data_8E1Y # _model_server_result.job_id WncF1AiJ6uFbF7zBedA3QQ _model_server_result.datetime_utc '2024-11-05 12:35:00' _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 8e1y # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":402}' # _entry.id 8E1Y # _exptl.entry_id 8E1Y _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 2 _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 8E1Y _cell.length_a 100.905 _cell.length_b 103.925 _cell.length_c 68.025 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8E1Y _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _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,F,G,H _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 F N 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 C _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 1.777 _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 8E1Y _atom_sites.fract_transf_matrix[1][1] 0.00991 _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] 0.009622 _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] 0.0147 _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 C 2 4WI A 1 401 401 4WI DRG . D 3 DMS A 1 402 402 DMS DMS . E 3 DMS B 1 401 401 DMS DMS . F 2 4WI B 1 402 402 4WI DRG . G 4 HOH A 1 501 18 HOH HOH . G 4 HOH A 2 502 10 HOH HOH . G 4 HOH A 3 503 29 HOH HOH . G 4 HOH A 4 504 16 HOH HOH . G 4 HOH A 5 505 21 HOH HOH . G 4 HOH A 6 506 20 HOH HOH . G 4 HOH A 7 507 22 HOH HOH . G 4 HOH A 8 508 4 HOH HOH . G 4 HOH A 9 509 28 HOH HOH . G 4 HOH A 10 510 1 HOH HOH . G 4 HOH A 11 511 26 HOH HOH . G 4 HOH A 12 512 2 HOH HOH . G 4 HOH A 13 513 19 HOH HOH . G 4 HOH A 14 514 5 HOH HOH . G 4 HOH A 15 515 13 HOH HOH . G 4 HOH A 16 516 27 HOH HOH . G 4 HOH A 17 517 24 HOH HOH . H 4 HOH B 1 501 3 HOH HOH . H 4 HOH B 2 502 11 HOH HOH . H 4 HOH B 3 503 9 HOH HOH . H 4 HOH B 4 504 17 HOH HOH . H 4 HOH B 5 505 15 HOH HOH . H 4 HOH B 6 506 6 HOH HOH . H 4 HOH B 7 507 7 HOH HOH . H 4 HOH B 8 508 8 HOH HOH . H 4 HOH B 9 509 12 HOH HOH . H 4 HOH B 10 510 25 HOH HOH . H 4 HOH B 11 511 14 HOH HOH . H 4 HOH B 12 512 23 HOH HOH . H 4 HOH B 13 513 30 HOH HOH . H 4 HOH B 14 514 31 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 . . . F 2 10.091 -7.722 13.275 1 64.44 0 C8 4WI 402 B 1 HETATM 2 C C3 4WI . . . F 2 13.314 -4.034 12.569 1 59.01 0 C3 4WI 402 B 1 HETATM 3 C C1 4WI . . . F 2 12.173 -2.5 14.894 1 73.56 0 C1 4WI 402 B 1 HETATM 4 C C13 4WI . . . F 2 10.488 -3.626 17.247 1 76.53 0 C13 4WI 402 B 1 HETATM 5 C C21 4WI . . . F 2 8.305 -3.201 19.833 1 90.95 0 C21 4WI 402 B 1 HETATM 6 C C6 4WI . . . F 2 12.352 -7.889 13.957 1 64.04 0 C6 4WI 402 B 1 HETATM 7 C C7 4WI . . . F 2 11.655 -9.23 14.136 1 64.85 0 C7 4WI 402 B 1 HETATM 8 C C10 4WI . . . F 2 11.82 -1.727 18.17 1 72.8 0 C10 4WI 402 B 1 HETATM 9 C C5 4WI . . . F 2 11.212 -6.888 13.857 1 63.47 0 C5 4WI 402 B 1 HETATM 10 C C9 4WI . . . F 2 11.193 -1.78 15.802 1 72.52 0 C9 4WI 402 B 1 HETATM 11 C C11 4WI . . . F 2 12.085 -0.361 17.575 1 70.71 0 C11 4WI 402 B 1 HETATM 12 C C12 4WI . . . F 2 11.69 -0.388 16.117 1 71.08 0 C12 4WI 402 B 1 HETATM 13 C C18 4WI . . . F 2 10.947 0.499 17.09 1 67.3 0 C18 4WI 402 B 1 HETATM 14 C C19 4WI . . . F 2 11.179 1.989 16.987 1 63.79 0 C19 4WI 402 B 1 HETATM 15 C C20 4WI . . . F 2 9.544 0.153 17.55 1 65.62 0 C20 4WI 402 B 1 HETATM 16 C C16 4WI . . . F 2 11.46 -5.448 20.443 1 82.76 0 C16 4WI 402 B 1 HETATM 17 C C17 4WI . . . F 2 12.118 -5.735 18.056 1 83.91 0 C17 4WI 402 B 1 HETATM 18 C C23 4WI . . . F 2 9.928 -6.622 18.866 1 82.68 0 C23 4WI 402 B 1 HETATM 19 C C4 4WI . . . F 2 11.436 -5.632 13.024 1 63.7 0 C4 4WI 402 B 1 HETATM 20 C C2 4WI . . . F 2 12.377 -4.558 13.615 1 65.13 0 C2 4WI 402 B 1 HETATM 21 C C14 4WI . . . F 2 10.264 -4.109 18.682 1 83.93 0 C14 4WI 402 B 1 HETATM 22 C C22 4WI . . . F 2 7.188 -3.716 20.751 1 93.58 0 C22 4WI 402 B 1 HETATM 23 C C15 4WI . . . F 2 10.934 -5.47 19.001 1 84.1 0 C15 4WI 402 B 1 HETATM 24 N N5 4WI . . . F 2 14.189 -4.269 11.302 1 60.92 0 N5 4WI 402 B 1 HETATM 25 N N2 4WI . . . F 2 10.336 -8.998 13.554 1 67.21 0 N2 4WI 402 B 1 HETATM 26 N N3 4WI . . . F 2 11.132 -2.457 17.096 1 73.23 0 N3 4WI 402 B 1 HETATM 27 N N1 4WI . . . F 2 11.577 -3.425 14.133 1 70.86 0 N1 4WI 402 B 1 HETATM 28 N N4 4WI . . . F 2 8.838 -4.082 18.982 1 88.94 0 N4 4WI 402 B 1 HETATM 29 O O1 4WI . . . F 2 9.107 -7.281 12.655 1 61.25 0 O1 4WI 402 B 1 HETATM 30 O O2 4WI . . . F 2 13.387 -2.266 14.906 1 76.03 0 O2 4WI 402 B 1 HETATM 31 O O3 4WI . . . F 2 10.113 -4.282 16.275 1 70.99 0 O3 4WI 402 B 1 HETATM 32 O O4 4WI . . . F 2 8.691 -2.051 19.963 1 86.62 0 O4 4WI 402 B 1 HETATM 33 F F1 4WI . . . F 2 7.399 -4.97 21.14 1 93.06 0 F1 4WI 402 B 1 HETATM 34 F F2 4WI . . . F 2 7.077 -2.981 21.853 1 92.1 0 F2 4WI 402 B 1 HETATM 35 F F3 4WI . . . F 2 6.005 -3.687 20.156 1 92.93 0 F3 4WI 402 B 1 HETATM 36 H H5 4WI . . . F 2 12.894 -7.884 13.144 1 63.79 0 H5 4WI 402 B 1 HETATM 37 H H6 4WI . . . F 2 12.927 -7.692 14.724 1 63.84 0 H6 4WI 402 B 1 HETATM 38 H H7 4WI . . . F 2 11.586 -9.473 15.086 1 64.79 0 H7 4WI 402 B 1 HETATM 39 H H8 4WI . . . F 2 12.132 -9.946 13.66 1 64.75 0 H8 4WI 402 B 1 HETATM 40 H H11 4WI . . . F 2 11.253 -1.652 18.963 1 72.38 0 H11 4WI 402 B 1 HETATM 41 H H12 4WI . . . F 2 12.656 -2.175 18.414 1 72.37 0 H12 4WI 402 B 1 HETATM 42 H H4 4WI . . . F 2 10.954 -6.611 14.773 1 63.62 0 H4 4WI 402 B 1 HETATM 43 H H10 4WI . . . F 2 10.298 -1.752 15.385 1 72.1 0 H10 4WI 402 B 1 HETATM 44 H H13 4WI . . . F 2 12.95 0.109 17.818 1 70.43 0 H13 4WI 402 B 1 HETATM 45 H H14 4WI . . . F 2 12.347 0.057 15.483 1 70.45 0 H14 4WI 402 B 1 HETATM 46 H H23 4WI . . . F 2 11.806 2.172 16.271 1 64.63 0 H23 4WI 402 B 1 HETATM 47 H H24 4WI . . . F 2 11.542 2.319 17.823 1 64.63 0 H24 4WI 402 B 1 HETATM 48 H H25 4WI . . . F 2 10.341 2.44 16.801 1 64.64 0 H25 4WI 402 B 1 HETATM 49 H H26 4WI . . . F 2 9.251 -0.668 17.127 1 65.91 0 H26 4WI 402 B 1 HETATM 50 H H27 4WI . . . F 2 8.934 0.868 17.311 1 65.96 0 H27 4WI 402 B 1 HETATM 51 H H28 4WI . . . F 2 9.538 0.035 18.512 1 66 0 H28 4WI 402 B 1 HETATM 52 H H17 4WI . . . F 2 11.265 -4.586 20.851 1 82.95 0 H17 4WI 402 B 1 HETATM 53 H H19 4WI . . . F 2 11.032 -6.15 20.961 1 82.95 0 H19 4WI 402 B 1 HETATM 54 H H18 4WI . . . F 2 12.422 -5.591 20.446 1 82.95 0 H18 4WI 402 B 1 HETATM 55 H H20 4WI . . . F 2 12.237 -4.982 17.454 1 83.68 0 H20 4WI 402 B 1 HETATM 56 H H21 4WI . . . F 2 11.95 -6.538 17.534 1 83.73 0 H21 4WI 402 B 1 HETATM 57 H H22 4WI . . . F 2 12.931 -5.856 18.575 1 83.73 0 H22 4WI 402 B 1 HETATM 58 H H29 4WI . . . F 2 9.067 -6.276 18.589 1 82.64 0 H29 4WI 402 B 1 HETATM 59 H H30 4WI . . . F 2 9.828 -7.076 19.719 1 82.84 0 H30 4WI 402 B 1 HETATM 60 H H31 4WI . . . F 2 10.242 -7.256 18.2 1 82.7 0 H31 4WI 402 B 1 HETATM 61 H H2 4WI . . . F 2 11.8 -5.902 12.152 1 63.82 0 H2 4WI 402 B 1 HETATM 62 H H3 4WI . . . F 2 10.565 -5.215 12.852 1 63.86 0 H3 4WI 402 B 1 HETATM 63 H H32 4WI . . . F 2 12.981 -5.008 14.4 1 64.56 0 H32 4WI 402 B 1 HETATM 64 H H15 4WI . . . F 2 10.69 -3.459 19.287 1 83.24 0 H15 4WI 402 B 1 HETATM 65 H H36 4WI . . . F 2 14.56 -4.626 11.48 0 58.51 0 H36 4WI 402 B 1 HETATM 66 H H9 4WI . . . F 2 9.754 -9.631 13.404 1 65.6 0 H9 4WI 402 B 1 HETATM 67 H H1 4WI . . . F 2 10.741 -3.312 13.874 1 69.77 0 H1 4WI 402 B 1 HETATM 68 H H16 4WI . . . F 2 8.296 -4.632 18.575 1 88.04 0 H16 4WI 402 B 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 28 _model_server_stats.query_time_ms 279 _model_server_stats.encode_time_ms 17 _model_server_stats.element_count 68 #