data_WBK
# 
_chem_comp.id                                    WBK 
_chem_comp.name                                  "2-cyano-D-phenylalanyl-2,4-dichloro-N-[(2S)-4-{[5-(dimethylamino)pentyl]amino}-1-(4-fluorophenyl)-4-oxobutan-2-yl]-D-phenylalaninamide" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C36 H43 Cl2 F N6 O3" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-09-29 
_chem_comp.pdbx_modified_date                    2024-12-27 
_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                        697.669 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     WBK 
_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        8UDO 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  RCSB 
_chem_comp.pdbx_pcm                              ? 
# 
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 
WBK C2  C1  C  0 1 N N R N N N 10.487 -2.065  22.402 -0.604 0.058  -0.826 C2  WBK 1  
WBK C3  C2  C  0 1 N N N N N N 10.711 -1.867  23.771 -1.003 0.269  -2.288 C3  WBK 2  
WBK C4  C3  C  0 1 Y N N N N N 9.725  -0.781  24.321 -1.612 1.638  -2.450 C4  WBK 3  
WBK C5  C4  C  0 1 Y N N N N N 8.472  -1.157  24.800 -2.930 1.856  -2.089 C5  WBK 4  
WBK C6  C5  C  0 1 Y N N N N N 7.588  -0.201  25.280 -3.489 3.113  -2.237 C6  WBK 5  
WBK C11 C6  C  0 1 N N S N N N 11.205 -5.491  21.314 1.955  -2.760 -1.236 C11 WBK 6  
WBK C13 C7  C  0 1 Y N N N N N 10.733 -6.447  23.576 -0.078 -4.058 -1.811 C13 WBK 7  
WBK C14 C8  C  0 1 Y N N N N N 11.897 -6.792  24.253 -1.103 -3.293 -2.336 C14 WBK 8  
WBK C15 C9  C  0 1 Y N N N N N 11.989 -6.561  25.621 -2.412 -3.554 -1.979 C15 WBK 9  
WBK CL1 CL1 CL 0 0 N N N N N N 7.977  -2.814  24.797 -3.882 0.552  -1.450 CL1 WBK 10 
WBK C17 C10 C  0 1 Y N N N N N 9.763  -5.644  25.628 -1.670 -5.347 -0.572 C17 WBK 11 
WBK C18 C11 C  0 1 Y N N N N N 9.668  -5.876  24.264 -0.361 -5.084 -0.929 C18 WBK 12 
WBK C19 C12 C  0 1 N N N N N N 11.036 -5.689  19.792 3.438  -2.567 -1.560 C19 WBK 13 
WBK CL2 CL2 CL 0 0 N N N N N N 6.821  2.303   25.897 -3.430 5.729  -2.932 CL2 WBK 14 
WBK C1  C13 C  0 1 N N N N N N 10.037 -0.262  20.821 -2.325 1.211  0.456  C1  WBK 15 
WBK C10 C14 C  0 1 N N N N N N 11.169 -3.136  21.991 0.116  -1.258 -0.687 C10 WBK 16 
WBK C12 C15 C  0 1 N N N N N N 10.625 -6.697  22.043 1.349  -3.776 -2.206 C12 WBK 17 
WBK C16 C16 C  0 1 Y N N N N N 10.923 -5.989  26.308 -2.697 -4.582 -1.096 C16 WBK 18 
WBK C20 C17 C  0 1 N N N N N N 11.829 -6.963  19.337 4.063  -1.661 -0.531 C20 WBK 19 
WBK C21 C18 C  0 1 N N N N N N 11.998 -9.028  18.001 5.979  -0.467 0.385  C21 WBK 20 
WBK C22 C19 C  0 1 N N N N N N 10.917 -10.115 17.679 7.463  -0.275 0.062  C22 WBK 21 
WBK C23 C20 C  0 1 N N N N N N 10.995 -10.576 16.197 8.097  0.646  1.106  C23 WBK 22 
WBK C24 C21 C  0 1 N N N N N N 9.907  -11.657 15.944 9.580  0.838  0.783  C24 WBK 23 
WBK C25 C22 C  0 1 N N R N N N 10.477 1.042   20.099 -3.561 1.201  1.318  C25 WBK 24 
WBK C26 C23 C  0 1 N N N N N N 10.279 0.902   18.590 -3.175 0.867  2.760  C26 WBK 25 
WBK C27 C24 C  0 1 Y N N N N N 11.069 -0.324  18.052 -4.421 0.737  3.597  C27 WBK 26 
WBK C28 C25 C  0 1 Y N N N N N 10.463 -1.166  17.130 -5.107 -0.478 3.647  C28 WBK 27 
WBK C29 C26 C  0 1 N N N N N N 9.042  -0.880  16.662 -4.632 -1.604 2.899  C29 WBK 28 
WBK C30 C27 C  0 1 Y N N N N N 11.248 -2.369  16.596 -6.258 -0.592 4.430  C30 WBK 29 
WBK C31 C28 C  0 1 Y N N N N N 12.541 -2.570  17.071 -6.709 0.496  5.148  C31 WBK 30 
WBK C32 C29 C  0 1 Y N N N N N 13.089 -1.684  18.001 -6.025 1.697  5.094  C32 WBK 31 
WBK C33 C30 C  0 1 Y N N N N N 12.373 -0.586  18.478 -4.884 1.816  4.321  C33 WBK 32 
WBK C34 C31 C  0 1 N N N N N N 10.533 -12.923 15.302 10.215 1.758  1.827  C34 WBK 33 
WBK C35 C32 C  0 1 N N N N N N 9.064  -12.662 13.413 12.227 3.000  2.350  C35 WBK 34 
WBK C36 C33 C  0 1 N N N N N N 10.055 -14.793 13.867 12.378 0.682  1.666  C36 WBK 35 
WBK C7  C34 C  0 1 Y N N N N N 7.949  1.138   25.290 -2.730 4.151  -2.746 C7  WBK 36 
WBK C8  C35 C  0 1 Y N N N N N 9.201  1.523   24.813 -1.412 3.932  -3.107 C8  WBK 37 
WBK C9  C36 C  0 1 Y N N N N N 10.088 0.564   24.329 -0.853 2.677  -2.954 C9  WBK 38 
WBK F1  F1  F  0 1 N N N N N N 11.012 -5.764  27.636 -3.977 -4.837 -0.746 F1  WBK 39 
WBK N1  N1  N  0 1 N N N N N N 10.865 -0.851  21.682 -1.805 0.049  0.012  N1  WBK 40 
WBK N2  N2  N  0 1 N N N N N N 10.518 -4.276  21.745 1.256  -1.479 -1.372 N2  WBK 41 
WBK N3  N3  N  0 1 N N N N N N 11.275 -7.801  18.464 5.372  -1.348 -0.615 N3  WBK 42 
WBK N4  N4  N  0 1 N N N N N N 9.508  -13.580 14.462 11.639 1.943  1.516  N4  WBK 43 
WBK N5  N5  N  0 1 N N N N N N 9.670  2.124   20.571 -4.197 2.525  1.276  N5  WBK 44 
WBK N6  N6  N  0 1 N N N N N N 8.004  -0.679  16.313 -4.255 -2.496 2.306  N6  WBK 45 
WBK O1  O1  O  0 1 N N N N N N 8.972  -0.732  20.595 -1.799 2.263  0.162  O1  WBK 46 
WBK O2  O2  O  0 1 N N N N N N 12.914 -7.179  19.768 3.389  -1.213 0.372  O2  WBK 47 
WBK O3  O3  O  0 1 N N N N N N 12.346 -3.080  21.861 -0.331 -2.120 0.040  O3  WBK 48 
WBK H1  H1  H  0 1 N N N N N N 9.411  -2.230  22.243 0.055  0.867  -0.509 H1  WBK 49 
WBK H2  H2  H  0 1 N N N N N N 10.548 -2.813  24.308 -0.120 0.188  -2.922 H2  WBK 50 
WBK H3  H3  H  0 1 N N N N N N 11.747 -1.531  23.926 -1.730 -0.488 -2.579 H3  WBK 51 
WBK H4  H4  H  0 1 N N N N N N 6.617  -0.500  25.646 -4.517 3.283  -1.955 H4  WBK 52 
WBK H5  H5  H  0 1 N N N N N N 12.278 -5.415  21.544 1.850  -3.124 -0.215 H5  WBK 53 
WBK H6  H6  H  0 1 N N N N N N 12.724 -7.237  23.720 -0.881 -2.492 -3.025 H6  WBK 54 
WBK H7  H7  H  0 1 N N N N N N 12.891 -6.827  26.152 -3.213 -2.956 -2.388 H7  WBK 55 
WBK H8  H8  H  0 1 N N N N N N 8.937  -5.196  26.160 -1.891 -6.149 0.117  H8  WBK 56 
WBK H9  H9  H  0 1 N N N N N N 8.764  -5.612  23.735 0.441  -5.681 -0.520 H9  WBK 57 
WBK H10 H10 H  0 1 N N N N N N 11.425 -4.807  19.262 3.941  -3.534 -1.546 H10 WBK 58 
WBK H11 H11 H  0 1 N N N N N N 9.969  -5.818  19.556 3.539  -2.119 -2.549 H11 WBK 59 
WBK H12 H12 H  0 1 N N N N N N 9.570  -6.828  21.762 1.373  -3.373 -3.218 H12 WBK 60 
WBK H13 H13 H  0 1 N N N N N N 11.191 -7.601  21.774 1.925  -4.701 -2.169 H13 WBK 61 
WBK H14 H14 H  0 1 N N N N N N 12.670 -9.389  18.793 5.878  -0.915 1.374  H14 WBK 62 
WBK H15 H15 H  0 1 N N N N N N 12.584 -8.801  17.098 5.476  0.500  0.372  H15 WBK 63 
WBK H16 H16 H  0 1 N N N N N N 9.919  -9.694  17.870 7.966  -1.242 0.075  H16 WBK 64 
WBK H17 H17 H  0 1 N N N N N N 11.079 -10.985 18.333 7.564  0.173  -0.927 H17 WBK 65 
WBK H18 H18 H  0 1 N N N N N N 11.990 -11.000 15.995 7.594  1.612  1.092  H18 WBK 66 
WBK H19 H19 H  0 1 N N N N N N 10.821 -9.716  15.534 7.996  0.197  2.095  H19 WBK 67 
WBK H20 H20 H  0 1 N N N N N N 9.143  -11.249 15.267 10.083 -0.129 0.796  H20 WBK 68 
WBK H21 H21 H  0 1 N N N N N N 9.440  -11.931 16.902 9.681  1.286  -0.206 H21 WBK 69 
WBK H22 H22 H  0 1 N N N N N N 11.540 1.228   20.311 -4.259 0.451  0.946  H22 WBK 70 
WBK H23 H23 H  0 1 N N N N N N 10.640 1.813   18.091 -2.624 -0.074 2.780  H23 WBK 71 
WBK H24 H24 H  0 1 N N N N N N 9.209  0.766   18.376 -2.548 1.663  3.163  H24 WBK 72 
WBK H25 H25 H  0 1 N N N N N N 10.811 -3.041  15.872 -6.793 -1.529 4.472  H25 WBK 73 
WBK H26 H26 H  0 1 N N N N N N 13.120 -3.411  16.720 -7.600 0.410  5.753  H26 WBK 74 
WBK H27 H27 H  0 1 N N N N N N 14.093 -1.853  18.360 -6.383 2.546  5.658  H27 WBK 75 
WBK H28 H28 H  0 1 N N N N N N 12.838 0.077   19.193 -4.352 2.756  4.287  H28 WBK 76 
WBK H29 H29 H  0 1 N N N N N N 10.864 -13.614 16.091 9.712  2.725  1.813  H29 WBK 77 
WBK H30 H30 H  0 1 N N N N N N 11.394 -12.636 14.680 10.114 1.310  2.816  H30 WBK 78 
WBK H31 H31 H  0 1 N N N N N N 8.653  -11.751 13.872 13.281 3.115  2.099  H31 WBK 79 
WBK H32 H32 H  0 1 N N N N N N 9.918  -12.397 12.772 11.705 3.939  2.167  H32 WBK 80 
WBK H33 H33 H  0 1 N N N N N N 8.287  -13.148 12.805 12.131 2.729  3.401  H33 WBK 81 
WBK H34 H34 H  0 1 N N N N N N 10.386 -15.476 14.664 12.347 0.364  2.708  H34 WBK 82 
WBK H35 H35 H  0 1 N N N N N N 9.281  -15.285 13.260 11.922 -0.083 1.038  H35 WBK 83 
WBK H36 H36 H  0 1 N N N N N N 10.912 -14.534 13.228 13.415 0.830  1.362  H36 WBK 84 
WBK H37 H37 H  0 1 N N N N N N 9.484  2.565   24.819 -0.820 4.743  -3.505 H37 WBK 85 
WBK H38 H38 H  0 1 N N N N N N 11.058 0.863   23.960 0.177  2.508  -3.232 H38 WBK 86 
WBK H39 H39 H  0 1 N N N N N N 11.768 -0.452  21.840 -2.226 -0.792 0.247  H39 WBK 87 
WBK H40 H40 H  0 1 N N N N N N 9.525  -4.299  21.860 1.613  -0.790 -1.954 H40 WBK 88 
WBK H41 H41 H  0 1 N N N N N N 10.360 -7.608  18.111 5.911  -1.707 -1.337 H41 WBK 89 
WBK H43 H43 H  0 1 N N N N N N 9.792  2.225   21.558 -3.570 3.238  1.617  H43 WBK 90 
WBK H44 H44 H  0 1 N N N N N N 9.945  2.969   20.113 -4.520 2.742  0.345  H44 WBK 91 
# 
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 
WBK C35 N4  SING N N 1  
WBK C36 N4  SING N N 2  
WBK N4  C34 SING N N 3  
WBK C34 C24 SING N N 4  
WBK C24 C23 SING N N 5  
WBK C23 C22 SING N N 6  
WBK N6  C29 TRIP N N 7  
WBK C30 C31 DOUB Y N 8  
WBK C30 C28 SING Y N 9  
WBK C29 C28 SING N N 10 
WBK C31 C32 SING Y N 11 
WBK C28 C27 DOUB Y N 12 
WBK C22 C21 SING N N 13 
WBK C32 C33 DOUB Y N 14 
WBK C21 N3  SING N N 15 
WBK C27 C33 SING Y N 16 
WBK C27 C26 SING N N 17 
WBK N3  C20 SING N N 18 
WBK C26 C25 SING N N 19 
WBK C20 O2  DOUB N N 20 
WBK C20 C19 SING N N 21 
WBK C19 C11 SING N N 22 
WBK C25 N5  SING N N 23 
WBK C25 C1  SING N N 24 
WBK O1  C1  DOUB N N 25 
WBK C1  N1  SING N N 26 
WBK C11 N2  SING N N 27 
WBK C11 C12 SING N N 28 
WBK N1  C2  SING N N 29 
WBK N2  C10 SING N N 30 
WBK O3  C10 DOUB N N 31 
WBK C10 C2  SING N N 32 
WBK C12 C13 SING N N 33 
WBK C2  C3  SING N N 34 
WBK C13 C14 DOUB Y N 35 
WBK C13 C18 SING Y N 36 
WBK C3  C4  SING N N 37 
WBK C14 C15 SING Y N 38 
WBK C18 C17 DOUB Y N 39 
WBK C4  C9  DOUB Y N 40 
WBK C4  C5  SING Y N 41 
WBK C9  C8  SING Y N 42 
WBK CL1 C5  SING N N 43 
WBK C5  C6  DOUB Y N 44 
WBK C8  C7  DOUB Y N 45 
WBK C6  C7  SING Y N 46 
WBK C7  CL2 SING N N 47 
WBK C15 C16 DOUB Y N 48 
WBK C17 C16 SING Y N 49 
WBK C16 F1  SING N N 50 
WBK C2  H1  SING N N 51 
WBK C3  H2  SING N N 52 
WBK C3  H3  SING N N 53 
WBK C6  H4  SING N N 54 
WBK C11 H5  SING N N 55 
WBK C14 H6  SING N N 56 
WBK C15 H7  SING N N 57 
WBK C17 H8  SING N N 58 
WBK C18 H9  SING N N 59 
WBK C19 H10 SING N N 60 
WBK C19 H11 SING N N 61 
WBK C12 H12 SING N N 62 
WBK C12 H13 SING N N 63 
WBK C21 H14 SING N N 64 
WBK C21 H15 SING N N 65 
WBK C22 H16 SING N N 66 
WBK C22 H17 SING N N 67 
WBK C23 H18 SING N N 68 
WBK C23 H19 SING N N 69 
WBK C24 H20 SING N N 70 
WBK C24 H21 SING N N 71 
WBK C25 H22 SING N N 72 
WBK C26 H23 SING N N 73 
WBK C26 H24 SING N N 74 
WBK C30 H25 SING N N 75 
WBK C31 H26 SING N N 76 
WBK C32 H27 SING N N 77 
WBK C33 H28 SING N N 78 
WBK C34 H29 SING N N 79 
WBK C34 H30 SING N N 80 
WBK C35 H31 SING N N 81 
WBK C35 H32 SING N N 82 
WBK C35 H33 SING N N 83 
WBK C36 H34 SING N N 84 
WBK C36 H35 SING N N 85 
WBK C36 H36 SING N N 86 
WBK C8  H37 SING N N 87 
WBK C9  H38 SING N N 88 
WBK N1  H39 SING N N 89 
WBK N2  H40 SING N N 90 
WBK N3  H41 SING N N 91 
WBK N5  H43 SING N N 92 
WBK N5  H44 SING N N 93 
# 
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 
WBK SMILES           ACDLabs              12.01 "Clc1cc(Cl)ccc1CC(NC(=O)C(N)Cc1ccccc1C#N)C(=O)NC(Cc1ccc(F)cc1)CC(=O)NCCCCCN(C)C"                                                                                                                                                                                           
WBK InChI            InChI                1.06  "InChI=1S/C36H43Cl2FN6O3/c1-45(2)17-7-3-6-16-42-34(46)22-30(18-24-10-14-29(39)15-11-24)43-36(48)33(20-26-12-13-28(37)21-31(26)38)44-35(47)32(41)19-25-8-4-5-9-27(25)23-40/h4-5,8-15,21,30,32-33H,3,6-7,16-20,22,41H2,1-2H3,(H,42,46)(H,43,48)(H,44,47)/t30-,32+,33+/m0/s1" 
WBK InChIKey         InChI                1.06  RRTRGOYSEXBKKY-FCIJAXDVSA-N                                                                                                                                                                                                                                                
WBK SMILES_CANONICAL CACTVS               3.385 "CN(C)CCCCCNC(=O)C[C@H](Cc1ccc(F)cc1)NC(=O)[C@@H](Cc2ccc(Cl)cc2Cl)NC(=O)[C@H](N)Cc3ccccc3C#N"                                                                                                                                                                              
WBK SMILES           CACTVS               3.385 "CN(C)CCCCCNC(=O)C[CH](Cc1ccc(F)cc1)NC(=O)[CH](Cc2ccc(Cl)cc2Cl)NC(=O)[CH](N)Cc3ccccc3C#N"                                                                                                                                                                                  
WBK SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CN(C)CCCCCNC(=O)C[C@H](Cc1ccc(cc1)F)NC(=O)[C@@H](Cc2ccc(cc2Cl)Cl)NC(=O)[C@@H](Cc3ccccc3C#N)N"                                                                                                                                                                             
WBK SMILES           "OpenEye OEToolkits" 2.0.7 "CN(C)CCCCCNC(=O)CC(Cc1ccc(cc1)F)NC(=O)C(Cc2ccc(cc2Cl)Cl)NC(=O)C(Cc3ccccc3C#N)N"                                                                                                                                                                                           
# 
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 
WBK "SYSTEMATIC NAME" ACDLabs              12.01 "2-cyano-D-phenylalanyl-2,4-dichloro-N-[(2S)-4-{[5-(dimethylamino)pentyl]amino}-1-(4-fluorophenyl)-4-oxobutan-2-yl]-D-phenylalaninamide"                                        
WBK "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "(3~{S})-3-[[(2~{R})-2-[[(2~{R})-2-azanyl-3-(2-cyanophenyl)propanoyl]amino]-3-(2,4-dichlorophenyl)propanoyl]amino]-~{N}-[5-(dimethylamino)pentyl]-4-(4-fluorophenyl)butanamide" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
WBK "Create component" 2023-09-29 RCSB 
WBK "Initial release"  2025-01-01 RCSB 
# 
