data_7RFS # _model_server_result.job_id V7DAjAuuxZv5A2myTkrAVA _model_server_result.datetime_utc '2025-04-25 23:44:18' _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 7rfs # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 7RFS # _exptl.entry_id 7RFS _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 102.52 _cell.angle_gamma 90 _cell.entry_id 7RFS _cell.length_a 114.2 _cell.length_b 53.03 _cell.length_c 45.68 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7RFS _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 _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 1.804 _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 7RFS _atom_sites.fract_transf_matrix[1][1] 0.008757 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001944 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.018857 _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] 0.022425 _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 1 4WI UNL . C 3 HOH A 1 501 12 HOH HOH . C 3 HOH A 2 502 85 HOH HOH . C 3 HOH A 3 503 52 HOH HOH . C 3 HOH A 4 504 27 HOH HOH . C 3 HOH A 5 505 29 HOH HOH . C 3 HOH A 6 506 3 HOH HOH . C 3 HOH A 7 507 23 HOH HOH . C 3 HOH A 8 508 55 HOH HOH . C 3 HOH A 9 509 42 HOH HOH . C 3 HOH A 10 510 53 HOH HOH . C 3 HOH A 11 511 32 HOH HOH . C 3 HOH A 12 512 24 HOH HOH . C 3 HOH A 13 513 10 HOH HOH . C 3 HOH A 14 514 78 HOH HOH . C 3 HOH A 15 515 50 HOH HOH . C 3 HOH A 16 516 13 HOH HOH . C 3 HOH A 17 517 15 HOH HOH . C 3 HOH A 18 518 37 HOH HOH . C 3 HOH A 19 519 1 HOH HOH . C 3 HOH A 20 520 40 HOH HOH . C 3 HOH A 21 521 2 HOH HOH . C 3 HOH A 22 522 57 HOH HOH . C 3 HOH A 23 523 7 HOH HOH . C 3 HOH A 24 524 56 HOH HOH . C 3 HOH A 25 525 4 HOH HOH . C 3 HOH A 26 526 8 HOH HOH . C 3 HOH A 27 527 20 HOH HOH . C 3 HOH A 28 528 22 HOH HOH . C 3 HOH A 29 529 16 HOH HOH . C 3 HOH A 30 530 6 HOH HOH . C 3 HOH A 31 531 77 HOH HOH . C 3 HOH A 32 532 49 HOH HOH . C 3 HOH A 33 533 33 HOH HOH . C 3 HOH A 34 534 68 HOH HOH . C 3 HOH A 35 535 46 HOH HOH . C 3 HOH A 36 536 14 HOH HOH . C 3 HOH A 37 537 39 HOH HOH . C 3 HOH A 38 538 5 HOH HOH . C 3 HOH A 39 539 28 HOH HOH . C 3 HOH A 40 540 30 HOH HOH . C 3 HOH A 41 541 70 HOH HOH . C 3 HOH A 42 542 43 HOH HOH . C 3 HOH A 43 543 87 HOH HOH . C 3 HOH A 44 544 65 HOH HOH . C 3 HOH A 45 545 18 HOH HOH . C 3 HOH A 46 546 63 HOH HOH . C 3 HOH A 47 547 9 HOH HOH . C 3 HOH A 48 548 58 HOH HOH . C 3 HOH A 49 549 80 HOH HOH . C 3 HOH A 50 550 69 HOH HOH . C 3 HOH A 51 551 71 HOH HOH . C 3 HOH A 52 552 79 HOH HOH . C 3 HOH A 53 553 47 HOH HOH . C 3 HOH A 54 554 41 HOH HOH . C 3 HOH A 55 555 45 HOH HOH . C 3 HOH A 56 556 38 HOH HOH . C 3 HOH A 57 557 35 HOH HOH . C 3 HOH A 58 558 59 HOH HOH . C 3 HOH A 59 559 51 HOH HOH . C 3 HOH A 60 560 21 HOH HOH . C 3 HOH A 61 561 17 HOH HOH . C 3 HOH A 62 562 19 HOH HOH . C 3 HOH A 63 563 25 HOH HOH . C 3 HOH A 64 564 61 HOH HOH . C 3 HOH A 65 565 36 HOH HOH . C 3 HOH A 66 566 60 HOH HOH . C 3 HOH A 67 567 31 HOH HOH . C 3 HOH A 68 568 72 HOH HOH . C 3 HOH A 69 569 84 HOH HOH . C 3 HOH A 70 570 75 HOH HOH . C 3 HOH A 71 571 54 HOH HOH . C 3 HOH A 72 572 82 HOH HOH . C 3 HOH A 73 573 73 HOH HOH . C 3 HOH A 74 574 76 HOH HOH . C 3 HOH A 75 575 11 HOH HOH . C 3 HOH A 76 576 64 HOH HOH . C 3 HOH A 77 577 44 HOH HOH . C 3 HOH A 78 578 34 HOH HOH . C 3 HOH A 79 579 66 HOH HOH . C 3 HOH A 80 580 83 HOH HOH . C 3 HOH A 81 581 62 HOH HOH . C 3 HOH A 82 582 67 HOH HOH . C 3 HOH A 83 583 86 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 6.572 1.373 18.105 1 48.45 ? C8 4WI 401 A 1 HETATM 2 C C3 4WI . . . B 2 7.852 -3.217 19.713 1 46.34 ? C3 4WI 401 A 1 HETATM 3 C C1 4WI . . . B 2 9.193 -0.664 21.659 1 50.51 ? C1 4WI 401 A 1 HETATM 4 C C13 4WI . . . B 2 10.255 2.169 22.026 1 51.87 ? C13 4WI 401 A 1 HETATM 5 C C21 4WI . . . B 2 12.25 4.895 22.778 1 54.13 ? C21 4WI 401 A 1 HETATM 6 C C6 4WI . . . B 2 5.62 0.469 20.076 1 48.65 ? C6 4WI 401 A 1 HETATM 7 C C7 4WI . . . B 2 5.047 1.849 19.806 1 48.74 ? C7 4WI 401 A 1 HETATM 8 C C10 4WI . . . B 2 11.164 0.893 24.031 1 51.53 ? C10 4WI 401 A 1 HETATM 9 C C5 4WI . . . B 2 6.931 0.492 19.282 1 48.61 ? C5 4WI 401 A 1 HETATM 10 C C9 4WI . . . B 2 10.609 -0.25 21.925 1 51.29 ? C9 4WI 401 A 1 HETATM 11 C C11 4WI . . . B 2 11.688 -0.488 24.08 1 51.42 ? C11 4WI 401 A 1 HETATM 12 C C12 4WI . . . B 2 11.354 -1.196 22.813 1 51.34 ? C12 4WI 401 A 1 HETATM 13 C C18 4WI . . . B 2 12.815 -1.019 23.214 1 51.38 ? C18 4WI 401 A 1 HETATM 14 C C19 4WI . . . B 2 13.636 -0.021 22.474 1 51.24 ? C19 4WI 401 A 1 HETATM 15 C C20 4WI . . . B 2 13.552 -2.205 23.718 1 51.45 ? C20 4WI 401 A 1 HETATM 16 C C16 4WI . . . B 2 8.922 5.082 24.062 1 50.59 ? C16 4WI 401 A 1 HETATM 17 C C17 4WI . . . B 2 7.919 2.927 23.533 1 50.19 ? C17 4WI 401 A 1 HETATM 18 C C23 4WI . . . B 2 8.301 4.608 21.742 1 50.37 ? C23 4WI 401 A 1 HETATM 19 C C4 4WI . . . B 2 7.333 -0.901 18.827 1 48.51 ? C4 4WI 401 A 1 HETATM 20 C C2 4WI . . . B 2 7.746 -1.749 20.019 1 48.17 ? C2 4WI 401 A 1 HETATM 21 C C14 4WI . . . B 2 10.252 3.427 22.86 1 52.08 ? C14 4WI 401 A 1 HETATM 22 C C22 4WI . . . B 2 13.138 5.636 21.809 1 54.28 ? C22 4WI 401 A 1 HETATM 23 C C15 4WI . . . B 2 8.851 3.997 23.015 1 50.92 ? C15 4WI 401 A 1 HETATM 24 N N5 4WI . . . B 2 6.776 -3.94 19.63 1 46 ? N5 4WI 401 A 1 HETATM 25 N N2 4WI . . . B 2 5.414 2.061 18.429 1 48.6 ? N2 4WI 401 A 1 HETATM 26 N N3 4WI . . . B 2 10.544 1.003 22.693 1 51.84 ? N3 4WI 401 A 1 HETATM 27 N N1 4WI . . . B 2 9.055 -1.335 20.472 1 49.33 ? N1 4WI 401 A 1 HETATM 28 N N4 4WI . . . B 2 11.163 4.306 22.15 1 53.32 ? N4 4WI 401 A 1 HETATM 29 O O1 4WI . . . B 2 7.211 1.469 17.073 1 48.62 ? O1 4WI 401 A 1 HETATM 30 O O2 4WI . . . B 2 8.28 -0.42 22.434 1 50.92 ? O2 4WI 401 A 1 HETATM 31 O O3 4WI . . . B 2 9.993 2.178 20.83 1 51.7 ? O3 4WI 401 A 1 HETATM 32 O O4 4WI . . . B 2 12.481 4.874 23.983 1 54.33 ? O4 4WI 401 A 1 HETATM 33 F F1 4WI . . . B 2 13.131 5.084 20.574 1 54.59 ? F1 4WI 401 A 1 HETATM 34 F F2 4WI . . . B 2 14.445 5.618 22.161 1 54.44 ? F2 4WI 401 A 1 HETATM 35 F F3 4WI . . . B 2 12.8 6.947 21.669 1 54.07 ? F3 4WI 401 A 1 HETATM 36 H H5 4WI . . . B 2 5.808 0.323 21.143 0 48.65 ? H5 4WI 401 A 1 HETATM 37 H H6 4WI . . . B 2 4.947 -0.312 19.714 0 48.65 ? H6 4WI 401 A 1 HETATM 38 H H7 4WI . . . B 2 3.959 1.875 19.9 0 48.74 ? H7 4WI 401 A 1 HETATM 39 H H8 4WI . . . B 2 5.51 2.621 20.427 0 48.74 ? H8 4WI 401 A 1 HETATM 40 H H11 4WI . . . B 2 10.414 1.084 24.803 0 51.53 ? H11 4WI 401 A 1 HETATM 41 H H12 4WI . . . B 2 12.01 1.579 24.125 0 51.53 ? H12 4WI 401 A 1 HETATM 42 H H4 4WI . . . B 2 7.726 0.984 19.852 0 48.61 ? H4 4WI 401 A 1 HETATM 43 H H10 4WI . . . B 2 11.151 -0.077 20.992 0 51.29 ? H10 4WI 401 A 1 HETATM 44 H H13 4WI . . . B 2 11.288 -1.016 24.944 0 51.42 ? H13 4WI 401 A 1 HETATM 45 H H14 4WI . . . B 2 10.889 -2.169 22.893 0 51.34 ? H14 4WI 401 A 1 HETATM 46 H H23 4WI . . . B 2 14.14 -0.509 21.635 0 51.24 ? H23 4WI 401 A 1 HETATM 47 H H24 4WI . . . B 2 14.401 0.391 23.137 0 51.24 ? H24 4WI 401 A 1 HETATM 48 H H25 4WI . . . B 2 13.045 0.807 22.08 0 51.24 ? H25 4WI 401 A 1 HETATM 49 H H26 4WI . . . B 2 13.997 -2.755 22.885 0 51.45 ? H26 4WI 401 A 1 HETATM 50 H H27 4WI . . . B 2 12.873 -2.872 24.256 0 51.45 ? H27 4WI 401 A 1 HETATM 51 H H28 4WI . . . B 2 14.349 -1.894 24.398 0 51.45 ? H28 4WI 401 A 1 HETATM 52 H H17 4WI . . . B 2 9.71 5.8 23.825 0 50.59 ? H17 4WI 401 A 1 HETATM 53 H H19 4WI . . . B 2 9.127 4.651 25.046 0 50.59 ? H19 4WI 401 A 1 HETATM 54 H H18 4WI . . . B 2 7.971 5.618 24.112 0 50.59 ? H18 4WI 401 A 1 HETATM 55 H H20 4WI . . . B 2 7.503 2.343 22.708 0 50.19 ? H20 4WI 401 A 1 HETATM 56 H H21 4WI . . . B 2 7.09 3.388 24.075 0 50.19 ? H21 4WI 401 A 1 HETATM 57 H H22 4WI . . . B 2 8.442 2.254 24.217 0 50.19 ? H22 4WI 401 A 1 HETATM 58 H H29 4WI . . . B 2 8.34 3.898 20.913 0 50.37 ? H29 4WI 401 A 1 HETATM 59 H H30 4WI . . . B 2 8.871 5.499 21.466 0 50.37 ? H30 4WI 401 A 1 HETATM 60 H H31 4WI . . . B 2 7.259 4.902 21.891 0 50.37 ? H31 4WI 401 A 1 HETATM 61 H H2 4WI . . . B 2 8.165 -0.817 18.124 0 48.51 ? H2 4WI 401 A 1 HETATM 62 H H3 4WI . . . B 2 6.5 -1.378 18.305 0 48.51 ? H3 4WI 401 A 1 HETATM 63 H H32 4WI . . . B 2 7.037 -1.691 20.851 0 48.17 ? H32 4WI 401 A 1 HETATM 64 H H15 4WI . . . B 2 10.641 3.273 23.86 0 52.08 ? H15 4WI 401 A 1 HETATM 65 H H36 4WI . . . B 2 6.965 -4.937 19.492 0 46 ? H36 4WI 401 A 1 HETATM 66 H H9 4WI . . . B 2 5.197 2.942 17.975 0 48.6 ? H9 4WI 401 A 1 HETATM 67 H H1 4WI . . . B 2 9.863 -1.522 19.888 0 49.33 ? H1 4WI 401 A 1 HETATM 68 H H16 4WI . . . B 2 11.075 4.381 21.141 0 53.32 ? H16 4WI 401 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 337 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 68 #