data_6EAG # _model_server_result.job_id LQWoSuRLyYSIQ1PqNXukcQ _model_server_result.datetime_utc '2025-01-14 11:50:33' _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 6eag # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":605}' # _entry.id 6EAG # _exptl.entry_id 6EAG _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 394.513 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-[[2-[[1-(2-azanylethyl)piperidin-4-yl]amino]-4-methyl-benzimidazol-1-yl]methyl]-6-methyl-pyridin-3-ol _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 6EAG _cell.length_a 170.34 _cell.length_b 170.34 _cell.length_c 170.34 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6EAG _symmetry.cell_setting ? _symmetry.Int_Tables_number 213 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 3 2' # _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 _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' 5_555 z,x,y 0 0 1 1 0 0 0 1 0 0 0 0 3 'crystal symmetry operation' 9_555 y,z,x 0 1 0 0 0 1 1 0 0 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id F _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 37 F CYS 37 1_555 A SG CYS 439 F CYS 439 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf2 A SG CYS 155 F CYS 155 1_555 A SG CYS 290 F CYS 290 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf3 A SG CYS 313 F CYS 313 1_555 A SG CYS 343 F CYS 343 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf4 A SG CYS 322 F CYS 322 1_555 A SG CYS 333 F CYS 333 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf5 A SG CYS 358 F CYS 358 1_555 A SG CYS 367 F CYS 367 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf6 A SG CYS 382 F CYS 382 1_555 A SG CYS 393 F CYS 393 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf7 A SG CYS 416 F CYS 416 1_555 A SG CYS 422 F CYS 422 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? # _chem_comp.formula 'C22 H30 N6 O' _chem_comp.formula_weight 394.513 _chem_comp.id 5NK _chem_comp.mon_nstd_flag . _chem_comp.name 2-[[2-[[1-(2-azanylethyl)piperidin-4-yl]amino]-4-methyl-benzimidazol-1-yl]methyl]-6-methyl-pyridin-3-ol _chem_comp.type non-polymer _chem_comp.pdbx_synonyms JNJ-2408068 # 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 C04 C03 5NK doub 1 n y C04 C06 5NK sing 2 n y C28 C14 5NK sing 3 n n C11 C12 5NK sing 4 n n C11 N07 5NK sing 5 n n N13 C14 5NK doub 6 n y N13 C12 5NK sing 7 n y C03 C02 5NK sing 8 n y C14 C15 5NK sing 9 n y C12 C17 5NK doub 10 n y C06 N07 5NK sing 11 n y C06 C05 5NK doub 12 n y N07 C08 5NK sing 13 n y C02 C01 5NK doub 14 n y C15 C16 5NK doub 15 n y C17 O29 5NK sing 16 n n C17 C16 5NK sing 17 n y C19 C24 5NK sing 18 n n C19 N18 5NK sing 19 n n C19 C20 5NK sing 20 n n C05 C01 5NK sing 21 n y C05 N09 5NK sing 22 n y C08 N18 5NK sing 23 n n C08 N09 5NK doub 24 n y C24 C23 5NK sing 25 n n C01 C10 5NK sing 26 n n C20 C21 5NK sing 27 n n C23 N22 5NK sing 28 n n C21 N22 5NK sing 29 n n C25 N22 5NK sing 30 n n C25 C26 5NK sing 31 n n C26 N27 5NK sing 32 n n C10 H1 5NK sing 33 n n C10 H2 5NK sing 34 n n C10 H3 5NK sing 35 n n C15 H4 5NK sing 36 n n C20 H5 5NK sing 37 n n C20 H6 5NK sing 38 n n C21 H7 5NK sing 39 n n C21 H8 5NK sing 40 n n C24 H9 5NK sing 41 n n C24 H10 5NK sing 42 n n C26 H11 5NK sing 43 n n C26 H12 5NK sing 44 n n C28 H13 5NK sing 45 n n C28 H14 5NK sing 46 n n C28 H15 5NK sing 47 n n C02 H16 5NK sing 48 n n C03 H17 5NK sing 49 n n C04 H18 5NK sing 50 n n C11 H19 5NK sing 51 n n C11 H20 5NK sing 52 n n C16 H21 5NK sing 53 n n N18 H22 5NK sing 54 n n C19 H23 5NK sing 55 n n C23 H25 5NK sing 56 n n C23 H26 5NK sing 57 n n C25 H27 5NK sing 58 n n C25 H28 5NK sing 59 n n N27 H29 5NK sing 60 n n N27 H30 5NK sing 61 n n O29 H32 5NK sing 62 n n # _atom_sites.entry_id 6EAG _atom_sites.fract_transf_matrix[1][1] 0.005871 _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] 0.005871 _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] 0.005871 _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 NHE F 1 601 1 NHE NHE . C 3 SO4 F 1 602 1 SO4 SO4 . D 3 SO4 F 1 603 2 SO4 SO4 . E 4 TAR F 1 604 1 TAR TAR . F 5 5NK F 1 605 1 5NK 5NK . # 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 5NK . . . F 5 23.645 17.041 23.566 0.33 90.75 ? C10 5NK 605 F 1 HETATM 2 C C15 5NK . . . F 5 16.309 22.168 22.708 0.33 86.2 ? C15 5NK 605 F 1 HETATM 3 C C17 5NK . . . F 5 17.439 20.804 20.815 0.33 83.52 ? C17 5NK 605 F 1 HETATM 4 C C20 5NK . . . F 5 24.298 22.622 22.552 0.33 95.98 ? C20 5NK 605 F 1 HETATM 5 C C21 5NK . . . F 5 24.398 22.679 24.077 0.33 98.74 ? C21 5NK 605 F 1 HETATM 6 C C24 5NK . . . F 5 22.899 24.581 22.544 0.33 97.04 ? C24 5NK 605 F 1 HETATM 7 C C26 5NK . . . F 5 25.459 25.429 25.771 0.33 107.89 ? C26 5NK 605 F 1 HETATM 8 C C28 5NK . . . F 5 17.761 23.821 24.178 0.33 86.19 ? C28 5NK 605 F 1 HETATM 9 C C01 5NK . . . F 5 22.594 17.316 22.493 0.33 86.08 ? C01 5NK 605 F 1 HETATM 10 C C02 5NK . . . F 5 22.01 16.184 21.69 0.33 82.24 ? C02 5NK 605 F 1 HETATM 11 C C03 5NK . . . F 5 20.991 16.472 20.653 0.33 80.81 ? C03 5NK 605 F 1 HETATM 12 C C04 5NK . . . F 5 20.551 17.89 20.413 0.33 85.58 ? C04 5NK 605 F 1 HETATM 13 C C05 5NK . . . F 5 22.121 18.801 22.227 0.33 95.23 ? C05 5NK 605 F 1 HETATM 14 C C06 5NK . . . F 5 21.172 19.068 21.263 0.33 85.46 ? C06 5NK 605 F 1 HETATM 15 N N07 5NK . . . F 5 20.964 20.389 21.249 0.33 90.12 ? N07 5NK 605 F 1 HETATM 16 C C08 5NK . . . F 5 21.768 20.955 22.194 0.33 89.9 ? C08 5NK 605 F 1 HETATM 17 N N09 5NK . . . F 5 22.478 19.957 22.792 0.33 87.22 ? N09 5NK 605 F 1 HETATM 18 C C11 5NK . . . F 5 20.036 21.086 20.378 0.33 89.19 ? C11 5NK 605 F 1 HETATM 19 C C12 5NK . . . F 5 18.778 21.448 21.166 0.33 85.23 ? C12 5NK 605 F 1 HETATM 20 N N13 5NK . . . F 5 18.86 22.434 22.267 0.33 74.97 ? N13 5NK 605 F 1 HETATM 21 C C14 5NK . . . F 5 17.655 22.804 23.044 0.33 86.42 ? C14 5NK 605 F 1 HETATM 22 C C16 5NK . . . F 5 16.212 21.169 21.595 0.33 80.62 ? C16 5NK 605 F 1 HETATM 23 N N18 5NK . . . F 5 21.854 22.372 22.514 0.33 91.57 ? N18 5NK 605 F 1 HETATM 24 C C19 5NK . . . F 5 23.06 23.215 22.05 0.33 93.67 ? C19 5NK 605 F 1 HETATM 25 N N22 5NK . . . F 5 24.18 24.017 24.611 0.33 99.01 ? N22 5NK 605 F 1 HETATM 26 C C23 5NK . . . F 5 22.992 24.662 24.068 0.33 97.74 ? C23 5NK 605 F 1 HETATM 27 C C25 5NK . . . F 5 25.144 24.701 24.465 0.33 101.62 ? C25 5NK 605 F 1 HETATM 28 N N27 5NK . . . F 5 26.784 26.017 25.686 0.33 112.45 ? N27 5NK 605 F 1 HETATM 29 O O29 5NK . . . F 5 17.357 19.871 19.774 0.33 83.77 ? O29 5NK 605 F 1 # _model_server_stats.io_time_ms 32 _model_server_stats.parse_time_ms 59 _model_server_stats.create_model_time_ms 29 _model_server_stats.query_time_ms 323 _model_server_stats.encode_time_ms 11 _model_server_stats.element_count 29 #