data_Y8N # _chem_comp.id Y8N _chem_comp.name "BBO-8520 (bound form)" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C35 H35 F6 N7 O2 S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "(4P)-2-amino-4-{4-[(2S,5R)-2,5-dimethyl-4-propanoylpiperazin-1-yl]-8-fluoro-2-{[(2R,4R,7aS)-2-fluorotetrahydro-1H-pyrrolizin-7a(5H)-yl]methoxy}-6-(trifluoromethyl)quinazolin-7-yl}-7-fluoro-1-benzothiophene-3-carbonitrile" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2023-11-28 _chem_comp.pdbx_modified_date 2024-12-13 _chem_comp.pdbx_ambiguous_flag N _chem_comp.pdbx_release_status REL _chem_comp.pdbx_replaced_by ? _chem_comp.pdbx_replaces ? _chem_comp.formula_weight 731.754 _chem_comp.one_letter_code ? _chem_comp.three_letter_code Y8N _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details Corina _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 8V39 _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB _chem_comp.pdbx_pcm Y # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.alt_atom_id _chem_comp_atom.type_symbol _chem_comp_atom.charge _chem_comp_atom.pdbx_align _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_leaving_atom_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_n_terminal_atom_flag _chem_comp_atom.pdbx_backbone_atom_flag _chem_comp_atom.pdbx_c_terminal_atom_flag _chem_comp_atom.model_Cartn_x _chem_comp_atom.model_Cartn_y _chem_comp_atom.model_Cartn_z _chem_comp_atom.pdbx_model_Cartn_x_ideal _chem_comp_atom.pdbx_model_Cartn_y_ideal _chem_comp_atom.pdbx_model_Cartn_z_ideal _chem_comp_atom.pdbx_component_atom_id _chem_comp_atom.pdbx_component_comp_id _chem_comp_atom.pdbx_ordinal Y8N N1 N1 N 0 1 Y N N N N N -6.905 5.509 -1.967 -2.487 0.390 0.411 N1 Y8N 1 Y8N N3 N2 N 0 1 N N N N N N -7.828 6.087 -3.973 -1.739 2.607 0.648 N3 Y8N 2 Y8N C4 C1 C 0 1 Y N N N N N -4.345 6.032 -2.683 0.015 -0.653 0.576 C4 Y8N 3 Y8N C5 C2 C 0 1 Y N N N N N -4.980 6.638 -4.947 0.931 1.594 0.832 C5 Y8N 4 Y8N C6 C3 C 0 1 Y N N N N N -3.670 6.892 -5.264 2.182 1.068 0.915 C6 Y8N 5 Y8N C7 C4 C 0 1 Y N N N N N -2.678 6.743 -4.282 2.385 -0.319 0.832 C7 Y8N 6 Y8N C8 C5 C 0 1 Y N N N N N -3.016 6.304 -3.009 1.311 -1.180 0.664 C8 Y8N 7 Y8N C10 C6 C 0 1 N N S N N N -7.370 4.037 1.878 -4.354 -3.917 -0.090 C10 Y8N 8 Y8N C13 C7 C 0 1 Y N N N N N 0.668 8.526 -4.565 5.563 -1.724 2.254 C13 Y8N 9 Y8N C15 C8 C 0 1 Y N N N N N 1.010 6.220 -5.030 5.824 -1.545 -0.141 C15 Y8N 10 Y8N C17 C9 C 0 1 N N S N N N -8.990 5.286 -3.558 -1.405 3.276 -0.617 C17 Y8N 11 Y8N C20 C10 C 0 1 N N N N N N -8.150 7.248 -4.814 -3.131 2.869 1.038 C20 Y8N 12 Y8N C21 C11 C 0 1 N N N N N N -5.223 3.281 2.716 -4.814 -6.032 0.941 C21 Y8N 13 Y8N C22 C12 C 0 1 N N R N N N -5.777 4.298 3.691 -5.983 -5.074 1.282 C22 Y8N 14 Y8N C24 C13 C 0 1 N N N N N N -8.715 3.449 2.343 -5.055 -3.500 -1.399 C24 Y8N 15 Y8N C26 C14 C 0 1 N N N N N N -7.212 1.662 2.433 -4.627 -5.864 -1.464 C26 Y8N 16 Y8N C28 C15 C 0 1 N N N N N N -8.177 6.287 -7.080 -2.489 4.793 2.504 C28 Y8N 17 Y8N C1 C16 C 0 1 Y N N N N N -5.888 5.379 -1.121 -2.265 -0.917 0.335 C1 Y8N 18 Y8N C11 C17 C 0 1 Y N N N N N -1.237 6.991 -4.557 3.758 -0.867 0.925 C11 Y8N 19 Y8N C12 C18 C 0 1 Y N N N N N -0.684 8.268 -4.362 4.282 -1.211 2.161 C12 Y8N 20 Y8N C14 C19 C 0 1 Y N N N N N 1.510 7.491 -4.885 6.329 -1.891 1.119 C14 Y8N 21 Y8N C16 C20 C 0 1 Y N N N N N -0.346 5.941 -4.846 4.537 -1.028 -0.251 C16 Y8N 22 Y8N C18 C21 C 0 1 N N N N N N -9.687 4.787 -4.780 -1.518 4.793 -0.434 C18 Y8N 23 Y8N C19 C22 C 0 1 N N R N N N -9.056 6.880 -5.990 -3.315 4.369 1.288 C19 Y8N 24 Y8N C2 C23 C 0 1 Y N N N N N -6.699 5.916 -3.222 -1.493 1.253 0.571 C2 Y8N 25 Y8N C23 C24 C 0 1 N N N N N N -6.724 5.077 2.803 -5.316 -3.686 1.092 C23 Y8N 26 Y8N C25 C25 C 0 1 N N N N N N -8.612 1.974 2.014 -4.643 -4.622 -2.389 C25 Y8N 27 Y8N C27 C26 C 0 1 N N N N N N -9.903 6.116 -2.656 -2.376 2.819 -1.707 C27 Y8N 28 Y8N C29 C27 C 0 1 N N N N N N -11.407 6.117 -5.913 -3.635 6.030 -0.488 C29 Y8N 29 Y8N C3 C28 C 0 1 Y N N N N N -5.366 6.211 -3.648 -0.173 0.748 0.662 C3 Y8N 30 Y8N C30 C29 C 0 1 N N N N N N -11.814 7.370 -6.597 -3.143 6.768 -1.706 C30 Y8N 31 Y8N C31 C30 C 0 1 N N N N N N -12.392 8.380 -5.635 -4.214 7.758 -2.170 C31 Y8N 32 Y8N C32 C31 C 0 1 Y N N N N N 0.560 3.831 -5.476 5.167 -1.007 -2.534 C32 Y8N 33 Y8N C33 C32 C 0 1 Y N N N N N -0.569 4.526 -5.141 4.179 -0.725 -1.636 C33 Y8N 34 Y8N C34 C33 C 0 1 N N N N N N -1.869 3.947 -5.126 2.908 -0.184 -2.015 C34 Y8N 35 Y8N C35 C34 C 0 1 N N N N N N -3.309 7.366 -6.637 3.365 1.984 1.098 C35 Y8N 36 Y8N C9 C35 C 0 1 N N N N N N -7.470 4.573 0.450 -3.045 -3.146 0.094 C9 Y8N 37 Y8N F1 F1 F 0 1 N N N N N N -2.066 6.139 -2.076 1.511 -2.514 0.585 F1 Y8N 38 Y8N F2 F2 F 0 1 N N N N N N -6.503 3.716 4.740 -7.047 -5.245 0.389 F2 Y8N 39 Y8N F3 F3 F 0 1 N N N N N N 2.816 7.696 -5.076 7.579 -2.393 1.223 F3 Y8N 40 Y8N F4 F4 F 0 1 N N N N N N -2.805 8.580 -6.615 2.923 3.310 1.153 F4 Y8N 41 Y8N F5 F5 F 0 1 N N N N N N -2.393 6.606 -7.242 4.024 1.662 2.289 F5 Y8N 42 Y8N F6 F6 F 0 1 N N N N N N -4.343 7.392 -7.463 4.245 1.830 0.022 F6 Y8N 43 Y8N N2 N3 N 0 1 Y N N N N N -4.623 5.621 -1.417 -1.059 -1.441 0.414 N2 Y8N 44 Y8N N4 N4 N 0 1 N N N N N N -10.115 5.942 -5.568 -2.854 5.101 0.098 N4 Y8N 45 Y8N N5 N5 N 0 1 N N N N N N -6.437 2.853 1.969 -4.100 -5.371 -0.174 N5 Y8N 46 Y8N N6 N6 N 0 1 N N N N N N 0.646 2.556 -5.869 5.067 -0.807 -3.894 N6 Y8N 47 Y8N N7 N7 N 0 1 N N N N N N -2.906 3.467 -5.249 1.901 0.246 -2.315 N7 Y8N 48 Y8N O1 O1 O 0 1 N N N N N N -6.130 4.950 0.109 -3.323 -1.747 0.171 O1 Y8N 49 Y8N O2 O2 O 0 1 N N N N N N -12.245 5.252 -5.685 -4.734 6.272 -0.035 O2 Y8N 50 Y8N S1 S1 S 0 1 Y N N N N N 1.973 4.837 -5.440 6.580 -1.655 -1.725 S1 Y8N 51 Y8N H1 H1 H 0 1 N N N N N N -5.738 6.766 -5.705 0.788 2.663 0.898 H1 Y8N 52 Y8N H2 H2 H 0 1 N N N N N N 1.051 9.531 -4.472 5.968 -1.991 3.219 H2 Y8N 53 Y8N H3 H3 H 0 1 N N N N N N -8.635 4.420 -2.980 -0.386 3.019 -0.906 H3 Y8N 54 Y8N H4 H4 H 0 1 N N N N N N -7.214 7.670 -5.208 -3.799 2.549 0.237 H4 Y8N 55 Y8N H5 H5 H 0 1 N N N N N N -8.661 8.001 -4.196 -3.364 2.316 1.948 H5 Y8N 56 Y8N H6 H6 H 0 1 N N N N N N -4.763 2.433 3.245 -4.153 -6.145 1.801 H6 Y8N 57 Y8N H7 H7 H 0 1 N N N N N N -4.483 3.738 2.043 -5.197 -7.002 0.627 H7 Y8N 58 Y8N H8 H8 H 0 1 N N N N N N -4.973 4.952 4.059 -6.313 -5.212 2.311 H8 Y8N 59 Y8N H9 H9 H 0 1 N N N N N N -8.853 3.598 3.424 -6.137 -3.481 -1.267 H9 Y8N 60 Y8N H10 H10 H 0 1 N N N N N N -9.552 3.912 1.799 -4.693 -2.530 -1.738 H10 Y8N 61 Y8N H11 H11 H 0 1 N N N N N N -6.851 0.744 1.947 -5.636 -6.256 -1.337 H11 Y8N 62 Y8N H12 H12 H 0 1 N N N N N N -7.144 1.549 3.525 -3.972 -6.633 -1.874 H12 Y8N 63 Y8N H13 H13 H 0 1 N N N N N N -7.404 7.015 -7.365 -2.608 5.863 2.669 H13 Y8N 64 Y8N H14 H14 H 0 1 N N N N N N -7.697 5.370 -6.706 -2.832 4.248 3.384 H14 Y8N 65 Y8N H15 H15 H 0 1 N N N N N N -8.794 6.046 -7.958 -1.438 4.567 2.325 H15 Y8N 66 Y8N H16 H16 H 0 1 N N N N N N -1.329 9.074 -4.045 3.689 -1.079 3.054 H16 Y8N 67 Y8N H17 H17 H 0 1 N N N N N N -10.564 4.189 -4.490 -0.757 5.135 0.267 H17 Y8N 68 Y8N H18 H18 H 0 1 N N N N N N -8.999 4.166 -5.373 -1.380 5.289 -1.395 H18 Y8N 69 Y8N H19 H19 H 0 1 N N N N N N -9.520 7.800 -6.375 -4.368 4.587 1.467 H19 Y8N 70 Y8N H20 H20 H 0 1 N N N N N N -6.172 5.824 2.214 -4.764 -3.399 1.987 H20 Y8N 71 Y8N H21 H21 H 0 1 N N N N N N -7.491 5.582 3.409 -6.062 -2.932 0.840 H21 Y8N 72 Y8N H22 H22 H 0 1 N N N N N N -9.342 1.384 2.588 -5.383 -4.734 -3.181 H22 Y8N 73 Y8N H23 H23 H 0 1 N N N N N N -8.758 1.793 0.939 -3.654 -4.431 -2.804 H23 Y8N 74 Y8N H24 H24 H 0 1 N N N N N N -9.339 6.456 -1.775 -3.395 3.077 -1.418 H24 Y8N 75 Y8N H25 H25 H 0 1 N N N N N N -10.273 6.989 -3.213 -2.128 3.315 -2.646 H25 Y8N 76 Y8N H26 H26 H 0 1 N N N N N N -10.755 5.501 -2.331 -2.297 1.740 -1.835 H26 Y8N 77 Y8N H27 H27 H 0 1 N N N N N N -10.932 7.810 -7.086 -2.230 7.310 -1.458 H27 Y8N 78 Y8N H28 H28 H 0 1 N N N N N N -12.572 7.129 -7.357 -2.937 6.056 -2.504 H28 Y8N 79 Y8N H29 H29 H 0 1 N N N N N N -12.678 9.289 -6.185 -3.858 8.292 -3.051 H29 Y8N 80 Y8N H30 H30 H 0 1 N N N N N N -13.279 7.953 -5.145 -5.126 7.216 -2.417 H30 Y8N 81 Y8N H31 H31 H 0 1 N N N N N N -11.639 8.634 -4.874 -4.419 8.471 -1.371 H31 Y8N 82 Y8N H32 H32 H 0 1 N N N N N N -8.141 5.444 0.409 -2.558 -3.471 1.014 H32 Y8N 83 Y8N H33 H33 H 0 1 N N N N N N -7.839 3.793 -0.232 -2.387 -3.340 -0.753 H33 Y8N 84 Y8N H35 H35 H 0 1 N N N N N N 1.594 2.343 -6.107 5.813 -1.031 -4.473 H35 Y8N 85 Y8N H36 H36 H 0 1 N N N N N N 0.347 1.957 -5.126 4.252 -0.444 -4.272 H36 Y8N 86 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal Y8N F6 C35 SING N N 1 Y8N F5 C35 SING N N 2 Y8N C28 C19 SING N N 3 Y8N C35 F4 SING N N 4 Y8N C35 C6 SING N N 5 Y8N C30 C29 SING N N 6 Y8N C30 C31 SING N N 7 Y8N C19 N4 SING N N 8 Y8N C19 C20 SING N N 9 Y8N C29 O2 DOUB N N 10 Y8N C29 N4 SING N N 11 Y8N N6 C32 SING N N 12 Y8N N4 C18 SING N N 13 Y8N C32 S1 SING Y N 14 Y8N C32 C33 DOUB Y N 15 Y8N S1 C15 SING Y N 16 Y8N C6 C5 DOUB Y N 17 Y8N C6 C7 SING Y N 18 Y8N N7 C34 TRIP N N 19 Y8N C33 C34 SING N N 20 Y8N C33 C16 SING Y N 21 Y8N F3 C14 SING N N 22 Y8N C15 C14 DOUB Y N 23 Y8N C15 C16 SING Y N 24 Y8N C5 C3 SING Y N 25 Y8N C14 C13 SING Y N 26 Y8N C16 C11 DOUB Y N 27 Y8N C20 N3 SING N N 28 Y8N C18 C17 SING N N 29 Y8N C13 C12 DOUB Y N 30 Y8N C11 C12 SING Y N 31 Y8N C11 C7 SING N N 32 Y8N C7 C8 DOUB Y N 33 Y8N N3 C17 SING N N 34 Y8N N3 C2 SING N N 35 Y8N C3 C2 DOUB Y N 36 Y8N C3 C4 SING Y N 37 Y8N C17 C27 SING N N 38 Y8N C2 N1 SING Y N 39 Y8N C8 C4 SING Y N 40 Y8N C8 F1 SING N N 41 Y8N C4 N2 DOUB Y N 42 Y8N N1 C1 DOUB Y N 43 Y8N N2 C1 SING Y N 44 Y8N C1 O1 SING N N 45 Y8N O1 C9 SING N N 46 Y8N C9 C10 SING N N 47 Y8N C10 N5 SING N N 48 Y8N C10 C24 SING N N 49 Y8N C10 C23 SING N N 50 Y8N N5 C26 SING N N 51 Y8N N5 C21 SING N N 52 Y8N C25 C24 SING N N 53 Y8N C25 C26 SING N N 54 Y8N C21 C22 SING N N 55 Y8N C23 C22 SING N N 56 Y8N C22 F2 SING N N 57 Y8N C5 H1 SING N N 58 Y8N C13 H2 SING N N 59 Y8N C17 H3 SING N N 60 Y8N C20 H4 SING N N 61 Y8N C20 H5 SING N N 62 Y8N C21 H6 SING N N 63 Y8N C21 H7 SING N N 64 Y8N C22 H8 SING N N 65 Y8N C24 H9 SING N N 66 Y8N C24 H10 SING N N 67 Y8N C26 H11 SING N N 68 Y8N C26 H12 SING N N 69 Y8N C28 H13 SING N N 70 Y8N C28 H14 SING N N 71 Y8N C28 H15 SING N N 72 Y8N C12 H16 SING N N 73 Y8N C18 H17 SING N N 74 Y8N C18 H18 SING N N 75 Y8N C19 H19 SING N N 76 Y8N C23 H20 SING N N 77 Y8N C23 H21 SING N N 78 Y8N C25 H22 SING N N 79 Y8N C25 H23 SING N N 80 Y8N C27 H24 SING N N 81 Y8N C27 H25 SING N N 82 Y8N C27 H26 SING N N 83 Y8N C30 H27 SING N N 84 Y8N C30 H28 SING N N 85 Y8N C31 H29 SING N N 86 Y8N C31 H30 SING N N 87 Y8N C31 H31 SING N N 88 Y8N C9 H32 SING N N 89 Y8N C9 H33 SING N N 90 Y8N N6 H35 SING N N 91 Y8N N6 H36 SING N N 92 # loop_ _pdbx_chem_comp_descriptor.comp_id _pdbx_chem_comp_descriptor.type _pdbx_chem_comp_descriptor.program _pdbx_chem_comp_descriptor.program_version _pdbx_chem_comp_descriptor.descriptor Y8N SMILES ACDLabs 12.01 "CCC(=O)N1CC(C)N(CC1C)c1nc(OCC23CCCN3CC(F)C2)nc2c1cc(c(c1ccc(F)c3sc(N)c(C#N)c13)c2F)C(F)(F)F" Y8N InChI InChI 1.06 "InChI=1S/C35H35F6N7O2S/c1-4-25(49)47-13-18(3)48(14-17(47)2)32-21-10-23(35(39,40)41)27(20-6-7-24(37)30-26(20)22(12-42)31(43)51-30)28(38)29(21)44-33(45-32)50-16-34-8-5-9-46(34)15-19(36)11-34/h6-7,10,17-19H,4-5,8-9,11,13-16,43H2,1-3H3/t17-,18+,19-,34+/m1/s1" Y8N InChIKey InChI 1.06 DWYHZCOHGXYZHA-VHJOERAISA-N Y8N SMILES_CANONICAL CACTVS 3.385 "CCC(=O)N1C[C@H](C)N(C[C@H]1C)c2nc(OC[C@@]34CCCN3C[C@H](F)C4)nc5c(F)c(c6ccc(F)c7sc(N)c(C#N)c67)c(cc25)C(F)(F)F" Y8N SMILES CACTVS 3.385 "CCC(=O)N1C[CH](C)N(C[CH]1C)c2nc(OC[C]34CCCN3C[CH](F)C4)nc5c(F)c(c6ccc(F)c7sc(N)c(C#N)c67)c(cc25)C(F)(F)F" Y8N SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CCC(=O)N1C[C@@H](N(C[C@H]1C)c2c3cc(c(c(c3nc(n2)OC[C@@]45CCCN4C[C@@H](C5)F)F)c6ccc(c7c6c(c(s7)N)C#N)F)C(F)(F)F)C" Y8N SMILES "OpenEye OEToolkits" 2.0.7 "CCC(=O)N1CC(N(CC1C)c2c3cc(c(c(c3nc(n2)OCC45CCCN4CC(C5)F)F)c6ccc(c7c6c(c(s7)N)C#N)F)C(F)(F)F)C" # loop_ _pdbx_chem_comp_identifier.comp_id _pdbx_chem_comp_identifier.type _pdbx_chem_comp_identifier.program _pdbx_chem_comp_identifier.program_version _pdbx_chem_comp_identifier.identifier Y8N "SYSTEMATIC NAME" ACDLabs 12.01 "(4P)-2-amino-4-{4-[(2S,5R)-2,5-dimethyl-4-propanoylpiperazin-1-yl]-8-fluoro-2-{[(2R,4R,7aS)-2-fluorotetrahydro-1H-pyrrolizin-7a(5H)-yl]methoxy}-6-(trifluoromethyl)quinazolin-7-yl}-7-fluoro-1-benzothiophene-3-carbonitrile" Y8N "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "2-azanyl-4-[4-[(2~{S},5~{R})-2,5-dimethyl-4-propanoyl-piperazin-1-yl]-8-fluoranyl-2-[[(2~{R},8~{S})-2-fluoranyl-1,2,3,5,6,7-hexahydropyrrolizin-8-yl]methoxy]-6-(trifluoromethyl)quinazolin-7-yl]-7-fluoranyl-1-benzothiophene-3-carbonitrile" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site Y8N "Create component" 2023-11-28 RCSB Y8N "Modify PCM" 2024-09-27 PDBE Y8N "Initial release" 2024-12-18 RCSB # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id Y8N _pdbx_chem_comp_synonyms.name "(4P)-2-amino-4-{4-[(2S,5R)-2,5-dimethyl-4-propanoylpiperazin-1-yl]-8-fluoro-2-{[(2R,4R,7aS)-2-fluorotetrahydro-1H-pyrrolizin-7a(5H)-yl]methoxy}-6-(trifluoromethyl)quinazolin-7-yl}-7-fluoro-1-benzothiophene-3-carbonitrile" _pdbx_chem_comp_synonyms.provenance PDB _pdbx_chem_comp_synonyms.type ? # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id Y8N _pdbx_chem_comp_pcm.modified_residue_id CYS _pdbx_chem_comp_pcm.type None _pdbx_chem_comp_pcm.category "Covalent chemical modification" _pdbx_chem_comp_pcm.position "Amino-acid side chain" _pdbx_chem_comp_pcm.polypeptide_position "Any position" _pdbx_chem_comp_pcm.comp_id_linking_atom C31 _pdbx_chem_comp_pcm.modified_residue_id_linking_atom SG _pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ? _pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ? #