data_7VLO # _model_server_result.job_id dNtCqUICfs2AE3TPsVt3yA _model_server_result.datetime_utc '2024-11-06 00:18:16' _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":"D","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 . . . D 2 38.69 -58.292 24.107 1 43.09 ? C8 4WI 401 B 1 HETATM 2 C C3 4WI . . . D 2 38.432 -56.314 28.582 1 34.96 ? C3 4WI 401 B 1 HETATM 3 C C1 4WI . . . D 2 35.872 -58.624 28.152 1 40.23 ? C1 4WI 401 B 1 HETATM 4 C C13 4WI . . . D 2 34.085 -60.363 26.247 1 43.44 ? C13 4WI 401 B 1 HETATM 5 C C21 4WI . . . D 2 31.307 -61.601 24.685 1 50.75 ? C21 4WI 401 B 1 HETATM 6 C C6 4WI . . . D 2 38.823 -59.872 25.981 1 39.61 ? C6 4WI 401 B 1 HETATM 7 C C7 4WI . . . D 2 39.271 -60.599 25.018 1 44.81 ? C7 4WI 401 B 1 HETATM 8 C C10 4WI . . . D 2 33.205 -60.68 28.664 1 42.77 ? C10 4WI 401 B 1 HETATM 9 C C5 4WI . . . D 2 38.16 -58.445 25.301 1 37.25 ? C5 4WI 401 B 1 HETATM 10 C C9 4WI . . . D 2 34.347 -58.707 28.095 1 40.58 ? C9 4WI 401 B 1 HETATM 11 C C11 4WI . . . D 2 32.702 -59.602 29.598 1 39.16 ? C11 4WI 401 B 1 HETATM 12 C C12 4WI . . . D 2 33.423 -58.339 29.218 1 44.52 ? C12 4WI 401 B 1 HETATM 13 C C18 4WI . . . D 2 31.959 -58.304 29.508 1 42.38 ? C18 4WI 401 B 1 HETATM 14 C C19 4WI . . . D 2 31.601 -57.593 30.816 1 40.85 ? C19 4WI 401 B 1 HETATM 15 C C20 4WI . . . D 2 31.04 -58.169 28.265 1 43.98 ? C20 4WI 401 B 1 HETATM 16 C C16 4WI . . . D 2 34.041 -64.105 25.17 1 40.45 ? C16 4WI 401 B 1 HETATM 17 C C17 4WI . . . D 2 35.585 -62.888 26.754 1 43.2 ? C17 4WI 401 B 1 HETATM 18 C C23 4WI . . . D 2 35.574 -62.267 24.31 1 37.66 ? C23 4WI 401 B 1 HETATM 19 C C4 4WI . . . D 2 38.563 -57.272 26.248 1 40.15 ? C4 4WI 401 B 1 HETATM 20 C C2 4WI . . . D 2 38.024 -57.464 27.69 1 37.3 ? C2 4WI 401 B 1 HETATM 21 C C14 4WI . . . D 2 33.551 -61.725 25.79 1 40.98 ? C14 4WI 401 B 1 HETATM 22 C C22 4WI . . . D 2 30.508 -61.325 23.408 1 50.13 ? C22 4WI 401 B 1 HETATM 23 C C15 4WI . . . D 2 34.686 -62.732 25.503 1 42.31 ? C15 4WI 401 B 1 HETATM 24 N N5 4WI . . . D 2 39.527 -56.379 29.202 1 38.51 ? N5 4WI 401 B 1 HETATM 25 N N2 4WI . . . D 2 39.482 -59.657 23.755 1 39.26 ? N2 4WI 401 B 1 HETATM 26 N N3 4WI . . . D 2 33.853 -59.94 27.632 1 42.68 ? N3 4WI 401 B 1 HETATM 27 N N1 4WI . . . D 2 36.583 -57.455 27.614 1 40.32 ? N1 4WI 401 B 1 HETATM 28 N N4 4WI . . . D 2 32.768 -61.485 24.61 1 42.07 ? N4 4WI 401 B 1 HETATM 29 O O1 4WI . . . D 2 38.622 -57.346 23.382 1 36.22 ? O1 4WI 401 B 1 HETATM 30 O O2 4WI . . . D 2 36.447 -59.545 28.615 1 42.84 ? O2 4WI 401 B 1 HETATM 31 O O3 4WI . . . D 2 34.653 -59.615 25.506 1 41.87 ? O3 4WI 401 B 1 HETATM 32 O O4 4WI . . . D 2 30.749 -61.892 25.699 1 48.53 ? O4 4WI 401 B 1 HETATM 33 F F1 4WI . . . D 2 31.007 -60.173 22.868 1 51.35 ? F1 4WI 401 B 1 HETATM 34 F F2 4WI . . . D 2 30.647 -62.358 22.521 1 53.74 ? F2 4WI 401 B 1 HETATM 35 F F3 4WI . . . D 2 29.198 -61.153 23.744 1 55.42 ? F3 4WI 401 B 1 # _model_server_stats.io_time_ms 25 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 280 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 35 #