data_5VDK # _model_server_result.job_id w2usXFYaDY1T2ozsT1KtEg _model_server_result.datetime_utc '2024-11-29 14:17:27' _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 5vdk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 5VDK # _exptl.entry_id 5VDK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 500.595 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1-[6-(2-hydroxypropan-2-yl)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 90 _cell.angle_gamma 120 _cell.entry_id 5VDK _cell.length_a 68.81 _cell.length_b 68.81 _cell.length_c 58.04 _cell.Z_PDB 3 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5VDK _symmetry.cell_setting ? _symmetry.Int_Tables_number 145 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32' # _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 _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 B _struct_conn.ptnr1_label_atom_id C21 _struct_conn.ptnr1_label_comp_id 8X7 _struct_conn.ptnr1_label_seq_id . _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id 8X7 _struct_conn.ptnr1_auth_seq_id 501 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id C _struct_conn.ptnr2_label_atom_id O1 _struct_conn.ptnr2_label_comp_id PO4 _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id PO4 _struct_conn.ptnr2_auth_seq_id 502 _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 1.377 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C27 H32 N8 O2' _chem_comp.formula_weight 500.595 _chem_comp.id 8X7 _chem_comp.mon_nstd_flag . _chem_comp.name 1-[6-(2-hydroxypropan-2-yl)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 8X7 sing 1 n n N02 C03 8X7 sing 2 n n N02 C07 8X7 sing 3 n n C03 C04 8X7 sing 4 n n C07 C06 8X7 sing 5 n n C04 N05 8X7 sing 6 n n C06 N05 8X7 sing 7 n n N05 C08 8X7 sing 8 n n C08 C37 8X7 doub 9 n y C08 C09 8X7 sing 10 n y C37 C36 8X7 sing 11 n y C09 C10 8X7 doub 12 n y C36 C11 8X7 doub 13 n y C10 C11 8X7 sing 14 n y C11 N12 8X7 sing 15 n n N12 C13 8X7 sing 16 n n C30 C29 8X7 doub 17 n y C30 C31 8X7 sing 18 n y C29 C28 8X7 sing 19 n y C33 C32 8X7 sing 20 n n C13 N25 8X7 doub 21 n y C13 N14 8X7 sing 22 n y C31 C26 8X7 doub 23 n y N25 C24 8X7 sing 24 n y C28 C32 8X7 sing 25 n n C28 N27 8X7 doub 26 n y O35 C32 8X7 sing 27 n n C32 C34 8X7 sing 28 n n N14 C15 8X7 doub 29 n y C26 N27 8X7 sing 30 n y C26 N23 8X7 sing 31 n n C24 N23 8X7 sing 32 n n C24 C16 8X7 doub 33 n y N23 N19 8X7 sing 34 n n C15 C16 8X7 sing 35 n y C16 C17 8X7 sing 36 n n N19 C17 8X7 sing 37 n n N19 C20 8X7 sing 38 n n C17 O18 8X7 doub 39 n n C20 C21 8X7 sing 40 n n C21 C22 8X7 doub 41 n n C01 H011 8X7 sing 42 n n C01 H013 8X7 sing 43 n n C01 H012 8X7 sing 44 n n C03 H031 8X7 sing 45 n n C03 H032 8X7 sing 46 n n C04 H041 8X7 sing 47 n n C04 H042 8X7 sing 48 n n C06 H061 8X7 sing 49 n n C06 H062 8X7 sing 50 n n C07 H072 8X7 sing 51 n n C07 H071 8X7 sing 52 n n C09 H091 8X7 sing 53 n n C10 H101 8X7 sing 54 n n N12 H121 8X7 sing 55 n n C15 H151 8X7 sing 56 n n C20 H202 8X7 sing 57 n n C20 H201 8X7 sing 58 n n C21 H211 8X7 sing 59 n n C22 H221 8X7 sing 60 n n C22 H222 8X7 sing 61 n n C29 H291 8X7 sing 62 n n C30 H301 8X7 sing 63 n n C31 H311 8X7 sing 64 n n C33 H331 8X7 sing 65 n n C33 H333 8X7 sing 66 n n C33 H332 8X7 sing 67 n n C34 H342 8X7 sing 68 n n C34 H341 8X7 sing 69 n n C34 H343 8X7 sing 70 n n O35 H351 8X7 sing 71 n n C36 H361 8X7 sing 72 n n C37 H371 8X7 sing 73 n n # _atom_sites.entry_id 5VDK _atom_sites.fract_transf_matrix[1][1] 0.014533 _atom_sites.fract_transf_matrix[1][2] 0.00839 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.016781 _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] 0.017229 _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 8X7 A 1 501 1 8X7 MK1 . C 3 PO4 A 1 502 1 PO4 PO4 . D 3 PO4 A 1 503 2 PO4 PO4 . E 3 PO4 A 1 504 3 PO4 PO4 . F 4 HOH A 1 601 3 HOH HOH . F 4 HOH A 2 602 4 HOH HOH . F 4 HOH A 3 603 1 HOH HOH . F 4 HOH A 4 604 6 HOH HOH . F 4 HOH A 5 605 7 HOH HOH . F 4 HOH A 6 606 8 HOH HOH . F 4 HOH A 7 607 9 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 C01 8X7 . . . B 2 -11.988 -23 -23.373 1 33.97 ? C01 8X7 501 A 1 HETATM 2 N N02 8X7 . . . B 2 -12.449 -23.227 -21.974 1 34.03 ? N02 8X7 501 A 1 HETATM 3 C C03 8X7 . . . B 2 -11.613 -22.54 -20.947 1 33.52 ? C03 8X7 501 A 1 HETATM 4 C C04 8X7 . . . B 2 -12.243 -22.676 -19.534 1 33.19 ? C04 8X7 501 A 1 HETATM 5 N N05 8X7 . . . B 2 -12.629 -24.045 -19.205 1 33.04 ? N05 8X7 501 A 1 HETATM 6 C C06 8X7 . . . B 2 -13.415 -24.694 -20.247 1 33.56 ? C06 8X7 501 A 1 HETATM 7 C C07 8X7 . . . B 2 -12.671 -24.658 -21.608 1 33.86 ? C07 8X7 501 A 1 HETATM 8 C C08 8X7 . . . B 2 -12.751 -24.434 -17.868 1 31.6 ? C08 8X7 501 A 1 HETATM 9 C C09 8X7 . . . B 2 -12.248 -23.65 -16.795 1 30.9 ? C09 8X7 501 A 1 HETATM 10 C C10 8X7 . . . B 2 -12.377 -24.047 -15.452 1 30.17 ? C10 8X7 501 A 1 HETATM 11 C C11 8X7 . . . B 2 -13.02 -25.263 -15.113 1 29.4 ? C11 8X7 501 A 1 HETATM 12 N N12 8X7 . . . B 2 -13.217 -25.77 -13.85 1 28.02 ? N12 8X7 501 A 1 HETATM 13 C C13 8X7 . . . B 2 -12.409 -25.743 -12.746 1 26.6 ? C13 8X7 501 A 1 HETATM 14 N N14 8X7 . . . B 2 -12.802 -26.397 -11.617 1 26.43 ? N14 8X7 501 A 1 HETATM 15 C C15 8X7 . . . B 2 -12.042 -26.407 -10.482 1 26.26 ? C15 8X7 501 A 1 HETATM 16 C C16 8X7 . . . B 2 -10.815 -25.72 -10.482 1 25.67 ? C16 8X7 501 A 1 HETATM 17 C C17 8X7 . . . B 2 -9.79 -25.511 -9.522 1 25.14 ? C17 8X7 501 A 1 HETATM 18 O O18 8X7 . . . B 2 -9.691 -25.921 -8.314 1 25.01 ? O18 8X7 501 A 1 HETATM 19 N N19 8X7 . . . B 2 -8.834 -24.751 -10.148 1 26.36 ? N19 8X7 501 A 1 HETATM 20 C C20 8X7 . . . B 2 -7.607 -24.282 -9.502 1 27.99 ? C20 8X7 501 A 1 HETATM 21 C C21 8X7 . . . B 2 -6.871 -25.228 -8.667 1 29.37 ? C21 8X7 501 A 1 HETATM 22 C C22 8X7 . . . B 2 -6.675 -26.494 -9.042 1 28.98 ? C22 8X7 501 A 1 HETATM 23 N N23 8X7 . . . B 2 -9.22 -24.479 -11.4 1 25.79 ? N23 8X7 501 A 1 HETATM 24 C C24 8X7 . . . B 2 -10.419 -25.061 -11.618 1 25.6 ? C24 8X7 501 A 1 HETATM 25 N N25 8X7 . . . B 2 -11.219 -25.088 -12.711 1 26.04 ? N25 8X7 501 A 1 HETATM 26 C C26 8X7 . . . B 2 -8.602 -23.739 -12.385 1 24.95 ? C26 8X7 501 A 1 HETATM 27 N N27 8X7 . . . B 2 -7.806 -22.714 -12.015 1 24.75 ? N27 8X7 501 A 1 HETATM 28 C C28 8X7 . . . B 2 -7.129 -21.886 -12.843 1 23.99 ? C28 8X7 501 A 1 HETATM 29 C C29 8X7 . . . B 2 -7.263 -22.084 -14.236 1 23.77 ? C29 8X7 501 A 1 HETATM 30 C C30 8X7 . . . B 2 -8.087 -23.126 -14.694 1 23.62 ? C30 8X7 501 A 1 HETATM 31 C C31 8X7 . . . B 2 -8.756 -23.956 -13.777 1 23.98 ? C31 8X7 501 A 1 HETATM 32 C C32 8X7 . . . B 2 -6.292 -20.83 -12.209 1 23.41 ? C32 8X7 501 A 1 HETATM 33 C C33 8X7 . . . B 2 -5.843 -19.711 -13.19 1 23.06 ? C33 8X7 501 A 1 HETATM 34 C C34 8X7 . . . B 2 -5.084 -21.517 -11.513 1 22.82 ? C34 8X7 501 A 1 HETATM 35 O O35 8X7 . . . B 2 -7.046 -20.19 -11.174 1 23.98 ? O35 8X7 501 A 1 HETATM 36 C C36 8X7 . . . B 2 -13.525 -26.044 -16.17 1 30.06 ? C36 8X7 501 A 1 HETATM 37 C C37 8X7 . . . B 2 -13.396 -25.645 -17.51 1 30.67 ? C37 8X7 501 A 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 40 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 916 _model_server_stats.encode_time_ms 17 _model_server_stats.element_count 37 #