data_6FKD # _model_server_result.job_id 54ZSsfa-ZGaY_WeBDkpYzA _model_server_result.datetime_utc '2024-11-08 10:47:38' _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 6fkd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":412}' # _entry.id 6FKD # _exptl.entry_id 6FKD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 360.792 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5-chloranyl-2-(2-oxidanylidene-2-spiro[1,3-benzodioxole-2,4'-piperidine]-1'-yl-ethyl)-3~{H}-pyridin-6-one" _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 6FKD _cell.length_a 243.431 _cell.length_b 243.431 _cell.length_c 111.782 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6FKD _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'H 3 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 _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 5 _struct_asym.id I _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 2 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 2 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 2 4 3 MAN BMA C1 O1 . O3 HO3 . sing 4 ? 2 5 3 MAN BMA C1 O1 . O6 HO6 . sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 2 n B NAG 1 B 1 NAG A 400 NAG 2 n B NAG 2 B 2 NAG A 401 NAG 2 n B BMA 3 B 3 BMA A 402 BMA 2 n B MAN 4 B 4 MAN A 403 MAN 2 n B MAN 5 B 5 MAN A 404 MAN # 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 A SG CYS 3 A CYS 2 1_555 A SG CYS 283 A CYS 282 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf2 A SG CYS 111 A CYS 110 1_555 A SG CYS 188 A CYS 187 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? covale ? covale1 A C ACE 1 A ACE 0 1_555 A N MET 2 A MET 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.342 ? covale ? covale2 A ND2 ASN 16 A ASN 15 1_555 B C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale3 A SG CYS 323 A CYS 322 1_555 C C1 PLM . A PLM 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.724 ? covale ? covale4 B O4 NAG . B NAG 1 1_555 B C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale5 B O4 NAG . B NAG 2 1_555 B C1 BMA . B BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.429 ? covale ? covale6 B O3 BMA . B BMA 3 1_555 B C1 MAN . B MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale7 B O6 BMA . B BMA 3 1_555 B C1 MAN . B MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? # _chem_comp.formula 'C18 H17 Cl N2 O4' _chem_comp.formula_weight 360.792 _chem_comp.id DL2 _chem_comp.mon_nstd_flag . _chem_comp.name "5-chloranyl-2-(2-oxidanylidene-2-spiro[1,3-benzodioxole-2,4'-piperidine]-1'-yl-ethyl)-3~{H}-pyridin-6-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 C1 C2 DL2 doub 161 n y C1 C6 DL2 sing 162 n y O9 C2 DL2 sing 163 n n O9 C8 DL2 sing 164 n n C2 C3 DL2 sing 165 n y C6 C5 DL2 doub 166 n y C14 C13 DL2 sing 167 n n C14 C15 DL2 sing 168 n n C22 C8 DL2 sing 169 n n C22 C21 DL2 sing 170 n n C11 C10 DL2 sing 171 n n C11 N12 DL2 sing 172 n n C8 C10 DL2 sing 173 n n C8 O7 DL2 sing 174 n n C13 O20 DL2 doub 175 n n C13 N12 DL2 sing 176 n n N12 C21 DL2 sing 177 n n N16 C15 DL2 doub 178 n n N16 C17 DL2 sing 179 n n C3 O7 DL2 sing 180 n n C3 C4 DL2 doub 181 n y C5 C4 DL2 sing 182 n y C15 C19 DL2 sing 183 n n O18 C17 DL2 doub 184 n n C17 C23 DL2 sing 185 n n C19 C25 DL2 sing 186 n n C23 C25 DL2 doub 187 n n C23 CL DL2 sing 188 n n C10 H1 DL2 sing 189 n n C10 H2 DL2 sing 190 n n C11 H3 DL2 sing 191 n n C11 H4 DL2 sing 192 n n C19 H5 DL2 sing 193 n n C19 H6 DL2 sing 194 n n C21 H7 DL2 sing 195 n n C21 H8 DL2 sing 196 n n C22 H9 DL2 sing 197 n n C22 H10 DL2 sing 198 n n C25 H11 DL2 sing 199 n n C1 H12 DL2 sing 200 n n C4 H13 DL2 sing 201 n n C5 H14 DL2 sing 202 n n C6 H15 DL2 sing 203 n n C14 H16 DL2 sing 204 n n C14 H17 DL2 sing 205 n n # _atom_sites.entry_id 6FKD _atom_sites.fract_transf_matrix[1][1] 0.004108 _atom_sites.fract_transf_matrix[1][2] 0.002372 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.004743 _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] 0.008946 _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 3 PLM A 1 401 1322 PLM P1L . D 4 BOG A 1 407 500 BOG BOG . E 4 BOG A 1 408 501 BOG BOG . F 4 BOG A 1 409 502 BOG BOG . G 4 BOG A 1 410 503 BOG BOG . H 4 BOG A 1 411 504 BOG BOG . I 5 DL2 A 1 412 600 DL2 L0R . J 6 HOH A 1 501 1006 HOH HOH . J 6 HOH A 2 502 1000 HOH HOH . J 6 HOH A 3 503 1004 HOH HOH . J 6 HOH A 4 504 1011 HOH HOH . J 6 HOH A 5 505 1002 HOH HOH . J 6 HOH A 6 506 1015 HOH HOH . J 6 HOH A 7 507 1022 HOH HOH . J 6 HOH A 8 508 1001 HOH HOH . J 6 HOH A 9 509 1016 HOH HOH . J 6 HOH A 10 510 1012 HOH HOH . J 6 HOH A 11 511 1010 HOH HOH . J 6 HOH A 12 512 1007 HOH HOH . J 6 HOH A 13 513 1018 HOH HOH . J 6 HOH A 14 514 1023 HOH HOH . J 6 HOH A 15 515 1009 HOH HOH . J 6 HOH A 16 516 1003 HOH HOH . J 6 HOH A 17 517 1024 HOH HOH . J 6 HOH A 18 518 1013 HOH HOH . J 6 HOH A 19 519 1005 HOH HOH . J 6 HOH A 20 520 1014 HOH HOH . J 6 HOH A 21 521 1021 HOH HOH . J 6 HOH A 22 522 1017 HOH HOH . J 6 HOH A 23 523 1019 HOH HOH . J 6 HOH A 24 524 1008 HOH HOH . J 6 HOH A 25 525 1020 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 C10 DL2 . . . I 5 -234.989 48.626 36.057 1 71.1 ? C10 DL2 412 A 1 HETATM 2 C C11 DL2 . . . I 5 -234.274 47.399 35.519 1 87.59 ? C11 DL2 412 A 1 HETATM 3 C C13 DL2 . . . I 5 -233.98 45.012 35.975 1 91.55 ? C13 DL2 412 A 1 HETATM 4 C C15 DL2 . . . I 5 -235.485 43.087 36.59 1 70.16 ? C15 DL2 412 A 1 HETATM 5 C C17 DL2 . . . I 5 -237.475 41.819 37.228 1 76.19 ? C17 DL2 412 A 1 HETATM 6 C C19 DL2 . . . I 5 -235.014 43.065 37.879 1 63.27 ? C19 DL2 412 A 1 HETATM 7 C C21 DL2 . . . I 5 -236.21 46.136 36.436 1 74.12 ? C21 DL2 412 A 1 HETATM 8 C C22 DL2 . . . I 5 -236.97 47.061 35.489 1 72.83 ? C22 DL2 412 A 1 HETATM 9 C C23 DL2 . . . I 5 -236.943 41.814 38.55 1 74.55 ? C23 DL2 412 A 1 HETATM 10 C C25 DL2 . . . I 5 -235.77 42.403 38.891 1 64.97 ? C25 DL2 412 A 1 HETATM 11 C C1 DL2 . . . I 5 -238.263 51.291 34.421 1 93.82 ? C1 DL2 412 A 1 HETATM 12 C C2 DL2 . . . I 5 -237.668 50.274 35.115 1 86.67 ? C2 DL2 412 A 1 HETATM 13 C C3 DL2 . . . I 5 -237.868 50.097 36.495 1 88.14 ? C3 DL2 412 A 1 HETATM 14 C C4 DL2 . . . I 5 -238.667 50.925 37.239 1 97.43 ? C4 DL2 412 A 1 HETATM 15 C C5 DL2 . . . I 5 -239.274 51.969 36.531 1 94.82 ? C5 DL2 412 A 1 HETATM 16 C C6 DL2 . . . I 5 -239.083 52.143 35.176 1 97.33 ? C6 DL2 412 A 1 HETATM 17 O O7 DL2 . . . I 5 -237.162 49.014 36.916 1 80.77 ? O7 DL2 412 A 1 HETATM 18 C C8 DL2 . . . I 5 -236.49 48.502 35.768 1 80.85 ? C8 DL2 412 A 1 HETATM 19 O O9 DL2 . . . I 5 -236.822 49.304 34.645 1 75.75 ? O9 DL2 412 A 1 HETATM 20 N N12 DL2 . . . I 5 -234.744 46.169 36.177 1 86.96 ? N12 DL2 412 A 1 HETATM 21 C C14 DL2 . . . I 5 -234.729 43.776 35.489 1 82.36 ? C14 DL2 412 A 1 HETATM 22 N N16 DL2 . . . I 5 -236.686 42.497 36.256 1 78.97 ? N16 DL2 412 A 1 HETATM 23 O O18 DL2 . . . I 5 -238.529 41.3 36.89 1 69.55 ? O18 DL2 412 A 1 HETATM 24 O O20 DL2 . . . I 5 -232.757 45.018 36.169 1 90.52 ? O20 DL2 412 A 1 HETATM 25 CL CL DL2 . . . I 5 -237.906 41.009 39.667 1 80.77 ? CL DL2 412 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 253 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 25 #