data_6FK9 # _model_server_result.job_id 1Md2iNU_dorKrJKV_WN3CQ _model_server_result.datetime_utc '2024-11-23 04:52:55' _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 6fk9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":411}' # _entry.id 6FK9 # _exptl.entry_id 6FK9 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 351.439 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "(2~{S})-3-methyl-2-phenyl-1-spiro[1,3-benzodioxole-2,4'-piperidine]-1'-yl-butan-1-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 6FK9 _cell.length_a 243.193 _cell.length_b 243.193 _cell.length_c 111.688 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6FK9 _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 _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 H _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 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf2 A SG CYS 111 A CYS 110 1_555 A SG CYS 188 A CYS 187 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? covale ? covale1 A C ACE 1 A ACE 0 1_555 A N MET 2 A MET 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale2 A ND2 ASN 16 A ASN 15 1_555 B C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale3 A SG CYS 323 A CYS 322 1_555 C C1 PLM . A PLM 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.727 ? covale ? covale4 B O4 NAG . B NAG 1 1_555 B C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale5 B O4 NAG . B NAG 2 1_555 B C1 BMA . B BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale6 B O3 BMA . B BMA 3 1_555 B C1 MAN . B MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale7 B O6 BMA . B BMA 3 1_555 B C1 MAN . B MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? # _chem_comp.formula 'C22 H25 N O3' _chem_comp.formula_weight 351.439 _chem_comp.id DNK _chem_comp.mon_nstd_flag . _chem_comp.name "(2~{S})-3-methyl-2-phenyl-1-spiro[1,3-benzodioxole-2,4'-piperidine]-1'-yl-butan-1-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 O9 C2 DNK sing 161 n n O9 C8 DNK sing 162 n n C26 C8 DNK sing 163 n n C26 C25 DNK sing 164 n n C1 C2 DNK doub 165 n y C1 C6 DNK sing 166 n y C2 C3 DNK sing 167 n y C17 C15 DNK sing 168 n n C8 C10 DNK sing 169 n n C8 O7 DNK sing 170 n n C10 C11 DNK sing 171 n n C6 C5 DNK doub 172 n y C25 N12 DNK sing 173 n n C14 C15 DNK sing 174 n n C14 C13 DNK sing 175 n n C14 C18 DNK sing 176 n n N12 C13 DNK sing 177 n n N12 C11 DNK sing 178 n n C15 C16 DNK sing 179 n n C13 O24 DNK doub 180 n n C19 C18 DNK doub 181 n y C19 C20 DNK sing 182 n y C3 O7 DNK sing 183 n n C3 C4 DNK doub 184 n y C18 C23 DNK sing 185 n y C5 C4 DNK sing 186 n y C20 C21 DNK doub 187 n y C23 C22 DNK doub 188 n y C21 C22 DNK sing 189 n y C10 H1 DNK sing 190 n n C10 H2 DNK sing 191 n n C11 H3 DNK sing 192 n n C11 H4 DNK sing 193 n n C15 H5 DNK sing 194 n n C16 H6 DNK sing 195 n n C16 H7 DNK sing 196 n n C16 H8 DNK sing 197 n n C17 H9 DNK sing 198 n n C17 H10 DNK sing 199 n n C17 H11 DNK sing 200 n n C19 H12 DNK sing 201 n n C20 H13 DNK sing 202 n n C21 H14 DNK sing 203 n n C22 H15 DNK sing 204 n n C23 H16 DNK sing 205 n n C25 H17 DNK sing 206 n n C25 H18 DNK sing 207 n n C26 H19 DNK sing 208 n n C26 H20 DNK sing 209 n n C1 H21 DNK sing 210 n n C4 H22 DNK sing 211 n n C5 H23 DNK sing 212 n n C6 H24 DNK sing 213 n n C14 H25 DNK sing 214 n n # _atom_sites.entry_id 6FK9 _atom_sites.fract_transf_matrix[1][1] 0.004112 _atom_sites.fract_transf_matrix[1][2] 0.002374 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.004748 _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] 0.008954 _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 1 409 503 BOG BOG . G 4 BOG A 1 410 504 BOG BOG . H 5 DNK A 1 411 600 DNK L0R . I 6 HOH A 1 1000 1000 HOH HOH . I 6 HOH A 2 1001 1001 HOH HOH . I 6 HOH A 3 1002 1002 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 DNK . . . H 5 -234.265 48.641 35.254 1 117.19 ? C10 DNK 411 A 1 HETATM 2 C C11 DNK . . . H 5 -233.601 47.683 36.257 1 104.34 ? C11 DNK 411 A 1 HETATM 3 C C13 DNK . . . H 5 -232.815 45.317 36.115 1 111.96 ? C13 DNK 411 A 1 HETATM 4 C C15 DNK . . . H 5 -231.7 43.007 36.052 1 100.23 ? C15 DNK 411 A 1 HETATM 5 C C16 DNK . . . H 5 -231.981 41.499 36.073 1 99.02 ? C16 DNK 411 A 1 HETATM 6 C C17 DNK . . . H 5 -230.668 43.318 34.954 1 92.77 ? C17 DNK 411 A 1 HETATM 7 C C18 DNK . . . H 5 -234.148 43.289 36.707 1 88.01 ? C18 DNK 411 A 1 HETATM 8 C C19 DNK . . . H 5 -235.256 42.641 36.143 1 93.82 ? C19 DNK 411 A 1 HETATM 9 C C20 DNK . . . H 5 -236.297 42.193 36.951 1 88.97 ? C20 DNK 411 A 1 HETATM 10 C C21 DNK . . . H 5 -236.253 42.388 38.324 1 82.96 ? C21 DNK 411 A 1 HETATM 11 C C22 DNK . . . H 5 -235.159 43.037 38.883 1 90.63 ? C22 DNK 411 A 1 HETATM 12 C C23 DNK . . . H 5 -234.114 43.493 38.083 1 81.16 ? C23 DNK 411 A 1 HETATM 13 C C25 DNK . . . H 5 -235.242 45.925 35.511 1 104.34 ? C25 DNK 411 A 1 HETATM 14 C C26 DNK . . . H 5 -235.741 46.832 34.402 1 110.44 ? C26 DNK 411 A 1 HETATM 15 C C1 DNK . . . H 5 -238.45 50.437 34.522 1 107.11 ? C1 DNK 411 A 1 HETATM 16 C C2 DNK . . . H 5 -237.481 49.541 34.902 1 109.65 ? C2 DNK 411 A 1 HETATM 17 C C3 DNK . . . H 5 -237.477 48.907 36.166 1 102.15 ? C3 DNK 411 A 1 HETATM 18 C C4 DNK . . . H 5 -238.437 49.138 37.101 1 102.84 ? C4 DNK 411 A 1 HETATM 19 C C5 DNK . . . H 5 -239.425 50.043 36.713 1 105.18 ? C5 DNK 411 A 1 HETATM 20 C C6 DNK . . . H 5 -239.436 50.68 35.482 1 101.65 ? C6 DNK 411 A 1 HETATM 21 O O7 DNK . . . H 5 -236.403 48.086 36.264 1 103.31 ? O7 DNK 411 A 1 HETATM 22 C C8 DNK . . . H 5 -235.714 48.195 35.025 1 113.88 ? C8 DNK 411 A 1 HETATM 23 O O9 DNK . . . H 5 -236.403 49.116 34.185 1 112.51 ? O9 DNK 411 A 1 HETATM 24 N N12 DNK . . . H 5 -233.86 46.25 35.951 1 107.06 ? N12 DNK 411 A 1 HETATM 25 C C14 DNK . . . H 5 -233.022 43.802 35.821 1 95.35 ? C14 DNK 411 A 1 HETATM 26 O O24 DNK . . . H 5 -231.727 45.759 36.498 1 118.71 ? O24 DNK 411 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 311 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 26 #