data_5NGU # _model_server_result.job_id oq7H5PmWPZmONpCo-KfEtg _model_server_result.datetime_utc '2025-08-31 00:24:44' _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 5ngu # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":403}' # _entry.id 5NGU # _exptl.entry_id 5NGU _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 403.48 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-[2-[[4-(4-methylpiperazin-1-yl)phenyl]amino]pyrimidin-4-yl]-1,5,6,7-tetrahydropyrrolo[3,2-c]pyridin-4-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 110.02 _cell.angle_gamma 90 _cell.entry_id 5NGU _cell.length_a 48.98 _cell.length_b 71.05 _cell.length_c 60.61 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5NGU _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _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,D,E _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 3 _struct_asym.id D _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 covale ? covale1 A C THR 179 A THR 160 1_555 A N CME 180 A CME 161 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale2 A C CME 180 A CME 161 1_555 A N ASP 181 A ASP 162 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? # _chem_comp.formula 'C22 H25 N7 O' _chem_comp.formula_weight 403.48 _chem_comp.id 8X2 _chem_comp.mon_nstd_flag . _chem_comp.name 2-[2-[[4-(4-methylpiperazin-1-yl)phenyl]amino]pyrimidin-4-yl]-1,5,6,7-tetrahydropyrrolo[3,2-c]pyridin-4-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 O C21 8X2 doub 1 n n C12 C13 8X2 doub 2 n y C12 N3 8X2 sing 3 n y C13 C14 8X2 sing 4 n y C16 C17 8X2 sing 5 n y C16 C15 8X2 doub 6 n y C21 C17 8X2 sing 7 n n C21 N6 8X2 sing 8 n n N3 C11 8X2 doub 9 n y C17 C18 8X2 doub 10 n y C14 C15 8X2 sing 11 n n C14 N4 8X2 doub 12 n y C15 N5 8X2 sing 13 n y N6 C20 8X2 sing 14 n n C11 N4 8X2 sing 15 n y C11 N2 8X2 sing 16 n n C18 N5 8X2 sing 17 n y C18 C19 8X2 sing 18 n n N2 C8 8X2 sing 19 n n C19 C20 8X2 sing 20 n n C8 C9 8X2 doub 21 n y C8 C7 8X2 sing 22 n y C9 C10 8X2 sing 23 n y C7 C6 8X2 doub 24 n y C10 C5 8X2 doub 25 n y C6 C5 8X2 sing 26 n y C5 N1 8X2 sing 27 n n C2 N1 8X2 sing 28 n n C2 C1 8X2 sing 29 n n C3 N1 8X2 sing 30 n n C3 C4 8X2 sing 31 n n N C1 8X2 sing 32 n n N C4 8X2 sing 33 n n N C 8X2 sing 34 n n C1 H1 8X2 sing 35 n n C1 H2 8X2 sing 36 n n C2 H3 8X2 sing 37 n n C2 H4 8X2 sing 38 n n C3 H5 8X2 sing 39 n n C3 H6 8X2 sing 40 n n N6 H7 8X2 sing 41 n n C7 H8 8X2 sing 42 n n C9 H9 8X2 sing 43 n n C10 H10 8X2 sing 44 n n C12 H11 8X2 sing 45 n n C13 H12 8X2 sing 46 n n C16 H13 8X2 sing 47 n n C19 H14 8X2 sing 48 n n C19 H15 8X2 sing 49 n n C20 H16 8X2 sing 50 n n C20 H17 8X2 sing 51 n n N5 H18 8X2 sing 52 n n N2 H19 8X2 sing 53 n n C6 H20 8X2 sing 54 n n C4 H21 8X2 sing 55 n n C4 H22 8X2 sing 56 n n C H24 8X2 sing 57 n n C H25 8X2 sing 58 n n C H26 8X2 sing 59 n n # _atom_sites.entry_id 5NGU _atom_sites.fract_transf_matrix[1][1] 0.020416 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.007439 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014075 _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] 0.01756 _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 SO4 A 1 401 1 SO4 SO4 . C 2 SO4 A 1 402 2 SO4 SO4 . D 3 8X2 A 1 403 1 8X2 INH . E 4 HOH A 1 501 2 HOH HOH . E 4 HOH A 2 502 13 HOH HOH . E 4 HOH A 3 503 14 HOH HOH . E 4 HOH A 4 504 3 HOH HOH . E 4 HOH A 5 505 6 HOH HOH . E 4 HOH A 6 506 11 HOH HOH . E 4 HOH A 7 507 12 HOH HOH . E 4 HOH A 8 508 10 HOH HOH . E 4 HOH A 9 509 7 HOH HOH . E 4 HOH A 10 510 5 HOH HOH . E 4 HOH A 11 511 8 HOH HOH . E 4 HOH A 12 512 4 HOH HOH . E 4 HOH A 13 513 9 HOH HOH . E 4 HOH A 14 514 1 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 8X2 . . . D 3 -19.403 19.656 45.888 1 57.02 ? C1 8X2 403 A 1 HETATM 2 C C2 8X2 . . . D 3 -19.574 18.402 45.023 1 55.98 ? C2 8X2 403 A 1 HETATM 3 C C3 8X2 . . . D 3 -17.236 17.885 45.32 1 55.04 ? C3 8X2 403 A 1 HETATM 4 N N6 8X2 . . . D 3 -9.857 13.765 41.32 1 49.88 ? N6 8X2 403 A 1 HETATM 5 C C7 8X2 . . . D 3 -17.79 14.025 43.794 1 52.49 ? C7 8X2 403 A 1 HETATM 6 C C8 8X2 . . . D 3 -18.911 13.779 43.004 1 51.84 ? C8 8X2 403 A 1 HETATM 7 C C9 8X2 . . . D 3 -19.954 14.702 43.014 1 51.51 ? C9 8X2 403 A 1 HETATM 8 C C10 8X2 . . . D 3 -19.857 15.855 43.801 1 52.05 ? C10 8X2 403 A 1 HETATM 9 C C11 8X2 . . . D 3 -17.917 12.045 41.392 1 51.75 ? C11 8X2 403 A 1 HETATM 10 C C12 8X2 . . . D 3 -17.224 10.446 39.804 1 52.1 ? C12 8X2 403 A 1 HETATM 11 C C13 8X2 . . . D 3 -15.926 10.933 39.857 1 52.33 ? C13 8X2 403 A 1 HETATM 12 C C14 8X2 . . . D 3 -15.65 12.001 40.707 1 51.71 ? C14 8X2 403 A 1 HETATM 13 C C15 8X2 . . . D 3 -14.247 12.501 40.774 1 50.82 ? C15 8X2 403 A 1 HETATM 14 C C16 8X2 . . . D 3 -13.088 12.037 40.175 1 51.24 ? C16 8X2 403 A 1 HETATM 15 C C19 8X2 . . . D 3 -11.93 14.936 42.193 1 50.23 ? C19 8X2 403 A 1 HETATM 16 C C20 8X2 . . . D 3 -10.462 14.528 42.416 1 49.95 ? C20 8X2 403 A 1 HETATM 17 C C21 8X2 . . . D 3 -10.655 12.966 40.438 1 50.03 ? C21 8X2 403 A 1 HETATM 18 O O 8X2 . . . D 3 -10.161 12.302 39.541 1 49.7 ? O 8X2 403 A 1 HETATM 19 C C17 8X2 . . . D 3 -12.124 12.895 40.647 1 50.77 ? C17 8X2 403 A 1 HETATM 20 C C18 8X2 . . . D 3 -12.699 13.835 41.489 1 50.21 ? C18 8X2 403 A 1 HETATM 21 N N5 8X2 . . . D 3 -14.016 13.571 41.557 1 49.9 ? N5 8X2 403 A 1 HETATM 22 N N3 8X2 . . . D 3 -18.184 11.002 40.566 1 51.97 ? N3 8X2 403 A 1 HETATM 23 N N4 8X2 . . . D 3 -16.648 12.54 41.461 1 51.65 ? N4 8X2 403 A 1 HETATM 24 N N2 8X2 . . . D 3 -19.008 12.586 42.186 1 51.91 ? N2 8X2 403 A 1 HETATM 25 C C6 8X2 . . . D 3 -17.718 15.182 44.566 1 52.97 ? C6 8X2 403 A 1 HETATM 26 C C5 8X2 . . . D 3 -18.735 16.156 44.607 1 53.37 ? C5 8X2 403 A 1 HETATM 27 N N1 8X2 . . . D 3 -18.61 17.359 45.429 1 54.85 ? N1 8X2 403 A 1 HETATM 28 C C4 8X2 . . . D 3 -17.064 19.105 46.225 1 56.04 ? C4 8X2 403 A 1 HETATM 29 N N 8X2 . . . D 3 -18.012 20.153 45.794 1 57.18 ? N 8X2 403 A 1 HETATM 30 C C 8X2 . . . D 3 -17.853 21.339 46.649 1 57.57 ? C 8X2 403 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 596 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 30 #