data_5VD7 # _model_server_result.job_id LBpa0oW5uhSdqWPUi968Vg _model_server_result.datetime_utc '2025-01-11 11:55:24' _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 5vd7 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":601}' # _entry.id 5VD7 # _exptl.entry_id 5VD7 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 518.586 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 6-{[3-fluoro-4-(4-methylpiperazin-1-yl)phenyl]amino}-1-[6-(2-hydroxypropan-2-yl)pyridin-2-yl]-2-(prop-2-en-1-yl)-1,2-dihydro-3H-pyrazolo[3,4-d]pyrimidin-3-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 102.05 _cell.angle_gamma 90 _cell.entry_id 5VD7 _cell.length_a 50.19 _cell.length_b 44.55 _cell.length_c 64.64 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5VD7 _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 author_and_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 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C27 H31 F N8 O2' _chem_comp.formula_weight 518.586 _chem_comp.id 99V _chem_comp.mon_nstd_flag . _chem_comp.name 6-{[3-fluoro-4-(4-methylpiperazin-1-yl)phenyl]amino}-1-[6-(2-hydroxypropan-2-yl)pyridin-2-yl]-2-(prop-2-en-1-yl)-1,2-dihydro-3H-pyrazolo[3,4-d]pyrimidin-3-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 N30 C31 99V sing 1 n n N30 C32 99V sing 2 n n N30 C29 99V sing 3 n n C32 C33 99V sing 4 n n C14 C11 99V sing 5 n n C29 C28 99V sing 6 n n C15 C16 99V doub 7 n y C15 C10 99V sing 8 n y C12 C11 99V sing 9 n n C11 C10 99V sing 10 n n C11 O13 99V sing 11 n n C16 C17 99V sing 12 n y C33 N27 99V sing 13 n n C10 N09 99V doub 14 n y C28 N27 99V sing 15 n n N27 C26 99V sing 16 n n C17 C08 99V doub 17 n y N09 C08 99V sing 18 n y C26 C34 99V doub 19 n y C26 C24 99V sing 20 n y C34 C35 99V sing 21 n y C08 N07 99V sing 22 n n C05 C06 99V doub 23 n n C05 C04 99V sing 24 n n C24 F25 99V sing 25 n n C24 C23 99V doub 26 n y C35 C22 99V doub 27 n y N07 N03 99V sing 28 n n N07 C18 99V sing 29 n n C04 N03 99V sing 30 n n N03 C02 99V sing 31 n n C23 C22 99V sing 32 n y C22 N21 99V sing 33 n n N19 C18 99V doub 34 n y N19 C20 99V sing 35 n y C18 C38 99V sing 36 n y N21 C20 99V sing 37 n n C20 N36 99V doub 38 n y C02 C38 99V sing 39 n n C02 O01 99V doub 40 n n C38 C37 99V doub 41 n y N36 C37 99V sing 42 n y C15 H151 99V sing 43 n n C17 H171 99V sing 44 n n C28 H282 99V sing 45 n n C28 H281 99V sing 46 n n C04 H041 99V sing 47 n n C04 H042 99V sing 48 n n C05 H051 99V sing 49 n n C06 H061 99V sing 50 n n C06 H062 99V sing 51 n n C12 H122 99V sing 52 n n C12 H121 99V sing 53 n n C12 H123 99V sing 54 n n O13 H131 99V sing 55 n n C14 H142 99V sing 56 n n C14 H143 99V sing 57 n n C14 H141 99V sing 58 n n C16 H161 99V sing 59 n n N21 H211 99V sing 60 n n C23 H231 99V sing 61 n n C29 H291 99V sing 62 n n C29 H292 99V sing 63 n n C31 H311 99V sing 64 n n C31 H312 99V sing 65 n n C31 H313 99V sing 66 n n C32 H322 99V sing 67 n n C32 H321 99V sing 68 n n C33 H331 99V sing 69 n n C33 H332 99V sing 70 n n C34 H341 99V sing 71 n n C35 H351 99V sing 72 n n C37 H371 99V sing 73 n n # _atom_sites.entry_id 5VD7 _atom_sites.fract_transf_matrix[1][1] 0.019924 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004254 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.022447 _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] 0.015819 _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 99V A 1 601 1 99V LIG . C 3 CL A 1 602 1 CL CL . D 4 EDO A 1 603 1 EDO EDO . E 5 HOH A 1 701 49 HOH HOH . E 5 HOH A 2 702 14 HOH HOH . E 5 HOH A 3 703 13 HOH HOH . E 5 HOH A 4 704 42 HOH HOH . E 5 HOH A 5 705 38 HOH HOH . E 5 HOH A 6 706 18 HOH HOH . E 5 HOH A 7 707 11 HOH HOH . E 5 HOH A 8 708 61 HOH HOH . E 5 HOH A 9 709 31 HOH HOH . E 5 HOH A 10 710 50 HOH HOH . E 5 HOH A 11 711 64 HOH HOH . E 5 HOH A 12 712 34 HOH HOH . E 5 HOH A 13 713 45 HOH HOH . E 5 HOH A 14 714 27 HOH HOH . E 5 HOH A 15 715 56 HOH HOH . E 5 HOH A 16 716 12 HOH HOH . E 5 HOH A 17 717 65 HOH HOH . E 5 HOH A 18 718 26 HOH HOH . E 5 HOH A 19 719 20 HOH HOH . E 5 HOH A 20 720 69 HOH HOH . E 5 HOH A 21 721 63 HOH HOH . E 5 HOH A 22 722 30 HOH HOH . E 5 HOH A 23 723 33 HOH HOH . E 5 HOH A 24 724 2 HOH HOH . E 5 HOH A 25 725 70 HOH HOH . E 5 HOH A 26 726 46 HOH HOH . E 5 HOH A 27 727 25 HOH HOH . E 5 HOH A 28 728 51 HOH HOH . E 5 HOH A 29 729 29 HOH HOH . E 5 HOH A 30 730 1 HOH HOH . E 5 HOH A 31 731 39 HOH HOH . E 5 HOH A 32 732 3 HOH HOH . E 5 HOH A 33 733 9 HOH HOH . E 5 HOH A 34 734 44 HOH HOH . E 5 HOH A 35 735 6 HOH HOH . E 5 HOH A 36 736 57 HOH HOH . E 5 HOH A 37 737 10 HOH HOH . E 5 HOH A 38 738 15 HOH HOH . E 5 HOH A 39 739 19 HOH HOH . E 5 HOH A 40 740 37 HOH HOH . E 5 HOH A 41 741 16 HOH HOH . E 5 HOH A 42 742 43 HOH HOH . E 5 HOH A 43 743 36 HOH HOH . E 5 HOH A 44 744 22 HOH HOH . E 5 HOH A 45 745 4 HOH HOH . E 5 HOH A 46 746 53 HOH HOH . E 5 HOH A 47 747 55 HOH HOH . E 5 HOH A 48 748 8 HOH HOH . E 5 HOH A 49 749 23 HOH HOH . E 5 HOH A 50 750 21 HOH HOH . E 5 HOH A 51 751 24 HOH HOH . E 5 HOH A 52 752 7 HOH HOH . E 5 HOH A 53 753 68 HOH HOH . E 5 HOH A 54 754 60 HOH HOH . E 5 HOH A 55 755 58 HOH HOH . E 5 HOH A 56 756 40 HOH HOH . E 5 HOH A 57 757 48 HOH HOH . E 5 HOH A 58 758 32 HOH HOH . E 5 HOH A 59 759 5 HOH HOH . E 5 HOH A 60 760 35 HOH HOH . E 5 HOH A 61 761 17 HOH HOH . E 5 HOH A 62 762 62 HOH HOH . E 5 HOH A 63 763 47 HOH HOH . E 5 HOH A 64 764 67 HOH HOH . E 5 HOH A 65 765 54 HOH HOH . E 5 HOH A 66 766 28 HOH HOH . E 5 HOH A 67 767 59 HOH HOH . E 5 HOH A 68 768 52 HOH HOH . E 5 HOH A 69 769 66 HOH HOH . E 5 HOH A 70 770 41 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 99V . . . B 2 -1.488 3.457 9 1 28.28 ? C10 99V 601 A 1 HETATM 2 C C15 99V . . . B 2 -2.319 4.225 8.185 1 27.07 ? C15 99V 601 A 1 HETATM 3 C C17 99V . . . B 2 -4.038 4.113 9.922 1 26.67 ? C17 99V 601 A 1 HETATM 4 C C20 99V . . . B 2 -5.722 5.131 13.887 1 23.82 ? C20 99V 601 A 1 HETATM 5 C C22 99V . . . B 2 -6.66 7.181 12.65 1 31.82 ? C22 99V 601 A 1 HETATM 6 C C24 99V . . . B 2 -7.98 8.893 11.537 1 39.88 ? C24 99V 601 A 1 HETATM 7 C C26 99V . . . B 2 -7.097 8.892 10.454 1 40.96 ? C26 99V 601 A 1 HETATM 8 C C28 99V . . . B 2 -6.445 10.843 9.129 1 48.62 ? C28 99V 601 A 1 HETATM 9 O O01 99V . . . B 2 -3.162 0.747 14.717 1 28.68 ? O01 99V 601 A 1 HETATM 10 C C02 99V . . . B 2 -3.403 1.622 13.899 1 27.59 ? C02 99V 601 A 1 HETATM 11 N N03 99V . . . B 2 -2.882 1.682 12.59 1 27.9 ? N03 99V 601 A 1 HETATM 12 C C04 99V . . . B 2 -2.024 0.693 12.02 1 28.13 ? C04 99V 601 A 1 HETATM 13 C C05 99V . . . B 2 -2.944 -0.273 11.284 1 29.06 ? C05 99V 601 A 1 HETATM 14 C C06 99V . . . B 2 -3.867 -0.993 11.966 1 28.48 ? C06 99V 601 A 1 HETATM 15 N N07 99V . . . B 2 -3.418 2.847 11.961 1 26.04 ? N07 99V 601 A 1 HETATM 16 C C08 99V . . . B 2 -3.134 3.335 10.639 1 26.92 ? C08 99V 601 A 1 HETATM 17 N N09 99V . . . B 2 -1.924 3.065 10.185 1 27.67 ? N09 99V 601 A 1 HETATM 18 C C11 99V . . . B 2 -0.064 3.026 8.615 1 29.57 ? C11 99V 601 A 1 HETATM 19 C C12 99V . . . B 2 -0.091 1.525 8.346 1 29.75 ? C12 99V 601 A 1 HETATM 20 O O13 99V . . . B 2 0.791 3.289 9.697 1 30.98 ? O13 99V 601 A 1 HETATM 21 C C14 99V . . . B 2 0.44 3.786 7.396 1 29.35 ? C14 99V 601 A 1 HETATM 22 C C16 99V . . . B 2 -3.625 4.568 8.636 1 26.49 ? C16 99V 601 A 1 HETATM 23 C C18 99V . . . B 2 -4.269 3.541 12.934 1 24.98 ? C18 99V 601 A 1 HETATM 24 N N19 99V . . . B 2 -5.003 4.706 12.855 1 24.64 ? N19 99V 601 A 1 HETATM 25 N N21 99V . . . B 2 -6.497 6.348 13.833 1 27.1 ? N21 99V 601 A 1 HETATM 26 C C23 99V . . . B 2 -7.761 8.04 12.626 1 35.45 ? C23 99V 601 A 1 HETATM 27 F F25 99V . . . B 2 -9.049 9.693 11.558 1 42.89 ? F25 99V 601 A 1 HETATM 28 N N27 99V . . . B 2 -7.301 9.782 9.312 1 46.05 ? N27 99V 601 A 1 HETATM 29 C C29 99V . . . B 2 -6.324 11.228 7.667 1 50.27 ? C29 99V 601 A 1 HETATM 30 N N30 99V . . . B 2 -7.557 11.445 7.059 1 50.85 ? N30 99V 601 A 1 HETATM 31 C C31 99V . . . B 2 -7.997 12.6 7.245 1 51.43 ? C31 99V 601 A 1 HETATM 32 C C32 99V . . . B 2 -8.5 10.455 7.348 1 50.32 ? C32 99V 601 A 1 HETATM 33 C C33 99V . . . B 2 -8.549 10.07 8.815 1 48.77 ? C33 99V 601 A 1 HETATM 34 C C34 99V . . . B 2 -5.987 8.042 10.481 1 37.17 ? C34 99V 601 A 1 HETATM 35 C C35 99V . . . B 2 -5.768 7.189 11.582 1 33.89 ? C35 99V 601 A 1 HETATM 36 N N36 99V . . . B 2 -5.745 4.468 15.013 1 22.95 ? N36 99V 601 A 1 HETATM 37 C C37 99V . . . B 2 -5.06 3.319 15.186 1 23.81 ? C37 99V 601 A 1 HETATM 38 C C38 99V . . . B 2 -4.271 2.81 14.092 1 24.93 ? C38 99V 601 A 1 HETATM 39 H H151 99V . . . B 2 -2.008 4.521 7.303 1 32.48 ? H151 99V 601 A 1 HETATM 40 H H171 99V . . . B 2 -4.925 4.321 10.277 1 32 ? H171 99V 601 A 1 HETATM 41 H H282 99V . . . B 2 -6.777 11.61 9.633 1 58.34 ? H282 99V 601 A 1 HETATM 42 H H281 99V . . . B 2 -5.557 10.599 9.468 1 58.34 ? H281 99V 601 A 1 HETATM 43 H H041 99V . . . B 2 -1.4 1.108 11.393 1 33.76 ? H041 99V 601 A 1 HETATM 44 H H042 99V . . . B 2 -1.534 0.222 12.725 1 33.76 ? H042 99V 601 A 1 HETATM 45 H H051 99V . . . B 2 -2.868 -0.374 10.318 1 34.88 ? H051 99V 601 A 1 HETATM 46 H H061 99V . . . B 2 -3.945 -0.893 12.941 1 34.17 ? H061 99V 601 A 1 HETATM 47 H H062 99V . . . B 2 -4.453 -1.61 11.491 1 34.17 ? H062 99V 601 A 1 HETATM 48 H H122 99V . . . B 2 -0.745 1.33 7.638 1 35.7 ? H122 99V 601 A 1 HETATM 49 H H121 99V . . . B 2 -0.346 1.051 9.164 1 35.7 ? H121 99V 601 A 1 HETATM 50 H H123 99V . . . B 2 0.798 1.228 8.06 1 35.7 ? H123 99V 601 A 1 HETATM 51 H H131 99V . . . B 2 0.936 4.167 9.754 1 37.17 ? H131 99V 601 A 1 HETATM 52 H H142 99V . . . B 2 -0.051 3.492 6.601 1 35.22 ? H142 99V 601 A 1 HETATM 53 H H143 99V . . . B 2 1.402 3.608 7.273 1 35.22 ? H143 99V 601 A 1 HETATM 54 H H141 99V . . . B 2 0.301 4.745 7.529 1 35.22 ? H141 99V 601 A 1 HETATM 55 H H161 99V . . . B 2 -4.225 5.103 8.077 1 31.79 ? H161 99V 601 A 1 HETATM 56 H H211 99V . . . B 2 -6.917 6.617 14.601 1 32.52 ? H211 99V 601 A 1 HETATM 57 H H231 99V . . . B 2 -8.386 8.047 13.38 1 42.54 ? H231 99V 601 A 1 HETATM 58 H H291 99V . . . B 2 -5.791 12.05 7.6 1 60.33 ? H291 99V 601 A 1 HETATM 59 H H292 99V . . . B 2 -5.861 10.512 7.191 1 60.33 ? H292 99V 601 A 1 HETATM 60 H H311 99V . . . B 2 -8.218 12.718 8.191 1 61.72 ? H311 99V 601 A 1 HETATM 61 H H312 99V . . . B 2 -8.805 12.734 6.701 1 61.72 ? H312 99V 601 A 1 HETATM 62 H H313 99V . . . B 2 -7.314 13.258 6.984 1 61.72 ? H313 99V 601 A 1 HETATM 63 H H322 99V . . . B 2 -8.285 9.656 6.822 1 60.38 ? H322 99V 601 A 1 HETATM 64 H H321 99V . . . B 2 -9.381 10.777 7.081 1 60.38 ? H321 99V 601 A 1 HETATM 65 H H331 99V . . . B 2 -9.123 9.28 8.918 1 58.52 ? H331 99V 601 A 1 HETATM 66 H H332 99V . . . B 2 -8.931 10.81 9.325 1 58.52 ? H332 99V 601 A 1 HETATM 67 H H341 99V . . . B 2 -5.359 8.037 9.73 1 44.6 ? H341 99V 601 A 1 HETATM 68 H H351 99V . . . B 2 -4.993 6.595 11.591 1 40.67 ? H351 99V 601 A 1 HETATM 69 H H371 99V . . . B 2 -5.104 2.835 16.035 1 28.58 ? H371 99V 601 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 269 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 69 #