data_7KPA
#
_model_server_result.job_id            NvrU-NY_oKWuBJVLnQ_3_A 
_model_server_result.datetime_utc      '2024-11-16 12:31:09' 
_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          7kpa 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":201}' 
#
_entry.id    7KPA 
#
_exptl.entry_id    7KPA 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              556.559 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            5-(1-{[2-(difluoromethoxy)phenyl]methyl}-2-{[3-(2-oxopyrrolidin-1-yl)phenoxy]methyl}-1H-benzimidazol-6-yl)pyridin-2(1H)-one 
_entity.pdbx_number_of_molecules    1 
_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            7KPA 
_cell.length_a            55.13 
_cell.length_b            82.13 
_cell.length_c            93.04 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7KPA 
_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    trimeric 
_pdbx_struct_assembly.oligomeric_count      3 
_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 
_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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      2 
_struct_asym.id                             D 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    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
disulf ? disulf1 A SG CYS 70 A CYS 69 1_555 A SG CYS 102 A CYS 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? 
disulf ? disulf2 B SG CYS 70 B CYS 69 1_555 B SG CYS 102 B CYS 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? 
disulf ? disulf3 C SG CYS 70 C CYS 69 1_555 C SG CYS 102 C CYS 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? 
#
_chem_comp.formula           'C31 H26 F2 N4 O4' 
_chem_comp.formula_weight    556.559 
_chem_comp.id                D84 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              5-(1-{[2-(difluoromethoxy)phenyl]methyl}-2-{[3-(2-oxopyrrolidin-1-yl)phenoxy]methyl}-1H-benzimidazol-6-yl)pyridin-2(1H)-one 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     ? 
#
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
O2 C19 D84 doub 83 n n 
C13 C12 D84 doub 84 n y 
C13 C14 D84 sing 85 n y 
C12 C11 D84 sing 86 n y 
C19 C18 D84 sing 87 n n 
C19 N1 D84 sing 88 n n 
C18 C17 D84 sing 89 n n 
C11 C10 D84 doub 90 n y 
C14 N1 D84 sing 91 n n 
C14 C15 D84 doub 92 n y 
N1 C16 D84 sing 93 n n 
C17 C16 D84 sing 94 n n 
C10 C15 D84 sing 95 n y 
C10 O1 D84 sing 96 n n 
N2 C8 D84 doub 97 n y 
N2 C20 D84 sing 98 n y 
O1 C9 D84 sing 99 n n 
C9 C8 D84 sing 100 n n 
C21 C20 D84 doub 101 n y 
C21 C22 D84 sing 102 n y 
C8 N D84 sing 103 n y 
C20 C25 D84 sing 104 n y 
C22 C23 D84 doub 105 n y 
N C25 D84 sing 106 n y 
N C7 D84 sing 107 n n 
C25 C24 D84 doub 108 n y 
C5 C4 D84 doub 109 n y 
C5 C6 D84 sing 110 n y 
C4 C3 D84 sing 111 n y 
C23 C24 D84 sing 112 n y 
C23 C26 D84 sing 113 n n 
C7 C6 D84 sing 114 n n 
C6 C1 D84 doub 115 n y 
C26 C27 D84 doub 116 n n 
C26 C30 D84 sing 117 n n 
C27 N3 D84 sing 118 n n 
C3 C2 D84 doub 119 n y 
C1 C2 D84 sing 120 n y 
C1 O D84 sing 121 n n 
C30 C29 D84 doub 122 n n 
N3 C28 D84 sing 123 n n 
O C D84 sing 124 n n 
C28 C29 D84 sing 125 n n 
C28 O3 D84 doub 126 n n 
C F1 D84 sing 127 n n 
C F D84 sing 128 n n 
C11 H1 D84 sing 129 n n 
C12 H2 D84 sing 130 n n 
C13 H3 D84 sing 131 n n 
C15 H4 D84 sing 132 n n 
C16 H5 D84 sing 133 n n 
C16 H6 D84 sing 134 n n 
C17 H7 D84 sing 135 n n 
C17 H8 D84 sing 136 n n 
C27 H9 D84 sing 137 n n 
C29 H10 D84 sing 138 n n 
C30 H11 D84 sing 139 n n 
C22 H13 D84 sing 140 n n 
C21 H14 D84 sing 141 n n 
C24 H15 D84 sing 142 n n 
C7 H16 D84 sing 143 n n 
C7 H17 D84 sing 144 n n 
C5 H18 D84 sing 145 n n 
C4 H19 D84 sing 146 n n 
C3 H20 D84 sing 147 n n 
C2 H21 D84 sing 148 n n 
C H22 D84 sing 149 n n 
C9 H23 D84 sing 150 n n 
C9 H24 D84 sing 151 n n 
C18 H25 D84 sing 152 n n 
C18 H26 D84 sing 153 n n 
N3 H27 D84 sing 154 n n 
#
_atom_sites.entry_id                     7KPA 
_atom_sites.fract_transf_matrix[1][1]    0.018139 
_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]    0.012176 
_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]    0.010748 
_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
D 2 D84 C 1 201 1 D84 733 . 
E 3 HOH A 1 201 44 HOH HOH . 
E 3 HOH A 2 202 38 HOH HOH . 
E 3 HOH A 3 203 43 HOH HOH . 
E 3 HOH A 4 204 29 HOH HOH . 
E 3 HOH A 5 205 4 HOH HOH . 
E 3 HOH A 6 206 12 HOH HOH . 
E 3 HOH A 7 207 13 HOH HOH . 
E 3 HOH A 8 208 35 HOH HOH . 
E 3 HOH A 9 209 15 HOH HOH . 
E 3 HOH A 10 210 9 HOH HOH . 
E 3 HOH A 11 211 8 HOH HOH . 
E 3 HOH A 12 212 17 HOH HOH . 
E 3 HOH A 13 213 57 HOH HOH . 
E 3 HOH A 14 214 10 HOH HOH . 
E 3 HOH A 15 215 6 HOH HOH . 
E 3 HOH A 16 216 22 HOH HOH . 
E 3 HOH A 17 217 14 HOH HOH . 
E 3 HOH A 18 218 5 HOH HOH . 
E 3 HOH A 19 219 36 HOH HOH . 
E 3 HOH A 20 220 42 HOH HOH . 
E 3 HOH A 21 221 37 HOH HOH . 
E 3 HOH A 22 222 11 HOH HOH . 
E 3 HOH A 23 223 41 HOH HOH . 
E 3 HOH A 24 224 60 HOH HOH . 
E 3 HOH A 25 225 7 HOH HOH . 
E 3 HOH A 26 226 20 HOH HOH . 
E 3 HOH A 27 227 56 HOH HOH . 
F 3 HOH B 1 201 52 HOH HOH . 
F 3 HOH B 2 202 25 HOH HOH . 
F 3 HOH B 3 203 28 HOH HOH . 
F 3 HOH B 4 204 26 HOH HOH . 
F 3 HOH B 5 205 58 HOH HOH . 
F 3 HOH B 6 206 16 HOH HOH . 
F 3 HOH B 7 207 31 HOH HOH . 
F 3 HOH B 8 208 24 HOH HOH . 
F 3 HOH B 9 209 47 HOH HOH . 
F 3 HOH B 10 210 23 HOH HOH . 
F 3 HOH B 11 211 59 HOH HOH . 
F 3 HOH B 12 212 18 HOH HOH . 
F 3 HOH B 13 213 55 HOH HOH . 
F 3 HOH B 14 214 54 HOH HOH . 
F 3 HOH B 15 215 45 HOH HOH . 
F 3 HOH B 16 216 27 HOH HOH . 
F 3 HOH B 17 217 39 HOH HOH . 
F 3 HOH B 18 218 32 HOH HOH . 
F 3 HOH B 19 219 21 HOH HOH . 
F 3 HOH B 20 220 53 HOH HOH . 
F 3 HOH B 21 221 51 HOH HOH . 
F 3 HOH B 22 222 49 HOH HOH . 
F 3 HOH B 23 223 46 HOH HOH . 
F 3 HOH B 24 224 48 HOH HOH . 
F 3 HOH B 25 225 40 HOH HOH . 
F 3 HOH B 26 226 62 HOH HOH . 
F 3 HOH B 27 227 1 HOH HOH . 
G 3 HOH C 1 301 63 HOH HOH . 
G 3 HOH C 2 302 34 HOH HOH . 
G 3 HOH C 3 303 30 HOH HOH . 
G 3 HOH C 4 304 61 HOH HOH . 
G 3 HOH C 5 305 3 HOH HOH . 
G 3 HOH C 6 306 19 HOH HOH . 
G 3 HOH C 7 307 2 HOH HOH . 
G 3 HOH C 8 308 50 HOH HOH . 
G 3 HOH C 9 309 33 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 C10 D84 . . . D 2 -9.707 -0.959 15.658 1 21.9 ? C10 D84 201 C 1 
HETATM 2 C C11 D84 . . . D 2 -10.645 -1.065 14.637 1 22.5 ? C11 D84 201 C 1 
HETATM 3 C C12 D84 . . . D 2 -10.431 -1.964 13.597 1 22.59 ? C12 D84 201 C 1 
HETATM 4 C C13 D84 . . . D 2 -9.282 -2.756 13.571 1 21.64 ? C13 D84 201 C 1 
HETATM 5 C C14 D84 . . . D 2 -8.356 -2.672 14.604 1 21.66 ? C14 D84 201 C 1 
HETATM 6 F F D84 . . . D 2 -11.353 -1.811 24.297 1 21.39 ? F D84 201 C 1 
HETATM 7 C C15 D84 . . . D 2 -8.577 -1.77 15.639 1 21.69 ? C15 D84 201 C 1 
HETATM 8 C C16 D84 . . . D 2 -6.103 -2.983 15.521 1 21.27 ? C16 D84 201 C 1 
HETATM 9 C C17 D84 . . . D 2 -4.991 -3.967 15.155 1 20.72 ? C17 D84 201 C 1 
HETATM 10 O O1 D84 . . . D 2 -9.867 -0.083 16.707 1 22.79 ? O1 D84 201 C 1 
HETATM 11 C C1 D84 . . . D 2 -11.264 -2.216 21.184 1 21.02 ? C1 D84 201 C 1 
HETATM 12 N N1 D84 . . . D 2 -7.178 -3.434 14.647 1 20.71 ? N1 D84 201 C 1 
HETATM 13 O O3 D84 . . . D 2 -19.272 -3.778 22.977 1 24.03 ? O3 D84 201 C 1 
HETATM 14 C C28 D84 . . . D 2 -18.463 -3.301 22.15 1 23.87 ? C28 D84 201 C 1 
HETATM 15 N N3 D84 . . . D 2 -18.89 -2.387 21.27 1 24.02 ? N3 D84 201 C 1 
HETATM 16 C C27 D84 . . . D 2 -18.058 -1.846 20.371 1 24.06 ? C27 D84 201 C 1 
HETATM 17 C C29 D84 . . . D 2 -17.133 -3.712 22.15 1 23.3 ? C29 D84 201 C 1 
HETATM 18 C C30 D84 . . . D 2 -16.244 -3.165 21.233 1 23.03 ? C30 D84 201 C 1 
HETATM 19 C C26 D84 . . . D 2 -16.717 -2.222 20.326 1 23.86 ? C26 D84 201 C 1 
HETATM 20 C C23 D84 . . . D 2 -15.833 -1.591 19.308 1 23.75 ? C23 D84 201 C 1 
HETATM 21 C C22 D84 . . . D 2 -16.4 -1.301 18.073 1 23.52 ? C22 D84 201 C 1 
HETATM 22 C C21 D84 . . . D 2 -15.631 -0.705 17.086 1 23.63 ? C21 D84 201 C 1 
HETATM 23 C C24 D84 . . . D 2 -14.501 -1.264 19.572 1 22.16 ? C24 D84 201 C 1 
HETATM 24 C C25 D84 . . . D 2 -13.726 -0.666 18.582 1 24.76 ? C25 D84 201 C 1 
HETATM 25 N N D84 . . . D 2 -12.449 -0.264 18.514 1 21.44 ? N D84 201 C 1 
HETATM 26 C C7 D84 . . . D 2 -11.445 -0.338 19.574 1 21.87 ? C7 D84 201 C 1 
HETATM 27 C C6 D84 . . . D 2 -11.142 -1.786 19.883 1 21.82 ? C6 D84 201 C 1 
HETATM 28 C C5 D84 . . . D 2 -10.752 -2.676 18.889 1 21.15 ? C5 D84 201 C 1 
HETATM 29 C C4 D84 . . . D 2 -10.506 -4.008 19.212 1 21.09 ? C4 D84 201 C 1 
HETATM 30 C C3 D84 . . . D 2 -10.644 -4.449 20.526 1 20.79 ? C3 D84 201 C 1 
HETATM 31 C C2 D84 . . . D 2 -11.039 -3.548 21.509 1 21.5 ? C2 D84 201 C 1 
HETATM 32 O O D84 . . . D 2 -11.704 -1.314 22.113 1 21.71 ? O D84 201 C 1 
HETATM 33 C C D84 . . . D 2 -10.963 -0.976 23.287 1 22.1 ? C D84 201 C 1 
HETATM 34 F F1 D84 . . . D 2 -11.244 0.318 23.661 1 21.71 ? F1 D84 201 C 1 
HETATM 35 C C20 D84 . . . D 2 -14.301 -0.399 17.346 1 22.12 ? C20 D84 201 C 1 
HETATM 36 N N2 D84 . . . D 2 -13.351 0.163 16.573 1 23.52 ? N2 D84 201 C 1 
HETATM 37 C C8 D84 . . . D 2 -12.215 0.237 17.294 1 22.79 ? C8 D84 201 C 1 
HETATM 38 C C9 D84 . . . D 2 -10.933 0.858 16.784 1 22.26 ? C9 D84 201 C 1 
HETATM 39 C C19 D84 . . . D 2 -6.952 -4.526 13.928 1 22.81 ? C19 D84 201 C 1 
HETATM 40 O O2 D84 . . . D 2 -7.725 -5.106 13.189 1 20.58 ? O2 D84 201 C 1 
HETATM 41 C C18 D84 . . . D 2 -5.535 -4.984 14.156 1 20.51 ? C18 D84 201 C 1 
#
_model_server_stats.io_time_ms              69 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    12 
_model_server_stats.query_time_ms           308 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           41 
#