data_6KRO # _model_server_result.job_id WvmFGpSpoptPkKDweFNX7g _model_server_result.datetime_utc '2025-01-12 04:08:34' _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 6kro # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1201}' # _entry.id 6KRO # _exptl.entry_id 6KRO _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 510.604 _entity.id 3 _entity.src_method nat _entity.type non-polymer _entity.pdbx_description "6-[(2S,6R)-2,6-dimethylmorpholin-4-yl]-4-fluoranyl-1-methyl-1'-(8-methyl-4-oxidanylidene-3,5,6,7-tetrahydropyrido[2,3-d]pyrimidin-2-yl)spiro[indole-3,4'-piperidine]-2-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 90 _cell.entry_id 6KRO _cell.length_a 66.116 _cell.length_b 66.116 _cell.length_c 114.758 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6KRO _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall 'P 4abw 2nw' _symmetry.space_group_name_H-M 'P 41 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 A SG CYS 135 A CYS 1081 1_555 D ZN ZN . A ZN 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.285 ? metalc ? metalc2 A ND1 HIS 138 A HIS 1084 1_555 D ZN ZN . A ZN 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.241 ? metalc ? metalc3 A SG CYS 143 A CYS 1089 1_555 D ZN ZN . A ZN 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.376 ? metalc ? metalc4 A SG CYS 146 A CYS 1092 1_555 D ZN ZN . A ZN 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.264 ? # _chem_comp.formula 'C27 H35 F N6 O3' _chem_comp.formula_weight 510.604 _chem_comp.id DU9 _chem_comp.mon_nstd_flag . _chem_comp.name "6-[(2S,6R)-2,6-dimethylmorpholin-4-yl]-4-fluoranyl-1-methyl-1'-(8-methyl-4-oxidanylidene-3,5,6,7-tetrahydropyrido[2,3-d]pyrimidin-2-yl)spiro[indole-3,4'-piperidine]-2-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 C37 C01 DU9 sing 83 n n C37 C36 DU9 sing 84 n n C01 C02 DU9 sing 85 n n C36 N34 DU9 sing 86 n n O04 C03 DU9 doub 87 n n C02 C03 DU9 sing 88 n n C02 C33 DU9 doub 89 n n C03 N05 DU9 sing 90 n n N34 C33 DU9 sing 91 n n N34 C35 DU9 sing 92 n n C33 N32 DU9 sing 93 n n N05 C06 DU9 sing 94 n n N32 C06 DU9 doub 95 n n C06 N07 DU9 sing 96 n n N07 C08 DU9 sing 97 n n N07 C31 DU9 sing 98 n n C08 C09 DU9 sing 99 n n C31 C30 DU9 sing 100 n n C09 C10 DU9 sing 101 n n C30 C10 DU9 sing 102 n n O29 C28 DU9 doub 103 n n C10 C28 DU9 sing 104 n n C10 C11 DU9 sing 105 n n C28 N26 DU9 sing 106 n n F13 C12 DU9 sing 107 n n C11 C12 DU9 doub 108 n y C11 C25 DU9 sing 109 n y N26 C27 DU9 sing 110 n n N26 C25 DU9 sing 111 n n C12 C14 DU9 sing 112 n y C25 C24 DU9 doub 113 n y C14 C15 DU9 doub 114 n y C24 C15 DU9 sing 115 n y C15 N16 DU9 sing 116 n n N16 C23 DU9 sing 117 n n N16 C17 DU9 sing 118 n n C23 C21 DU9 sing 119 n n C17 C18 DU9 sing 120 n n C21 C22 DU9 sing 121 n n C21 O20 DU9 sing 122 n n C18 O20 DU9 sing 123 n n C18 C19 DU9 sing 124 n n C14 H1 DU9 sing 125 n n C01 H2 DU9 sing 126 n n C01 H3 DU9 sing 127 n n C08 H4 DU9 sing 128 n n C08 H5 DU9 sing 129 n n C09 H6 DU9 sing 130 n n C09 H7 DU9 sing 131 n n C17 H8 DU9 sing 132 n n C17 H9 DU9 sing 133 n n C18 H10 DU9 sing 134 n n C19 H11 DU9 sing 135 n n C19 H12 DU9 sing 136 n n C19 H13 DU9 sing 137 n n C21 H14 DU9 sing 138 n n C22 H15 DU9 sing 139 n n C22 H16 DU9 sing 140 n n C22 H17 DU9 sing 141 n n C23 H18 DU9 sing 142 n n C23 H19 DU9 sing 143 n n C24 H20 DU9 sing 144 n n C27 H21 DU9 sing 145 n n C27 H22 DU9 sing 146 n n C27 H23 DU9 sing 147 n n C30 H24 DU9 sing 148 n n C30 H25 DU9 sing 149 n n C31 H26 DU9 sing 150 n n C31 H27 DU9 sing 151 n n C35 H28 DU9 sing 152 n n C35 H29 DU9 sing 153 n n C35 H30 DU9 sing 154 n n C36 H31 DU9 sing 155 n n C36 H32 DU9 sing 156 n n C37 H33 DU9 sing 157 n n C37 H34 DU9 sing 158 n n N05 H35 DU9 sing 159 n n # _atom_sites.entry_id 6KRO _atom_sites.fract_transf_matrix[1][1] 0.015125 _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] 0.015125 _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] 0.008714 _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 DU9 A 1 1201 1163 DU9 XXX . D 4 ZN A 1 1202 1201 ZN ZN . E 5 PO4 A 1 1203 1203 PO4 PO4 . F 6 GOL A 1 1204 1204 GOL GOL . G 6 GOL A 1 1205 1205 GOL GOL . H 7 HOH A 1 1301 85 HOH HOH . H 7 HOH A 2 1302 77 HOH HOH . H 7 HOH A 3 1303 36 HOH HOH . H 7 HOH A 4 1304 50 HOH HOH . H 7 HOH A 5 1305 111 HOH HOH . H 7 HOH A 6 1306 5 HOH HOH . H 7 HOH A 7 1307 54 HOH HOH . H 7 HOH A 8 1308 20 HOH HOH . H 7 HOH A 9 1309 79 HOH HOH . H 7 HOH A 10 1310 6 HOH HOH . H 7 HOH A 11 1311 108 HOH HOH . H 7 HOH A 12 1312 22 HOH HOH . H 7 HOH A 13 1313 102 HOH HOH . H 7 HOH A 14 1314 66 HOH HOH . H 7 HOH A 15 1315 51 HOH HOH . H 7 HOH A 16 1316 18 HOH HOH . H 7 HOH A 17 1317 34 HOH HOH . H 7 HOH A 18 1318 48 HOH HOH . H 7 HOH A 19 1319 32 HOH HOH . H 7 HOH A 20 1320 41 HOH HOH . H 7 HOH A 21 1321 25 HOH HOH . H 7 HOH A 22 1322 2 HOH HOH . H 7 HOH A 23 1323 101 HOH HOH . H 7 HOH A 24 1324 33 HOH HOH . H 7 HOH A 25 1325 14 HOH HOH . H 7 HOH A 26 1326 100 HOH HOH . H 7 HOH A 27 1327 15 HOH HOH . H 7 HOH A 28 1328 64 HOH HOH . H 7 HOH A 29 1329 30 HOH HOH . H 7 HOH A 30 1330 29 HOH HOH . H 7 HOH A 31 1331 39 HOH HOH . H 7 HOH A 32 1332 84 HOH HOH . H 7 HOH A 33 1333 104 HOH HOH . H 7 HOH A 34 1334 8 HOH HOH . H 7 HOH A 35 1335 26 HOH HOH . H 7 HOH A 36 1336 7 HOH HOH . H 7 HOH A 37 1337 59 HOH HOH . H 7 HOH A 38 1338 27 HOH HOH . H 7 HOH A 39 1339 9 HOH HOH . H 7 HOH A 40 1340 116 HOH HOH . H 7 HOH A 41 1341 65 HOH HOH . H 7 HOH A 42 1342 109 HOH HOH . H 7 HOH A 43 1343 40 HOH HOH . H 7 HOH A 44 1344 42 HOH HOH . H 7 HOH A 45 1345 43 HOH HOH . H 7 HOH A 46 1346 47 HOH HOH . H 7 HOH A 47 1347 13 HOH HOH . H 7 HOH A 48 1348 11 HOH HOH . H 7 HOH A 49 1349 49 HOH HOH . H 7 HOH A 50 1350 63 HOH HOH . H 7 HOH A 51 1351 46 HOH HOH . H 7 HOH A 52 1352 82 HOH HOH . H 7 HOH A 53 1353 95 HOH HOH . H 7 HOH A 54 1354 37 HOH HOH . H 7 HOH A 55 1355 105 HOH HOH . H 7 HOH A 56 1356 83 HOH HOH . H 7 HOH A 57 1357 61 HOH HOH . H 7 HOH A 58 1358 106 HOH HOH . H 7 HOH A 59 1359 76 HOH HOH . H 7 HOH A 60 1360 44 HOH HOH . H 7 HOH A 61 1361 4 HOH HOH . H 7 HOH A 62 1362 35 HOH HOH . H 7 HOH A 63 1363 75 HOH HOH . H 7 HOH A 64 1364 103 HOH HOH . H 7 HOH A 65 1365 74 HOH HOH . H 7 HOH A 66 1366 107 HOH HOH . H 7 HOH A 67 1367 12 HOH HOH . H 7 HOH A 68 1368 55 HOH HOH . H 7 HOH A 69 1369 98 HOH HOH . H 7 HOH A 70 1370 68 HOH HOH . H 7 HOH A 71 1371 28 HOH HOH . H 7 HOH A 72 1372 70 HOH HOH . H 7 HOH A 73 1373 72 HOH HOH . H 7 HOH A 74 1374 52 HOH HOH . H 7 HOH A 75 1375 71 HOH HOH . H 7 HOH A 76 1376 58 HOH HOH . H 7 HOH A 77 1377 94 HOH HOH . H 7 HOH A 78 1378 31 HOH HOH . H 7 HOH A 79 1379 92 HOH HOH . H 7 HOH A 80 1380 67 HOH HOH . H 7 HOH A 81 1381 60 HOH HOH . H 7 HOH A 82 1382 113 HOH HOH . H 7 HOH A 83 1383 17 HOH HOH . H 7 HOH A 84 1384 89 HOH HOH . H 7 HOH A 85 1385 53 HOH HOH . H 7 HOH A 86 1386 78 HOH HOH . H 7 HOH A 87 1387 118 HOH HOH . H 7 HOH A 88 1388 73 HOH HOH . H 7 HOH A 89 1389 115 HOH HOH . H 7 HOH A 90 1390 91 HOH HOH . H 7 HOH A 91 1391 99 HOH HOH . H 7 HOH A 92 1392 62 HOH HOH . H 7 HOH A 93 1393 114 HOH HOH . H 7 HOH A 94 1394 80 HOH HOH . H 7 HOH A 95 1395 96 HOH HOH . I 7 HOH B 1 1201 57 HOH HOH . I 7 HOH B 2 1202 117 HOH HOH . I 7 HOH B 3 1203 45 HOH HOH . I 7 HOH B 4 1204 23 HOH HOH . I 7 HOH B 5 1205 19 HOH HOH . I 7 HOH B 6 1206 3 HOH HOH . I 7 HOH B 7 1207 56 HOH HOH . I 7 HOH B 8 1208 10 HOH HOH . I 7 HOH B 9 1209 24 HOH HOH . I 7 HOH B 10 1210 1 HOH HOH . I 7 HOH B 11 1211 21 HOH HOH . I 7 HOH B 12 1212 38 HOH HOH . I 7 HOH B 13 1213 16 HOH HOH . I 7 HOH B 14 1214 86 HOH HOH . I 7 HOH B 15 1215 110 HOH HOH . I 7 HOH B 16 1216 93 HOH HOH . I 7 HOH B 17 1217 81 HOH HOH . I 7 HOH B 18 1218 97 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 DU9 . . . C 3 1.938 -11.474 -7.224 1 28.91 ? C10 DU9 1201 A 1 HETATM 2 C C11 DU9 . . . C 3 1.702 -12.043 -5.867 1 31.24 ? C11 DU9 1201 A 1 HETATM 3 C C12 DU9 . . . C 3 1.384 -13.326 -5.463 1 37.58 ? C12 DU9 1201 A 1 HETATM 4 C C14 DU9 . . . C 3 1.208 -13.739 -4.134 1 41.24 ? C14 DU9 1201 A 1 HETATM 5 C C15 DU9 . . . C 3 1.351 -12.754 -3.133 1 46.79 ? C15 DU9 1201 A 1 HETATM 6 C C01 DU9 . . . C 3 3.279 -12.454 -15.76 1 27.66 ? C01 DU9 1201 A 1 HETATM 7 C C02 DU9 . . . C 3 2.983 -12.255 -14.307 1 27.5 ? C02 DU9 1201 A 1 HETATM 8 C C03 DU9 . . . C 3 1.595 -12.161 -13.862 1 27.34 ? C03 DU9 1201 A 1 HETATM 9 C C06 DU9 . . . C 3 2.47 -11.836 -11.586 1 32.57 ? C06 DU9 1201 A 1 HETATM 10 C C08 DU9 . . . C 3 0.877 -11.451 -9.609 1 32.66 ? C08 DU9 1201 A 1 HETATM 11 C C09 DU9 . . . C 3 0.695 -11.645 -8.1 1 28.56 ? C09 DU9 1201 A 1 HETATM 12 C C17 DU9 . . . C 3 1.036 -11.869 -0.702 1 65.66 ? C17 DU9 1201 A 1 HETATM 13 C C18 DU9 . . . C 3 1.821 -12.203 0.629 1 70.6 ? C18 DU9 1201 A 1 HETATM 14 C C19 DU9 . . . C 3 1.748 -11.061 1.662 1 68.5 ? C19 DU9 1201 A 1 HETATM 15 C C21 DU9 . . . C 3 1.51 -14.536 0.232 1 66.39 ? C21 DU9 1201 A 1 HETATM 16 C C22 DU9 . . . C 3 1.175 -15.908 0.852 1 64.24 ? C22 DU9 1201 A 1 HETATM 17 C C23 DU9 . . . C 3 0.67 -14.245 -1.071 1 62.74 ? C23 DU9 1201 A 1 HETATM 18 C C24 DU9 . . . C 3 1.684 -11.419 -3.519 1 39.24 ? C24 DU9 1201 A 1 HETATM 19 C C25 DU9 . . . C 3 1.848 -11.043 -4.868 1 41.59 ? C25 DU9 1201 A 1 HETATM 20 C C27 DU9 . . . C 3 2.416 -8.433 -4.876 1 38.73 ? C27 DU9 1201 A 1 HETATM 21 C C28 DU9 . . . C 3 2.199 -9.983 -6.914 1 34.74 ? C28 DU9 1201 A 1 HETATM 22 C C30 DU9 . . . C 3 3.134 -12.106 -7.895 1 28.24 ? C30 DU9 1201 A 1 HETATM 23 C C31 DU9 . . . C 3 3.435 -11.521 -9.27 1 30.23 ? C31 DU9 1201 A 1 HETATM 24 C C33 DU9 . . . C 3 4.01 -12.126 -13.379 1 29.91 ? C33 DU9 1201 A 1 HETATM 25 C C35 DU9 . . . C 3 6.502 -12.091 -12.645 1 26.6 ? C35 DU9 1201 A 1 HETATM 26 C C36 DU9 . . . C 3 5.744 -12.447 -15.197 1 24.95 ? C36 DU9 1201 A 1 HETATM 27 C C37 DU9 . . . C 3 4.672 -11.826 -16.1 1 31.33 ? C37 DU9 1201 A 1 HETATM 28 F F13 DU9 . . . C 3 1.222 -14.307 -6.424 1 37.13 ? F13 DU9 1201 A 1 HETATM 29 N N05 DU9 . . . C 3 1.368 -11.936 -12.443 1 28.5 ? N05 DU9 1201 A 1 HETATM 30 N N07 DU9 . . . C 3 2.26 -11.636 -10.213 1 31.35 ? N07 DU9 1201 A 1 HETATM 31 N N16 DU9 . . . C 3 1.209 -12.997 -1.679 1 53 ? N16 DU9 1201 A 1 HETATM 32 N N26 DU9 . . . C 3 2.164 -9.775 -5.502 1 37.5 ? N26 DU9 1201 A 1 HETATM 33 N N32 DU9 . . . C 3 3.715 -11.914 -12.009 1 28.73 ? N32 DU9 1201 A 1 HETATM 34 N N34 DU9 . . . C 3 5.4 -12.207 -13.736 1 29.91 ? N34 DU9 1201 A 1 HETATM 35 O O04 DU9 . . . C 3 0.583 -12.255 -14.578 1 28.7 ? O04 DU9 1201 A 1 HETATM 36 O O20 DU9 . . . C 3 1.363 -13.444 1.129 1 70.19 ? O20 DU9 1201 A 1 HETATM 37 O O29 DU9 . . . C 3 2.465 -9.108 -7.743 1 38.28 ? O29 DU9 1201 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 27 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 280 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 37 #