data_7KPB
#
_model_server_result.job_id            hz59dptHH0F2gqbGIWxMsQ 
_model_server_result.datetime_utc      '2024-11-16 10:41:21' 
_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          7kpb 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"K","auth_seq_id":201}' 
#
_entry.id    7KPB 
#
_exptl.entry_id    7KPB 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              556.559 
_entity.id                          6 
_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            7KPB 
_cell.length_a            99.51 
_cell.length_b            99.51 
_cell.length_c            311.35 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7KPB 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        92 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 41 21 2' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    heptameric 
_pdbx_struct_assembly.oligomeric_count      7 
_pdbx_struct_assembly.details               author_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,M,N,O,P,Q,R,S,T,U,V,W,X 
_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                      6 
_struct_asym.id                             K 
_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 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? 
disulf ? disulf2 B SG CYS 70 B CYS 69 1_555 B SG CYS 102 B CYS 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf3 C SG CYS 70 C CYS 69 1_555 C SG CYS 102 C CYS 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
disulf ? disulf4 D SG CYS 4 F CYS 15 1_555 D SG CYS 18 F CYS 29 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
disulf ? disulf5 D SG CYS 19 F CYS 30 1_555 D SG CYS 32 F CYS 43 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? 
disulf ? disulf6 D SG CYS 22 F CYS 33 1_555 D SG CYS 41 F CYS 52 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
disulf ? disulf7 D SG CYS 44 F CYS 55 1_555 D SG CYS 59 F CYS 70 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf8 D SG CYS 62 F CYS 73 1_555 D SG CYS 77 F CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
disulf ? disulf9 D SG CYS 65 F CYS 76 1_555 D SG CYS 85 F CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf10 D SG CYS 87 F CYS 98 1_555 D SG CYS 103 F CYS 114 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf11 D SG CYS 106 F CYS 117 1_555 D SG CYS 118 F CYS 129 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf12 D SG CYS 109 F CYS 120 1_555 D SG CYS 126 F CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf13 D SG CYS 128 F CYS 139 1_555 D SG CYS 139 F CYS 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf14 E SG CYS 4 E CYS 15 1_555 E SG CYS 18 E CYS 29 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf15 E SG CYS 19 E CYS 30 1_555 E SG CYS 32 E CYS 43 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
disulf ? disulf16 E SG CYS 22 E CYS 33 1_555 E SG CYS 41 E CYS 52 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf17 E SG CYS 44 E CYS 55 1_555 E SG CYS 59 E CYS 70 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf18 E SG CYS 62 E CYS 73 1_555 E SG CYS 77 E CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf19 E SG CYS 65 E CYS 76 1_555 E SG CYS 85 E CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? 
disulf ? disulf20 E SG CYS 87 E CYS 98 1_555 E SG CYS 103 E CYS 114 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? 
disulf ? disulf21 E SG CYS 106 E CYS 117 1_555 E SG CYS 118 E CYS 129 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? 
disulf ? disulf22 E SG CYS 109 E CYS 120 1_555 E SG CYS 126 E CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? 
disulf ? disulf23 E SG CYS 128 E CYS 139 1_555 E SG CYS 139 E CYS 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf24 F SG CYS 23 L CYS 23 1_555 F SG CYS 88 L CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf25 F SG CYS 134 L CYS 134 1_555 F SG CYS 194 L CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? 
disulf ? disulf26 G SG CYS 22 H CYS 22 1_555 G SG CYS 96 H CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf27 G SG CYS 148 H CYS 148 1_555 G SG CYS 203 H CYS 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? 
covale ? covale1 E ND2 ASN 111 E ASN 122 1_555 O C1 NAG . E NAG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? 
#
_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                     7KPB 
_atom_sites.fract_transf_matrix[1][1]    0.010049 
_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]    0.010049 
_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]    0.003212 
_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
H 5 GOL A 1 201 1 GOL GOL . 
I 5 GOL B 1 201 7 GOL GOL . 
J 5 GOL B 1 202 8 GOL GOL . 
K 6 D84 C 1 201 1 D84 733 . 
L 5 GOL F 1 201 2 GOL GOL . 
M 5 GOL F 1 202 3 GOL GOL . 
N 5 GOL F 1 203 4 GOL GOL . 
O 7 NAG E 1 201 200 NAG NAG . 
P 5 GOL E 1 202 5 GOL GOL . 
Q 5 GOL E 1 203 6 GOL GOL . 
R 5 GOL L 1 301 9 GOL GOL . 
S 8 HOH A 1 301 3 HOH HOH . 
S 8 HOH A 2 302 17 HOH HOH . 
S 8 HOH A 3 303 15 HOH HOH . 
S 8 HOH A 4 304 1 HOH HOH . 
T 8 HOH B 1 301 2 HOH HOH . 
T 8 HOH B 2 302 5 HOH HOH . 
T 8 HOH B 3 303 13 HOH HOH . 
T 8 HOH B 4 304 14 HOH HOH . 
T 8 HOH B 5 305 4 HOH HOH . 
U 8 HOH C 1 301 16 HOH HOH . 
U 8 HOH C 2 302 11 HOH HOH . 
U 8 HOH C 3 303 6 HOH HOH . 
U 8 HOH C 4 304 12 HOH HOH . 
U 8 HOH C 5 305 7 HOH HOH . 
V 8 HOH F 1 301 8 HOH HOH . 
W 8 HOH E 1 301 19 HOH HOH . 
W 8 HOH E 2 302 18 HOH HOH . 
W 8 HOH E 3 303 20 HOH HOH . 
W 8 HOH E 4 304 9 HOH HOH . 
X 8 HOH L 1 401 10 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 . . . K 6 -55.293 93.34 -5.994 1 35.44 ? C10 D84 201 C 1 
HETATM 2 C C11 D84 . . . K 6 -54.647 93.582 -7.201 1 33.96 ? C11 D84 201 C 1 
HETATM 3 C C12 D84 . . . K 6 -53.274 93.395 -7.297 1 33.28 ? C12 D84 201 C 1 
HETATM 4 C C13 D84 . . . K 6 -52.551 92.971 -6.189 1 32.77 ? C13 D84 201 C 1 
HETATM 5 C C14 D84 . . . K 6 -53.193 92.718 -4.982 1 29.21 ? C14 D84 201 C 1 
HETATM 6 F F D84 . . . K 6 -61.601 88.011 -4.203 1 41.73 ? F D84 201 C 1 
HETATM 7 C C15 D84 . . . K 6 -54.566 92.912 -4.89 1 30.74 ? C15 D84 201 C 1 
HETATM 8 C C16 D84 . . . K 6 -53.146 92.384 -2.544 1 32.55 ? C16 D84 201 C 1 
HETATM 9 C C17 D84 . . . K 6 -52.056 91.831 -1.626 1 38.78 ? C17 D84 201 C 1 
HETATM 10 O O1 D84 . . . K 6 -56.647 93.526 -5.892 1 37.94 ? O1 D84 201 C 1 
HETATM 11 C C1 D84 . . . K 6 -59.355 89.417 -5.55 1 42.04 ? C1 D84 201 C 1 
HETATM 12 N N1 D84 . . . K 6 -52.496 92.292 -3.841 1 32.55 ? N1 D84 201 C 1 
HETATM 13 O O3 D84 . . . K 6 -62.255 85.381 -12.096 1 49.7 ? O3 D84 201 C 1 
HETATM 14 C C28 D84 . . . K 6 -61.618 86.392 -11.727 1 44.22 ? C28 D84 201 C 1 
HETATM 15 N N3 D84 . . . K 6 -61.564 87.468 -12.52 1 37 ? N3 D84 201 C 1 
HETATM 16 C C27 D84 . . . K 6 -60.894 88.568 -12.153 1 34.89 ? C27 D84 201 C 1 
HETATM 17 C C29 D84 . . . K 6 -60.973 86.391 -10.495 1 33.83 ? C29 D84 201 C 1 
HETATM 18 C C30 D84 . . . K 6 -60.27 87.519 -10.088 1 37.99 ? C30 D84 201 C 1 
HETATM 19 C C26 D84 . . . K 6 -60.23 88.62 -10.933 1 34.13 ? C26 D84 201 C 1 
HETATM 20 C C23 D84 . . . K 6 -59.482 89.847 -10.547 1 34.56 ? C23 D84 201 C 1 
HETATM 21 C C22 D84 . . . K 6 -58.76 90.531 -11.519 1 34.97 ? C22 D84 201 C 1 
HETATM 22 C C21 D84 . . . K 6 -58.046 91.675 -11.184 1 34.78 ? C21 D84 201 C 1 
HETATM 23 C C24 D84 . . . K 6 -59.479 90.301 -9.231 1 33.46 ? C24 D84 201 C 1 
HETATM 24 C C25 D84 . . . K 6 -58.768 91.45 -8.896 1 38.54 ? C25 D84 201 C 1 
HETATM 25 N N D84 . . . K 6 -58.595 92.109 -7.742 1 34.32 ? N D84 201 C 1 
HETATM 26 C C7 D84 . . . K 6 -59.179 91.743 -6.453 1 30.57 ? C7 D84 201 C 1 
HETATM 27 C C6 D84 . . . K 6 -58.547 90.471 -5.936 1 41.06 ? C6 D84 201 C 1 
HETATM 28 C C5 D84 . . . K 6 -57.165 90.364 -5.833 1 37.08 ? C5 D84 201 C 1 
HETATM 29 C C4 D84 . . . K 6 -56.595 89.193 -5.347 1 31.41 ? C4 D84 201 C 1 
HETATM 30 C C3 D84 . . . K 6 -57.406 88.13 -4.964 1 28.29 ? C3 D84 201 C 1 
HETATM 31 C C2 D84 . . . K 6 -58.788 88.243 -5.066 1 32.49 ? C2 D84 201 C 1 
HETATM 32 O O D84 . . . K 6 -60.716 89.536 -5.651 1 37.07 ? O D84 201 C 1 
HETATM 33 C C D84 . . . K 6 -61.526 89.348 -4.495 1 38.7 ? C D84 201 C 1 
HETATM 34 F F1 D84 . . . K 6 -62.781 89.845 -4.728 1 43.04 ? F1 D84 201 C 1 
HETATM 35 C C20 D84 . . . K 6 -58.055 92.135 -9.872 1 38.32 ? C20 D84 201 C 1 
HETATM 36 N N2 D84 . . . K 6 -57.469 93.194 -9.276 1 32.13 ? N2 D84 201 C 1 
HETATM 37 C C8 D84 . . . K 6 -57.805 93.167 -7.968 1 32.37 ? C8 D84 201 C 1 
HETATM 38 C C9 D84 . . . K 6 -57.364 94.179 -6.938 1 30.59 ? C9 D84 201 C 1 
HETATM 39 C C19 D84 . . . K 6 -51.264 91.796 -3.874 1 35.37 ? C19 D84 201 C 1 
HETATM 40 O O2 D84 . . . K 6 -50.549 91.607 -4.845 1 32.18 ? O2 D84 201 C 1 
HETATM 41 C C18 D84 . . . K 6 -50.837 91.46 -2.468 1 36.48 ? C18 D84 201 C 1 
#
_model_server_stats.io_time_ms              72 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    17 
_model_server_stats.query_time_ms           294 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           41 
#