data_8QK5 # _model_server_result.job_id bOanRTDjmAJnyTIe6A347g _model_server_result.datetime_utc '2024-10-23 14:27:58' _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 8qk5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":303}' # _entry.id 8QK5 # _exptl.entry_id 8QK5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 667.802 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 5-[[3-(aminomethyl)azetidin-1-yl]methyl]-N-[4-[4-(4-cyano-6-methyl-pyrimidin-2-yl)piperazin-1-yl]sulfonylphenyl]-2-[methyl(methylsulfonyl)amino]benzamide _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 8QK5 _cell.length_a 60.418 _cell.length_b 60.418 _cell.length_c 287.692 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8QK5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 12_565 x,x-y+1,-z+1/6 0.5 0.866025 0 0.866025 -0.5 0 0 0 -1 -30.209 52.323523 47.948667 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id D _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 A OD1 ASP 8 A ASP 8 1_555 B MN MN . A MN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.133 ? metalc ? metalc2 A NE2 HIS 10 A HIS 10 1_555 B MN MN . A MN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.241 ? metalc ? metalc3 A OD2 ASP 41 A ASP 41 1_555 B MN MN . A MN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.211 ? metalc ? metalc4 A OD2 ASP 41 A ASP 41 1_555 C MN MN . A MN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.22 ? metalc ? metalc5 A OD1 ASN 79 A ASN 79 1_555 C MN MN . A MN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.121 ? metalc ? metalc6 A NE2 HIS 114 A HIS 114 1_555 C MN MN . A MN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.289 ? metalc ? metalc7 A ND1 HIS 195 A HIS 195 1_555 C MN MN . A MN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.324 ? metalc ? metalc8 A NE2 HIS 197 A HIS 197 1_555 B MN MN . A MN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.24 ? metalc ? metalc9 B MN MN . A MN 301 1_555 E O HOH . A HOH 428 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.137 ? metalc ? metalc10 C MN MN . A MN 302 1_555 E O HOH . A HOH 428 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.224 ? # _chem_comp.formula 'C30 H37 N9 O5 S2' _chem_comp.formula_weight 667.802 _chem_comp.id VN6 _chem_comp.mon_nstd_flag . _chem_comp.name 5-[[3-(aminomethyl)azetidin-1-yl]methyl]-N-[4-[4-(4-cyano-6-methyl-pyrimidin-2-yl)piperazin-1-yl]sulfonylphenyl]-2-[methyl(methylsulfonyl)amino]benzamide _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 N39 C38 VN6 trip 376 n n C10 C11 VN6 sing 377 n n C10 N7 VN6 sing 378 n n O16 S13 VN6 doub 379 n n C38 C1 VN6 sing 380 n n C11 N12 VN6 sing 381 n n N2 C1 VN6 doub 382 n y N2 C3 VN6 sing 383 n y C1 C6 VN6 sing 384 n y N12 S13 VN6 sing 385 n n N12 C9 VN6 sing 386 n n N7 C3 VN6 sing 387 n n N7 C8 VN6 sing 388 n n C3 N4 VN6 doub 389 n y C8 C9 VN6 sing 390 n n S13 O15 VN6 doub 391 n n S13 C14 VN6 sing 392 n n C6 C5 VN6 doub 393 n y N4 C5 VN6 sing 394 n y C5 C37 VN6 sing 395 n n C17 C14 VN6 doub 396 n y C17 C18 VN6 sing 397 n y C14 C20 VN6 sing 398 n y C18 C19 VN6 doub 399 n y C20 C21 VN6 doub 400 n y C19 C21 VN6 sing 401 n y C19 N22 VN6 sing 402 n n N46 C45 VN6 sing 403 n n C45 C44 VN6 sing 404 n n N22 C23 VN6 sing 405 n n O36 S33 VN6 doub 406 n n C23 O24 VN6 doub 407 n n C23 C25 VN6 sing 408 n n C44 C43 VN6 sing 409 n n C44 C42 VN6 sing 410 n n C43 N41 VN6 sing 411 n n N41 C42 VN6 sing 412 n n N41 C40 VN6 sing 413 n n C26 C25 VN6 doub 414 n y C26 C27 VN6 sing 415 n y C25 C30 VN6 sing 416 n y S33 O35 VN6 doub 417 n n S33 C34 VN6 sing 418 n n S33 N31 VN6 sing 419 n n C27 C40 VN6 sing 420 n n C27 C28 VN6 doub 421 n y C30 N31 VN6 sing 422 n n C30 C29 VN6 doub 423 n y N31 C32 VN6 sing 424 n n C28 C29 VN6 sing 425 n y C6 H1 VN6 sing 426 n n C8 H2 VN6 sing 427 n n C8 H3 VN6 sing 428 n n C26 H4 VN6 sing 429 n n C28 H5 VN6 sing 430 n n C29 H6 VN6 sing 431 n n C32 H7 VN6 sing 432 n n C32 H8 VN6 sing 433 n n C32 H9 VN6 sing 434 n n C37 H10 VN6 sing 435 n n C37 H11 VN6 sing 436 n n C37 H12 VN6 sing 437 n n C40 H13 VN6 sing 438 n n C40 H14 VN6 sing 439 n n C42 H15 VN6 sing 440 n n C42 H16 VN6 sing 441 n n C9 H17 VN6 sing 442 n n C9 H18 VN6 sing 443 n n C10 H19 VN6 sing 444 n n C10 H20 VN6 sing 445 n n C11 H21 VN6 sing 446 n n C11 H22 VN6 sing 447 n n C17 H23 VN6 sing 448 n n C18 H24 VN6 sing 449 n n C20 H25 VN6 sing 450 n n C21 H26 VN6 sing 451 n n N22 H27 VN6 sing 452 n n C34 H28 VN6 sing 453 n n C34 H29 VN6 sing 454 n n C34 H30 VN6 sing 455 n n C43 H32 VN6 sing 456 n n C43 H33 VN6 sing 457 n n C44 H34 VN6 sing 458 n n C45 H35 VN6 sing 459 n n C45 H36 VN6 sing 460 n n N46 H37 VN6 sing 461 n n N46 H38 VN6 sing 462 n n # _atom_sites.entry_id 8QK5 _atom_sites.fract_transf_matrix[1][1] 0.016551 _atom_sites.fract_transf_matrix[1][2] 0.009556 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.019112 _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] 0.003476 _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 MN A 1 301 301 MN MN . C 2 MN A 1 302 302 MN MN . D 3 VN6 A 1 303 401 VN6 M24 . E 4 HOH A 1 401 31 HOH HOH . E 4 HOH A 2 402 6 HOH HOH . E 4 HOH A 3 403 47 HOH HOH . E 4 HOH A 4 404 9 HOH HOH . E 4 HOH A 5 405 33 HOH HOH . E 4 HOH A 6 406 38 HOH HOH . E 4 HOH A 7 407 11 HOH HOH . E 4 HOH A 8 408 45 HOH HOH . E 4 HOH A 9 409 14 HOH HOH . E 4 HOH A 10 410 10 HOH HOH . E 4 HOH A 11 411 43 HOH HOH . E 4 HOH A 12 412 46 HOH HOH . E 4 HOH A 13 413 39 HOH HOH . E 4 HOH A 14 414 30 HOH HOH . E 4 HOH A 15 415 27 HOH HOH . E 4 HOH A 16 416 3 HOH HOH . E 4 HOH A 17 417 7 HOH HOH . E 4 HOH A 18 418 24 HOH HOH . E 4 HOH A 19 419 2 HOH HOH . E 4 HOH A 20 420 25 HOH HOH . E 4 HOH A 21 421 32 HOH HOH . E 4 HOH A 22 422 12 HOH HOH . E 4 HOH A 23 423 5 HOH HOH . E 4 HOH A 24 424 26 HOH HOH . E 4 HOH A 25 425 13 HOH HOH . E 4 HOH A 26 426 18 HOH HOH . E 4 HOH A 27 427 22 HOH HOH . E 4 HOH A 28 428 1 HOH HOH . E 4 HOH A 29 429 21 HOH HOH . E 4 HOH A 30 430 34 HOH HOH . E 4 HOH A 31 431 42 HOH HOH . E 4 HOH A 32 432 44 HOH HOH . E 4 HOH A 33 433 1 HOH HOH . E 4 HOH A 34 434 37 HOH HOH . E 4 HOH A 35 435 35 HOH HOH . E 4 HOH A 36 436 23 HOH HOH . E 4 HOH A 37 437 4 HOH HOH . E 4 HOH A 38 438 41 HOH HOH . E 4 HOH A 39 439 36 HOH HOH . E 4 HOH A 40 440 8 HOH HOH . E 4 HOH A 41 441 15 HOH HOH . E 4 HOH A 42 442 29 HOH HOH . E 4 HOH A 43 443 20 HOH HOH . E 4 HOH A 44 444 40 HOH HOH . E 4 HOH A 45 445 17 HOH HOH . E 4 HOH A 46 446 28 HOH HOH . E 4 HOH A 47 447 19 HOH HOH . E 4 HOH A 48 448 16 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 C5 VN6 . . . D 3 5.753 7.685 5.623 1 51.38 ? C5 VN6 303 A 1 HETATM 2 C C6 VN6 . . . D 3 4.864 6.747 5.145 1 49.56 ? C6 VN6 303 A 1 HETATM 3 N N7 VN6 . . . D 3 4.004 10.72 4.792 1 46.62 ? N7 VN6 303 A 1 HETATM 4 C C8 VN6 . . . D 3 5.107 11.651 4.987 1 45.95 ? C8 VN6 303 A 1 HETATM 5 C C26 VN6 . . . D 3 -2.175 12.287 11.944 1 47.88 ? C26 VN6 303 A 1 HETATM 6 C C27 VN6 . . . D 3 -3.214 11.905 12.798 1 51.77 ? C27 VN6 303 A 1 HETATM 7 C C28 VN6 . . . D 3 -3.721 12.801 13.734 1 48.9 ? C28 VN6 303 A 1 HETATM 8 C C29 VN6 . . . D 3 -3.213 14.091 13.823 1 48.89 ? C29 VN6 303 A 1 HETATM 9 C C30 VN6 . . . D 3 -2.2 14.507 12.966 1 49.31 ? C30 VN6 303 A 1 HETATM 10 C C32 VN6 . . . D 3 -1.849 16.344 14.506 1 48.5 ? C32 VN6 303 A 1 HETATM 11 C C37 VN6 . . . D 3 7.048 7.255 6.32 1 36.29 ? C37 VN6 303 A 1 HETATM 12 C C38 VN6 . . . D 3 2.744 6.239 4.054 1 57.73 ? C38 VN6 303 A 1 HETATM 13 C C40 VN6 . . . D 3 -3.785 10.521 12.799 1 60.51 ? C40 VN6 303 A 1 HETATM 14 C C42 VN6 . . . D 3 -4.899 8.744 11.747 1 65.49 ? C42 VN6 303 A 1 HETATM 15 C C1 VN6 . . . D 3 3.689 7.174 4.537 1 52.1 ? C1 VN6 303 A 1 HETATM 16 N N2 VN6 . . . D 3 3.441 8.467 4.406 1 49.75 ? N2 VN6 303 A 1 HETATM 17 C C3 VN6 . . . D 3 4.352 9.381 4.809 1 49.54 ? C3 VN6 303 A 1 HETATM 18 N N4 VN6 . . . D 3 5.47 8.995 5.47 1 46.35 ? N4 VN6 303 A 1 HETATM 19 C C9 VN6 . . . D 3 4.482 12.931 5.542 1 39.37 ? C9 VN6 303 A 1 HETATM 20 C C10 VN6 . . . D 3 3.158 11.113 3.715 1 40.73 ? C10 VN6 303 A 1 HETATM 21 C C11 VN6 . . . D 3 2.447 12.41 4.171 1 41.36 ? C11 VN6 303 A 1 HETATM 22 N N12 VN6 . . . D 3 3.491 13.454 4.548 1 45.33 ? N12 VN6 303 A 1 HETATM 23 S S13 VN6 . . . D 3 2.788 14.87 5.071 1 41.74 ? S13 VN6 303 A 1 HETATM 24 C C14 VN6 . . . D 3 1.8 14.576 6.484 1 40.21 ? C14 VN6 303 A 1 HETATM 25 O O15 VN6 . . . D 3 3.839 15.8 5.363 1 45.46 ? O15 VN6 303 A 1 HETATM 26 O O16 VN6 . . . D 3 1.966 15.354 4.01 1 42.61 ? O16 VN6 303 A 1 HETATM 27 C C17 VN6 . . . D 3 0.483 14.287 6.305 1 46.19 ? C17 VN6 303 A 1 HETATM 28 C C18 VN6 . . . D 3 -0.331 14.047 7.384 1 44.25 ? C18 VN6 303 A 1 HETATM 29 C C19 VN6 . . . D 3 0.165 14.078 8.682 1 38.82 ? C19 VN6 303 A 1 HETATM 30 C C20 VN6 . . . D 3 2.346 14.603 7.798 1 41.89 ? C20 VN6 303 A 1 HETATM 31 C C21 VN6 . . . D 3 1.504 14.331 8.903 1 37.28 ? C21 VN6 303 A 1 HETATM 32 N N22 VN6 . . . D 3 -0.722 13.743 9.719 1 45.03 ? N22 VN6 303 A 1 HETATM 33 C C23 VN6 . . . D 3 -0.533 14.025 11.046 1 50.86 ? C23 VN6 303 A 1 HETATM 34 O O24 VN6 . . . D 3 0.488 14.601 11.441 1 47.93 ? O24 VN6 303 A 1 HETATM 35 C C25 VN6 . . . D 3 -1.635 13.584 12.036 1 51.91 ? C25 VN6 303 A 1 HETATM 36 N N31 VN6 . . . D 3 -1.643 15.837 13.113 1 52.76 ? N31 VN6 303 A 1 HETATM 37 S S33 VN6 . . . D 3 -2.295 16.881 12.037 1 49.34 ? S33 VN6 303 A 1 HETATM 38 C C34 VN6 . . . D 3 -4.021 17.149 12.439 1 46.5 ? C34 VN6 303 A 1 HETATM 39 O O35 VN6 . . . D 3 -1.565 18.095 12.112 1 51.91 ? O35 VN6 303 A 1 HETATM 40 O O36 VN6 . . . D 3 -2.189 16.347 10.712 1 48.82 ? O36 VN6 303 A 1 HETATM 41 N N39 VN6 . . . D 3 1.966 5.524 3.664 1 63.69 ? N39 VN6 303 A 1 HETATM 42 N N41 VN6 . . . D 3 -4.281 10.086 11.52 1 67.9 ? N41 VN6 303 A 1 HETATM 43 C C43 VN6 . . . D 3 -5.618 10.675 11.254 1 70.83 ? C43 VN6 303 A 1 HETATM 44 C C44 VN6 . . . D 3 -6.167 9.27 11.09 1 69.22 ? C44 VN6 303 A 1 HETATM 45 C C45 VN6 . . . D 3 -6.137 8.881 9.61 1 69.4 ? C45 VN6 303 A 1 HETATM 46 N N46 VN6 . . . D 3 -7.288 8.017 9.278 1 71.54 ? N46 VN6 303 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 307 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 46 #