data_8H4Y # _model_server_result.job_id 3TF7NhPMuQ1wYFq4UdB7Ag _model_server_result.datetime_utc '2024-10-15 18:23:34' _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 8h4y # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 8H4Y # _exptl.entry_id 8H4Y _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 8H4Y _cell.length_a 45.965 _cell.length_b 64.457 _cell.length_c 105.116 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8H4Y _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_565 -x,-y+1,z -1 0 0 0 -1 0 0 0 1 0 64.457 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 1.768 _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 8H4Y _atom_sites.fract_transf_matrix[1][1] 0.021756 _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] 0.015514 _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] 0.009513 _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 27 HOH HOH . C 3 HOH A 2 502 46 HOH HOH . C 3 HOH A 3 503 23 HOH HOH . C 3 HOH A 4 504 29 HOH HOH . C 3 HOH A 5 505 43 HOH HOH . C 3 HOH A 6 506 11 HOH HOH . C 3 HOH A 7 507 25 HOH HOH . C 3 HOH A 8 508 4 HOH HOH . C 3 HOH A 9 509 10 HOH HOH . C 3 HOH A 10 510 7 HOH HOH . C 3 HOH A 11 511 12 HOH HOH . C 3 HOH A 12 512 3 HOH HOH . C 3 HOH A 13 513 44 HOH HOH . C 3 HOH A 14 514 6 HOH HOH . C 3 HOH A 15 515 16 HOH HOH . C 3 HOH A 16 516 24 HOH HOH . C 3 HOH A 17 517 47 HOH HOH . C 3 HOH A 18 518 8 HOH HOH . C 3 HOH A 19 519 52 HOH HOH . C 3 HOH A 20 520 38 HOH HOH . C 3 HOH A 21 521 55 HOH HOH . C 3 HOH A 22 522 13 HOH HOH . C 3 HOH A 23 523 20 HOH HOH . C 3 HOH A 24 524 1 HOH HOH . C 3 HOH A 25 525 17 HOH HOH . C 3 HOH A 26 526 2 HOH HOH . C 3 HOH A 27 527 15 HOH HOH . C 3 HOH A 28 528 45 HOH HOH . C 3 HOH A 29 529 28 HOH HOH . C 3 HOH A 30 530 32 HOH HOH . C 3 HOH A 31 531 9 HOH HOH . C 3 HOH A 32 532 30 HOH HOH . C 3 HOH A 33 533 5 HOH HOH . C 3 HOH A 34 534 14 HOH HOH . C 3 HOH A 35 535 26 HOH HOH . C 3 HOH A 36 536 41 HOH HOH . C 3 HOH A 37 537 18 HOH HOH . C 3 HOH A 38 538 49 HOH HOH . C 3 HOH A 39 539 54 HOH HOH . C 3 HOH A 40 540 19 HOH HOH . C 3 HOH A 41 541 39 HOH HOH . C 3 HOH A 42 542 35 HOH HOH . C 3 HOH A 43 543 37 HOH HOH . C 3 HOH A 44 544 48 HOH HOH . C 3 HOH A 45 545 50 HOH HOH . C 3 HOH A 46 546 56 HOH HOH . C 3 HOH A 47 547 31 HOH HOH . C 3 HOH A 48 548 21 HOH HOH . C 3 HOH A 49 549 51 HOH HOH . C 3 HOH A 50 550 36 HOH HOH . C 3 HOH A 51 551 22 HOH HOH . C 3 HOH A 52 552 40 HOH HOH . C 3 HOH A 53 553 42 HOH HOH . C 3 HOH A 54 554 33 HOH HOH . C 3 HOH A 55 555 34 HOH HOH . C 3 HOH A 56 556 53 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 -16.165 21.646 -24.995 1 46.43 ? C8 4WI 401 A 1 HETATM 2 C C3 4WI . . . B 2 -17.169 19.994 -29.762 1 43.68 ? C3 4WI 401 A 1 HETATM 3 C C1 4WI . . . B 2 -18.827 18.087 -27.145 1 42.83 ? C1 4WI 401 A 1 HETATM 4 C C13 4WI . . . B 2 -19.103 17.099 -24.318 1 41.26 ? C13 4WI 401 A 1 HETATM 5 C C21 4WI . . . B 2 -19.513 14.955 -21.677 1 45.09 ? C21 4WI 401 A 1 HETATM 6 C C6 4WI . . . B 2 -18.416 21.67 -25.854 1 42.86 ? C6 4WI 401 A 1 HETATM 7 C C7 4WI . . . B 2 -18.292 22.575 -24.544 1 42.31 ? C7 4WI 401 A 1 HETATM 8 C C10 4WI . . . B 2 -20.92 15.794 -25.891 1 43.08 ? C10 4WI 401 A 1 HETATM 9 C C5 4WI . . . B 2 -17.251 20.916 -25.937 1 44.17 ? C5 4WI 401 A 1 HETATM 10 C C9 4WI . . . B 2 -18.782 16.647 -26.683 1 44.48 ? C9 4WI 401 A 1 HETATM 11 C C11 4WI . . . B 2 -20.744 15.098 -27.106 1 43.97 ? C11 4WI 401 A 1 HETATM 12 C C12 4WI . . . B 2 -19.39 15.561 -27.68 1 41.05 ? C12 4WI 401 A 1 HETATM 13 C C18 4WI . . . B 2 -19.721 14.068 -27.626 1 48.59 ? C18 4WI 401 A 1 HETATM 14 C C19 4WI . . . B 2 -18.857 13.353 -26.55 1 43.03 ? C19 4WI 401 A 1 HETATM 15 C C20 4WI . . . B 2 -20.011 13.4 -28.985 1 45.51 ? C20 4WI 401 A 1 HETATM 16 C C16 4WI . . . B 2 -21.395 18.958 -23.648 1 42.39 ? C16 4WI 401 A 1 HETATM 17 C C17 4WI . . . B 2 -21.465 17.986 -21.327 1 42.5 ? C17 4WI 401 A 1 HETATM 18 C C23 4WI . . . B 2 -19.36 19.142 -22.114 1 40.7 ? C23 4WI 401 A 1 HETATM 19 C C4 4WI . . . B 2 -16.707 20.835 -27.412 1 40.98 ? C4 4WI 401 A 1 HETATM 20 C C2 4WI . . . B 2 -17.642 20.006 -28.317 1 42.62 ? C2 4WI 401 A 1 HETATM 21 C C14 4WI . . . B 2 -20.01 16.918 -23.111 1 45.65 ? C14 4WI 401 A 1 HETATM 22 C C22 4WI . . . B 2 -18.569 14.22 -20.708 1 50.53 ? C22 4WI 401 A 1 HETATM 23 C C15 4WI . . . B 2 -20.553 18.258 -22.554 1 48.21 ? C15 4WI 401 A 1 HETATM 24 N N5 4WI . . . B 2 -17.467 20.97 -30.49 1 42.89 ? N5 4WI 401 A 1 HETATM 25 N N2 4WI . . . B 2 -16.784 22.58 -24.215 1 43.25 ? N2 4WI 401 A 1 HETATM 26 N N3 4WI . . . B 2 -19.539 16.54 -25.598 1 43.07 ? N3 4WI 401 A 1 HETATM 27 N N1 4WI . . . B 2 -17.642 18.621 -27.865 1 45.18 ? N1 4WI 401 A 1 HETATM 28 N N4 4WI . . . B 2 -19.143 16.259 -22.177 1 44.99 ? N4 4WI 401 A 1 HETATM 29 O O1 4WI . . . B 2 -14.991 21.378 -24.982 1 46.93 ? O1 4WI 401 A 1 HETATM 30 O O2 4WI . . . B 2 -19.77 18.75 -26.88 1 39.67 ? O2 4WI 401 A 1 HETATM 31 O O3 4WI . . . B 2 -18.03 17.602 -24.3 1 41.33 ? O3 4WI 401 A 1 HETATM 32 O O4 4WI . . . B 2 -20.533 14.478 -22.042 1 49.36 ? O4 4WI 401 A 1 HETATM 33 F F1 4WI . . . B 2 -18.973 14.314 -19.413 1 56 ? F1 4WI 401 A 1 HETATM 34 F F2 4WI . . . B 2 -17.295 14.685 -20.805 1 51.16 ? F2 4WI 401 A 1 HETATM 35 F F3 4WI . . . B 2 -18.545 12.92 -21.093 1 56.53 ? F3 4WI 401 A 1 # _model_server_stats.io_time_ms 49 _model_server_stats.parse_time_ms 37 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 305 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 35 #