data_WB5
#
_chem_comp.id WB5
_chem_comp.name "2-cyano-D-phenylalanyl-2,4-dichloro-N-[(2S)-4-(methylamino)-4-oxo-1-phenylbutan-2-yl]-D-phenylalaninamide"
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C30 H31 Cl2 N5 O3"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2023-09-29
_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 580.505
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code WB5
_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 8UDJ
_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
WB5 C10 C1 C 0 1 Y N N N N N 10.101 -7.419 26.102 2.803 -0.893 -3.880 C10 WB5 1
WB5 C11 C2 C 0 1 Y N N N N N 10.051 -7.321 24.714 3.551 -0.428 -2.814 C11 WB5 2
WB5 C13 C3 C 0 1 N N R N N N 8.807 -1.568 22.865 0.747 0.469 0.117 C13 WB5 3
WB5 C15 C4 C 0 1 Y N N N N N 7.838 -0.452 24.812 -0.238 2.490 -0.929 C15 WB5 4
WB5 C17 C5 C 0 1 Y N N N N N 5.617 -0.289 25.772 -1.144 4.514 -0.023 C17 WB5 5
WB5 C19 C6 C 0 1 Y N N N N N 6.902 1.744 25.138 -2.412 3.234 -1.602 C19 WB5 6
WB5 C21 C7 C 0 1 N N N N N N 8.363 0.053 21.098 -1.656 0.171 0.393 C21 WB5 7
WB5 C22 C8 C 0 1 N N R N N N 8.694 1.293 20.308 -2.920 -0.626 0.203 C22 WB5 8
WB5 C23 C9 C 0 1 N N N N N N 8.896 0.924 18.859 -2.994 -1.726 1.265 C23 WB5 9
WB5 C25 C10 C 0 1 Y N N N N N 9.250 -1.357 17.892 -4.102 -3.661 0.100 C25 WB5 10
WB5 C1 C11 C 0 1 N N N N N N 11.620 -8.396 19.241 4.186 -0.522 5.247 C1 WB5 11
WB5 C2 C12 C 0 1 N N N N N N 11.031 -6.221 20.167 4.412 -0.693 2.827 C2 WB5 12
WB5 C3 C13 C 0 1 N N N N N N 9.996 -5.213 20.562 5.188 -0.480 1.553 C3 WB5 13
WB5 C4 C14 C 0 1 N N S N N N 9.861 -5.144 22.054 4.321 -0.877 0.356 C4 WB5 14
WB5 C5 C15 C 0 1 N N N N N N 9.148 -6.370 22.568 5.152 -0.794 -0.926 C5 WB5 15
WB5 C6 C16 C 0 1 Y N N N N N 9.175 -6.444 24.073 4.336 -1.302 -2.087 C6 WB5 16
WB5 C8 C17 C 0 1 Y N N N N N 8.326 -5.692 26.215 3.626 -3.108 -3.489 C8 WB5 17
WB5 C14 C18 C 0 1 N N N N N N 8.976 -1.304 24.337 0.883 1.487 -1.017 C14 WB5 18
WB5 C12 C19 C 0 1 N N N N N N 9.669 -2.748 22.516 1.933 -0.460 0.104 C12 WB5 19
WB5 C16 C20 C 0 1 Y N N N N N 6.691 -1.055 25.331 -0.115 3.593 -0.103 C16 WB5 20
WB5 C18 C21 C 0 1 Y N N N N N 5.674 1.095 25.695 -2.295 4.332 -0.769 C18 WB5 21
WB5 C20 C22 C 0 1 Y N N N N N 7.945 0.933 24.715 -1.385 2.312 -1.678 C20 WB5 22
WB5 C24 C23 C 0 1 Y N N N N N 9.762 -0.293 18.626 -4.194 -2.599 1.001 C24 WB5 23
WB5 C26 C24 C 0 1 Y N N N N N 10.022 -2.491 17.645 -5.218 -4.465 -0.139 C26 WB5 24
WB5 C27 C25 C 0 1 Y N N N N N 11.325 -2.565 18.132 -6.404 -4.205 0.517 C27 WB5 25
WB5 C28 C26 C 0 1 Y N N N N N 11.844 -1.498 18.859 -6.488 -3.151 1.408 C28 WB5 26
WB5 C29 C27 C 0 1 Y N N N N N 11.068 -0.367 19.107 -5.386 -2.350 1.649 C29 WB5 27
WB5 C30 C28 C 0 1 N N N N N N 7.847 -1.261 17.378 -2.869 -3.922 -0.582 C30 WB5 28
WB5 C7 C29 C 0 1 Y N N N N N 8.316 -5.642 24.825 4.374 -2.642 -2.424 C7 WB5 29
WB5 C9 C30 C 0 1 Y N N N N N 9.269 -6.634 26.893 2.841 -2.233 -4.218 C9 WB5 30
WB5 CL1 CL1 CL 0 0 N N N N N N 4.342 2.055 26.243 -3.592 5.480 -0.658 CL1 WB5 31
WB5 CL2 CL2 CL 0 0 N N N N N N 6.588 -2.779 25.434 1.329 3.821 0.834 CL2 WB5 32
WB5 N1 N1 N 0 1 N N N N N N 10.644 -7.386 19.642 4.940 -0.315 4.008 N1 WB5 33
WB5 N2 N2 N 0 1 N N N N N N 9.091 -3.943 22.375 3.178 0.034 0.257 N2 WB5 34
WB5 N3 N3 N 0 1 N N N N N N 9.143 -0.360 22.099 -0.482 -0.306 -0.068 N3 WB5 35
WB5 N4 N4 N 0 1 N N N N N N 7.611 2.294 20.397 -4.083 0.261 0.336 N4 WB5 36
WB5 N5 N5 N 0 1 N N N N N N 6.762 -1.177 16.990 -1.892 -4.128 -1.122 N5 WB5 37
WB5 O1 O1 O 0 1 N N N N N N 7.370 -0.607 20.804 -1.694 1.242 0.961 O1 WB5 38
WB5 O2 O2 O 0 1 N N N N N N 10.887 -2.617 22.391 1.768 -1.652 -0.046 O2 WB5 39
WB5 O3 O3 O 0 1 N N N N N N 12.225 -5.955 20.327 3.313 -1.205 2.790 O3 WB5 40
WB5 H1 H1 H 0 1 N N N N N N 10.790 -8.109 26.567 2.186 -0.211 -4.446 H1 WB5 41
WB5 H2 H2 H 0 1 N N N N N N 10.707 -7.939 24.119 3.522 0.619 -2.551 H2 WB5 42
WB5 H3 H3 H 0 1 N N N N N N 7.756 -1.833 22.675 0.706 0.993 1.072 H3 WB5 43
WB5 H4 H4 H 0 1 N N N N N N 4.739 -0.772 26.174 -1.049 5.375 0.623 H4 WB5 44
WB5 H5 H5 H 0 1 N N N N N N 6.975 2.819 25.067 -3.310 3.092 -2.185 H5 WB5 45
WB5 H6 H6 H 0 1 N N N N N N 9.626 1.728 20.699 -2.919 -1.078 -0.789 H6 WB5 46
WB5 H7 H7 H 0 1 N N N N N N 9.365 1.779 18.351 -2.089 -2.331 1.224 H7 WB5 47
WB5 H8 H8 H 0 1 N N N N N N 7.908 0.730 18.415 -3.085 -1.272 2.252 H8 WB5 48
WB5 H9 H9 H 0 1 N N N N N N 11.095 -9.274 18.836 4.769 -0.156 6.093 H9 WB5 49
WB5 H10 H10 H 0 1 N N N N N N 12.284 -7.978 18.470 3.243 0.023 5.194 H10 WB5 50
WB5 H11 H11 H 0 1 N N N N N N 12.216 -8.697 20.115 3.985 -1.585 5.377 H11 WB5 51
WB5 H12 H12 H 0 1 N N N N N N 10.292 -4.224 20.181 5.465 0.570 1.468 H12 WB5 52
WB5 H13 H13 H 0 1 N N N N N N 9.028 -5.500 20.125 6.088 -1.094 1.569 H13 WB5 53
WB5 H14 H14 H 0 1 N N N N N N 10.860 -5.084 22.511 3.961 -1.898 0.491 H14 WB5 54
WB5 H15 H15 H 0 1 N N N N N N 8.101 -6.340 22.232 5.437 0.242 -1.107 H15 WB5 55
WB5 H16 H16 H 0 1 N N N N N N 9.639 -7.265 22.159 6.049 -1.404 -0.817 H16 WB5 56
WB5 H17 H17 H 0 1 N N N N N N 7.666 -5.063 26.793 3.655 -4.154 -3.753 H17 WB5 57
WB5 H18 H18 H 0 1 N N N N N N 8.977 -2.258 24.885 1.840 2.002 -0.930 H18 WB5 58
WB5 H19 H19 H 0 1 N N N N N N 9.927 -0.780 24.511 0.835 0.971 -1.976 H19 WB5 59
WB5 H20 H20 H 0 1 N N N N N N 8.842 1.377 24.309 -1.480 1.451 -2.323 H20 WB5 60
WB5 H21 H21 H 0 1 N N N N N N 9.610 -3.312 17.076 -5.154 -5.289 -0.835 H21 WB5 61
WB5 H22 H22 H 0 1 N N N N N N 11.927 -3.442 17.947 -7.268 -4.826 0.334 H22 WB5 62
WB5 H23 H23 H 0 1 N N N N N N 12.856 -1.547 19.234 -7.419 -2.951 1.918 H23 WB5 63
WB5 H24 H24 H 0 1 N N N N N N 11.480 0.455 19.674 -5.458 -1.528 2.346 H24 WB5 64
WB5 H25 H25 H 0 1 N N N N N N 7.634 -4.973 24.321 4.987 -3.325 -1.856 H25 WB5 65
WB5 H26 H26 H 0 1 N N N N N N 9.303 -6.703 27.970 2.253 -2.598 -5.047 H26 WB5 66
WB5 H27 H27 H 0 1 N N N N N N 9.669 -7.570 19.521 5.819 0.094 4.038 H27 WB5 67
WB5 H28 H28 H 0 1 N N N N N N 8.101 -4.019 22.493 3.317 0.993 0.303 H28 WB5 68
WB5 H29 H29 H 0 1 N N N N N N 9.966 0.159 22.331 -0.452 -1.163 -0.522 H29 WB5 69
WB5 H30 H30 H 0 1 N N N N N N 7.468 2.547 21.354 -4.107 0.693 1.247 H30 WB5 70
WB5 H31 H31 H 0 1 N N N N N N 7.864 3.107 19.872 -4.092 0.958 -0.395 H31 WB5 71
#
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
WB5 N5 C30 TRIP N N 1
WB5 C30 C25 SING N N 2
WB5 C26 C25 DOUB Y N 3
WB5 C26 C27 SING Y N 4
WB5 C25 C24 SING Y N 5
WB5 C27 C28 DOUB Y N 6
WB5 C24 C23 SING N N 7
WB5 C24 C29 DOUB Y N 8
WB5 C28 C29 SING Y N 9
WB5 C23 C22 SING N N 10
WB5 C1 N1 SING N N 11
WB5 N1 C2 SING N N 12
WB5 C2 O3 DOUB N N 13
WB5 C2 C3 SING N N 14
WB5 C22 N4 SING N N 15
WB5 C22 C21 SING N N 16
WB5 C3 C4 SING N N 17
WB5 O1 C21 DOUB N N 18
WB5 C21 N3 SING N N 19
WB5 C4 N2 SING N N 20
WB5 C4 C5 SING N N 21
WB5 N3 C13 SING N N 22
WB5 N2 C12 SING N N 23
WB5 O2 C12 DOUB N N 24
WB5 C12 C13 SING N N 25
WB5 C5 C6 SING N N 26
WB5 C13 C14 SING N N 27
WB5 C6 C11 DOUB Y N 28
WB5 C6 C7 SING Y N 29
WB5 C14 C15 SING N N 30
WB5 C11 C10 SING Y N 31
WB5 C20 C15 DOUB Y N 32
WB5 C20 C19 SING Y N 33
WB5 C15 C16 SING Y N 34
WB5 C7 C8 DOUB Y N 35
WB5 C19 C18 DOUB Y N 36
WB5 C16 CL2 SING N N 37
WB5 C16 C17 DOUB Y N 38
WB5 C18 C17 SING Y N 39
WB5 C18 CL1 SING N N 40
WB5 C10 C9 DOUB Y N 41
WB5 C8 C9 SING Y N 42
WB5 C10 H1 SING N N 43
WB5 C11 H2 SING N N 44
WB5 C13 H3 SING N N 45
WB5 C17 H4 SING N N 46
WB5 C19 H5 SING N N 47
WB5 C22 H6 SING N N 48
WB5 C23 H7 SING N N 49
WB5 C23 H8 SING N N 50
WB5 C1 H9 SING N N 51
WB5 C1 H10 SING N N 52
WB5 C1 H11 SING N N 53
WB5 C3 H12 SING N N 54
WB5 C3 H13 SING N N 55
WB5 C4 H14 SING N N 56
WB5 C5 H15 SING N N 57
WB5 C5 H16 SING N N 58
WB5 C8 H17 SING N N 59
WB5 C14 H18 SING N N 60
WB5 C14 H19 SING N N 61
WB5 C20 H20 SING N N 62
WB5 C26 H21 SING N N 63
WB5 C27 H22 SING N N 64
WB5 C28 H23 SING N N 65
WB5 C29 H24 SING N N 66
WB5 C7 H25 SING N N 67
WB5 C9 H26 SING N N 68
WB5 N1 H27 SING N N 69
WB5 N2 H28 SING N N 70
WB5 N3 H29 SING N N 71
WB5 N4 H30 SING N N 72
WB5 N4 H31 SING N N 73
#
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
WB5 SMILES ACDLabs 12.01 "Clc1cc(Cl)ccc1CC(NC(=O)C(N)Cc1ccccc1C#N)C(=O)NC(Cc1ccccc1)CC(=O)NC"
WB5 InChI InChI 1.06 "InChI=1S/C30H31Cl2N5O3/c1-35-28(38)17-24(13-19-7-3-2-4-8-19)36-30(40)27(15-21-11-12-23(31)16-25(21)32)37-29(39)26(34)14-20-9-5-6-10-22(20)18-33/h2-12,16,24,26-27H,13-15,17,34H2,1H3,(H,35,38)(H,36,40)(H,37,39)/t24-,26+,27+/m0/s1"
WB5 InChIKey InChI 1.06 PQNNKOZAACJZJY-WYMJOSIYSA-N
WB5 SMILES_CANONICAL CACTVS 3.385 "CNC(=O)C[C@H](Cc1ccccc1)NC(=O)[C@@H](Cc2ccc(Cl)cc2Cl)NC(=O)[C@H](N)Cc3ccccc3C#N"
WB5 SMILES CACTVS 3.385 "CNC(=O)C[CH](Cc1ccccc1)NC(=O)[CH](Cc2ccc(Cl)cc2Cl)NC(=O)[CH](N)Cc3ccccc3C#N"
WB5 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CNC(=O)C[C@H](Cc1ccccc1)NC(=O)[C@@H](Cc2ccc(cc2Cl)Cl)NC(=O)[C@@H](Cc3ccccc3C#N)N"
WB5 SMILES "OpenEye OEToolkits" 2.0.7 "CNC(=O)CC(Cc1ccccc1)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
WB5 "SYSTEMATIC NAME" ACDLabs 12.01 "2-cyano-D-phenylalanyl-2,4-dichloro-N-[(2S)-4-(methylamino)-4-oxo-1-phenylbutan-2-yl]-D-phenylalaninamide"
WB5 "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}-methyl-4-phenyl-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
WB5 "Create component" 2023-09-29 RCSB
WB5 "Initial release" 2024-12-25 RCSB
#