data_A1JWY # _chem_comp.id A1JWY _chem_comp.name "~{N}-[3-[1-[[4-[5-[(2-methylpyridin-3-yl)methyl]-3-phenyl-pyridin-2-yl]phenyl]methyl]piperidin-4-yl]-2-oxidanylidene-1~{H}-benzimidazol-5-yl]propanamide" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C40 H38 N6 O2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2025-12-17 _chem_comp.pdbx_modified_date 2026-09-11 _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 634.769 _chem_comp.one_letter_code ? _chem_comp.three_letter_code A1JWY _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 9TN3 _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBE _chem_comp.pdbx_pcm Y _chem_comp.pdbx_comp_type ? # 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_n_terminal_atom_flag _chem_comp_atom.pdbx_backbone_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 A1JWY C10 C1 C 0 1 Y N N N N N -12.325 19.396 -16.043 -0.720 0.087 -1.536 C10 A1JWY 1 A1JWY C13 C2 C 0 1 Y N N N N N -11.801 21.856 -18.917 -4.006 0.026 0.287 C13 A1JWY 2 A1JWY C15 C3 C 0 1 Y N N N N N -12.042 21.524 -21.201 -5.200 1.657 1.403 C15 A1JWY 3 A1JWY C17 C4 C 0 1 N N N N N N -12.255 23.339 -22.904 -7.603 1.387 2.067 C17 A1JWY 4 A1JWY C20 C5 C 0 1 N N N N N N -14.943 23.243 -23.972 -7.137 4.086 1.145 C20 A1JWY 5 A1JWY C22 C6 C 0 1 Y N N N N N -14.515 26.861 -23.478 -10.052 3.153 -0.891 C22 A1JWY 6 A1JWY C24 C7 C 0 1 Y N N N N N -12.481 25.862 -22.770 -9.543 1.263 0.475 C24 A1JWY 7 A1JWY C26 C8 C 0 1 Y N N N N N -11.835 23.245 -19.074 -5.123 -0.824 0.266 C26 A1JWY 8 A1JWY C28 C9 C 0 1 Y N N N N N -10.782 25.263 -18.003 -5.480 -3.291 0.326 C28 A1JWY 9 A1JWY C02 C10 C 0 1 N N N N N N -11.477 13.054 -14.693 5.370 -1.401 2.275 C02 A1JWY 10 A1JWY C04 C11 C 0 1 N N N N N N -9.898 15.015 -14.063 4.594 -0.811 -0.031 C04 A1JWY 11 A1JWY C05 C12 C 0 1 N N N N N N -10.930 15.422 -13.134 3.293 -0.145 0.423 C05 A1JWY 12 A1JWY C06 C13 C 0 1 N N N N N N -10.930 16.938 -12.887 2.274 -0.198 -0.718 C06 A1JWY 13 A1JWY C08 C14 C 0 1 N N N N N N -11.000 18.894 -13.918 0.950 -1.693 -2.087 C08 A1JWY 14 A1JWY C09 C15 C 0 1 Y N N N N N -11.231 19.669 -15.232 -0.349 -1.244 -1.469 C09 A1JWY 15 A1JWY C11 C16 C 0 1 Y N N N N N -12.506 20.105 -17.226 -1.906 0.505 -0.968 C11 A1JWY 16 A1JWY C12 C17 C 0 1 Y N N N N N -11.616 21.102 -17.594 -2.731 -0.417 -0.325 C12 A1JWY 17 A1JWY C16 C18 C 0 1 Y N N N N N -12.097 22.884 -21.444 -6.340 0.873 1.426 C16 A1JWY 18 A1JWY C18 C19 C 0 1 Y N N N N N -13.044 24.632 -23.088 -8.492 1.992 1.010 C18 A1JWY 19 A1JWY C19 C20 C 0 1 Y N N N N N -14.325 24.588 -23.606 -8.273 3.282 0.567 C19 A1JWY 20 A1JWY C23 C21 C 0 1 Y N N N N N -13.241 27.003 -22.963 -10.335 1.860 -0.493 C23 A1JWY 21 A1JWY C25 C22 C 0 1 Y N N N N N -11.983 23.751 -20.364 -6.313 -0.387 0.849 C25 A1JWY 22 A1JWY C27 C23 C 0 1 Y N N N N N -11.713 24.234 -17.920 -5.040 -2.163 -0.365 C27 A1JWY 23 A1JWY C29 C24 C 0 1 Y N N N N N -10.651 26.180 -16.971 -5.396 -4.535 -0.264 C29 A1JWY 24 A1JWY C30 C25 C 0 1 Y N N N N N -11.449 26.077 -15.847 -4.876 -4.665 -1.539 C30 A1JWY 25 A1JWY C31 C26 C 0 1 Y N N N N N -12.381 25.050 -15.761 -4.437 -3.549 -2.230 C31 A1JWY 26 A1JWY C32 C27 C 0 1 Y N N N N N -12.513 24.137 -16.794 -4.521 -2.299 -1.651 C32 A1JWY 27 A1JWY C33 C28 C 0 1 Y N N N N N -10.515 21.366 -16.794 -2.352 -1.757 -0.261 C33 A1JWY 28 A1JWY C34 C29 C 0 1 Y N N N N N -10.333 20.660 -15.612 -1.166 -2.164 -0.837 C34 A1JWY 29 A1JWY C35 C30 C 0 1 N N N N N N -9.826 17.322 -14.938 3.251 -2.243 -1.574 C35 A1JWY 30 A1JWY C36 C31 C 0 1 N N N N N N -9.856 15.825 -15.253 4.299 -2.252 -0.459 C36 A1JWY 31 A1JWY C37 C32 C 0 1 Y N N N N N -9.405 12.455 -13.749 6.811 -0.216 1.068 C37 A1JWY 32 A1JWY C38 C33 C 0 1 Y N N N N N -8.118 12.380 -13.175 7.510 0.511 0.118 C38 A1JWY 33 A1JWY C39 C34 C 0 1 Y N N N N N -7.544 11.134 -12.886 8.778 0.991 0.412 C39 A1JWY 34 A1JWY C41 C35 C 0 1 N N N N N N -5.197 10.157 -12.861 8.826 2.527 -1.405 C41 A1JWY 35 A1JWY C42 C36 C 0 1 N N N N N N -3.809 10.004 -12.242 9.559 3.220 -2.475 C42 A1JWY 36 A1JWY C43 C37 C 0 1 N N N N N N -3.128 11.343 -11.978 8.907 4.011 -3.322 C43 A1JWY 37 A1JWY C45 C38 C 0 1 Y N N N N N -8.266 9.948 -13.168 9.346 0.744 1.657 C45 A1JWY 38 A1JWY C46 C39 C 0 1 Y N N N N N -9.540 10.017 -13.734 8.652 0.019 2.606 C46 A1JWY 39 A1JWY C47 C40 C 0 1 Y N N N N N -10.108 11.269 -14.026 7.383 -0.460 2.319 C47 A1JWY 40 A1JWY N03 N1 N 0 1 N N N N N N -10.254 13.597 -14.156 5.554 -0.816 1.076 N03 A1JWY 41 A1JWY N07 N2 N 0 1 N N N N N N -10.945 17.689 -14.116 2.025 -1.596 -1.090 N07 A1JWY 42 A1JWY N14 N3 N 0 1 Y N N N N N -11.896 21.082 -19.975 -4.086 1.225 0.848 N14 A1JWY 43 A1JWY N21 N4 N 0 1 Y N N N N N -15.032 25.686 -23.786 -9.044 3.816 -0.361 N21 A1JWY 44 A1JWY N40 N5 N 0 1 N N N N N N -6.220 11.020 -12.285 9.487 1.725 -0.546 N40 A1JWY 45 A1JWY N48 N6 N 0 1 N N N N N N -11.406 11.627 -14.617 6.454 -1.201 3.048 N48 A1JWY 46 A1JWY O01 O1 O 0 1 N N N N N N -12.400 13.654 -15.126 4.374 -2.014 2.610 O01 A1JWY 47 A1JWY O44 O2 O 0 1 N N N N N N -5.421 9.539 -13.829 7.624 2.676 -1.295 O44 A1JWY 48 A1JWY H101 H1 H 0 0 N N N N N N -13.034 18.634 -15.755 -0.078 0.802 -2.031 H101 A1JWY 49 A1JWY H151 H2 H 0 0 N N N N N N -12.119 20.826 -22.021 -5.224 2.640 1.849 H151 A1JWY 50 A1JWY H171 H3 H 0 0 N N N N N N -12.772 22.541 -23.457 -8.126 0.563 2.553 H171 A1JWY 51 A1JWY H172 H4 H 0 0 N N N N N N -11.251 23.488 -23.327 -7.352 2.146 2.808 H172 A1JWY 52 A1JWY H201 H5 H 0 0 N N N N N N -15.960 23.400 -24.360 -6.217 3.851 0.611 H201 A1JWY 53 A1JWY H202 H6 H 0 0 N N N N N N -14.328 22.755 -24.742 -7.356 5.149 1.043 H202 A1JWY 54 A1JWY H203 H7 H 0 0 N N N N N N -14.986 22.604 -23.078 -7.018 3.839 2.200 H203 A1JWY 55 A1JWY H221 H8 H 0 0 N N N N N N -15.112 27.747 -23.635 -10.661 3.623 -1.649 H221 A1JWY 56 A1JWY H241 H9 H 0 0 N N N N N N -11.475 25.926 -22.382 -9.740 0.253 0.806 H241 A1JWY 57 A1JWY H281 H10 H 0 0 N N N N N N -10.156 25.349 -18.879 -5.883 -3.192 1.323 H281 A1JWY 58 A1JWY H041 H11 H 0 0 N N N N N N -8.925 15.091 -13.555 5.013 -0.260 -0.873 H041 A1JWY 59 A1JWY H051 H12 H 0 0 N N N N N N -11.909 15.131 -13.543 2.896 -0.674 1.290 H051 A1JWY 60 A1JWY H052 H13 H 0 0 N N N N N N -10.765 14.908 -12.176 3.489 0.893 0.689 H052 A1JWY 61 A1JWY H061 H14 H 0 0 N N N N N N -11.822 17.201 -12.300 1.341 0.263 -0.393 H061 A1JWY 62 A1JWY H062 H15 H 0 0 N N N N N N -10.026 17.205 -12.320 2.665 0.343 -1.579 H062 A1JWY 63 A1JWY H081 H16 H 0 0 N N N N N N -10.053 19.227 -13.468 0.856 -2.726 -2.421 H081 A1JWY 64 A1JWY H082 H17 H 0 0 N N N N N N -11.829 19.106 -13.227 1.187 -1.056 -2.939 H082 A1JWY 65 A1JWY H111 H18 H 0 0 N N N N N N -13.347 19.877 -17.863 -2.195 1.545 -1.021 H111 A1JWY 66 A1JWY H231 H19 H 0 0 N N N N N N -12.848 27.979 -22.717 -11.162 1.321 -0.932 H231 A1JWY 67 A1JWY H251 H20 H 0 0 N N N N N N -12.009 24.819 -20.525 -7.192 -1.015 0.851 H251 A1JWY 68 A1JWY H291 H21 H 0 0 N N N N N N -9.925 26.976 -17.046 -5.737 -5.410 0.270 H291 A1JWY 69 A1JWY H301 H22 H 0 0 N N N N N N -11.349 26.790 -15.042 -4.811 -5.641 -1.998 H301 A1JWY 70 A1JWY H311 H23 H 0 0 N N N N N N -13.006 24.963 -14.884 -4.031 -3.657 -3.225 H311 A1JWY 71 A1JWY H321 H24 H 0 0 N N N N N N -13.244 23.345 -16.721 -4.178 -1.429 -2.191 H321 A1JWY 72 A1JWY H331 H25 H 0 0 N N N N N N -9.800 22.120 -17.090 -2.987 -2.476 0.236 H331 A1JWY 73 A1JWY H341 H26 H 0 0 N N N N N N -9.485 20.883 -14.981 -0.871 -3.202 -0.788 H341 A1JWY 74 A1JWY H351 H27 H 0 0 N N N N N N -9.867 17.890 -15.879 3.638 -1.692 -2.431 H351 A1JWY 75 A1JWY H352 H28 H 0 0 N N N N N N -8.893 17.561 -14.406 3.029 -3.268 -1.871 H352 A1JWY 76 A1JWY H361 H29 H 0 0 N N N N N N -10.748 15.609 -15.859 5.215 -2.718 -0.823 H361 A1JWY 77 A1JWY H362 H30 H 0 0 N N N N N N -8.953 15.566 -15.825 3.919 -2.814 0.394 H362 A1JWY 78 A1JWY H381 H31 H 0 0 N N N N N N -7.573 13.287 -12.957 7.069 0.703 -0.849 H381 A1JWY 79 A1JWY H421 H32 H 0 0 N N N N N N -3.358 9.049 -12.015 10.627 3.088 -2.572 H421 A1JWY 80 A1JWY H431 H34 H 0 0 N N N N N N -2.141 11.370 -11.541 9.446 4.521 -4.108 H431 A1JWY 81 A1JWY H432 H35 H 0 0 N N N N N N -3.633 12.264 -12.228 7.840 4.144 -3.225 H432 A1JWY 82 A1JWY H451 H37 H 0 0 N N N N N N -7.829 8.986 -12.944 10.333 1.119 1.882 H451 A1JWY 83 A1JWY H461 H38 H 0 0 N N N N N N -10.088 9.111 -13.947 9.096 -0.171 3.571 H461 A1JWY 84 A1JWY H401 H40 H 0 0 N N N N N N -6.010 11.545 -11.460 10.453 1.657 -0.591 H401 A1JWY 85 A1JWY H481 H41 H 0 0 N N N N N N -12.114 10.986 -14.913 6.569 -1.519 3.958 H481 A1JWY 86 # 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 A1JWY C02 O01 DOUB N N 1 A1JWY N03 C02 SING N N 2 A1JWY C05 C04 SING N N 3 A1JWY C06 C05 SING N N 4 A1JWY N07 C06 SING N N 5 A1JWY C09 C08 SING N N 6 A1JWY C10 C09 DOUB Y N 7 A1JWY C11 C10 SING Y N 8 A1JWY C12 C11 DOUB Y N 9 A1JWY N14 C13 DOUB Y N 10 A1JWY C15 N14 SING Y N 11 A1JWY C16 C15 DOUB Y N 12 A1JWY C18 C17 SING N N 13 A1JWY C19 C18 DOUB Y N 14 A1JWY C20 C19 SING N N 15 A1JWY N21 C19 SING Y N 16 A1JWY C22 N21 DOUB Y N 17 A1JWY C23 C22 SING Y N 18 A1JWY C24 C23 DOUB Y N 19 A1JWY C17 C16 SING N N 20 A1JWY C25 C16 SING Y N 21 A1JWY C26 C25 DOUB Y N 22 A1JWY C27 C26 SING N N 23 A1JWY C28 C27 DOUB Y N 24 A1JWY C29 C28 SING Y N 25 A1JWY C30 C29 DOUB Y N 26 A1JWY C31 C30 SING Y N 27 A1JWY C32 C31 DOUB Y N 28 A1JWY C13 C12 SING N N 29 A1JWY C33 C12 SING Y N 30 A1JWY C34 C33 DOUB Y N 31 A1JWY C08 N07 SING N N 32 A1JWY C35 N07 SING N N 33 A1JWY C36 C35 SING N N 34 A1JWY C04 N03 SING N N 35 A1JWY C37 N03 SING N N 36 A1JWY C38 C37 DOUB Y N 37 A1JWY C39 C38 SING Y N 38 A1JWY C41 N40 SING N N 39 A1JWY C43 C42 DOUB N N 40 A1JWY C42 C41 SING N N 41 A1JWY O44 C41 DOUB N N 42 A1JWY N40 C39 SING N N 43 A1JWY C45 C39 DOUB Y N 44 A1JWY C46 C45 SING Y N 45 A1JWY C47 C46 DOUB Y N 46 A1JWY N48 C47 SING N N 47 A1JWY C02 N48 SING N N 48 A1JWY C04 C36 SING N N 49 A1JWY C09 C34 SING Y N 50 A1JWY C13 C26 SING Y N 51 A1JWY C18 C24 SING Y N 52 A1JWY C27 C32 SING Y N 53 A1JWY C37 C47 SING Y N 54 A1JWY C10 H101 SING N N 55 A1JWY C15 H151 SING N N 56 A1JWY C17 H171 SING N N 57 A1JWY C17 H172 SING N N 58 A1JWY C20 H201 SING N N 59 A1JWY C20 H202 SING N N 60 A1JWY C20 H203 SING N N 61 A1JWY C22 H221 SING N N 62 A1JWY C24 H241 SING N N 63 A1JWY C28 H281 SING N N 64 A1JWY C04 H041 SING N N 65 A1JWY C05 H051 SING N N 66 A1JWY C05 H052 SING N N 67 A1JWY C06 H061 SING N N 68 A1JWY C06 H062 SING N N 69 A1JWY C08 H081 SING N N 70 A1JWY C08 H082 SING N N 71 A1JWY C11 H111 SING N N 72 A1JWY C23 H231 SING N N 73 A1JWY C25 H251 SING N N 74 A1JWY C29 H291 SING N N 75 A1JWY C30 H301 SING N N 76 A1JWY C31 H311 SING N N 77 A1JWY C32 H321 SING N N 78 A1JWY C33 H331 SING N N 79 A1JWY C34 H341 SING N N 80 A1JWY C35 H351 SING N N 81 A1JWY C35 H352 SING N N 82 A1JWY C36 H361 SING N N 83 A1JWY C36 H362 SING N N 84 A1JWY C38 H381 SING N N 85 A1JWY C42 H421 SING N N 86 A1JWY C43 H431 SING N N 87 A1JWY C43 H432 SING N N 88 A1JWY C45 H451 SING N N 89 A1JWY C46 H461 SING N N 90 A1JWY N40 H401 SING N N 91 A1JWY N48 H481 SING N N 92 # 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 A1JWY InChI InChI 1.06 "InChI=1S/C40H38N6O2/c1-3-38(47)43-33-15-16-36-37(24-33)46(40(48)44-36)34-17-20-45(21-18-34)26-28-11-13-31(14-12-28)39-35(30-8-5-4-6-9-30)23-29(25-42-39)22-32-10-7-19-41-27(32)2/h3-16,19,23-25,34H,1,17-18,20-22,26H2,2H3,(H,43,47)(H,44,48)" A1JWY InChIKey InChI 1.06 AOBAUNYNDIPEOE-UHFFFAOYSA-N A1JWY SMILES_CANONICAL CACTVS 3.385 "Cc1ncccc1Cc2cnc(c3ccc(CN4CCC(CC4)N5C(=O)Nc6ccc(NC(=O)C=C)cc56)cc3)c(c2)c7ccccc7" A1JWY SMILES CACTVS 3.385 "Cc1ncccc1Cc2cnc(c3ccc(CN4CCC(CC4)N5C(=O)Nc6ccc(NC(=O)C=C)cc56)cc3)c(c2)c7ccccc7" A1JWY SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "Cc1c(cccn1)Cc2cc(c(nc2)c3ccc(cc3)CN4CCC(CC4)N5c6cc(ccc6NC5=O)NC(=O)C=C)c7ccccc7" A1JWY SMILES "OpenEye OEToolkits" 2.0.7 "Cc1c(cccn1)Cc2cc(c(nc2)c3ccc(cc3)CN4CCC(CC4)N5c6cc(ccc6NC5=O)NC(=O)C=C)c7ccccc7" # _pdbx_chem_comp_identifier.comp_id A1JWY _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 2.0.7 _pdbx_chem_comp_identifier.identifier "~{N}-[3-[1-[[4-[5-[(2-methylpyridin-3-yl)methyl]-3-phenyl-pyridin-2-yl]phenyl]methyl]piperidin-4-yl]-2-oxidanylidene-1~{H}-benzimidazol-5-yl]prop-2-enamide" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site A1JWY "Create component" 2025-12-17 PDBE A1JWY "Modify PCM" 2025-12-18 PDBE A1JWY "Initial release" 2026-09-16 RCSB # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id A1JWY _pdbx_chem_comp_pcm.modified_residue_id CYS _pdbx_chem_comp_pcm.type None _pdbx_chem_comp_pcm.category "Covalent chemical modification" _pdbx_chem_comp_pcm.position "Amino-acid side chain" _pdbx_chem_comp_pcm.polypeptide_position "Any position" _pdbx_chem_comp_pcm.comp_id_linking_atom C43 _pdbx_chem_comp_pcm.modified_residue_id_linking_atom SG _pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ? _pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ? #