data_5EA3 # _model_server_result.job_id 5rpUejKna5EqxCaX0VI3AQ _model_server_result.datetime_utc '2024-10-18 02:20:54' _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 5ea3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":608}' # _entry.id 5EA3 # _exptl.entry_id 5EA3 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 394.513 _entity.id 4 _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 5EA3 _cell.length_a 170.11 _cell.length_b 170.11 _cell.length_c 170.11 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5EA3 _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,G,H,I,J _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 4 _struct_asym.id I _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 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf3 A SG CYS 313 F CYS 313 1_555 A SG CYS 343 F CYS 343 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf4 A SG CYS 322 F CYS 322 1_555 A SG CYS 333 F CYS 333 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf5 A SG CYS 358 F CYS 358 1_555 A SG CYS 367 F CYS 367 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? disulf ? disulf6 A SG CYS 382 F CYS 382 1_555 A SG CYS 393 F CYS 393 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf7 A SG CYS 416 F CYS 416 1_555 A SG CYS 422 F CYS 422 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? # _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 5EA3 _atom_sites.fract_transf_matrix[1][1] 0.005879 _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] 0.005879 _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] 0.005879 _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 3 SO4 F 1 604 3 SO4 SO4 . F 3 SO4 F 1 605 4 SO4 SO4 . G 3 SO4 F 1 606 5 SO4 SO4 . H 3 SO4 F 1 607 6 SO4 SO4 . I 4 5NK F 1 608 1 5NK LIG . J 5 HOH F 1 701 10 HOH HOH . J 5 HOH F 2 702 15 HOH HOH . J 5 HOH F 3 703 21 HOH HOH . J 5 HOH F 4 704 1 HOH HOH . J 5 HOH F 5 705 20 HOH HOH . J 5 HOH F 6 706 17 HOH HOH . J 5 HOH F 7 707 6 HOH HOH . J 5 HOH F 8 708 25 HOH HOH . J 5 HOH F 9 709 32 HOH HOH . J 5 HOH F 10 710 27 HOH HOH . J 5 HOH F 11 711 19 HOH HOH . J 5 HOH F 12 712 26 HOH HOH . J 5 HOH F 13 713 2 HOH HOH . J 5 HOH F 14 714 28 HOH HOH . J 5 HOH F 15 715 9 HOH HOH . J 5 HOH F 16 716 24 HOH HOH . J 5 HOH F 17 717 23 HOH HOH . J 5 HOH F 18 718 11 HOH HOH . J 5 HOH F 19 719 14 HOH HOH . J 5 HOH F 20 720 13 HOH HOH . J 5 HOH F 21 721 12 HOH HOH . J 5 HOH F 22 722 5 HOH HOH . J 5 HOH F 23 723 16 HOH HOH . J 5 HOH F 24 724 33 HOH HOH . J 5 HOH F 25 725 3 HOH HOH . J 5 HOH F 26 726 7 HOH HOH . J 5 HOH F 27 727 8 HOH HOH . J 5 HOH F 28 728 36 HOH HOH . J 5 HOH F 29 729 18 HOH HOH . J 5 HOH F 30 730 22 HOH HOH . J 5 HOH F 31 731 4 HOH HOH . J 5 HOH F 32 732 31 HOH HOH . J 5 HOH F 33 733 30 HOH HOH . J 5 HOH F 34 734 29 HOH HOH . J 5 HOH F 35 735 34 HOH HOH . J 5 HOH F 36 736 35 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 5NK . . . I 4 23.738 16.92 23.869 0.33 44.98 ? C10 5NK 608 F 1 HETATM 2 C C15 5NK . . . I 4 16.094 21.366 22.018 0.33 35.79 ? C15 5NK 608 F 1 HETATM 3 C C17 5NK . . . I 4 18.462 22.28 22.034 0.33 35.95 ? C17 5NK 608 F 1 HETATM 4 C C20 5NK . . . I 4 24.482 22.656 22.928 0.33 36.49 ? C20 5NK 608 F 1 HETATM 5 C C21 5NK . . . I 4 24.406 22.795 24.437 0.33 38.43 ? C21 5NK 608 F 1 HETATM 6 C C24 5NK . . . I 4 23.065 24.596 22.656 0.33 37.13 ? C24 5NK 608 F 1 HETATM 7 C C26 5NK . . . I 4 25.79 25.665 25.968 0.33 39.39 ? C26 5NK 608 F 1 HETATM 8 C C28 5NK . . . I 4 15.506 19.244 20.527 0.33 35.56 ? C28 5NK 608 F 1 HETATM 9 C C01 5NK . . . I 4 22.743 17.239 22.721 0.33 35.46 ? C01 5NK 608 F 1 HETATM 10 C C02 5NK . . . I 4 22.19 16.133 21.845 0.33 35.65 ? C02 5NK 608 F 1 HETATM 11 C C03 5NK . . . I 4 21.237 16.461 20.748 0.33 35.6 ? C03 5NK 608 F 1 HETATM 12 C C04 5NK . . . I 4 20.837 17.894 20.52 0.33 36.08 ? C04 5NK 608 F 1 HETATM 13 C C05 5NK . . . I 4 22.319 18.723 22.471 0.33 35.35 ? C05 5NK 608 F 1 HETATM 14 C C06 5NK . . . I 4 21.426 19.031 21.439 0.33 36.24 ? C06 5NK 608 F 1 HETATM 15 N N07 5NK . . . I 4 21.224 20.396 21.451 0.33 36.77 ? N07 5NK 608 F 1 HETATM 16 C C08 5NK . . . I 4 21.998 20.947 22.486 0.33 36.43 ? C08 5NK 608 F 1 HETATM 17 N N09 5NK . . . I 4 22.67 19.902 23.111 0.33 35.21 ? N09 5NK 608 F 1 HETATM 18 C C11 5NK . . . I 4 20.367 21.12 20.53 0.33 38.03 ? C11 5NK 608 F 1 HETATM 19 C C12 5NK . . . I 4 18.893 21.184 21.042 0.33 35.83 ? C12 5NK 608 F 1 HETATM 20 N N13 5NK . . . I 4 17.921 20.217 20.565 0.33 36.08 ? N13 5NK 608 F 1 HETATM 21 C C14 5NK . . . I 4 16.526 20.274 21.031 0.33 35.49 ? C14 5NK 608 F 1 HETATM 22 C C16 5NK . . . I 4 17.07 22.347 22.498 0.33 35.33 ? C16 5NK 608 F 1 HETATM 23 N N18 5NK . . . I 4 22.088 22.367 22.847 0.33 34.57 ? N18 5NK 608 F 1 HETATM 24 C C19 5NK . . . I 4 23.243 23.176 22.324 0.33 36.98 ? C19 5NK 608 F 1 HETATM 25 N N22 5NK . . . I 4 24.265 24.183 24.864 0.33 37.69 ? N22 5NK 608 F 1 HETATM 26 C C23 5NK . . . I 4 23.182 24.897 24.137 0.33 39.14 ? C23 5NK 608 F 1 HETATM 27 C C25 5NK . . . I 4 25.467 24.855 24.692 0.33 40.56 ? C25 5NK 608 F 1 HETATM 28 N N27 5NK . . . I 4 25.714 24.817 27.134 0.33 39.02 ? N27 5NK 608 F 1 HETATM 29 O O29 5NK . . . I 4 19.391 23.216 22.484 0.33 35.29 ? O29 5NK 608 F 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 21 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 318 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 29 #