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
#