data_5NGE # _model_server_result.job_id 9qgUeEDpIwlEFuBWHF4Qsg _model_server_result.datetime_utc '2024-10-28 02:31:18' _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 5nge # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":601}' # _entry.id 5NGE # _exptl.entry_id 5NGE _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 533.478 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 5-[[1-[(3~{S})-4,4-bis(fluoranyl)-3-(3-fluoranylpyrazol-1-yl)butanoyl]-4-oxidanyl-piperidin-4-yl]methyl]-1-(4-fluorophenyl)pyrazolo[3,4-d]pyrimidin-4-one _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 97.17 _cell.angle_gamma 90 _cell.entry_id 5NGE _cell.length_a 71.28 _cell.length_b 70.3 _cell.length_c 78.56 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5NGE _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,E 1 1 B,D,F 2 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 D N N # _struct_conn.conn_type_id disulf _struct_conn.details ? _struct_conn.id disulf1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id SG _struct_conn.ptnr1_label_comp_id CYS _struct_conn.ptnr1_label_seq_id 110 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id CYS _struct_conn.ptnr1_auth_seq_id 315 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id B _struct_conn.ptnr2_label_atom_id SG _struct_conn.ptnr2_label_comp_id CYS _struct_conn.ptnr2_label_seq_id 110 _struct_conn.ptnr2_auth_asym_id B _struct_conn.ptnr2_auth_comp_id CYS _struct_conn.ptnr2_auth_seq_id 315 _struct_conn.ptnr2_symmetry 1_555 _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 2.087 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C24 H23 F4 N7 O3' _chem_comp.formula_weight 533.478 _chem_comp.id 8WK _chem_comp.mon_nstd_flag . _chem_comp.name 5-[[1-[(3~{S})-4,4-bis(fluoranyl)-3-(3-fluoranylpyrazol-1-yl)butanoyl]-4-oxidanyl-piperidin-4-yl]methyl]-1-(4-fluorophenyl)pyrazolo[3,4-d]pyrimidin-4-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 FAD CAZ 8WK sing 1 n n CAH CAZ 8WK doub 2 n y CAH CAJ 8WK sing 3 n y CAZ CAI 8WK sing 4 n y CAJ CBB 8WK doub 5 n y CAI CAK 8WK doub 6 n y CAK CBB 8WK sing 7 n y CBB NBJ 8WK sing 8 n n NAV CAO 8WK doub 9 n n NAV CBE 8WK sing 10 n n CAO NBH 8WK sing 11 n n NBJ CBE 8WK sing 12 n y NBJ NAW 8WK sing 13 n y CBE CBD 8WK doub 14 n y NBH CAU 8WK sing 15 n n NBH CBC 8WK sing 16 n n CAU CBK 8WK sing 17 n n NAW CAN 8WK doub 18 n y CBD CBC 8WK sing 19 n n CBD CAN 8WK sing 20 n y CBC OAB 8WK doub 21 n n OAC CBK 8WK sing 22 n n CBK CAR 8WK sing 23 n n CBK CAS 8WK sing 24 n n CAR CAP 8WK sing 25 n n CAP NBG 8WK sing 26 n n CAS CAQ 8WK sing 27 n n FAE CBA 8WK sing 28 n n NBG CAQ 8WK sing 29 n n NBG CAY 8WK sing 30 n n CBA CAL 8WK sing 31 n y CBA NAX 8WK doub 32 n y CAL CAM 8WK doub 33 n y OAA CAY 8WK doub 34 n n CAY CAT 8WK sing 35 n n NAX NBI 8WK sing 36 n y CAM NBI 8WK sing 37 n y NBI CBL 8WK sing 38 n n CAT CBL 8WK sing 39 n n CBL CBF 8WK sing 40 n n CBF FAF 8WK sing 41 n n CBF FAG 8WK sing 42 n n CAJ H1 8WK sing 43 n n CAH H2 8WK sing 44 n n CAI H3 8WK sing 45 n n CAK H4 8WK sing 46 n n CAN H5 8WK sing 47 n n CAO H6 8WK sing 48 n n CAU H7 8WK sing 49 n n CAU H8 8WK sing 50 n n CAR H9 8WK sing 51 n n CAR H10 8WK sing 52 n n CAP H11 8WK sing 53 n n CAP H12 8WK sing 54 n n OAC H13 8WK sing 55 n n CAS H14 8WK sing 56 n n CAS H15 8WK sing 57 n n CAQ H16 8WK sing 58 n n CAQ H17 8WK sing 59 n n CAT H18 8WK sing 60 n n CAT H19 8WK sing 61 n n CBL H20 8WK sing 62 n n CBF H21 8WK sing 63 n n CAL H22 8WK sing 64 n n CAM H23 8WK sing 65 n n # _atom_sites.entry_id 5NGE _atom_sites.fract_transf_matrix[1][1] 0.014029 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001765 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014225 _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] 0.012829 _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 8WK A 1 601 1 8WK DRG . D 2 8WK B 1 601 2 8WK DRG . E 3 HOH A 1 701 27 HOH HOH . E 3 HOH A 2 702 56 HOH HOH . E 3 HOH A 3 703 4 HOH HOH . E 3 HOH A 4 704 41 HOH HOH . E 3 HOH A 5 705 2 HOH HOH . E 3 HOH A 6 706 38 HOH HOH . E 3 HOH A 7 707 6 HOH HOH . E 3 HOH A 8 708 19 HOH HOH . E 3 HOH A 9 709 44 HOH HOH . E 3 HOH A 10 710 26 HOH HOH . E 3 HOH A 11 711 37 HOH HOH . E 3 HOH A 12 712 1 HOH HOH . E 3 HOH A 13 713 28 HOH HOH . E 3 HOH A 14 714 23 HOH HOH . E 3 HOH A 15 715 35 HOH HOH . E 3 HOH A 16 716 3 HOH HOH . E 3 HOH A 17 717 18 HOH HOH . E 3 HOH A 18 718 25 HOH HOH . E 3 HOH A 19 719 34 HOH HOH . E 3 HOH A 20 720 40 HOH HOH . E 3 HOH A 21 721 39 HOH HOH . E 3 HOH A 22 722 43 HOH HOH . E 3 HOH A 23 723 22 HOH HOH . E 3 HOH A 24 724 20 HOH HOH . E 3 HOH A 25 725 29 HOH HOH . E 3 HOH A 26 726 42 HOH HOH . E 3 HOH A 27 727 5 HOH HOH . F 3 HOH B 1 701 57 HOH HOH . F 3 HOH B 2 702 17 HOH HOH . F 3 HOH B 3 703 52 HOH HOH . F 3 HOH B 4 704 32 HOH HOH . F 3 HOH B 5 705 8 HOH HOH . F 3 HOH B 6 706 10 HOH HOH . F 3 HOH B 7 707 49 HOH HOH . F 3 HOH B 8 708 58 HOH HOH . F 3 HOH B 9 709 16 HOH HOH . F 3 HOH B 10 710 21 HOH HOH . F 3 HOH B 11 711 30 HOH HOH . F 3 HOH B 12 712 55 HOH HOH . F 3 HOH B 13 713 50 HOH HOH . F 3 HOH B 14 714 48 HOH HOH . F 3 HOH B 15 715 14 HOH HOH . F 3 HOH B 16 716 53 HOH HOH . F 3 HOH B 17 717 31 HOH HOH . F 3 HOH B 18 718 13 HOH HOH . F 3 HOH B 19 719 51 HOH HOH . F 3 HOH B 20 720 12 HOH HOH . F 3 HOH B 21 721 7 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 CAJ 8WK . . . C 2 59.874 -43.348 86.722 1 51.92 ? CAJ 8WK 601 A 1 HETATM 2 C CAH 8WK . . . C 2 59.384 -42.357 85.868 1 58.58 ? CAH 8WK 601 A 1 HETATM 3 C CAZ 8WK . . . C 2 59.92 -41.069 85.877 1 58.37 ? CAZ 8WK 601 A 1 HETATM 4 F FAD 8WK . . . C 2 59.408 -40.055 84.998 1 55.76 ? FAD 8WK 601 A 1 HETATM 5 C CAI 8WK . . . C 2 60.975 -40.81 86.746 1 53.32 ? CAI 8WK 601 A 1 HETATM 6 C CAK 8WK . . . C 2 61.442 -41.837 87.566 1 53.19 ? CAK 8WK 601 A 1 HETATM 7 C CBB 8WK . . . C 2 60.899 -43.111 87.568 1 46.11 ? CBB 8WK 601 A 1 HETATM 8 N NBJ 8WK . . . C 2 61.394 -44.106 88.359 1 57.68 ? NBJ 8WK 601 A 1 HETATM 9 N NAW 8WK . . . C 2 60.731 -44.906 89.204 1 55.51 ? NAW 8WK 601 A 1 HETATM 10 C CAN 8WK . . . C 2 61.582 -45.772 89.762 1 53.49 ? CAN 8WK 601 A 1 HETATM 11 C CBD 8WK . . . C 2 62.791 -45.555 89.288 1 53.17 ? CBD 8WK 601 A 1 HETATM 12 C CBC 8WK . . . C 2 63.955 -46.179 89.552 1 54.51 ? CBC 8WK 601 A 1 HETATM 13 O OAB 8WK . . . C 2 63.981 -47.136 90.367 1 46.62 ? OAB 8WK 601 A 1 HETATM 14 C CBE 8WK . . . C 2 62.681 -44.531 88.407 1 56.42 ? CBE 8WK 601 A 1 HETATM 15 N NAV 8WK . . . C 2 63.777 -44.096 87.736 1 52.94 ? NAV 8WK 601 A 1 HETATM 16 C CAO 8WK . . . C 2 65.012 -44.72 88.002 1 47.44 ? CAO 8WK 601 A 1 HETATM 17 N NBH 8WK . . . C 2 65.095 -45.753 88.896 1 46.47 ? NBH 8WK 601 A 1 HETATM 18 C CAU 8WK . . . C 2 66.416 -46.32 89.141 1 41.18 ? CAU 8WK 601 A 1 HETATM 19 C CBK 8WK . . . C 2 67.144 -45.452 90.205 1 46.49 ? CBK 8WK 601 A 1 HETATM 20 C CAR 8WK . . . C 2 68.508 -45.972 90.378 1 49.22 ? CAR 8WK 601 A 1 HETATM 21 C CAP 8WK . . . C 2 69.248 -45 91.327 1 49.44 ? CAP 8WK 601 A 1 HETATM 22 O OAC 8WK . . . C 2 67.307 -44.009 89.817 1 43.78 ? OAC 8WK 601 A 1 HETATM 23 C CAS 8WK . . . C 2 66.411 -45.559 91.563 1 44.61 ? CAS 8WK 601 A 1 HETATM 24 C CAQ 8WK . . . C 2 67.171 -44.838 92.677 1 46.82 ? CAQ 8WK 601 A 1 HETATM 25 N NBG 8WK . . . C 2 68.619 -45.186 92.667 1 47.89 ? NBG 8WK 601 A 1 HETATM 26 C CAY 8WK . . . C 2 69.35 -45.611 93.754 1 57.51 ? CAY 8WK 601 A 1 HETATM 27 O OAA 8WK . . . C 2 70.557 -45.851 93.709 1 63.47 ? OAA 8WK 601 A 1 HETATM 28 C CAT 8WK . . . C 2 68.68 -45.786 95.134 1 55.67 ? CAT 8WK 601 A 1 HETATM 29 C CBL 8WK . . . C 2 68.798 -47.242 95.545 1 58.45 ? CBL 8WK 601 A 1 HETATM 30 C CBF 8WK . . . C 2 67.949 -47.613 96.824 1 64.18 ? CBF 8WK 601 A 1 HETATM 31 F FAF 8WK . . . C 2 68.266 -48.859 97.265 1 63.83 ? FAF 8WK 601 A 1 HETATM 32 F FAG 8WK . . . C 2 68.185 -46.705 97.898 1 66 ? FAG 8WK 601 A 1 HETATM 33 N NBI 8WK . . . C 2 68.351 -48.057 94.467 1 55.87 ? NBI 8WK 601 A 1 HETATM 34 N NAX 8WK . . . C 2 67.177 -48 93.854 1 51.91 ? NAX 8WK 601 A 1 HETATM 35 C CBA 8WK . . . C 2 67.23 -48.996 92.952 1 53 ? CBA 8WK 601 A 1 HETATM 36 F FAE 8WK . . . C 2 66.355 -49.279 92.2 1 59.37 ? FAE 8WK 601 A 1 HETATM 37 C CAL 8WK . . . C 2 68.37 -49.666 93.003 1 52.91 ? CAL 8WK 601 A 1 HETATM 38 C CAM 8WK . . . C 2 69.076 -49.073 93.966 1 52.63 ? CAM 8WK 601 A 1 # _model_server_stats.io_time_ms 76 _model_server_stats.parse_time_ms 28 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 308 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 38 #