data_5VD8
#
_model_server_result.job_id            GvjY2126w7hOO1ciZNrmQA 
_model_server_result.datetime_utc      '2025-01-11 09:05:40' 
_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          5vd8 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":601}' 
#
_entry.id    5VD8 
#
_exptl.entry_id    5VD8 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              535.04 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            6-{[3-chloro-4-(4-methylpiperazin-1-yl)phenyl]amino}-1-[6-(2-hydroxypropan-2-yl)pyridin-2-yl]-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          101.94 
_cell.angle_gamma         90 
_cell.entry_id            5VD8 
_cell.length_a            50.29 
_cell.length_b            44.56 
_cell.length_c            64.98 
_cell.Z_PDB               2 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5VD8 
_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 
_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 H31 Cl N8 O2' 
_chem_comp.formula_weight    535.04 
_chem_comp.id                98M 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              6-{[3-chloro-4-(4-methylpiperazin-1-yl)phenyl]amino}-1-[6-(2-hydroxypropan-2-yl)pyridin-2-yl]-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     RAC-IV-099 
#
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
C31 N30 98M sing 1 n n 
N30 C29 98M sing 2 n n 
N30 C32 98M sing 3 n n 
C14 C11 98M sing 4 n n 
C29 C28 98M sing 5 n n 
C32 C33 98M sing 6 n n 
C15 C16 98M doub 7 n y 
C15 C10 98M sing 8 n y 
C12 C11 98M sing 9 n n 
C28 N27 98M sing 10 n n 
C11 C10 98M sing 11 n n 
C11 O13 98M sing 12 n n 
C16 C17 98M sing 13 n y 
C33 N27 98M sing 14 n n 
C10 N09 98M doub 15 n y 
N27 C26 98M sing 16 n n 
C17 C08 98M doub 17 n y 
N09 C08 98M sing 18 n y 
C34 C26 98M doub 19 n y 
C34 C35 98M sing 20 n y 
C26 C24 98M sing 21 n y 
C08 N07 98M sing 22 n n 
C05 C06 98M doub 23 n n 
C05 C04 98M sing 24 n n 
C35 C22 98M doub 25 n y 
C24 CL25 98M sing 26 n n 
C24 C23 98M doub 27 n y 
N07 N03 98M sing 28 n n 
N07 C18 98M sing 29 n n 
C04 N03 98M sing 30 n n 
C22 C23 98M sing 31 n y 
C22 N21 98M sing 32 n n 
N03 C02 98M sing 33 n n 
N19 C18 98M doub 34 n y 
N19 C20 98M sing 35 n y 
C18 C38 98M sing 36 n y 
N21 C20 98M sing 37 n n 
C20 N36 98M doub 38 n y 
C02 C38 98M sing 39 n n 
C02 O01 98M doub 40 n n 
C38 C37 98M doub 41 n y 
N36 C37 98M sing 42 n y 
C15 H151 98M sing 43 n n 
C17 H171 98M sing 44 n n 
C28 H281 98M sing 45 n n 
C28 H282 98M sing 46 n n 
C04 H042 98M sing 47 n n 
C04 H041 98M sing 48 n n 
C05 H051 98M sing 49 n n 
C06 H061 98M sing 50 n n 
C06 H062 98M sing 51 n n 
C12 H122 98M sing 52 n n 
C12 H121 98M sing 53 n n 
C12 H123 98M sing 54 n n 
O13 H131 98M sing 55 n n 
C14 H142 98M sing 56 n n 
C14 H141 98M sing 57 n n 
C14 H143 98M sing 58 n n 
C16 H161 98M sing 59 n n 
N21 H211 98M sing 60 n n 
C23 H231 98M sing 61 n n 
C29 H292 98M sing 62 n n 
C29 H291 98M sing 63 n n 
C31 H312 98M sing 64 n n 
C31 H311 98M sing 65 n n 
C31 H313 98M sing 66 n n 
C32 H322 98M sing 67 n n 
C32 H321 98M sing 68 n n 
C33 H331 98M sing 69 n n 
C33 H332 98M sing 70 n n 
C34 H341 98M sing 71 n n 
C35 H351 98M sing 72 n n 
C37 H371 98M sing 73 n n 
#
_atom_sites.entry_id                     5VD8 
_atom_sites.fract_transf_matrix[1][1]    0.019885 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.004205 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.022442 
_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]    0.01573 
_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 98M A 1 601 1 98M LIG . 
C 3 CL A 1 602 1 CL CL . 
D 4 EDO A 1 603 1 EDO EDO . 
E 4 EDO A 1 604 2 EDO EDO . 
F 5 HOH A 1 701 60 HOH HOH . 
F 5 HOH A 2 702 39 HOH HOH . 
F 5 HOH A 3 703 28 HOH HOH . 
F 5 HOH A 4 704 64 HOH HOH . 
F 5 HOH A 5 705 57 HOH HOH . 
F 5 HOH A 6 706 30 HOH HOH . 
F 5 HOH A 7 707 46 HOH HOH . 
F 5 HOH A 8 708 17 HOH HOH . 
F 5 HOH A 9 709 29 HOH HOH . 
F 5 HOH A 10 710 63 HOH HOH . 
F 5 HOH A 11 711 49 HOH HOH . 
F 5 HOH A 12 712 48 HOH HOH . 
F 5 HOH A 13 713 14 HOH HOH . 
F 5 HOH A 14 714 24 HOH HOH . 
F 5 HOH A 15 715 27 HOH HOH . 
F 5 HOH A 16 716 10 HOH HOH . 
F 5 HOH A 17 717 66 HOH HOH . 
F 5 HOH A 18 718 35 HOH HOH . 
F 5 HOH A 19 719 19 HOH HOH . 
F 5 HOH A 20 720 56 HOH HOH . 
F 5 HOH A 21 721 6 HOH HOH . 
F 5 HOH A 22 722 11 HOH HOH . 
F 5 HOH A 23 723 32 HOH HOH . 
F 5 HOH A 24 724 9 HOH HOH . 
F 5 HOH A 25 725 33 HOH HOH . 
F 5 HOH A 26 726 40 HOH HOH . 
F 5 HOH A 27 727 51 HOH HOH . 
F 5 HOH A 28 728 20 HOH HOH . 
F 5 HOH A 29 729 5 HOH HOH . 
F 5 HOH A 30 730 18 HOH HOH . 
F 5 HOH A 31 731 31 HOH HOH . 
F 5 HOH A 32 732 22 HOH HOH . 
F 5 HOH A 33 733 62 HOH HOH . 
F 5 HOH A 34 734 21 HOH HOH . 
F 5 HOH A 35 735 15 HOH HOH . 
F 5 HOH A 36 736 47 HOH HOH . 
F 5 HOH A 37 737 37 HOH HOH . 
F 5 HOH A 38 738 4 HOH HOH . 
F 5 HOH A 39 739 8 HOH HOH . 
F 5 HOH A 40 740 65 HOH HOH . 
F 5 HOH A 41 741 36 HOH HOH . 
F 5 HOH A 42 742 16 HOH HOH . 
F 5 HOH A 43 743 3 HOH HOH . 
F 5 HOH A 44 744 1 HOH HOH . 
F 5 HOH A 45 745 13 HOH HOH . 
F 5 HOH A 46 746 42 HOH HOH . 
F 5 HOH A 47 747 26 HOH HOH . 
F 5 HOH A 48 748 52 HOH HOH . 
F 5 HOH A 49 749 68 HOH HOH . 
F 5 HOH A 50 750 23 HOH HOH . 
F 5 HOH A 51 751 58 HOH HOH . 
F 5 HOH A 52 752 61 HOH HOH . 
F 5 HOH A 53 753 12 HOH HOH . 
F 5 HOH A 54 754 41 HOH HOH . 
F 5 HOH A 55 755 55 HOH HOH . 
F 5 HOH A 56 756 59 HOH HOH . 
F 5 HOH A 57 757 54 HOH HOH . 
F 5 HOH A 58 758 38 HOH HOH . 
F 5 HOH A 59 759 7 HOH HOH . 
F 5 HOH A 60 760 2 HOH HOH . 
F 5 HOH A 61 761 67 HOH HOH . 
F 5 HOH A 62 762 43 HOH HOH . 
F 5 HOH A 63 763 45 HOH HOH . 
F 5 HOH A 64 764 34 HOH HOH . 
F 5 HOH A 65 765 25 HOH HOH . 
F 5 HOH A 66 766 53 HOH HOH . 
F 5 HOH A 67 767 50 HOH HOH . 
F 5 HOH A 68 768 44 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 98M . . . B 2 -1.492 3.747 9.167 1 28.86 ? C10 98M 601 A 1 
HETATM 2 C C15 98M . . . B 2 -2.335 4.557 8.372 1 28.67 ? C15 98M 601 A 1 
HETATM 3 C C17 98M . . . B 2 -4.057 4.445 10.103 1 28.54 ? C17 98M 601 A 1 
HETATM 4 C C20 98M . . . B 2 -5.696 5.386 13.896 1 28.5 ? C20 98M 601 A 1 
HETATM 5 C C22 98M . . . B 2 -6.552 7.367 12.709 1 29.64 ? C22 98M 601 A 1 
HETATM 6 C C24 98M . . . B 2 -7.842 9.232 11.766 1 30.42 ? C24 98M 601 A 1 
HETATM 7 C C26 98M . . . B 2 -7.008 9.258 10.62 1 30.37 ? C26 98M 601 A 1 
HETATM 8 C C28 98M . . . B 2 -8.371 10.032 8.783 1 30.94 ? C28 98M 601 A 1 
HETATM 9 O O01 98M . . . B 2 -3.097 1.108 14.83 1 28.9 ? O01 98M 601 A 1 
HETATM 10 C C02 98M . . . B 2 -3.376 1.992 13.987 1 28.74 ? C02 98M 601 A 1 
HETATM 11 N N03 98M . . . B 2 -2.915 2.074 12.718 1 28.67 ? N03 98M 601 A 1 
HETATM 12 C C04 98M . . . B 2 -2.041 1.07 12.173 1 28.71 ? C04 98M 601 A 1 
HETATM 13 C C05 98M . . . B 2 -2.869 0.152 11.405 1 28.75 ? C05 98M 601 A 1 
HETATM 14 C C06 98M . . . B 2 -3.825 -0.616 11.954 1 28.66 ? C06 98M 601 A 1 
HETATM 15 N N07 98M . . . B 2 -3.446 3.126 12.111 1 28.53 ? N07 98M 601 A 1 
HETATM 16 C C08 98M . . . B 2 -3.204 3.613 10.86 1 28.53 ? C08 98M 601 A 1 
HETATM 17 N N09 98M . . . B 2 -1.976 3.346 10.363 1 28.56 ? N09 98M 601 A 1 
HETATM 18 C C11 98M . . . B 2 -0.113 3.287 8.81 1 28.79 ? C11 98M 601 A 1 
HETATM 19 C C12 98M . . . B 2 -0.119 1.753 8.532 1 29.14 ? C12 98M 601 A 1 
HETATM 20 O O13 98M . . . B 2 0.791 3.505 9.895 1 29.03 ? O13 98M 601 A 1 
HETATM 21 C C14 98M . . . B 2 0.471 4.077 7.61 1 28.97 ? C14 98M 601 A 1 
HETATM 22 C C16 98M . . . B 2 -3.617 4.901 8.846 1 28.64 ? C16 98M 601 A 1 
HETATM 23 C C18 98M . . . B 2 -4.217 3.771 13.001 1 28.47 ? C18 98M 601 A 1 
HETATM 24 N N19 98M . . . B 2 -4.948 4.9 12.873 1 28.45 ? N19 98M 601 A 1 
HETATM 25 N N21 98M . . . B 2 -6.435 6.526 13.789 1 29.03 ? N21 98M 601 A 1 
HETATM 26 C C23 98M . . . B 2 -7.611 8.291 12.786 1 29.99 ? C23 98M 601 A 1 
HETATM 27 CL CL25 98M . . . B 2 -9.149 10.287 11.987 1 30.88 ? CL25 98M 601 A 1 
HETATM 28 N N27 98M . . . B 2 -7.168 10.148 9.583 1 30.7 ? N27 98M 601 A 1 
HETATM 29 C C29 98M . . . B 2 -8.701 11.362 8.067 1 31.04 ? C29 98M 601 A 1 
HETATM 30 N N30 98M . . . B 2 -7.512 11.886 7.332 1 31.12 ? N30 98M 601 A 1 
HETATM 31 C C31 98M . . . B 2 -7.245 11.096 6.094 1 31.13 ? C31 98M 601 A 1 
HETATM 32 C C32 98M . . . B 2 -6.301 12.001 8.201 1 31.08 ? C32 98M 601 A 1 
HETATM 33 C C33 98M . . . B 2 -5.991 10.667 8.925 1 30.98 ? C33 98M 601 A 1 
HETATM 34 C C34 98M . . . B 2 -5.94 8.336 10.541 1 30.04 ? C34 98M 601 A 1 
HETATM 35 C C35 98M . . . B 2 -5.715 7.406 11.567 1 29.79 ? C35 98M 601 A 1 
HETATM 36 N N36 98M . . . B 2 -5.69 4.699 15.073 1 28.47 ? N36 98M 601 A 1 
HETATM 37 C C37 98M . . . B 2 -4.968 3.557 15.262 1 28.51 ? C37 98M 601 A 1 
HETATM 38 C C38 98M . . . B 2 -4.21 3.074 14.191 1 28.58 ? C38 98M 601 A 1 
HETATM 39 H H151 98M . . . B 2 -2.04 4.896 7.454 1 34.41 ? H151 98M 601 A 1 
HETATM 40 H H171 98M . . . B 2 -4.989 4.698 10.442 1 34.25 ? H171 98M 601 A 1 
HETATM 41 H H281 98M . . . B 2 -8.221 9.243 8.041 1 37.13 ? H281 98M 601 A 1 
HETATM 42 H H282 98M . . . B 2 -9.244 9.742 9.376 1 37.13 ? H282 98M 601 A 1 
HETATM 43 H H042 98M . . . B 2 -1.256 1.49 11.539 1 34.46 ? H042 98M 601 A 1 
HETATM 44 H H041 98M . . . B 2 -1.548 0.536 12.989 1 34.46 ? H041 98M 601 A 1 
HETATM 45 H H051 98M . . . B 2 -2.72 0.091 10.423 1 34.5 ? H051 98M 601 A 1 
HETATM 46 H H061 98M . . . B 2 -4.016 -0.594 12.927 1 34.39 ? H061 98M 601 A 1 
HETATM 47 H H062 98M . . . B 2 -4.361 -1.225 11.381 1 34.39 ? H062 98M 601 A 1 
HETATM 48 H H122 98M . . . B 2 -0.735 1.58 7.596 1 34.97 ? H122 98M 601 A 1 
HETATM 49 H H121 98M . . . B 2 -0.532 1.239 9.504 1 34.97 ? H121 98M 601 A 1 
HETATM 50 H H123 98M . . . B 2 0.931 1.455 8.233 1 34.97 ? H123 98M 601 A 1 
HETATM 51 H H131 98M . . . B 2 0.931 4.474 9.937 1 34.84 ? H131 98M 601 A 1 
HETATM 52 H H142 98M . . . B 2 -0.116 3.897 6.704 1 34.76 ? H142 98M 601 A 1 
HETATM 53 H H141 98M . . . B 2 1.5 3.767 7.418 1 34.76 ? H141 98M 601 A 1 
HETATM 54 H H143 98M . . . B 2 0.47 5.149 7.818 1 34.76 ? H143 98M 601 A 1 
HETATM 55 H H161 98M . . . B 2 -4.233 5.484 8.275 1 34.37 ? H161 98M 601 A 1 
HETATM 56 H H211 98M . . . B 2 -6.943 6.774 14.575 1 34.83 ? H211 98M 601 A 1 
HETATM 57 H H231 98M . . . B 2 -8.219 8.286 13.609 1 35.99 ? H231 98M 601 A 1 
HETATM 58 H H292 98M . . . B 2 -9.533 11.192 7.377 1 37.24 ? H292 98M 601 A 1 
HETATM 59 H H291 98M . . . B 2 -9.031 12.082 8.821 1 37.24 ? H291 98M 601 A 1 
HETATM 60 H H312 98M . . . B 2 -6.957 10.076 6.352 1 37.36 ? H312 98M 601 A 1 
HETATM 61 H H311 98M . . . B 2 -6.449 11.545 5.496 1 37.36 ? H311 98M 601 A 1 
HETATM 62 H H313 98M . . . B 2 -8.148 11.034 5.482 1 37.36 ? H313 98M 601 A 1 
HETATM 63 H H322 98M . . . B 2 -6.459 12.773 8.958 1 37.29 ? H322 98M 601 A 1 
HETATM 64 H H321 98M . . . B 2 -5.428 12.285 7.606 1 37.29 ? H321 98M 601 A 1 
HETATM 65 H H331 98M . . . B 2 -5.17 10.837 9.63 1 37.17 ? H331 98M 601 A 1 
HETATM 66 H H332 98M . . . B 2 -5.642 9.933 8.193 1 37.17 ? H332 98M 601 A 1 
HETATM 67 H H341 98M . . . B 2 -5.32 8.334 9.725 1 36.04 ? H341 98M 601 A 1 
HETATM 68 H H351 98M . . . B 2 -4.934 6.756 11.466 1 35.74 ? H351 98M 601 A 1 
HETATM 69 H H371 98M . . . B 2 -4.995 3.065 16.156 1 34.21 ? H371 98M 601 A 1 
#
_model_server_stats.io_time_ms              14 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           287 
_model_server_stats.encode_time_ms          8 
_model_server_stats.element_count           69 
#