data_8INW # _model_server_result.job_id hSmqHqammQHMxQCVDbnkFg _model_server_result.datetime_utc '2025-06-22 16:00:55' _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 8inw # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 8INW # _exptl.entry_id 8INW _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 501.542 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide _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 8INW _cell.length_a 45.627 _cell.length_b 64.033 _cell.length_c 105.14 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8INW _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 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 _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_555 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 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 # _struct_conn.conn_type_id covale _struct_conn.details ? _struct_conn.id covale1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id SG _struct_conn.ptnr1_label_comp_id CYS _struct_conn.ptnr1_label_seq_id 145 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id CYS _struct_conn.ptnr1_auth_seq_id 145 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id B _struct_conn.ptnr2_label_atom_id C3 _struct_conn.ptnr2_label_comp_id 4WI _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id 4WI _struct_conn.ptnr2_auth_seq_id 401 _struct_conn.ptnr2_symmetry 1_555 _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 1.766 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C23 H34 F3 N5 O4' _chem_comp.formula_weight 501.542 _chem_comp.id 4WI _chem_comp.mon_nstd_flag . _chem_comp.name (1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'PF-07321332, bound form;nirmatrelvir, bound form;Paxlovid, bound form' # 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 O1 C8 4WI doub 1 n n C8 N2 4WI sing 2 n n C8 C5 4WI sing 3 n n N2 C7 4WI sing 4 n n C4 C5 4WI sing 5 n n C4 C2 4WI sing 6 n n C5 C6 4WI sing 7 n n N5 C3 4WI doub 8 n n C3 C2 4WI sing 9 n n C7 C6 4WI sing 10 n n C2 N1 4WI sing 11 n n N1 C1 4WI sing 12 n n F1 C22 4WI sing 13 n n O3 C13 4WI doub 14 n n C1 C9 4WI sing 15 n n C1 O2 4WI doub 16 n n F3 C22 4WI sing 17 n n C23 C15 4WI sing 18 n n C22 F2 4WI sing 19 n n C22 C21 4WI sing 20 n n C9 N3 4WI sing 21 n n C9 C12 4WI sing 22 n n C13 N3 4WI sing 23 n n C13 C14 4WI sing 24 n n N4 C21 4WI sing 25 n n N4 C14 4WI sing 26 n n C19 C18 4WI sing 27 n n N3 C10 4WI sing 28 n n C21 O4 4WI doub 29 n n C12 C18 4WI sing 30 n n C12 C11 4WI sing 31 n n C14 C15 4WI sing 32 n n C15 C17 4WI sing 33 n n C15 C16 4WI sing 34 n n C18 C20 4WI sing 35 n n C18 C11 4WI sing 36 n n C10 C11 4WI sing 37 n n C3 H33 4WI sing 38 n n C6 H5 4WI sing 39 n n C6 H6 4WI sing 40 n n C7 H7 4WI sing 41 n n C7 H8 4WI sing 42 n n C10 H11 4WI sing 43 n n C10 H12 4WI sing 44 n n C5 H4 4WI sing 45 n n C9 H10 4WI sing 46 n n C11 H13 4WI sing 47 n n C12 H14 4WI sing 48 n n C19 H23 4WI sing 49 n n C19 H24 4WI sing 50 n n C19 H25 4WI sing 51 n n C20 H26 4WI sing 52 n n C20 H27 4WI sing 53 n n C20 H28 4WI sing 54 n n C16 H17 4WI sing 55 n n C16 H19 4WI sing 56 n n C16 H18 4WI sing 57 n n C17 H20 4WI sing 58 n n C17 H21 4WI sing 59 n n C17 H22 4WI sing 60 n n C23 H29 4WI sing 61 n n C23 H30 4WI sing 62 n n C23 H31 4WI sing 63 n n C4 H2 4WI sing 64 n n C4 H3 4WI sing 65 n n C2 H32 4WI sing 66 n n C14 H15 4WI sing 67 n n N5 H36 4WI sing 68 n n N2 H9 4WI sing 69 n n N1 H1 4WI sing 70 n n N4 H16 4WI sing 71 n n # _atom_sites.entry_id 8INW _atom_sites.fract_transf_matrix[1][1] 0.021917 _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] 0.015617 _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] 0.009511 _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 4WI A 1 401 401 4WI 4WI . C 3 HOH A 1 501 33 HOH HOH . C 3 HOH A 2 502 37 HOH HOH . C 3 HOH A 3 503 85 HOH HOH . C 3 HOH A 4 504 86 HOH HOH . C 3 HOH A 5 505 3 HOH HOH . C 3 HOH A 6 506 50 HOH HOH . C 3 HOH A 7 507 1 HOH HOH . C 3 HOH A 8 508 45 HOH HOH . C 3 HOH A 9 509 15 HOH HOH . C 3 HOH A 10 510 23 HOH HOH . C 3 HOH A 11 511 14 HOH HOH . C 3 HOH A 12 512 2 HOH HOH . C 3 HOH A 13 513 57 HOH HOH . C 3 HOH A 14 514 19 HOH HOH . C 3 HOH A 15 515 6 HOH HOH . C 3 HOH A 16 516 32 HOH HOH . C 3 HOH A 17 517 11 HOH HOH . C 3 HOH A 18 518 82 HOH HOH . C 3 HOH A 19 519 51 HOH HOH . C 3 HOH A 20 520 4 HOH HOH . C 3 HOH A 21 521 53 HOH HOH . C 3 HOH A 22 522 17 HOH HOH . C 3 HOH A 23 523 7 HOH HOH . C 3 HOH A 24 524 30 HOH HOH . C 3 HOH A 25 525 20 HOH HOH . C 3 HOH A 26 526 81 HOH HOH . C 3 HOH A 27 527 21 HOH HOH . C 3 HOH A 28 528 42 HOH HOH . C 3 HOH A 29 529 5 HOH HOH . C 3 HOH A 30 530 8 HOH HOH . C 3 HOH A 31 531 38 HOH HOH . C 3 HOH A 32 532 39 HOH HOH . C 3 HOH A 33 533 49 HOH HOH . C 3 HOH A 34 534 36 HOH HOH . C 3 HOH A 35 535 41 HOH HOH . C 3 HOH A 36 536 43 HOH HOH . C 3 HOH A 37 537 9 HOH HOH . C 3 HOH A 38 538 27 HOH HOH . C 3 HOH A 39 539 18 HOH HOH . C 3 HOH A 40 540 63 HOH HOH . C 3 HOH A 41 541 58 HOH HOH . C 3 HOH A 42 542 54 HOH HOH . C 3 HOH A 43 543 28 HOH HOH . C 3 HOH A 44 544 75 HOH HOH . C 3 HOH A 45 545 25 HOH HOH . C 3 HOH A 46 546 59 HOH HOH . C 3 HOH A 47 547 52 HOH HOH . C 3 HOH A 48 548 87 HOH HOH . C 3 HOH A 49 549 10 HOH HOH . C 3 HOH A 50 550 67 HOH HOH . C 3 HOH A 51 551 62 HOH HOH . C 3 HOH A 52 552 34 HOH HOH . C 3 HOH A 53 553 91 HOH HOH . C 3 HOH A 54 554 76 HOH HOH . C 3 HOH A 55 555 16 HOH HOH . C 3 HOH A 56 556 13 HOH HOH . C 3 HOH A 57 557 47 HOH HOH . C 3 HOH A 58 558 89 HOH HOH . C 3 HOH A 59 559 26 HOH HOH . C 3 HOH A 60 560 60 HOH HOH . C 3 HOH A 61 561 40 HOH HOH . C 3 HOH A 62 562 46 HOH HOH . C 3 HOH A 63 563 44 HOH HOH . C 3 HOH A 64 564 64 HOH HOH . C 3 HOH A 65 565 31 HOH HOH . C 3 HOH A 66 566 79 HOH HOH . C 3 HOH A 67 567 78 HOH HOH . C 3 HOH A 68 568 71 HOH HOH . C 3 HOH A 69 569 29 HOH HOH . C 3 HOH A 70 570 61 HOH HOH . C 3 HOH A 71 571 22 HOH HOH . C 3 HOH A 72 572 24 HOH HOH . C 3 HOH A 73 573 66 HOH HOH . C 3 HOH A 74 574 74 HOH HOH . C 3 HOH A 75 575 68 HOH HOH . C 3 HOH A 76 576 84 HOH HOH . C 3 HOH A 77 577 90 HOH HOH . C 3 HOH A 78 578 80 HOH HOH . C 3 HOH A 79 579 12 HOH HOH . C 3 HOH A 80 580 48 HOH HOH . C 3 HOH A 81 581 83 HOH HOH . C 3 HOH A 82 582 88 HOH HOH . C 3 HOH A 83 583 56 HOH HOH . C 3 HOH A 84 584 72 HOH HOH . C 3 HOH A 85 585 69 HOH HOH . C 3 HOH A 86 586 73 HOH HOH . C 3 HOH A 87 587 70 HOH HOH . C 3 HOH A 88 588 55 HOH HOH . C 3 HOH A 89 589 35 HOH HOH . C 3 HOH A 90 590 77 HOH HOH . C 3 HOH A 91 591 65 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 C8 4WI . . . B 2 -16.12 10.605 -27.597 1 31.29 ? C8 4WI 401 A 1 HETATM 2 C C3 4WI . . . B 2 -17.226 12.035 -22.824 1 24.52 ? C3 4WI 401 A 1 HETATM 3 C C1 4WI . . . B 2 -18.913 14.001 -25.391 1 24.3 ? C1 4WI 401 A 1 HETATM 4 C C13 4WI . . . B 2 -19.065 15.055 -28.409 1 27.85 ? C13 4WI 401 A 1 HETATM 5 C C21 4WI . . . B 2 -19.288 17.326 -31.035 1 34.57 ? C21 4WI 401 A 1 HETATM 6 C C6 4WI . . . B 2 -18.368 10.42 -26.737 1 26.22 ? C6 4WI 401 A 1 HETATM 7 C C7 4WI . . . B 2 -18.221 9.704 -28.153 1 23.12 ? C7 4WI 401 A 1 HETATM 8 C C10 4WI . . . B 2 -20.892 16.354 -26.803 1 29.27 ? C10 4WI 401 A 1 HETATM 9 C C5 4WI . . . B 2 -17.241 11.211 -26.609 1 28.19 ? C5 4WI 401 A 1 HETATM 10 C C9 4WI . . . B 2 -18.83 15.429 -25.937 1 29.7 ? C9 4WI 401 A 1 HETATM 11 C C11 4WI . . . B 2 -20.772 16.984 -25.539 1 34.67 ? C11 4WI 401 A 1 HETATM 12 C C12 4WI . . . B 2 -19.397 16.575 -24.96 1 26.89 ? C12 4WI 401 A 1 HETATM 13 C C18 4WI . . . B 2 -19.828 18.054 -24.958 1 34.99 ? C18 4WI 401 A 1 HETATM 14 C C19 4WI . . . B 2 -19.105 18.906 -26.023 1 32.51 ? C19 4WI 401 A 1 HETATM 15 C C20 4WI . . . B 2 -20.211 18.666 -23.593 1 30.63 ? C20 4WI 401 A 1 HETATM 16 C C16 4WI . . . B 2 -21.315 13.242 -29.183 1 21.41 ? C16 4WI 401 A 1 HETATM 17 C C17 4WI . . . B 2 -21.425 14.366 -31.442 1 24.08 ? C17 4WI 401 A 1 HETATM 18 C C23 4WI . . . B 2 -19.366 13.059 -30.799 1 22.6 ? C23 4WI 401 A 1 HETATM 19 C C4 4WI . . . B 2 -16.744 11.185 -25.131 1 24.35 ? C4 4WI 401 A 1 HETATM 20 C C2 4WI . . . B 2 -17.693 12.039 -24.27 1 27.21 ? C2 4WI 401 A 1 HETATM 21 C C14 4WI . . . B 2 -19.906 15.293 -29.66 1 26.25 ? C14 4WI 401 A 1 HETATM 22 C C22 4WI . . . B 2 -18.314 18.008 -32.015 1 35.23 ? C22 4WI 401 A 1 HETATM 23 C C15 4WI . . . B 2 -20.491 13.985 -30.262 1 27.83 ? C15 4WI 401 A 1 HETATM 24 N N5 4WI . . . B 2 -17.613 11.122 -22.048 1 26.38 ? N5 4WI 401 A 1 HETATM 25 N N2 4WI . . . B 2 -16.711 9.754 -28.467 1 29.93 ? N2 4WI 401 A 1 HETATM 26 N N3 4WI . . . B 2 -19.529 15.567 -27.08 1 26.53 ? N3 4WI 401 A 1 HETATM 27 N N1 4WI . . . B 2 -17.683 13.403 -24.791 1 25.49 ? N1 4WI 401 A 1 HETATM 28 N N4 4WI . . . B 2 -19.018 15.952 -30.594 1 29.9 ? N4 4WI 401 A 1 HETATM 29 O O1 4WI . . . B 2 -14.96 10.869 -27.572 1 29.52 ? O1 4WI 401 A 1 HETATM 30 O O2 4WI . . . B 2 -19.922 13.377 -25.463 1 26.3 ? O2 4WI 401 A 1 HETATM 31 O O3 4WI . . . B 2 -18.015 14.497 -28.471 1 27.48 ? O3 4WI 401 A 1 HETATM 32 O O4 4WI . . . B 2 -20.245 17.905 -30.645 1 32.98 ? O4 4WI 401 A 1 HETATM 33 F F1 4WI . . . B 2 -18.484 17.5 -33.273 1 43.12 ? F1 4WI 401 A 1 HETATM 34 F F2 4WI . . . B 2 -17.032 17.775 -31.598 1 40.16 ? F2 4WI 401 A 1 HETATM 35 F F3 4WI . . . B 2 -18.552 19.355 -32.019 1 41.51 ? F3 4WI 401 A 1 # _model_server_stats.io_time_ms 56 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 298 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 35 #