data_5VD0 # _model_server_result.job_id azTzRA5lEoIqXNKLxSGBmw _model_server_result.datetime_utc '2024-11-28 06:07:20' _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 5vd0 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 5VD0 # _exptl.entry_id 5VD0 _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 90 _cell.entry_id 5VD0 _cell.length_a 46.78 _cell.length_b 53.87 _cell.length_c 113.62 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5VD0 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _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 _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 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 5VD0 _atom_sites.fract_transf_matrix[1][1] 0.021377 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.018563 _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] 0.008801 _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 1 401 1 8X7 MK1 . C 3 PEG A 1 402 1 PEG PEG . D 4 HOH A 1 501 42 HOH HOH . D 4 HOH A 2 502 1 HOH HOH . D 4 HOH A 3 503 19 HOH HOH . D 4 HOH A 4 504 45 HOH HOH . D 4 HOH A 5 505 40 HOH HOH . D 4 HOH A 6 506 11 HOH HOH . D 4 HOH A 7 507 43 HOH HOH . D 4 HOH A 8 508 31 HOH HOH . D 4 HOH A 9 509 28 HOH HOH . D 4 HOH A 10 510 26 HOH HOH . D 4 HOH A 11 511 66 HOH HOH . D 4 HOH A 12 512 22 HOH HOH . D 4 HOH A 13 513 57 HOH HOH . D 4 HOH A 14 514 15 HOH HOH . D 4 HOH A 15 515 36 HOH HOH . D 4 HOH A 16 516 49 HOH HOH . D 4 HOH A 17 517 44 HOH HOH . D 4 HOH A 18 518 61 HOH HOH . D 4 HOH A 19 519 17 HOH HOH . D 4 HOH A 20 520 5 HOH HOH . D 4 HOH A 21 521 20 HOH HOH . D 4 HOH A 22 522 58 HOH HOH . D 4 HOH A 23 523 27 HOH HOH . D 4 HOH A 24 524 18 HOH HOH . D 4 HOH A 25 525 10 HOH HOH . D 4 HOH A 26 526 68 HOH HOH . D 4 HOH A 27 527 65 HOH HOH . D 4 HOH A 28 528 13 HOH HOH . D 4 HOH A 29 529 9 HOH HOH . D 4 HOH A 30 530 53 HOH HOH . D 4 HOH A 31 531 6 HOH HOH . D 4 HOH A 32 532 33 HOH HOH . D 4 HOH A 33 533 3 HOH HOH . D 4 HOH A 34 534 63 HOH HOH . D 4 HOH A 35 535 54 HOH HOH . D 4 HOH A 36 536 23 HOH HOH . D 4 HOH A 37 537 52 HOH HOH . D 4 HOH A 38 538 21 HOH HOH . D 4 HOH A 39 539 50 HOH HOH . D 4 HOH A 40 540 47 HOH HOH . D 4 HOH A 41 541 25 HOH HOH . D 4 HOH A 42 542 7 HOH HOH . D 4 HOH A 43 543 41 HOH HOH . D 4 HOH A 44 544 56 HOH HOH . D 4 HOH A 45 545 64 HOH HOH . D 4 HOH A 46 546 32 HOH HOH . D 4 HOH A 47 547 39 HOH HOH . D 4 HOH A 48 548 38 HOH HOH . D 4 HOH A 49 549 14 HOH HOH . D 4 HOH A 50 550 67 HOH HOH . D 4 HOH A 51 551 12 HOH HOH . D 4 HOH A 52 552 35 HOH HOH . D 4 HOH A 53 553 16 HOH HOH . D 4 HOH A 54 554 34 HOH HOH . D 4 HOH A 55 555 2 HOH HOH . D 4 HOH A 56 556 55 HOH HOH . D 4 HOH A 57 557 51 HOH HOH . D 4 HOH A 58 558 48 HOH HOH . D 4 HOH A 59 559 46 HOH HOH . D 4 HOH A 60 560 37 HOH HOH . D 4 HOH A 61 561 59 HOH HOH . D 4 HOH A 62 562 29 HOH HOH . D 4 HOH A 63 563 4 HOH HOH . D 4 HOH A 64 564 60 HOH HOH . D 4 HOH A 65 565 30 HOH HOH . D 4 HOH A 66 566 8 HOH HOH . D 4 HOH A 67 567 24 HOH HOH . D 4 HOH A 68 568 62 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 -9.173 9.252 3.424 1 39.54 ? C01 8X7 401 A 1 HETATM 2 N N02 8X7 . . . B 2 -9.408 8.046 2.587 1 38.51 ? N02 8X7 401 A 1 HETATM 3 C C03 8X7 . . . B 2 -10.842 7.886 2.215 1 37.91 ? C03 8X7 401 A 1 HETATM 4 C C04 8X7 . . . B 2 -11.001 6.69 1.246 1 36.22 ? C04 8X7 401 A 1 HETATM 5 N N05 8X7 . . . B 2 -10.486 5.474 1.859 1 34.24 ? N05 8X7 401 A 1 HETATM 6 C C06 8X7 . . . B 2 -9.072 5.596 2.196 1 34.17 ? C06 8X7 401 A 1 HETATM 7 C C07 8X7 . . . B 2 -8.842 6.789 3.167 1 39.44 ? C07 8X7 401 A 1 HETATM 8 C C08 8X7 . . . B 2 -11.212 4.272 1.898 1 31.76 ? C08 8X7 401 A 1 HETATM 9 C C09 8X7 . . . B 2 -12.625 4.226 1.74 1 30.13 ? C09 8X7 401 A 1 HETATM 10 C C10 8X7 . . . B 2 -13.342 3.024 1.782 1 29.12 ? C10 8X7 401 A 1 HETATM 11 C C11 8X7 . . . B 2 -12.688 1.792 1.986 1 28.96 ? C11 8X7 401 A 1 HETATM 12 N N12 8X7 . . . B 2 -13.281 0.56 2.049 1 27.9 ? N12 8X7 401 A 1 HETATM 13 C C13 8X7 . . . B 2 -14.597 0.268 2.237 1 27.06 ? C13 8X7 401 A 1 HETATM 14 N N14 8X7 . . . B 2 -14.963 -1.039 2.249 1 27.72 ? N14 8X7 401 A 1 HETATM 15 C C15 8X7 . . . B 2 -16.25 -1.442 2.426 1 28.07 ? C15 8X7 401 A 1 HETATM 16 C C16 8X7 . . . B 2 -17.225 -0.452 2.604 1 27.76 ? C16 8X7 401 A 1 HETATM 17 C C17 8X7 . . . B 2 -18.626 -0.473 2.803 1 28.2 ? C17 8X7 401 A 1 HETATM 18 O O18 8X7 . . . B 2 -19.455 -1.443 2.891 1 28.6 ? O18 8X7 401 A 1 HETATM 19 N N19 8X7 . . . B 2 -19.003 0.835 2.898 1 28.23 ? N19 8X7 401 A 1 HETATM 20 C C20 8X7 . . . B 2 -20.378 1.214 3.13 1 30.33 ? C20 8X7 401 A 1 HETATM 21 C C21 8X7 . . . B 2 -20.707 0.798 4.48 1 32.23 ? C21 8X7 401 A 1 HETATM 22 C C22 8X7 . . . B 2 -21.751 0.017 4.782 1 33.22 ? C22 8X7 401 A 1 HETATM 23 N N23 8X7 . . . B 2 -17.948 1.635 2.792 1 26.17 ? N23 8X7 401 A 1 HETATM 24 C C24 8X7 . . . B 2 -16.857 0.871 2.598 1 26.57 ? C24 8X7 401 A 1 HETATM 25 N N25 8X7 . . . B 2 -15.565 1.207 2.415 1 25.99 ? N25 8X7 401 A 1 HETATM 26 C C26 8X7 . . . B 2 -17.874 3.001 2.788 1 25.13 ? C26 8X7 401 A 1 HETATM 27 N N27 8X7 . . . B 2 -18.9 3.654 2.21 1 24.91 ? N27 8X7 401 A 1 HETATM 28 C C28 8X7 . . . B 2 -19.012 4.997 2.074 1 25.03 ? C28 8X7 401 A 1 HETATM 29 C C29 8X7 . . . B 2 -17.961 5.796 2.571 1 24.85 ? C29 8X7 401 A 1 HETATM 30 C C30 8X7 . . . B 2 -16.853 5.173 3.17 1 25.01 ? C30 8X7 401 A 1 HETATM 31 C C31 8X7 . . . B 2 -16.793 3.771 3.273 1 25.03 ? C31 8X7 401 A 1 HETATM 32 C C32 8X7 . . . B 2 -20.238 5.55 1.432 1 24.56 ? C32 8X7 401 A 1 HETATM 33 C C33 8X7 . . . B 2 -21.432 5.565 2.427 1 25.95 ? C33 8X7 401 A 1 HETATM 34 C C34 8X7 . . . B 2 -20.611 4.678 0.199 1 29.95 ? C34 8X7 401 A 1 HETATM 35 O O35 8X7 . . . B 2 -20.018 6.891 0.98 1 24.09 ? O35 8X7 401 A 1 HETATM 36 C C36 8X7 . . . B 2 -11.293 1.813 2.147 1 29.98 ? C36 8X7 401 A 1 HETATM 37 C C37 8X7 . . . B 2 -10.577 3.019 2.103 1 30.84 ? C37 8X7 401 A 1 HETATM 38 H H011 8X7 . . . B 2 -8.275 9.207 3.82 1 47.44 ? H011 8X7 401 A 1 HETATM 39 H H013 8X7 . . . B 2 -9.846 9.29 4.14 1 47.44 ? H013 8X7 401 A 1 HETATM 40 H H012 8X7 . . . B 2 -9.244 10.058 2.865 1 47.44 ? H012 8X7 401 A 1 HETATM 41 H H031 8X7 . . . B 2 -11.373 7.723 3.026 1 45.49 ? H031 8X7 401 A 1 HETATM 42 H H032 8X7 . . . B 2 -11.159 8.707 1.775 1 45.49 ? H032 8X7 401 A 1 HETATM 43 H H041 8X7 . . . B 2 -10.503 6.873 0.419 1 43.47 ? H041 8X7 401 A 1 HETATM 44 H H042 8X7 . . . B 2 -11.954 6.569 1.033 1 43.47 ? H042 8X7 401 A 1 HETATM 45 H H061 8X7 . . . B 2 -8.553 5.745 1.372 1 41 ? H061 8X7 401 A 1 HETATM 46 H H062 8X7 . . . B 2 -8.767 4.766 2.625 1 41 ? H062 8X7 401 A 1 HETATM 47 H H072 8X7 . . . B 2 -7.878 6.905 3.317 1 47.32 ? H072 8X7 401 A 1 HETATM 48 H H071 8X7 . . . B 2 -9.284 6.599 4.026 1 47.32 ? H071 8X7 401 A 1 HETATM 49 H H091 8X7 . . . B 2 -13.113 5.063 1.595 1 36.16 ? H091 8X7 401 A 1 HETATM 50 H H101 8X7 . . . B 2 -14.315 3.04 1.668 1 34.95 ? H101 8X7 401 A 1 HETATM 51 H H121 8X7 . . . B 2 -12.721 -0.161 1.953 1 33.47 ? H121 8X7 401 A 1 HETATM 52 H H151 8X7 . . . B 2 -16.487 -2.394 2.431 1 33.69 ? H151 8X7 401 A 1 HETATM 53 H H202 8X7 . . . B 2 -20.477 2.186 3.046 1 36.39 ? H202 8X7 401 A 1 HETATM 54 H H201 8X7 . . . B 2 -20.965 0.759 2.486 1 36.39 ? H201 8X7 401 A 1 HETATM 55 H H211 8X7 . . . B 2 -20.128 1.109 5.209 1 38.68 ? H211 8X7 401 A 1 HETATM 56 H H221 8X7 . . . B 2 -22.344 -0.306 4.07 1 39.87 ? H221 8X7 401 A 1 HETATM 57 H H222 8X7 . . . B 2 -21.924 -0.232 5.715 1 39.87 ? H222 8X7 401 A 1 HETATM 58 H H291 8X7 . . . B 2 -18.003 6.773 2.499 1 29.82 ? H291 8X7 401 A 1 HETATM 59 H H301 8X7 . . . B 2 -16.114 5.72 3.516 1 30.01 ? H301 8X7 401 A 1 HETATM 60 H H311 8X7 . . . B 2 -16.021 3.335 3.692 1 30.03 ? H311 8X7 401 A 1 HETATM 61 H H331 8X7 . . . B 2 -21.209 6.133 3.199 1 31.14 ? H331 8X7 401 A 1 HETATM 62 H H333 8X7 . . . B 2 -22.23 5.924 1.976 1 31.14 ? H333 8X7 401 A 1 HETATM 63 H H332 8X7 . . . B 2 -21.614 4.649 2.735 1 31.14 ? H332 8X7 401 A 1 HETATM 64 H H342 8X7 . . . B 2 -19.918 4.773 -0.492 1 35.94 ? H342 8X7 401 A 1 HETATM 65 H H341 8X7 . . . B 2 -20.676 3.737 0.471 1 35.94 ? H341 8X7 401 A 1 HETATM 66 H H343 8X7 . . . B 2 -21.476 4.975 -0.163 1 35.94 ? H343 8X7 401 A 1 HETATM 67 H H351 8X7 . . . B 2 -20.147 7.457 1.656 1 28.91 ? H351 8X7 401 A 1 HETATM 68 H H361 8X7 . . . B 2 -10.81 0.972 2.291 1 35.97 ? H361 8X7 401 A 1 HETATM 69 H H371 8X7 . . . B 2 -9.603 2.995 2.219 1 37.01 ? H371 8X7 401 A 1 # _model_server_stats.io_time_ms 53 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 286 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 69 #