data_8UDY # _model_server_result.job_id DTE8KF28ejWwFBL3z-sU4g _model_server_result.datetime_utc '2025-01-18 08:07:51' _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 8udy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 8UDY # _exptl.entry_id 8UDY _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 622.517 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-cyano-D-phenylalanyl-2,4-dichloro-N-{(2S)-1-(4-fluorophenyl)-4-oxo-4-[(prop-2-yn-1-yl)amino]butan-2-yl}-D-phenylalaninamide _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 114.87 _cell.angle_gamma 90 _cell.entry_id 8UDY _cell.length_a 96.306 _cell.length_b 81.593 _cell.length_c 51.806 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8UDY _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _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' 2_557 -x,y,-z+2 -1 0 0 0 1 0 0 0 -1 -43.575149 0 94.003473 # _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 # 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 covale ? covale1 A C SER 144 A SER 144 1_555 A N CSO 145 A CSO 145 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale2 A C CSO 145 A CSO 145 1_555 A N GLY 146 A GLY 146 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? metalc ? metalc1 A O ASN 221 A ASN 221 1_555 D CA CA . A CA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.712 ? metalc ? metalc2 A OD1 ASN 221 A ASN 221 1_555 D CA CA . A CA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.279 ? metalc ? metalc3 A O PHE 223 A PHE 223 1_555 D CA CA . A CA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.004 ? metalc ? metalc4 A O ASP 263 A ASP 263 1_555 D CA CA . A CA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.719 ? metalc ? metalc5 A OD1 ASP 263 A ASP 263 1_555 D CA CA . A CA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.331 ? metalc ? metalc6 C NA NA . A NA 402 1_555 E O HOH . A HOH 571 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.118 ? metalc ? metalc7 C NA NA . A NA 402 1_555 E O HOH . A HOH 571 2_557 ? ? ? ? ? ? ? ? ? ? ? ? 2.119 ? metalc ? metalc8 D CA CA . A CA 403 1_555 E O HOH . A HOH 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.973 ? # _chem_comp.formula 'C32 H30 Cl2 F N5 O3' _chem_comp.formula_weight 622.517 _chem_comp.id WD6 _chem_comp.mon_nstd_flag . _chem_comp.name 2-cyano-D-phenylalanyl-2,4-dichloro-N-{(2S)-1-(4-fluorophenyl)-4-oxo-4-[(prop-2-yn-1-yl)amino]butan-2-yl}-D-phenylalaninamide _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 N5 C28 WD6 trip 390 n n C28 C27 WD6 sing 391 n n C29 C27 WD6 doub 392 n y C29 C30 WD6 sing 393 n y C23 C22 WD6 trip 394 n n C27 C26 WD6 sing 395 n y C30 C31 WD6 doub 396 n y C22 C21 WD6 sing 397 n n C26 C25 WD6 sing 398 n n C26 C32 WD6 doub 399 n y C31 C32 WD6 sing 400 n y C25 C24 WD6 sing 401 n n C21 N3 WD6 sing 402 n n N3 C20 WD6 sing 403 n n C20 O2 WD6 doub 404 n n C20 C19 WD6 sing 405 n n C24 N4 WD6 sing 406 n n C24 C1 WD6 sing 407 n n C19 C11 WD6 sing 408 n n O1 C1 WD6 doub 409 n n C1 N1 WD6 sing 410 n n N1 C2 WD6 sing 411 n n O3 C10 WD6 doub 412 n n C11 N2 WD6 sing 413 n n C11 C12 WD6 sing 414 n n C10 N2 WD6 sing 415 n n C10 C2 WD6 sing 416 n n C12 C13 WD6 sing 417 n n C2 C3 WD6 sing 418 n n C13 C14 WD6 doub 419 n y C13 C18 WD6 sing 420 n y C3 C4 WD6 sing 421 n n C9 C4 WD6 doub 422 n y C9 C8 WD6 sing 423 n y C4 C5 WD6 sing 424 n y C14 C15 WD6 sing 425 n y C18 C17 WD6 doub 426 n y C8 C7 WD6 doub 427 n y C5 CL1 WD6 sing 428 n n C5 C6 WD6 doub 429 n y C7 C6 WD6 sing 430 n y C7 CL2 WD6 sing 431 n n C15 C16 WD6 doub 432 n y C17 C16 WD6 sing 433 n y C16 F1 WD6 sing 434 n n C2 H1 WD6 sing 435 n n C3 H2 WD6 sing 436 n n C3 H3 WD6 sing 437 n n C6 H4 WD6 sing 438 n n C9 H5 WD6 sing 439 n n C11 H6 WD6 sing 440 n n C14 H7 WD6 sing 441 n n C15 H8 WD6 sing 442 n n C17 H9 WD6 sing 443 n n C18 H10 WD6 sing 444 n n C19 H11 WD6 sing 445 n n C19 H12 WD6 sing 446 n n C12 H13 WD6 sing 447 n n C12 H14 WD6 sing 448 n n C21 H15 WD6 sing 449 n n C21 H16 WD6 sing 450 n n C23 H17 WD6 sing 451 n n C24 H18 WD6 sing 452 n n C25 H19 WD6 sing 453 n n C25 H20 WD6 sing 454 n n C29 H21 WD6 sing 455 n n C30 H22 WD6 sing 456 n n C31 H23 WD6 sing 457 n n C32 H24 WD6 sing 458 n n C8 H25 WD6 sing 459 n n N1 H26 WD6 sing 460 n n N2 H27 WD6 sing 461 n n N3 H28 WD6 sing 462 n n N4 H29 WD6 sing 463 n n N4 H30 WD6 sing 464 n n # _atom_sites.entry_id 8UDY _atom_sites.fract_transf_matrix[1][1] 0.010384 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004813 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012256 _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] 0.021276 _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 WD6 A 1 401 401 WD6 DH2 . C 3 NA A 1 402 402 NA NA . D 4 CA A 1 403 403 CA CA . E 5 HOH A 1 501 47 HOH HOH . E 5 HOH A 2 502 40 HOH HOH . E 5 HOH A 3 503 41 HOH HOH . E 5 HOH A 4 504 57 HOH HOH . E 5 HOH A 5 505 58 HOH HOH . E 5 HOH A 6 506 10 HOH HOH . E 5 HOH A 7 507 62 HOH HOH . E 5 HOH A 8 508 50 HOH HOH . E 5 HOH A 9 509 56 HOH HOH . E 5 HOH A 10 510 6 HOH HOH . E 5 HOH A 11 511 68 HOH HOH . E 5 HOH A 12 512 3 HOH HOH . E 5 HOH A 13 513 21 HOH HOH . E 5 HOH A 14 514 12 HOH HOH . E 5 HOH A 15 515 2 HOH HOH . E 5 HOH A 16 516 60 HOH HOH . E 5 HOH A 17 517 25 HOH HOH . E 5 HOH A 18 518 31 HOH HOH . E 5 HOH A 19 519 24 HOH HOH . E 5 HOH A 20 520 55 HOH HOH . E 5 HOH A 21 521 4 HOH HOH . E 5 HOH A 22 522 28 HOH HOH . E 5 HOH A 23 523 5 HOH HOH . E 5 HOH A 24 524 15 HOH HOH . E 5 HOH A 25 525 11 HOH HOH . E 5 HOH A 26 526 39 HOH HOH . E 5 HOH A 27 527 74 HOH HOH . E 5 HOH A 28 528 9 HOH HOH . E 5 HOH A 29 529 26 HOH HOH . E 5 HOH A 30 530 71 HOH HOH . E 5 HOH A 31 531 35 HOH HOH . E 5 HOH A 32 532 36 HOH HOH . E 5 HOH A 33 533 16 HOH HOH . E 5 HOH A 34 534 70 HOH HOH . E 5 HOH A 35 535 79 HOH HOH . E 5 HOH A 36 536 42 HOH HOH . E 5 HOH A 37 537 18 HOH HOH . E 5 HOH A 38 538 17 HOH HOH . E 5 HOH A 39 539 22 HOH HOH . E 5 HOH A 40 540 53 HOH HOH . E 5 HOH A 41 541 8 HOH HOH . E 5 HOH A 42 542 43 HOH HOH . E 5 HOH A 43 543 44 HOH HOH . E 5 HOH A 44 544 61 HOH HOH . E 5 HOH A 45 545 51 HOH HOH . E 5 HOH A 46 546 75 HOH HOH . E 5 HOH A 47 547 13 HOH HOH . E 5 HOH A 48 548 14 HOH HOH . E 5 HOH A 49 549 19 HOH HOH . E 5 HOH A 50 550 32 HOH HOH . E 5 HOH A 51 551 65 HOH HOH . E 5 HOH A 52 552 23 HOH HOH . E 5 HOH A 53 553 33 HOH HOH . E 5 HOH A 54 554 67 HOH HOH . E 5 HOH A 55 555 27 HOH HOH . E 5 HOH A 56 556 49 HOH HOH . E 5 HOH A 57 557 7 HOH HOH . E 5 HOH A 58 558 72 HOH HOH . E 5 HOH A 59 559 52 HOH HOH . E 5 HOH A 60 560 20 HOH HOH . E 5 HOH A 61 561 29 HOH HOH . E 5 HOH A 62 562 34 HOH HOH . E 5 HOH A 63 563 30 HOH HOH . E 5 HOH A 64 564 46 HOH HOH . E 5 HOH A 65 565 54 HOH HOH . E 5 HOH A 66 566 81 HOH HOH . E 5 HOH A 67 567 1 HOH HOH . E 5 HOH A 68 568 82 HOH HOH . E 5 HOH A 69 569 76 HOH HOH . E 5 HOH A 70 570 59 HOH HOH . E 5 HOH A 71 571 80 HOH HOH . E 5 HOH A 72 572 37 HOH HOH . E 5 HOH A 73 573 63 HOH HOH . E 5 HOH A 74 574 73 HOH HOH . E 5 HOH A 75 575 77 HOH HOH . E 5 HOH A 76 576 66 HOH HOH . E 5 HOH A 77 577 78 HOH HOH . E 5 HOH A 78 578 45 HOH HOH . E 5 HOH A 79 579 38 HOH HOH . E 5 HOH A 80 580 64 HOH HOH . E 5 HOH A 81 581 69 HOH HOH . E 5 HOH A 82 582 48 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 C1 WD6 . . . B 2 -11.446 13.786 67.135 1 61.38 ? C1 WD6 401 A 1 HETATM 2 C C2 WD6 . . . B 2 -11.002 12.135 68.916 1 56.25 ? C2 WD6 401 A 1 HETATM 3 C C3 WD6 . . . B 2 -10.649 12.385 70.383 1 61.95 ? C3 WD6 401 A 1 HETATM 4 C C4 WD6 . . . B 2 -11.773 13.237 70.948 1 56.43 ? C4 WD6 401 A 1 HETATM 5 C C5 WD6 . . . B 2 -12.914 12.643 71.483 1 53.56 ? C5 WD6 401 A 1 HETATM 6 C C6 WD6 . . . B 2 -13.93 13.436 71.981 1 56.34 ? C6 WD6 401 A 1 HETATM 7 C C9 WD6 . . . B 2 -11.648 14.621 70.903 1 59.08 ? C9 WD6 401 A 1 HETATM 8 C C10 WD6 . . . B 2 -10.205 10.906 68.49 1 68.04 ? C10 WD6 401 A 1 HETATM 9 C C11 WD6 . . . B 2 -10.041 8.489 68.193 1 75.87 ? C11 WD6 401 A 1 HETATM 10 C C14 WD6 . . . B 2 -9.34 7.233 71.025 1 83.22 ? C14 WD6 401 A 1 HETATM 11 C C15 WD6 . . . B 2 -9.223 7.433 72.4 1 86.73 ? C15 WD6 401 A 1 HETATM 12 C C16 WD6 . . . B 2 -10.317 7.874 73.138 1 84.41 ? C16 WD6 401 A 1 HETATM 13 C C17 WD6 . . . B 2 -11.526 8.119 72.495 1 79.96 ? C17 WD6 401 A 1 HETATM 14 C C18 WD6 . . . B 2 -11.642 7.922 71.123 1 75.03 ? C18 WD6 401 A 1 HETATM 15 C C19 WD6 . . . B 2 -10.044 8.327 66.675 1 80.36 ? C19 WD6 401 A 1 HETATM 16 C C12 WD6 . . . B 2 -10.678 7.273 68.874 1 73.05 ? C12 WD6 401 A 1 HETATM 17 C C13 WD6 . . . B 2 -10.551 7.478 70.385 1 77.2 ? C13 WD6 401 A 1 HETATM 18 C C20 WD6 . . . B 2 -9.186 7.132 66.262 1 89.34 ? C20 WD6 401 A 1 HETATM 19 C C21 WD6 . . . B 2 -9.026 4.843 65.496 1 94.18 ? C21 WD6 401 A 1 HETATM 20 C C22 WD6 . . . B 2 -9.805 4.12 64.405 1 92.6 ? C22 WD6 401 A 1 HETATM 21 C C23 WD6 . . . B 2 -10.417 3.551 63.516 1 92.74 ? C23 WD6 401 A 1 HETATM 22 C C24 WD6 . . . B 2 -10.953 14.975 66.285 1 60.96 ? C24 WD6 401 A 1 HETATM 23 C C25 WD6 . . . B 2 -11.149 14.635 64.806 1 55.59 ? C25 WD6 401 A 1 HETATM 24 C C26 WD6 . . . B 2 -10.319 13.407 64.433 1 56.01 ? C26 WD6 401 A 1 HETATM 25 C C27 WD6 . . . B 2 -10.901 12.408 63.67 1 50.61 ? C27 WD6 401 A 1 HETATM 26 C C28 WD6 . . . B 2 -12.349 12.573 63.239 1 50.1 ? C28 WD6 401 A 1 HETATM 27 C C29 WD6 . . . B 2 -10.181 11.275 63.291 1 46.53 ? C29 WD6 401 A 1 HETATM 28 C C30 WD6 . . . B 2 -8.861 11.144 63.698 1 54.88 ? C30 WD6 401 A 1 HETATM 29 C C31 WD6 . . . B 2 -8.27 12.146 64.472 1 59.9 ? C31 WD6 401 A 1 HETATM 30 C C32 WD6 . . . B 2 -8.996 13.272 64.846 1 55.53 ? C32 WD6 401 A 1 HETATM 31 C C7 WD6 . . . B 2 -13.814 14.815 71.938 1 70.64 ? C7 WD6 401 A 1 HETATM 32 C C8 WD6 . . . B 2 -12.675 15.412 71.399 1 66.74 ? C8 WD6 401 A 1 HETATM 33 CL CL1 WD6 . . . B 2 -13.129 10.927 71.548 1 64.15 ? CL1 WD6 401 A 1 HETATM 34 CL CL2 WD6 . . . B 2 -15.116 15.765 72.561 1 81.83 ? CL2 WD6 401 A 1 HETATM 35 F F1 WD6 . . . B 2 -10.211 8.068 74.473 1 81.46 ? F1 WD6 401 A 1 HETATM 36 N N1 WD6 . . . B 2 -10.643 13.279 68.087 1 56.48 ? N1 WD6 401 A 1 HETATM 37 N N2 WD6 . . . B 2 -10.763 9.696 68.571 1 71.13 ? N2 WD6 401 A 1 HETATM 38 N N3 WD6 . . . B 2 -9.79 6.002 65.899 1 92.01 ? N3 WD6 401 A 1 HETATM 39 N N4 WD6 . . . B 2 -11.501 16.319 66.553 1 65.64 ? N4 WD6 401 A 1 HETATM 40 N N5 WD6 . . . B 2 -13.406 12.701 62.934 1 45.67 ? N5 WD6 401 A 1 HETATM 41 O O1 WD6 . . . B 2 -12.502 13.288 66.912 1 53.88 ? O1 WD6 401 A 1 HETATM 42 O O2 WD6 . . . B 2 -8.001 7.214 66.26 1 89.61 ? O2 WD6 401 A 1 HETATM 43 O O3 WD6 . . . B 2 -9.09 11.039 68.109 1 70.29 ? O3 WD6 401 A 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 324 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 43 #