data_8DZ6 # _model_server_result.job_id c5oa1GNlwA6cDiovWKWfuw _model_server_result.datetime_utc '2024-11-16 11:01:44' _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":"F","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 . . . F 2 13.622 -10.484 7.142 1 50.34 0 C8 4WI 401 B 1 HETATM 2 C C3 4WI . . . F 2 12.058 -13.099 3.065 1 40.48 0 C3 4WI 401 B 1 HETATM 3 C C1 4WI . . . F 2 15.178 -12.186 2.384 1 44.18 0 C1 4WI 401 B 1 HETATM 4 C C13 4WI . . . F 2 17.673 -10.629 3.491 1 47.1 0 C13 4WI 401 B 1 HETATM 5 C C21 4WI . . . F 2 20.027 -8.272 2.653 1 52.43 0 C21 4WI 401 B 1 HETATM 6 C C6 4WI . . . F 2 14.681 -12.581 6.787 1 51.25 0 C6 4WI 401 B 1 HETATM 7 C C7 4WI . . . F 2 15.299 -11.872 7.981 1 51.57 0 C7 4WI 401 B 1 HETATM 8 C C10 4WI . . . F 2 18.44 -11.757 1.383 1 43.65 0 C10 4WI 401 B 1 HETATM 9 C C5 4WI . . . F 2 13.977 -11.456 6.033 1 49.24 0 C5 4WI 401 B 1 HETATM 10 C C9 4WI . . . F 2 16.08 -11.154 1.714 1 43.19 0 C9 4WI 401 B 1 HETATM 11 C C11 4WI . . . F 2 17.728 -11.926 0.055 1 41.75 0 C11 4WI 401 B 1 HETATM 12 C C12 4WI . . . F 2 16.28 -11.53 0.254 1 41.85 0 C12 4WI 401 B 1 HETATM 13 C C18 4WI . . . F 2 17.161 -10.737 -0.689 1 40.35 0 C18 4WI 401 B 1 HETATM 14 C C19 4WI . . . F 2 17.718 -9.365 -0.368 1 37.84 0 C19 4WI 401 B 1 HETATM 15 C C20 4WI . . . F 2 16.873 -10.913 -2.165 1 40.74 0 C20 4WI 401 B 1 HETATM 16 C C16 4WI . . . F 2 19.367 -9.619 6.304 1 50.41 0 C16 4WI 401 B 1 HETATM 17 C C17 4WI . . . F 2 19.085 -12.012 5.672 1 51.7 0 C17 4WI 401 B 1 HETATM 18 C C23 4WI . . . F 2 21.202 -10.816 5.122 1 50.26 0 C23 4WI 401 B 1 HETATM 19 C C4 4WI . . . F 2 12.804 -11.826 5.125 1 45.85 0 C4 4WI 401 B 1 HETATM 20 C C2 4WI . . . F 2 13.255 -12.567 3.863 1 43.67 0 C2 4WI 401 B 1 HETATM 21 C C14 4WI . . . F 2 19.117 -10.23 3.829 1 49.99 0 C14 4WI 401 B 1 HETATM 22 C C22 4WI . . . F 2 20.375 -6.784 2.77 1 54.79 0 C22 4WI 401 B 1 HETATM 23 C C15 4WI . . . F 2 19.675 -10.665 5.222 1 50.57 0 C15 4WI 401 B 1 HETATM 24 N N5 4WI . . . F 2 11.615 -14.291 3.176 1 41.18 0 N5 4WI 401 B 1 HETATM 25 N N2 4WI . . . F 2 14.338 -10.8 8.223 1 51.65 0 N2 4WI 401 B 1 HETATM 26 N N3 4WI . . . F 2 17.433 -11.163 2.277 1 44.14 0 N3 4WI 401 B 1 HETATM 27 N N1 4WI . . . F 2 14.099 -11.714 3.035 1 44.06 0 N1 4WI 401 B 1 HETATM 28 N N4 4WI . . . F 2 19.254 -8.793 3.612 1 51.08 0 N4 4WI 401 B 1 HETATM 29 O O1 4WI . . . F 2 12.823 -9.538 7.047 1 50.04 0 O1 4WI 401 B 1 HETATM 30 O O2 4WI . . . F 2 15.454 -13.384 2.314 1 46.4 0 O2 4WI 401 B 1 HETATM 31 O O3 4WI . . . F 2 16.759 -10.47 4.295 1 46.26 0 O3 4WI 401 B 1 HETATM 32 O O4 4WI . . . F 2 20.47 -8.897 1.71 1 50.56 0 O4 4WI 401 B 1 HETATM 33 F F1 4WI . . . F 2 20.661 -6.432 4.017 1 55.31 0 F1 4WI 401 B 1 HETATM 34 F F2 4WI . . . F 2 21.429 -6.465 2.028 1 54.86 0 F2 4WI 401 B 1 HETATM 35 F F3 4WI . . . F 2 19.37 -6.016 2.373 1 57.5 0 F3 4WI 401 B 1 HETATM 36 H H5 4WI . . . F 2 14.043 -13.264 7.078 1 50.79 0 H5 4WI 401 B 1 HETATM 37 H H6 4WI . . . F 2 15.37 -13.002 6.234 1 50.79 0 H6 4WI 401 B 1 HETATM 38 H H7 4WI . . . F 2 16.188 -11.513 7.764 1 51.48 0 H7 4WI 401 B 1 HETATM 39 H H8 4WI . . . F 2 15.374 -12.47 8.757 1 51.48 0 H8 4WI 401 B 1 HETATM 40 H H11 4WI . . . F 2 19.214 -11.167 1.286 1 43.32 0 H11 4WI 401 B 1 HETATM 41 H H12 4WI . . . F 2 18.744 -12.622 1.729 1 43.29 0 H12 4WI 401 B 1 HETATM 42 H H4 4WI . . . F 2 14.66 -11.006 5.477 1 49.07 0 H4 4WI 401 B 1 HETATM 43 H H10 4WI . . . F 2 15.683 -10.255 1.792 1 43.14 0 H10 4WI 401 B 1 HETATM 44 H H13 4WI . . . F 2 17.954 -12.7 -0.493 1 41.82 0 H13 4WI 401 B 1 HETATM 45 H H14 4WI . . . F 2 15.572 -12.1 -0.167 1 41.75 0 H14 4WI 401 B 1 HETATM 46 H H23 4WI . . . F 2 17.457 -9.107 0.528 1 38.36 0 H23 4WI 401 B 1 HETATM 47 H H24 4WI . . . F 2 17.375 -8.715 -1.001 1 38.4 0 H24 4WI 401 B 1 HETATM 48 H H25 4WI . . . F 2 18.686 -9.387 -0.425 1 38.39 0 H25 4WI 401 B 1 HETATM 49 H H26 4WI . . . F 2 16.173 -11.57 -2.284 1 40.5 0 H26 4WI 401 B 1 HETATM 50 H H27 4WI . . . F 2 17.675 -11.215 -2.62 1 40.51 0 H27 4WI 401 B 1 HETATM 51 H H28 4WI . . . F 2 16.587 -10.068 -2.547 1 40.5 0 H28 4WI 401 B 1 HETATM 52 H H17 4WI . . . F 2 18.825 -8.909 5.929 1 50.29 0 H17 4WI 401 B 1 HETATM 53 H H19 4WI . . . F 2 18.88 -10.035 7.036 1 50.35 0 H19 4WI 401 B 1 HETATM 54 H H18 4WI . . . F 2 20.196 -9.242 6.646 1 50.34 0 H18 4WI 401 B 1 HETATM 55 H H20 4WI . . . F 2 18.478 -12.35 4.992 1 51.3 0 H20 4WI 401 B 1 HETATM 56 H H21 4WI . . . F 2 18.597 -11.897 6.506 1 51.31 0 H21 4WI 401 B 1 HETATM 57 H H22 4WI . . . F 2 19.8 -12.657 5.808 1 51.31 0 H22 4WI 401 B 1 HETATM 58 H H29 4WI . . . F 2 21.494 -10.595 4.22 1 50.28 0 H29 4WI 401 B 1 HETATM 59 H H30 4WI . . . F 2 21.457 -11.733 5.324 1 50.28 0 H30 4WI 401 B 1 HETATM 60 H H31 4WI . . . F 2 21.636 -10.218 5.753 1 50.28 0 H31 4WI 401 B 1 HETATM 61 H H2 4WI . . . F 2 12.179 -12.393 5.624 1 46.01 0 H2 4WI 401 B 1 HETATM 62 H H3 4WI . . . F 2 12.33 -11.009 4.865 1 46.02 0 H3 4WI 401 B 1 HETATM 63 H H32 4WI . . . F 2 13.794 -13.348 4.149 1 43.52 0 H32 4WI 401 B 1 HETATM 64 H H15 4WI . . . F 2 19.704 -10.67 3.171 1 49.66 0 H15 4WI 401 B 1 HETATM 65 H H36 4WI . . . F 2 11.049 -14.507 2.558 0 51.73 0 H36 4WI 401 B 1 HETATM 66 H H9 4WI . . . F 2 14.231 -10.405 8.996 1 51.26 0 H9 4WI 401 B 1 HETATM 67 H H1 4WI . . . F 2 13.891 -10.876 2.96 1 43.89 0 H1 4WI 401 B 1 HETATM 68 H H16 4WI . . . F 2 18.797 -8.239 4.108 1 51.08 0 H16 4WI 401 B 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 22 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 308 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 68 #