data_89B
# 
_chem_comp.id                                    89B 
_chem_comp.name                                  "N-[(2S)-3-(4-fluorophenyl)-1-oxidanylidene-1-[[(2R,3S)-3-oxidanyl-4-oxidanylidene-1-[(3S)-2-oxidanylidenepiperidin-3-yl]-4-[(phenylmethyl)amino]butan-2-yl]amino]propan-2-yl]-1-benzofuran-2-carboxamide" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C34 H35 F N4 O6" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2021-11-30 
_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                        614.663 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     89B 
_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        7W33 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBJ 
_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 
89B O01 O1  O 0 1 N N N N N N -3.441  -16.448 21.691 2.629  -0.292 1.825  O01 89B 1  
89B C02 C1  C 0 1 N N N N N N -3.763  -17.413 22.274 2.543  -0.436 0.620  C02 89B 2  
89B N03 N1  N 0 1 N N N N N N -2.711  -18.418 22.720 1.516  0.118  -0.054 N03 89B 3  
89B C04 C2  C 0 1 N N S N N N -1.250  -18.190 22.415 0.502  0.894  0.664  C04 89B 4  
89B C05 C3  C 0 1 N N N N N N -0.294  -19.039 23.340 0.984  2.337  0.825  C05 89B 5  
89B C06 C4  C 0 1 Y N N N N N -0.386  -18.651 24.889 2.205  2.364  1.707  C06 89B 6  
89B C07 C5  C 0 1 Y N N N N N -0.687  -19.637 25.831 2.066  2.497  3.076  C07 89B 7  
89B C08 C6  C 0 1 Y N N N N N -0.766  -19.312 27.176 3.186  2.521  3.886  C08 89B 8  
89B C09 C7  C 0 1 Y N N N N N -0.540  -17.964 27.596 4.447  2.413  3.325  C09 89B 9  
89B C11 C8  C 0 1 Y N N N N N -0.242  -16.994 26.669 4.585  2.280  1.954  C11 89B 10 
89B C12 C9  C 0 1 Y N N N N N -0.162  -17.329 25.301 3.464  2.250  1.147  C12 89B 11 
89B C13 C10 C 0 1 N N N N N N -0.860  -18.289 20.875 -0.788 0.878  -0.115 C13 89B 12 
89B N14 N2  N 0 1 N N N N N N 0.290   -17.522 20.401 -1.868 1.531  0.357  N14 89B 13 
89B C15 C11 C 0 1 N N R N N N 0.787   -17.509 18.972 -3.122 1.516  -0.400 C15 89B 14 
89B C16 C12 C 0 1 N N N N N N -0.351  -17.872 17.889 -3.095 2.624  -1.454 C16 89B 15 
89B C17 C13 C 0 1 N N S N N N -1.590  -16.868 17.898 -2.026 2.306  -2.501 C17 89B 16 
89B C18 C14 C 0 1 N N N N N N -2.621  -17.456 17.116 -1.847 3.511  -3.428 C18 89B 17 
89B C19 C15 C 0 1 N N N N N N -2.478  -17.278 15.675 -0.987 3.081  -4.622 C19 89B 18 
89B C20 C16 C 0 1 N N N N N N -2.534  -15.867 15.252 -1.781 2.081  -5.464 C20 89B 19 
89B N21 N3  N 0 1 N N N N N N -1.624  -14.942 16.039 -2.314 1.016  -4.622 N21 89B 20 
89B C22 C17 C 0 1 N N N N N N -1.117  -15.428 17.395 -2.452 1.108  -3.300 C22 89B 21 
89B O23 O2  O 0 1 N N N N N N -0.386  -14.724 18.071 -2.945 0.171  -2.709 O23 89B 22 
89B C24 C18 C 0 1 N N S N N N 2.111   -18.421 18.853 -4.296 1.747  0.553  C24 89B 23 
89B O25 O3  O 0 1 N N N N N N 3.208   -17.839 19.607 -4.207 3.060  1.110  O25 89B 24 
89B C26 C19 C 0 1 N N N N N N 2.520   -18.729 17.353 -4.252 0.727  1.662  C26 89B 25 
89B N27 N4  N 0 1 N N N N N N 3.316   -17.768 16.585 -4.422 -0.580 1.383  N27 89B 26 
89B C28 C20 C 0 1 N N N N N N 3.691   -18.073 15.162 -4.379 -1.571 2.461  C28 89B 27 
89B C29 C21 C 0 1 Y N N N N N 2.495   -17.722 14.208 -4.596 -2.948 1.887  C29 89B 28 
89B C30 C22 C 0 1 Y N N N N N 2.160   -18.572 13.162 -5.877 -3.456 1.776  C30 89B 29 
89B C31 C23 C 0 1 Y N N N N N 1.090   -18.249 12.319 -6.077 -4.716 1.245  C31 89B 30 
89B C32 C24 C 0 1 Y N N N N N 0.335   -17.028 12.544 -4.996 -5.468 0.823  C32 89B 31 
89B C33 C25 C 0 1 Y N N N N N 0.671   -16.183 13.588 -3.716 -4.959 0.933  C33 89B 32 
89B C34 C26 C 0 1 Y N N N N N 1.734   -16.501 14.429 -3.516 -3.699 1.465  C34 89B 33 
89B O35 O4  O 0 1 N N N N N N 2.181   -19.730 16.855 -4.062 1.083  2.806  O35 89B 34 
89B O36 O5  O 0 1 N N N N N N -1.494  -18.978 20.167 -0.854 0.278  -1.166 O36 89B 35 
89B C37 C27 C 0 1 Y N N N N N -5.231  -17.694 22.608 3.564  -1.210 -0.101 C37 89B 36 
89B C38 C28 C 0 1 Y N N N N N -6.340  -16.858 22.380 4.639  -1.811 0.471  C38 89B 37 
89B C39 C29 C 0 1 Y N N N N N -7.511  -17.551 22.857 5.370  -2.457 -0.619 C39 89B 38 
89B C40 C30 C 0 1 Y N N N N N -8.911  -17.275 22.926 6.537  -3.221 -0.689 C40 89B 39 
89B C41 C31 C 0 1 Y N N N N N -9.769  -18.203 23.467 6.966  -3.691 -1.899 C41 89B 40 
89B C42 C32 C 0 1 Y N N N N N -9.262  -19.440 23.959 6.250  -3.415 -3.055 C42 89B 41 
89B C43 C33 C 0 1 Y N N N N N -7.887  -19.710 23.892 5.096  -2.663 -3.007 C43 89B 42 
89B C44 C34 C 0 1 Y N N N N N -7.018  -18.775 23.346 4.640  -2.174 -1.788 C44 89B 43 
89B O45 O6  O 0 1 Y N N N N N -5.685  -18.828 23.185 3.571  -1.435 -1.432 O45 89B 44 
89B F10 F1  F 0 1 N N N N N N -0.616  -17.644 28.920 5.542  2.437  4.116  F10 89B 45 
89B H1  H1  H 0 1 N N N N N N -2.990  -19.238 23.220 1.448  0.002  -1.015 H1  89B 46 
89B H2  H2  H 0 1 N N N N N N -1.051  -17.143 22.688 0.338  0.454  1.648  H2  89B 47 
89B H3  H3  H 0 1 N N N N N N -0.559  -20.101 23.232 1.233  2.748  -0.154 H3  89B 48 
89B H4  H4  H 0 1 N N N N N N 0.742   -18.884 23.004 0.194  2.935  1.280  H4  89B 49 
89B H5  H5  H 0 1 N N N N N N -0.858  -20.654 25.511 1.082  2.582  3.513  H5  89B 50 
89B H6  H6  H 0 1 N N N N N N -0.998  -20.075 27.905 3.077  2.625  4.955  H6  89B 51 
89B H7  H7  H 0 1 N N N N N N -0.069  -15.977 26.987 5.569  2.196  1.516  H7  89B 52 
89B H8  H8  H 0 1 N N N N N N 0.072   -16.568 24.571 3.572  2.142  0.078  H8  89B 53 
89B H9  H9  H 0 1 N N N N N N 0.784   -16.966 21.069 -1.815 2.011  1.199  H9  89B 54 
89B H10 H10 H 0 1 N N N N N N 1.104   -16.480 18.748 -3.238 0.550  -0.891 H10 89B 55 
89B H11 H11 H 0 1 N N N N N N -0.723  -18.885 18.103 -4.069 2.690  -1.938 H11 89B 56 
89B H12 H12 H 0 1 N N N N N N 0.104   -17.853 16.888 -2.862 3.575  -0.975 H12 89B 57 
89B H13 H13 H 0 1 N N N N N N -1.926  -16.763 18.940 -1.082 2.091  -2.001 H13 89B 58 
89B H14 H14 H 0 1 N N N N N N -3.579  -17.009 17.422 -2.821 3.850  -3.781 H14 89B 59 
89B H15 H15 H 0 1 N N N N N N -2.636  -18.535 17.327 -1.351 4.318  -2.889 H15 89B 60 
89B H16 H16 H 0 1 N N N N N N -3.290  -17.825 15.174 -0.739 3.953  -5.228 H16 89B 61 
89B H17 H17 H 0 1 N N N N N N -1.509  -17.697 15.366 -0.070 2.613  -4.263 H17 89B 62 
89B H18 H18 H 0 1 N N N N N N -2.246  -15.814 14.192 -2.606 2.598  -5.955 H18 89B 63 
89B H19 H19 H 0 1 N N N N N N -3.569  -15.513 15.369 -1.128 1.649  -6.222 H19 89B 64 
89B H20 H20 H 0 1 N N N N N N -1.365  -14.045 15.682 -2.586 0.190  -5.052 H20 89B 65 
89B H21 H21 H 0 1 N N N N N N 1.859   -19.388 19.312 -5.234 1.647  0.006  H21 89B 66 
89B H22 H22 H 0 1 N N N N N N 2.925   -17.669 20.498 -3.396 3.220  1.612  H22 89B 67 
89B H23 H23 H 0 1 N N N N N N 3.609   -16.910 17.007 -4.574 -0.865 0.468  H23 89B 68 
89B H24 H24 H 0 1 N N N N N N 3.930   -19.143 15.069 -3.407 -1.532 2.951  H24 89B 69 
89B H25 H25 H 0 1 N N N N N N 4.570   -17.475 14.880 -5.162 -1.353 3.187  H25 89B 70 
89B H26 H26 H 0 1 N N N N N N 2.723   -19.479 12.999 -6.721 -2.869 2.106  H26 89B 71 
89B H27 H27 H 0 1 N N N N N N 0.826   -18.906 11.503 -7.077 -5.114 1.160  H27 89B 72 
89B H28 H28 H 0 1 N N N N N N -0.491  -16.779 11.895 -5.152 -6.453 0.409  H28 89B 73 
89B H29 H29 H 0 1 N N N N N N 0.108   -15.276 13.750 -2.871 -5.547 0.603  H29 89B 74 
89B H30 H30 H 0 1 N N N N N N 1.994   -15.842 15.245 -2.515 -3.300 1.547  H30 89B 75 
89B H31 H31 H 0 1 N N N N N N -6.318  -15.877 21.930 4.901  -1.811 1.519  H31 89B 76 
89B H32 H32 H 0 1 N N N N N N -9.295  -16.337 22.553 7.098  -3.438 0.207  H32 89B 77 
89B H33 H33 H 0 1 N N N N N N -10.827 -17.994 23.519 7.868  -4.282 -1.955 H33 89B 78 
89B H34 H34 H 0 1 N N N N N N -9.936  -20.170 24.383 6.601  -3.793 -4.004 H34 89B 79 
89B H35 H35 H 0 1 N N N N N N -7.503  -20.648 24.266 4.547  -2.454 -3.913 H35 89B 80 
# 
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 
89B C31 C32 DOUB Y N 1  
89B C31 C30 SING Y N 2  
89B C32 C33 SING Y N 3  
89B C30 C29 DOUB Y N 4  
89B C33 C34 DOUB Y N 5  
89B C29 C34 SING Y N 6  
89B C29 C28 SING N N 7  
89B C28 N27 SING N N 8  
89B C20 C19 SING N N 9  
89B C20 N21 SING N N 10 
89B C19 C18 SING N N 11 
89B N21 C22 SING N N 12 
89B N27 C26 SING N N 13 
89B O35 C26 DOUB N N 14 
89B C18 C17 SING N N 15 
89B C26 C24 SING N N 16 
89B C22 C17 SING N N 17 
89B C22 O23 DOUB N N 18 
89B C16 C17 SING N N 19 
89B C16 C15 SING N N 20 
89B C24 C15 SING N N 21 
89B C24 O25 SING N N 22 
89B C15 N14 SING N N 23 
89B O36 C13 DOUB N N 24 
89B N14 C13 SING N N 25 
89B C13 C04 SING N N 26 
89B O01 C02 DOUB N N 27 
89B C02 C37 SING N N 28 
89B C02 N03 SING N N 29 
89B C38 C37 DOUB Y N 30 
89B C38 C39 SING Y N 31 
89B C04 N03 SING N N 32 
89B C04 C05 SING N N 33 
89B C37 O45 SING Y N 34 
89B C39 C40 DOUB Y N 35 
89B C39 C44 SING Y N 36 
89B C40 C41 SING Y N 37 
89B O45 C44 SING Y N 38 
89B C05 C06 SING N N 39 
89B C44 C43 DOUB Y N 40 
89B C41 C42 DOUB Y N 41 
89B C43 C42 SING Y N 42 
89B C06 C12 DOUB Y N 43 
89B C06 C07 SING Y N 44 
89B C12 C11 SING Y N 45 
89B C07 C08 DOUB Y N 46 
89B C11 C09 DOUB Y N 47 
89B C08 C09 SING Y N 48 
89B C09 F10 SING N N 49 
89B N03 H1  SING N N 50 
89B C04 H2  SING N N 51 
89B C05 H3  SING N N 52 
89B C05 H4  SING N N 53 
89B C07 H5  SING N N 54 
89B C08 H6  SING N N 55 
89B C11 H7  SING N N 56 
89B C12 H8  SING N N 57 
89B N14 H9  SING N N 58 
89B C15 H10 SING N N 59 
89B C16 H11 SING N N 60 
89B C16 H12 SING N N 61 
89B C17 H13 SING N N 62 
89B C18 H14 SING N N 63 
89B C18 H15 SING N N 64 
89B C19 H16 SING N N 65 
89B C19 H17 SING N N 66 
89B C20 H18 SING N N 67 
89B C20 H19 SING N N 68 
89B N21 H20 SING N N 69 
89B C24 H21 SING N N 70 
89B O25 H22 SING N N 71 
89B N27 H23 SING N N 72 
89B C28 H24 SING N N 73 
89B C28 H25 SING N N 74 
89B C30 H26 SING N N 75 
89B C31 H27 SING N N 76 
89B C32 H28 SING N N 77 
89B C33 H29 SING N N 78 
89B C34 H30 SING N N 79 
89B C38 H31 SING N N 80 
89B C40 H32 SING N N 81 
89B C41 H33 SING N N 82 
89B C42 H34 SING N N 83 
89B C43 H35 SING N N 84 
# 
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 
89B InChI            InChI                1.03  "InChI=1S/C34H35FN4O6/c35-25-14-12-21(13-15-25)17-27(39-33(43)29-19-23-9-4-5-11-28(23)45-29)32(42)38-26(18-24-10-6-16-36-31(24)41)30(40)34(44)37-20-22-7-2-1-3-8-22/h1-5,7-9,11-15,19,24,26-27,30,40H,6,10,16-18,20H2,(H,36,41)(H,37,44)(H,38,42)(H,39,43)/t24-,26+,27-,30-/m0/s1" 
89B InChIKey         InChI                1.03  RXCWWLZLSPDOKP-SNJIXJEUSA-N                                                                                                                                                                                                                                                        
89B SMILES_CANONICAL CACTVS               3.385 "O[C@@H]([C@@H](C[C@@H]1CCCNC1=O)NC(=O)[C@H](Cc2ccc(F)cc2)NC(=O)c3oc4ccccc4c3)C(=O)NCc5ccccc5"                                                                                                                                                                                     
89B SMILES           CACTVS               3.385 "O[CH]([CH](C[CH]1CCCNC1=O)NC(=O)[CH](Cc2ccc(F)cc2)NC(=O)c3oc4ccccc4c3)C(=O)NCc5ccccc5"                                                                                                                                                                                            
89B SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1ccc(cc1)CNC(=O)[C@H]([C@@H](C[C@@H]2CCCNC2=O)NC(=O)[C@H](Cc3ccc(cc3)F)NC(=O)c4cc5ccccc5o4)O"                                                                                                                                                                                    
89B SMILES           "OpenEye OEToolkits" 2.0.7 "c1ccc(cc1)CNC(=O)C(C(CC2CCCNC2=O)NC(=O)C(Cc3ccc(cc3)F)NC(=O)c4cc5ccccc5o4)O"                                                                                                                                                                                                      
# 
_pdbx_chem_comp_identifier.comp_id           89B 
_pdbx_chem_comp_identifier.type              "SYSTEMATIC NAME" 
_pdbx_chem_comp_identifier.program           "OpenEye OEToolkits" 
_pdbx_chem_comp_identifier.program_version   2.0.7 
_pdbx_chem_comp_identifier.identifier        "~{N}-[(2~{S})-3-(4-fluorophenyl)-1-oxidanylidene-1-[[(2~{R},3~{S})-3-oxidanyl-4-oxidanylidene-1-[(3~{S})-2-oxidanylidenepiperidin-3-yl]-4-[(phenylmethyl)amino]butan-2-yl]amino]propan-2-yl]-1-benzofuran-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 
89B "Create component" 2021-11-30 PDBJ 
89B "Initial release"  2023-05-31 RCSB 
89B "Modify PCM"       2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            89B 
_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               C24 
_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      ? 
# 
