161 45.803 48.273 1 109.03 ? N4 RN6 502 B 1 
HETATM 49 N N5 RN6 . . . E 5 67.709 49.332 47.373 1 117.49 ? N5 RN6 502 B 1 
HETATM 50 N N6 RN6 . . . E 5 75.552 33.389 53.421 1 141.57 ? N6 RN6 502 B 1 
HETATM 51 N N7 RN6 . . . E 5 75.032 33.584 56.382 1 150.62 ? N7 RN6 502 B 1 
HETATM 52 O O1 RN6 . . . E 5 65.869 50.598 47.05 1 142.71 ? O1 RN6 502 B 1 
HETATM 53 O O2 RN6 . . . E 5 69.608 48.136 47.686 1 112 ? O2 RN6 502 B 1 
HETATM 54 O O3 RN6 . . . E 5 68.617 47.053 50.18 1 129.02 ? O3 RN6 502 B 1 
HETATM 55 O O4 RN6 . . . E 5 67.966 44.035 46.777 1 149.84 ? O4 RN6 502 B 1 
HETATM 56 O O5 RN6 . . . E 5 71.986 40.279 47.737 1 135.9 ? O5 RN6 502 B 1 
HETATM 57 O O6 RN6 . . . E 5 74.449 29.811 52.191 1 149.81 ? O6 RN6 502 B 1 
HETATM 58 S S RN6 . . . E 5 72.451 34.474 56.822 1 157.64 ? S RN6 502 B 1 
HETATM 59 CL CL RN6 . . . E 5 76.23 39.137 50.174 1 153.28 ? CL RN6 502 B 1 
#
_model_server_stats.io_time_ms              113 
_model_server_stats.parse_time_ms           13 
_model_server_stats.create_model_time_ms    10 
_model_server_stats.query_time_ms           312 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           59 
#