data_9BO4 # _model_server_result.job_id 9ZEmjMR_nvCRHrcnerBSzA _model_server_result.datetime_utc '2025-03-12 16:12:41' _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 9bo4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":401}' # _entry.id 9BO4 # _exptl.entry_id 9BO4 _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 100.54 _cell.angle_gamma 90 _cell.entry_id 9BO4 _cell.length_a 45.64 _cell.length_b 53.7 _cell.length_c 114.41 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9BO4 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall 'P 2yb' _symmetry.space_group_name_H-M 'P 1 21 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,D,E,F _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 D N N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _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 _struct_conn.pdbx_value_order covale ? covale1 A SG CYS 145 A CYS 145 1_555 C C3 4WI . A 4WI 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.766 ? covale ? covale2 B SG CYS 145 B CYS 145 1_555 D C3 4WI . B 4WI 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.766 ? # _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 9BO4 _atom_sites.fract_transf_matrix[1][1] 0.021911 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004077 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.018622 _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] 0.008891 _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 1 401 999 4WI NMA . D 2 4WI B 1 401 999 4WI NMB . E 3 HOH A 1 501 9 HOH HOH . E 3 HOH A 2 502 32 HOH HOH . E 3 HOH A 3 503 58 HOH HOH . E 3 HOH A 4 504 24 HOH HOH . E 3 HOH A 5 505 35 HOH HOH . E 3 HOH A 6 506 43 HOH HOH . E 3 HOH A 7 507 10 HOH HOH . E 3 HOH A 8 508 11 HOH HOH . E 3 HOH A 9 509 28 HOH HOH . E 3 HOH A 10 510 23 HOH HOH . E 3 HOH A 11 511 34 HOH HOH . E 3 HOH A 12 512 6 HOH HOH . E 3 HOH A 13 513 22 HOH HOH . E 3 HOH A 14 514 14 HOH HOH . E 3 HOH A 15 515 47 HOH HOH . E 3 HOH A 16 516 48 HOH HOH . E 3 HOH A 17 517 26 HOH HOH . E 3 HOH A 18 518 19 HOH HOH . E 3 HOH A 19 519 40 HOH HOH . E 3 HOH A 20 520 46 HOH HOH . E 3 HOH A 21 521 54 HOH HOH . E 3 HOH A 22 522 44 HOH HOH . E 3 HOH A 23 523 21 HOH HOH . E 3 HOH A 24 524 37 HOH HOH . E 3 HOH A 25 525 38 HOH HOH . F 3 HOH B 1 501 4 HOH HOH . F 3 HOH B 2 502 8 HOH HOH . F 3 HOH B 3 503 7 HOH HOH . F 3 HOH B 4 504 49 HOH HOH . F 3 HOH B 5 505 29 HOH HOH . F 3 HOH B 6 506 1 HOH HOH . F 3 HOH B 7 507 25 HOH HOH . F 3 HOH B 8 508 36 HOH HOH . F 3 HOH B 9 509 20 HOH HOH . F 3 HOH B 10 510 39 HOH HOH . F 3 HOH B 11 511 13 HOH HOH . F 3 HOH B 12 512 18 HOH HOH . F 3 HOH B 13 513 50 HOH HOH . F 3 HOH B 14 514 16 HOH HOH . F 3 HOH B 15 515 5 HOH HOH . F 3 HOH B 16 516 57 HOH HOH . F 3 HOH B 17 517 52 HOH HOH . F 3 HOH B 18 518 3 HOH HOH . F 3 HOH B 19 519 2 HOH HOH . F 3 HOH B 20 520 41 HOH HOH . F 3 HOH B 21 521 56 HOH HOH . F 3 HOH B 22 522 27 HOH HOH . F 3 HOH B 23 523 31 HOH HOH . F 3 HOH B 24 524 15 HOH HOH . F 3 HOH B 25 525 51 HOH HOH . F 3 HOH B 26 526 30 HOH HOH . F 3 HOH B 27 527 12 HOH HOH . F 3 HOH B 28 528 55 HOH HOH . F 3 HOH B 29 529 33 HOH HOH . F 3 HOH B 30 530 53 HOH HOH . F 3 HOH B 31 531 59 HOH HOH . F 3 HOH B 32 532 42 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 . . . D 2 -34.704 -0.08 -38.573 1 42.19 ? C8 4WI 401 B 1 HETATM 2 C C3 4WI . . . D 2 -36.427 4.291 -40.1 1 45.48 ? C3 4WI 401 B 1 HETATM 3 C C1 4WI . . . D 2 -37.77 1.923 -42.077 1 50.25 ? C1 4WI 401 B 1 HETATM 4 C C13 4WI . . . D 2 -37.755 -0.779 -43.299 1 44.41 ? C13 4WI 401 B 1 HETATM 5 C C21 4WI . . . D 2 -37.963 -3.483 -45.521 1 50.11 ? C21 4WI 401 B 1 HETATM 6 C C6 4WI . . . D 2 -37.128 0.2 -38.543 1 52.76 ? C6 4WI 401 B 1 HETATM 7 C C7 4WI . . . D 2 -36.708 -0.944 -37.636 1 51.62 ? C7 4WI 401 B 1 HETATM 8 C C10 4WI . . . D 2 -39.447 0.559 -44.613 1 41.7 ? C10 4WI 401 B 1 HETATM 9 C C5 4WI . . . D 2 -35.857 0.645 -39.256 1 40.66 ? C5 4WI 401 B 1 HETATM 10 C C9 4WI . . . D 2 -37.595 1.679 -43.551 1 41.76 ? C9 4WI 401 B 1 HETATM 11 C C11 4WI . . . D 2 -39.508 2.047 -45.002 1 45.81 ? C11 4WI 401 B 1 HETATM 12 C C12 4WI . . . D 2 -38.351 2.753 -44.353 1 51.61 ? C12 4WI 401 B 1 HETATM 13 C C18 4WI . . . D 2 -38.299 2.457 -45.851 1 48.36 ? C18 4WI 401 B 1 HETATM 14 C C19 4WI . . . D 2 -38.502 3.609 -46.791 1 40.08 ? C19 4WI 401 B 1 HETATM 15 C C20 4WI . . . D 2 -37.301 1.511 -46.467 1 45.71 ? C20 4WI 401 B 1 HETATM 16 C C16 4WI . . . D 2 -37.922 -2.934 -41.331 1 50.48 ? C16 4WI 401 B 1 HETATM 17 C C17 4WI . . . D 2 -39.846 -3.888 -42.657 1 40.32 ? C17 4WI 401 B 1 HETATM 18 C C23 4WI . . . D 2 -40.024 -1.583 -41.669 1 45.66 ? C23 4WI 401 B 1 HETATM 19 C C4 4WI . . . D 2 -35.671 2.134 -39.199 1 52.87 ? C4 4WI 401 B 1 HETATM 20 C C2 4WI . . . D 2 -36.702 2.817 -40.053 1 51.27 ? C2 4WI 401 B 1 HETATM 21 C C14 4WI . . . D 2 -38.541 -2.033 -43.599 1 45.93 ? C14 4WI 401 B 1 HETATM 22 C C22 4WI . . . D 2 -36.905 -4.418 -46.039 1 64.95 ? C22 4WI 401 B 1 HETATM 23 C C15 4WI . . . D 2 -39.072 -2.612 -42.304 1 46.28 ? C15 4WI 401 B 1 HETATM 24 N N5 4WI . . . D 2 -36.333 5.02 -38.935 1 48.85 ? N5 4WI 401 B 1 HETATM 25 N N2 4WI . . . D 2 -35.251 -0.928 -37.701 1 48.01 ? N2 4WI 401 B 1 HETATM 26 N N3 4WI . . . D 2 -38.234 0.389 -43.807 1 43.34 ? N3 4WI 401 B 1 HETATM 27 N N1 4WI . . . D 2 -36.673 2.278 -41.413 1 41.97 ? N1 4WI 401 B 1 HETATM 28 N N4 4WI . . . D 2 -37.683 -2.978 -44.316 1 48.28 ? N4 4WI 401 B 1 HETATM 29 O O1 4WI . . . D 2 -33.506 0.074 -38.779 1 43.25 ? O1 4WI 401 B 1 HETATM 30 O O2 4WI . . . D 2 -38.836 1.733 -41.494 1 52.79 ? O2 4WI 401 B 1 HETATM 31 O O3 4WI . . . D 2 -36.723 -0.813 -42.618 1 43.95 ? O3 4WI 401 B 1 HETATM 32 O O4 4WI . . . D 2 -38.992 -3.192 -46.121 1 44.27 ? O4 4WI 401 B 1 HETATM 33 F F1 4WI . . . D 2 -35.754 -4.17 -45.411 1 58.8 ? F1 4WI 401 B 1 HETATM 34 F F2 4WI . . . D 2 -36.755 -4.214 -47.351 1 59.29 ? F2 4WI 401 B 1 HETATM 35 F F3 4WI . . . D 2 -37.286 -5.673 -45.818 1 65.6 ? F3 4WI 401 B 1 HETATM 36 H H5 4WI . . . D 2 -37.861 -0.148 -39.268 1 63.31 ? H5 4WI 401 B 1 HETATM 37 H H6 4WI . . . D 2 -37.528 1.02 -37.948 1 63.31 ? H6 4WI 401 B 1 HETATM 38 H H7 4WI . . . D 2 -37.093 -1.888 -38.017 1 61.93 ? H7 4WI 401 B 1 HETATM 39 H H8 4WI . . . D 2 -37.043 -0.761 -36.617 1 61.93 ? H8 4WI 401 B 1 HETATM 40 H H11 4WI . . . D 2 -40.32 0.865 -44.033 1 50.04 ? H11 4WI 401 B 1 HETATM 41 H H12 4WI . . . D 2 -39.276 0.474 -45.687 1 50.04 ? H12 4WI 401 B 1 HETATM 42 H H10 4WI . . . D 2 -36.57 1.69 -43.924 1 50.1 ? H10 4WI 401 B 1 HETATM 43 H H14 4WI . . . D 2 -38.29 3.827 -44.182 1 61.93 ? H14 4WI 401 B 1 HETATM 44 H H23 4WI . . . D 2 -39.054 4.398 -46.285 1 48.09 ? H23 4WI 401 B 1 HETATM 45 H H24 4WI . . . D 2 -39.065 3.275 -47.66 1 48.09 ? H24 4WI 401 B 1 HETATM 46 H H25 4WI . . . D 2 -37.536 3.992 -47.111 1 48.09 ? H25 4WI 401 B 1 HETATM 47 H H26 4WI . . . D 2 -37.089 0.701 -45.766 1 54.84 ? H26 4WI 401 B 1 HETATM 48 H H27 4WI . . . D 2 -37.715 1.097 -47.389 1 54.84 ? H27 4WI 401 B 1 HETATM 49 H H28 4WI . . . D 2 -36.379 2.052 -46.69 1 54.84 ? H28 4WI 401 B 1 HETATM 50 H H17 4WI . . . D 2 -37.82 -2.125 -40.612 1 60.57 ? H17 4WI 401 B 1 HETATM 51 H H19 4WI . . . D 2 -36.996 -3.043 -41.89 1 60.57 ? H19 4WI 401 B 1 HETATM 52 H H18 4WI . . . D 2 -38.141 -3.861 -40.807 1 60.57 ? H18 4WI 401 B 1 HETATM 53 H H20 4WI . . . D 2 -40.64 -3.649 -43.361 1 48.38 ? H20 4WI 401 B 1 HETATM 54 H H21 4WI . . . D 2 -39.168 -4.611 -43.107 1 48.38 ? H21 4WI 401 B 1 HETATM 55 H H22 4WI . . . D 2 -40.278 -4.312 -41.753 1 48.38 ? H22 4WI 401 B 1 HETATM 56 H H29 4WI . . . D 2 -39.447 -0.743 -41.28 1 54.78 ? H29 4WI 401 B 1 HETATM 57 H H30 4WI . . . D 2 -40.577 -2.052 -40.855 1 54.78 ? H30 4WI 401 B 1 HETATM 58 H H31 4WI . . . D 2 -40.725 -1.222 -42.423 1 54.78 ? H31 4WI 401 B 1 HETATM 59 H H2 4WI . . . D 2 -34.677 2.388 -39.563 1 63.44 ? H2 4WI 401 B 1 HETATM 60 H H3 4WI . . . D 2 -35.777 2.472 -38.169 1 63.44 ? H3 4WI 401 B 1 HETATM 61 H H32 4WI . . . D 2 -37.683 2.64 -39.619 1 61.52 ? H32 4WI 401 B 1 HETATM 62 H H15 4WI . . . D 2 -39.395 -1.807 -44.236 1 55.11 ? H15 4WI 401 B 1 HETATM 63 H H9 4WI . . . D 2 -34.689 -1.525 -37.12 1 57.61 ? H9 4WI 401 B 1 HETATM 64 H H1 4WI . . . D 2 -36.065 2.822 -41.997 1 50.36 ? H1 4WI 401 B 1 HETATM 65 H H16 4WI . . . D 2 -36.827 -3.267 -43.874 1 57.94 ? H16 4WI 401 B 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 26 _model_server_stats.query_time_ms 289 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 65 #