data_8DZ6 # _model_server_result.job_id PdSZXWqU1En49kmSAqEVQQ _model_server_result.datetime_utc '2024-11-16 10:53:52' _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 8dz6 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":401}' # _entry.id 8DZ6 # _exptl.entry_id 8DZ6 _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 8DZ6 _cell.length_a 67.782 _cell.length_b 101.572 _cell.length_c 103.561 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8DZ6 _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,I _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 # 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 ? ? ? ? ? ? ? ? ? ? ? ? 1.758 ? covale ? covale2 B SG CYS 145 B CYS 145 1_555 F C3 4WI . B 4WI 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.762 ? # _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 8DZ6 _atom_sites.fract_transf_matrix[1][1] 0.014753 _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] 0.009845 _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] 0.009656 _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 A 1 403 403 DMS DMS . F 2 4WI B 1 401 401 4WI DRG . G 3 DMS B 1 402 402 DMS DMS . H 4 HOH A 1 501 4 HOH HOH . H 4 HOH A 2 502 76 HOH HOH . H 4 HOH A 3 503 5 HOH HOH . H 4 HOH A 4 504 34 HOH HOH . H 4 HOH A 5 505 29 HOH HOH . H 4 HOH A 6 506 36 HOH HOH . H 4 HOH A 7 507 42 HOH HOH . H 4 HOH A 8 508 69 HOH HOH . H 4 HOH A 9 509 32 HOH HOH . H 4 HOH A 10 510 15 HOH HOH . H 4 HOH A 11 511 13 HOH HOH . H 4 HOH A 12 512 25 HOH HOH . H 4 HOH A 13 513 28 HOH HOH . H 4 HOH A 14 514 27 HOH HOH . H 4 HOH A 15 515 39 HOH HOH . H 4 HOH A 16 516 67 HOH HOH . H 4 HOH A 17 517 19 HOH HOH . H 4 HOH A 18 518 41 HOH HOH . H 4 HOH A 19 519 11 HOH HOH . H 4 HOH A 20 520 22 HOH HOH . H 4 HOH A 21 521 6 HOH HOH . H 4 HOH A 22 522 48 HOH HOH . H 4 HOH A 23 523 20 HOH HOH . H 4 HOH A 24 524 50 HOH HOH . H 4 HOH A 25 525 14 HOH HOH . H 4 HOH A 26 526 3 HOH HOH . H 4 HOH A 27 527 10 HOH HOH . H 4 HOH A 28 528 38 HOH HOH . H 4 HOH A 29 529 37 HOH HOH . H 4 HOH A 30 530 16 HOH HOH . H 4 HOH A 31 531 52 HOH HOH . H 4 HOH A 32 532 49 HOH HOH . H 4 HOH A 33 533 1 HOH HOH . H 4 HOH A 34 534 70 HOH HOH . H 4 HOH A 35 535 46 HOH HOH . H 4 HOH A 36 536 54 HOH HOH . H 4 HOH A 37 537 74 HOH HOH . H 4 HOH A 38 538 72 HOH HOH . H 4 HOH A 39 539 53 HOH HOH . H 4 HOH A 40 540 73 HOH HOH . H 4 HOH A 41 541 62 HOH HOH . H 4 HOH A 42 542 75 HOH HOH . I 4 HOH B 1 501 17 HOH HOH . I 4 HOH B 2 502 35 HOH HOH . I 4 HOH B 3 503 21 HOH HOH . I 4 HOH B 4 504 31 HOH HOH . I 4 HOH B 5 505 24 HOH HOH . I 4 HOH B 6 506 8 HOH HOH . I 4 HOH B 7 507 26 HOH HOH . I 4 HOH B 8 508 68 HOH HOH . I 4 HOH B 9 509 30 HOH HOH . I 4 HOH B 10 510 2 HOH HOH . I 4 HOH B 11 511 71 HOH HOH . I 4 HOH B 12 512 51 HOH HOH . I 4 HOH B 13 513 65 HOH HOH . I 4 HOH B 14 514 45 HOH HOH . I 4 HOH B 15 515 44 HOH HOH . I 4 HOH B 16 516 9 HOH HOH . I 4 HOH B 17 517 55 HOH HOH . I 4 HOH B 18 518 40 HOH HOH . I 4 HOH B 19 519 18 HOH HOH . I 4 HOH B 20 520 43 HOH HOH . I 4 HOH B 21 521 57 HOH HOH . I 4 HOH B 22 522 33 HOH HOH . I 4 HOH B 23 523 12 HOH HOH . I 4 HOH B 24 524 56 HOH HOH . I 4 HOH B 25 525 61 HOH HOH . I 4 HOH B 26 526 64 HOH HOH . I 4 HOH B 27 527 23 HOH HOH . I 4 HOH B 28 528 58 HOH HOH . I 4 HOH B 29 529 59 HOH HOH . I 4 HOH B 30 530 60 HOH HOH . I 4 HOH B 31 531 7 HOH HOH . I 4 HOH B 32 532 63 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 -16.844 5.035 25.465 1 45.71 0 C8 4WI 401 A 1 HETATM 2 C C3 4WI . . . C 2 -21.043 2.807 24.364 1 37.67 0 C3 4WI 401 A 1 HETATM 3 C C1 4WI . . . C 2 -21.725 4.224 27.491 1 50.56 0 C1 4WI 401 A 1 HETATM 4 C C13 4WI . . . C 2 -20.354 5.658 29.819 1 55.89 0 C13 4WI 401 A 1 HETATM 5 C C21 4WI . . . C 2 -19.822 6.386 33.209 1 61.17 0 C21 4WI 401 A 1 HETATM 6 C C6 4WI . . . C 2 -18.78 6.423 25.273 1 47.87 0 C6 4WI 401 A 1 HETATM 7 C C7 4WI . . . C 2 -17.518 7.267 25.29 1 48.41 0 C7 4WI 401 A 1 HETATM 8 C C10 4WI . . . C 2 -22.749 5.453 30.605 1 53.83 0 C10 4WI 401 A 1 HETATM 9 C C5 4WI . . . C 2 -18.319 5.072 25.816 1 46.54 0 C5 4WI 401 A 1 HETATM 10 C C9 4WI . . . C 2 -21.778 3.881 28.976 1 52.08 0 C9 4WI 401 A 1 HETATM 11 C C11 4WI . . . C 2 -23.733 4.307 30.417 1 53.06 0 C11 4WI 401 A 1 HETATM 12 C C12 4WI . . . C 2 -23.164 3.385 29.357 1 51.63 0 C12 4WI 401 A 1 HETATM 13 C C18 4WI . . . C 2 -23.385 2.874 30.764 1 52.61 0 C18 4WI 401 A 1 HETATM 14 C C19 4WI . . . C 2 -24.501 1.866 30.943 1 53.39 0 C19 4WI 401 A 1 HETATM 15 C C20 4WI . . . C 2 -22.225 2.609 31.703 1 50.48 0 C20 4WI 401 A 1 HETATM 16 C C16 4WI . . . C 2 -18.995 8.005 28.788 1 58.25 0 C16 4WI 401 A 1 HETATM 17 C C17 4WI . . . C 2 -20.475 9.252 30.34 1 61.62 0 C17 4WI 401 A 1 HETATM 18 C C23 4WI . . . C 2 -18.214 8.528 31.09 1 60.68 0 C23 4WI 401 A 1 HETATM 19 C C4 4WI . . . C 2 -19.002 3.814 25.293 1 45.18 0 C4 4WI 401 A 1 HETATM 20 C C2 4WI . . . C 2 -20.526 3.79 25.395 1 42.98 0 C2 4WI 401 A 1 HETATM 21 C C14 4WI . . . C 2 -20.108 6.805 30.808 1 58.93 0 C14 4WI 401 A 1 HETATM 22 C C22 4WI . . . C 2 -19.086 5.595 34.297 1 61.81 0 C22 4WI 401 A 1 HETATM 23 C C15 4WI . . . C 2 -19.442 8.117 30.256 1 60.28 0 C15 4WI 401 A 1 HETATM 24 N N5 4WI . . . C 2 -21.507 3.166 23.238 1 38.1 0 N5 4WI 401 A 1 HETATM 25 N N2 4WI . . . C 2 -16.469 6.266 25.114 1 47.78 0 N2 4WI 401 A 1 HETATM 26 N N3 4WI . . . C 2 -21.568 5.068 29.814 1 54.01 0 N3 4WI 401 A 1 HETATM 27 N N1 4WI . . . C 2 -20.961 3.42 26.734 1 46.82 0 N1 4WI 401 A 1 HETATM 28 N N4 4WI . . . C 2 -19.401 6.232 31.949 1 58.95 0 N4 4WI 401 A 1 HETATM 29 O O1 4WI . . . C 2 -16.117 4.019 25.486 1 39.74 0 O1 4WI 401 A 1 HETATM 30 O O2 4WI . . . C 2 -22.319 5.208 27.05 1 52.53 0 O2 4WI 401 A 1 HETATM 31 O O3 4WI . . . C 2 -19.459 5.244 29.083 1 51.76 0 O3 4WI 401 A 1 HETATM 32 O O4 4WI . . . C 2 -20.738 7.113 33.54 1 65.68 0 O4 4WI 401 A 1 HETATM 33 F F1 4WI . . . C 2 -19.707 5.668 35.467 1 61.46 0 F1 4WI 401 A 1 HETATM 34 F F2 4WI . . . C 2 -18.985 4.307 33.993 1 59.01 0 F2 4WI 401 A 1 HETATM 35 F F3 4WI . . . C 2 -17.858 6.055 34.494 1 62.72 0 F3 4WI 401 A 1 HETATM 36 H H5 4WI . . . C 2 -19.127 6.336 24.362 1 47.64 0 H5 4WI 401 A 1 HETATM 37 H H6 4WI . . . C 2 -19.473 6.816 25.842 1 47.66 0 H6 4WI 401 A 1 HETATM 38 H H7 4WI . . . C 2 -17.418 7.743 26.145 1 48.13 0 H7 4WI 401 A 1 HETATM 39 H H8 4WI . . . C 2 -17.514 7.922 24.557 1 48.13 0 H8 4WI 401 A 1 HETATM 40 H H11 4WI . . . C 2 -22.517 5.56 31.551 1 53.65 0 H11 4WI 401 A 1 HETATM 41 H H12 4WI . . . C 2 -23.127 6.295 30.275 1 53.63 0 H12 4WI 401 A 1 HETATM 42 H H4 4WI . . . C 2 -18.398 5.082 26.801 1 46.36 0 H4 4WI 401 A 1 HETATM 43 H H10 4WI . . . C 2 -21.097 3.197 29.183 1 51.95 0 H10 4WI 401 A 1 HETATM 44 H H13 4WI . . . C 2 -24.682 4.519 30.42 1 52.8 0 H13 4WI 401 A 1 HETATM 45 H H14 4WI . . . C 2 -23.753 3.014 28.643 1 52.05 0 H14 4WI 401 A 1 HETATM 46 H H23 4WI . . . C 2 -24.943 1.715 30.093 1 52.82 0 H23 4WI 401 A 1 HETATM 47 H H24 4WI . . . C 2 -25.146 2.204 31.583 1 52.88 0 H24 4WI 401 A 1 HETATM 48 H H25 4WI . . . C 2 -24.138 1.027 31.267 1 52.87 0 H25 4WI 401 A 1 HETATM 49 H H26 4WI . . . C 2 -21.396 2.871 31.285 1 50.72 0 H26 4WI 401 A 1 HETATM 50 H H27 4WI . . . C 2 -22.188 1.664 31.921 1 50.8 0 H27 4WI 401 A 1 HETATM 51 H H28 4WI . . . C 2 -22.344 3.12 32.519 1 50.81 0 H28 4WI 401 A 1 HETATM 52 H H17 4WI . . . C 2 -19.225 7.133 28.434 1 58.65 0 H17 4WI 401 A 1 HETATM 53 H H19 4WI . . . C 2 -19.439 8.688 28.256 1 58.69 0 H19 4WI 401 A 1 HETATM 54 H H18 4WI . . . C 2 -18.033 8.131 28.725 1 58.68 0 H18 4WI 401 A 1 HETATM 55 H H20 4WI . . . C 2 -21.309 8.913 30.707 1 61.09 0 H20 4WI 401 A 1 HETATM 56 H H21 4WI . . . C 2 -20.643 9.613 29.452 1 61.11 0 H21 4WI 401 A 1 HETATM 57 H H22 4WI . . . C 2 -20.14 9.962 30.914 1 61.12 0 H22 4WI 401 A 1 HETATM 58 H H29 4WI . . . C 2 -18.079 7.899 31.815 1 60.31 0 H29 4WI 401 A 1 HETATM 59 H H30 4WI . . . C 2 -18.352 9.416 31.462 1 60.39 0 H30 4WI 401 A 1 HETATM 60 H H31 4WI . . . C 2 -17.422 8.538 30.527 1 60.38 0 H31 4WI 401 A 1 HETATM 61 H H2 4WI . . . C 2 -18.755 3.699 24.351 1 44.9 0 H2 4WI 401 A 1 HETATM 62 H H3 4WI . . . C 2 -18.647 3.043 25.783 1 44.9 0 H3 4WI 401 A 1 HETATM 63 H H32 4WI . . . C 2 -20.877 4.69 25.176 1 43.01 0 H32 4WI 401 A 1 HETATM 64 H H15 4WI . . . C 2 -20.989 7.088 31.148 1 58.51 0 H15 4WI 401 A 1 HETATM 65 H H36 4WI . . . C 2 -21.672 2.637 22.653 0 45.27 0 H36 4WI 401 A 1 HETATM 66 H H9 4WI . . . C 2 -15.673 6.446 24.803 1 47.38 0 H9 4WI 401 A 1 HETATM 67 H H1 4WI . . . C 2 -20.716 2.648 27.05 1 46.71 0 H1 4WI 401 A 1 HETATM 68 H H16 4WI . . . C 2 -18.675 5.764 31.811 1 59.34 0 H16 4WI 401 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 24 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 251 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 68 #