data_6P39 # _model_server_result.job_id O-mLM2eIuQt_EVLXNahsFg _model_server_result.datetime_utc '2025-08-01 04:07:23' _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 6p39 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":4000}' # _entry.id 6P39 # _exptl.entry_id 6P39 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 478.587 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "3-methoxy-4-{[(6aR)-5-methyl-6-oxo-6,6a,7,8,9,10-hexahydro-5H-dipyrido[1,2-a:3',2'-e]pyrazin-2-yl]amino}-N-(1-methylpiperidin-4-yl)benzamide" _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 6P39 _cell.length_a 96.6 _cell.length_b 96.6 _cell.length_c 91.13 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6P39 _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 2 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B _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 # _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 122 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id CYS _struct_conn.ptnr1_auth_seq_id 1640 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id A _struct_conn.ptnr2_label_atom_id SG _struct_conn.ptnr2_label_comp_id CYS _struct_conn.ptnr2_label_seq_id 122 _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id CYS _struct_conn.ptnr2_auth_seq_id 1640 _struct_conn.ptnr2_symmetry 6_554 _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 2.022 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C26 H34 N6 O3' _chem_comp.formula_weight 478.587 _chem_comp.id NQY _chem_comp.mon_nstd_flag . _chem_comp.name "3-methoxy-4-{[(6aR)-5-methyl-6-oxo-6,6a,7,8,9,10-hexahydro-5H-dipyrido[1,2-a:3',2'-e]pyrazin-2-yl]amino}-N-(1-methylpiperidin-4-yl)benzamide" _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 C14 C13 NQY sing 235 n n C14 N4 NQY sing 236 n n C15 N4 NQY sing 237 n n C13 C12 NQY sing 238 n n N4 C16 NQY sing 239 n n O2 C11 NQY doub 240 n n C12 N3 NQY sing 241 n n C12 C17 NQY sing 242 n n C16 C17 NQY sing 243 n n C11 N3 NQY sing 244 n n C11 C10 NQY sing 245 n n C9 C10 NQY doub 246 n y C9 C8 NQY sing 247 n y C10 C18 NQY sing 248 n y C8 C7 NQY doub 249 n y C18 C19 NQY doub 250 n y C5 C4 NQY doub 251 n y C5 C6 NQY sing 252 n y C4 C3 NQY sing 253 n y C2 N1 NQY sing 254 n n C7 C19 NQY sing 255 n y C7 N2 NQY sing 256 n n C19 O3 NQY sing 257 n n C6 N2 NQY sing 258 n n C6 N5 NQY doub 259 n y C3 N1 NQY sing 260 n n C3 C21 NQY doub 261 n y N1 C1 NQY sing 262 n n O3 C20 NQY sing 263 n n N5 C21 NQY sing 264 n y C21 N6 NQY sing 265 n n C1 O1 NQY doub 266 n n C1 C22 NQY sing 267 n n N6 C22 NQY sing 268 n n N6 C26 NQY sing 269 n n C22 C23 NQY sing 270 n n C26 C25 NQY sing 271 n n C23 C24 NQY sing 272 n n C24 C25 NQY sing 273 n n C4 H1 NQY sing 274 n n C14 H2 NQY sing 275 n n C14 H3 NQY sing 276 n n C5 H4 NQY sing 277 n n C8 H5 NQY sing 278 n n C9 H6 NQY sing 279 n n C12 H7 NQY sing 280 n n C13 H8 NQY sing 281 n n C13 H9 NQY sing 282 n n N2 H10 NQY sing 283 n n N3 H11 NQY sing 284 n n C15 H12 NQY sing 285 n n C15 H13 NQY sing 286 n n C15 H14 NQY sing 287 n n C16 H15 NQY sing 288 n n C16 H16 NQY sing 289 n n C17 H17 NQY sing 290 n n C17 H18 NQY sing 291 n n C18 H19 NQY sing 292 n n C2 H20 NQY sing 293 n n C2 H21 NQY sing 294 n n C2 H22 NQY sing 295 n n C20 H23 NQY sing 296 n n C20 H24 NQY sing 297 n n C20 H25 NQY sing 298 n n C22 H26 NQY sing 299 n n C23 H27 NQY sing 300 n n C23 H28 NQY sing 301 n n C24 H29 NQY sing 302 n n C24 H30 NQY sing 303 n n C25 H31 NQY sing 304 n n C25 H32 NQY sing 305 n n C26 H33 NQY sing 306 n n C26 H34 NQY sing 307 n n # _atom_sites.entry_id 6P39 _atom_sites.fract_transf_matrix[1][1] 0.010352 _atom_sites.fract_transf_matrix[1][2] 0.005977 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011953 _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] 0.010973 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # _pdbx_nonpoly_scheme.asym_id B _pdbx_nonpoly_scheme.entity_id 2 _pdbx_nonpoly_scheme.mon_id NQY _pdbx_nonpoly_scheme.pdb_strand_id A _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 4000 _pdbx_nonpoly_scheme.auth_seq_num 4000 _pdbx_nonpoly_scheme.pdb_mon_id NQY _pdbx_nonpoly_scheme.auth_mon_id DRG _pdbx_nonpoly_scheme.pdb_ins_code . # 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 NQY . . . B 2 53.15 -33.435 -8.815 1 142.15 ? C4 NQY 4000 A 1 HETATM 2 C C14 NQY . . . B 2 63.177 -27.526 -13.272 1 161.69 ? C14 NQY 4000 A 1 HETATM 3 C C5 NQY . . . B 2 54.234 -32.596 -8.841 1 138.14 ? C5 NQY 4000 A 1 HETATM 4 C C6 NQY . . . B 2 54.613 -31.94 -7.639 1 125.82 ? C6 NQY 4000 A 1 HETATM 5 C C11 NQY . . . B 2 59.622 -29.591 -11.387 1 136.4 ? C11 NQY 4000 A 1 HETATM 6 C C7 NQY . . . B 2 56.669 -30.773 -8.547 1 105.65 ? C7 NQY 4000 A 1 HETATM 7 C C8 NQY . . . B 2 57.077 -31.667 -9.538 1 104.05 ? C8 NQY 4000 A 1 HETATM 8 C C9 NQY . . . B 2 58.033 -31.283 -10.453 1 112.81 ? C9 NQY 4000 A 1 HETATM 9 C C10 NQY . . . B 2 58.579 -30.008 -10.402 1 125.49 ? C10 NQY 4000 A 1 HETATM 10 C C12 NQY . . . B 2 61.396 -27.86 -11.566 1 158.82 ? C12 NQY 4000 A 1 HETATM 11 C C13 NQY . . . B 2 61.754 -27.997 -13.038 1 160.47 ? C13 NQY 4000 A 1 HETATM 12 N N1 NQY . . . B 2 51.33 -34.461 -7.539 1 124.94 ? N1 NQY 4000 A 1 HETATM 13 N N2 NQY . . . B 2 55.685 -31.079 -7.579 1 106.57 ? N2 NQY 4000 A 1 HETATM 14 C C3 NQY . . . B 2 52.459 -33.608 -7.62 1 133.9 ? C3 NQY 4000 A 1 HETATM 15 N N3 NQY . . . B 2 60.024 -28.293 -11.293 1 148.52 ? N3 NQY 4000 A 1 HETATM 16 C C1 NQY . . . B 2 50.673 -34.721 -6.353 1 114.74 ? C1 NQY 4000 A 1 HETATM 17 C C15 NQY . . . B 2 64.743 -25.705 -13.079 1 161.59 ? C15 NQY 4000 A 1 HETATM 18 C C16 NQY . . . B 2 63.027 -25.982 -11.412 1 166.64 ? C16 NQY 4000 A 1 HETATM 19 C C17 NQY . . . B 2 61.605 -26.42 -11.123 1 164.91 ? C17 NQY 4000 A 1 HETATM 20 C C18 NQY . . . B 2 58.17 -29.119 -9.413 1 121.92 ? C18 NQY 4000 A 1 HETATM 21 C C19 NQY . . . B 2 57.216 -29.487 -8.491 1 109.82 ? C19 NQY 4000 A 1 HETATM 22 C C2 NQY . . . B 2 50.833 -35.111 -8.765 1 127.48 ? C2 NQY 4000 A 1 HETATM 23 C C20 NQY . . . B 2 57.37 -27.372 -7.385 1 108.34 ? C20 NQY 4000 A 1 HETATM 24 C C21 NQY . . . B 2 52.889 -32.922 -6.482 1 132.79 ? C21 NQY 4000 A 1 HETATM 25 C C22 NQY . . . B 2 51.179 -34.068 -5.084 1 120.71 ? C22 NQY 4000 A 1 HETATM 26 C C23 NQY . . . B 2 51.674 -35.122 -4.09 1 110.02 ? C23 NQY 4000 A 1 HETATM 27 C C24 NQY . . . B 2 52.77 -34.57 -3.189 1 108.17 ? C24 NQY 4000 A 1 HETATM 28 C C25 NQY . . . B 2 52.498 -33.116 -2.84 1 112.25 ? C25 NQY 4000 A 1 HETATM 29 C C26 NQY . . . B 2 52.589 -32.273 -4.094 1 120.4 ? C26 NQY 4000 A 1 HETATM 30 N N4 NQY . . . B 2 63.359 -26.136 -12.834 1 164.94 ? N4 NQY 4000 A 1 HETATM 31 N N5 NQY . . . B 2 53.95 -32.101 -6.505 1 131.3 ? N5 NQY 4000 A 1 HETATM 32 N N6 NQY . . . B 2 52.236 -33.066 -5.271 1 131.26 ? N6 NQY 4000 A 1 HETATM 33 O O1 NQY . . . B 2 49.711 -35.469 -6.303 1 104.17 ? O1 NQY 4000 A 1 HETATM 34 O O2 NQY . . . B 2 60.113 -30.404 -12.17 1 134.74 ? O2 NQY 4000 A 1 HETATM 35 O O3 NQY . . . B 2 56.77 -28.658 -7.499 1 104.96 ? O3 NQY 4000 A 1 # _model_server_stats.io_time_ms 42 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 262 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 35 #