data_5VD9 # _model_server_result.job_id fnz7b2ZeQQfiobbXRY_anQ _model_server_result.datetime_utc '2024-11-08 19:55:16' _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 5vd9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":601}' # _entry.id 5VD9 # _exptl.entry_id 5VD9 _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-[(1R)-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 102.14 _cell.angle_gamma 90 _cell.entry_id 5VD9 _cell.length_a 50.37 _cell.length_b 44.59 _cell.length_c 64.59 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5VD9 _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 98G _chem_comp.mon_nstd_flag . _chem_comp.name 1-{6-[(1R)-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 98G sing 1 n n N02 C36 98G sing 2 n n N02 C03 98G sing 3 n n C36 C35 98G sing 4 n n C21 C20 98G sing 5 n n C35 N05 98G sing 6 n n O22 C20 98G sing 7 n n C03 C04 98G sing 8 n n C23 C24 98G doub 9 n y C23 C19 98G sing 10 n y C24 C25 98G sing 11 n y C20 C19 98G sing 12 n n C04 N05 98G sing 13 n n C19 N18 98G doub 14 n y N05 C06 98G sing 15 n n C25 C17 98G doub 16 n y N18 C17 98G sing 17 n y C06 C34 98G doub 18 n y C06 C07 98G sing 19 n y C34 C33 98G sing 20 n y C17 N16 98G sing 21 n n C28 C27 98G sing 22 n n C28 C29 98G doub 23 n n C07 C08 98G doub 24 n y C33 C09 98G doub 25 n y N16 N26 98G sing 26 n n N16 C15 98G sing 27 n n C27 N26 98G sing 28 n n N26 C30 98G sing 29 n n C09 C08 98G sing 30 n y C09 N10 98G sing 31 n n N32 C15 98G doub 32 n y N32 C11 98G sing 33 n y C15 C14 98G sing 34 n y N10 C11 98G sing 35 n n C11 N12 98G doub 36 n y C30 C14 98G sing 37 n n C30 O31 98G doub 38 n n C14 C13 98G doub 39 n y N12 C13 98G sing 40 n y C13 H131 98G sing 41 n n C20 H201 98G sing 42 n n C21 H212 98G sing 43 n n C21 H213 98G sing 44 n n C21 H211 98G sing 45 n n C24 H241 98G sing 46 n n C28 H281 98G sing 47 n n C01 H012 98G sing 48 n n C01 H013 98G sing 49 n n C01 H011 98G sing 50 n n C03 H032 98G sing 51 n n C03 H031 98G sing 52 n n C04 H042 98G sing 53 n n C04 H041 98G sing 54 n n C07 H071 98G sing 55 n n C08 H081 98G sing 56 n n N10 H101 98G sing 57 n n O22 H221 98G sing 58 n n C23 H231 98G sing 59 n n C25 H251 98G sing 60 n n C27 H272 98G sing 61 n n C27 H271 98G sing 62 n n C29 H292 98G sing 63 n n C29 H291 98G sing 64 n n C33 H331 98G sing 65 n n C34 H341 98G sing 66 n n C35 H352 98G sing 67 n n C35 H351 98G sing 68 n n C36 H361 98G sing 69 n n C36 H362 98G sing 70 n n # _atom_sites.entry_id 5VD9 _atom_sites.fract_transf_matrix[1][1] 0.019853 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00427 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.022427 _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] 0.015836 _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 98G A 1 601 1 98G 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 48 HOH HOH . E 5 HOH A 2 702 42 HOH HOH . E 5 HOH A 3 703 58 HOH HOH . E 5 HOH A 4 704 25 HOH HOH . E 5 HOH A 5 705 23 HOH HOH . E 5 HOH A 6 706 41 HOH HOH . E 5 HOH A 7 707 44 HOH HOH . E 5 HOH A 8 708 39 HOH HOH . E 5 HOH A 9 709 26 HOH HOH . E 5 HOH A 10 710 8 HOH HOH . E 5 HOH A 11 711 7 HOH HOH . E 5 HOH A 12 712 17 HOH HOH . E 5 HOH A 13 713 45 HOH HOH . E 5 HOH A 14 714 5 HOH HOH . E 5 HOH A 15 715 18 HOH HOH . E 5 HOH A 16 716 2 HOH HOH . E 5 HOH A 17 717 55 HOH HOH . E 5 HOH A 18 718 3 HOH HOH . E 5 HOH A 19 719 61 HOH HOH . E 5 HOH A 20 720 43 HOH HOH . E 5 HOH A 21 721 9 HOH HOH . E 5 HOH A 22 722 51 HOH HOH . E 5 HOH A 23 723 60 HOH HOH . E 5 HOH A 24 724 11 HOH HOH . E 5 HOH A 25 725 52 HOH HOH . E 5 HOH A 26 726 20 HOH HOH . E 5 HOH A 27 727 19 HOH HOH . E 5 HOH A 28 728 54 HOH HOH . E 5 HOH A 29 729 22 HOH HOH . E 5 HOH A 30 730 4 HOH HOH . E 5 HOH A 31 731 28 HOH HOH . E 5 HOH A 32 732 57 HOH HOH . E 5 HOH A 33 733 10 HOH HOH . E 5 HOH A 34 734 1 HOH HOH . E 5 HOH A 35 735 21 HOH HOH . E 5 HOH A 36 736 50 HOH HOH . E 5 HOH A 37 737 14 HOH HOH . E 5 HOH A 38 738 35 HOH HOH . E 5 HOH A 39 739 13 HOH HOH . E 5 HOH A 40 740 12 HOH HOH . E 5 HOH A 41 741 53 HOH HOH . E 5 HOH A 42 742 37 HOH HOH . E 5 HOH A 43 743 15 HOH HOH . E 5 HOH A 44 744 16 HOH HOH . E 5 HOH A 45 745 49 HOH HOH . E 5 HOH A 46 746 27 HOH HOH . E 5 HOH A 47 747 46 HOH HOH . E 5 HOH A 48 748 38 HOH HOH . E 5 HOH A 49 749 34 HOH HOH . E 5 HOH A 50 750 6 HOH HOH . E 5 HOH A 51 751 24 HOH HOH . E 5 HOH A 52 752 31 HOH HOH . E 5 HOH A 53 753 47 HOH HOH . E 5 HOH A 54 754 40 HOH HOH . E 5 HOH A 55 755 29 HOH HOH . E 5 HOH A 56 756 36 HOH HOH . E 5 HOH A 57 757 62 HOH HOH . E 5 HOH A 58 758 56 HOH HOH . E 5 HOH A 59 759 32 HOH HOH . E 5 HOH A 60 760 33 HOH HOH . E 5 HOH A 61 761 59 HOH HOH . E 5 HOH A 62 762 30 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 98G . . . B 2 -5.728 4.757 15.107 1 24.55 ? N12 98G 601 A 1 HETATM 2 C C13 98G . . . B 2 -4.967 3.635 15.26 1 26.67 ? C13 98G 601 A 1 HETATM 3 C C15 98G . . . B 2 -4.464 3.777 12.936 1 25.95 ? C15 98G 601 A 1 HETATM 4 C C17 98G . . . B 2 -3.53 3.586 10.785 1 30.82 ? C17 98G 601 A 1 HETATM 5 C C20 98G . . . B 2 -0.204 3.75 8.969 1 42.2 ? C20 98G 601 A 1 HETATM 6 C C21 98G . . . B 2 -0.121 2.494 8.087 1 42.09 ? C21 98G 601 A 1 HETATM 7 C C24 98G . . . B 2 -3.759 4.952 8.81 1 31.68 ? C24 98G 601 A 1 HETATM 8 C C28 98G . . . B 2 -3.201 0.162 11.497 1 30.48 ? C28 98G 601 A 1 HETATM 9 C C01 98G . . . B 2 -8.264 12.957 6.614 1 57.88 ? C01 98G 601 A 1 HETATM 10 N N02 98G . . . B 2 -8.09 11.615 7.241 1 53.6 ? N02 98G 601 A 1 HETATM 11 C C03 98G . . . B 2 -9.003 11.467 8.409 1 53.22 ? C03 98G 601 A 1 HETATM 12 C C04 98G . . . B 2 -8.882 10.059 9.021 1 46.53 ? C04 98G 601 A 1 HETATM 13 N N05 98G . . . B 2 -7.516 9.835 9.414 1 33.29 ? N05 98G 601 A 1 HETATM 14 C C06 98G . . . B 2 -7.25 8.986 10.472 1 27.7 ? C06 98G 601 A 1 HETATM 15 C C07 98G . . . B 2 -8.135 8.873 11.552 1 26.72 ? C07 98G 601 A 1 HETATM 16 C C08 98G . . . B 2 -7.904 8.032 12.637 1 23.52 ? C08 98G 601 A 1 HETATM 17 C C09 98G . . . B 2 -6.743 7.244 12.626 1 19.96 ? C09 98G 601 A 1 HETATM 18 N N10 98G . . . B 2 -6.607 6.476 13.765 1 22.91 ? N10 98G 601 A 1 HETATM 19 C C11 98G . . . B 2 -5.871 5.365 13.908 1 20.58 ? C11 98G 601 A 1 HETATM 20 C C14 98G . . . B 2 -4.293 3.124 14.153 1 24.29 ? C14 98G 601 A 1 HETATM 21 N N16 98G . . . B 2 -3.785 3.103 12.003 1 24.82 ? N16 98G 601 A 1 HETATM 22 N N18 98G . . . B 2 -2.209 3.503 10.439 1 26.14 ? N18 98G 601 A 1 HETATM 23 C C19 98G . . . B 2 -1.632 4.004 9.298 1 31.72 ? C19 98G 601 A 1 HETATM 24 O O22 98G . . . B 2 0.423 4.906 8.36 1 41.24 ? O22 98G 601 A 1 HETATM 25 C C23 98G . . . B 2 -2.433 4.772 8.45 1 24.44 ? C23 98G 601 A 1 HETATM 26 C C25 98G . . . B 2 -4.303 4.433 9.995 1 26.14 ? C25 98G 601 A 1 HETATM 27 N N26 98G . . . B 2 -3.094 2.14 12.622 1 31.45 ? N26 98G 601 A 1 HETATM 28 C C27 98G . . . B 2 -2.283 1.138 12.048 1 29.1 ? C27 98G 601 A 1 HETATM 29 C C29 98G . . . B 2 -4.306 -0.343 12.08 1 37.53 ? C29 98G 601 A 1 HETATM 30 C C30 98G . . . B 2 -3.414 2.066 13.916 1 30.55 ? C30 98G 601 A 1 HETATM 31 O O31 98G . . . B 2 -2.964 1.16 14.679 1 29.15 ? O31 98G 601 A 1 HETATM 32 N N32 98G . . . B 2 -5.244 4.881 12.817 1 22.79 ? N32 98G 601 A 1 HETATM 33 C C33 98G . . . B 2 -5.848 7.361 11.558 1 29.29 ? C33 98G 601 A 1 HETATM 34 C C34 98G . . . B 2 -6.072 8.211 10.491 1 24.98 ? C34 98G 601 A 1 HETATM 35 C C35 98G . . . B 2 -6.54 10.005 8.349 1 48.72 ? C35 98G 601 A 1 HETATM 36 C C36 98G . . . B 2 -6.684 11.381 7.654 1 62.86 ? C36 98G 601 A 1 HETATM 37 H H131 98G . . . B 2 -4.899 3.18 16.173 1 32 ? H131 98G 601 A 1 HETATM 38 H H201 98G . . . B 2 0.348 3.551 9.892 1 50.65 ? H201 98G 601 A 1 HETATM 39 H H212 98G . . . B 2 -0.558 2.687 7.104 1 50.5 ? H212 98G 601 A 1 HETATM 40 H H213 98G . . . B 2 -0.654 1.665 8.555 1 50.5 ? H213 98G 601 A 1 HETATM 41 H H211 98G . . . B 2 0.922 2.199 7.95 1 50.5 ? H211 98G 601 A 1 HETATM 42 H H241 98G . . . B 2 -4.361 5.507 8.198 1 38.01 ? H241 98G 601 A 1 HETATM 43 H H281 98G . . . B 2 -2.987 -0.173 10.583 1 36.57 ? H281 98G 601 A 1 HETATM 44 H H012 98G . . . B 2 -7.637 13.043 5.724 1 69.46 ? H012 98G 601 A 1 HETATM 45 H H013 98G . . . B 2 -7.963 13.747 7.307 1 69.46 ? H013 98G 601 A 1 HETATM 46 H H011 98G . . . B 2 -9.307 13.126 6.326 1 69.46 ? H011 98G 601 A 1 HETATM 47 H H032 98G . . . B 2 -10.04 11.624 8.093 1 63.87 ? H032 98G 601 A 1 HETATM 48 H H031 98G . . . B 2 -8.761 12.209 9.175 1 63.87 ? H031 98G 601 A 1 HETATM 49 H H042 98G . . . B 2 -9.171 9.309 8.277 1 55.83 ? H042 98G 601 A 1 HETATM 50 H H041 98G . . . B 2 -9.575 9.975 9.863 1 55.83 ? H041 98G 601 A 1 HETATM 51 H H071 98G . . . B 2 -8.989 9.436 11.549 1 32.06 ? H071 98G 601 A 1 HETATM 52 H H081 98G . . . B 2 -8.579 7.98 13.404 1 28.23 ? H081 98G 601 A 1 HETATM 53 H H101 98G . . . B 2 -7.096 6.772 14.547 1 27.49 ? H101 98G 601 A 1 HETATM 54 H H221 98G . . . B 2 0.185 5.664 8.935 1 49.48 ? H221 98G 601 A 1 HETATM 55 H H231 98G . . . B 2 -2.071 5.167 7.577 1 29.32 ? H231 98G 601 A 1 HETATM 56 H H251 98G . . . B 2 -5.29 4.587 10.212 1 31.36 ? H251 98G 601 A 1 HETATM 57 H H272 98G . . . B 2 -1.605 1.563 11.3 1 34.92 ? H272 98G 601 A 1 HETATM 58 H H271 98G . . . B 2 -1.649 0.645 12.782 1 34.92 ? H271 98G 601 A 1 HETATM 59 H H292 98G . . . B 2 -4.568 -0.045 12.991 1 45.03 ? H292 98G 601 A 1 HETATM 60 H H291 98G . . . B 2 -4.877 -1.013 11.62 1 45.03 ? H291 98G 601 A 1 HETATM 61 H H331 98G . . . B 2 -4.988 6.812 11.547 1 35.15 ? H331 98G 601 A 1 HETATM 62 H H341 98G . . . B 2 -5.402 8.251 9.721 1 29.97 ? H341 98G 601 A 1 HETATM 63 H H352 98G . . . B 2 -5.512 9.907 8.712 1 58.46 ? H352 98G 601 A 1 HETATM 64 H H351 98G . . . B 2 -6.692 9.212 7.611 1 58.46 ? H351 98G 601 A 1 HETATM 65 H H361 98G . . . B 2 -6.366 12.158 8.356 1 75.44 ? H361 98G 601 A 1 HETATM 66 H H362 98G . . . B 2 -6.023 11.412 6.782 1 75.44 ? H362 98G 601 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 227 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 66 #