data_6H0F # _model_server_result.job_id iGHhmFwvBILTIbCuW1lUng _model_server_result.datetime_utc '2024-12-02 09:12:21' _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 6h0f # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"W","auth_seq_id":502}' # _entry.id 6H0F # _exptl.entry_id 6H0F _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 273.244 _entity.id 5 _entity.src_method man _entity.type non-polymer _entity.pdbx_description S-Pomalidomide _entity.pdbx_number_of_molecules 4 _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 90 _cell.entry_id 6H0F _cell.length_a 161.45 _cell.length_b 177.86 _cell.length_c 242.47 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6H0F _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? trimeric 3 author_defined_assembly 1 ? trimeric 3 author_defined_assembly 2 ? trimeric 3 author_defined_assembly 3 ? trimeric 3 author_defined_assembly 4 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,M,N,O,Y,Z,AA 1 1 D,E,F,P,Q,R,BA 2 1 G,H,I,S,T,U,CA,DA 3 1 J,K,L,V,W,X,EA 4 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 N N N ? 5 Q N N ? 5 T N N ? 5 W 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 metalc ? metalc1 B SG CYS 307 B CYS 323 1_555 M ZN ZN . B ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.205 ? metalc ? metalc2 B SG CYS 310 B CYS 326 1_555 M ZN ZN . B ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.494 ? metalc ? metalc3 B SG CYS 375 B CYS 391 1_555 M ZN ZN . B ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.324 ? metalc ? metalc4 B SG CYS 378 B CYS 394 1_555 M ZN ZN . B ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.237 ? metalc ? metalc5 C SG CYS 11 C CYS 147 1_555 O ZN ZN . C ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.329 ? metalc ? metalc6 C SG CYS 14 C CYS 150 1_555 O ZN ZN . C ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.215 ? metalc ? metalc7 C NE2 HIS 27 C HIS 163 1_555 O ZN ZN . C ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.973 ? metalc ? metalc8 C NE2 HIS 31 C HIS 167 1_555 O ZN ZN . C ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.918 ? metalc ? metalc9 E SG CYS 307 E CYS 323 1_555 P ZN ZN . E ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.268 ? metalc ? metalc10 E SG CYS 310 E CYS 326 1_555 P ZN ZN . E ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.481 ? metalc ? metalc11 E SG CYS 375 E CYS 391 1_555 P ZN ZN . E ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.502 ? metalc ? metalc12 E SG CYS 378 E CYS 394 1_555 P ZN ZN . E ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.154 ? metalc ? metalc13 F SG CYS 11 F CYS 147 1_555 R ZN ZN . F ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.325 ? metalc ? metalc14 F SG CYS 14 F CYS 150 1_555 R ZN ZN . F ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.16 ? metalc ? metalc15 F NE2 HIS 27 F HIS 163 1_555 R ZN ZN . F ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.98 ? metalc ? metalc16 F NE2 HIS 31 F HIS 167 1_555 R ZN ZN . F ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.005 ? metalc ? metalc17 H SG CYS 307 H CYS 323 1_555 S ZN ZN . H ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.417 ? metalc ? metalc18 H SG CYS 310 H CYS 326 1_555 S ZN ZN . H ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.277 ? metalc ? metalc19 H SG CYS 375 H CYS 391 1_555 S ZN ZN . H ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.449 ? metalc ? metalc20 H SG CYS 378 H CYS 394 1_555 S ZN ZN . H ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.381 ? metalc ? metalc21 I SG CYS 11 I CYS 147 1_555 U ZN ZN . I ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.299 ? metalc ? metalc22 I SG CYS 14 I CYS 150 1_555 U ZN ZN . I ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.166 ? metalc ? metalc23 I NE2 HIS 27 I HIS 163 1_555 U ZN ZN . I ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? metalc ? metalc24 I NE2 HIS 31 I HIS 167 1_555 U ZN ZN . I ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.984 ? metalc ? metalc25 K SG CYS 307 K CYS 323 1_555 V ZN ZN . K ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.347 ? metalc ? metalc26 K SG CYS 310 K CYS 326 1_555 V ZN ZN . K ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.466 ? metalc ? metalc27 K SG CYS 375 K CYS 391 1_555 V ZN ZN . K ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.292 ? metalc ? metalc28 K SG CYS 378 K CYS 394 1_555 V ZN ZN . K ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.294 ? metalc ? metalc29 L SG CYS 11 L CYS 147 1_555 X ZN ZN . L ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.249 ? metalc ? metalc30 L SG CYS 14 L CYS 150 1_555 X ZN ZN . L ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.185 ? metalc ? metalc31 L NE2 HIS 27 L HIS 163 1_555 X ZN ZN . L ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.137 ? metalc ? metalc32 L NE2 HIS 31 L HIS 167 1_555 X ZN ZN . L ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.959 ? # _chem_comp.formula 'C13 H11 N3 O4' _chem_comp.formula_weight 273.244 _chem_comp.id Y70 _chem_comp.mon_nstd_flag . _chem_comp.name S-Pomalidomide _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 Y70 sing 376 n y C1 C6 Y70 doub 377 n y C2 C3 Y70 doub 378 n y C3 C4 Y70 sing 379 n y C4 C5 Y70 doub 380 n y C4 C7 Y70 sing 381 n n C5 C6 Y70 sing 382 n y C5 C9 Y70 sing 383 n n C6 N10 Y70 sing 384 n n C7 N8 Y70 sing 385 n n C7 O13 Y70 doub 386 n n N8 C9 Y70 sing 387 n n N8 C12 Y70 sing 388 n n C9 O11 Y70 doub 389 n n C12 C14 Y70 sing 390 n n C12 C15 Y70 sing 391 n n C14 C18 Y70 sing 392 n n C15 N16 Y70 sing 393 n n C15 O19 Y70 doub 394 n n N16 C17 Y70 sing 395 n n C17 C18 Y70 sing 396 n n C17 O20 Y70 doub 397 n n C1 H1 Y70 sing 398 n n C2 H2 Y70 sing 399 n n C3 H3 Y70 sing 400 n n N10 H101 Y70 sing 401 n n N10 H102 Y70 sing 402 n n C12 H12 Y70 sing 403 n n C14 H141 Y70 sing 404 n n C14 H142 Y70 sing 405 n n C18 H181 Y70 sing 406 n n C18 H182 Y70 sing 407 n n N16 H16 Y70 sing 408 n n # _atom_sites.entry_id 6H0F _atom_sites.fract_transf_matrix[1][1] 0.006194 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.005622 _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] 0.004124 _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 M 4 ZN B 1 501 999 ZN ZN . N 5 Y70 B 1 502 1000 Y70 Y70 . O 4 ZN C 1 201 999 ZN ZN . P 4 ZN E 1 501 999 ZN ZN . Q 5 Y70 E 1 502 1000 Y70 Y70 . R 4 ZN F 1 201 999 ZN ZN . S 4 ZN H 1 501 999 ZN ZN . T 5 Y70 H 1 502 1000 Y70 Y70 . U 4 ZN I 1 201 999 ZN ZN . V 4 ZN K 1 501 999 ZN ZN . W 5 Y70 K 1 502 1000 Y70 Y70 . X 4 ZN L 1 201 999 ZN ZN . Y 6 HOH A 1 1201 8 HOH HOH . Y 6 HOH A 2 1202 16 HOH HOH . Y 6 HOH A 3 1203 15 HOH HOH . Y 6 HOH A 4 1204 18 HOH HOH . Y 6 HOH A 5 1205 17 HOH HOH . Y 6 HOH A 6 1206 20 HOH HOH . Y 6 HOH A 7 1207 22 HOH HOH . Y 6 HOH A 8 1208 13 HOH HOH . Z 6 HOH B 1 601 29 HOH HOH . Z 6 HOH B 2 602 31 HOH HOH . Z 6 HOH B 3 603 12 HOH HOH . AA 6 HOH C 1 301 34 HOH HOH . AA 6 HOH C 2 302 6 HOH HOH . AA 6 HOH C 3 303 7 HOH HOH . BA 6 HOH E 1 601 19 HOH HOH . BA 6 HOH E 2 602 33 HOH HOH . BA 6 HOH E 3 603 21 HOH HOH . BA 6 HOH E 4 604 9 HOH HOH . CA 6 HOH G 1 1201 32 HOH HOH . CA 6 HOH G 2 1202 24 HOH HOH . CA 6 HOH G 3 1203 23 HOH HOH . DA 6 HOH H 1 601 26 HOH HOH . DA 6 HOH H 2 602 27 HOH HOH . DA 6 HOH H 3 603 10 HOH HOH . DA 6 HOH H 4 604 25 HOH HOH . DA 6 HOH H 5 605 1 HOH HOH . EA 6 HOH J 1 1201 30 HOH HOH . EA 6 HOH J 2 1202 3 HOH HOH . EA 6 HOH J 3 1203 5 HOH HOH . EA 6 HOH J 4 1204 2 HOH HOH . EA 6 HOH J 5 1205 28 HOH HOH . EA 6 HOH J 6 1206 4 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 C1 Y70 . . . W 5 0.386 -46.973 14.214 1 69.03 ? C1 Y70 502 K 1 HETATM 2 C C2 Y70 . . . W 5 -0.608 -47.162 13.267 1 63.5 ? C2 Y70 502 K 1 HETATM 3 C C3 Y70 . . . W 5 -1.408 -46.101 12.871 1 63.04 ? C3 Y70 502 K 1 HETATM 4 C C4 Y70 . . . W 5 -1.205 -44.847 13.449 1 66.03 ? C4 Y70 502 K 1 HETATM 5 C C5 Y70 . . . W 5 -0.226 -44.631 14.406 1 68.59 ? C5 Y70 502 K 1 HETATM 6 C C6 Y70 . . . W 5 0.592 -45.72 14.816 1 73.44 ? C6 Y70 502 K 1 HETATM 7 C C7 Y70 . . . W 5 -1.91 -43.563 13.212 1 66.45 ? C7 Y70 502 K 1 HETATM 8 N N8 Y70 . . . W 5 -1.29 -42.625 14.046 1 66.96 ? N8 Y70 502 K 1 HETATM 9 C C9 Y70 . . . W 5 -0.27 -43.209 14.81 1 67.46 ? C9 Y70 502 K 1 HETATM 10 N N10 Y70 . . . W 5 1.534 -45.574 15.812 1 81.87 ? N10 Y70 502 K 1 HETATM 11 O O11 Y70 . . . W 5 0.382 -42.637 15.656 1 68.5 ? O11 Y70 502 K 1 HETATM 12 C C12 Y70 . . . W 5 -1.671 -41.214 14.099 1 69.37 ? C12 Y70 502 K 1 HETATM 13 O O13 Y70 . . . W 5 -2.845 -43.328 12.471 1 66.52 ? O13 Y70 502 K 1 HETATM 14 C C14 Y70 . . . W 5 -2.562 -41.038 15.317 1 71.76 ? C14 Y70 502 K 1 HETATM 15 C C15 Y70 . . . W 5 -0.445 -40.316 14.127 1 75.57 ? C15 Y70 502 K 1 HETATM 16 N N16 Y70 . . . W 5 -0.477 -39.224 14.961 1 78.82 ? N16 Y70 502 K 1 HETATM 17 C C17 Y70 . . . W 5 -1.54 -38.795 15.709 1 76.11 ? C17 Y70 502 K 1 HETATM 18 C C18 Y70 . . . W 5 -2.819 -39.556 15.556 1 76.03 ? C18 Y70 502 K 1 HETATM 19 O O19 Y70 . . . W 5 0.517 -40.528 13.395 1 77.82 ? O19 Y70 502 K 1 HETATM 20 O O20 Y70 . . . W 5 -1.415 -37.845 16.472 1 74.69 ? O20 Y70 502 K 1 HETATM 21 H H1 Y70 . . . W 5 1.04 -47.807 14.461 0 69.21 ? H1 Y70 502 K 1 HETATM 22 H H2 Y70 . . . W 5 -0.764 -48.152 12.842 0 60.1 ? H2 Y70 502 K 1 HETATM 23 H H3 Y70 . . . W 5 -2.186 -46.226 12.12 0 60.31 ? H3 Y70 502 K 1 HETATM 24 H H101 Y70 . . . W 5 1.675 -44.688 16.286 0 86.23 ? H101 Y70 502 K 1 HETATM 25 H H102 Y70 . . . W 5 2.111 -46.357 16.104 0 84.96 ? H102 Y70 502 K 1 HETATM 26 H H12 Y70 . . . W 5 -2.224 -40.946 13.2 0 65.33 ? H12 Y70 502 K 1 HETATM 27 H H141 Y70 . . . W 5 -2.095 -41.474 16.197 0 72.28 ? H141 Y70 502 K 1 HETATM 28 H H142 Y70 . . . W 5 -3.493 -41.587 15.191 0 70.52 ? H142 Y70 502 K 1 HETATM 29 H H181 Y70 . . . W 5 -3.49 -39.396 16.399 0 78.66 ? H181 Y70 502 K 1 HETATM 30 H H182 Y70 . . . W 5 -3.334 -39.121 14.701 0 77.57 ? H182 Y70 502 K 1 HETATM 31 H H16 Y70 . . . W 5 0.378 -38.681 15.023 0 84.55 ? H16 Y70 502 K 1 # _model_server_stats.io_time_ms 179 _model_server_stats.parse_time_ms 347 _model_server_stats.create_model_time_ms 360 _model_server_stats.query_time_ms 671 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 31 #