data_WDK
# 
_chem_comp.id                                    WDK 
_chem_comp.name                                  "2-cyano-D-phenylalanyl-2,4-dichloro-N-[(2S)-4-{[3-(dimethylamino)propyl]amino}-1-(4-fluorophenyl)-4-oxobutan-2-yl]-D-phenylalaninamide" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C34 H39 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                     2023-10-02 
_chem_comp.pdbx_modified_date                    2024-12-20 
_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                        669.616 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     WDK 
_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        8UDW 
_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 
WDK C1  C1  C  0 1 N N N N N N -11.416 13.560 67.374 2.196   0.885  -0.619 C1  WDK 1  
WDK C10 C2  C  0 1 N N N N N N -10.070 10.683 68.514 -0.607  -1.025 0.746  C10 WDK 2  
WDK C11 C3  C  0 1 N N S N N N -9.916  8.345  67.833 -2.644  -2.198 1.386  C11 WDK 3  
WDK C12 C4  C  0 1 N N N N N N -10.573 7.100  68.432 -2.264  -2.972 2.650  C12 WDK 4  
WDK C13 C5  C  0 1 Y N N N N N -10.473 7.256  69.950 -0.839  -3.447 2.539  C13 WDK 5  
WDK C14 C6  C  0 1 Y N N N N N -11.547 7.761  70.669 -0.563  -4.679 1.974  C14 WDK 6  
WDK C15 C7  C  0 1 Y N N N N N -11.459 7.914  72.045 0.744   -5.115 1.871  C15 WDK 7  
WDK C16 C8  C  0 1 Y N N N N N -10.291 7.563  72.707 1.778   -4.319 2.334  C16 WDK 8  
WDK C17 C9  C  0 1 Y N N N N N -9.211  7.055  71.992 1.500   -3.086 2.900  C17 WDK 9  
WDK C18 C10 C  0 1 Y N N N N N -9.302  6.904  70.612 0.193   -2.649 2.997  C18 WDK 10 
WDK C19 C11 C  0 1 N N N N N N -9.913  8.286  66.308 -4.126  -1.823 1.443  C19 WDK 11 
WDK C2  C12 C  0 1 N N R N N N -10.914 11.847 69.023 0.226   0.228  0.656  C2  WDK 12 
WDK C20 C13 C  0 1 N N N N N N -9.078  7.101  65.816 -4.529  -1.169 0.146  C20 WDK 13 
WDK C21 C14 C  0 1 N N N N N N -8.936  4.988  64.574 -6.191  -0.117 -1.293 C21 WDK 14 
WDK C22 C15 C  0 1 N N N N N N -9.934  3.867  64.270 -7.673  0.257  -1.235 C22 WDK 15 
WDK C23 C16 C  0 1 N N N N N N -9.350  2.820  63.314 -8.082  0.921  -2.552 C23 WDK 16 
WDK C24 C17 C  0 1 N N N N N N -8.276  2.612  61.193 -9.879  2.128  -3.638 C24 WDK 17 
WDK C25 C18 C  0 1 N N N N N N -10.618 2.988  61.286 -10.350 0.081  -2.433 C25 WDK 18 
WDK C26 C19 C  0 1 N N R N N N -10.984 14.807 66.607 3.516   0.566  -1.272 C26 WDK 19 
WDK C27 C20 C  0 1 N N N N N N -11.224 14.622 65.092 3.266   -0.100 -2.627 C27 WDK 20 
WDK C28 C21 C  0 1 Y N N N N N -10.411 13.417 64.614 4.581   -0.530 -3.225 C28 WDK 21 
WDK C29 C22 C  0 1 Y N N N N N -10.980 12.434 63.814 5.137   -1.763 -2.878 C29 WDK 22 
WDK C3  C23 C  0 1 N N N N N N -10.611 12.080 70.503 0.472   0.779  2.062  C3  WDK 23 
WDK C30 C24 C  0 1 N N N N N N -12.435 12.558 63.390 4.464   -2.620 -1.951 C30 WDK 24 
WDK C31 C25 C  0 1 Y N N N N N -10.236 11.336 63.386 6.353   -2.156 -3.441 C31 WDK 25 
WDK C32 C26 C  0 1 Y N N N N N -8.905  11.219 63.780 6.997   -1.325 -4.335 C32 WDK 26 
WDK C33 C27 C  0 1 Y N N N N N -8.328  12.196 64.589 6.440   -0.104 -4.674 C33 WDK 27 
WDK C34 C28 C  0 1 Y N N N N N -9.076  13.291 65.008 5.235   0.292  -4.120 C34 WDK 28 
WDK C4  C29 C  0 1 Y N N N N N -11.690 13.005 71.067 1.198   2.096  1.965  C4  WDK 29 
WDK C5  C30 C  0 1 Y N N N N N -12.834 12.469 71.654 0.485   3.267  1.775  C5  WDK 30 
WDK C6  C31 C  0 1 Y N N N N N -13.818 13.306 72.157 1.151   4.476  1.687  C6  WDK 31 
WDK C7  C32 C  0 1 Y N N N N N -13.672 14.680 72.069 2.531   4.514  1.788  C7  WDK 32 
WDK C8  C33 C  0 1 Y N N N N N -12.531 15.222 71.477 3.242   3.343  1.977  C8  WDK 33 
WDK C9  C34 C  0 1 Y N N N N N -11.541 14.385 70.978 2.575   2.135  2.072  C9  WDK 34 
WDK CL1 CL1 CL 0 0 N N N N N N -13.063 10.760 71.775 -1.246  3.218  1.648  CL1 WDK 35 
WDK CL2 CL2 CL 0 0 N N N N N N -14.926 15.691 72.702 3.368   6.030  1.676  CL2 WDK 36 
WDK F1  F1  F  0 1 N N N N N N -10.216 7.718  74.042 3.056   -4.745 2.235  F1  WDK 37 
WDK N1  N1  N  0 1 N N N N N N -10.580 13.030 68.258 1.509   -0.082 0.021  N1  WDK 38 
WDK N2  N2  N  0 1 N N N N N N -10.651 9.504  68.303 -1.835  -0.980 1.298  N2  WDK 39 
WDK N3  N3  N  0 1 N N N N N N -9.660  6.146  65.082 -5.799  -0.753 -0.032 N3  WDK 40 
WDK N4  N4  N  0 1 N N N N N N -9.344  3.277  61.926 -9.505  1.281  -2.497 N4  WDK 41 
WDK N5  N5  N  0 1 N N N N N N -11.706 15.955 67.138 4.277   1.807  -1.469 N5  WDK 42 
WDK N6  N6  N  0 1 N N N N N N -13.494 12.639 63.083 3.929   -3.301 -1.215 N6  WDK 43 
WDK O1  O1  O  0 1 N N N N N N -12.482 13.070 67.171 1.754   2.014  -0.664 O1  WDK 44 
WDK O2  O2  O  0 1 N N N N N N -7.924  7.046  66.083 -3.712  -1.018 -0.737 O2  WDK 45 
WDK O3  O3  O  0 1 N N N N N N -8.910  10.838 68.314 -0.170  -2.074 0.322  O3  WDK 46 
WDK H1  H1  H  0 1 N N N N N N -8.875  8.398  68.186 -2.460  -2.820 0.510  H1  WDK 47 
WDK H2  H2  H  0 1 N N N N N N -11.627 7.039  68.123 -2.364  -2.321 3.518  H2  WDK 48 
WDK H3  H3  H  0 1 N N N N N N -10.042 6.194  68.106 -2.926  -3.831 2.762  H3  WDK 49 
WDK H4  H4  H  0 1 N N N N N N -12.456 8.036  70.155 -1.369  -5.300 1.613  H4  WDK 50 
WDK H5  H5  H  0 1 N N N N N N -12.298 8.306  72.600 0.959   -6.077 1.430  H5  WDK 51 
WDK H6  H6  H  0 1 N N N N N N -8.303  6.778  72.508 2.306   -2.464 3.262  H6  WDK 52 
WDK H7  H7  H  0 1 N N N N N N -8.463  6.513  70.055 -0.023  -1.686 3.434  H7  WDK 53 
WDK H8  H8  H  0 1 N N N N N N -9.486  9.219  65.911 -4.723  -2.722 1.597  H8  WDK 54 
WDK H9  H9  H  0 1 N N N N N N -10.947 8.174  65.949 -4.294  -1.130 2.267  H9  WDK 55 
WDK H10 H10 H  0 1 N N N N N N -11.980 11.602 68.905 -0.303  0.974  0.061  H10 WDK 56 
WDK H11 H11 H  0 1 N N N N N N -8.215  4.644  65.330 -6.023  -0.811 -2.117 H11 WDK 57 
WDK H12 H12 H  0 1 N N N N N N -8.400  5.263  63.654 -5.594  0.782  -1.447 H12 WDK 58 
WDK H13 H13 H  0 1 N N N N N N -10.832 4.306  63.810 -8.269  -0.642 -1.081 H13 WDK 59 
WDK H14 H14 H  0 1 N N N N N N -10.210 3.372  65.213 -7.841  0.951  -0.411 H14 WDK 60 
WDK H15 H15 H  0 1 N N N N N N -9.954  1.903  63.382 -7.486  1.820  -2.706 H15 WDK 61 
WDK H16 H16 H  0 1 N N N N N N -8.316  2.601  63.619 -7.914  0.228  -3.376 H16 WDK 62 
WDK H17 H17 H  0 1 N N N N N N -7.311  2.828  61.674 -10.937 2.379  -3.572 H17 WDK 63 
WDK H18 H18 H  0 1 N N N N N N -8.451  1.526  61.195 -9.286  3.042  -3.621 H18 WDK 64 
WDK H19 H19 H  0 1 N N N N N N -8.259  2.979  60.156 -9.690  1.589  -4.567 H19 WDK 65 
WDK H20 H20 H  0 1 N N N N N N -11.428 3.489  61.837 -10.231 -0.496 -3.350 H20 WDK 66 
WDK H21 H21 H  0 1 N N N N N N -10.599 3.355  60.249 -10.052 -0.528 -1.579 H21 WDK 67 
WDK H22 H22 H  0 1 N N N N N N -10.791 1.902  61.288 -11.393 0.376  -2.323 H22 WDK 68 
WDK H23 H23 H  0 1 N N N N N N -9.905  14.953 66.766 4.083   -0.111 -0.633 H23 WDK 69 
WDK H24 H24 H  0 1 N N N N N N -10.901 15.525 64.552 2.627   -0.971 -2.491 H24 WDK 70 
WDK H25 H25 H  0 1 N N N N N N -12.294 14.446 64.905 2.778   0.609  -3.296 H25 WDK 71 
WDK H26 H26 H  0 1 N N N N N N -10.623 11.121 71.042 -0.482  0.927  2.567  H26 WDK 72 
WDK H27 H27 H  0 1 N N N N N N -9.622  12.550 70.612 1.077   0.071  2.628  H27 WDK 73 
WDK H28 H28 H  0 1 N N N N N N -10.687 10.584 62.756 6.789   -3.108 -3.178 H28 WDK 74 
WDK H29 H29 H  0 1 N N N N N N -8.320  10.370 63.458 7.937   -1.628 -4.771 H29 WDK 75 
WDK H30 H30 H  0 1 N N N N N N -7.296  12.102 64.892 6.948   0.543  -5.374 H30 WDK 76 
WDK H31 H31 H  0 1 N N N N N N -8.625  14.044 65.638 4.804   1.244  -4.392 H31 WDK 77 
WDK H32 H32 H  0 1 N N N N N N -14.700 12.886 72.618 0.595   5.390  1.538  H32 WDK 78 
WDK H33 H33 H  0 1 N N N N N N -12.417 16.294 71.407 4.319   3.372  2.056  H33 WDK 79 
WDK H34 H34 H  0 1 N N N N N N -10.657 14.805 70.522 3.131   1.222  2.224  H34 WDK 80 
WDK H35 H35 H  0 1 N N N N N N -9.690  13.462 68.401 1.864   -0.984 0.060  H35 WDK 81 
WDK H36 H36 H  0 1 N N N N N N -11.632 9.414  68.475 -2.184  -0.141 1.637  H36 WDK 82 
WDK H37 H37 H  0 1 N N N N N N -10.634 6.230  64.873 -6.453  -0.874 0.674  H37 WDK 83 
WDK H39 H39 H  0 1 N N N N N N -11.525 16.039 68.118 5.193   1.613  -1.846 H39 WDK 84 
WDK H40 H40 H  0 1 N N N N N N -11.402 16.785 66.670 3.772   2.451  -2.058 H40 WDK 85 
# 
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 
WDK C24 N4  SING N N 1  
WDK C25 N4  SING N N 2  
WDK N4  C23 SING N N 3  
WDK N6  C30 TRIP N N 4  
WDK C23 C22 SING N N 5  
WDK C31 C32 DOUB Y N 6  
WDK C31 C29 SING Y N 7  
WDK C30 C29 SING N N 8  
WDK C32 C33 SING Y N 9  
WDK C29 C28 DOUB Y N 10 
WDK C22 C21 SING N N 11 
WDK C21 N3  SING N N 12 
WDK C33 C34 DOUB Y N 13 
WDK C28 C34 SING Y N 14 
WDK C28 C27 SING N N 15 
WDK N3  C20 SING N N 16 
WDK C27 C26 SING N N 17 
WDK C20 O2  DOUB N N 18 
WDK C20 C19 SING N N 19 
WDK C19 C11 SING N N 20 
WDK C26 N5  SING N N 21 
WDK C26 C1  SING N N 22 
WDK O1  C1  DOUB N N 23 
WDK C1  N1  SING N N 24 
WDK C11 N2  SING N N 25 
WDK C11 C12 SING N N 26 
WDK N1  C2  SING N N 27 
WDK N2  C10 SING N N 28 
WDK O3  C10 DOUB N N 29 
WDK C12 C13 SING N N 30 
WDK C10 C2  SING N N 31 
WDK C2  C3  SING N N 32 
WDK C13 C18 DOUB Y N 33 
WDK C13 C14 SING Y N 34 
WDK C3  C4  SING N N 35 
WDK C18 C17 SING Y N 36 
WDK C14 C15 DOUB Y N 37 
WDK C9  C4  DOUB Y N 38 
WDK C9  C8  SING Y N 39 
WDK C4  C5  SING Y N 40 
WDK C8  C7  DOUB Y N 41 
WDK C5  CL1 SING N N 42 
WDK C5  C6  DOUB Y N 43 
WDK C17 C16 DOUB Y N 44 
WDK C15 C16 SING Y N 45 
WDK C7  C6  SING Y N 46 
WDK C7  CL2 SING N N 47 
WDK C16 F1  SING N N 48 
WDK C11 H1  SING N N 49 
WDK C12 H2  SING N N 50 
WDK C12 H3  SING N N 51 
WDK C14 H4  SING N N 52 
WDK C15 H5  SING N N 53 
WDK C17 H6  SING N N 54 
WDK C18 H7  SING N N 55 
WDK C19 H8  SING N N 56 
WDK C19 H9  SING N N 57 
WDK C2  H10 SING N N 58 
WDK C21 H11 SING N N 59 
WDK C21 H12 SING N N 60 
WDK C22 H13 SING N N 61 
WDK C22 H14 SING N N 62 
WDK C23 H15 SING N N 63 
WDK C23 H16 SING N N 64 
WDK C24 H17 SING N N 65 
WDK C24 H18 SING N N 66 
WDK C24 H19 SING N N 67 
WDK C25 H20 SING N N 68 
WDK C25 H21 SING N N 69 
WDK C25 H22 SING N N 70 
WDK C26 H23 SING N N 71 
WDK C27 H24 SING N N 72 
WDK C27 H25 SING N N 73 
WDK C3  H26 SING N N 74 
WDK C3  H27 SING N N 75 
WDK C31 H28 SING N N 76 
WDK C32 H29 SING N N 77 
WDK C33 H30 SING N N 78 
WDK C34 H31 SING N N 79 
WDK C6  H32 SING N N 80 
WDK C8  H33 SING N N 81 
WDK C9  H34 SING N N 82 
WDK N1  H35 SING N N 83 
WDK N2  H36 SING N N 84 
WDK N3  H37 SING N N 85 
WDK N5  H39 SING N N 86 
WDK N5  H40 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 
WDK SMILES           ACDLabs              12.01 "Clc1cc(Cl)ccc1CC(NC(=O)C(N)Cc1ccccc1C#N)C(=O)NC(Cc1ccc(F)cc1)CC(=O)NCCCN(C)C"                                                                                                                                                                                   
WDK InChI            InChI                1.06  "InChI=1S/C34H39Cl2FN6O3/c1-43(2)15-5-14-40-32(44)20-28(16-22-8-12-27(37)13-9-22)41-34(46)31(18-24-10-11-26(35)19-29(24)36)42-33(45)30(39)17-23-6-3-4-7-25(23)21-38/h3-4,6-13,19,28,30-31H,5,14-18,20,39H2,1-2H3,(H,40,44)(H,41,46)(H,42,45)/t28-,30+,31+/m0/s1" 
WDK InChIKey         InChI                1.06  TYVGHVUYGAWXBC-FAOMPSFFSA-N                                                                                                                                                                                                                                      
WDK SMILES_CANONICAL CACTVS               3.385 "CN(C)CCCNC(=O)C[C@H](Cc1ccc(F)cc1)NC(=O)[C@@H](Cc2ccc(Cl)cc2Cl)NC(=O)[C@H](N)Cc3ccccc3C#N"                                                                                                                                                                      
WDK SMILES           CACTVS               3.385 "CN(C)CCCNC(=O)C[CH](Cc1ccc(F)cc1)NC(=O)[CH](Cc2ccc(Cl)cc2Cl)NC(=O)[CH](N)Cc3ccccc3C#N"                                                                                                                                                                          
WDK SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CN(C)CCCNC(=O)C[C@H](Cc1ccc(cc1)F)NC(=O)[C@@H](Cc2ccc(cc2Cl)Cl)NC(=O)[C@@H](Cc3ccccc3C#N)N"                                                                                                                                                                     
WDK SMILES           "OpenEye OEToolkits" 2.0.7 "CN(C)CCCNC(=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 
WDK "SYSTEMATIC NAME" ACDLabs              12.01 "2-cyano-D-phenylalanyl-2,4-dichloro-N-[(2S)-4-{[3-(dimethylamino)propyl]amino}-1-(4-fluorophenyl)-4-oxobutan-2-yl]-D-phenylalaninamide"                                        
WDK "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}-[3-(dimethylamino)propyl]-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 
WDK "Create component" 2023-10-02 RCSB 
WDK "Initial release"  2024-12-25 RCSB 
# 
