data_5P9J # _model_server_result.job_id ySzWGUQoB3KtbOV8TOXKVw _model_server_result.datetime_utc '2024-11-27 00:28:48' _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 5p9j # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":701}' # _entry.id 5P9J # _exptl.entry_id 5P9J _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 442.513 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1-[(3~{R})-3-[4-azanyl-3-(4-phenoxyphenyl)pyrazolo[3,4-d]pyrimidin-1-yl]piperidin-1-yl]propan-1-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 90 _cell.angle_gamma 90 _cell.entry_id 5P9J _cell.length_a 72.25 _cell.length_b 104.61 _cell.length_c 38.1 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5P9J _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _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 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _struct_conn.conn_type_id covale _struct_conn.details ? _struct_conn.id covale1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id SG _struct_conn.ptnr1_label_comp_id CYS _struct_conn.ptnr1_label_seq_id 101 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id CYS _struct_conn.ptnr1_auth_seq_id 481 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id B _struct_conn.ptnr2_label_atom_id CAA _struct_conn.ptnr2_label_comp_id 8E8 _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id 8E8 _struct_conn.ptnr2_auth_seq_id 701 _struct_conn.ptnr2_symmetry 1_555 _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 1.85 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C25 H26 N6 O2' _chem_comp.formula_weight 442.513 _chem_comp.id 8E8 _chem_comp.mon_nstd_flag . _chem_comp.name 1-[(3~{R})-3-[4-azanyl-3-(4-phenoxyphenyl)pyrazolo[3,4-d]pyrimidin-1-yl]piperidin-1-yl]propan-1-one _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'Ibrutinib (bound form)' # 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 OAC CAW 8E8 doub 1 n n CAD CAW 8E8 sing 2 n n CAD CAA 8E8 sing 3 n n CAW NBG 8E8 sing 4 n n C2 N3 8E8 doub 5 n y C2 N1 8E8 sing 6 n y N3 C4 8E8 sing 7 n y N1 C6 8E8 doub 8 n y NBG CAR 8E8 sing 9 n n NBG CAQ 8E8 sing 10 n n CAR CBE 8E8 sing 11 n n C4 NBF 8E8 sing 12 n y C4 C5 8E8 doub 13 n y CBE NBF 8E8 sing 14 n n CBE CAP 8E8 sing 15 n n C6 C5 8E8 sing 16 n y C6 NAB 8E8 sing 17 n n CAQ CAO 8E8 sing 18 n n CAO CAP 8E8 sing 19 n n NBF NAU 8E8 sing 20 n y C5 CBB 8E8 sing 21 n y NAU CBB 8E8 doub 22 n y CBB CBA 8E8 sing 23 n n CBA CAM 8E8 doub 24 n y CBA CAN 8E8 sing 25 n y CAM CAK 8E8 sing 26 n y CAN CAL 8E8 doub 27 n y CAK CAZ 8E8 doub 28 n y CAL CAZ 8E8 sing 29 n y CAZ OAV 8E8 sing 30 n n CAI CAF 8E8 doub 31 n y CAI CAY 8E8 sing 32 n y OAV CAY 8E8 sing 33 n n CAF CAE 8E8 sing 34 n y CAY CAJ 8E8 doub 35 n y CAE CAG 8E8 doub 36 n y CAJ CAG 8E8 sing 37 n y C2 H1 8E8 sing 38 n n CAA H2 8E8 sing 39 n n CAA H3 8E8 sing 40 n n CAA H4 8E8 sing 41 n n NAB H5 8E8 sing 42 n n NAB H6 8E8 sing 43 n n CAD H7 8E8 sing 44 n n CAD H8 8E8 sing 45 n n CAE H9 8E8 sing 46 n n CAF H10 8E8 sing 47 n n CAG H11 8E8 sing 48 n n CAI H12 8E8 sing 49 n n CAJ H13 8E8 sing 50 n n CAK H14 8E8 sing 51 n n CAL H15 8E8 sing 52 n n CAM H16 8E8 sing 53 n n CAN H17 8E8 sing 54 n n CAO H18 8E8 sing 55 n n CAO H19 8E8 sing 56 n n CAP H20 8E8 sing 57 n n CAP H21 8E8 sing 58 n n CAQ H22 8E8 sing 59 n n CAQ H23 8E8 sing 60 n n CAR H24 8E8 sing 61 n n CAR H25 8E8 sing 62 n n CBE H26 8E8 sing 63 n n # _atom_sites.entry_id 5P9J _atom_sites.fract_transf_matrix[1][1] 0.013841 _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] 0.009559 _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] 0.026247 _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 8E8 A 1 701 0 8E8 INH . C 3 HOH A 1 801 168 HOH HOH . C 3 HOH A 2 802 173 HOH HOH . C 3 HOH A 3 803 160 HOH HOH . C 3 HOH A 4 804 144 HOH HOH . C 3 HOH A 5 805 163 HOH HOH . C 3 HOH A 6 806 132 HOH HOH . C 3 HOH A 7 807 103 HOH HOH . C 3 HOH A 8 808 82 HOH HOH . C 3 HOH A 9 809 50 HOH HOH . C 3 HOH A 10 810 60 HOH HOH . C 3 HOH A 11 811 110 HOH HOH . C 3 HOH A 12 812 171 HOH HOH . C 3 HOH A 13 813 98 HOH HOH . C 3 HOH A 14 814 108 HOH HOH . C 3 HOH A 15 815 26 HOH HOH . C 3 HOH A 16 816 70 HOH HOH . C 3 HOH A 17 817 140 HOH HOH . C 3 HOH A 18 818 174 HOH HOH . C 3 HOH A 19 819 88 HOH HOH . C 3 HOH A 20 820 6 HOH HOH . C 3 HOH A 21 821 117 HOH HOH . C 3 HOH A 22 822 29 HOH HOH . C 3 HOH A 23 823 25 HOH HOH . C 3 HOH A 24 824 69 HOH HOH . C 3 HOH A 25 825 28 HOH HOH . C 3 HOH A 26 826 91 HOH HOH . C 3 HOH A 27 827 65 HOH HOH . C 3 HOH A 28 828 156 HOH HOH . C 3 HOH A 29 829 97 HOH HOH . C 3 HOH A 30 830 114 HOH HOH . C 3 HOH A 31 831 116 HOH HOH . C 3 HOH A 32 832 102 HOH HOH . C 3 HOH A 33 833 151 HOH HOH . C 3 HOH A 34 834 96 HOH HOH . C 3 HOH A 35 835 58 HOH HOH . C 3 HOH A 36 836 9 HOH HOH . C 3 HOH A 37 837 4 HOH HOH . C 3 HOH A 38 838 130 HOH HOH . C 3 HOH A 39 839 3 HOH HOH . C 3 HOH A 40 840 30 HOH HOH . C 3 HOH A 41 841 2 HOH HOH . C 3 HOH A 42 842 68 HOH HOH . C 3 HOH A 43 843 67 HOH HOH . C 3 HOH A 44 844 86 HOH HOH . C 3 HOH A 45 845 170 HOH HOH . C 3 HOH A 46 846 7 HOH HOH . C 3 HOH A 47 847 48 HOH HOH . C 3 HOH A 48 848 74 HOH HOH . C 3 HOH A 49 849 172 HOH HOH . C 3 HOH A 50 850 15 HOH HOH . C 3 HOH A 51 851 124 HOH HOH . C 3 HOH A 52 852 8 HOH HOH . C 3 HOH A 53 853 49 HOH HOH . C 3 HOH A 54 854 33 HOH HOH . C 3 HOH A 55 855 64 HOH HOH . C 3 HOH A 56 856 23 HOH HOH . C 3 HOH A 57 857 122 HOH HOH . C 3 HOH A 58 858 5 HOH HOH . C 3 HOH A 59 859 21 HOH HOH . C 3 HOH A 60 860 138 HOH HOH . C 3 HOH A 61 861 31 HOH HOH . C 3 HOH A 62 862 169 HOH HOH . C 3 HOH A 63 863 20 HOH HOH . C 3 HOH A 64 864 121 HOH HOH . C 3 HOH A 65 865 40 HOH HOH . C 3 HOH A 66 866 148 HOH HOH . C 3 HOH A 67 867 53 HOH HOH . C 3 HOH A 68 868 11 HOH HOH . C 3 HOH A 69 869 24 HOH HOH . C 3 HOH A 70 870 37 HOH HOH . C 3 HOH A 71 871 36 HOH HOH . C 3 HOH A 72 872 149 HOH HOH . C 3 HOH A 73 873 56 HOH HOH . C 3 HOH A 74 874 101 HOH HOH . C 3 HOH A 75 875 78 HOH HOH . C 3 HOH A 76 876 107 HOH HOH . C 3 HOH A 77 877 52 HOH HOH . C 3 HOH A 78 878 22 HOH HOH . C 3 HOH A 79 879 158 HOH HOH . C 3 HOH A 80 880 55 HOH HOH . C 3 HOH A 81 881 75 HOH HOH . C 3 HOH A 82 882 95 HOH HOH . C 3 HOH A 83 883 63 HOH HOH . C 3 HOH A 84 884 10 HOH HOH . C 3 HOH A 85 885 73 HOH HOH . C 3 HOH A 86 886 77 HOH HOH . C 3 HOH A 87 887 153 HOH HOH . C 3 HOH A 88 888 19 HOH HOH . C 3 HOH A 89 889 32 HOH HOH . C 3 HOH A 90 890 13 HOH HOH . C 3 HOH A 91 891 61 HOH HOH . C 3 HOH A 92 892 155 HOH HOH . C 3 HOH A 93 893 17 HOH HOH . C 3 HOH A 94 894 175 HOH HOH . C 3 HOH A 95 895 59 HOH HOH . C 3 HOH A 96 896 166 HOH HOH . C 3 HOH A 97 897 39 HOH HOH . C 3 HOH A 98 898 79 HOH HOH . C 3 HOH A 99 899 45 HOH HOH . C 3 HOH A 100 900 137 HOH HOH . C 3 HOH A 101 901 152 HOH HOH . C 3 HOH A 102 902 106 HOH HOH . C 3 HOH A 103 903 164 HOH HOH . C 3 HOH A 104 904 76 HOH HOH . C 3 HOH A 105 905 51 HOH HOH . C 3 HOH A 106 906 12 HOH HOH . C 3 HOH A 107 907 38 HOH HOH . C 3 HOH A 108 908 1 HOH HOH . C 3 HOH A 109 909 90 HOH HOH . C 3 HOH A 110 910 44 HOH HOH . C 3 HOH A 111 911 84 HOH HOH . C 3 HOH A 112 912 87 HOH HOH . C 3 HOH A 113 913 83 HOH HOH . C 3 HOH A 114 914 72 HOH HOH . C 3 HOH A 115 915 154 HOH HOH . C 3 HOH A 116 916 165 HOH HOH . C 3 HOH A 117 917 146 HOH HOH . C 3 HOH A 118 918 41 HOH HOH . C 3 HOH A 119 919 159 HOH HOH . C 3 HOH A 120 920 47 HOH HOH . C 3 HOH A 121 921 54 HOH HOH . C 3 HOH A 122 922 150 HOH HOH . C 3 HOH A 123 923 80 HOH HOH . C 3 HOH A 124 924 99 HOH HOH . C 3 HOH A 125 925 111 HOH HOH . C 3 HOH A 126 926 18 HOH HOH . C 3 HOH A 127 927 27 HOH HOH . C 3 HOH A 128 928 34 HOH HOH . C 3 HOH A 129 929 57 HOH HOH . C 3 HOH A 130 930 113 HOH HOH . C 3 HOH A 131 931 14 HOH HOH . C 3 HOH A 132 932 134 HOH HOH . C 3 HOH A 133 933 162 HOH HOH . C 3 HOH A 134 934 145 HOH HOH . C 3 HOH A 135 935 141 HOH HOH . C 3 HOH A 136 936 62 HOH HOH . C 3 HOH A 137 937 128 HOH HOH . C 3 HOH A 138 938 115 HOH HOH . C 3 HOH A 139 939 118 HOH HOH . C 3 HOH A 140 940 89 HOH HOH . C 3 HOH A 141 941 46 HOH HOH . C 3 HOH A 142 942 123 HOH HOH . C 3 HOH A 143 943 127 HOH HOH . C 3 HOH A 144 944 43 HOH HOH . C 3 HOH A 145 945 92 HOH HOH . C 3 HOH A 146 946 42 HOH HOH . C 3 HOH A 147 947 126 HOH HOH . C 3 HOH A 148 948 136 HOH HOH . C 3 HOH A 149 949 16 HOH HOH . C 3 HOH A 150 950 35 HOH HOH . C 3 HOH A 151 951 167 HOH HOH . C 3 HOH A 152 952 85 HOH HOH . C 3 HOH A 153 953 133 HOH HOH . C 3 HOH A 154 954 120 HOH HOH . C 3 HOH A 155 955 143 HOH HOH . C 3 HOH A 156 956 109 HOH HOH . C 3 HOH A 157 957 157 HOH HOH . C 3 HOH A 158 958 81 HOH HOH . C 3 HOH A 159 959 104 HOH HOH . C 3 HOH A 160 960 71 HOH HOH . C 3 HOH A 161 961 131 HOH HOH . C 3 HOH A 162 962 161 HOH HOH . C 3 HOH A 163 963 119 HOH HOH . C 3 HOH A 164 964 93 HOH HOH . C 3 HOH A 165 965 112 HOH HOH . C 3 HOH A 166 966 139 HOH HOH . C 3 HOH A 167 967 142 HOH HOH . C 3 HOH A 168 968 135 HOH HOH . C 3 HOH A 169 969 125 HOH HOH . C 3 HOH A 170 970 66 HOH HOH . C 3 HOH A 171 971 129 HOH HOH . C 3 HOH A 172 972 105 HOH HOH . C 3 HOH A 173 973 100 HOH HOH . C 3 HOH A 174 974 147 HOH HOH . C 3 HOH A 175 975 94 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 N N1 8E8 . . . B 2 17.996 4.906 0.251 1 12.4 ? N1 8E8 701 A 1 HETATM 2 C C2 8E8 . . . B 2 19.029 5.21 -0.502 1 13.21 ? C2 8E8 701 A 1 HETATM 3 N N3 8E8 . . . B 2 20.165 5.774 -0.209 1 13.78 ? N3 8E8 701 A 1 HETATM 4 C C4 8E8 . . . B 2 20.287 6.087 1.106 1 13.59 ? C4 8E8 701 A 1 HETATM 5 C C5 8E8 . . . B 2 19.244 5.77 2.045 1 13.49 ? C5 8E8 701 A 1 HETATM 6 C C6 8E8 . . . B 2 18.035 5.202 1.583 1 12.52 ? C6 8E8 701 A 1 HETATM 7 C CAA 8E8 . . . B 2 24.636 11.914 -0.796 1 20.77 ? CAA 8E8 701 A 1 HETATM 8 N NAB 8E8 . . . B 2 16.993 4.962 2.344 1 12.25 ? NAB 8E8 701 A 1 HETATM 9 O OAC 8E8 . . . B 2 22.896 9.271 -1.719 1 19.14 ? OAC 8E8 701 A 1 HETATM 10 C CAD 8E8 . . . B 2 24.926 10.401 -1.225 1 21.68 ? CAD 8E8 701 A 1 HETATM 11 C CAE 8E8 . . . B 2 14.681 8.437 10.029 1 18.37 ? CAE 8E8 701 A 1 HETATM 12 C CAF 8E8 . . . B 2 14.539 8.013 8.709 1 17.58 ? CAF 8E8 701 A 1 HETATM 13 C CAG 8E8 . . . B 2 15.731 7.994 10.795 1 20.38 ? CAG 8E8 701 A 1 HETATM 14 C CAI 8E8 . . . B 2 15.458 7.201 8.143 1 17.54 ? CAI 8E8 701 A 1 HETATM 15 C CAJ 8E8 . . . B 2 16.634 7.082 10.226 1 18.02 ? CAJ 8E8 701 A 1 HETATM 16 C CAK 8E8 . . . B 2 18.227 4.86 6.454 1 17.33 ? CAK 8E8 701 A 1 HETATM 17 C CAL 8E8 . . . B 2 18.403 7.301 6.655 1 17.38 ? CAL 8E8 701 A 1 HETATM 18 C CAM 8E8 . . . B 2 18.766 4.955 5.197 1 16.86 ? CAM 8E8 701 A 1 HETATM 19 C CAN 8E8 . . . B 2 19.004 7.377 5.43 1 17.48 ? CAN 8E8 701 A 1 HETATM 20 C CAO 8E8 . . . B 2 24.944 7.933 1.767 1 23.32 ? CAO 8E8 701 A 1 HETATM 21 C CAP 8E8 . . . B 2 23.791 6.994 2.161 1 22.36 ? CAP 8E8 701 A 1 HETATM 22 C CAQ 8E8 . . . B 2 24.375 9.395 1.601 1 21.53 ? CAQ 8E8 701 A 1 HETATM 23 C CAR 8E8 . . . B 2 22.234 8.54 0.826 1 21.89 ? CAR 8E8 701 A 1 HETATM 24 N NAU 8E8 . . . B 2 20.956 6.785 3.152 1 15.16 ? NAU 8E8 701 A 1 HETATM 25 O OAV 8E8 . . . B 2 17.473 5.899 8.446 1 18.42 ? OAV 8E8 701 A 1 HETATM 26 C CAW 8E8 . . . B 2 23.702 9.561 -0.811 1 21.67 ? CAW 8E8 701 A 1 HETATM 27 C CAY 8E8 . . . B 2 16.539 6.777 8.917 1 16.54 ? CAY 8E8 701 A 1 HETATM 28 C CAZ 8E8 . . . B 2 18.005 6.032 7.186 1 17.48 ? CAZ 8E8 701 A 1 HETATM 29 C CBA 8E8 . . . B 2 19.109 6.221 4.675 1 15.69 ? CBA 8E8 701 A 1 HETATM 30 C CBB 8E8 . . . B 2 19.757 6.277 3.36 1 14.48 ? CBB 8E8 701 A 1 HETATM 31 C CBE 8E8 . . . B 2 22.532 7.127 1.261 1 17.72 ? CBE 8E8 701 A 1 HETATM 32 N NBF 8E8 . . . B 2 21.24 6.66 1.801 1 15.5 ? NBF 8E8 701 A 1 HETATM 33 N NBG 8E8 . . . B 2 23.477 9.237 0.497 1 21.51 ? NBG 8E8 701 A 1 # _model_server_stats.io_time_ms 46 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 296 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 33 #