data_7UMY # _model_server_result.job_id YaY-YBOtlSKNjhj7mejIyw _model_server_result.datetime_utc '2024-12-03 20:15:36' _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 7umy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"O","auth_seq_id":301}' # _entry.id 7UMY # _exptl.entry_id 7UMY _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 404.462 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (2E)-3-[(7S)-7-amino-8-oxo-6,7,8,9-tetrahydro-5H-pyrido[2,3-b]azepin-3-yl]-N-methyl-N-[(3-methyl-1-benzofuran-2-yl)methyl]prop-2-enamide _entity.pdbx_number_of_molecules 6 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 110.297 _cell.angle_gamma 90 _cell.entry_id 7UMY _cell.length_a 256.215 _cell.length_b 79.137 _cell.length_c 89.425 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7UMY _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall 'C 2y' _symmetry.space_group_name_H-M 'C 1 2 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 ? tetrameric 4 author_defined_assembly 1 ? tetrameric 4 author_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,F,G,H,K,L,O,P,Q,R,S,U,W,X 1 1 B,I,J,T 2 1,3 D,M,N,V 2 2,4 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 1_556 x,y,z+1 1 0 0 0 1 0 0 0 1 -31.020329 0 83.872342 3 'crystal symmetry operation' 2_556 -x,y,-z+1 -1 0 0 0 1 0 0 0 -1 -31.020329 0 83.872342 4 'crystal symmetry operation' 2_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 H N N ? 3 I N N ? 3 K N N ? 3 N N N ? 3 O N N ? 3 Q 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 covale ? covale1 A N ILE 26 A ILE 22 1_555 G O2N NAD . A NAD 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.303 ? covale ? covale2 A NZ LYS 170 A LYS 166 1_555 G O2D NAD . A NAD 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.3 ? covale ? covale3 C N ILE 26 C ILE 22 1_555 L O2N NAD . C NAD 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.302 ? covale ? covale4 C NZ LYS 170 C LYS 166 1_555 L O2D NAD . C NAD 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.3 ? covale ? covale5 D N ILE 26 D ILE 22 1_555 M O2N NAD . D NAD 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.301 ? covale ? covale6 F N ILE 26 F ILE 22 1_555 R O2N NAD . F NAD 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.301 ? # _chem_comp.formula 'C23 H24 N4 O3' _chem_comp.formula_weight 404.462 _chem_comp.id NUC _chem_comp.mon_nstd_flag . _chem_comp.name (2E)-3-[(7S)-7-amino-8-oxo-6,7,8,9-tetrahydro-5H-pyrido[2,3-b]azepin-3-yl]-N-methyl-N-[(3-methyl-1-benzofuran-2-yl)methyl]prop-2-enamide _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 C13 N4 NUC sing 312 n n O1 C1 NUC doub 313 n n N4 C1 NUC sing 314 n n N4 C14 NUC sing 315 n n C1 C2 NUC sing 316 n n C17 C16 NUC sing 317 n n C2 C3 NUC doub 318 e n C14 C15 NUC sing 319 n n C3 C4 NUC sing 320 n n C16 C15 NUC doub 321 n y C16 C18 NUC sing 322 n y C15 O3 NUC sing 323 n y C18 C19 NUC doub 324 n y C18 C23 NUC sing 325 n y C5 C4 NUC doub 326 n y C5 N1 NUC sing 327 n y C19 C20 NUC sing 328 n y C4 C12 NUC sing 329 n y O3 C23 NUC sing 330 n y C23 C22 NUC doub 331 n y C20 C21 NUC doub 332 n y N1 C6 NUC doub 333 n y C22 C21 NUC sing 334 n y C12 C11 NUC doub 335 n y C6 C11 NUC sing 336 n y C6 N2 NUC sing 337 n n C11 C10 NUC sing 338 n n N2 C7 NUC sing 339 n n C10 C9 NUC sing 340 n n C8 C7 NUC sing 341 n n C8 C9 NUC sing 342 n n C8 N3 NUC sing 343 n n C7 O2 NUC doub 344 n n N3 H1 NUC sing 345 n n N3 H2 NUC sing 346 n n C2 H4 NUC sing 347 n n C5 H5 NUC sing 348 n n C10 H6 NUC sing 349 n n C10 H7 NUC sing 350 n n C12 H8 NUC sing 351 n n C13 H9 NUC sing 352 n n C13 H10 NUC sing 353 n n C13 H11 NUC sing 354 n n C14 H12 NUC sing 355 n n C14 H13 NUC sing 356 n n C17 H14 NUC sing 357 n n C17 H15 NUC sing 358 n n C17 H16 NUC sing 359 n n C19 H17 NUC sing 360 n n C20 H18 NUC sing 361 n n C21 H19 NUC sing 362 n n C22 H20 NUC sing 363 n n C3 H21 NUC sing 364 n n C8 H22 NUC sing 365 n n C9 H23 NUC sing 366 n n C9 H24 NUC sing 367 n n N2 H25 NUC sing 368 n n # _atom_sites.entry_id 7UMY _atom_sites.fract_transf_matrix[1][1] 0.003903 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001444 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012636 _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] 0.011923 _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 G 2 NAD A 1 301 301 NAD NAD . H 3 NUC A 1 302 302 NUC BRD . I 3 NUC B 1 301 301 NUC BRD . J 2 NAD B 1 302 302 NAD NAD . K 3 NUC C 1 301 301 NUC BRD . L 2 NAD C 1 302 302 NAD NAD . M 2 NAD D 1 301 301 NAD NAD . N 3 NUC D 1 302 302 NUC BRD . O 3 NUC E 1 301 301 NUC BRD . P 2 NAD E 1 302 302 NAD NAD . Q 3 NUC F 1 301 301 NUC BRD . R 2 NAD F 1 302 302 NAD NAD . S 4 HOH A 1 401 5 HOH HOH . S 4 HOH A 2 402 14 HOH HOH . S 4 HOH A 3 403 21 HOH HOH . S 4 HOH A 4 404 11 HOH HOH . T 4 HOH B 1 401 27 HOH HOH . T 4 HOH B 2 402 7 HOH HOH . U 4 HOH C 1 401 13 HOH HOH . U 4 HOH C 2 402 18 HOH HOH . U 4 HOH C 3 403 9 HOH HOH . U 4 HOH C 4 404 36 HOH HOH . U 4 HOH C 5 405 12 HOH HOH . U 4 HOH C 6 406 32 HOH HOH . U 4 HOH C 7 407 24 HOH HOH . U 4 HOH C 8 408 15 HOH HOH . U 4 HOH C 9 409 22 HOH HOH . V 4 HOH D 1 401 17 HOH HOH . W 4 HOH E 1 401 33 HOH HOH . W 4 HOH E 2 402 31 HOH HOH . X 4 HOH F 1 401 26 HOH HOH . X 4 HOH F 2 402 4 HOH HOH . X 4 HOH F 3 403 16 HOH HOH . X 4 HOH F 4 404 1 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 NUC . . . O 3 52.949 -12.415 29.011 1 91.19 ? C4 NUC 301 E 1 HETATM 2 N N3 NUC . . . O 3 57.429 -11.917 33.545 1 108 ? N3 NUC 301 E 1 HETATM 3 C C2 NUC . . . O 3 50.936 -13.48 27.882 1 85.81 ? C2 NUC 301 E 1 HETATM 4 N N1 NUC . . . O 3 55.266 -13.002 28.671 1 89.9 ? N1 NUC 301 E 1 HETATM 5 C C7 NUC . . . O 3 57.498 -11.844 31.03 1 96.46 ? C7 NUC 301 E 1 HETATM 6 C C6 NUC . . . O 3 55.598 -12.06 29.548 1 89.94 ? C6 NUC 301 E 1 HETATM 7 O O2 NUC . . . O 3 58.702 -11.692 31.059 1 93.54 ? O2 NUC 301 E 1 HETATM 8 C C5 NUC . . . O 3 53.97 -13.18 28.407 1 91.44 ? C5 NUC 301 E 1 HETATM 9 C C1 NUC . . . O 3 49.492 -13.557 27.69 1 79.9 ? C1 NUC 301 E 1 HETATM 10 C C10 NUC . . . O 3 55.187 -10.203 31.191 1 104.25 ? C10 NUC 301 E 1 HETATM 11 C C11 NUC . . . O 3 54.684 -11.25 30.211 1 94.96 ? C11 NUC 301 E 1 HETATM 12 C C12 NUC . . . O 3 53.336 -11.428 29.933 1 96.64 ? C12 NUC 301 E 1 HETATM 13 C C13 NUC . . . O 3 48.414 -12.017 29.328 1 91.78 ? C13 NUC 301 E 1 HETATM 14 C C14 NUC . . . O 3 47.878 -11.904 26.822 1 79.5 ? C14 NUC 301 E 1 HETATM 15 C C15 NUC . . . O 3 48.734 -10.937 26.026 1 82.68 ? C15 NUC 301 E 1 HETATM 16 C C16 NUC . . . O 3 48.373 -9.761 25.474 1 84.13 ? C16 NUC 301 E 1 HETATM 17 C C17 NUC . . . O 3 46.997 -9.151 25.539 1 88.21 ? C17 NUC 301 E 1 HETATM 18 C C18 NUC . . . O 3 49.512 -9.22 24.837 1 86.29 ? C18 NUC 301 E 1 HETATM 19 C C19 NUC . . . O 3 49.772 -8.051 24.105 1 93.81 ? C19 NUC 301 E 1 HETATM 20 C C20 NUC . . . O 3 51.054 -7.837 23.608 1 90.66 ? C20 NUC 301 E 1 HETATM 21 C C21 NUC . . . O 3 52.079 -8.778 23.834 1 90.97 ? C21 NUC 301 E 1 HETATM 22 C C22 NUC . . . O 3 51.823 -9.936 24.559 1 91.87 ? C22 NUC 301 E 1 HETATM 23 C C23 NUC . . . O 3 50.532 -10.131 25.048 1 87.45 ? C23 NUC 301 E 1 HETATM 24 C C3 NUC . . . O 3 51.522 -12.588 28.736 1 91.4 ? C3 NUC 301 E 1 HETATM 25 C C8 NUC . . . O 3 56.629 -11.98 32.306 1 98.97 ? C8 NUC 301 E 1 HETATM 26 C C9 NUC . . . O 3 55.598 -10.855 32.519 1 101.9 ? C9 NUC 301 E 1 HETATM 27 N N2 NUC . . . O 3 56.936 -11.908 29.801 1 94.64 ? N2 NUC 301 E 1 HETATM 28 N N4 NUC . . . O 3 48.686 -12.46 27.944 1 81.03 ? N4 NUC 301 E 1 HETATM 29 O O1 NUC . . . O 3 48.93 -14.583 27.31 1 76.28 ? O1 NUC 301 E 1 HETATM 30 O O3 NUC . . . O 3 50.062 -11.193 25.781 1 85.51 ? O3 NUC 301 E 1 HETATM 31 H H1 NUC . . . O 3 58.004 -12.744 33.606 1 131.01 ? H1 NUC 301 E 1 HETATM 32 H H2 NUC . . . O 3 58.054 -11.122 33.453 1 131.01 ? H2 NUC 301 E 1 HETATM 33 H H4 NUC . . . O 3 51.517 -14.157 27.32 1 104.38 ? H4 NUC 301 E 1 HETATM 34 H H5 NUC . . . O 3 53.724 -13.936 27.709 1 111.13 ? H5 NUC 301 E 1 HETATM 35 H H6 NUC . . . O 3 54.406 -9.467 31.387 1 126.5 ? H6 NUC 301 E 1 HETATM 36 H H7 NUC . . . O 3 56.049 -9.682 30.773 1 126.5 ? H7 NUC 301 E 1 HETATM 37 H H8 NUC . . . O 3 52.599 -10.831 30.406 1 117.38 ? H8 NUC 301 E 1 HETATM 38 H H9 NUC . . . O 3 48.513 -12.871 29.985 1 111.54 ? H9 NUC 301 E 1 HETATM 39 H H10 NUC . . . O 3 47.408 -11.622 29.368 1 111.54 ? H10 NUC 301 E 1 HETATM 40 H H11 NUC . . . O 3 49.133 -11.252 29.588 1 111.54 ? H11 NUC 301 E 1 HETATM 41 H H12 NUC . . . O 3 47.572 -12.696 26.15 1 96.8 ? H12 NUC 301 E 1 HETATM 42 H H13 NUC . . . O 3 47.032 -11.348 27.207 1 96.8 ? H13 NUC 301 E 1 HETATM 43 H H14 NUC . . . O 3 46.46 -9.435 24.633 1 107.26 ? H14 NUC 301 E 1 HETATM 44 H H15 NUC . . . O 3 47.111 -8.069 25.601 1 107.26 ? H15 NUC 301 E 1 HETATM 45 H H16 NUC . . . O 3 46.498 -9.541 26.425 1 107.26 ? H16 NUC 301 E 1 HETATM 46 H H17 NUC . . . O 3 49.001 -7.345 23.936 1 113.98 ? H17 NUC 301 E 1 HETATM 47 H H18 NUC . . . O 3 51.265 -6.959 23.052 1 110.2 ? H18 NUC 301 E 1 HETATM 48 H H19 NUC . . . O 3 53.049 -8.598 23.449 1 110.57 ? H19 NUC 301 E 1 HETATM 49 H H20 NUC . . . O 3 52.578 -10.656 24.741 1 111.65 ? H20 NUC 301 E 1 HETATM 50 H H21 NUC . . . O 3 50.884 -11.932 29.275 1 111.08 ? H21 NUC 301 E 1 HETATM 51 H H22 NUC . . . O 3 56.149 -12.948 32.231 1 120.17 ? H22 NUC 301 E 1 HETATM 52 H H23 NUC . . . O 3 54.716 -11.272 33.006 1 123.68 ? H23 NUC 301 E 1 HETATM 53 H H24 NUC . . . O 3 56.032 -10.098 33.174 1 123.68 ? H24 NUC 301 E 1 HETATM 54 H H25 NUC . . . O 3 57.564 -11.837 28.993 1 114.97 ? H25 NUC 301 E 1 # _model_server_stats.io_time_ms 49 _model_server_stats.parse_time_ms 293 _model_server_stats.create_model_time_ms 101 _model_server_stats.query_time_ms 272 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 54 #