data_3DA6 # _model_server_result.job_id xohDyN-KKCeDTFKC0lQSwQ _model_server_result.datetime_utc '2024-11-04 23:16:16' _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 3da6 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":1}' # _entry.id 3DA6 # _exptl.entry_id 3DA6 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 473.529 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description N-[3-methyl-4-({3-[2-(methylamino)pyrimidin-4-yl]pyridin-2-yl}oxy)naphthalen-1-yl]-1H-benzimidazol-2-amine _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 3DA6 _cell.length_a 52.483 _cell.length_b 71.283 _cell.length_c 106.957 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3DA6 _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 monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _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 B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C28 H23 N7 O' _chem_comp.formula_weight 473.529 _chem_comp.id BZ9 _chem_comp.mon_nstd_flag . _chem_comp.name N-[3-methyl-4-({3-[2-(methylamino)pyrimidin-4-yl]pyridin-2-yl}oxy)naphthalen-1-yl]-1H-benzimidazol-2-amine _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 N1 C9 BZ9 sing 70 n y N1 HN1 BZ9 sing 71 n n C4 N2 BZ9 sing 72 n y C5 C4 BZ9 doub 73 n y C5 H5 BZ9 sing 74 n n C6 C5 BZ9 sing 75 n y C6 H6 BZ9 sing 76 n n C7 C6 BZ9 doub 77 n y C7 C8 BZ9 sing 78 n y C7 H7 BZ9 sing 79 n n C8 C3 BZ9 doub 80 n y C8 H8 BZ9 sing 81 n n C10 C17 BZ9 sing 82 n y C13 C14 BZ9 doub 83 n y C13 C12 BZ9 sing 84 n y C13 H13 BZ9 sing 85 n n C15 C10 BZ9 doub 86 n y C15 H15 BZ9 sing 87 n n C17 O33 BZ9 sing 88 n n C17 C18 BZ9 doub 89 n y C20 N16 BZ9 sing 90 n n C20 C19 BZ9 doub 91 n y C21 C22 BZ9 doub 92 n y C21 C26 BZ9 sing 93 n y C22 C23 BZ9 sing 94 n y C22 H22 BZ9 sing 95 n n C24 H24 BZ9 sing 96 n n C26 N25 BZ9 doub 97 n y C28 C21 BZ9 sing 98 n y C28 N27 BZ9 sing 99 n y C35 H35 BZ9 sing 100 n n C35 H35A BZ9 sing 101 n n N34 C35 BZ9 sing 102 n n C32 N34 BZ9 sing 103 n n C32 N27 BZ9 doub 104 n y N31 C32 BZ9 sing 105 n y C30 N31 BZ9 doub 106 n y C30 C29 BZ9 sing 107 n y C30 H30 BZ9 sing 108 n n C29 C28 BZ9 doub 109 n y C29 H29 BZ9 sing 110 n n C23 C24 BZ9 doub 111 n y C23 H23 BZ9 sing 112 n n N25 C24 BZ9 sing 113 n y O33 C26 BZ9 sing 114 n n C18 C36 BZ9 sing 115 n n C36 H36 BZ9 sing 116 n n C36 H36A BZ9 sing 117 n n C36 H36B BZ9 sing 118 n n C19 C18 BZ9 sing 119 n y C19 H19 BZ9 sing 120 n n C14 C15 BZ9 sing 121 n y C14 H14 BZ9 sing 122 n n C12 C11 BZ9 doub 123 n y C12 H12 BZ9 sing 124 n n C11 C10 BZ9 sing 125 n y C11 C20 BZ9 sing 126 n y N16 HN16 BZ9 sing 127 n n C9 N16 BZ9 sing 128 n n N2 C9 BZ9 doub 129 n y C3 N1 BZ9 sing 130 n y C3 C4 BZ9 sing 131 n y C35 H221 BZ9 sing 132 n n N34 H231 BZ9 sing 133 n n # _atom_sites.entry_id 3DA6 _atom_sites.fract_transf_matrix[1][1] 0.019054 _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] 0.014029 _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] 0.00935 _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 B 2 BZ9 A 1 1 1 BZ9 BZ9 . C 3 HOH A 1 403 1 HOH HOH . C 3 HOH A 2 404 2 HOH HOH . C 3 HOH A 3 405 3 HOH HOH . C 3 HOH A 4 406 4 HOH HOH . C 3 HOH A 5 407 5 HOH HOH . C 3 HOH A 6 408 6 HOH HOH . C 3 HOH A 7 409 7 HOH HOH . C 3 HOH A 8 410 8 HOH HOH . C 3 HOH A 9 411 9 HOH HOH . C 3 HOH A 10 412 10 HOH HOH . C 3 HOH A 11 413 11 HOH HOH . C 3 HOH A 12 414 12 HOH HOH . C 3 HOH A 13 415 13 HOH HOH . C 3 HOH A 14 416 14 HOH HOH . C 3 HOH A 15 417 15 HOH HOH . C 3 HOH A 16 418 16 HOH HOH . C 3 HOH A 17 419 17 HOH HOH . C 3 HOH A 18 420 18 HOH HOH . C 3 HOH A 19 421 19 HOH HOH . C 3 HOH A 20 422 20 HOH HOH . C 3 HOH A 21 423 21 HOH HOH . C 3 HOH A 22 424 22 HOH HOH . C 3 HOH A 23 425 23 HOH HOH . C 3 HOH A 24 426 24 HOH HOH . C 3 HOH A 25 427 25 HOH HOH . C 3 HOH A 26 428 26 HOH HOH . C 3 HOH A 27 429 27 HOH HOH . C 3 HOH A 28 430 28 HOH HOH . C 3 HOH A 29 431 29 HOH HOH . C 3 HOH A 30 432 30 HOH HOH . C 3 HOH A 31 433 31 HOH HOH . C 3 HOH A 32 434 32 HOH HOH . C 3 HOH A 33 435 33 HOH HOH . C 3 HOH A 34 436 34 HOH HOH . C 3 HOH A 35 437 35 HOH HOH . C 3 HOH A 36 438 36 HOH HOH . C 3 HOH A 37 439 37 HOH HOH . C 3 HOH A 38 440 38 HOH HOH . C 3 HOH A 39 441 39 HOH HOH . C 3 HOH A 40 442 40 HOH HOH . C 3 HOH A 41 443 41 HOH HOH . C 3 HOH A 42 444 42 HOH HOH . C 3 HOH A 43 445 43 HOH HOH . C 3 HOH A 44 446 44 HOH HOH . C 3 HOH A 45 447 45 HOH HOH . C 3 HOH A 46 448 46 HOH HOH . C 3 HOH A 47 449 47 HOH HOH . C 3 HOH A 48 450 48 HOH HOH . C 3 HOH A 49 451 49 HOH HOH . C 3 HOH A 50 452 50 HOH HOH . C 3 HOH A 51 453 51 HOH HOH . C 3 HOH A 52 454 52 HOH HOH . C 3 HOH A 53 455 53 HOH HOH . C 3 HOH A 54 456 54 HOH HOH . C 3 HOH A 55 457 55 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 N N1 BZ9 . . . B 2 -19.257 17.145 -33.167 1 34.25 ? N1 BZ9 1 A 1 HETATM 2 C C4 BZ9 . . . B 2 -17.501 18.317 -33.835 1 43.45 ? C4 BZ9 1 A 1 HETATM 3 C C5 BZ9 . . . B 2 -16.828 19.315 -34.584 1 45.96 ? C5 BZ9 1 A 1 HETATM 4 C C6 BZ9 . . . B 2 -17.567 20.201 -35.385 1 43.21 ? C6 BZ9 1 A 1 HETATM 5 C C7 BZ9 . . . B 2 -18.982 20.029 -35.414 1 43.81 ? C7 BZ9 1 A 1 HETATM 6 C C8 BZ9 . . . B 2 -19.64 19.014 -34.728 1 36.49 ? C8 BZ9 1 A 1 HETATM 7 C C10 BZ9 . . . B 2 -19.759 12.661 -33.049 1 26.5 ? C10 BZ9 1 A 1 HETATM 8 C C13 BZ9 . . . B 2 -18.451 13.275 -35.39 1 29.42 ? C13 BZ9 1 A 1 HETATM 9 C C15 BZ9 . . . B 2 -19.906 11.858 -34.171 1 33.15 ? C15 BZ9 1 A 1 HETATM 10 C C17 BZ9 . . . B 2 -20.445 12.334 -31.88 1 28.4 ? C17 BZ9 1 A 1 HETATM 11 C C20 BZ9 . . . B 2 -18.854 14.598 -31.915 1 34.79 ? C20 BZ9 1 A 1 HETATM 12 C C21 BZ9 . . . B 2 -22.834 9.602 -31.769 1 27.92 ? C21 BZ9 1 A 1 HETATM 13 C C22 BZ9 . . . B 2 -24.22 9.361 -31.768 1 35.21 ? C22 BZ9 1 A 1 HETATM 14 C C24 BZ9 . . . B 2 -24.527 11.749 -31.619 1 35.9 ? C24 BZ9 1 A 1 HETATM 15 C C26 BZ9 . . . B 2 -22.414 10.919 -31.743 1 26.02 ? C26 BZ9 1 A 1 HETATM 16 C C28 BZ9 . . . B 2 -22.018 8.502 -31.928 1 30.55 ? C28 BZ9 1 A 1 HETATM 17 C C35 BZ9 . . . B 2 -23.899 4.856 -30.744 1 30.33 ? C35 BZ9 1 A 1 HETATM 18 N N34 BZ9 . . . B 2 -22.579 4.976 -31.397 1 31.94 ? N34 BZ9 1 A 1 HETATM 19 C C32 BZ9 . . . B 2 -21.978 6.132 -31.739 1 26.58 ? C32 BZ9 1 A 1 HETATM 20 N N27 BZ9 . . . B 2 -22.558 7.315 -31.59 1 23.39 ? N27 BZ9 1 A 1 HETATM 21 N N31 BZ9 . . . B 2 -20.791 6.108 -32.336 1 28.62 ? N31 BZ9 1 A 1 HETATM 22 C C30 BZ9 . . . B 2 -20.191 7.222 -32.638 1 25.35 ? C30 BZ9 1 A 1 HETATM 23 C C29 BZ9 . . . B 2 -20.713 8.502 -32.494 1 23.6 ? C29 BZ9 1 A 1 HETATM 24 C C23 BZ9 . . . B 2 -25.06 10.479 -31.671 1 28.92 ? C23 BZ9 1 A 1 HETATM 25 N N25 BZ9 . . . B 2 -23.197 11.94 -31.679 1 31.33 ? N25 BZ9 1 A 1 HETATM 26 O O33 BZ9 . . . B 2 -21.125 11.147 -31.835 1 33.32 ? O33 BZ9 1 A 1 HETATM 27 C C18 BZ9 . . . B 2 -20.349 13.124 -30.735 1 29.63 ? C18 BZ9 1 A 1 HETATM 28 C C36 BZ9 . . . B 2 -21.106 12.755 -29.45 1 24.99 ? C36 BZ9 1 A 1 HETATM 29 C C19 BZ9 . . . B 2 -19.577 14.283 -30.776 1 29.38 ? C19 BZ9 1 A 1 HETATM 30 C C14 BZ9 . . . B 2 -19.219 12.141 -35.369 1 30.91 ? C14 BZ9 1 A 1 HETATM 31 C C12 BZ9 . . . B 2 -18.262 14.074 -34.271 1 30.24 ? C12 BZ9 1 A 1 HETATM 32 C C11 BZ9 . . . B 2 -18.937 13.79 -33.077 1 26.68 ? C11 BZ9 1 A 1 HETATM 33 N N16 BZ9 . . . B 2 -18.102 15.692 -31.776 1 34.39 ? N16 BZ9 1 A 1 HETATM 34 C C9 BZ9 . . . B 2 -18.135 16.691 -32.618 1 43.68 ? C9 BZ9 1 A 1 HETATM 35 N N2 BZ9 . . . B 2 -17.042 17.374 -33.003 1 43.53 ? N2 BZ9 1 A 1 HETATM 36 C C3 BZ9 . . . B 2 -18.899 18.172 -33.921 1 35.02 ? C3 BZ9 1 A 1 # _model_server_stats.io_time_ms 61 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 273 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 36 #