data_7VLO # _model_server_result.job_id pd_iKduYl-7zP5767EzmEA _model_server_result.datetime_utc '2025-06-24 17:44:42' _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 7vlo # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":401}' # _entry.id 7VLO # _exptl.entry_id 7VLO _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 91.921 _cell.angle_beta 102.421 _cell.angle_gamma 108.764 _cell.entry_id 7VLO _cell.length_a 55.464 _cell.length_b 60.461 _cell.length_c 68.137 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7VLO _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall 'P 1' _symmetry.space_group_name_H-M 'P 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 # _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 7VLO _atom_sites.fract_transf_matrix[1][1] 0.01803 _atom_sites.fract_transf_matrix[1][2] 0.006125 _atom_sites.fract_transf_matrix[1][3] 0.00468 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.017468 _atom_sites.fract_transf_matrix[2][3] 0.001952 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.015122 _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 5 4WI 9I7 . D 2 4WI B 1 401 6 4WI 9I7 . E 3 HOH A 1 501 58 HOH HOH . E 3 HOH A 2 502 16 HOH HOH . E 3 HOH A 3 503 54 HOH HOH . E 3 HOH A 4 504 19 HOH HOH . E 3 HOH A 5 505 10 HOH HOH . E 3 HOH A 6 506 15 HOH HOH . E 3 HOH A 7 507 23 HOH HOH . E 3 HOH A 8 508 46 HOH HOH . E 3 HOH A 9 509 36 HOH HOH . E 3 HOH A 10 510 1 HOH HOH . E 3 HOH A 11 511 57 HOH HOH . E 3 HOH A 12 512 2 HOH HOH . E 3 HOH A 13 513 25 HOH HOH . E 3 HOH A 14 514 34 HOH HOH . E 3 HOH A 15 515 12 HOH HOH . E 3 HOH A 16 516 8 HOH HOH . E 3 HOH A 17 517 3 HOH HOH . E 3 HOH A 18 518 47 HOH HOH . E 3 HOH A 19 519 18 HOH HOH . E 3 HOH A 20 520 13 HOH HOH . E 3 HOH A 21 521 37 HOH HOH . E 3 HOH A 22 522 17 HOH HOH . E 3 HOH A 23 523 5 HOH HOH . E 3 HOH A 24 524 33 HOH HOH . E 3 HOH A 25 525 9 HOH HOH . E 3 HOH A 26 526 45 HOH HOH . E 3 HOH A 27 527 42 HOH HOH . E 3 HOH A 28 528 50 HOH HOH . E 3 HOH A 29 529 59 HOH HOH . E 3 HOH A 30 530 64 HOH HOH . E 3 HOH A 31 531 51 HOH HOH . E 3 HOH A 32 532 6 HOH HOH . E 3 HOH A 33 533 41 HOH HOH . E 3 HOH A 34 534 67 HOH HOH . E 3 HOH A 35 535 62 HOH HOH . F 3 HOH B 1 501 14 HOH HOH . F 3 HOH B 2 502 52 HOH HOH . F 3 HOH B 3 503 30 HOH HOH . F 3 HOH B 4 504 56 HOH HOH . F 3 HOH B 5 505 44 HOH HOH . F 3 HOH B 6 506 39 HOH HOH . F 3 HOH B 7 507 7 HOH HOH . F 3 HOH B 8 508 20 HOH HOH . F 3 HOH B 9 509 40 HOH HOH . F 3 HOH B 10 510 53 HOH HOH . F 3 HOH B 11 511 61 HOH HOH . F 3 HOH B 12 512 21 HOH HOH . F 3 HOH B 13 513 28 HOH HOH . F 3 HOH B 14 514 4 HOH HOH . F 3 HOH B 15 515 22 HOH HOH . F 3 HOH B 16 516 24 HOH HOH . F 3 HOH B 17 517 32 HOH HOH . F 3 HOH B 18 518 11 HOH HOH . F 3 HOH B 19 519 38 HOH HOH . F 3 HOH B 20 520 49 HOH HOH . F 3 HOH B 21 521 35 HOH HOH . F 3 HOH B 22 522 31 HOH HOH . F 3 HOH B 23 523 55 HOH HOH . F 3 HOH B 24 524 26 HOH HOH . F 3 HOH B 25 525 43 HOH HOH . F 3 HOH B 26 526 48 HOH HOH . F 3 HOH B 27 527 27 HOH HOH . F 3 HOH B 28 528 65 HOH HOH . F 3 HOH B 29 529 60 HOH HOH . F 3 HOH B 30 530 66 HOH HOH . F 3 HOH B 31 531 29 HOH HOH . F 3 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 60.68 -36.128 1.168 1 37.04 ? C8 4WI 401 A 1 HETATM 2 C C3 4WI . . . C 2 63.056 -32.739 3.917 1 36.65 ? C3 4WI 401 A 1 HETATM 3 C C1 4WI . . . C 2 64.511 -32.951 0.713 1 37.83 ? C1 4WI 401 A 1 HETATM 4 C C13 4WI . . . C 2 64.913 -34.55 -1.897 1 41.9 ? C13 4WI 401 A 1 HETATM 5 C C21 4WI . . . C 2 66.552 -36.128 -4.471 1 42.68 ? C21 4WI 401 A 1 HETATM 6 C C6 4WI . . . C 2 60.69 -33.858 0.246 1 39.83 ? C6 4WI 401 A 1 HETATM 7 C C7 4WI . . . C 2 59.697 -34.377 -0.398 1 40.98 ? C7 4WI 401 A 1 HETATM 8 C C10 4WI . . . C 2 66.479 -32.495 -2.035 1 39.41 ? C10 4WI 401 A 1 HETATM 9 C C5 4WI . . . C 2 61.507 -35.098 1.115 1 33.86 ? C5 4WI 401 A 1 HETATM 10 C C9 4WI . . . C 2 65.849 -33.324 0.07 1 37.73 ? C9 4WI 401 A 1 HETATM 11 C C11 4WI . . . C 2 67.537 -32.077 -1.047 1 38.54 ? C11 4WI 401 A 1 HETATM 12 C C12 4WI . . . C 2 67.189 -32.672 0.286 1 38.18 ? C12 4WI 401 A 1 HETATM 13 C C18 4WI . . . C 2 68.59 -32.762 -0.242 1 40.35 ? C18 4WI 401 A 1 HETATM 14 C C19 4WI . . . C 2 69.654 -31.864 0.439 1 38.02 ? C19 4WI 401 A 1 HETATM 15 C C20 4WI . . . C 2 68.995 -34.118 -0.874 1 36.47 ? C20 4WI 401 A 1 HETATM 16 C C16 4WI . . . C 2 63.393 -34.296 -5.479 1 38.51 ? C16 4WI 401 A 1 HETATM 17 C C17 4WI . . . C 2 63.104 -32.827 -3.447 1 39.11 ? C17 4WI 401 A 1 HETATM 18 C C23 4WI . . . C 2 62.32 -35.215 -3.366 1 37.02 ? C23 4WI 401 A 1 HETATM 19 C C4 4WI . . . C 2 61.893 -34.524 2.52 1 33.94 ? C4 4WI 401 A 1 HETATM 20 C C2 4WI . . . C 2 62.795 -33.254 2.504 1 37.47 ? C2 4WI 401 A 1 HETATM 21 C C14 4WI . . . C 2 64.852 -34.625 -3.425 1 36.03 ? C14 4WI 401 A 1 HETATM 22 C C22 4WI . . . C 2 67.018 -37.55 -4.804 1 44.06 ? C22 4WI 401 A 1 HETATM 23 C C15 4WI . . . C 2 63.427 -34.266 -3.927 1 37.97 ? C15 4WI 401 A 1 HETATM 24 N N5 4WI . . . C 2 62.244 -31.947 4.478 1 41.91 ? N5 4WI 401 A 1 HETATM 25 N N2 4WI . . . C 2 59.412 -35.816 0.223 1 33.6 ? N2 4WI 401 A 1 HETATM 26 N N3 4WI . . . C 2 65.756 -33.491 -1.32 1 40.83 ? N3 4WI 401 A 1 HETATM 27 N N1 4WI . . . C 2 64.085 -33.611 1.95 1 33.7 ? N1 4WI 401 A 1 HETATM 28 N N4 4WI . . . C 2 65.291 -35.952 -3.764 1 35.12 ? N4 4WI 401 A 1 HETATM 29 O O1 4WI . . . C 2 60.795 -37.142 1.775 1 33.56 ? O1 4WI 401 A 1 HETATM 30 O O2 4WI . . . C 2 63.826 -32.164 0.147 1 37.89 ? O2 4WI 401 A 1 HETATM 31 O O3 4WI . . . C 2 64.322 -35.331 -1.177 1 38.63 ? O3 4WI 401 A 1 HETATM 32 O O4 4WI . . . C 2 67.206 -35.179 -4.786 1 43.77 ? O4 4WI 401 A 1 HETATM 33 F F1 4WI . . . C 2 68.38 -37.63 -4.688 1 52.08 ? F1 4WI 401 A 1 HETATM 34 F F2 4WI . . . C 2 66.456 -38.422 -3.935 1 45.21 ? F2 4WI 401 A 1 HETATM 35 F F3 4WI . . . C 2 66.655 -37.875 -6.072 1 51.58 ? F3 4WI 401 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 322 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 35 #