data_9IM5 # _model_server_result.job_id UANdk3Lsyful7DMa9LOLqQ _model_server_result.datetime_utc '2025-03-07 00:11:25' _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 9im5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"V","auth_seq_id":503}' # _entry.id 9IM5 # _exptl.entry_id 9IM5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 359.381 _entity.id 10 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description ~{N}4-(1,3-benzodioxol-5-ylmethyl)-6-(1~{H}-indol-4-yl)pyrimidine-2,4-diamine _entity.pdbx_number_of_molecules 2 _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 9IM5 _cell.length_a 107.35 _cell.length_b 160.78 _cell.length_c 184.54 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9IM5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall 'P 2ac 2ab' _symmetry.space_group_name_H-M 'P 21 21 21' # _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 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,X,Y 1 1 F,W 1 2 # 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' 3_545 -x,y-1/2,-z+1/2 -1 0 0 0 1 0 0 0 -1 0 -80.39 92.27 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 10 O N N ? 10 V N 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 metalc ? metalc1 A OD1 ASP 39 A ASP 39 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.394 ? metalc ? metalc2 A OD2 ASP 39 A ASP 39 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.458 ? metalc ? metalc3 A O THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.465 ? metalc ? metalc4 A OG1 THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.197 ? metalc ? metalc5 A O GLY 44 A GLY 44 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.628 ? metalc ? metalc6 A OE1 GLU 55 A GLU 55 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.844 ? metalc ? metalc7 A OE2 GLU 55 A GLU 55 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.653 ? metalc ? metalc8 G O1G GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.253 ? metalc ? metalc9 G O1B GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.476 ? metalc ? metalc10 B OE1 GLU 111 B GLU 111 1_555 L CA CA . B CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.005 ? metalc ? metalc11 B OE2 GLU 111 B GLU 111 1_555 L CA CA . B CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.594 ? metalc ? metalc12 K MG MG . B MG 501 1_555 P O1A GDP . B GDP 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.216 ? metalc ? metalc13 C OD1 ASP 39 C ASP 39 1_555 S CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.484 ? metalc ? metalc14 C OD2 ASP 39 C ASP 39 1_555 S CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.454 ? metalc ? metalc15 C O THR 41 C THR 41 1_555 S CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.327 ? metalc ? metalc16 C OG1 THR 41 C THR 41 1_555 S CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.45 ? metalc ? metalc17 C O GLY 44 C GLY 44 1_555 S CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.523 ? metalc ? metalc18 C OE1 GLU 55 C GLU 55 1_555 S CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.724 ? metalc ? metalc19 C OE2 GLU 55 C GLU 55 1_555 S CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.439 ? metalc ? metalc20 Q O1G GTP . C GTP 501 1_555 R MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.259 ? metalc ? metalc21 Q O1B GTP . C GTP 501 1_555 R MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.275 ? # _chem_comp.formula 'C20 H17 N5 O2' _chem_comp.formula_weight 359.381 _chem_comp.id A1L2T _chem_comp.mon_nstd_flag . _chem_comp.name ~{N}4-(1,3-benzodioxol-5-ylmethyl)-6-(1~{H}-indol-4-yl)pyrimidine-2,4-diamine _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 C21 C20 A1L2T doub 1 n y C21 C22 A1L2T sing 2 n y N23 C22 A1L2T sing 3 n y N23 C24 A1L2T sing 4 n y C20 C19 A1L2T sing 5 n y C22 C26 A1L2T doub 6 n y C24 C25 A1L2T doub 7 n y C19 C18 A1L2T doub 8 n y C26 C25 A1L2T sing 9 n y C26 C18 A1L2T sing 10 n y C18 C17 A1L2T sing 11 n n C17 C16 A1L2T doub 12 n y C17 N27 A1L2T sing 13 n y C16 C04 A1L2T sing 14 n y N27 C02 A1L2T doub 15 n y C04 N05 A1L2T sing 16 n n C04 N03 A1L2T doub 17 n y C02 N03 A1L2T sing 18 n y C02 N01 A1L2T sing 19 n n N05 C06 A1L2T sing 20 n n C06 C07 A1L2T sing 21 n n C07 C08 A1L2T doub 22 n y C07 C12 A1L2T sing 23 n y C08 C09 A1L2T sing 24 n y C12 C11 A1L2T doub 25 n y C09 C10 A1L2T doub 26 n y C11 C10 A1L2T sing 27 n y C11 O13 A1L2T sing 28 n n C10 O15 A1L2T sing 29 n n O13 C14 A1L2T sing 30 n n O15 C14 A1L2T sing 31 n n C20 H201 A1L2T sing 32 n n C21 H211 A1L2T sing 33 n n C24 H241 A1L2T sing 34 n n C06 H062 A1L2T sing 35 n n C06 H061 A1L2T sing 36 n n C08 H081 A1L2T sing 37 n n C09 H091 A1L2T sing 38 n n C12 H121 A1L2T sing 39 n n C14 H142 A1L2T sing 40 n n C14 H141 A1L2T sing 41 n n C16 H161 A1L2T sing 42 n n C19 H191 A1L2T sing 43 n n C25 H251 A1L2T sing 44 n n N01 H011 A1L2T sing 45 n n N01 H012 A1L2T sing 46 n n N05 H051 A1L2T sing 47 n n N23 H231 A1L2T sing 48 n n # _atom_sites.entry_id 9IM5 _atom_sites.fract_transf_matrix[1][1] 0.009315 _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] 0.00622 _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] 0.005419 _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 G 5 GTP A 1 501 501 GTP GTP . H 6 MG A 1 502 502 MG MG . I 7 CA A 1 503 503 CA CA . J 8 CL A 1 504 504 CL CL . K 6 MG B 1 501 502 MG MG . L 7 CA B 1 502 503 CA CA . M 9 MES B 1 503 504 MES MES . N 9 MES B 1 504 505 MES MES . O 10 A1L2T B 1 505 601 A1L2T LIG . P 11 GDP B 1 506 501 GDP GDP . Q 5 GTP C 1 501 501 GTP GTP . R 6 MG C 1 502 502 MG MG . S 7 CA C 1 503 503 CA CA . T 5 GTP D 1 501 501 GTP GTP . U 6 MG D 1 502 502 MG MG . V 10 A1L2T D 1 503 601 A1L2T LIG . W 12 ACP F 1 401 401 ACP ACP . X 13 HOH A 1 601 2 HOH HOH . Y 13 HOH B 1 601 4 HOH HOH . Y 13 HOH B 2 602 1 HOH HOH . Y 13 HOH B 3 603 5 HOH HOH . Y 13 HOH B 4 604 6 HOH HOH . Y 13 HOH B 5 605 3 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 A1L2T . . . V 10 13.124 9.377 -21.573 1 58.93 ? C10 A1L2T 503 D 1 HETATM 2 C C17 A1L2T . . . V 10 17.15 5.567 -27.236 1 40.67 ? C17 A1L2T 503 D 1 HETATM 3 C C20 A1L2T . . . V 10 19.286 4.613 -30.208 1 43.04 ? C20 A1L2T 503 D 1 HETATM 4 C C21 A1L2T . . . V 10 19.051 5.597 -31.134 1 47.01 ? C21 A1L2T 503 D 1 HETATM 5 C C22 A1L2T . . . V 10 18.151 6.613 -30.771 1 38.3 ? C22 A1L2T 503 D 1 HETATM 6 C C24 A1L2T . . . V 10 16.831 8.429 -30.732 1 34.17 ? C24 A1L2T 503 D 1 HETATM 7 C C26 A1L2T . . . V 10 17.509 6.629 -29.51 1 38.67 ? C26 A1L2T 503 D 1 HETATM 8 C C02 A1L2T . . . V 10 17.429 5.145 -24.98 1 41.23 ? C02 A1L2T 503 D 1 HETATM 9 C C04 A1L2T . . . V 10 15.344 5.844 -25.673 1 43.23 ? C04 A1L2T 503 D 1 HETATM 10 C C06 A1L2T . . . V 10 13.411 5.95 -24.113 1 39.41 ? C06 A1L2T 503 D 1 HETATM 11 C C07 A1L2T . . . V 10 13.313 7.137 -23.223 1 46.92 ? C07 A1L2T 503 D 1 HETATM 12 C C08 A1L2T . . . V 10 12.386 8.161 -23.458 1 46.37 ? C08 A1L2T 503 D 1 HETATM 13 C C09 A1L2T . . . V 10 12.266 9.3 -22.644 1 51.06 ? C09 A1L2T 503 D 1 HETATM 14 C C11 A1L2T . . . V 10 14.077 8.354 -21.323 1 52.83 ? C11 A1L2T 503 D 1 HETATM 15 C C12 A1L2T . . . V 10 14.186 7.249 -22.124 1 43.19 ? C12 A1L2T 503 D 1 HETATM 16 C C14 A1L2T . . . V 10 14.214 9.879 -19.683 1 57.78 ? C14 A1L2T 503 D 1 HETATM 17 C C16 A1L2T . . . V 10 15.837 5.909 -26.995 1 39.68 ? C16 A1L2T 503 D 1 HETATM 18 C C18 A1L2T . . . V 10 17.762 5.613 -28.584 1 42.84 ? C18 A1L2T 503 D 1 HETATM 19 C C19 A1L2T . . . V 10 18.65 4.618 -28.949 1 44.11 ? C19 A1L2T 503 D 1 HETATM 20 C C25 A1L2T . . . V 10 16.676 7.801 -29.516 1 35.46 ? C25 A1L2T 503 D 1 HETATM 21 N N01 A1L2T . . . V 10 18.261 4.748 -23.947 1 40.21 ? N01 A1L2T 503 D 1 HETATM 22 N N03 A1L2T . . . V 10 16.143 5.455 -24.627 1 41.41 ? N03 A1L2T 503 D 1 HETATM 23 N N05 A1L2T . . . V 10 14.045 6.156 -25.392 1 45.41 ? N05 A1L2T 503 D 1 HETATM 24 N N23 A1L2T . . . V 10 17.733 7.712 -31.49 1 33.67 ? N23 A1L2T 503 D 1 HETATM 25 N N27 A1L2T . . . V 10 18 5.182 -26.243 1 40.65 ? N27 A1L2T 503 D 1 HETATM 26 O O13 A1L2T . . . V 10 14.798 8.69 -20.204 1 51.06 ? O13 A1L2T 503 D 1 HETATM 27 O O15 A1L2T . . . V 10 13.237 10.351 -20.623 1 60.31 ? O15 A1L2T 503 D 1 HETATM 28 H H201 A1L2T . . . V 10 19.982 3.807 -30.45 1 51.65 ? H201 A1L2T 503 D 1 HETATM 29 H H211 A1L2T . . . V 10 19.533 5.604 -32.115 1 56.41 ? H211 A1L2T 503 D 1 HETATM 30 H H241 A1L2T . . . V 10 16.358 9.331 -31.098 1 41 ? H241 A1L2T 503 D 1 HETATM 31 H H062 A1L2T . . . V 10 13.948 5.141 -23.558 1 47.29 ? H062 A1L2T 503 D 1 HETATM 32 H H061 A1L2T . . . V 10 12.381 5.545 -24.27 1 47.29 ? H061 A1L2T 503 D 1 HETATM 33 H H081 A1L2T . . . V 10 11.702 8.112 -24.307 1 55.64 ? H081 A1L2T 503 D 1 HETATM 34 H H091 A1L2T . . . V 10 11.54 10.092 -22.832 1 61.27 ? H091 A1L2T 503 D 1 HETATM 35 H H121 A1L2T . . . V 10 14.935 6.493 -21.897 1 51.83 ? H121 A1L2T 503 D 1 HETATM 36 H H142 A1L2T . . . V 10 14.987 10.659 -19.522 1 69.33 ? H142 A1L2T 503 D 1 HETATM 37 H H141 A1L2T . . . V 10 13.728 9.683 -18.705 1 69.33 ? H141 A1L2T 503 D 1 HETATM 38 H H161 A1L2T . . . V 10 15.223 6.218 -27.835 1 47.62 ? H161 A1L2T 503 D 1 HETATM 39 H H191 A1L2T . . . V 10 18.886 3.801 -28.27 1 52.94 ? H191 A1L2T 503 D 1 HETATM 40 H H251 A1L2T . . . V 10 16.048 8.118 -28.703 1 42.55 ? H251 A1L2T 503 D 1 HETATM 41 H H011 A1L2T . . . V 10 18.708 3.859 -23.952 1 48.26 ? H011 A1L2T 503 D 1 HETATM 42 H H012 A1L2T . . . V 10 18.425 5.351 -23.165 1 48.26 ? H012 A1L2T 503 D 1 HETATM 43 H H051 A1L2T . . . V 10 13.5 6.557 -26.139 1 54.49 ? H051 A1L2T 503 D 1 HETATM 44 H H231 A1L2T . . . V 10 18.039 7.956 -32.427 1 40.4 ? H231 A1L2T 503 D 1 # _model_server_stats.io_time_ms 27 _model_server_stats.parse_time_ms 25 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 321 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 44 #