data_WBO
#
_chem_comp.id WBO
_chem_comp.name "2-cyano-D-phenylalanyl-2,4-dichloro-N-[(2S)-4-{[4-(dimethylamino)butyl]amino}-1-(4-fluorophenyl)-4-oxobutan-2-yl]-D-phenylalaninamide"
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C35 H41 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 683.643
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code WBO
_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 8UDP
_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
WBO C1 C1 C 0 1 N N N N N N 8.454 -0.422 21.656 2.091 1.139 -0.492 C1 WBO 1
WBO C2 C2 C 0 1 N N R N N N 8.778 -2.163 23.292 0.285 0.143 0.806 C2 WBO 2
WBO C3 C3 C 0 1 N N N N N N 8.958 -1.941 24.796 0.658 0.421 2.264 C3 WBO 3
WBO N4 N1 N 0 1 N N N N N N 9.531 -13.291 16.747 -10.349 2.139 -2.197 N4 WBO 4
WBO C5 C4 C 0 1 Y N N N N N 6.647 -1.313 25.601 2.663 1.903 2.032 C5 WBO 5
WBO N6 N2 N 0 1 N N N N N N 6.881 -0.881 16.919 3.885 -2.757 -2.080 N6 WBO 6
WBO C8 C5 C 0 1 Y N N N N N 7.297 1.379 25.663 1.216 4.104 2.877 C8 WBO 7
WBO C9 C6 C 0 1 Y N N N N N 8.253 0.448 25.268 0.604 2.868 2.785 C9 WBO 8
WBO C12 C7 C 0 1 N N N N N N 9.038 -6.855 22.664 -1.879 -3.511 2.348 C12 WBO 9
WBO C13 C8 C 0 1 Y N N N N N 9.021 -6.670 24.187 -0.458 -3.880 2.010 C13 WBO 10
WBO C26 C9 C 0 1 N N N N N N 8.830 0.713 19.462 2.981 0.622 -2.749 C26 WBO 11
WBO C27 C10 C 0 1 Y N N N N N 9.707 -0.452 18.984 4.241 0.387 -3.542 C27 WBO 12
WBO C22 C11 C 0 1 N N N N N N 9.491 -10.001 18.302 -7.762 0.125 -0.287 C22 WBO 13
WBO C23 C12 C 0 1 N N N N N N 9.955 -10.927 17.183 -8.327 1.011 -1.400 C23 WBO 14
WBO C25 C13 C 0 1 N N R N N N 8.923 0.860 20.979 3.347 1.023 -1.318 C25 WBO 15
WBO C10 C14 C 0 1 N N N N N N 9.606 -3.376 22.874 -0.491 -1.145 0.723 C10 WBO 16
WBO C11 C15 C 0 1 N N S N N N 9.743 -5.643 22.045 -2.412 -2.527 1.305 C11 WBO 17
WBO C14 C16 C 0 1 Y N N N N N 10.062 -7.162 24.969 -0.201 -4.961 1.188 C14 WBO 18
WBO C15 C17 C 0 1 Y N N N N N 10.044 -6.989 26.348 1.102 -5.300 0.877 C15 WBO 19
WBO C16 C18 C 0 1 Y N N N N N 8.987 -6.319 26.950 2.151 -4.556 1.390 C16 WBO 20
WBO C17 C19 C 0 1 Y N N N N N 7.948 -5.827 26.173 1.893 -3.474 2.213 C17 WBO 21
WBO C18 C20 C 0 1 Y N N N N N 7.968 -6.003 24.798 0.589 -3.134 2.519 C18 WBO 22
WBO C19 C21 C 0 1 N N N N N N 9.855 -5.772 20.527 -3.892 -2.249 1.576 C19 WBO 23
WBO C20 C22 C 0 1 N N N N N N 10.519 -7.099 20.165 -4.448 -1.377 0.480 C20 WBO 24
WBO C21 C23 C 0 1 N N N N N N 10.630 -9.084 18.760 -6.282 -0.153 -0.557 C21 WBO 25
WBO C24 C24 C 0 1 N N N N N N 8.896 -11.996 16.932 -9.807 1.289 -1.129 C24 WBO 26
WBO C28 C25 C 0 1 Y N N N N N 9.248 -1.298 17.982 4.870 -0.859 -3.502 C28 WBO 27
WBO C29 C26 C 0 1 N N N N N N 7.881 -1.054 17.374 4.321 -1.918 -2.709 C29 WBO 28
WBO C30 C27 C 0 1 Y N N N N N 10.031 -2.358 17.536 6.037 -1.069 -4.240 C30 WBO 29
WBO C31 C28 C 0 1 Y N N N N N 11.285 -2.584 18.100 6.560 -0.045 -5.002 C31 WBO 30
WBO C32 C29 C 0 1 Y N N N N N 11.750 -1.738 19.095 5.932 1.187 -5.036 C32 WBO 31
WBO C33 C30 C 0 1 Y N N N N N 10.965 -0.677 19.540 4.772 1.400 -4.312 C33 WBO 32
WBO C34 C31 C 0 1 N N N N N N 9.247 -13.786 15.413 -10.356 1.428 -3.483 C34 WBO 33
WBO C35 C32 C 0 1 N N N N N N 9.038 -14.229 17.742 -11.693 2.622 -1.855 C35 WBO 34
WBO C4 C33 C 0 1 Y N N N N N 7.926 -0.903 25.240 1.326 1.768 2.363 C4 WBO 35
WBO C6 C34 C 0 1 Y N N N N N 5.695 -0.386 25.996 3.276 3.139 2.123 C6 WBO 36
WBO C7 C35 C 0 1 Y N N N N N 6.019 0.961 26.028 2.552 4.240 2.546 C7 WBO 37
WBO CL1 CL1 CL 0 0 N N N N N N 6.219 -2.985 25.563 3.572 0.520 1.509 CL1 WBO 38
WBO CL2 CL2 CL 0 0 N N N N N N 4.816 2.102 26.525 3.321 5.793 2.661 CL2 WBO 39
WBO F1 F1 F 0 1 N N N N N N 8.959 -6.145 28.289 3.425 -4.887 1.087 F1 WBO 40
WBO N1 N3 N 0 1 N N N N N N 9.198 -0.956 22.614 1.506 0.031 0.003 N1 WBO 41
WBO N2 N4 N 0 1 N N N N N N 8.990 -4.458 22.412 -1.657 -1.274 1.386 N2 WBO 42
WBO N3 N5 N 0 1 N N N N N N 10.042 -7.813 19.148 -5.742 -1.000 0.508 N3 WBO 43
WBO N5 N6 N 0 1 N N N N N N 8.063 1.941 21.431 4.043 2.316 -1.334 N5 WBO 44
WBO O1 O1 O 0 1 N N N N N N 7.438 -0.937 21.325 1.610 2.230 -0.270 O1 WBO 45
WBO O2 O2 O 0 1 N N N N N N 11.458 -7.484 20.773 -3.731 -1.013 -0.429 O2 WBO 46
WBO O3 O3 O 0 1 N N N N N N 10.786 -3.360 22.978 -0.067 -2.067 0.058 O3 WBO 47
WBO H1 H1 H 0 1 N N N N N N 7.717 -2.364 23.084 -0.326 0.961 0.424 H1 WBO 48
WBO H2 H2 H 0 1 N N N N N N 8.796 -2.885 25.336 -0.244 0.417 2.876 H2 WBO 49
WBO H3 H3 H 0 1 N N N N N N 9.973 -1.571 25.001 1.341 -0.351 2.618 H3 WBO 50
WBO H5 H5 H 0 1 N N N N N N 7.547 2.429 25.687 0.651 4.964 3.206 H5 WBO 51
WBO H6 H6 H 0 1 N N N N N N 9.243 0.773 24.985 -0.440 2.762 3.044 H6 WBO 52
WBO H7 H7 H 0 1 N N N N N N 8.007 -6.921 22.285 -2.497 -4.409 2.349 H7 WBO 53
WBO H8 H8 H 0 1 N N N N N N 9.583 -7.775 22.406 -1.910 -3.048 3.334 H8 WBO 54
WBO H9 H9 H 0 1 N N N N N N 9.172 1.644 18.986 2.403 1.421 -3.213 H9 WBO 55
WBO H10 H10 H 0 1 N N N N N N 7.785 0.520 19.180 2.388 -0.292 -2.730 H10 WBO 56
WBO H11 H11 H 0 1 N N N N N N 8.657 -9.384 17.936 -7.867 0.635 0.671 H11 WBO 57
WBO H12 H12 H 0 1 N N N N N N 9.152 -10.608 19.155 -8.310 -0.817 -0.259 H12 WBO 58
WBO H13 H13 H 0 1 N N N N N N 10.900 -11.409 17.475 -7.779 1.953 -1.427 H13 WBO 59
WBO H14 H14 H 0 1 N N N N N N 10.110 -10.342 16.264 -8.222 0.501 -2.357 H14 WBO 60
WBO H15 H15 H 0 1 N N N N N N 9.967 1.060 21.261 3.999 0.265 -0.883 H15 WBO 61
WBO H16 H16 H 0 1 N N N N N N 10.757 -5.578 22.466 -2.299 -2.955 0.309 H16 WBO 62
WBO H17 H17 H 0 1 N N N N N N 10.887 -7.680 24.503 -1.020 -5.542 0.788 H17 WBO 63
WBO H18 H18 H 0 1 N N N N N N 10.852 -7.376 26.951 1.302 -6.145 0.235 H18 WBO 64
WBO H19 H19 H 0 1 N N N N N N 7.124 -5.307 26.639 2.711 -2.893 2.614 H19 WBO 65
WBO H20 H20 H 0 1 N N N N N N 7.157 -5.618 24.197 0.387 -2.286 3.157 H20 WBO 66
WBO H21 H21 H 0 1 N N N N N N 10.461 -4.942 20.134 -4.440 -3.191 1.604 H21 WBO 67
WBO H22 H22 H 0 1 N N N N N N 8.849 -5.734 20.083 -3.997 -1.739 2.534 H22 WBO 68
WBO H23 H23 H 0 1 N N N N N N 11.151 -9.533 19.618 -6.178 -0.662 -1.515 H23 WBO 69
WBO H24 H24 H 0 1 N N N N N N 11.343 -8.932 17.936 -5.735 0.789 -0.585 H24 WBO 70
WBO H25 H25 H 0 1 N N N N N N 8.325 -11.738 16.028 -9.911 1.798 -0.171 H25 WBO 71
WBO H26 H26 H 0 1 N N N N N N 8.215 -12.044 17.795 -10.354 0.347 -1.101 H26 WBO 72
WBO H27 H27 H 0 1 N N N N N N 9.667 -3.006 16.752 6.528 -2.030 -4.214 H27 WBO 73
WBO H28 H28 H 0 1 N N N N N N 11.891 -3.413 17.764 7.463 -0.206 -5.573 H28 WBO 74
WBO H29 H29 H 0 1 N N N N N N 12.726 -1.902 19.527 6.346 1.985 -5.635 H29 WBO 75
WBO H30 H30 H 0 1 N N N N N N 11.333 -0.026 20.319 4.284 2.363 -4.347 H30 WBO 76
WBO H31 H31 H 0 1 N N N N N N 9.728 -14.766 15.275 -10.974 0.534 -3.400 H31 WBO 77
WBO H32 H32 H 0 1 N N N N N N 8.160 -13.890 15.285 -10.762 2.080 -4.256 H32 WBO 78
WBO H33 H33 H 0 1 N N N N N N 9.638 -13.077 14.668 -9.337 1.143 -3.746 H33 WBO 79
WBO H34 H34 H 0 1 N N N N N N 9.258 -13.845 18.749 -11.647 3.204 -0.935 H34 WBO 80
WBO H35 H35 H 0 1 N N N N N N 7.951 -14.350 17.625 -12.071 3.249 -2.663 H35 WBO 81
WBO H36 H36 H 0 1 N N N N N N 9.532 -15.202 17.605 -12.359 1.771 -1.714 H36 WBO 82
WBO H37 H37 H 0 1 N N N N N N 4.705 -0.712 26.278 4.319 3.245 1.865 H37 WBO 83
WBO H38 H38 H 0 1 N N N N N N 10.060 -0.519 22.871 1.893 -0.842 -0.171 H38 WBO 84
WBO H39 H39 H 0 1 N N N N N N 7.995 -4.456 22.316 -1.996 -0.536 1.917 H39 WBO 85
WBO H40 H40 H 0 1 N N N N N N 9.257 -7.465 18.636 -6.315 -1.291 1.235 H40 WBO 86
WBO H41 H41 H 0 1 N N N N N N 8.131 2.029 22.425 4.921 2.248 -1.827 H41 WBO 87
WBO H42 H42 H 0 1 N N N N N N 8.349 2.797 21.001 3.459 3.036 -1.733 H42 WBO 88
#
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
WBO C34 N4 SING N N 1
WBO N4 C24 SING N N 2
WBO N4 C35 SING N N 3
WBO N6 C29 TRIP N N 4
WBO C24 C23 SING N N 5
WBO C23 C22 SING N N 6
WBO C29 C28 SING N N 7
WBO C30 C28 DOUB Y N 8
WBO C30 C31 SING Y N 9
WBO C28 C27 SING Y N 10
WBO C31 C32 DOUB Y N 11
WBO C22 C21 SING N N 12
WBO C21 N3 SING N N 13
WBO C27 C26 SING N N 14
WBO C27 C33 DOUB Y N 15
WBO C32 C33 SING Y N 16
WBO N3 C20 SING N N 17
WBO C26 C25 SING N N 18
WBO C20 C19 SING N N 19
WBO C20 O2 DOUB N N 20
WBO C19 C11 SING N N 21
WBO C25 N5 SING N N 22
WBO C25 C1 SING N N 23
WBO O1 C1 DOUB N N 24
WBO C1 N1 SING N N 25
WBO C11 N2 SING N N 26
WBO C11 C12 SING N N 27
WBO N2 C10 SING N N 28
WBO N1 C2 SING N N 29
WBO C12 C13 SING N N 30
WBO C10 O3 DOUB N N 31
WBO C10 C2 SING N N 32
WBO C2 C3 SING N N 33
WBO C13 C18 DOUB Y N 34
WBO C13 C14 SING Y N 35
WBO C3 C4 SING N N 36
WBO C18 C17 SING Y N 37
WBO C14 C15 DOUB Y N 38
WBO C4 C9 DOUB Y N 39
WBO C4 C5 SING Y N 40
WBO C9 C8 SING Y N 41
WBO CL1 C5 SING N N 42
WBO C5 C6 DOUB Y N 43
WBO C8 C7 DOUB Y N 44
WBO C6 C7 SING Y N 45
WBO C7 CL2 SING N N 46
WBO C17 C16 DOUB Y N 47
WBO C15 C16 SING Y N 48
WBO C16 F1 SING N N 49
WBO C2 H1 SING N N 50
WBO C3 H2 SING N N 51
WBO C3 H3 SING N N 52
WBO C8 H5 SING N N 53
WBO C9 H6 SING N N 54
WBO C12 H7 SING N N 55
WBO C12 H8 SING N N 56
WBO C26 H9 SING N N 57
WBO C26 H10 SING N N 58
WBO C22 H11 SING N N 59
WBO C22 H12 SING N N 60
WBO C23 H13 SING N N 61
WBO C23 H14 SING N N 62
WBO C25 H15 SING N N 63
WBO C11 H16 SING N N 64
WBO C14 H17 SING N N 65
WBO C15 H18 SING N N 66
WBO C17 H19 SING N N 67
WBO C18 H20 SING N N 68
WBO C19 H21 SING N N 69
WBO C19 H22 SING N N 70
WBO C21 H23 SING N N 71
WBO C21 H24 SING N N 72
WBO C24 H25 SING N N 73
WBO C24 H26 SING N N 74
WBO C30 H27 SING N N 75
WBO C31 H28 SING N N 76
WBO C32 H29 SING N N 77
WBO C33 H30 SING N N 78
WBO C34 H31 SING N N 79
WBO C34 H32 SING N N 80
WBO C34 H33 SING N N 81
WBO C35 H34 SING N N 82
WBO C35 H35 SING N N 83
WBO C35 H36 SING N N 84
WBO C6 H37 SING N N 85
WBO N1 H38 SING N N 86
WBO N2 H39 SING N N 87
WBO N3 H40 SING N N 88
WBO N5 H41 SING N N 89
WBO N5 H42 SING N N 90
#
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
WBO SMILES ACDLabs 12.01 "Clc1cc(Cl)ccc1CC(NC(=O)C(N)Cc1ccccc1C#N)C(=O)NC(Cc1ccc(F)cc1)CC(=O)NCCCCN(C)C"
WBO InChI InChI 1.06 "InChI=1S/C35H41Cl2FN6O3/c1-44(2)16-6-5-15-41-33(45)21-29(17-23-9-13-28(38)14-10-23)42-35(47)32(19-25-11-12-27(36)20-30(25)37)43-34(46)31(40)18-24-7-3-4-8-26(24)22-39/h3-4,7-14,20,29,31-32H,5-6,15-19,21,40H2,1-2H3,(H,41,45)(H,42,47)(H,43,46)/t29-,31+,32+/m0/s1"
WBO InChIKey InChI 1.06 GHJNNBYANWGVQR-JIZBBPSKSA-N
WBO SMILES_CANONICAL CACTVS 3.385 "CN(C)CCCCNC(=O)C[C@H](Cc1ccc(F)cc1)NC(=O)[C@@H](Cc2ccc(Cl)cc2Cl)NC(=O)[C@H](N)Cc3ccccc3C#N"
WBO SMILES CACTVS 3.385 "CN(C)CCCCNC(=O)C[CH](Cc1ccc(F)cc1)NC(=O)[CH](Cc2ccc(Cl)cc2Cl)NC(=O)[CH](N)Cc3ccccc3C#N"
WBO SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CN(C)CCCCNC(=O)C[C@H](Cc1ccc(cc1)F)NC(=O)[C@@H](Cc2ccc(cc2Cl)Cl)NC(=O)[C@@H](Cc3ccccc3C#N)N"
WBO SMILES "OpenEye OEToolkits" 2.0.7 "CN(C)CCCCNC(=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
WBO "SYSTEMATIC NAME" ACDLabs 12.01 "2-cyano-D-phenylalanyl-2,4-dichloro-N-[(2S)-4-{[4-(dimethylamino)butyl]amino}-1-(4-fluorophenyl)-4-oxobutan-2-yl]-D-phenylalaninamide"
WBO "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}-[4-(dimethylamino)butyl]-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
WBO "Create component" 2023-09-29 RCSB
WBO "Initial release" 2025-01-01 RCSB
#