data_9GDV # _model_server_result.job_id aBE8RYz2QRG620tnSiIPUQ _model_server_result.datetime_utc '2025-02-25 23:18:05' _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 9gdv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":1101}' # _entry.id 9GDV # _exptl.entry_id 9GDV _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 501.623 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description ~{N}-[2-[2-(dimethylamino)ethyl-methyl-amino]-4-methoxy-5-[[4-(1-methylindol-3-yl)pyrimidin-2-yl]amino]phenyl]propanamide _entity.pdbx_number_of_molecules 2 _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 9GDV _cell.length_a 75.025 _cell.length_b 82.31 _cell.length_c 89.297 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9GDV _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 ? monomeric 1 author_defined_assembly 1 ? monomeric 1 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,D,E,I 1 1 B,F,G,H,J 2 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 ? 2 C N N ? 2 F 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 SG CYS 105 A CYS 797 1_555 C C32 Q6K . A Q6K 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.805 ? covale ? covale2 B SG CYS 105 B CYS 797 1_555 F C32 Q6K . B Q6K 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.782 ? # _chem_comp.formula 'C28 H35 N7 O2' _chem_comp.formula_weight 501.623 _chem_comp.id Q6K _chem_comp.mon_nstd_flag . _chem_comp.name ~{N}-[2-[2-(dimethylamino)ethyl-methyl-amino]-4-methoxy-5-[[4-(1-methylindol-3-yl)pyrimidin-2-yl]amino]phenyl]propanamide _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 C32 C31 Q6K sing 277 n n C31 C30 Q6K sing 278 n n C22 N21 Q6K sing 279 n n C30 O33 Q6K doub 280 n n C30 N29 Q6K sing 281 n n N29 C28 Q6K sing 282 n n C28 C34 Q6K doub 283 n y C28 C20 Q6K sing 284 n y N21 C20 Q6K sing 285 n n N21 C23 Q6K sing 286 n n C34 C15 Q6K sing 287 n y C20 C19 Q6K doub 288 n y C15 C16 Q6K doub 289 n y C15 N14 Q6K sing 290 n n C19 C16 Q6K sing 291 n y C23 C24 Q6K sing 292 n n C16 O17 Q6K sing 293 n n N14 C13 Q6K sing 294 n n N35 C13 Q6K doub 295 n y N35 C36 Q6K sing 296 n y C13 N12 Q6K sing 297 n y C24 N25 Q6K sing 298 n n C36 C37 Q6K doub 299 n y N12 C11 Q6K doub 300 n y C37 C11 Q6K sing 301 n y C11 C10 Q6K sing 302 n n C18 O17 Q6K sing 303 n n C09 C10 Q6K doub 304 n y C09 N02 Q6K sing 305 n y C10 C04 Q6K sing 306 n y C01 N02 Q6K sing 307 n n N02 C03 Q6K sing 308 n y C04 C03 Q6K doub 309 n y C04 C05 Q6K sing 310 n y C03 C08 Q6K sing 311 n y C05 C06 Q6K doub 312 n y C08 C07 Q6K doub 313 n y C06 C07 Q6K sing 314 n y N25 C27 Q6K sing 315 n n N25 C26 Q6K sing 316 n n C22 H1 Q6K sing 317 n n C22 H2 Q6K sing 318 n n C22 H3 Q6K sing 319 n n C24 H4 Q6K sing 320 n n C24 H5 Q6K sing 321 n n C26 H6 Q6K sing 322 n n C26 H7 Q6K sing 323 n n C26 H8 Q6K sing 324 n n C01 H9 Q6K sing 325 n n C01 H10 Q6K sing 326 n n C01 H11 Q6K sing 327 n n C05 H12 Q6K sing 328 n n C06 H13 Q6K sing 329 n n C07 H14 Q6K sing 330 n n C08 H15 Q6K sing 331 n n C09 H16 Q6K sing 332 n n C18 H17 Q6K sing 333 n n C18 H18 Q6K sing 334 n n C18 H19 Q6K sing 335 n n C19 H20 Q6K sing 336 n n C23 H21 Q6K sing 337 n n C23 H22 Q6K sing 338 n n C27 H23 Q6K sing 339 n n C27 H24 Q6K sing 340 n n C27 H25 Q6K sing 341 n n C31 H26 Q6K sing 342 n n C31 H27 Q6K sing 343 n n C32 H28 Q6K sing 344 n n C32 H29 Q6K sing 345 n n C32 H30 Q6K sing 346 n n C34 H31 Q6K sing 347 n n C36 H32 Q6K sing 348 n n C37 H33 Q6K sing 349 n n N14 H34 Q6K sing 350 n n N29 H36 Q6K sing 351 n n # _atom_sites.entry_id 9GDV _atom_sites.fract_transf_matrix[1][1] 0.013329 _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] 0.012149 _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] 0.011199 _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 2 Q6K A 1 1101 1001 Q6K INH . D 3 SO4 A 1 1102 1101 SO4 SO4 . E 3 SO4 A 1 1103 1101 SO4 SO4 . F 2 Q6K B 1 1101 1001 Q6K INH . G 3 SO4 B 1 1102 1201 SO4 SO4 . H 3 SO4 B 1 1103 1301 SO4 SO4 . I 4 HOH A 1 1201 29 HOH HOH . I 4 HOH A 2 1202 20 HOH HOH . I 4 HOH A 3 1203 77 HOH HOH . I 4 HOH A 4 1204 57 HOH HOH . I 4 HOH A 5 1205 78 HOH HOH . I 4 HOH A 6 1206 81 HOH HOH . I 4 HOH A 7 1207 7 HOH HOH . I 4 HOH A 8 1208 47 HOH HOH . I 4 HOH A 9 1209 38 HOH HOH . I 4 HOH A 10 1210 41 HOH HOH . I 4 HOH A 11 1211 54 HOH HOH . I 4 HOH A 12 1212 70 HOH HOH . I 4 HOH A 13 1213 8 HOH HOH . I 4 HOH A 14 1214 58 HOH HOH . I 4 HOH A 15 1215 11 HOH HOH . I 4 HOH A 16 1216 18 HOH HOH . I 4 HOH A 17 1217 46 HOH HOH . I 4 HOH A 18 1218 35 HOH HOH . I 4 HOH A 19 1219 17 HOH HOH . I 4 HOH A 20 1220 9 HOH HOH . I 4 HOH A 21 1221 51 HOH HOH . I 4 HOH A 22 1222 40 HOH HOH . I 4 HOH A 23 1223 72 HOH HOH . I 4 HOH A 24 1224 12 HOH HOH . I 4 HOH A 25 1225 80 HOH HOH . I 4 HOH A 26 1226 21 HOH HOH . I 4 HOH A 27 1227 37 HOH HOH . I 4 HOH A 28 1228 32 HOH HOH . I 4 HOH A 29 1229 43 HOH HOH . I 4 HOH A 30 1230 60 HOH HOH . I 4 HOH A 31 1231 65 HOH HOH . I 4 HOH A 32 1232 61 HOH HOH . I 4 HOH A 33 1233 5 HOH HOH . I 4 HOH A 34 1234 59 HOH HOH . I 4 HOH A 35 1235 49 HOH HOH . I 4 HOH A 36 1236 63 HOH HOH . I 4 HOH A 37 1237 48 HOH HOH . I 4 HOH A 38 1238 36 HOH HOH . I 4 HOH A 39 1239 22 HOH HOH . I 4 HOH A 40 1240 33 HOH HOH . I 4 HOH A 41 1241 39 HOH HOH . I 4 HOH A 42 1242 68 HOH HOH . I 4 HOH A 43 1243 19 HOH HOH . I 4 HOH A 44 1244 23 HOH HOH . I 4 HOH A 45 1245 74 HOH HOH . I 4 HOH A 46 1246 50 HOH HOH . J 4 HOH B 1 1201 79 HOH HOH . J 4 HOH B 2 1202 62 HOH HOH . J 4 HOH B 3 1203 44 HOH HOH . J 4 HOH B 4 1204 75 HOH HOH . J 4 HOH B 5 1205 73 HOH HOH . J 4 HOH B 6 1206 76 HOH HOH . J 4 HOH B 7 1207 16 HOH HOH . J 4 HOH B 8 1208 27 HOH HOH . J 4 HOH B 9 1209 24 HOH HOH . J 4 HOH B 10 1210 13 HOH HOH . J 4 HOH B 11 1211 14 HOH HOH . J 4 HOH B 12 1212 15 HOH HOH . J 4 HOH B 13 1213 66 HOH HOH . J 4 HOH B 14 1214 34 HOH HOH . J 4 HOH B 15 1215 10 HOH HOH . J 4 HOH B 16 1216 71 HOH HOH . J 4 HOH B 17 1217 25 HOH HOH . J 4 HOH B 18 1218 6 HOH HOH . J 4 HOH B 19 1219 30 HOH HOH . J 4 HOH B 20 1220 45 HOH HOH . J 4 HOH B 21 1221 28 HOH HOH . J 4 HOH B 22 1222 53 HOH HOH . J 4 HOH B 23 1223 26 HOH HOH . J 4 HOH B 24 1224 67 HOH HOH . J 4 HOH B 25 1225 52 HOH HOH . J 4 HOH B 26 1226 42 HOH HOH . J 4 HOH B 27 1227 64 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 Q6K . . . F 2 21.33 -12.05 7.001 1 44.69 ? C10 Q6K 1101 B 1 HETATM 2 N N12 Q6K . . . F 2 19.938 -12.082 5.054 1 43.72 ? N12 Q6K 1101 B 1 HETATM 3 C C13 Q6K . . . F 2 18.713 -12.096 4.501 1 43.38 ? C13 Q6K 1101 B 1 HETATM 4 C C15 Q6K . . . F 2 19.574 -11.859 2.129 1 43.44 ? C15 Q6K 1101 B 1 HETATM 5 C C20 Q6K . . . F 2 21.398 -11.642 0.031 1 45.25 ? C20 Q6K 1101 B 1 HETATM 6 C C22 Q6K . . . F 2 23.065 -12.79 -1.261 1 47.39 ? C22 Q6K 1101 B 1 HETATM 7 C C24 Q6K . . . F 2 22.795 -10.742 -3.39 1 49.7 ? C24 Q6K 1101 B 1 HETATM 8 C C26 Q6K . . . F 2 23.482 -8.908 -4.779 1 50.65 ? C26 Q6K 1101 B 1 HETATM 9 C C28 Q6K . . . F 2 21.734 -11.16 1.304 1 43.92 ? C28 Q6K 1101 B 1 HETATM 10 C C01 Q6K . . . F 2 23.614 -11.474 9.792 1 46.2 ? C01 Q6K 1101 B 1 HETATM 11 C C03 Q6K . . . F 2 23.607 -11.956 7.316 1 45.5 ? C03 Q6K 1101 B 1 HETATM 12 C C04 Q6K . . . F 2 22.626 -12.181 6.335 1 45.19 ? C04 Q6K 1101 B 1 HETATM 13 C C05 Q6K . . . F 2 23.034 -12.479 5.035 1 45.28 ? C05 Q6K 1101 B 1 HETATM 14 C C06 Q6K . . . F 2 24.39 -12.516 4.733 1 45.27 ? C06 Q6K 1101 B 1 HETATM 15 C C07 Q6K . . . F 2 25.342 -12.265 5.71 1 45.12 ? C07 Q6K 1101 B 1 HETATM 16 C C08 Q6K . . . F 2 24.963 -11.988 7.017 1 45.2 ? C08 Q6K 1101 B 1 HETATM 17 C C09 Q6K . . . F 2 21.612 -11.782 8.305 1 45.15 ? C09 Q6K 1101 B 1 HETATM 18 C C11 Q6K . . . F 2 19.995 -12.058 6.393 1 43.94 ? C11 Q6K 1101 B 1 HETATM 19 C C16 Q6K . . . F 2 19.261 -12.348 0.86 1 43.71 ? C16 Q6K 1101 B 1 HETATM 20 C C18 Q6K . . . F 2 17.757 -13.743 -0.379 1 43.76 ? C18 Q6K 1101 B 1 HETATM 21 C C19 Q6K . . . F 2 20.159 -12.236 -0.183 1 44.35 ? C19 Q6K 1101 B 1 HETATM 22 C C23 Q6K . . . F 2 21.803 -10.817 -2.224 1 48.52 ? C23 Q6K 1101 B 1 HETATM 23 C C27 Q6K . . . F 2 22.05 -10.603 -5.674 1 50.62 ? C27 Q6K 1101 B 1 HETATM 24 C C30 Q6K . . . F 2 23.522 -9.771 2.424 1 42.97 ? C30 Q6K 1101 B 1 HETATM 25 C C31 Q6K . . . F 2 24.865 -9.2 2.058 1 42.43 ? C31 Q6K 1101 B 1 HETATM 26 C C32 Q6K . . . F 2 24.968 -7.721 2.317 1 42.55 ? C32 Q6K 1101 B 1 HETATM 27 C C34 Q6K . . . F 2 20.813 -11.262 2.341 1 43.53 ? C34 Q6K 1101 B 1 HETATM 28 C C36 Q6K . . . F 2 17.646 -12.06 6.501 1 43.12 ? C36 Q6K 1101 B 1 HETATM 29 C C37 Q6K . . . F 2 18.849 -12.018 7.173 1 43.32 ? C37 Q6K 1101 B 1 HETATM 30 N N02 Q6K . . . F 2 22.963 -11.72 8.513 1 45.81 ? N02 Q6K 1101 B 1 HETATM 31 N N14 Q6K . . . F 2 18.608 -11.994 3.142 1 43.28 ? N14 Q6K 1101 B 1 HETATM 32 N N21 Q6K . . . F 2 22.349 -11.535 -1.034 1 47.23 ? N21 Q6K 1101 B 1 HETATM 33 N N25 Q6K . . . F 2 22.394 -9.839 -4.475 1 50.36 ? N25 Q6K 1101 B 1 HETATM 34 N N29 Q6K . . . F 2 23.031 -10.622 1.491 1 43.4 ? N29 Q6K 1101 B 1 HETATM 35 N N35 Q6K . . . F 2 17.545 -12.115 5.164 1 43.27 ? N35 Q6K 1101 B 1 HETATM 36 O O17 Q6K . . . F 2 18.021 -12.917 0.756 1 43.85 ? O17 Q6K 1101 B 1 HETATM 37 O O33 Q6K . . . F 2 22.941 -9.475 3.463 1 43.24 ? O33 Q6K 1101 B 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 477 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 37 #