data_8E1Y # _model_server_result.job_id t7s6Sw7iXdVbAcrVqbpqlw _model_server_result.datetime_utc '2024-11-05 12:30:34' _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 8e1y # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":401}' # _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 . . . C 2 -4.74 -26.093 -16.873 1 48.49 0 C8 4WI 401 A 1 HETATM 2 C C3 4WI . . . C 2 -3.14 -24.989 -21.268 1 41.06 0 C3 4WI 401 A 1 HETATM 3 C C1 4WI . . . C 2 -4.299 -28.054 -22.023 1 55.3 0 C1 4WI 401 A 1 HETATM 4 C C13 4WI . . . C 2 -5.678 -30.486 -20.557 1 66.75 0 C13 4WI 401 A 1 HETATM 5 C C21 4WI . . . C 2 -5.735 -33.813 -19.856 1 81.07 0 C21 4WI 401 A 1 HETATM 6 C C6 4WI . . . C 2 -6.732 -26.254 -18.139 1 48.82 0 C6 4WI 401 A 1 HETATM 7 C C7 4WI . . . C 2 -6.879 -25.19 -17.053 1 49.33 0 C7 4WI 401 A 1 HETATM 8 C C10 4WI . . . C 2 -5.387 -31.286 -22.891 1 61.51 0 C10 4WI 401 A 1 HETATM 9 C C5 4WI . . . C 2 -5.224 -26.412 -18.279 1 48.49 0 C5 4WI 401 A 1 HETATM 10 C C9 4WI . . . C 2 -3.895 -29.533 -21.996 1 60.45 0 C9 4WI 401 A 1 HETATM 11 C C11 4WI . . . C 2 -4.285 -31.051 -23.9 1 60.75 0 C11 4WI 401 A 1 HETATM 12 C C12 4WI . . . C 2 -3.36 -29.981 -23.362 1 60.43 0 C12 4WI 401 A 1 HETATM 13 C C18 4WI . . . C 2 -2.846 -31.387 -23.603 1 59.34 0 C18 4WI 401 A 1 HETATM 14 C C19 4WI . . . C 2 -2.508 -32.274 -22.422 1 58.64 0 C19 4WI 401 A 1 HETATM 15 C C20 4WI . . . C 2 -2 -31.696 -24.82 1 59.09 0 C20 4WI 401 A 1 HETATM 16 C C16 4WI . . . C 2 -8.177 -30.489 -18.599 1 67.74 0 C16 4WI 401 A 1 HETATM 17 C C17 4WI . . . C 2 -8.669 -30.253 -21.043 1 71.22 0 C17 4WI 401 A 1 HETATM 18 C C23 4WI . . . C 2 -8.995 -32.456 -19.904 1 71.79 0 C23 4WI 401 A 1 HETATM 19 C C4 4WI . . . C 2 -4.478 -25.522 -19.275 1 47.62 0 C4 4WI 401 A 1 HETATM 20 C C2 4WI . . . C 2 -4.296 -25.914 -20.75 1 46.59 0 C2 4WI 401 A 1 HETATM 21 C C14 4WI . . . C 2 -6.685 -31.626 -20.348 1 71.4 0 C14 4WI 401 A 1 HETATM 22 C C22 4WI . . . C 2 -6.141 -35.06 -19.06 1 85.12 0 C22 4WI 401 A 1 HETATM 23 C C15 4WI . . . C 2 -8.118 -31.196 -19.963 1 71.31 0 C15 4WI 401 A 1 HETATM 24 N N5 4WI . . . C 2 -3.347 -23.683 -21.951 1 42.9 0 N5 4WI 401 A 1 HETATM 25 N N2 4WI . . . C 2 -5.657 -25.354 -16.271 1 47.96 0 N2 4WI 401 A 1 HETATM 26 N N3 4WI . . . C 2 -5.034 -30.432 -21.743 1 63.16 0 N3 4WI 401 A 1 HETATM 27 N N1 4WI . . . C 2 -3.976 -27.332 -20.928 1 50.34 0 N1 4WI 401 A 1 HETATM 28 N N4 4WI . . . C 2 -6.18 -32.63 -19.421 1 74.6 0 N4 4WI 401 A 1 HETATM 29 O O1 4WI . . . C 2 -3.66 -26.448 -16.373 1 47.09 0 O1 4WI 401 A 1 HETATM 30 O O2 4WI . . . C 2 -4.887 -27.581 -22.998 1 56.31 0 O2 4WI 401 A 1 HETATM 31 O O3 4WI . . . C 2 -5.482 -29.636 -19.691 1 64.08 0 O3 4WI 401 A 1 HETATM 32 O O4 4WI . . . C 2 -5.092 -33.963 -20.876 1 82.56 0 O4 4WI 401 A 1 HETATM 33 F F1 4WI . . . C 2 -5.245 -36.034 -19.176 1 81.94 0 F1 4WI 401 A 1 HETATM 34 F F2 4WI . . . C 2 -7.299 -35.557 -19.477 1 89.29 0 F2 4WI 401 A 1 HETATM 35 F F3 4WI . . . C 2 -6.273 -34.801 -17.767 1 87.51 0 F3 4WI 401 A 1 HETATM 36 H H5 4WI . . . C 2 -7.138 -25.956 -18.978 1 48.77 0 H5 4WI 401 A 1 HETATM 37 H H6 4WI . . . C 2 -7.15 -27.094 -17.861 1 48.77 0 H6 4WI 401 A 1 HETATM 38 H H7 4WI . . . C 2 -7.677 -25.348 -16.502 1 48.79 0 H7 4WI 401 A 1 HETATM 39 H H8 4WI . . . C 2 -6.935 -24.29 -17.444 1 48.74 0 H8 4WI 401 A 1 HETATM 40 H H11 4WI . . . C 2 -5.418 -32.228 -22.631 1 61.64 0 H11 4WI 401 A 1 HETATM 41 H H12 4WI . . . C 2 -6.258 -31.029 -23.257 1 61.58 0 H12 4WI 401 A 1 HETATM 42 H H4 4WI . . . C 2 -5.012 -27.36 -18.479 1 48.34 0 H4 4WI 401 A 1 HETATM 43 H H10 4WI . . . C 2 -3.206 -29.669 -21.302 1 59.78 0 H10 4WI 401 A 1 HETATM 44 H H13 4WI . . . C 2 -4.539 -31.021 -24.873 1 60.46 0 H13 4WI 401 A 1 HETATM 45 H H14 4WI . . . C 2 -3.02 -29.263 -24.026 1 60.15 0 H14 4WI 401 A 1 HETATM 46 H H23 4WI . . . C 2 -2.688 -31.805 -21.598 1 58.36 0 H23 4WI 401 A 1 HETATM 47 H H24 4WI . . . C 2 -1.568 -32.516 -22.453 1 58.55 0 H24 4WI 401 A 1 HETATM 48 H H25 4WI . . . C 2 -3.047 -33.079 -22.456 1 58.58 0 H25 4WI 401 A 1 HETATM 49 H H26 4WI . . . C 2 -1.888 -30.892 -25.35 1 58.92 0 H26 4WI 401 A 1 HETATM 50 H H27 4WI . . . C 2 -2.437 -32.375 -25.357 1 58.92 0 H27 4WI 401 A 1 HETATM 51 H H28 4WI . . . C 2 -1.129 -32.019 -24.541 1 58.92 0 H28 4WI 401 A 1 HETATM 52 H H17 4WI . . . C 2 -7.285 -30.441 -18.216 1 68.46 0 H17 4WI 401 A 1 HETATM 53 H H19 4WI . . . C 2 -8.526 -29.588 -18.709 1 68.55 0 H19 4WI 401 A 1 HETATM 54 H H18 4WI . . . C 2 -8.757 -30.984 -17.995 1 68.56 0 H18 4WI 401 A 1 HETATM 55 H H20 4WI . . . C 2 -8.004 -30.133 -21.743 1 71.05 0 H20 4WI 401 A 1 HETATM 56 H H21 4WI . . . C 2 -8.881 -29.389 -20.651 1 71.04 0 H21 4WI 401 A 1 HETATM 57 H H22 4WI . . . C 2 -9.475 -30.634 -21.433 1 71.06 0 H22 4WI 401 A 1 HETATM 58 H H29 4WI . . . C 2 -8.462 -33.238 -20.128 1 71.5 0 H29 4WI 401 A 1 HETATM 59 H H30 4WI . . . C 2 -9.726 -32.379 -20.541 1 71.46 0 H30 4WI 401 A 1 HETATM 60 H H31 4WI . . . C 2 -9.361 -32.564 -19.01 1 71.45 0 H31 4WI 401 A 1 HETATM 61 H H2 4WI . . . C 2 -4.918 -24.646 -19.265 1 47.47 0 H2 4WI 401 A 1 HETATM 62 H H3 4WI . . . C 2 -3.579 -25.376 -18.906 1 47.43 0 H3 4WI 401 A 1 HETATM 63 H H32 4WI . . . C 2 -5.134 -25.702 -21.248 1 46.3 0 H32 4WI 401 A 1 HETATM 64 H H15 4WI . . . C 2 -6.789 -32.088 -21.214 1 70.9 0 H15 4WI 401 A 1 HETATM 65 H H36 4WI . . . C 2 -2.208 -23.737 -22.318 0 39.4 0 H36 4WI 401 A 1 HETATM 66 H H9 4WI . . . C 2 -5.539 -25.012 -15.477 1 48.19 0 H9 4WI 401 A 1 HETATM 67 H H1 4WI . . . C 2 -3.549 -27.734 -20.286 1 50.48 0 H1 4WI 401 A 1 HETATM 68 H H16 4WI . . . C 2 -6.156 -32.468 -18.563 1 75.08 0 H16 4WI 401 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 21 _model_server_stats.create_model_time_ms 32 _model_server_stats.query_time_ms 354 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 68 #