data_5HE3 # _model_server_result.job_id MZ5FzlydQQTtBtweWipGVg _model_server_result.datetime_utc '2025-07-03 14:08:59' _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 5he3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":702}' # _entry.id 5HE3 # _exptl.entry_id 5HE3 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 540.588 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (4~{S})-4-[3-[2-(2,6-dimethylphenyl)ethylcarbamoyl]-4-fluoranyl-phenyl]-~{N}-(1~{H}-indazol-5-yl)-6-methyl-2-oxidanylidene-3,4-dihydro-1~{H}-pyrimidine-5-carboxamide _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 5HE3 _cell.length_a 60.031 _cell.length_b 239.412 _cell.length_c 208.625 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5HE3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 2 2 21' # _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 _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 5 _struct_asym.id E _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 metalc ? metalc1 A O HIS 319 A HIS 348 1_555 D MG MG . A MG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.29 ? metalc ? metalc2 A O GLU 331 A GLU 360 1_555 D MG MG . A MG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.939 ? metalc ? metalc3 A O VAL 332 A VAL 361 1_555 D MG MG . A MG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.35 ? metalc ? metalc4 A O GLN 334 A GLN 363 1_555 D MG MG . A MG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.56 ? metalc ? metalc5 A O VAL 337 A VAL 366 1_555 D MG MG . A MG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.849 ? # _chem_comp.formula 'C30 H29 F N6 O3' _chem_comp.formula_weight 540.588 _chem_comp.id FF1 _chem_comp.mon_nstd_flag . _chem_comp.name (4~{S})-4-[3-[2-(2,6-dimethylphenyl)ethylcarbamoyl]-4-fluoranyl-phenyl]-~{N}-(1~{H}-indazol-5-yl)-6-methyl-2-oxidanylidene-3,4-dihydro-1~{H}-pyrimidine-5-carboxamide _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 C15 C14 FF1 doub 83 n y C15 C16 FF1 sing 84 n y C14 C13 FF1 sing 85 n y C C1 FF1 sing 86 n n F C16 FF1 sing 87 n n C2 C1 FF1 doub 88 n y C2 C3 FF1 sing 89 n y C16 C11 FF1 doub 90 n y C27 N5 FF1 doub 91 n y C27 C28 FF1 sing 92 n y O2 C22 FF1 doub 93 n n C13 C17 FF1 sing 94 n n C13 C12 FF1 doub 95 n y N5 N4 FF1 sing 96 n y C1 C7 FF1 sing 97 n y C17 N1 FF1 sing 98 n n C17 C21 FF1 sing 99 n n C3 C4 FF1 doub 100 n y C29 C28 FF1 sing 101 n y C29 C23 FF1 doub 102 n y C28 C26 FF1 doub 103 n y C11 C12 FF1 sing 104 n y C11 C10 FF1 sing 105 n n C22 C21 FF1 sing 106 n n C22 N3 FF1 sing 107 n n N1 C18 FF1 sing 108 n n N4 C26 FF1 sing 109 n y C21 C19 FF1 doub 110 n n C7 C8 FF1 sing 111 n n C7 C5 FF1 doub 112 n y C23 N3 FF1 sing 113 n n C23 C24 FF1 sing 114 n y C26 C25 FF1 sing 115 n y C10 N FF1 sing 116 n n C10 O FF1 doub 117 n n C4 C5 FF1 sing 118 n y N C9 FF1 sing 119 n n C8 C9 FF1 sing 120 n n C5 C6 FF1 sing 121 n n C18 O1 FF1 doub 122 n n C18 N2 FF1 sing 123 n n C25 C24 FF1 doub 124 n y C19 N2 FF1 sing 125 n n C19 C20 FF1 sing 126 n n N3 H1 FF1 sing 127 n n C29 H2 FF1 sing 128 n n C27 H3 FF1 sing 129 n n C25 H5 FF1 sing 130 n n C24 H6 FF1 sing 131 n n C20 H7 FF1 sing 132 n n C20 H8 FF1 sing 133 n n C20 H9 FF1 sing 134 n n N2 H10 FF1 sing 135 n n N1 H11 FF1 sing 136 n n C17 H12 FF1 sing 137 n n C12 H13 FF1 sing 138 n n C14 H14 FF1 sing 139 n n C15 H15 FF1 sing 140 n n N H16 FF1 sing 141 n n C9 H17 FF1 sing 142 n n C9 H18 FF1 sing 143 n n C8 H19 FF1 sing 144 n n C8 H20 FF1 sing 145 n n C H21 FF1 sing 146 n n C H22 FF1 sing 147 n n C H23 FF1 sing 148 n n C6 H24 FF1 sing 149 n n C6 H25 FF1 sing 150 n n C6 H26 FF1 sing 151 n n C4 H27 FF1 sing 152 n n C3 H28 FF1 sing 153 n n C2 H29 FF1 sing 154 n n N4 H4 FF1 sing 155 n n # _atom_sites.entry_id 5HE3 _atom_sites.fract_transf_matrix[1][1] 0.016658 _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] 0.004177 _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] 0.004793 _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 D 4 MG A 1 701 1 MG MG . E 5 FF1 A 1 702 1 FF1 FF1 . F 6 HOH A 1 801 58 HOH HOH . F 6 HOH A 2 802 20 HOH HOH . F 6 HOH A 3 803 3 HOH HOH . F 6 HOH A 4 804 22 HOH HOH . F 6 HOH A 5 805 53 HOH HOH . F 6 HOH A 6 806 42 HOH HOH . F 6 HOH A 7 807 62 HOH HOH . F 6 HOH A 8 808 49 HOH HOH . F 6 HOH A 9 809 10 HOH HOH . F 6 HOH A 10 810 56 HOH HOH . F 6 HOH A 11 811 4 HOH HOH . F 6 HOH A 12 812 60 HOH HOH . F 6 HOH A 13 813 12 HOH HOH . F 6 HOH A 14 814 26 HOH HOH . F 6 HOH A 15 815 59 HOH HOH . F 6 HOH A 16 816 33 HOH HOH . F 6 HOH A 17 817 61 HOH HOH . G 6 HOH B 1 401 5 HOH HOH . G 6 HOH B 2 402 47 HOH HOH . G 6 HOH B 3 403 7 HOH HOH . G 6 HOH B 4 404 54 HOH HOH . G 6 HOH B 5 405 18 HOH HOH . G 6 HOH B 6 406 70 HOH HOH . G 6 HOH B 7 407 1 HOH HOH . G 6 HOH B 8 408 46 HOH HOH . G 6 HOH B 9 409 48 HOH HOH . G 6 HOH B 10 410 17 HOH HOH . G 6 HOH B 11 411 9 HOH HOH . G 6 HOH B 12 412 69 HOH HOH . G 6 HOH B 13 413 15 HOH HOH . G 6 HOH B 14 414 65 HOH HOH . G 6 HOH B 15 415 30 HOH HOH . G 6 HOH B 16 416 38 HOH HOH . G 6 HOH B 17 417 68 HOH HOH . G 6 HOH B 18 418 67 HOH HOH . G 6 HOH B 19 419 66 HOH HOH . G 6 HOH B 20 420 64 HOH HOH . H 6 HOH G 1 101 55 HOH HOH . H 6 HOH G 2 102 44 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 O O2 FF1 . . . E 5 -19.99 28.387 15.565 1 100.32 ? O2 FF1 702 A 1 HETATM 2 C C22 FF1 . . . E 5 -19.373 27.819 16.464 1 102.39 ? C22 FF1 702 A 1 HETATM 3 N N3 FF1 . . . E 5 -19.724 26.689 17.098 1 91.68 ? N3 FF1 702 A 1 HETATM 4 C C23 FF1 . . . E 5 -20.963 26.114 17.085 1 78.51 ? C23 FF1 702 A 1 HETATM 5 C C29 FF1 . . . E 5 -22.042 26.518 16.279 1 73.71 ? C29 FF1 702 A 1 HETATM 6 C C28 FF1 . . . E 5 -23.27 25.849 16.347 1 67.86 ? C28 FF1 702 A 1 HETATM 7 C C27 FF1 . . . E 5 -24.473 26.086 15.616 1 63.65 ? C27 FF1 702 A 1 HETATM 8 N N5 FF1 . . . E 5 -25.388 25.187 16.024 1 62.63 ? N5 FF1 702 A 1 HETATM 9 N N4 FF1 . . . E 5 -24.714 24.415 17.004 1 64.52 ? N4 FF1 702 A 1 HETATM 10 C C26 FF1 . . . E 5 -23.445 24.801 17.212 1 66.31 ? C26 FF1 702 A 1 HETATM 11 C C25 FF1 . . . E 5 -22.399 24.4 18.032 1 73.04 ? C25 FF1 702 A 1 HETATM 12 C C24 FF1 . . . E 5 -21.168 25.058 17.977 1 76.66 ? C24 FF1 702 A 1 HETATM 13 C C21 FF1 . . . E 5 -18.197 28.571 16.993 1 114.65 ? C21 FF1 702 A 1 HETATM 14 C C19 FF1 . . . E 5 -18.171 28.993 18.437 1 110.27 ? C19 FF1 702 A 1 HETATM 15 C C20 FF1 . . . E 5 -19.269 28.703 19.444 1 97.21 ? C20 FF1 702 A 1 HETATM 16 N N2 FF1 . . . E 5 -17.149 29.756 18.835 1 120.22 ? N2 FF1 702 A 1 HETATM 17 C C18 FF1 . . . E 5 -16.426 30.448 17.924 1 122.28 ? C18 FF1 702 A 1 HETATM 18 O O1 FF1 . . . E 5 -15.777 31.443 18.32 1 119.67 ? O1 FF1 702 A 1 HETATM 19 N N1 FF1 . . . E 5 -16.415 30.148 16.604 1 121.36 ? N1 FF1 702 A 1 HETATM 20 C C17 FF1 . . . E 5 -17.07 28.931 16.093 1 120.96 ? C17 FF1 702 A 1 HETATM 21 C C13 FF1 . . . E 5 -16.052 27.815 15.981 1 122.93 ? C13 FF1 702 A 1 HETATM 22 C C12 FF1 . . . E 5 -14.874 27.757 16.768 1 129.95 ? C12 FF1 702 A 1 HETATM 23 C C14 FF1 . . . E 5 -16.248 26.8 15.043 1 114.54 ? C14 FF1 702 A 1 HETATM 24 C C15 FF1 . . . E 5 -15.312 25.768 14.898 1 115.27 ? C15 FF1 702 A 1 HETATM 25 C C16 FF1 . . . E 5 -14.16 25.722 15.687 1 116.45 ? C16 FF1 702 A 1 HETATM 26 F F FF1 . . . E 5 -13.259 24.734 15.54 1 103.34 ? F FF1 702 A 1 HETATM 27 C C11 FF1 . . . E 5 -13.932 26.715 16.631 1 127.6 ? C11 FF1 702 A 1 HETATM 28 C C10 FF1 . . . E 5 -12.659 26.658 17.457 1 133.83 ? C10 FF1 702 A 1 HETATM 29 O O FF1 . . . E 5 -12.355 25.582 17.96 1 123.48 ? O FF1 702 A 1 HETATM 30 N N FF1 . . . E 5 -11.884 27.768 17.553 1 148.47 ? N FF1 702 A 1 HETATM 31 C C9 FF1 . . . E 5 -10.56 27.836 18.197 1 158.4 ? C9 FF1 702 A 1 HETATM 32 C C8 FF1 . . . E 5 -9.896 29.235 18.203 1 162.86 ? C8 FF1 702 A 1 HETATM 33 C C7 FF1 . . . E 5 -8.462 29.275 17.635 1 168.88 ? C7 FF1 702 A 1 HETATM 34 C C1 FF1 . . . E 5 -8.183 29.741 16.324 1 163.64 ? C1 FF1 702 A 1 HETATM 35 C C FF1 . . . E 5 -9.265 30.224 15.379 1 155.28 ? C FF1 702 A 1 HETATM 36 C C5 FF1 . . . E 5 -7.38 28.857 18.437 1 165.72 ? C5 FF1 702 A 1 HETATM 37 C C6 FF1 . . . E 5 -7.599 28.353 19.851 1 155.08 ? C6 FF1 702 A 1 HETATM 38 C C4 FF1 . . . E 5 -6.067 28.894 17.931 1 162.22 ? C4 FF1 702 A 1 HETATM 39 C C3 FF1 . . . E 5 -5.807 29.349 16.637 1 156.43 ? C3 FF1 702 A 1 HETATM 40 C C2 FF1 . . . E 5 -6.865 29.773 15.838 1 158 ? C2 FF1 702 A 1 # _model_server_stats.io_time_ms 23 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 311 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 40 #