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
#