data_3KPE
#
_model_server_result.job_id            JsF1M0wI9hMBdz5Vu8xDPw 
_model_server_result.datetime_utc      '2024-11-07 13:46:35' 
_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          3kpe 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":1}' 
#
_entry.id    3KPE 
#
_exptl.entry_id    3KPE 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              558.714 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            2-[[6-[[[2-(3-hydroxypropyl)-5-methylphenyl]amino]methyl]-2-[[3-(4-morpholinyl)propyl]amino]-1H-benzimidazol-1-yl]methyl]-6-methyl-3-pyridinol 
_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            3KPE 
_cell.length_a            63.248 
_cell.length_b            63.248 
_cell.length_c            63.248 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3KPE 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        198 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 3' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    hexameric 
_pdbx_struct_assembly.oligomeric_count      6 
_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    1,2,3 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 6_555 z+1/2,-x+1/2,-y 0 0 1 -1 0 0 0 -1 0 31.624 31.624 0 
3 'crystal symmetry operation' 12_554 -y+1/2,-z,x-1/2 0 -1 0 0 0 -1 1 0 0 31.624 0 -31.624 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      3 
_struct_asym.id                             C 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    N 
#
_chem_comp.formula           'C32 H42 N6 O3' 
_chem_comp.formula_weight    558.714 
_chem_comp.id                TM3 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              2-[[6-[[[2-(3-hydroxypropyl)-5-methylphenyl]amino]methyl]-2-[[3-(4-morpholinyl)propyl]amino]-1H-benzimidazol-1-yl]methyl]-6-methyl-3-pyridinol 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     TMC353121 
#
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
C1 C2 TM3 sing 304 n n 
C1 O6 TM3 sing 305 n n 
C1 H1 TM3 sing 306 n n 
C1 H1A TM3 sing 307 n n 
C2 N3 TM3 sing 308 n n 
C2 H2 TM3 sing 309 n n 
C2 H2A TM3 sing 310 n n 
N3 C13 TM3 sing 311 n n 
N3 C4 TM3 sing 312 n n 
C5 C4 TM3 sing 313 n n 
C4 H4 TM3 sing 314 n n 
C4 H4A TM3 sing 315 n n 
O6 C5 TM3 sing 316 n n 
C5 H5 TM3 sing 317 n n 
C5 H5A TM3 sing 318 n n 
C13 C14 TM3 sing 319 n n 
C13 H13 TM3 sing 320 n n 
C13 H13A TM3 sing 321 n n 
C14 C15 TM3 sing 322 n n 
C14 H14 TM3 sing 323 n n 
C14 H14A TM3 sing 324 n n 
C15 N16 TM3 sing 325 n n 
C15 H15 TM3 sing 326 n n 
C15 H15A TM3 sing 327 n n 
N16 C17 TM3 sing 328 n n 
N16 HN16 TM3 sing 329 n n 
C17 N26 TM3 sing 330 n y 
C17 N23 TM3 doub 331 n y 
N23 C24 TM3 sing 332 n y 
C25 C24 TM3 doub 333 n y 
C24 C35 TM3 sing 334 n y 
N26 C25 TM3 sing 335 n y 
C25 C32 TM3 sing 336 n y 
C41 N26 TM3 sing 337 n n 
C32 C33 TM3 doub 338 n y 
C32 H32 TM3 sing 339 n n 
C33 C34 TM3 sing 340 n y 
C33 C60 TM3 sing 341 n n 
C35 C34 TM3 doub 342 n y 
C34 H34 TM3 sing 343 n n 
C35 H35 TM3 sing 344 n n 
C41 C42 TM3 sing 345 n n 
C41 H41 TM3 sing 346 n n 
C41 H41A TM3 sing 347 n n 
C45 C42 TM3 doub 348 n y 
C42 N49 TM3 sing 349 n y 
O56 C45 TM3 sing 350 n n 
C45 C46 TM3 sing 351 n y 
C46 C47 TM3 doub 352 n y 
C46 H46 TM3 sing 353 n n 
C47 C48 TM3 sing 354 n y 
C47 H47 TM3 sing 355 n n 
N49 C48 TM3 doub 356 n y 
C48 C58 TM3 sing 357 n n 
O56 HO56 TM3 sing 358 n n 
C58 H58 TM3 sing 359 n n 
C58 H58A TM3 sing 360 n n 
C58 H58B TM3 sing 361 n n 
N61 C60 TM3 sing 362 n n 
C60 H60 TM3 sing 363 n n 
N61 C62 TM3 sing 364 n n 
C70 C62 TM3 doub 365 n y 
C62 C66 TM3 sing 366 n y 
C66 C67 TM3 doub 367 n y 
C66 H66 TM3 sing 368 n n 
C68 C67 TM3 sing 369 n y 
C67 C77 TM3 sing 370 n n 
C69 C68 TM3 doub 371 n y 
C68 H68 TM3 sing 372 n n 
C70 C69 TM3 sing 373 n y 
C69 H69 TM3 sing 374 n n 
C79 C70 TM3 sing 375 n n 
C77 H77 TM3 sing 376 n n 
C77 H77A TM3 sing 377 n n 
C77 H77B TM3 sing 378 n n 
C80 C79 TM3 sing 379 n n 
C79 H79 TM3 sing 380 n n 
C79 H79A TM3 sing 381 n n 
C80 C81 TM3 sing 382 n n 
C80 H80 TM3 sing 383 n n 
C80 H80A TM3 sing 384 n n 
O82 C81 TM3 sing 385 n n 
C81 H81 TM3 sing 386 n n 
C81 H81A TM3 sing 387 n n 
O82 HO82 TM3 sing 388 n n 
N61 HO83 TM3 sing 389 n n 
C60 HO84 TM3 sing 390 n n 
#
_atom_sites.entry_id                     3KPE 
_atom_sites.fract_transf_matrix[1][1]    0.015811 
_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]    0.015811 
_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]    0.015811 
_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 3 TM3 A 1 1 1 TM3 TTZ . 
D 4 PG4 A 1 210 1 PG4 PG4 . 
E 5 HOH A 1 2 2 HOH HOH . 
E 5 HOH A 2 3 3 HOH HOH . 
E 5 HOH A 3 6 6 HOH HOH . 
E 5 HOH A 4 9 9 HOH HOH . 
E 5 HOH A 5 10 10 HOH HOH . 
E 5 HOH A 6 12 12 HOH HOH . 
E 5 HOH A 7 13 13 HOH HOH . 
E 5 HOH A 8 16 16 HOH HOH . 
E 5 HOH A 9 17 17 HOH HOH . 
E 5 HOH A 10 22 22 HOH HOH . 
E 5 HOH A 11 24 24 HOH HOH . 
E 5 HOH A 12 28 28 HOH HOH . 
E 5 HOH A 13 32 32 HOH HOH . 
E 5 HOH A 14 34 34 HOH HOH . 
E 5 HOH A 15 37 37 HOH HOH . 
E 5 HOH A 16 211 1 HOH HOH . 
F 5 HOH B 1 4 4 HOH HOH . 
F 5 HOH B 2 5 5 HOH HOH . 
F 5 HOH B 3 7 7 HOH HOH . 
F 5 HOH B 4 8 8 HOH HOH . 
F 5 HOH B 5 11 11 HOH HOH . 
F 5 HOH B 6 14 14 HOH HOH . 
F 5 HOH B 7 15 15 HOH HOH . 
F 5 HOH B 8 18 18 HOH HOH . 
F 5 HOH B 9 19 19 HOH HOH . 
F 5 HOH B 10 20 20 HOH HOH . 
F 5 HOH B 11 21 21 HOH HOH . 
F 5 HOH B 12 23 23 HOH HOH . 
F 5 HOH B 13 25 25 HOH HOH . 
F 5 HOH B 14 26 26 HOH HOH . 
F 5 HOH B 15 27 27 HOH HOH . 
F 5 HOH B 16 29 29 HOH HOH . 
F 5 HOH B 17 30 30 HOH HOH . 
F 5 HOH B 18 31 31 HOH HOH . 
F 5 HOH B 19 33 33 HOH HOH . 
F 5 HOH B 20 35 35 HOH HOH . 
F 5 HOH B 21 36 36 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 C1 TM3 . . . C 3 27.938 -10.313 -9.907 1 43.91 ? C1 TM3 1 A 1 
HETATM 2 C C2 TM3 . . . C 3 26.511 -9.888 -9.531 1 42.52 ? C2 TM3 1 A 1 
HETATM 3 N N3 TM3 . . . C 3 26.218 -10.335 -8.156 1 39.94 ? N3 TM3 1 A 1 
HETATM 4 C C4 TM3 . . . C 3 27.25 -9.756 -7.268 1 41.59 ? C4 TM3 1 A 1 
HETATM 5 C C5 TM3 . . . C 3 28.637 -10.279 -7.63 1 42.62 ? C5 TM3 1 A 1 
HETATM 6 O O6 TM3 . . . C 3 28.924 -9.85 -8.958 1 44 ? O6 TM3 1 A 1 
HETATM 7 C C13 TM3 . . . C 3 24.844 -9.931 -7.731 1 36.38 ? C13 TM3 1 A 1 
HETATM 8 C C14 TM3 . . . C 3 24.29 -10.788 -6.591 1 30.4 ? C14 TM3 1 A 1 
HETATM 9 C C15 TM3 . . . C 3 22.8 -10.628 -6.379 1 21.67 ? C15 TM3 1 A 1 
HETATM 10 N N16 TM3 . . . C 3 22.508 -9.301 -5.818 1 19.45 ? N16 TM3 1 A 1 
HETATM 11 C C17 TM3 . . . C 3 22.316 -9.089 -4.502 1 18.9 ? C17 TM3 1 A 1 
HETATM 12 N N23 TM3 . . . C 3 22.417 -10.071 -3.597 1 18.37 ? N23 TM3 1 A 1 
HETATM 13 C C24 TM3 . . . C 3 22.15 -9.474 -2.394 1 17.18 ? C24 TM3 1 A 1 
HETATM 14 C C25 TM3 . . . C 3 21.891 -8.116 -2.607 1 16.9 ? C25 TM3 1 A 1 
HETATM 15 N N26 TM3 . . . C 3 21.989 -7.914 -3.957 1 17.49 ? N26 TM3 1 A 1 
HETATM 16 C C32 TM3 . . . C 3 21.572 -7.224 -1.566 1 18.52 ? C32 TM3 1 A 1 
HETATM 17 C C33 TM3 . . . C 3 21.528 -7.763 -0.269 1 17.65 ? C33 TM3 1 A 1 
HETATM 18 C C34 TM3 . . . C 3 21.832 -9.131 -0.043 1 18.45 ? C34 TM3 1 A 1 
HETATM 19 C C35 TM3 . . . C 3 22.132 -9.987 -1.097 1 18.81 ? C35 TM3 1 A 1 
HETATM 20 C C41 TM3 . . . C 3 21.711 -6.66 -4.692 1 17.33 ? C41 TM3 1 A 1 
HETATM 21 C C42 TM3 . . . C 3 22.589 -5.522 -4.351 1 15.46 ? C42 TM3 1 A 1 
HETATM 22 C C45 TM3 . . . C 3 23.943 -5.608 -4.457 1 16.47 ? C45 TM3 1 A 1 
HETATM 23 C C46 TM3 . . . C 3 24.733 -4.515 -4.179 1 17.08 ? C46 TM3 1 A 1 
HETATM 24 C C47 TM3 . . . C 3 24.056 -3.355 -3.725 1 15.21 ? C47 TM3 1 A 1 
HETATM 25 C C48 TM3 . . . C 3 22.681 -3.312 -3.631 1 16.54 ? C48 TM3 1 A 1 
HETATM 26 N N49 TM3 . . . C 3 21.938 -4.395 -3.917 1 16.21 ? N49 TM3 1 A 1 
HETATM 27 O O56 TM3 . . . C 3 24.455 -6.787 -4.924 1 18.37 ? O56 TM3 1 A 1 
HETATM 28 C C58 TM3 . . . C 3 21.956 -2.07 -3.161 1 16.64 ? C58 TM3 1 A 1 
HETATM 29 C C60 TM3 . . . C 3 21.223 -6.912 0.939 1 17.52 ? C60 TM3 1 A 1 
HETATM 30 N N61 TM3 . . . C 3 20.893 -5.496 0.655 1 18.38 ? N61 TM3 1 A 1 
HETATM 31 C C62 TM3 . . . C 3 20.737 -4.58 1.665 1 17.77 ? C62 TM3 1 A 1 
HETATM 32 C C66 TM3 . . . C 3 20.895 -4.976 3.003 1 19.4 ? C66 TM3 1 A 1 
HETATM 33 C C67 TM3 . . . C 3 20.753 -4.068 4.054 1 18.64 ? C67 TM3 1 A 1 
HETATM 34 C C68 TM3 . . . C 3 20.43 -2.747 3.772 1 20.4 ? C68 TM3 1 A 1 
HETATM 35 C C69 TM3 . . . C 3 20.299 -2.34 2.46 1 18.23 ? C69 TM3 1 A 1 
HETATM 36 C C70 TM3 . . . C 3 20.418 -3.248 1.414 1 16.47 ? C70 TM3 1 A 1 
HETATM 37 C C77 TM3 . . . C 3 20.897 -4.514 5.495 1 19.37 ? C77 TM3 1 A 1 
HETATM 38 C C79 TM3 . . . C 3 20.258 -2.722 -0.007 1 18.51 ? C79 TM3 1 A 1 
HETATM 39 C C80 TM3 . . . C 3 18.809 -2.664 -0.499 1 18.73 ? C80 TM3 1 A 1 
HETATM 40 C C81 TM3 . . . C 3 18.036 -3.996 -0.409 1 21.08 ? C81 TM3 1 A 1 
HETATM 41 O O82 TM3 . . . C 3 18.7 -5.006 -1.186 1 21.75 ? O82 TM3 1 A 1 
#
_model_server_stats.io_time_ms              5 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           306 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           41 
#