data_XA8 # _chem_comp.id XA8 _chem_comp.name "(1R,2S,5S)-N-[(2S,3R)-4-(azetidin-1-yl)-3-hydroxy-4-oxo-1-(2-oxopiperidin-1-yl)butan-2-yl]-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C28 H42 F3 N5 O6" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2022-11-08 _chem_comp.pdbx_modified_date 2024-09-27 _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 601.658 _chem_comp.one_letter_code ? _chem_comp.three_letter_code XA8 _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 8F2D _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_backbone_atom_flag _chem_comp_atom.pdbx_n_terminal_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 XA8 N1 N1 N 0 1 N N N N N N -19.425 15.787 -27.577 0.382 1.692 -1.114 N1 XA8 1 XA8 N3 N2 N 0 1 N N N N N N -17.879 13.452 -25.337 -2.041 -0.269 0.861 N3 XA8 2 XA8 C4 C1 C 0 1 N N S N N N -20.587 17.085 -25.995 -1.403 3.204 -1.623 C4 XA8 3 XA8 C5 C2 C 0 1 N N N N N N -19.405 17.921 -25.571 -0.887 4.115 -0.507 C5 XA8 4 XA8 C6 C3 C 0 1 N N N N N N -19.508 18.812 -24.343 -1.691 5.381 -0.202 C6 XA8 5 XA8 C7 C4 C 0 1 N N N N N N -18.633 18.560 -26.701 0.629 4.243 -0.345 C7 XA8 6 XA8 C8 C5 C 0 1 N N N N N N -20.628 16.633 -27.432 -0.417 2.198 -2.254 C8 XA8 7 XA8 C10 C6 C 0 1 N N S N N N -19.847 15.439 -29.944 2.338 0.902 0.179 C10 XA8 8 XA8 C13 C7 C 0 1 N N N N N N -19.366 13.122 -30.981 1.307 2.509 1.791 C13 XA8 9 XA8 C15 C8 C 0 1 N N N N N N -19.411 17.333 -31.408 4.086 -0.723 0.669 C15 XA8 10 XA8 C17 C9 C 0 1 N N S N N N -18.002 12.203 -24.590 -2.738 -1.548 0.714 C17 XA8 11 XA8 C20 C10 C 0 1 N N N N N N -20.298 12.421 -21.100 -6.573 0.482 -0.129 C20 XA8 12 XA8 C21 C11 C 0 1 N N N N N N -20.773 11.501 -19.965 -6.149 -0.015 -1.522 C21 XA8 13 XA8 C22 C12 C 0 1 N N N N N N -19.752 10.443 -20.433 -5.656 -1.287 -0.809 C22 XA8 14 XA8 C24 C13 C 0 1 N N N N N N -18.562 9.898 -26.580 0.546 -2.031 0.183 C24 XA8 15 XA8 C26 C14 C 0 1 N N N N N N -18.092 9.540 -28.919 1.086 -2.314 -2.230 C26 XA8 16 XA8 C28 C15 C 0 1 N N N N N N -16.440 10.862 -27.424 -1.027 -3.223 -1.296 C28 XA8 17 XA8 C1 C16 C 0 1 N N N N N N -18.933 14.039 -25.908 -1.391 0.270 -0.190 C1 XA8 18 XA8 O1 O1 O 0 1 N N N N N N -19.983 13.428 -26.073 -1.443 -0.268 -1.275 O1 XA8 19 XA8 C2 C17 C 0 1 N N S N N N -18.750 15.491 -26.326 -0.600 1.541 -0.016 C2 XA8 20 XA8 N2 N3 N 0 1 N N N N N N -19.048 16.160 -30.922 3.597 0.230 -0.149 N2 XA8 21 XA8 O2 O2 O 0 1 N N N N N N -20.456 17.917 -31.205 3.483 -1.024 1.677 O2 XA8 22 XA8 C3 C18 C 0 1 N N R N N N -19.411 16.432 -25.326 -1.524 2.771 -0.147 C3 XA8 23 XA8 O3 O3 O 0 1 N N N N N N -17.945 14.618 -28.744 2.381 1.604 -2.074 O3 XA8 24 XA8 N4 N4 N 0 1 N N N N N N -19.267 11.422 -21.408 -5.559 -0.449 0.402 N4 XA8 25 XA8 O4 O4 O 0 1 N N N N N N -18.911 13.586 -22.804 -3.305 -1.549 3.063 O4 XA8 26 XA8 N5 N5 N 0 1 N N N N N N -17.292 10.654 -26.417 -0.730 -2.667 -0.121 N5 XA8 27 XA8 O5 O5 O 0 1 N N N N N N -17.489 10.418 -22.265 -4.965 0.346 2.387 O5 XA8 28 XA8 O6 O6 O 0 1 N N N N N N -15.466 11.605 -27.283 -2.137 -3.687 -1.447 O6 XA8 29 XA8 C9 C19 C 0 1 N N N N N N -18.964 15.276 -28.713 1.703 1.424 -1.084 C9 XA8 30 XA8 C11 C20 C 0 1 N N N N N N -20.432 14.109 -30.482 2.615 2.068 1.130 C11 XA8 31 XA8 C12 C21 C 0 1 N N N N N N -21.229 13.466 -29.340 3.605 1.622 2.208 C12 XA8 32 XA8 C14 C22 C 0 1 N N N N N N -21.380 14.459 -31.639 3.209 3.238 0.344 C14 XA8 33 XA8 C16 C23 C 0 1 N N N N N N -18.378 17.976 -32.324 5.381 -1.414 0.331 C16 XA8 34 XA8 C18 C24 C 0 1 N N R N N N -17.917 12.594 -23.098 -3.861 -1.640 1.750 C18 XA8 35 XA8 C19 C25 C 0 1 N N N N N N -18.221 11.381 -22.223 -4.834 -0.510 1.537 C19 XA8 36 XA8 C23 C26 C 0 1 N N N N N N -16.978 11.166 -25.074 -1.750 -2.696 0.930 C23 XA8 37 XA8 C25 C27 C 0 1 N N N N N N -19.059 10.046 -27.984 1.621 -2.490 -0.803 C25 XA8 38 XA8 C27 C28 C 0 1 N N N N N N -16.743 10.203 -28.751 -0.060 -3.306 -2.442 C27 XA8 39 XA8 F1 F1 F 0 1 N N N N N N -17.600 18.858 -31.709 5.680 -2.356 1.322 F1 XA8 40 XA8 F2 F2 F 0 1 N N N N N N -18.995 18.371 -33.436 5.257 -2.061 -0.903 F2 XA8 41 XA8 F3 F3 F 0 1 N N N N N N -17.491 17.105 -32.723 6.410 -0.469 0.262 F3 XA8 42 XA8 H1 H1 H 0 1 N N N N N N -16.979 13.880 -25.423 -2.046 0.191 1.716 H1 XA8 43 XA8 H2 H2 H 0 1 N N N N N N -21.532 17.180 -25.440 -2.272 3.508 -2.206 H2 XA8 44 XA8 H3 H3 H 0 1 N N N N N N -20.079 18.293 -23.559 -2.629 5.358 -0.756 H3 XA8 45 XA8 H4 H4 H 0 1 N N N N N N -18.499 19.041 -23.971 -1.902 5.428 0.867 H4 XA8 46 XA8 H5 H5 H 0 1 N N N N N N -20.021 19.748 -24.611 -1.115 6.257 -0.498 H5 XA8 47 XA8 H6 H6 H 0 1 N N N N N N -17.797 19.144 -26.290 0.984 5.101 -0.917 H6 XA8 48 XA8 H7 H7 H 0 1 N N N N N N -18.241 17.776 -27.366 0.871 4.384 0.708 H7 XA8 49 XA8 H8 H8 H 0 1 N N N N N N -19.299 19.225 -27.270 1.111 3.337 -0.711 H8 XA8 50 XA8 H9 H9 H 0 1 N N N N N N -20.584 17.495 -28.114 0.227 2.698 -2.977 H9 XA8 51 XA8 H10 H10 H 0 1 N N N N N N -21.540 16.052 -27.633 -0.960 1.381 -2.730 H10 XA8 52 XA8 H11 H11 H 0 1 N N N N N N -20.698 16.075 -29.657 1.662 0.194 0.659 H11 XA8 53 XA8 H12 H12 H 0 1 N N N N N N -18.685 12.869 -30.155 0.943 1.715 2.442 H12 XA8 54 XA8 H13 H13 H 0 1 N N N N N N -19.856 12.207 -31.346 1.483 3.410 2.379 H13 XA8 55 XA8 H14 H14 H 0 1 N N N N N N -18.794 13.583 -31.800 0.563 2.717 1.021 H14 XA8 56 XA8 H15 H15 H 0 1 N N N N N N -19.005 11.787 -24.766 -3.162 -1.618 -0.288 H15 XA8 57 XA8 H16 H16 H 0 1 N N N N N N -19.907 13.393 -20.767 -6.343 1.532 0.052 H16 XA8 58 XA8 H17 H17 H 0 1 N N N N N N -21.036 12.578 -21.900 -7.597 0.219 0.139 H17 XA8 59 XA8 H18 H18 H 0 1 N N N N N N -20.587 11.895 -18.955 -6.985 -0.187 -2.200 H18 XA8 60 XA8 H19 H19 H 0 1 N N N N N N -21.823 11.185 -20.048 -5.350 0.574 -1.974 H19 XA8 61 XA8 H20 H20 H 0 1 N N N N N N -20.199 9.540 -20.875 -6.410 -2.072 -0.740 H20 XA8 62 XA8 H21 H21 H 0 1 N N N N N N -19.014 10.152 -19.671 -4.695 -1.650 -1.172 H21 XA8 63 XA8 H22 H22 H 0 1 N N N N N N -19.315 10.293 -25.882 0.434 -0.949 0.117 H22 XA8 64 XA8 H23 H23 H 0 1 N N N N N N -18.385 8.834 -26.365 0.851 -2.301 1.194 H23 XA8 65 XA8 H24 H24 H 0 1 N N N N N N -18.455 9.726 -29.941 0.719 -1.296 -2.361 H24 XA8 66 XA8 H25 H25 H 0 1 N N N N N N -17.978 8.457 -28.762 1.882 -2.513 -2.947 H25 XA8 67 XA8 H26 H26 H 0 1 N N N N N N -17.677 15.723 -26.399 -0.095 1.544 0.950 H26 XA8 68 XA8 H27 H27 H 0 1 N N N N N N -18.191 15.752 -31.238 4.080 0.471 -0.956 H27 XA8 69 XA8 H28 H28 H 0 1 N N N N N N -19.532 16.078 -24.292 -2.483 2.752 0.369 H28 XA8 70 XA8 H29 H29 H 0 1 N N N N N N -18.858 13.826 -21.886 -2.827 -0.726 3.232 H29 XA8 71 XA8 H30 H30 H 0 1 N N N N N N -20.549 13.216 -28.513 3.182 0.789 2.768 H30 XA8 72 XA8 H31 H31 H 0 1 N N N N N N -21.995 14.172 -28.985 4.537 1.308 1.737 H31 XA8 73 XA8 H32 H32 H 0 1 N N N N N N -21.716 12.549 -29.704 3.803 2.453 2.886 H32 XA8 74 XA8 H33 H33 H 0 1 N N N N N N -22.145 15.166 -31.286 3.436 4.057 1.026 H33 XA8 75 XA8 H34 H34 H 0 1 N N N N N N -20.806 14.919 -32.457 4.124 2.915 -0.153 H34 XA8 76 XA8 H35 H35 H 0 1 N N N N N N -21.868 13.543 -32.003 2.490 3.576 -0.403 H35 XA8 77 XA8 H36 H36 H 0 1 N N N N N N -16.907 12.969 -22.874 -4.380 -2.592 1.640 H36 XA8 78 XA8 H37 H37 H 0 1 N N N N N N -16.968 10.323 -24.368 -1.272 -2.586 1.903 H37 XA8 79 XA8 H38 H38 H 0 1 N N N N N N -15.984 11.636 -25.098 -2.283 -3.647 0.892 H38 XA8 80 XA8 H39 H39 H 0 1 N N N N N N -19.241 11.111 -28.193 2.519 -1.886 -0.672 H39 XA8 81 XA8 H40 H40 H 0 1 N N N N N N -19.998 9.485 -28.096 1.854 -3.540 -0.627 H40 XA8 82 XA8 H41 H41 H 0 1 N N N N N N -15.976 9.432 -28.917 -0.578 -3.067 -3.371 H41 XA8 83 XA8 H42 H42 H 0 1 N N N N N N -16.659 10.977 -29.528 0.343 -4.317 -2.504 H42 XA8 84 # 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 XA8 F2 C16 SING N N 1 XA8 F3 C16 SING N N 2 XA8 C16 F1 SING N N 3 XA8 C16 C15 SING N N 4 XA8 C14 C11 SING N N 5 XA8 C15 O2 DOUB N N 6 XA8 C15 N2 SING N N 7 XA8 C13 C11 SING N N 8 XA8 N2 C10 SING N N 9 XA8 C11 C10 SING N N 10 XA8 C11 C12 SING N N 11 XA8 C10 C9 SING N N 12 XA8 C26 C27 SING N N 13 XA8 C26 C25 SING N N 14 XA8 C27 C28 SING N N 15 XA8 O3 C9 DOUB N N 16 XA8 C9 N1 SING N N 17 XA8 C25 C24 SING N N 18 XA8 N1 C8 SING N N 19 XA8 N1 C2 SING N N 20 XA8 C8 C4 SING N N 21 XA8 C28 O6 DOUB N N 22 XA8 C28 N5 SING N N 23 XA8 C7 C5 SING N N 24 XA8 C24 N5 SING N N 25 XA8 N5 C23 SING N N 26 XA8 C2 C1 SING N N 27 XA8 C2 C3 SING N N 28 XA8 O1 C1 DOUB N N 29 XA8 C4 C5 SING N N 30 XA8 C4 C3 SING N N 31 XA8 C1 N3 SING N N 32 XA8 C5 C3 SING N N 33 XA8 C5 C6 SING N N 34 XA8 N3 C17 SING N N 35 XA8 C23 C17 SING N N 36 XA8 C17 C18 SING N N 37 XA8 C18 O4 SING N N 38 XA8 C18 C19 SING N N 39 XA8 O5 C19 DOUB N N 40 XA8 C19 N4 SING N N 41 XA8 N4 C20 SING N N 42 XA8 N4 C22 SING N N 43 XA8 C20 C21 SING N N 44 XA8 C22 C21 SING N N 45 XA8 N3 H1 SING N N 46 XA8 C4 H2 SING N N 47 XA8 C6 H3 SING N N 48 XA8 C6 H4 SING N N 49 XA8 C6 H5 SING N N 50 XA8 C7 H6 SING N N 51 XA8 C7 H7 SING N N 52 XA8 C7 H8 SING N N 53 XA8 C8 H9 SING N N 54 XA8 C8 H10 SING N N 55 XA8 C10 H11 SING N N 56 XA8 C13 H12 SING N N 57 XA8 C13 H13 SING N N 58 XA8 C13 H14 SING N N 59 XA8 C17 H15 SING N N 60 XA8 C20 H16 SING N N 61 XA8 C20 H17 SING N N 62 XA8 C21 H18 SING N N 63 XA8 C21 H19 SING N N 64 XA8 C22 H20 SING N N 65 XA8 C22 H21 SING N N 66 XA8 C24 H22 SING N N 67 XA8 C24 H23 SING N N 68 XA8 C26 H24 SING N N 69 XA8 C26 H25 SING N N 70 XA8 C2 H26 SING N N 71 XA8 N2 H27 SING N N 72 XA8 C3 H28 SING N N 73 XA8 O4 H29 SING N N 74 XA8 C12 H30 SING N N 75 XA8 C12 H31 SING N N 76 XA8 C12 H32 SING N N 77 XA8 C14 H33 SING N N 78 XA8 C14 H34 SING N N 79 XA8 C14 H35 SING N N 80 XA8 C18 H36 SING N N 81 XA8 C23 H37 SING N N 82 XA8 C23 H38 SING N N 83 XA8 C25 H39 SING N N 84 XA8 C25 H40 SING N N 85 XA8 C27 H41 SING N N 86 XA8 C27 H42 SING N N 87 # 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 XA8 SMILES ACDLabs 12.01 "CC1(C)C2C(C(=O)NC(CN3CCCCC3=O)C(O)C(=O)N3CCC3)N(CC21)C(=O)C(NC(=O)C(F)(F)F)C(C)(C)C" XA8 InChI InChI 1.06 "InChI=1S/C28H42F3N5O6/c1-26(2,3)21(33-25(42)28(29,30)31)24(41)36-13-15-18(27(15,4)5)19(36)22(39)32-16(14-35-10-7-6-9-17(35)37)20(38)23(40)34-11-8-12-34/h15-16,18-21,38H,6-14H2,1-5H3,(H,32,39)(H,33,42)/t15-,16-,18-,19-,20+,21+/m0/s1" XA8 InChIKey InChI 1.06 CEVFDXICNWCNKE-NLNBCDFGSA-N XA8 SMILES_CANONICAL CACTVS 3.385 "CC(C)(C)[C@H](NC(=O)C(F)(F)F)C(=O)N1C[C@H]2[C@@H]([C@H]1C(=O)N[C@@H](CN3CCCCC3=O)[C@@H](O)C(=O)N4CCC4)C2(C)C" XA8 SMILES CACTVS 3.385 "CC(C)(C)[CH](NC(=O)C(F)(F)F)C(=O)N1C[CH]2[CH]([CH]1C(=O)N[CH](CN3CCCCC3=O)[CH](O)C(=O)N4CCC4)C2(C)C" XA8 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC1([C@@H]2[C@H]1[C@H](N(C2)C(=O)[C@H](C(C)(C)C)NC(=O)C(F)(F)F)C(=O)N[C@@H](CN3CCCCC3=O)[C@H](C(=O)N4CCC4)O)C" XA8 SMILES "OpenEye OEToolkits" 2.0.7 "CC1(C2C1C(N(C2)C(=O)C(C(C)(C)C)NC(=O)C(F)(F)F)C(=O)NC(CN3CCCCC3=O)C(C(=O)N4CCC4)O)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 XA8 "SYSTEMATIC NAME" ACDLabs 12.01 "(1R,2S,5S)-N-[(2S,3R)-4-(azetidin-1-yl)-3-hydroxy-4-oxo-1-(2-oxopiperidin-1-yl)butan-2-yl]-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide" XA8 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "(1~{R},2~{S},5~{S})-~{N}-[(2~{S},3~{R})-4-(azetidin-1-yl)-3-oxidanyl-4-oxidanylidene-1-(2-oxidanylidenepiperidin-1-yl)butan-2-yl]-3-[(2~{S})-3,3-dimethyl-2-[2,2,2-tris(fluoranyl)ethanoylamino]butanoyl]-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-2-carboxamide" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site XA8 "Create component" 2022-11-08 RCSB XA8 "Initial release" 2023-10-11 RCSB XA8 "Modify PCM" 2024-09-27 PDBE # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id XA8 _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 C18 _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 ? #