data_WD6
#
_chem_comp.id WD6
_chem_comp.name "2-cyano-D-phenylalanyl-2,4-dichloro-N-{(2S)-1-(4-fluorophenyl)-4-oxo-4-[(prop-2-yn-1-yl)amino]butan-2-yl}-D-phenylalaninamide"
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C32 H30 Cl2 F N5 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 2025-01-10
_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 622.517
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code WD6
_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 8UDY
_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
WD6 C1 C1 C 0 1 N N N N N N -11.439 13.711 67.141 1.753 0.675 -0.567 C1 WD6 1
WD6 C2 C2 C 0 1 N N R N N N -10.997 12.091 68.920 -0.537 0.431 0.230 C2 WD6 2
WD6 C3 C3 C 0 1 N N N N N N -10.660 12.357 70.387 -0.560 1.163 1.573 C3 WD6 3
WD6 C4 C4 C 0 1 Y N N N N N -11.778 13.222 70.949 0.344 2.366 1.505 C4 WD6 4
WD6 C5 C5 C 0 1 Y N N N N N -12.922 12.641 71.493 -0.133 3.562 0.996 C5 WD6 5
WD6 C6 C6 C 0 1 Y N N N N N -13.931 13.444 71.991 0.697 4.666 0.933 C6 WD6 6
WD6 C9 C7 C 0 1 Y N N N N N -11.643 14.605 70.898 1.648 2.278 1.956 C9 WD6 7
WD6 C10 C8 C 0 1 N N N N N N -10.179 10.883 68.484 -1.533 -0.700 0.257 C10 WD6 8
WD6 C11 C9 C 0 1 N N S N N N -10.012 8.464 68.168 -3.807 -1.543 0.491 C11 WD6 9
WD6 C14 C10 C 0 1 Y N N N N N -9.444 6.914 71.013 -1.530 -2.033 2.819 C14 WD6 10
WD6 C15 C11 C 0 1 Y N N N N N -9.330 7.070 72.393 -0.309 -2.612 3.112 C15 WD6 11
WD6 C16 C12 C 0 1 Y N N N N N -10.329 7.723 73.108 -0.079 -3.940 2.793 C16 WD6 12
WD6 C17 C13 C 0 1 Y N N N N N -11.441 8.219 72.440 -1.073 -4.686 2.182 C17 WD6 13
WD6 C18 C14 C 0 1 Y N N N N N -11.555 8.062 71.063 -2.292 -4.105 1.891 C18 WD6 14
WD6 C19 C15 C 0 1 N N N N N N -9.991 8.329 66.645 -5.193 -1.011 0.120 C19 WD6 15
WD6 C12 C16 C 0 1 N N N N N N -10.685 7.255 68.826 -3.853 -2.148 1.896 C12 WD6 16
WD6 C13 C17 C 0 1 Y N N N N N -10.558 7.412 70.345 -2.522 -2.780 2.214 C13 WD6 17
WD6 C20 C18 C 0 1 N N N N N N -9.153 7.116 66.237 -5.179 -0.526 -1.307 C20 WD6 18
WD6 C21 C19 C 0 1 N N N N N N -9.023 4.828 65.470 -6.284 0.459 -3.242 C21 WD6 19
WD6 C22 C20 C 0 1 N N N N N N -9.833 4.087 64.414 -7.617 0.970 -3.600 C22 WD6 20
WD6 C23 C21 C 0 1 N N N N N N -10.461 3.496 63.548 -8.680 1.378 -3.885 C23 WD6 21
WD6 C24 C22 C 0 1 N N R N N N -10.965 14.914 66.323 3.133 0.123 -0.815 C24 WD6 22
WD6 C25 C23 C 0 1 N N N N N N -11.134 14.631 64.833 3.125 -0.713 -2.096 C25 WD6 23
WD6 C26 C24 C 0 1 Y N N N N N -10.312 13.402 64.442 4.472 -1.365 -2.279 C26 WD6 24
WD6 C27 C25 C 0 1 Y N N N N N -10.895 12.413 63.669 4.752 -2.581 -1.653 C27 WD6 25
WD6 C28 C26 C 0 1 N N N N N N -12.342 12.578 63.234 3.761 -3.214 -0.835 C28 WD6 26
WD6 C29 C27 C 0 1 Y N N N N N -10.176 11.283 63.282 6.002 -3.178 -1.828 C29 WD6 27
WD6 C30 C28 C 0 1 Y N N N N N -8.856 11.142 63.687 6.951 -2.563 -2.617 C30 WD6 28
WD6 C31 C29 C 0 1 Y N N N N N -8.265 12.136 64.472 6.668 -1.358 -3.234 C31 WD6 29
WD6 C32 C30 C 0 1 Y N N N N N -8.990 13.258 64.854 5.429 -0.764 -3.070 C32 WD6 30
WD6 C7 C31 C 0 1 Y N N N N N -13.802 14.822 71.942 2.004 4.576 1.380 C7 WD6 31
WD6 C8 C32 C 0 1 Y N N N N N -12.661 15.407 71.396 2.477 3.382 1.894 C8 WD6 32
WD6 CL1 CL1 CL 0 0 N N N N N N -13.151 10.926 71.565 -1.772 3.674 0.436 CL1 WD6 33
WD6 CL2 CL2 CL 0 0 N N N N N N -15.094 15.784 72.566 3.046 5.962 1.301 CL2 WD6 34
WD6 F1 F1 F 0 1 N N N N N N -10.230 7.879 74.447 1.113 -4.506 3.079 F1 WD6 35
WD6 N1 N1 N 0 1 N N N N N N -10.643 13.237 68.103 0.805 -0.105 -0.012 N1 WD6 36
WD6 N2 N2 N 0 1 N N N N N N -10.730 9.670 68.549 -2.839 -0.443 0.465 N2 WD6 37
WD6 N3 N3 N 0 1 N N N N N N -9.770 5.992 65.877 -6.298 -0.012 -1.855 N3 WD6 38
WD6 N4 N4 N 0 1 N N N N N N -11.718 16.110 66.674 4.085 1.233 -0.961 N4 WD6 39
WD6 N5 N5 N 0 1 N N N N N N -13.398 12.707 62.925 2.974 -3.716 -0.186 N5 WD6 40
WD6 O1 O1 O 0 1 N N N N N N -12.493 13.211 66.905 1.496 1.823 -0.863 O1 WD6 41
WD6 O2 O2 O 0 1 N N N N N N -7.965 7.183 66.238 -4.161 -0.599 -1.962 O2 WD6 42
WD6 O3 O3 O 0 1 N N N N N N -9.065 11.035 68.106 -1.158 -1.842 0.091 O3 WD6 43
WD6 H1 H1 H 0 1 N N N N N N -12.069 11.864 68.825 -0.799 1.126 -0.568 H1 WD6 44
WD6 H2 H2 H 0 1 N N N N N N -10.602 11.408 70.940 -1.578 1.485 1.794 H2 WD6 45
WD6 H3 H3 H 0 1 N N N N N N -9.698 12.885 70.464 -0.213 0.491 2.358 H3 WD6 46
WD6 H4 H4 H 0 1 N N N N N N -14.817 12.998 72.417 0.326 5.599 0.536 H4 WD6 47
WD6 H5 H5 H 0 1 N N N N N N -10.755 15.051 70.475 2.018 1.346 2.357 H5 WD6 48
WD6 H6 H6 H 0 1 N N N N N N -8.974 8.525 68.528 -3.507 -2.308 -0.225 H6 WD6 49
WD6 H7 H7 H 0 1 N N N N N N -8.667 6.406 70.461 -1.709 -0.998 3.068 H7 WD6 50
WD6 H8 H8 H 0 1 N N N N N N -8.464 6.683 72.909 0.465 -2.029 3.589 H8 WD6 51
WD6 H9 H9 H 0 1 N N N N N N -12.218 8.727 72.991 -0.894 -5.721 1.933 H9 WD6 52
WD6 H10 H10 H 0 1 N N N N N N -12.423 8.447 70.549 -3.067 -4.687 1.413 H10 WD6 53
WD6 H11 H11 H 0 1 N N N N N N -9.554 9.238 66.205 -5.928 -1.809 0.225 H11 WD6 54
WD6 H12 H12 H 0 1 N N N N N N -11.020 8.201 66.277 -5.455 -0.185 0.781 H12 WD6 55
WD6 H13 H13 H 0 1 N N N N N N -11.747 7.218 68.542 -4.066 -1.364 2.623 H13 WD6 56
WD6 H14 H14 H 0 1 N N N N N N -10.187 6.329 68.503 -4.635 -2.906 1.939 H14 WD6 57
WD6 H15 H15 H 0 1 N N N N N N -8.854 4.173 66.337 -6.022 -0.367 -3.904 H15 WD6 58
WD6 H16 H16 H 0 1 N N N N N N -8.055 5.136 65.048 -5.549 1.257 -3.348 H16 WD6 59
WD6 H17 H17 H 0 1 N N N N N N -11.006 2.983 62.797 -9.631 1.742 -4.140 H17 WD6 60
WD6 H18 H18 H 0 1 N N N N N N -9.897 15.078 66.530 3.431 -0.503 0.026 H18 WD6 61
WD6 H19 H19 H 0 1 N N N N N N -10.788 15.501 64.255 2.356 -1.482 -2.023 H19 WD6 62
WD6 H20 H20 H 0 1 N N N N N N -12.196 14.444 64.615 2.914 -0.069 -2.950 H20 WD6 63
WD6 H21 H21 H 0 1 N N N N N N -10.642 10.524 62.672 6.225 -4.118 -1.346 H21 WD6 64
WD6 H22 H22 H 0 1 N N N N N N -8.289 10.270 63.397 7.919 -3.024 -2.753 H22 WD6 65
WD6 H23 H23 H 0 1 N N N N N N -7.236 12.031 64.784 7.415 -0.881 -3.851 H23 WD6 66
WD6 H24 H24 H 0 1 N N N N N N -8.529 14.017 65.469 5.212 0.175 -3.558 H24 WD6 67
WD6 H25 H25 H 0 1 N N N N N N -12.569 16.482 71.360 3.496 3.312 2.247 H25 WD6 68
WD6 H26 H26 H 0 1 N N N N N N -9.767 13.690 68.267 1.011 -1.022 0.229 H26 WD6 69
WD6 H27 H27 H 0 1 N N N N N N -11.673 9.587 68.872 -3.139 0.470 0.598 H27 WD6 70
WD6 H28 H28 H 0 1 N N N N N N -10.769 5.955 65.889 -7.112 0.045 -1.331 H28 WD6 71
WD6 H29 H29 H 0 1 N N N N N N -11.609 16.298 67.650 5.028 0.889 -1.064 H29 WD6 72
WD6 H30 H30 H 0 1 N N N N N N -11.376 16.886 66.145 3.830 1.828 -1.735 H30 WD6 73
#
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
WD6 N5 C28 TRIP N N 1
WD6 C28 C27 SING N N 2
WD6 C29 C27 DOUB Y N 3
WD6 C29 C30 SING Y N 4
WD6 C23 C22 TRIP N N 5
WD6 C27 C26 SING Y N 6
WD6 C30 C31 DOUB Y N 7
WD6 C22 C21 SING N N 8
WD6 C26 C25 SING N N 9
WD6 C26 C32 DOUB Y N 10
WD6 C31 C32 SING Y N 11
WD6 C25 C24 SING N N 12
WD6 C21 N3 SING N N 13
WD6 N3 C20 SING N N 14
WD6 C20 O2 DOUB N N 15
WD6 C20 C19 SING N N 16
WD6 C24 N4 SING N N 17
WD6 C24 C1 SING N N 18
WD6 C19 C11 SING N N 19
WD6 O1 C1 DOUB N N 20
WD6 C1 N1 SING N N 21
WD6 N1 C2 SING N N 22
WD6 O3 C10 DOUB N N 23
WD6 C11 N2 SING N N 24
WD6 C11 C12 SING N N 25
WD6 C10 N2 SING N N 26
WD6 C10 C2 SING N N 27
WD6 C12 C13 SING N N 28
WD6 C2 C3 SING N N 29
WD6 C13 C14 DOUB Y N 30
WD6 C13 C18 SING Y N 31
WD6 C3 C4 SING N N 32
WD6 C9 C4 DOUB Y N 33
WD6 C9 C8 SING Y N 34
WD6 C4 C5 SING Y N 35
WD6 C14 C15 SING Y N 36
WD6 C18 C17 DOUB Y N 37
WD6 C8 C7 DOUB Y N 38
WD6 C5 CL1 SING N N 39
WD6 C5 C6 DOUB Y N 40
WD6 C7 C6 SING Y N 41
WD6 C7 CL2 SING N N 42
WD6 C15 C16 DOUB Y N 43
WD6 C17 C16 SING Y N 44
WD6 C16 F1 SING N N 45
WD6 C2 H1 SING N N 46
WD6 C3 H2 SING N N 47
WD6 C3 H3 SING N N 48
WD6 C6 H4 SING N N 49
WD6 C9 H5 SING N N 50
WD6 C11 H6 SING N N 51
WD6 C14 H7 SING N N 52
WD6 C15 H8 SING N N 53
WD6 C17 H9 SING N N 54
WD6 C18 H10 SING N N 55
WD6 C19 H11 SING N N 56
WD6 C19 H12 SING N N 57
WD6 C12 H13 SING N N 58
WD6 C12 H14 SING N N 59
WD6 C21 H15 SING N N 60
WD6 C21 H16 SING N N 61
WD6 C23 H17 SING N N 62
WD6 C24 H18 SING N N 63
WD6 C25 H19 SING N N 64
WD6 C25 H20 SING N N 65
WD6 C29 H21 SING N N 66
WD6 C30 H22 SING N N 67
WD6 C31 H23 SING N N 68
WD6 C32 H24 SING N N 69
WD6 C8 H25 SING N N 70
WD6 N1 H26 SING N N 71
WD6 N2 H27 SING N N 72
WD6 N3 H28 SING N N 73
WD6 N4 H29 SING N N 74
WD6 N4 H30 SING N N 75
#
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
WD6 SMILES ACDLabs 12.01 "Clc1cc(Cl)ccc1CC(NC(=O)C(N)Cc1ccccc1C#N)C(=O)NC(Cc1ccc(F)cc1)CC(=O)NCC#C"
WD6 InChI InChI 1.06 "InChI=1S/C32H30Cl2FN5O3/c1-2-13-38-30(41)18-26(14-20-7-11-25(35)12-8-20)39-32(43)29(16-22-9-10-24(33)17-27(22)34)40-31(42)28(37)15-21-5-3-4-6-23(21)19-36/h1,3-12,17,26,28-29H,13-16,18,37H2,(H,38,41)(H,39,43)(H,40,42)/t26-,28+,29+/m0/s1"
WD6 InChIKey InChI 1.06 MOLWDJQRPLMKDR-WIIGKZCBSA-N
WD6 SMILES_CANONICAL CACTVS 3.385 "N[C@H](Cc1ccccc1C#N)C(=O)N[C@H](Cc2ccc(Cl)cc2Cl)C(=O)N[C@H](CC(=O)NCC#C)Cc3ccc(F)cc3"
WD6 SMILES CACTVS 3.385 "N[CH](Cc1ccccc1C#N)C(=O)N[CH](Cc2ccc(Cl)cc2Cl)C(=O)N[CH](CC(=O)NCC#C)Cc3ccc(F)cc3"
WD6 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C#CCNC(=O)C[C@H](Cc1ccc(cc1)F)NC(=O)[C@@H](Cc2ccc(cc2Cl)Cl)NC(=O)[C@@H](Cc3ccccc3C#N)N"
WD6 SMILES "OpenEye OEToolkits" 2.0.7 "C#CCNC(=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
WD6 "SYSTEMATIC NAME" ACDLabs 12.01 "2-cyano-D-phenylalanyl-2,4-dichloro-N-{(2S)-1-(4-fluorophenyl)-4-oxo-4-[(prop-2-yn-1-yl)amino]butan-2-yl}-D-phenylalaninamide"
WD6 "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]-4-(4-fluorophenyl)-~{N}-prop-2-ynyl-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
WD6 "Create component" 2023-10-02 RCSB
WD6 "Initial release" 2025-01-15 RCSB
#