data_8DCZ # _model_server_result.job_id yMtqudCQwF5K_JYa4Fjjkg _model_server_result.datetime_utc '2024-11-19 15:21:58' _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 8dcz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":401}' # _entry.id 8DCZ # _exptl.entry_id 8DCZ _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 100.53 _cell.angle_gamma 90 _cell.entry_id 8DCZ _cell.length_a 45.566 _cell.length_b 53.786 _cell.length_c 114.76 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8DCZ _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _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 ? ? ? ? ? ? ? ? ? ? ? ? 1.742 ? covale ? covale2 B SG CYS 145 B CYS 145 1_555 D C3 4WI . B 4WI 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.76 ? # _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 8DCZ _atom_sites.fract_transf_matrix[1][1] 0.021946 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004081 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.018592 _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] 0.008863 _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 4WI . D 2 4WI B 1 401 401 4WI 4WI . E 3 HOH A 1 501 22 HOH HOH . E 3 HOH A 2 502 54 HOH HOH . E 3 HOH A 3 503 67 HOH HOH . E 3 HOH A 4 504 114 HOH HOH . E 3 HOH A 5 505 9 HOH HOH . E 3 HOH A 6 506 105 HOH HOH . E 3 HOH A 7 507 84 HOH HOH . E 3 HOH A 8 508 79 HOH HOH . E 3 HOH A 9 509 100 HOH HOH . E 3 HOH A 10 510 104 HOH HOH . E 3 HOH A 11 511 151 HOH HOH . E 3 HOH A 12 512 66 HOH HOH . E 3 HOH A 13 513 55 HOH HOH . E 3 HOH A 14 514 1 HOH HOH . E 3 HOH A 15 515 38 HOH HOH . E 3 HOH A 16 516 34 HOH HOH . E 3 HOH A 17 517 74 HOH HOH . E 3 HOH A 18 518 3 HOH HOH . E 3 HOH A 19 519 44 HOH HOH . E 3 HOH A 20 520 28 HOH HOH . E 3 HOH A 21 521 47 HOH HOH . E 3 HOH A 22 522 88 HOH HOH . E 3 HOH A 23 523 57 HOH HOH . E 3 HOH A 24 524 27 HOH HOH . E 3 HOH A 25 525 4 HOH HOH . E 3 HOH A 26 526 71 HOH HOH . E 3 HOH A 27 527 86 HOH HOH . E 3 HOH A 28 528 125 HOH HOH . E 3 HOH A 29 529 62 HOH HOH . E 3 HOH A 30 530 61 HOH HOH . E 3 HOH A 31 531 45 HOH HOH . E 3 HOH A 32 532 70 HOH HOH . E 3 HOH A 33 533 31 HOH HOH . E 3 HOH A 34 534 103 HOH HOH . E 3 HOH A 35 535 19 HOH HOH . E 3 HOH A 36 536 106 HOH HOH . E 3 HOH A 37 537 94 HOH HOH . E 3 HOH A 38 538 140 HOH HOH . E 3 HOH A 39 539 30 HOH HOH . E 3 HOH A 40 540 63 HOH HOH . E 3 HOH A 41 541 122 HOH HOH . E 3 HOH A 42 542 12 HOH HOH . E 3 HOH A 43 543 97 HOH HOH . E 3 HOH A 44 544 124 HOH HOH . E 3 HOH A 45 545 25 HOH HOH . E 3 HOH A 46 546 5 HOH HOH . E 3 HOH A 47 547 80 HOH HOH . E 3 HOH A 48 548 76 HOH HOH . E 3 HOH A 49 549 101 HOH HOH . E 3 HOH A 50 550 123 HOH HOH . E 3 HOH A 51 551 137 HOH HOH . E 3 HOH A 52 552 120 HOH HOH . E 3 HOH A 53 553 90 HOH HOH . E 3 HOH A 54 554 2 HOH HOH . E 3 HOH A 55 555 6 HOH HOH . E 3 HOH A 56 556 108 HOH HOH . E 3 HOH A 57 557 102 HOH HOH . E 3 HOH A 58 558 53 HOH HOH . E 3 HOH A 59 559 138 HOH HOH . E 3 HOH A 60 560 82 HOH HOH . E 3 HOH A 61 561 118 HOH HOH . E 3 HOH A 62 562 52 HOH HOH . E 3 HOH A 63 563 126 HOH HOH . E 3 HOH A 64 564 149 HOH HOH . E 3 HOH A 65 565 135 HOH HOH . E 3 HOH A 66 566 65 HOH HOH . E 3 HOH A 67 567 10 HOH HOH . E 3 HOH A 68 568 142 HOH HOH . E 3 HOH A 69 569 49 HOH HOH . E 3 HOH A 70 570 143 HOH HOH . E 3 HOH A 71 571 150 HOH HOH . E 3 HOH A 72 572 146 HOH HOH . E 3 HOH A 73 573 141 HOH HOH . E 3 HOH A 74 574 92 HOH HOH . E 3 HOH A 75 575 139 HOH HOH . E 3 HOH A 76 576 131 HOH HOH . E 3 HOH A 77 577 147 HOH HOH . F 3 HOH B 1 501 35 HOH HOH . F 3 HOH B 2 502 132 HOH HOH . F 3 HOH B 3 503 89 HOH HOH . F 3 HOH B 4 504 51 HOH HOH . F 3 HOH B 5 505 87 HOH HOH . F 3 HOH B 6 506 56 HOH HOH . F 3 HOH B 7 507 78 HOH HOH . F 3 HOH B 8 508 43 HOH HOH . F 3 HOH B 9 509 58 HOH HOH . F 3 HOH B 10 510 115 HOH HOH . F 3 HOH B 11 511 112 HOH HOH . F 3 HOH B 12 512 37 HOH HOH . F 3 HOH B 13 513 68 HOH HOH . F 3 HOH B 14 514 107 HOH HOH . F 3 HOH B 15 515 48 HOH HOH . F 3 HOH B 16 516 46 HOH HOH . F 3 HOH B 17 517 99 HOH HOH . F 3 HOH B 18 518 23 HOH HOH . F 3 HOH B 19 519 73 HOH HOH . F 3 HOH B 20 520 42 HOH HOH . F 3 HOH B 21 521 8 HOH HOH . F 3 HOH B 22 522 20 HOH HOH . F 3 HOH B 23 523 32 HOH HOH . F 3 HOH B 24 524 24 HOH HOH . F 3 HOH B 25 525 11 HOH HOH . F 3 HOH B 26 526 16 HOH HOH . F 3 HOH B 27 527 110 HOH HOH . F 3 HOH B 28 528 39 HOH HOH . F 3 HOH B 29 529 14 HOH HOH . F 3 HOH B 30 530 36 HOH HOH . F 3 HOH B 31 531 15 HOH HOH . F 3 HOH B 32 532 109 HOH HOH . F 3 HOH B 33 533 81 HOH HOH . F 3 HOH B 34 534 93 HOH HOH . F 3 HOH B 35 535 95 HOH HOH . F 3 HOH B 36 536 133 HOH HOH . F 3 HOH B 37 537 83 HOH HOH . F 3 HOH B 38 538 128 HOH HOH . F 3 HOH B 39 539 119 HOH HOH . F 3 HOH B 40 540 111 HOH HOH . F 3 HOH B 41 541 59 HOH HOH . F 3 HOH B 42 542 13 HOH HOH . F 3 HOH B 43 543 21 HOH HOH . F 3 HOH B 44 544 64 HOH HOH . F 3 HOH B 45 545 26 HOH HOH . F 3 HOH B 46 546 98 HOH HOH . F 3 HOH B 47 547 18 HOH HOH . F 3 HOH B 48 548 117 HOH HOH . F 3 HOH B 49 549 77 HOH HOH . F 3 HOH B 50 550 91 HOH HOH . F 3 HOH B 51 551 29 HOH HOH . F 3 HOH B 52 552 152 HOH HOH . F 3 HOH B 53 553 144 HOH HOH . F 3 HOH B 54 554 136 HOH HOH . F 3 HOH B 55 555 7 HOH HOH . F 3 HOH B 56 556 116 HOH HOH . F 3 HOH B 57 557 148 HOH HOH . F 3 HOH B 58 558 130 HOH HOH . F 3 HOH B 59 559 145 HOH HOH . F 3 HOH B 60 560 127 HOH HOH . F 3 HOH B 61 561 129 HOH HOH . F 3 HOH B 62 562 153 HOH HOH . F 3 HOH B 63 563 134 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 -9.92 0.043 38.601 1 30.54 ? C8 4WI 401 B 1 HETATM 2 C C3 4WI . . . D 2 -10.777 -4.559 40.239 1 26.37 ? C3 4WI 401 B 1 HETATM 3 C C1 4WI . . . D 2 -12.67 -2.276 42.189 1 31.73 ? C1 4WI 401 B 1 HETATM 4 C C13 4WI . . . D 2 -12.98 0.506 43.213 1 31.13 ? C13 4WI 401 B 1 HETATM 5 C C21 4WI . . . D 2 -13.888 3.602 44.702 1 39.87 ? C21 4WI 401 B 1 HETATM 6 C C6 4WI . . . D 2 -12.079 -0.882 38.375 1 29.64 ? C6 4WI 401 B 1 HETATM 7 C C7 4WI . . . D 2 -12.011 0.454 37.643 1 30.28 ? C7 4WI 401 B 1 HETATM 8 C C10 4WI . . . D 2 -14.744 -0.695 44.51 1 32.49 ? C10 4WI 401 B 1 HETATM 9 C C5 4WI . . . D 2 -10.907 -0.836 39.34 1 29.34 ? C5 4WI 401 B 1 HETATM 10 C C9 4WI . . . D 2 -12.738 -1.852 43.651 1 30.81 ? C9 4WI 401 B 1 HETATM 11 C C11 4WI . . . D 2 -14.808 -2.143 44.938 1 32.27 ? C11 4WI 401 B 1 HETATM 12 C C12 4WI . . . D 2 -13.555 -2.843 44.452 1 31.6 ? C12 4WI 401 B 1 HETATM 13 C C18 4WI . . . D 2 -13.794 -2.647 45.935 1 32.61 ? C18 4WI 401 B 1 HETATM 14 C C19 4WI . . . D 2 -12.956 -1.66 46.726 1 31.98 ? C19 4WI 401 B 1 HETATM 15 C C20 4WI . . . D 2 -14.172 -3.872 46.745 1 32.91 ? C20 4WI 401 B 1 HETATM 16 C C16 4WI . . . D 2 -15.148 0.841 41.156 1 31.95 ? C16 4WI 401 B 1 HETATM 17 C C17 4WI . . . D 2 -13.25 2.446 40.821 1 32.46 ? C17 4WI 401 B 1 HETATM 18 C C23 4WI . . . D 2 -15.387 3.23 41.789 1 31.82 ? C23 4WI 401 B 1 HETATM 19 C C4 4WI . . . D 2 -10.277 -2.16 39.795 1 28.51 ? C4 4WI 401 B 1 HETATM 20 C C2 4WI . . . D 2 -11.278 -3.15 40.391 1 27.14 ? C2 4WI 401 B 1 HETATM 21 C C14 4WI . . . D 2 -13.911 1.717 43.162 1 32.09 ? C14 4WI 401 B 1 HETATM 22 C C22 4WI . . . D 2 -13.375 5.039 44.848 1 41.67 ? C22 4WI 401 B 1 HETATM 23 C C15 4WI . . . D 2 -14.412 2.052 41.743 1 31.85 ? C15 4WI 401 B 1 HETATM 24 N N5 4WI . . . D 2 -11.254 -5.344 39.364 1 24.7 ? N5 4WI 401 B 1 HETATM 25 N N2 4WI . . . D 2 -10.583 0.744 37.674 1 31.15 ? N2 4WI 401 B 1 HETATM 26 N N3 4WI . . . D 2 -13.472 -0.6 43.778 1 31.34 ? N3 4WI 401 B 1 HETATM 27 N N1 4WI . . . D 2 -11.529 -2.869 41.791 1 29.33 ? N1 4WI 401 B 1 HETATM 28 N N4 4WI . . . D 2 -13.266 2.853 43.79 1 35.4 ? N4 4WI 401 B 1 HETATM 29 O O1 4WI . . . D 2 -8.699 0.094 38.829 1 29.49 ? O1 4WI 401 B 1 HETATM 30 O O2 4WI . . . D 2 -13.621 -2.063 41.436 1 33.59 ? O2 4WI 401 B 1 HETATM 31 O O3 4WI . . . D 2 -11.851 0.513 42.737 1 29.46 ? O3 4WI 401 B 1 HETATM 32 O O4 4WI . . . D 2 -14.878 3.253 45.314 1 38.85 ? O4 4WI 401 B 1 HETATM 33 F F1 4WI . . . D 2 -13.363 5.677 43.682 1 44.14 ? F1 4WI 401 B 1 HETATM 34 F F2 4WI . . . D 2 -12.133 5.049 45.31 1 49.45 ? F2 4WI 401 B 1 HETATM 35 F F3 4WI . . . D 2 -14.109 5.769 45.679 1 40.29 ? F3 4WI 401 B 1 # _model_server_stats.io_time_ms 85 _model_server_stats.parse_time_ms 21 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 231 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 35 #