data_4L42 # _model_server_result.job_id bF4DjqbzjeUE6BHHTYPCdA _model_server_result.datetime_utc '2024-10-19 03:36:38' _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 4l42 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 4L42 # _exptl.entry_id 4L42 _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 4L42 _cell.length_a 67.656 _cell.length_b 67.656 _cell.length_c 377.735 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4L42 _symmetry.cell_setting ? _symmetry.Int_Tables_number 179 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65 2 2' # _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,G,H,I,J,K _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 metalc ? metalc1 A SG CYS 169 A CYS 217 1_555 J ZN ZN . A ZN 409 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.268 ? metalc ? metalc2 A ND1 HIS 174 A HIS 222 1_555 J ZN ZN . A ZN 409 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.139 ? metalc ? metalc3 A ND1 HIS 180 A HIS 228 1_555 J ZN ZN . A ZN 409 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.113 ? metalc ? metalc4 A SG CYS 183 A CYS 231 1_555 J ZN ZN . A ZN 409 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.188 ? # _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 4L42 _atom_sites.fract_transf_matrix[1][1] 0.014781 _atom_sites.fract_transf_matrix[1][2] 0.008534 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.017067 _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] 0.002647 _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 3 SO4 A 1 403 3 SO4 SO4 . E 3 SO4 A 1 404 4 SO4 SO4 . F 3 SO4 A 1 405 5 SO4 SO4 . G 3 SO4 A 1 406 6 SO4 SO4 . H 3 SO4 A 1 407 9 SO4 SO4 . I 3 SO4 A 1 408 12 SO4 SO4 . J 4 ZN A 1 409 1 ZN ZN . K 5 HOH A 1 501 1 HOH HOH . K 5 HOH A 2 502 2 HOH HOH . K 5 HOH A 3 503 3 HOH HOH . K 5 HOH A 4 504 4 HOH HOH . K 5 HOH A 5 505 6 HOH HOH . K 5 HOH A 6 506 7 HOH HOH . K 5 HOH A 7 507 8 HOH HOH . K 5 HOH A 8 508 9 HOH HOH . K 5 HOH A 9 509 10 HOH HOH . K 5 HOH A 10 510 11 HOH HOH . K 5 HOH A 11 511 12 HOH HOH . K 5 HOH A 12 512 13 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 C4 5FI . . . B 2 38.354 -26.05 -0.341 1 56.13 ? C4 5FI 401 A 1 HETATM 2 C C5 5FI . . . B 2 37.106 -26.466 0.157 1 53.11 ? C5 5FI 401 A 1 HETATM 3 C C6 5FI . . . B 2 36.786 -27.814 0.048 1 52.88 ? C6 5FI 401 A 1 HETATM 4 N N1 5FI . . . B 2 37.632 -28.657 -0.51 1 54.69 ? N1 5FI 401 A 1 HETATM 5 N N3 5FI . . . B 2 39.158 -26.983 -0.904 1 56.9 ? N3 5FI 401 A 1 HETATM 6 F FAB 5FI . . . B 2 40.597 -18.559 7.279 1 84.77 ? FAB 5FI 401 A 1 HETATM 7 C CBB 5FI . . . B 2 40.198 -17.793 6.277 1 82.36 ? CBB 5FI 401 A 1 HETATM 8 F FAC 5FI . . . B 2 40.662 -16.551 6.405 1 83.49 ? FAC 5FI 401 A 1 HETATM 9 F FAD 5FI . . . B 2 38.878 -17.806 6.237 1 81.28 ? FAD 5FI 401 A 1 HETATM 10 C CAU 5FI . . . B 2 40.723 -18.344 4.97 1 79.24 ? CAU 5FI 401 A 1 HETATM 11 C CAE 5FI . . . B 2 42.092 -18.441 4.742 1 77.62 ? CAE 5FI 401 A 1 HETATM 12 C CAF 5FI . . . B 2 42.551 -18.94 3.529 1 77.39 ? CAF 5FI 401 A 1 HETATM 13 C CAI 5FI . . . B 2 39.817 -18.733 3.995 1 77.37 ? CAI 5FI 401 A 1 HETATM 14 C CAX 5FI . . . B 2 40.276 -19.229 2.788 1 76.33 ? CAX 5FI 401 A 1 HETATM 15 C CAY 5FI . . . B 2 41.639 -19.333 2.553 1 77.32 ? CAY 5FI 401 A 1 HETATM 16 N NAS 5FI . . . B 2 41.786 -19.831 1.329 1 77.56 ? NAS 5FI 401 A 1 HETATM 17 N NAR 5FI . . . B 2 39.649 -19.659 1.704 1 75.74 ? NAR 5FI 401 A 1 HETATM 18 C CAV 5FI . . . B 2 40.571 -20.024 0.813 1 76.91 ? CAV 5FI 401 A 1 HETATM 19 C CAO 5FI . . . B 2 40.266 -20.616 -0.566 1 76.14 ? CAO 5FI 401 A 1 HETATM 20 N NAZ 5FI . . . B 2 39.778 -22.002 -0.339 1 73.34 ? NAZ 5FI 401 A 1 HETATM 21 C CAL 5FI . . . B 2 40.817 -23.072 -0.357 1 69.97 ? CAL 5FI 401 A 1 HETATM 22 C CAN 5FI . . . B 2 40.271 -24.466 -0.722 1 63.27 ? CAN 5FI 401 A 1 HETATM 23 C CAK 5FI . . . B 2 38.485 -22.326 -0.951 1 68.3 ? CAK 5FI 401 A 1 HETATM 24 C CAM 5FI . . . B 2 37.911 -23.526 -0.195 1 62.32 ? CAM 5FI 401 A 1 HETATM 25 N NBA 5FI . . . B 2 38.836 -24.695 -0.339 1 59.52 ? NBA 5FI 401 A 1 HETATM 26 C CAJ 5FI . . . B 2 36.045 -25.586 0.812 1 51.87 ? CAJ 5FI 401 A 1 HETATM 27 C CAA 5FI . . . B 2 36.617 -24.848 2.021 1 51.76 ? CAA 5FI 401 A 1 HETATM 28 C C2 5FI . . . B 2 38.802 -28.255 -0.981 1 56.13 ? C2 5FI 401 A 1 # _model_server_stats.io_time_ms 69 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 341 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #