data_9CJP
#
_model_server_result.job_id            Do_b84meEw5wU_Vak6n5jA 
_model_server_result.datetime_utc      '2025-07-13 01:04:16' 
_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          9cjp 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":401}' 
#
_entry.id    9CJP 
#
_exptl.entry_id    9CJP 
_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          103.61 
_cell.angle_gamma         90 
_cell.entry_id            9CJP 
_cell.length_a            48.095 
_cell.length_b            105.665 
_cell.length_c            53.1 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 9CJP 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    'P 2yb' 
_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,G,H,I,J,K,L 
_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 ? ? ? ? ? ? ? ? ? ? ? ? 1.798 ? 
covale ? covale2 B SG CYS 145 B CYS 145 1_555 F C3 4WI . B 4WI 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.793 ? 
#
_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                     9CJP 
_atom_sites.fract_transf_matrix[1][1]    0.020792 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.005034 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.009464 
_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]    0.019376 
_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 3 EDO A 1 402 402 EDO EDO . 
E 4 BR A 1 403 2 BR BR . 
F 2 4WI B 1 401 401 4WI 4WI . 
G 3 EDO B 1 402 403 EDO EDO . 
H 4 BR B 1 403 1 BR BR . 
I 4 BR B 1 404 3 BR BR . 
J 5 SO4 B 1 405 1 SO4 SO4 . 
K 6 HOH A 1 501 52 HOH HOH . 
K 6 HOH A 2 502 56 HOH HOH . 
K 6 HOH A 3 503 1 HOH HOH . 
K 6 HOH A 4 504 3 HOH HOH . 
K 6 HOH A 5 505 66 HOH HOH . 
K 6 HOH A 6 506 34 HOH HOH . 
K 6 HOH A 7 507 90 HOH HOH . 
K 6 HOH A 8 508 6 HOH HOH . 
K 6 HOH A 9 509 22 HOH HOH . 
K 6 HOH A 10 510 5 HOH HOH . 
K 6 HOH A 11 511 41 HOH HOH . 
K 6 HOH A 12 512 89 HOH HOH . 
K 6 HOH A 13 513 21 HOH HOH . 
K 6 HOH A 14 514 24 HOH HOH . 
K 6 HOH A 15 515 4 HOH HOH . 
K 6 HOH A 16 516 38 HOH HOH . 
K 6 HOH A 17 517 59 HOH HOH . 
K 6 HOH A 18 518 2 HOH HOH . 
K 6 HOH A 19 519 44 HOH HOH . 
K 6 HOH A 20 520 65 HOH HOH . 
K 6 HOH A 21 521 68 HOH HOH . 
K 6 HOH A 22 522 88 HOH HOH . 
K 6 HOH A 23 523 31 HOH HOH . 
K 6 HOH A 24 524 74 HOH HOH . 
K 6 HOH A 25 525 42 HOH HOH . 
K 6 HOH A 26 526 57 HOH HOH . 
K 6 HOH A 27 527 63 HOH HOH . 
K 6 HOH A 28 528 36 HOH HOH . 
K 6 HOH A 29 529 70 HOH HOH . 
K 6 HOH A 30 530 71 HOH HOH . 
K 6 HOH A 31 531 91 HOH HOH . 
L 6 HOH B 1 501 64 HOH HOH . 
L 6 HOH B 2 502 51 HOH HOH . 
L 6 HOH B 3 503 26 HOH HOH . 
L 6 HOH B 4 504 50 HOH HOH . 
L 6 HOH B 5 505 53 HOH HOH . 
L 6 HOH B 6 506 37 HOH HOH . 
L 6 HOH B 7 507 67 HOH HOH . 
L 6 HOH B 8 508 81 HOH HOH . 
L 6 HOH B 9 509 61 HOH HOH . 
L 6 HOH B 10 510 69 HOH HOH . 
L 6 HOH B 11 511 27 HOH HOH . 
L 6 HOH B 12 512 14 HOH HOH . 
L 6 HOH B 13 513 55 HOH HOH . 
L 6 HOH B 14 514 25 HOH HOH . 
L 6 HOH B 15 515 43 HOH HOH . 
L 6 HOH B 16 516 78 HOH HOH . 
L 6 HOH B 17 517 23 HOH HOH . 
L 6 HOH B 18 518 93 HOH HOH . 
L 6 HOH B 19 519 48 HOH HOH . 
L 6 HOH B 20 520 10 HOH HOH . 
L 6 HOH B 21 521 40 HOH HOH . 
L 6 HOH B 22 522 49 HOH HOH . 
L 6 HOH B 23 523 12 HOH HOH . 
L 6 HOH B 24 524 9 HOH HOH . 
L 6 HOH B 25 525 54 HOH HOH . 
L 6 HOH B 26 526 8 HOH HOH . 
L 6 HOH B 27 527 35 HOH HOH . 
L 6 HOH B 28 528 13 HOH HOH . 
L 6 HOH B 29 529 29 HOH HOH . 
L 6 HOH B 30 530 60 HOH HOH . 
L 6 HOH B 31 531 79 HOH HOH . 
L 6 HOH B 32 532 84 HOH HOH . 
L 6 HOH B 33 533 28 HOH HOH . 
L 6 HOH B 34 534 20 HOH HOH . 
L 6 HOH B 35 535 45 HOH HOH . 
L 6 HOH B 36 536 75 HOH HOH . 
L 6 HOH B 37 537 46 HOH HOH . 
L 6 HOH B 38 538 39 HOH HOH . 
L 6 HOH B 39 539 17 HOH HOH . 
L 6 HOH B 40 540 83 HOH HOH . 
L 6 HOH B 41 541 80 HOH HOH . 
L 6 HOH B 42 542 11 HOH HOH . 
L 6 HOH B 43 543 85 HOH HOH . 
L 6 HOH B 44 544 76 HOH HOH . 
L 6 HOH B 45 545 30 HOH HOH . 
L 6 HOH B 46 546 19 HOH HOH . 
L 6 HOH B 47 547 7 HOH HOH . 
L 6 HOH B 48 548 73 HOH HOH . 
L 6 HOH B 49 549 33 HOH HOH . 
L 6 HOH B 50 550 16 HOH HOH . 
L 6 HOH B 51 551 82 HOH HOH . 
L 6 HOH B 52 552 58 HOH HOH . 
L 6 HOH B 53 553 32 HOH HOH . 
L 6 HOH B 54 554 62 HOH HOH . 
L 6 HOH B 55 555 18 HOH HOH . 
L 6 HOH B 56 556 47 HOH HOH . 
L 6 HOH B 57 557 15 HOH HOH . 
L 6 HOH B 58 558 86 HOH HOH . 
L 6 HOH B 59 559 77 HOH HOH . 
L 6 HOH B 60 560 72 HOH HOH . 
L 6 HOH B 61 561 92 HOH HOH . 
L 6 HOH B 62 562 87 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 -9.901 -5.606 21.397 1 41.01 ? C8 4WI 401 A 1 
HETATM 2 C C3 4WI . . . C 2 -11.083 -10.365 22.327 1 30.36 ? C3 4WI 401 A 1 
HETATM 3 C C1 4WI . . . C 2 -13.226 -8.355 24.204 1 42.53 ? C1 4WI 401 A 1 
HETATM 4 C C13 4WI . . . C 2 -13.833 -5.759 25.642 1 39.17 ? C13 4WI 401 A 1 
HETATM 5 C C21 4WI . . . C 2 -14.337 -3.462 27.999 1 46.36 ? C21 4WI 401 A 1 
HETATM 6 C C6 4WI . . . C 2 -12.144 -6.262 20.836 1 44.12 ? C6 4WI 401 A 1 
HETATM 7 C C7 4WI . . . C 2 -11.804 -4.897 20.271 1 39.49 ? C7 4WI 401 A 1 
HETATM 8 C C10 4WI . . . C 2 -15.595 -7.292 26.535 1 48.23 ? C10 4WI 401 A 1 
HETATM 9 C C5 4WI . . . C 2 -11.028 -6.523 21.851 1 31.93 ? C5 4WI 401 A 1 
HETATM 10 C C9 4WI . . . C 2 -13.453 -8.161 25.696 1 37.73 ? C9 4WI 401 A 1 
HETATM 11 C C11 4WI . . . C 2 -15.575 -8.78 26.781 1 43.25 ? C11 4WI 401 A 1 
HETATM 12 C C12 4WI . . . C 2 -14.255 -9.32 26.284 1 43.85 ? C12 4WI 401 A 1 
HETATM 13 C C18 4WI . . . C 2 -14.574 -9.342 27.763 1 43.49 ? C18 4WI 401 A 1 
HETATM 14 C C19 4WI . . . C 2 -13.884 -8.385 28.712 1 41.34 ? C19 4WI 401 A 1 
HETATM 15 C C20 4WI . . . C 2 -14.942 -10.656 28.416 1 42.58 ? C20 4WI 401 A 1 
HETATM 16 C C16 4WI . . . C 2 -16.408 -2.908 24.973 1 51.58 ? C16 4WI 401 A 1 
HETATM 17 C C17 4WI . . . C 2 -16.026 -5.046 23.74 1 45.54 ? C17 4WI 401 A 1 
HETATM 18 C C23 4WI . . . C 2 -14.264 -3.28 23.763 1 37.54 ? C23 4WI 401 A 1 
HETATM 19 C C4 4WI . . . C 2 -10.567 -7.971 21.964 1 38.05 ? C4 4WI 401 A 1 
HETATM 20 C C2 4WI . . . C 2 -11.635 -8.955 22.444 1 36.21 ? C2 4WI 401 A 1 
HETATM 21 C C14 4WI . . . C 2 -14.763 -4.573 25.88 1 46.03 ? C14 4WI 401 A 1 
HETATM 22 C C22 4WI . . . C 2 -13.496 -2.431 28.75 1 51.17 ? C22 4WI 401 A 1 
HETATM 23 C C15 4WI . . . C 2 -15.361 -3.958 24.589 1 46.9 ? C15 4WI 401 A 1 
HETATM 24 N N5 4WI . . . C 2 -11.407 -11.187 21.362 1 37.94 ? N5 4WI 401 A 1 
HETATM 25 N N2 4WI . . . C 2 -10.356 -4.855 20.405 1 33.96 ? N2 4WI 401 A 1 
HETATM 26 N N3 4WI . . . C 2 -14.282 -6.983 25.941 1 39.4 ? N3 4WI 401 A 1 
HETATM 27 N N1 4WI . . . C 2 -11.983 -8.676 23.827 1 42.24 ? N1 4WI 401 A 1 
HETATM 28 N N4 4WI . . . C 2 -14.074 -3.581 26.705 1 39.09 ? N4 4WI 401 A 1 
HETATM 29 O O1 4WI . . . C 2 -8.759 -5.562 21.888 1 43.78 ? O1 4WI 401 A 1 
HETATM 30 O O2 4WI . . . C 2 -14.143 -8.188 23.403 1 49.78 ? O2 4WI 401 A 1 
HETATM 31 O O3 4WI . . . C 2 -12.711 -5.592 25.198 1 48.29 ? O3 4WI 401 A 1 
HETATM 32 O O4 4WI . . . C 2 -15.153 -4.101 28.63 1 51.03 ? O4 4WI 401 A 1 
HETATM 33 F F1 4WI . . . C 2 -12.224 -2.783 28.766 1 47.68 ? F1 4WI 401 A 1 
HETATM 34 F F2 4WI . . . C 2 -13.885 -2.316 30.006 1 63.19 ? F2 4WI 401 A 1 
HETATM 35 F F3 4WI . . . C 2 -13.565 -1.234 28.202 1 57.36 ? F3 4WI 401 A 1 
#
_model_server_stats.io_time_ms              0 
_model_server_stats.parse_time_ms           13 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           328 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           35 
#