data_5VD4 # _model_server_result.job_id rZ0r-4zV620XOe_GXgPYbQ _model_server_result.datetime_utc '2024-12-03 17:30:43' _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 5vd4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":601}' # _entry.id 5VD4 # _exptl.entry_id 5VD4 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 540.54 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 6-{[4-(4-methylpiperazin-1-yl)phenyl]amino}-2-(prop-2-en-1-yl)-1-{6-[(1S)-2,2,2-trifluoro-1-hydroxyethyl]pyridin-2-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 103.04 _cell.angle_gamma 90 _cell.entry_id 5VD4 _cell.length_a 50.31 _cell.length_b 43.78 _cell.length_c 64.86 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5VD4 _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,F,G,H,I _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 H27 F3 N8 O2' _chem_comp.formula_weight 540.54 _chem_comp.id 99J _chem_comp.mon_nstd_flag . _chem_comp.name 6-{[4-(4-methylpiperazin-1-yl)phenyl]amino}-2-(prop-2-en-1-yl)-1-{6-[(1S)-2,2,2-trifluoro-1-hydroxyethyl]pyridin-2-yl}-1,2-dihydro-3H-pyrazolo[3,4-d]pyrimidin-3-one _chem_comp.type non-polymer _chem_comp.pdbx_synonyms RAC-IV-016 # 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 F36 C34 99J sing 1 n n C01 N02 99J sing 2 n n N02 C07 99J sing 3 n n N02 C03 99J sing 4 n n F35 C34 99J sing 5 n n C34 F37 99J sing 6 n n C34 C32 99J sing 7 n n C07 C06 99J sing 8 n n O33 C32 99J sing 9 n n C03 C04 99J sing 10 n n C29 C30 99J doub 11 n y C29 C28 99J sing 12 n y C32 C28 99J sing 13 n n C04 N05 99J sing 14 n n C30 C31 99J sing 15 n y C28 N27 99J doub 16 n y C06 N05 99J sing 17 n n N05 C08 99J sing 18 n n C31 C26 99J doub 19 n y N27 C26 99J sing 20 n y C08 C39 99J doub 21 n y C08 C09 99J sing 22 n y C39 C38 99J sing 23 n y C26 N23 99J sing 24 n n C21 C22 99J doub 25 n n C21 C20 99J sing 26 n n C38 C11 99J doub 27 n y C09 C10 99J doub 28 n y C20 N19 99J sing 29 n n N23 N19 99J sing 30 n n N23 C24 99J sing 31 n n N19 C17 99J sing 32 n n C10 C11 99J sing 33 n y C11 N12 99J sing 34 n n N25 C24 99J doub 35 n y N25 C13 99J sing 36 n y C24 C16 99J sing 37 n y N12 C13 99J sing 38 n n C17 C16 99J sing 39 n n C17 O18 99J doub 40 n n C13 N14 99J doub 41 n y C16 C15 99J doub 42 n y N14 C15 99J sing 43 n y C10 H101 99J sing 44 n n N12 H121 99J sing 45 n n C15 H151 99J sing 46 n n C20 H201 99J sing 47 n n C20 H202 99J sing 48 n n C21 H211 99J sing 49 n n C22 H221 99J sing 50 n n C22 H222 99J sing 51 n n C01 H012 99J sing 52 n n C01 H013 99J sing 53 n n C01 H011 99J sing 54 n n C03 H032 99J sing 55 n n C03 H031 99J sing 56 n n C04 H042 99J sing 57 n n C04 H041 99J sing 58 n n C06 H062 99J sing 59 n n C06 H061 99J sing 60 n n C07 H071 99J sing 61 n n C07 H072 99J sing 62 n n C09 H091 99J sing 63 n n C29 H291 99J sing 64 n n C30 H301 99J sing 65 n n C31 H311 99J sing 66 n n C32 H321 99J sing 67 n n O33 H331 99J sing 68 n n C38 H381 99J sing 69 n n C39 H391 99J sing 70 n n # _atom_sites.entry_id 5VD4 _atom_sites.fract_transf_matrix[1][1] 0.019877 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004605 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.022841 _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] 0.015826 _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 99J A 1 601 1 99J LIG . C 3 PO4 A 1 602 1 PO4 PO4 . D 3 PO4 A 1 603 2 PO4 PO4 . E 4 EDO A 1 604 1 EDO EDO . F 4 EDO A 1 605 2 EDO EDO . G 4 EDO A 1 606 3 EDO EDO . H 5 CL A 1 607 1 CL CL . I 6 HOH A 1 701 28 HOH HOH . I 6 HOH A 2 702 51 HOH HOH . I 6 HOH A 3 703 5 HOH HOH . I 6 HOH A 4 704 15 HOH HOH . I 6 HOH A 5 705 21 HOH HOH . I 6 HOH A 6 706 43 HOH HOH . I 6 HOH A 7 707 17 HOH HOH . I 6 HOH A 8 708 9 HOH HOH . I 6 HOH A 9 709 1 HOH HOH . I 6 HOH A 10 710 23 HOH HOH . I 6 HOH A 11 711 4 HOH HOH . I 6 HOH A 12 712 18 HOH HOH . I 6 HOH A 13 713 6 HOH HOH . I 6 HOH A 14 714 49 HOH HOH . I 6 HOH A 15 715 39 HOH HOH . I 6 HOH A 16 716 8 HOH HOH . I 6 HOH A 17 717 22 HOH HOH . I 6 HOH A 18 718 45 HOH HOH . I 6 HOH A 19 719 29 HOH HOH . I 6 HOH A 20 720 2 HOH HOH . I 6 HOH A 21 721 31 HOH HOH . I 6 HOH A 22 722 10 HOH HOH . I 6 HOH A 23 723 3 HOH HOH . I 6 HOH A 24 724 52 HOH HOH . I 6 HOH A 25 725 13 HOH HOH . I 6 HOH A 26 726 26 HOH HOH . I 6 HOH A 27 727 44 HOH HOH . I 6 HOH A 28 728 48 HOH HOH . I 6 HOH A 29 729 30 HOH HOH . I 6 HOH A 30 730 32 HOH HOH . I 6 HOH A 31 731 7 HOH HOH . I 6 HOH A 32 732 14 HOH HOH . I 6 HOH A 33 733 25 HOH HOH . I 6 HOH A 34 734 12 HOH HOH . I 6 HOH A 35 735 46 HOH HOH . I 6 HOH A 36 736 24 HOH HOH . I 6 HOH A 37 737 11 HOH HOH . I 6 HOH A 38 738 36 HOH HOH . I 6 HOH A 39 739 16 HOH HOH . I 6 HOH A 40 740 40 HOH HOH . I 6 HOH A 41 741 47 HOH HOH . I 6 HOH A 42 742 34 HOH HOH . I 6 HOH A 43 743 38 HOH HOH . I 6 HOH A 44 744 27 HOH HOH . I 6 HOH A 45 745 50 HOH HOH . I 6 HOH A 46 746 41 HOH HOH . I 6 HOH A 47 747 19 HOH HOH . I 6 HOH A 48 748 42 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 99J . . . B 2 -7.962 7.952 12.792 1 34.34 ? C10 99J 601 A 1 HETATM 2 N N12 99J . . . B 2 -6.678 6.334 13.933 1 26.77 ? N12 99J 601 A 1 HETATM 3 C C13 99J . . . B 2 -5.945 5.169 14.026 1 24.68 ? C13 99J 601 A 1 HETATM 4 C C15 99J . . . B 2 -5.246 3.286 15.339 1 26 ? C15 99J 601 A 1 HETATM 5 C C17 99J . . . B 2 -3.669 1.739 14.003 1 48.89 ? C17 99J 601 A 1 HETATM 6 C C20 99J . . . B 2 -2.347 0.873 12.146 1 47.34 ? C20 99J 601 A 1 HETATM 7 C C21 99J . . . B 2 -3.209 -0.066 11.441 1 40.58 ? C21 99J 601 A 1 HETATM 8 C C22 99J . . . B 2 -4.217 -0.748 12.014 1 20.17 ? C22 99J 601 A 1 HETATM 9 C C24 99J . . . B 2 -4.497 3.555 13.091 1 42.79 ? C24 99J 601 A 1 HETATM 10 C C26 99J . . . B 2 -3.52 3.477 10.933 1 42.44 ? C26 99J 601 A 1 HETATM 11 C C28 99J . . . B 2 -1.869 3.779 9.211 1 33.63 ? C28 99J 601 A 1 HETATM 12 C C01 99J . . . B 2 -8.325 12.828 6.693 1 51.67 ? C01 99J 601 A 1 HETATM 13 N N02 99J . . . B 2 -7.91 11.534 7.304 1 42.87 ? N02 99J 601 A 1 HETATM 14 C C03 99J . . . B 2 -6.82 11.696 8.308 1 48.76 ? C03 99J 601 A 1 HETATM 15 C C04 99J . . . B 2 -6.433 10.309 8.863 1 34.46 ? C04 99J 601 A 1 HETATM 16 N N05 99J . . . B 2 -7.563 9.719 9.549 1 34.12 ? N05 99J 601 A 1 HETATM 17 C C06 99J . . . B 2 -8.882 10.265 9.301 1 55.9 ? C06 99J 601 A 1 HETATM 18 C C07 99J . . . B 2 -9.065 10.734 7.83 1 42.73 ? C07 99J 601 A 1 HETATM 19 C C08 99J . . . B 2 -7.326 8.875 10.611 1 32.44 ? C08 99J 601 A 1 HETATM 20 C C09 99J . . . B 2 -8.214 8.812 11.708 1 32.56 ? C09 99J 601 A 1 HETATM 21 C C11 99J . . . B 2 -6.819 7.12 12.812 1 32.05 ? C11 99J 601 A 1 HETATM 22 N N14 99J . . . B 2 -5.948 4.448 15.185 1 30.37 ? N14 99J 601 A 1 HETATM 23 C C16 99J . . . B 2 -4.494 2.821 14.256 1 25.78 ? C16 99J 601 A 1 HETATM 24 O O18 99J . . . B 2 -3.39 0.817 14.801 1 25.34 ? O18 99J 601 A 1 HETATM 25 N N19 99J . . . B 2 -3.212 1.863 12.733 1 46.75 ? N19 99J 601 A 1 HETATM 26 N N23 99J . . . B 2 -3.728 2.946 12.176 1 32.05 ? N23 99J 601 A 1 HETATM 27 N N25 99J . . . B 2 -5.209 4.694 12.993 1 23.03 ? N25 99J 601 A 1 HETATM 28 N N27 99J . . . B 2 -2.283 3.313 10.411 1 38.72 ? N27 99J 601 A 1 HETATM 29 C C29 99J . . . B 2 -2.788 4.52 8.434 1 25.46 ? C29 99J 601 A 1 HETATM 30 C C30 99J . . . B 2 -4.087 4.74 8.934 1 25.83 ? C30 99J 601 A 1 HETATM 31 C C31 99J . . . B 2 -4.461 4.229 10.192 1 25.6 ? C31 99J 601 A 1 HETATM 32 C C32 99J . . . B 2 -0.474 3.471 8.805 1 30.55 ? C32 99J 601 A 1 HETATM 33 O O33 99J . . . B 2 0.167 4.614 8.24 1 36.58 ? O33 99J 601 A 1 HETATM 34 C C34 99J . . . B 2 -0.422 2.286 7.809 1 39.45 ? C34 99J 601 A 1 HETATM 35 F F35 99J . . . B 2 0.874 1.993 7.447 1 44.27 ? F35 99J 601 A 1 HETATM 36 F F36 99J . . . B 2 -1.152 2.565 6.68 1 37.44 ? F36 99J 601 A 1 HETATM 37 F F37 99J . . . B 2 -0.973 1.16 8.377 1 34.46 ? F37 99J 601 A 1 HETATM 38 C C38 99J . . . B 2 -5.924 7.192 11.706 1 29.66 ? C38 99J 601 A 1 HETATM 39 C C39 99J . . . B 2 -6.177 8.05 10.625 1 38.01 ? C39 99J 601 A 1 HETATM 40 H H101 99J . . . B 2 -8.591 7.925 13.544 1 41.21 ? H101 99J 601 A 1 HETATM 41 H H121 99J . . . B 2 -7.114 6.611 14.692 1 32.13 ? H121 99J 601 A 1 HETATM 42 H H151 99J . . . B 2 -5.272 2.789 16.185 1 31.2 ? H151 99J 601 A 1 HETATM 43 H H201 99J . . . B 2 -1.728 1.3 11.514 1 56.81 ? H201 99J 601 A 1 HETATM 44 H H202 99J . . . B 2 -1.844 0.406 12.849 1 56.81 ? H202 99J 601 A 1 HETATM 45 H H211 99J . . . B 2 -3.038 -0.207 10.487 1 48.69 ? H211 99J 601 A 1 HETATM 46 H H221 99J . . . B 2 -4.41 -0.627 12.967 1 24.21 ? H221 99J 601 A 1 HETATM 47 H H222 99J . . . B 2 -4.758 -1.366 11.478 1 24.21 ? H222 99J 601 A 1 HETATM 48 H H012 99J . . . B 2 -8.963 12.657 5.966 1 62 ? H012 99J 601 A 1 HETATM 49 H H013 99J . . . B 2 -7.534 13.289 6.333 1 62 ? H013 99J 601 A 1 HETATM 50 H H011 99J . . . B 2 -8.75 13.392 7.377 1 62 ? H011 99J 601 A 1 HETATM 51 H H032 99J . . . B 2 -7.132 12.269 9.044 1 58.51 ? H032 99J 601 A 1 HETATM 52 H H031 99J . . . B 2 -6.036 12.11 7.88 1 58.51 ? H031 99J 601 A 1 HETATM 53 H H042 99J . . . B 2 -5.684 10.406 9.491 1 41.36 ? H042 99J 601 A 1 HETATM 54 H H041 99J . . . B 2 -6.162 9.724 8.119 1 41.36 ? H041 99J 601 A 1 HETATM 55 H H062 99J . . . B 2 -9.553 9.575 9.5 1 67.08 ? H062 99J 601 A 1 HETATM 56 H H061 99J . . . B 2 -9.026 11.032 9.9 1 67.08 ? H061 99J 601 A 1 HETATM 57 H H071 99J . . . B 2 -9.183 9.942 7.26 1 51.27 ? H071 99J 601 A 1 HETATM 58 H H072 99J . . . B 2 -9.878 11.285 7.775 1 51.27 ? H072 99J 601 A 1 HETATM 59 H H091 99J . . . B 2 -9.015 9.378 11.716 1 39.07 ? H091 99J 601 A 1 HETATM 60 H H291 99J . . . B 2 -2.526 4.872 7.557 1 30.55 ? H291 99J 601 A 1 HETATM 61 H H301 99J . . . B 2 -4.733 5.251 8.403 1 30.99 ? H301 99J 601 A 1 HETATM 62 H H311 99J . . . B 2 -5.365 4.38 10.542 1 30.72 ? H311 99J 601 A 1 HETATM 63 H H321 99J . . . B 2 0.024 3.211 9.61 1 36.66 ? H321 99J 601 A 1 HETATM 64 H H331 99J . . . B 2 0.746 4.351 7.614 1 43.9 ? H331 99J 601 A 1 HETATM 65 H H381 99J . . . B 2 -5.122 6.629 11.696 1 35.59 ? H381 99J 601 A 1 HETATM 66 H H391 99J . . . B 2 -5.549 8.08 9.873 1 45.61 ? H391 99J 601 A 1 # _model_server_stats.io_time_ms 54 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 270 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 66 #