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      ? 
# 
