data_5K4L # _model_server_result.job_id pwAOIpngvgvauL3iUDLVtg _model_server_result.datetime_utc '2025-04-11 15:16:09' _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 5k4l # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":904}' # _entry.id 5K4L # _exptl.entry_id 5K4L _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 233.223 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description ~{N}-ethyl-4-oxidanyl-2-oxidanylidene-1~{H}-1,7-naphthyridine-3-carboxamide _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 120 _cell.entry_id 5K4L _cell.length_a 159.141 _cell.length_b 159.141 _cell.length_c 92.109 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5K4L _symmetry.cell_setting ? _symmetry.Int_Tables_number 144 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? dimeric 2 author_defined_assembly 1 PISA tetrameric 4 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,B,E,F,G,H,I,J,K,L,M,N 1 1 A,B,C,D,E,F,G,H,I,J,K,L,M,N 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 ? 5 H N N ? 5 L N 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 disulf ? disulf1 B SG CYS 682 B CYS 692 1_555 B SG CYS 697 B CYS 707 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? metalc ? metalc1 A NE2 HIS 473 A HIS 483 1_555 E NI NI . A NI 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? metalc ? metalc2 A OE1 GLU 475 A GLU 485 1_555 E NI NI . A NI 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? metalc ? metalc3 A OE2 GLU 475 A GLU 485 1_555 E NI NI . A NI 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? metalc ? metalc4 A NE2 HIS 561 A HIS 571 1_555 E NI NI . A NI 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.998 ? metalc ? metalc5 A SG CYS 666 A CYS 676 1_555 F ZN ZN . A ZN 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.292 ? metalc ? metalc6 A SG CYS 669 A CYS 679 1_555 F ZN ZN . A ZN 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.7 ? metalc ? metalc7 A SG CYS 680 A CYS 690 1_555 G ZN ZN . A ZN 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.246 ? metalc ? metalc8 A SG CYS 699 A CYS 709 1_555 G ZN ZN . A ZN 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.459 ? metalc ? metalc9 E NI NI . A NI 901 1_555 H N11 6QN . A 6QN 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? metalc ? metalc10 B NE2 HIS 473 B HIS 483 1_555 I NI NI . B NI 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.992 ? metalc ? metalc11 B OE2 GLU 475 B GLU 485 1_555 I NI NI . B NI 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.985 ? metalc ? metalc12 B NE2 HIS 561 B HIS 571 1_555 I NI NI . B NI 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.006 ? metalc ? metalc13 B SG CYS 666 B CYS 676 1_555 J ZN ZN . B ZN 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.426 ? metalc ? metalc14 B SG CYS 669 B CYS 679 1_555 J ZN ZN . B ZN 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.11 ? metalc ? metalc15 B SG CYS 689 B CYS 699 1_555 J ZN ZN . B ZN 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.28 ? metalc ? metalc16 B ND1 HIS 692 B HIS 702 1_555 J ZN ZN . B ZN 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.009 ? metalc ? metalc17 B SG CYS 697 B CYS 707 1_555 K ZN ZN . B ZN 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.294 ? metalc ? metalc18 B O CYS 699 B CYS 709 1_555 K ZN ZN . B ZN 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.583 ? metalc ? metalc19 I NI NI . B NI 901 1_555 L N11 6QN . B 6QN 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.957 ? # _chem_comp.formula 'C11 H11 N3 O3' _chem_comp.formula_weight 233.223 _chem_comp.id 6QN _chem_comp.mon_nstd_flag . _chem_comp.name ~{N}-ethyl-4-oxidanyl-2-oxidanylidene-1~{H}-1,7-naphthyridine-3-carboxamide _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 C1 C2 6QN sing 1 n n C2 N3 6QN sing 2 n n N3 C4 6QN sing 3 n n O17 C16 6QN doub 4 n n C4 O5 6QN doub 5 n n C4 C6 6QN sing 6 n n C16 C6 6QN sing 7 n n C16 N14 6QN sing 8 n n C6 C7 6QN doub 9 n n N14 C13 6QN sing 10 n n C7 O18 6QN sing 11 n n C7 C8 6QN sing 12 n n C13 C8 6QN doub 13 n y C13 C12 6QN sing 14 n y C8 C9 6QN sing 15 n y C12 N11 6QN doub 16 n y C9 C10 6QN doub 17 n y N11 C10 6QN sing 18 n y C9 H25 6QN sing 19 n n C10 H26 6QN sing 20 n n C12 H27 6QN sing 21 n n N3 H24 6QN sing 22 n n C1 H19 6QN sing 23 n n C1 H20 6QN sing 24 n n C1 H21 6QN sing 25 n n C2 H23 6QN sing 26 n n C2 H22 6QN sing 27 n n N14 H15 6QN sing 28 n n O18 H28 6QN sing 29 n n # _atom_sites.entry_id 5K4L _atom_sites.fract_transf_matrix[1][1] 0.006284 _atom_sites.fract_transf_matrix[1][2] 0.003628 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007256 _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] 0.010857 _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 E 3 NI A 1 901 1500 NI NI . F 4 ZN A 1 902 1502 ZN ZN . G 4 ZN A 1 903 1501 ZN ZN . H 5 6QN A 1 904 1 6QN DRG . I 3 NI B 1 901 1500 NI NI . J 4 ZN B 1 902 1502 ZN ZN . K 4 ZN B 1 903 1501 ZN ZN . L 5 6QN B 1 904 1 6QN DRG . M 6 HOH A 1 1001 1 HOH HOH . M 6 HOH A 2 1002 8 HOH HOH . M 6 HOH A 3 1003 21 HOH HOH . M 6 HOH A 4 1004 5 HOH HOH . M 6 HOH A 5 1005 4 HOH HOH . M 6 HOH A 6 1006 20 HOH HOH . M 6 HOH A 7 1007 22 HOH HOH . N 6 HOH B 1 1001 30 HOH HOH . N 6 HOH B 2 1002 24 HOH HOH . N 6 HOH B 3 1003 28 HOH HOH . N 6 HOH B 4 1004 31 HOH HOH . N 6 HOH B 5 1005 16 HOH HOH . N 6 HOH B 6 1006 15 HOH HOH . N 6 HOH B 7 1007 29 HOH HOH . N 6 HOH B 8 1008 23 HOH HOH . N 6 HOH B 9 1009 13 HOH HOH . N 6 HOH B 10 1010 25 HOH HOH . N 6 HOH B 11 1011 19 HOH HOH . N 6 HOH B 12 1012 27 HOH HOH . N 6 HOH B 13 1013 26 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 6QN . . . H 5 190.084 2.501 -19.018 1 93.42 ? C4 6QN 904 A 1 HETATM 2 C C6 6QN . . . H 5 189.392 1.74 -17.949 1 110.04 ? C6 6QN 904 A 1 HETATM 3 C C7 6QN . . . H 5 189.028 2.417 -16.787 1 113.57 ? C7 6QN 904 A 1 HETATM 4 C C8 6QN . . . H 5 188.359 1.729 -15.701 1 114.36 ? C8 6QN 904 A 1 HETATM 5 C C9 6QN . . . H 5 187.955 2.362 -14.528 1 113.97 ? C9 6QN 904 A 1 HETATM 6 C C10 6QN . . . H 5 187.305 1.614 -13.561 1 110.49 ? C10 6QN 904 A 1 HETATM 7 C C12 6QN . . . H 5 187.453 -0.282 -14.81 1 107.73 ? C12 6QN 904 A 1 HETATM 8 C C13 6QN . . . H 5 188.101 0.355 -15.861 1 112.94 ? C13 6QN 904 A 1 HETATM 9 N N3 6QN . . . H 5 190.417 1.808 -20.11 1 72.61 ? N3 6QN 904 A 1 HETATM 10 C C1 6QN . . . H 5 190.336 2.726 -22.378 1 53.72 ? C1 6QN 904 A 1 HETATM 11 C C2 6QN . . . H 5 191.194 2.384 -21.205 1 63.13 ? C2 6QN 904 A 1 HETATM 12 O O5 6QN . . . H 5 190.333 3.699 -18.886 1 97.1 ? O5 6QN 904 A 1 HETATM 13 N N11 6QN . . . H 5 187.046 0.311 -13.682 1 105.62 ? N11 6QN 904 A 1 HETATM 14 N N14 6QN . . . H 5 188.485 -0.272 -17.043 1 120.01 ? N14 6QN 904 A 1 HETATM 15 C C16 6QN . . . H 5 189.105 0.331 -18.084 1 119.15 ? C16 6QN 904 A 1 HETATM 16 O O17 6QN . . . H 5 189.388 -0.329 -19.082 1 123.09 ? O17 6QN 904 A 1 HETATM 17 O O18 6QN . . . H 5 189.27 3.713 -16.583 1 108.89 ? O18 6QN 904 A 1 HETATM 18 H H25 6QN . . . H 5 188.145 3.423 -14.374 1 136.53 ? H25 6QN 904 A 1 HETATM 19 H H26 6QN . . . H 5 186.964 2.064 -12.63 1 132.36 ? H26 6QN 904 A 1 HETATM 20 H H27 6QN . . . H 5 187.23 -1.347 -14.851 1 129.05 ? H27 6QN 904 A 1 HETATM 21 H H24 6QN . . . H 5 190.128 0.84 -20.204 1 86.9 ? H24 6QN 904 A 1 HETATM 22 H H19 6QN . . . H 5 190.931 3.154 -23.184 1 64.23 ? H19 6QN 904 A 1 HETATM 23 H H20 6QN . . . H 5 189.824 1.862 -22.799 1 64.23 ? H20 6QN 904 A 1 HETATM 24 H H21 6QN . . . H 5 189.567 3.46 -22.143 1 64.23 ? H21 6QN 904 A 1 HETATM 25 H H23 6QN . . . H 5 191.981 1.691 -21.498 1 75.53 ? H23 6QN 904 A 1 HETATM 26 H H22 6QN . . . H 5 191.723 3.266 -20.847 1 75.53 ? H22 6QN 904 A 1 HETATM 27 H H15 6QN . . . H 5 188.277 -1.263 -17.117 1 143.78 ? H15 6QN 904 A 1 HETATM 28 H H28 6QN . . . H 5 189.737 4.129 -17.354 1 130.44 ? H28 6QN 904 A 1 # _model_server_stats.io_time_ms 29 _model_server_stats.parse_time_ms 35 _model_server_stats.create_model_time_ms 60 _model_server_stats.query_time_ms 432 _model_server_stats.encode_time_ms 56 _model_server_stats.element_count 28 #