data_4L46 # _model_server_result.job_id uK2Oy3YsOeZ7jIBGUfRd8w _model_server_result.datetime_utc '2024-11-05 08:04:30' _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 4l46 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 4L46 # _exptl.entry_id 4L46 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 390.405 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-{[4-(5-ethylpyrimidin-4-yl)piperazin-1-yl]methyl}-5-(trifluoromethyl)-1H-benzimidazole _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 4L46 _cell.length_a 81.139 _cell.length_b 81.139 _cell.length_c 111.047 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4L46 _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 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 _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 # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _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 _struct_conn.pdbx_value_order covale ? covale1 A C PHE 340 A PHE 388 1_555 A N TPO 341 A TPO 389 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.321 ? covale ? covale2 A C TPO 341 A TPO 389 1_555 A N TYR 342 A TYR 390 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? metalc ? metalc1 A ND1 HIS 174 A HIS 222 1_555 D ZN ZN . A ZN 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.652 ? metalc ? metalc2 A SG CYS 183 A CYS 231 1_555 D ZN ZN . A ZN 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.594 ? # _chem_comp.formula 'C19 H21 F3 N6' _chem_comp.formula_weight 390.405 _chem_comp.id 5FI _chem_comp.mon_nstd_flag . _chem_comp.name 2-{[4-(5-ethylpyrimidin-4-yl)piperazin-1-yl]methyl}-5-(trifluoromethyl)-1H-benzimidazole _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 FAB CBB 5FI sing 1 n n FAD CBB 5FI sing 2 n n CBB FAC 5FI sing 3 n n CBB CAU 5FI sing 4 n n CAU CAI 5FI doub 5 n y CAU CAE 5FI sing 6 n y CAI CAX 5FI sing 7 n y CAE CAF 5FI doub 8 n y CAX NAR 5FI sing 9 n y CAX CAY 5FI doub 10 n y NAR CAV 5FI doub 11 n y CAA CAJ 5FI sing 12 n n CAJ C5 5FI sing 13 n n CAF CAY 5FI sing 14 n y CAY NAS 5FI sing 15 n y CAV NAS 5FI sing 16 n y CAV CAO 5FI sing 17 n n CAM CAK 5FI sing 18 n n CAM NBA 5FI sing 19 n n C5 C6 5FI doub 20 n y C5 C4 5FI sing 21 n y CAO NAZ 5FI sing 22 n n CAK NAZ 5FI sing 23 n n C6 N1 5FI sing 24 n y NAZ CAL 5FI sing 25 n n NBA C4 5FI sing 26 n n NBA CAN 5FI sing 27 n n C4 N3 5FI doub 28 n y N1 C2 5FI doub 29 n y CAN CAL 5FI sing 30 n n N3 C2 5FI sing 31 n y C6 H1 5FI sing 32 n n CAE H2 5FI sing 33 n n CAF H3 5FI sing 34 n n CAI H4 5FI sing 35 n n CAO H7 5FI sing 36 n n CAO H8 5FI sing 37 n n CAL H10 5FI sing 38 n n CAL H11 5FI sing 39 n n CAN H12 5FI sing 40 n n CAN H13 5FI sing 41 n n CAK H14 5FI sing 42 n n CAK H15 5FI sing 43 n n CAM H16 5FI sing 44 n n CAM H17 5FI sing 45 n n CAJ H18 5FI sing 46 n n CAJ H19 5FI sing 47 n n CAA H20 5FI sing 48 n n CAA H21 5FI sing 49 n n CAA H22 5FI sing 50 n n C2 H23 5FI sing 51 n n NAS H5 5FI sing 52 n n # _atom_sites.entry_id 4L46 _atom_sites.fract_transf_matrix[1][1] 0.012325 _atom_sites.fract_transf_matrix[1][2] 0.007116 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014231 _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] 0.009005 _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 5FI A 1 401 1 5FI DRG . C 3 SO4 A 1 402 1 SO4 SO4 . D 4 ZN A 1 403 1 ZN ZN . # 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 C4 5FI . . . B 2 47.917 -17.056 12.692 1 67.48 ? C4 5FI 401 A 1 HETATM 2 C C5 5FI . . . B 2 47.452 -16.232 11.642 1 65.2 ? C5 5FI 401 A 1 HETATM 3 C C6 5FI . . . B 2 46.871 -15.003 11.934 1 65.45 ? C6 5FI 401 A 1 HETATM 4 N N1 5FI . . . B 2 46.753 -14.601 13.198 1 67.01 ? N1 5FI 401 A 1 HETATM 5 N N3 5FI . . . B 2 47.766 -16.569 13.958 1 67.42 ? N3 5FI 401 A 1 HETATM 6 F FAB 5FI . . . B 2 54.749 -21.516 5.588 1 73.68 ? FAB 5FI 401 A 1 HETATM 7 C CBB 5FI . . . B 2 55.635 -21.601 6.566 1 74.46 ? CBB 5FI 401 A 1 HETATM 8 F FAC 5FI . . . B 2 56.382 -20.521 6.616 1 77.61 ? FAC 5FI 401 A 1 HETATM 9 F FAD 5FI . . . B 2 56.521 -22.594 6.328 1 79.19 ? FAD 5FI 401 A 1 HETATM 10 C CAU 5FI . . . B 2 54.861 -21.67 7.864 1 71.42 ? CAU 5FI 401 A 1 HETATM 11 C CAE 5FI . . . B 2 55.588 -21.539 9.027 1 71.27 ? CAE 5FI 401 A 1 HETATM 12 C CAF 5FI . . . B 2 54.951 -21.597 10.261 1 71.78 ? CAF 5FI 401 A 1 HETATM 13 C CAI 5FI . . . B 2 53.478 -21.838 7.926 1 69.9 ? CAI 5FI 401 A 1 HETATM 14 C CAX 5FI . . . B 2 52.836 -21.904 9.159 1 68.92 ? CAX 5FI 401 A 1 HETATM 15 C CAY 5FI . . . B 2 53.571 -21.763 10.313 1 69.89 ? CAY 5FI 401 A 1 HETATM 16 N NAS 5FI . . . B 2 52.737 -21.826 11.354 1 68.71 ? NAS 5FI 401 A 1 HETATM 17 N NAR 5FI . . . B 2 51.56 -22.074 9.548 1 68.65 ? NAR 5FI 401 A 1 HETATM 18 C CAV 5FI . . . B 2 51.497 -22.029 10.892 1 68.29 ? CAV 5FI 401 A 1 HETATM 19 C CAO 5FI . . . B 2 50.281 -22.148 11.786 1 67.68 ? CAO 5FI 401 A 1 HETATM 20 N NAZ 5FI . . . B 2 49.832 -20.754 12.027 1 69.59 ? NAZ 5FI 401 A 1 HETATM 21 C CAL 5FI . . . B 2 50.092 -20.124 13.348 1 67.3 ? CAL 5FI 401 A 1 HETATM 22 C CAN 5FI . . . B 2 49.788 -18.632 13.281 1 66.84 ? CAN 5FI 401 A 1 HETATM 23 C CAK 5FI . . . B 2 48.39 -20.714 11.879 1 71.47 ? CAK 5FI 401 A 1 HETATM 24 C CAM 5FI . . . B 2 48.04 -19.25 11.535 1 69.82 ? CAM 5FI 401 A 1 HETATM 25 N NBA 5FI . . . B 2 48.568 -18.318 12.52 1 67.18 ? NBA 5FI 401 A 1 HETATM 26 C CAJ 5FI . . . B 2 47.512 -16.591 10.195 1 63.13 ? CAJ 5FI 401 A 1 HETATM 27 C CAA 5FI . . . B 2 48.842 -16.289 9.56 1 64.2 ? CAA 5FI 401 A 1 HETATM 28 C C2 5FI . . . B 2 47.19 -15.379 14.194 1 66.8 ? C2 5FI 401 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 232 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 28 #