data_5WBR
#
_model_server_result.job_id            0ELb1a9ohWoSOPfg64zIyA 
_model_server_result.datetime_utc      '2024-12-21 17:18:19' 
_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          5wbr 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":301}' 
#
_entry.id    5WBR 
#
_exptl.entry_id    5WBR 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              413.437 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            6-[4-(2-hydroxyethyl)piperazin-1-yl]-2-[(3S)-3-(hydroxymethyl)piperidin-1-yl]-4-(trifluoromethyl)pyridine-3-carbonitrile 
_entity.pdbx_number_of_molecules    2 
_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            5WBR 
_cell.length_a            83.19 
_cell.length_b            86.16 
_cell.length_c            137.97 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5WBR 
_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    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_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,J,K,L,M 
_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 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 2 C N N 
? 2 F N N 
#
_chem_comp.formula           'C19 H26 F3 N5 O2' 
_chem_comp.formula_weight    413.437 
_chem_comp.id                A3Y 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              6-[4-(2-hydroxyethyl)piperazin-1-yl]-2-[(3S)-3-(hydroxymethyl)piperidin-1-yl]-4-(trifluoromethyl)pyridine-3-carbonitrile 
_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
C10 C11 A3Y sing 1 n n 
C10 N3 A3Y sing 2 n n 
C11 O1 A3Y sing 3 n n 
C7 N3 A3Y sing 4 n n 
C7 C6 A3Y sing 5 n n 
N3 C8 A3Y sing 6 n n 
C6 N2 A3Y sing 7 n n 
C8 C9 A3Y sing 8 n n 
F1 C19 A3Y sing 9 n n 
F3 C19 A3Y sing 10 n n 
C1 C5 A3Y doub 11 n y 
C1 C2 A3Y sing 12 n y 
N2 C5 A3Y sing 13 n n 
N2 C9 A3Y sing 14 n n 
C19 C2 A3Y sing 15 n n 
C19 F2 A3Y sing 16 n n 
C5 N1 A3Y sing 17 n y 
C2 C3 A3Y doub 18 n y 
N1 C4 A3Y doub 19 n y 
C3 C18 A3Y sing 20 n n 
C3 C4 A3Y sing 21 n y 
C18 N5 A3Y trip 22 n n 
C4 N4 A3Y sing 23 n n 
N4 C16 A3Y sing 24 n n 
N4 C12 A3Y sing 25 n n 
C16 C15 A3Y sing 26 n n 
O2 C17 A3Y sing 27 n n 
C12 C13 A3Y sing 28 n n 
C15 C17 A3Y sing 29 n n 
C15 C14 A3Y sing 30 n n 
C13 C14 A3Y sing 31 n n 
C7 H4 A3Y sing 32 n n 
C7 H5 A3Y sing 33 n n 
C6 H2 A3Y sing 34 n n 
C6 H3 A3Y sing 35 n n 
C9 H8 A3Y sing 36 n n 
C9 H9 A3Y sing 37 n n 
C13 H18 A3Y sing 38 n n 
C13 H17 A3Y sing 39 n n 
C8 H7 A3Y sing 40 n n 
C8 H6 A3Y sing 41 n n 
C16 H23 A3Y sing 42 n n 
C16 H22 A3Y sing 43 n n 
C1 H1 A3Y sing 44 n n 
C10 H10 A3Y sing 45 n n 
C10 H11 A3Y sing 46 n n 
C11 H13 A3Y sing 47 n n 
C11 H12 A3Y sing 48 n n 
O1 H14 A3Y sing 49 n n 
C12 H16 A3Y sing 50 n n 
C12 H15 A3Y sing 51 n n 
C14 H19 A3Y sing 52 n n 
C14 H20 A3Y sing 53 n n 
C15 H21 A3Y sing 54 n n 
C17 H24 A3Y sing 55 n n 
C17 H25 A3Y sing 56 n n 
O2 H26 A3Y sing 57 n n 
#
_atom_sites.entry_id                     5WBR 
_atom_sites.fract_transf_matrix[1][1]    0.012021 
_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]    0.011606 
_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]    0.007248 
_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
C 2 A3Y A 1 301 2 A3Y PFE . 
D 3 SO4 A 1 302 1 SO4 SO4 . 
E 4 CIT A 1 303 1 CIT CIT . 
F 2 A3Y B 1 301 1 A3Y PFE . 
G 3 SO4 B 1 302 2 SO4 SO4 . 
H 3 SO4 B 1 303 3 SO4 SO4 . 
I 3 SO4 B 1 304 4 SO4 SO4 . 
J 3 SO4 B 1 305 5 SO4 SO4 . 
K 5 GOL B 1 306 1 GOL GOL . 
L 6 HOH A 1 401 10 HOH HOH . 
L 6 HOH A 2 402 24 HOH HOH . 
L 6 HOH A 3 403 2 HOH HOH . 
L 6 HOH A 4 404 4 HOH HOH . 
L 6 HOH A 5 405 16 HOH HOH . 
L 6 HOH A 6 406 12 HOH HOH . 
L 6 HOH A 7 407 25 HOH HOH . 
L 6 HOH A 8 408 6 HOH HOH . 
L 6 HOH A 9 409 18 HOH HOH . 
L 6 HOH A 10 410 11 HOH HOH . 
L 6 HOH A 11 411 5 HOH HOH . 
L 6 HOH A 12 412 23 HOH HOH . 
L 6 HOH A 13 413 21 HOH HOH . 
M 6 HOH B 1 401 1 HOH HOH . 
M 6 HOH B 2 402 33 HOH HOH . 
M 6 HOH B 3 403 14 HOH HOH . 
M 6 HOH B 4 404 13 HOH HOH . 
M 6 HOH B 5 405 27 HOH HOH . 
M 6 HOH B 6 406 36 HOH HOH . 
M 6 HOH B 7 407 35 HOH HOH . 
M 6 HOH B 8 408 34 HOH HOH . 
M 6 HOH B 9 409 20 HOH HOH . 
M 6 HOH B 10 410 7 HOH HOH . 
M 6 HOH B 11 411 30 HOH HOH . 
M 6 HOH B 12 412 17 HOH HOH . 
M 6 HOH B 13 413 32 HOH HOH . 
M 6 HOH B 14 414 19 HOH HOH . 
M 6 HOH B 15 415 28 HOH HOH . 
M 6 HOH B 16 416 31 HOH HOH . 
M 6 HOH B 17 417 26 HOH HOH . 
M 6 HOH B 18 418 22 HOH HOH . 
M 6 HOH B 19 419 15 HOH HOH . 
M 6 HOH B 20 420 8 HOH HOH . 
M 6 HOH B 21 421 9 HOH HOH . 
M 6 HOH B 22 422 37 HOH HOH . 
M 6 HOH B 23 423 3 HOH HOH . 
M 6 HOH B 24 424 29 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 N3 A3Y . . . C 2 -10.306 -1.216 22.776 1 115.36 ? N3 A3Y 301 A 1 
HETATM 2 C C4 A3Y . . . C 2 -4.866 -0.408 19.57 1 103.9 ? C4 A3Y 301 A 1 
HETATM 3 N N2 A3Y . . . C 2 -7.564 -0.823 21.945 1 109.22 ? N2 A3Y 301 A 1 
HETATM 4 C C7 A3Y . . . C 2 -9.975 -0.533 21.512 1 113.3 ? C7 A3Y 301 A 1 
HETATM 5 C C6 A3Y . . . C 2 -8.613 0.156 21.6 1 110.88 ? C6 A3Y 301 A 1 
HETATM 6 C C9 A3Y . . . C 2 -7.901 -1.454 23.229 1 112.2 ? C9 A3Y 301 A 1 
HETATM 7 C C13 A3Y . . . C 2 -3.914 2.732 17.906 1 103.36 ? C13 A3Y 301 A 1 
HETATM 8 C C8 A3Y . . . C 2 -9.234 -2.17 23.114 1 114.47 ? C8 A3Y 301 A 1 
HETATM 9 N N5 A3Y . . . C 2 -1.723 -1.891 18.792 1 105.64 ? N5 A3Y 301 A 1 
HETATM 10 C C18 A3Y . . . C 2 -2.778 -1.739 19.218 1 103.7 ? C18 A3Y 301 A 1 
HETATM 11 C C16 A3Y . . . C 2 -4.299 -0.016 17.264 1 107.92 ? C16 A3Y 301 A 1 
HETATM 12 C C19 A3Y . . . C 2 -3.926 -3.98 20.826 1 95.43 ? C19 A3Y 301 A 1 
HETATM 13 C C1 A3Y . . . C 2 -5.76 -2.365 21.352 1 101.64 ? C1 A3Y 301 A 1 
HETATM 14 C C2 A3Y . . . C 2 -4.585 -2.586 20.663 1 99.79 ? C2 A3Y 301 A 1 
HETATM 15 C C3 A3Y . . . C 2 -4.071 -1.604 19.783 1 102.31 ? C3 A3Y 301 A 1 
HETATM 16 N N1 A3Y . . . C 2 -6.04 -0.172 20.284 1 103.05 ? N1 A3Y 301 A 1 
HETATM 17 C C5 A3Y . . . C 2 -6.509 -1.103 21.2 1 104.49 ? C5 A3Y 301 A 1 
HETATM 18 C C10 A3Y . . . C 2 -11.641 -1.851 22.721 1 116.26 ? C10 A3Y 301 A 1 
HETATM 19 C C11 A3Y . . . C 2 -12.029 -2.679 23.942 1 115.32 ? C11 A3Y 301 A 1 
HETATM 20 O O1 A3Y . . . C 2 -13.408 -3.02 23.949 1 114.27 ? O1 A3Y 301 A 1 
HETATM 21 N N4 A3Y . . . C 2 -4.552 0.459 18.625 1 106.21 ? N4 A3Y 301 A 1 
HETATM 22 C C12 A3Y . . . C 2 -4.961 1.87 18.588 1 105 ? C12 A3Y 301 A 1 
HETATM 23 C C14 A3Y . . . C 2 -3.432 2.111 16.591 1 104.35 ? C14 A3Y 301 A 1 
HETATM 24 C C15 A3Y . . . C 2 -3.037 0.637 16.724 1 106.19 ? C15 A3Y 301 A 1 
HETATM 25 C C17 A3Y . . . C 2 -2.76 -0.033 15.388 1 105.14 ? C17 A3Y 301 A 1 
HETATM 26 O O2 A3Y . . . C 2 -2.373 -1.398 15.533 1 103.45 ? O2 A3Y 301 A 1 
HETATM 27 F F1 A3Y . . . C 2 -4.012 -4.506 22.06 1 93.6 ? F1 A3Y 301 A 1 
HETATM 28 F F2 A3Y . . . C 2 -4.548 -4.874 20.079 1 95.43 ? F2 A3Y 301 A 1 
HETATM 29 F F3 A3Y . . . C 2 -2.619 -4.079 20.513 1 93.63 ? F3 A3Y 301 A 1 
HETATM 30 H H4 A3Y . . . C 2 -10.719 0.239 21.32 1 113.27 ? H4 A3Y 301 A 1 
HETATM 31 H H5 A3Y . . . C 2 -9.996 -1.182 20.638 1 113.41 ? H5 A3Y 301 A 1 
HETATM 32 H H2 A3Y . . . C 2 -8.623 0.921 22.375 1 110.74 ? H2 A3Y 301 A 1 
HETATM 33 H H3 A3Y . . . C 2 -8.432 0.705 20.677 1 110.9 ? H3 A3Y 301 A 1 
HETATM 34 H H8 A3Y . . . C 2 -7.14 -2.126 23.624 1 112.09 ? H8 A3Y 301 A 1 
HETATM 35 H H9 A3Y . . . C 2 -7.989 -0.671 23.98 1 112.51 ? H9 A3Y 301 A 1 
HETATM 36 H H18 A3Y . . . C 2 -3.064 2.854 18.569 1 103.16 ? H18 A3Y 301 A 1 
HETATM 37 H H17 A3Y . . . C 2 -4.331 3.724 17.742 1 103.04 ? H17 A3Y 301 A 1 
HETATM 38 H H7 A3Y . . . C 2 -9.151 -3.01 22.428 1 114.54 ? H7 A3Y 301 A 1 
HETATM 39 H H6 A3Y . . . C 2 -9.414 -2.658 24.071 1 114.76 ? H6 A3Y 301 A 1 
HETATM 40 H H23 A3Y . . . C 2 -5.134 0.253 16.619 1 108.49 ? H23 A3Y 301 A 1 
HETATM 41 H H22 A3Y . . . C 2 -4.246 -1.101 17.205 1 107.92 ? H22 A3Y 301 A 1 
HETATM 42 H H1 A3Y . . . C 2 -6.166 -3.154 21.983 1 101.7 ? H1 A3Y 301 A 1 
HETATM 43 H H10 A3Y . . . C 2 -12.361 -1.038 22.634 1 116.32 ? H10 A3Y 301 A 1 
HETATM 44 H H11 A3Y . . . C 2 -11.811 -2.465 21.837 1 116.53 ? H11 A3Y 301 A 1 
HETATM 45 H H13 A3Y . . . C 2 -11.695 -2.254 24.886 1 115.35 ? H13 A3Y 301 A 1 
HETATM 46 H H12 A3Y . . . C 2 -11.55 -3.656 23.897 1 115.41 ? H12 A3Y 301 A 1 
HETATM 47 H H14 A3Y . . . C 2 -13.6 -3.456 24.82 1 114.15 ? H14 A3Y 301 A 1 
HETATM 48 H H16 A3Y . . . C 2 -5.153 2.25 19.591 1 105.1 ? H16 A3Y 301 A 1 
HETATM 49 H H15 A3Y . . . C 2 -5.917 1.967 18.075 1 105.15 ? H15 A3Y 301 A 1 
HETATM 50 H H19 A3Y . . . C 2 -4.187 2.245 15.819 1 104.36 ? H19 A3Y 301 A 1 
HETATM 51 H H20 A3Y . . . C 2 -2.581 2.685 16.23 1 104.35 ? H20 A3Y 301 A 1 
HETATM 52 H H21 A3Y . . . C 2 -2.191 0.526 17.401 1 106.08 ? H21 A3Y 301 A 1 
HETATM 53 H H24 A3Y . . . C 2 -3.662 0.008 14.782 1 104.96 ? H24 A3Y 301 A 1 
HETATM 54 H H25 A3Y . . . C 2 -1.998 0.504 14.824 1 105.37 ? H25 A3Y 301 A 1 
HETATM 55 H H26 A3Y . . . C 2 -1.385 -1.403 15.44 1 103.42 ? H26 A3Y 301 A 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           319 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           55 
#