data_5VDA # _model_server_result.job_id Q16_ha-cx_e8y_4Xm7KjLw _model_server_result.datetime_utc '2024-12-21 18:07:22' _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 5vda # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":601}' # _entry.id 5VDA # _exptl.entry_id 5VDA _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 486.569 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1-{6-[(1S)-1-hydroxyethyl]pyridin-2-yl}-6-{[4-(4-methylpiperazin-1-yl)phenyl]amino}-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 102.18 _cell.angle_gamma 90 _cell.entry_id 5VDA _cell.length_a 50.36 _cell.length_b 44.64 _cell.length_c 64.62 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5VDA _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 'C26 H30 N8 O2' _chem_comp.formula_weight 486.569 _chem_comp.id 98D _chem_comp.mon_nstd_flag . _chem_comp.name 1-{6-[(1S)-1-hydroxyethyl]pyridin-2-yl}-6-{[4-(4-methylpiperazin-1-yl)phenyl]amino}-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 C01 N02 98D sing 1 n n N02 C03 98D sing 2 n n N02 C36 98D sing 3 n n C03 C04 98D sing 4 n n C36 C35 98D sing 5 n n C23 C24 98D doub 6 n y C23 C19 98D sing 7 n y C21 C20 98D sing 8 n n C04 N05 98D sing 9 n n C20 C19 98D sing 10 n n C20 O22 98D sing 11 n n C24 C25 98D sing 12 n y C19 N18 98D doub 13 n y C35 N05 98D sing 14 n n N05 C06 98D sing 15 n n C25 C17 98D doub 16 n y N18 C17 98D sing 17 n y C06 C07 98D doub 18 n y C06 C34 98D sing 19 n y C07 C08 98D sing 20 n y C17 N16 98D sing 21 n n C28 C27 98D sing 22 n n C28 C29 98D doub 23 n n C34 C33 98D doub 24 n y C08 C09 98D doub 25 n y N16 N26 98D sing 26 n n N16 C15 98D sing 27 n n C27 N26 98D sing 28 n n N26 C30 98D sing 29 n n C33 C09 98D sing 30 n y C09 N10 98D sing 31 n n N32 C15 98D doub 32 n y N32 C11 98D sing 33 n y C15 C14 98D sing 34 n y N10 C11 98D sing 35 n n C30 C14 98D sing 36 n n C30 O31 98D doub 37 n n C11 N12 98D doub 38 n y C14 C13 98D doub 39 n y N12 C13 98D sing 40 n y C13 H131 98D sing 41 n n C20 H201 98D sing 42 n n C21 H213 98D sing 43 n n C21 H212 98D sing 44 n n C21 H211 98D sing 45 n n C24 H241 98D sing 46 n n C28 H281 98D sing 47 n n C01 H012 98D sing 48 n n C01 H013 98D sing 49 n n C01 H011 98D sing 50 n n C03 H031 98D sing 51 n n C03 H032 98D sing 52 n n C04 H041 98D sing 53 n n C04 H042 98D sing 54 n n C07 H071 98D sing 55 n n C08 H081 98D sing 56 n n N10 H101 98D sing 57 n n O22 H221 98D sing 58 n n C23 H231 98D sing 59 n n C25 H251 98D sing 60 n n C27 H271 98D sing 61 n n C27 H272 98D sing 62 n n C29 H291 98D sing 63 n n C29 H292 98D sing 64 n n C33 H331 98D sing 65 n n C34 H341 98D sing 66 n n C35 H351 98D sing 67 n n C35 H352 98D sing 68 n n C36 H361 98D sing 69 n n C36 H362 98D sing 70 n n # _atom_sites.entry_id 5VDA _atom_sites.fract_transf_matrix[1][1] 0.019857 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004287 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.022401 _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] 0.015832 _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 98D A 1 601 1 98D 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 76 HOH HOH . E 5 HOH A 2 702 26 HOH HOH . E 5 HOH A 3 703 53 HOH HOH . E 5 HOH A 4 704 18 HOH HOH . E 5 HOH A 5 705 10 HOH HOH . E 5 HOH A 6 706 30 HOH HOH . E 5 HOH A 7 707 75 HOH HOH . E 5 HOH A 8 708 32 HOH HOH . E 5 HOH A 9 709 79 HOH HOH . E 5 HOH A 10 710 9 HOH HOH . E 5 HOH A 11 711 69 HOH HOH . E 5 HOH A 12 712 45 HOH HOH . E 5 HOH A 13 713 40 HOH HOH . E 5 HOH A 14 714 19 HOH HOH . E 5 HOH A 15 715 27 HOH HOH . E 5 HOH A 16 716 29 HOH HOH . E 5 HOH A 17 717 8 HOH HOH . E 5 HOH A 18 718 43 HOH HOH . E 5 HOH A 19 719 41 HOH HOH . E 5 HOH A 20 720 3 HOH HOH . E 5 HOH A 21 721 4 HOH HOH . E 5 HOH A 22 722 17 HOH HOH . E 5 HOH A 23 723 13 HOH HOH . E 5 HOH A 24 724 14 HOH HOH . E 5 HOH A 25 725 65 HOH HOH . E 5 HOH A 26 726 11 HOH HOH . E 5 HOH A 27 727 12 HOH HOH . E 5 HOH A 28 728 23 HOH HOH . E 5 HOH A 29 729 42 HOH HOH . E 5 HOH A 30 730 78 HOH HOH . E 5 HOH A 31 731 68 HOH HOH . E 5 HOH A 32 732 6 HOH HOH . E 5 HOH A 33 733 33 HOH HOH . E 5 HOH A 34 734 46 HOH HOH . E 5 HOH A 35 735 2 HOH HOH . E 5 HOH A 36 736 49 HOH HOH . E 5 HOH A 37 737 55 HOH HOH . E 5 HOH A 38 738 77 HOH HOH . E 5 HOH A 39 739 37 HOH HOH . E 5 HOH A 40 740 1 HOH HOH . E 5 HOH A 41 741 15 HOH HOH . E 5 HOH A 42 742 58 HOH HOH . E 5 HOH A 43 743 57 HOH HOH . E 5 HOH A 44 744 66 HOH HOH . E 5 HOH A 45 745 60 HOH HOH . E 5 HOH A 46 746 20 HOH HOH . E 5 HOH A 47 747 71 HOH HOH . E 5 HOH A 48 748 21 HOH HOH . E 5 HOH A 49 749 28 HOH HOH . E 5 HOH A 50 750 62 HOH HOH . E 5 HOH A 51 751 22 HOH HOH . E 5 HOH A 52 752 67 HOH HOH . E 5 HOH A 53 753 44 HOH HOH . E 5 HOH A 54 754 83 HOH HOH . E 5 HOH A 55 755 52 HOH HOH . E 5 HOH A 56 756 34 HOH HOH . E 5 HOH A 57 757 64 HOH HOH . E 5 HOH A 58 758 48 HOH HOH . E 5 HOH A 59 759 16 HOH HOH . E 5 HOH A 60 760 73 HOH HOH . E 5 HOH A 61 761 59 HOH HOH . E 5 HOH A 62 762 63 HOH HOH . E 5 HOH A 63 763 70 HOH HOH . E 5 HOH A 64 764 31 HOH HOH . E 5 HOH A 65 765 74 HOH HOH . E 5 HOH A 66 766 7 HOH HOH . E 5 HOH A 67 767 51 HOH HOH . E 5 HOH A 68 768 24 HOH HOH . E 5 HOH A 69 769 39 HOH HOH . E 5 HOH A 70 770 36 HOH HOH . E 5 HOH A 71 771 50 HOH HOH . E 5 HOH A 72 772 25 HOH HOH . E 5 HOH A 73 773 84 HOH HOH . E 5 HOH A 74 774 38 HOH HOH . E 5 HOH A 75 775 54 HOH HOH . E 5 HOH A 76 776 5 HOH HOH . E 5 HOH A 77 777 81 HOH HOH . E 5 HOH A 78 778 82 HOH HOH . E 5 HOH A 79 779 61 HOH HOH . E 5 HOH A 80 780 80 HOH HOH . E 5 HOH A 81 781 72 HOH HOH . E 5 HOH A 82 782 56 HOH HOH . E 5 HOH A 83 783 35 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 N12 98D . . . B 2 -5.661 4.491 14.993 1 17.52 ? N12 98D 601 A 1 HETATM 2 C C13 98D . . . B 2 -4.867 3.391 15.152 1 24.11 ? C13 98D 601 A 1 HETATM 3 C C15 98D . . . B 2 -4.366 3.594 12.812 1 23.48 ? C15 98D 601 A 1 HETATM 4 C C17 98D . . . B 2 -3.497 3.425 10.64 1 24.29 ? C17 98D 601 A 1 HETATM 5 C C20 98D . . . B 2 -0.421 3.451 8.489 1 22.82 ? C20 98D 601 A 1 HETATM 6 C C21 98D . . . B 2 -0.244 1.929 8.404 1 18.62 ? C21 98D 601 A 1 HETATM 7 C C24 98D . . . B 2 -4.068 4.787 8.719 1 20.34 ? C24 98D 601 A 1 HETATM 8 C C28 98D . . . B 2 -2.994 -0.086 11.444 1 38.65 ? C28 98D 601 A 1 HETATM 9 C C01 98D . . . B 2 -8.639 11.487 5.599 1 76.86 ? C01 98D 601 A 1 HETATM 10 N N02 98D . . . B 2 -8.29 10.876 6.905 1 70.16 ? N02 98D 601 A 1 HETATM 11 C C03 98D . . . B 2 -6.878 11.035 7.313 1 58.72 ? C03 98D 601 A 1 HETATM 12 C C04 98D . . . B 2 -6.563 9.998 8.417 1 47.33 ? C04 98D 601 A 1 HETATM 13 N N05 98D . . . B 2 -7.642 9.66 9.337 1 28.54 ? N05 98D 601 A 1 HETATM 14 C C06 98D . . . B 2 -7.384 8.822 10.428 1 22.67 ? C06 98D 601 A 1 HETATM 15 C C07 98D . . . B 2 -6.187 8.075 10.508 1 19.94 ? C07 98D 601 A 1 HETATM 16 C C08 98D . . . B 2 -5.899 7.238 11.586 1 21.75 ? C08 98D 601 A 1 HETATM 17 C C09 98D . . . B 2 -6.806 7.047 12.631 1 21.46 ? C09 98D 601 A 1 HETATM 18 N N10 98D . . . B 2 -6.597 6.241 13.724 1 21.98 ? N10 98D 601 A 1 HETATM 19 C C11 98D . . . B 2 -5.819 5.143 13.811 1 13.5 ? C11 98D 601 A 1 HETATM 20 C C14 98D . . . B 2 -4.209 2.937 14.023 1 20.86 ? C14 98D 601 A 1 HETATM 21 N N16 98D . . . B 2 -3.649 2.935 11.893 1 27.93 ? N16 98D 601 A 1 HETATM 22 N N18 98D . . . B 2 -2.231 3.299 10.148 1 27.03 ? N18 98D 601 A 1 HETATM 23 C C19 98D . . . B 2 -1.771 3.746 8.969 1 21.44 ? C19 98D 601 A 1 HETATM 24 O O22 98D . . . B 2 0.514 4 9.416 1 25.2 ? O22 98D 601 A 1 HETATM 25 C C23 98D . . . B 2 -2.743 4.542 8.232 1 16.75 ? C23 98D 601 A 1 HETATM 26 C C25 98D . . . B 2 -4.418 4.268 9.962 1 24.86 ? C25 98D 601 A 1 HETATM 27 N N26 98D . . . B 2 -3.008 1.952 12.501 1 31.74 ? N26 98D 601 A 1 HETATM 28 C C27 98D . . . B 2 -2.151 0.975 11.951 1 32.75 ? C27 98D 601 A 1 HETATM 29 C C29 98D . . . B 2 -4.055 -0.616 12.069 1 29.8 ? C29 98D 601 A 1 HETATM 30 C C30 98D . . . B 2 -3.321 1.904 13.805 1 25.15 ? C30 98D 601 A 1 HETATM 31 O O31 98D . . . B 2 -2.923 1.065 14.647 1 25.03 ? O31 98D 601 A 1 HETATM 32 N N32 98D . . . B 2 -5.173 4.668 12.695 1 13.46 ? N32 98D 601 A 1 HETATM 33 C C33 98D . . . B 2 -7.999 7.795 12.589 1 20.21 ? C33 98D 601 A 1 HETATM 34 C C34 98D . . . B 2 -8.278 8.633 11.507 1 16.53 ? C34 98D 601 A 1 HETATM 35 C C35 98D . . . B 2 -8.983 10.237 9.152 1 30.35 ? C35 98D 601 A 1 HETATM 36 C C36 98D . . . B 2 -9.152 11.289 8.036 1 68.46 ? C36 98D 601 A 1 HETATM 37 H H131 98D . . . B 2 -4.779 2.926 16.057 1 28.94 ? H131 98D 601 A 1 HETATM 38 H H201 98D . . . B 2 -0.247 3.908 7.512 1 27.38 ? H201 98D 601 A 1 HETATM 39 H H213 98D . . . B 2 0.435 1.573 9.182 1 22.35 ? H213 98D 601 A 1 HETATM 40 H H212 98D . . . B 2 0.137 1.639 7.422 1 22.35 ? H212 98D 601 A 1 HETATM 41 H H211 98D . . . B 2 -1.212 1.444 8.547 1 22.35 ? H211 98D 601 A 1 HETATM 42 H H241 98D . . . B 2 -4.728 5.347 8.178 1 24.41 ? H241 98D 601 A 1 HETATM 43 H H281 98D . . . B 2 -2.765 -0.457 10.55 1 46.38 ? H281 98D 601 A 1 HETATM 44 H H012 98D . . . B 2 -7.954 11.127 4.83 1 92.24 ? H012 98D 601 A 1 HETATM 45 H H013 98D . . . B 2 -8.532 12.573 5.651 1 92.24 ? H013 98D 601 A 1 HETATM 46 H H011 98D . . . B 2 -9.663 11.244 5.31 1 92.24 ? H011 98D 601 A 1 HETATM 47 H H031 98D . . . B 2 -6.693 12.04 7.703 1 70.47 ? H031 98D 601 A 1 HETATM 48 H H032 98D . . . B 2 -6.211 10.887 6.454 1 70.47 ? H032 98D 601 A 1 HETATM 49 H H041 98D . . . B 2 -5.723 10.377 9.009 1 56.8 ? H041 98D 601 A 1 HETATM 50 H H042 98D . . . B 2 -6.228 9.101 7.894 1 56.8 ? H042 98D 601 A 1 HETATM 51 H H071 98D . . . B 2 -5.474 8.138 9.781 1 23.93 ? H071 98D 601 A 1 HETATM 52 H H081 98D . . . B 2 -5.016 6.722 11.574 1 26.1 ? H081 98D 601 A 1 HETATM 53 H H101 98D . . . B 2 -7.068 6.493 14.535 1 26.37 ? H101 98D 601 A 1 HETATM 54 H H221 98D . . . B 2 0.351 4.967 9.389 1 30.24 ? H221 98D 601 A 1 HETATM 55 H H231 98D . . . B 2 -2.569 4.981 7.271 1 20.11 ? H231 98D 601 A 1 HETATM 56 H H251 98D . . . B 2 -5.359 4.426 10.33 1 29.83 ? H251 98D 601 A 1 HETATM 57 H H271 98D . . . B 2 -1.548 1.416 11.155 1 39.3 ? H271 98D 601 A 1 HETATM 58 H H272 98D . . . B 2 -1.452 0.559 12.683 1 39.3 ? H272 98D 601 A 1 HETATM 59 H H291 98D . . . B 2 -4.339 -0.292 12.965 1 35.76 ? H291 98D 601 A 1 HETATM 60 H H292 98D . . . B 2 -4.576 -1.345 11.64 1 35.76 ? H292 98D 601 A 1 HETATM 61 H H331 98D . . . B 2 -8.691 7.696 13.335 1 24.25 ? H331 98D 601 A 1 HETATM 62 H H341 98D . . . B 2 -9.169 9.125 11.54 1 19.84 ? H341 98D 601 A 1 HETATM 63 H H351 98D . . . B 2 -9.699 9.435 8.954 1 36.42 ? H351 98D 601 A 1 HETATM 64 H H352 98D . . . B 2 -9.276 10.737 10.08 1 36.42 ? H352 98D 601 A 1 HETATM 65 H H361 98D . . . B 2 -10.203 11.365 7.735 1 82.15 ? H361 98D 601 A 1 HETATM 66 H H362 98D . . . B 2 -8.847 12.266 8.422 1 82.15 ? H362 98D 601 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 289 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 66 #