data_A1JWW # _chem_comp.id A1JWW _chem_comp.name "~{N}-[3-[1-[[4-[5-[(6-azanyl-2-methyl-pyridin-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 H41 N7 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 651.799 _chem_comp.one_letter_code ? _chem_comp.three_letter_code A1JWW _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 9TN4 _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBE _chem_comp.pdbx_pcm Y # 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 A1JWW C10 C1 C 0 1 Y N N N N N 12.067 -16.078 15.964 -0.859 -1.724 -2.886 C10 A1JWW 1 A1JWW C13 C2 C 0 1 Y N N N N N 11.580 -13.699 18.985 -4.127 -0.874 -1.237 C13 A1JWW 2 A1JWW C15 C3 C 0 1 Y N N N N N 11.851 -13.910 21.301 -5.874 0.505 -1.852 C15 A1JWW 3 A1JWW C17 C4 C 0 1 N N N N N N 12.146 -11.893 22.878 -8.132 0.430 -0.765 C17 A1JWW 4 A1JWW C20 C5 C 0 1 N N N N N N 15.004 -11.275 22.887 -8.097 0.132 2.105 C20 A1JWW 5 A1JWW C22 C6 C 0 1 Y N N N N N 14.908 -14.100 25.254 -8.216 3.797 1.792 C22 A1JWW 6 A1JWW C24 C7 C 0 1 Y N N N N N 13.571 -14.466 25.315 -8.235 4.010 0.417 C24 A1JWW 7 A1JWW C26 C8 C 0 1 Y N N N N N 11.844 -11.713 20.333 -6.235 -1.064 -0.083 C26 A1JWW 8 A1JWW C28 C9 C 0 1 Y N N N N N 11.552 -11.384 17.860 -4.355 -2.563 0.602 C28 A1JWW 9 A1JWW C02 C10 C 0 1 N N N N N N 11.036 -22.654 14.347 4.946 2.502 -1.684 C02 A1JWW 10 A1JWW C04 C11 C 0 1 N N N N N N 9.809 -20.515 13.497 4.451 0.172 -0.915 C04 A1JWW 11 A1JWW C05 C12 C 0 1 N N N N N N 9.857 -19.985 14.840 3.011 0.467 -0.484 C05 A1JWW 12 A1JWW C06 C13 C 0 1 N N N N N N 9.814 -18.437 14.866 2.196 -0.828 -0.524 C06 A1JWW 13 A1JWW C08 C14 C 0 1 N N N N N N 10.605 -16.613 13.910 1.331 -2.546 -1.995 C08 A1JWW 14 A1JWW C09 C15 C 0 1 Y N N N N N 10.897 -15.857 15.251 -0.099 -2.112 -1.797 C09 A1JWW 15 A1JWW C11 C16 C 0 1 Y N N N N N 12.299 -15.385 17.165 -2.167 -1.322 -2.711 C11 A1JWW 16 A1JWW C12 C17 C 0 1 Y N N N N N 11.357 -14.464 17.639 -2.723 -1.306 -1.433 C12 A1JWW 17 A1JWW C16 C18 C 0 1 Y N N N N N 11.947 -12.530 21.463 -6.711 -0.054 -0.904 C16 A1JWW 18 A1JWW C18 C19 C 0 1 Y N N N N N 13.121 -12.719 23.752 -8.163 1.647 0.123 C18 A1JWW 19 A1JWW C19 C20 C 0 1 Y N N N N N 14.482 -12.422 23.758 -8.146 1.510 1.496 C19 A1JWW 20 A1JWW C25 C21 C 0 1 Y N N N N N 12.652 -13.756 24.547 -8.208 2.919 -0.433 C25 A1JWW 21 A1JWW C27 C22 C 0 1 Y N N N N N 11.660 -12.301 19.075 -4.915 -1.487 -0.249 C27 A1JWW 22 A1JWW C29 C23 C 0 1 Y N N N N N 12.436 -11.503 16.805 -3.687 -3.640 0.020 C29 A1JWW 23 A1JWW C30 C24 C 0 1 Y N N N N N 12.325 -10.662 15.719 -3.168 -4.639 0.817 C30 A1JWW 24 A1JWW C31 C25 C 0 1 Y N N N N N 11.334 -9.693 15.689 -3.309 -4.574 2.191 C31 A1JWW 25 A1JWW C32 C26 C 0 1 Y N N N N N 10.457 -9.567 16.746 -3.970 -3.509 2.775 C32 A1JWW 26 A1JWW C33 C27 C 0 1 Y N N N N N 10.566 -10.411 17.834 -4.489 -2.501 1.988 C33 A1JWW 27 A1JWW C34 C28 C 0 1 Y N N N N N 10.180 -14.256 16.926 -1.953 -1.698 -0.338 C34 A1JWW 28 A1JWW C35 C29 C 0 1 Y N N N N N 9.952 -14.941 15.733 -0.647 -2.104 -0.527 C35 A1JWW 29 A1JWW C36 C30 C 0 1 N N N N N N 10.739 -18.376 12.674 3.583 -1.713 -2.304 C36 A1JWW 30 A1JWW C37 C31 C 0 1 N N N N N N 10.804 -19.912 12.651 4.439 -0.445 -2.317 C37 A1JWW 31 A1JWW C38 C32 C 0 1 Y N N N N N 8.903 -22.988 13.412 6.362 1.682 -0.182 C38 A1JWW 32 A1JWW C39 C33 C 0 1 Y N N N N N 7.628 -22.887 12.813 7.082 0.942 0.743 C39 A1JWW 33 A1JWW C40 C34 C 0 1 Y N N N N N 6.844 -24.045 12.610 8.207 1.493 1.341 C40 A1JWW 34 A1JWW C42 C35 C 0 1 N N N N N N 4.324 -24.579 12.520 9.034 -0.590 2.143 C42 A1JWW 35 A1JWW C43 C36 C 0 1 N N N N N N 2.986 -24.390 11.789 9.732 -1.404 3.202 C43 A1JWW 36 A1JWW C44 C37 C 0 1 N N N N N N 1.774 -24.598 12.701 9.703 -2.883 2.811 C44 A1JWW 37 A1JWW C46 C38 C 0 1 Y N N N N N 7.341 -25.306 12.997 8.609 2.782 1.015 C46 A1JWW 38 A1JWW C47 C39 C 0 1 Y N N N N N 8.610 -25.411 13.593 7.894 3.522 0.095 C47 A1JWW 39 A1JWW C48 C40 C 0 1 Y N N N N N 9.393 -24.247 13.801 6.772 2.976 -0.510 C48 A1JWW 40 A1JWW N03 N1 N 0 1 N N N N N N 9.924 -21.968 13.752 5.221 1.418 -0.935 N03 A1JWW 41 A1JWW N07 N2 N 0 1 N N N N N N 10.787 -17.821 14.004 2.215 -1.378 -1.886 N07 A1JWW 42 A1JWW N14 N3 N 0 1 Y N N N N N 11.674 -14.430 20.089 -4.631 0.091 -1.993 N14 A1JWW 43 A1JWW N21 N4 N 0 1 Y N N N N N 15.334 -13.107 24.495 -8.172 2.569 2.283 N21 A1JWW 44 A1JWW N23 N5 N 0 1 N N N N N N 15.872 -14.828 26.047 -8.236 4.885 2.658 N23 A1JWW 45 A1JWW N41 N6 N 0 1 N N N N N N 5.532 -23.920 11.984 8.937 0.747 2.275 N41 A1JWW 46 A1JWW N49 N7 N 0 1 N N N N N N 10.729 -24.060 14.390 5.865 3.458 -1.453 N49 A1JWW 47 A1JWW O01 O1 O 0 1 N N N N N N 12.034 -22.161 14.740 4.011 2.600 -2.458 O01 A1JWW 48 A1JWW O45 O2 O 0 1 N N N N N N 4.374 -25.254 13.503 8.560 -1.139 1.170 O45 A1JWW 49 A1JWW H101 H1 H 0 0 N N N N N N 12.799 -16.782 15.596 -0.425 -1.732 -3.875 H101 A1JWW 50 A1JWW H151 H2 H 0 0 N N N N N N 11.920 -14.560 22.161 -6.245 1.295 -2.488 H151 A1JWW 51 A1JWW H171 H3 H 0 0 N N N N N N 11.171 -11.841 23.385 -8.526 0.687 -1.748 H171 A1JWW 52 A1JWW H172 H4 H 0 0 N N N N N N 12.551 -10.877 22.757 -8.742 -0.357 -0.323 H172 A1JWW 53 A1JWW H201 H5 H 0 0 N N N N N N 16.093 -11.184 23.013 -7.063 -0.206 2.157 H201 A1JWW 54 A1JWW H202 H6 H 0 0 N N N N N N 14.773 -11.482 21.832 -8.520 0.163 3.109 H202 A1JWW 55 A1JWW H203 H7 H 0 0 N N N N N N 14.520 -10.335 23.190 -8.675 -0.558 1.489 H203 A1JWW 56 A1JWW H241 H8 H 0 0 N N N N N N 13.250 -15.283 25.944 -8.270 5.014 0.019 H241 A1JWW 57 A1JWW H261 H9 H 0 0 N N N N N N 11.906 -10.639 20.429 -6.870 -1.515 0.664 H261 A1JWW 58 A1JWW H041 H10 H 0 0 N N N N N N 8.814 -20.316 13.073 4.906 -0.527 -0.214 H041 A1JWW 59 A1JWW H051 H11 H 0 0 N N N N N N 8.995 -20.372 15.403 3.010 0.866 0.530 H051 A1JWW 60 A1JWW H052 H12 H 0 0 N N N N N N 10.789 -20.321 15.319 2.570 1.196 -1.163 H052 A1JWW 61 A1JWW H061 H13 H 0 0 N N N N N N 8.812 -18.111 14.549 2.630 -1.552 0.166 H061 A1JWW 62 A1JWW H062 H14 H 0 0 N N N N N N 10.000 -18.101 15.897 1.167 -0.619 -0.231 H062 A1JWW 63 A1JWW H081 H15 H 0 0 N N N N N N 9.557 -16.435 13.625 1.598 -3.276 -1.231 H081 A1JWW 64 A1JWW H082 H16 H 0 0 N N N N N N 11.270 -16.216 13.129 1.441 -2.994 -2.981 H082 A1JWW 65 A1JWW H111 H17 H 0 0 N N N N N N 13.206 -15.564 17.723 -2.758 -1.019 -3.562 H111 A1JWW 66 A1JWW H251 H18 H 0 0 N N N N N N 11.601 -14.006 24.569 -8.222 3.054 -1.504 H251 A1JWW 67 A1JWW H291 H19 H 0 0 N N N N N N 13.212 -12.253 16.831 -3.577 -3.692 -1.054 H291 A1JWW 68 A1JWW H301 H20 H 0 0 N N N N N N 13.011 -10.758 14.890 -2.651 -5.474 0.367 H301 A1JWW 69 A1JWW H311 H21 H 0 0 N N N N N N 11.249 -9.036 14.836 -2.901 -5.359 2.812 H311 A1JWW 70 A1JWW H321 H22 H 0 0 N N N N N N 9.687 -8.810 16.723 -4.077 -3.464 3.849 H321 A1JWW 71 A1JWW H331 H23 H 0 0 N N N N N N 9.883 -10.312 18.664 -5.001 -1.667 2.445 H331 A1JWW 72 A1JWW H341 H24 H 0 0 N N N N N N 9.441 -13.562 17.298 -2.378 -1.689 0.654 H341 A1JWW 73 A1JWW H351 H25 H 0 0 N N N N N N 9.043 -14.765 15.178 -0.050 -2.407 0.320 H351 A1JWW 74 A1JWW H361 H26 H 0 0 N N N N N N 9.799 -18.060 12.198 3.560 -2.147 -3.304 H361 A1JWW 75 A1JWW H362 H27 H 0 0 N N N N N N 11.591 -17.982 12.101 4.010 -2.432 -1.606 H362 A1JWW 76 A1JWW H371 H28 H 0 0 N N N N N N 10.646 -20.257 11.618 4.020 0.270 -3.025 H371 A1JWW 77 A1JWW H372 H29 H 0 0 N N N N N N 11.800 -20.229 12.995 5.457 -0.696 -2.612 H372 A1JWW 78 A1JWW H391 H30 H 0 0 N N N N N N 7.251 -21.922 12.509 6.769 -0.060 0.997 H391 A1JWW 79 A1JWW H431 H31 H 0 0 N N N N N N 2.932 -25.114 10.963 10.766 -1.072 3.292 H431 A1JWW 80 A1JWW H432 H32 H 0 0 N N N N N N 2.949 -23.368 11.384 9.223 -1.270 4.156 H432 A1JWW 81 A1JWW H441 H33 H 0 0 N N N N N N 0.850 -24.450 12.123 8.668 -3.214 2.720 H441 A1JWW 82 A1JWW H442 H34 H 0 0 N N N N N N 1.792 -25.620 13.107 10.212 -3.016 1.856 H442 A1JWW 83 A1JWW H443 H35 H 0 0 N N N N N N 1.809 -23.874 13.528 10.208 -3.471 3.577 H443 A1JWW 84 A1JWW H461 H36 H 0 0 N N N N N N 6.746 -26.193 12.835 9.485 3.207 1.483 H461 A1JWW 85 A1JWW H471 H37 H 0 0 N N N N N N 8.988 -26.377 13.892 8.209 4.524 -0.155 H471 A1JWW 86 A1JWW H231 H39 H 0 0 N N N N N N 16.784 -14.448 25.895 -8.219 4.742 3.617 H231 A1JWW 87 A1JWW H232 H40 H 0 0 N N N N N N 15.635 -14.749 27.015 -8.268 5.787 2.302 H232 A1JWW 88 A1JWW H411 H41 H 0 0 N N N N N N 5.447 -23.364 11.157 9.372 1.194 3.018 H411 A1JWW 89 A1JWW H491 H42 H 0 0 N N N N N N 11.318 -24.781 14.755 5.892 4.333 -1.872 H491 A1JWW 90 # 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 A1JWW C02 O01 DOUB N N 1 A1JWW N03 C02 SING N N 2 A1JWW C05 C04 SING N N 3 A1JWW C06 C05 SING N N 4 A1JWW N07 C06 SING N N 5 A1JWW C09 C08 SING N N 6 A1JWW C10 C09 DOUB Y N 7 A1JWW C11 C10 SING Y N 8 A1JWW C12 C11 DOUB Y N 9 A1JWW N14 C13 DOUB Y N 10 A1JWW C15 N14 SING Y N 11 A1JWW C16 C15 DOUB Y N 12 A1JWW C18 C17 SING N N 13 A1JWW C19 C18 DOUB Y N 14 A1JWW C20 C19 SING N N 15 A1JWW N21 C19 SING Y N 16 A1JWW C22 N21 DOUB Y N 17 A1JWW N23 C22 SING N N 18 A1JWW C24 C22 SING Y N 19 A1JWW C25 C24 DOUB Y N 20 A1JWW C17 C16 SING N N 21 A1JWW C26 C16 SING Y N 22 A1JWW C27 C26 DOUB Y N 23 A1JWW C28 C27 SING N N 24 A1JWW C29 C28 DOUB Y N 25 A1JWW C30 C29 SING Y N 26 A1JWW C31 C30 DOUB Y N 27 A1JWW C32 C31 SING Y N 28 A1JWW C33 C32 DOUB Y N 29 A1JWW C13 C12 SING N N 30 A1JWW C34 C12 SING Y N 31 A1JWW C35 C34 DOUB Y N 32 A1JWW C08 N07 SING N N 33 A1JWW C36 N07 SING N N 34 A1JWW C37 C36 SING N N 35 A1JWW C04 N03 SING N N 36 A1JWW C38 N03 SING N N 37 A1JWW C39 C38 DOUB Y N 38 A1JWW C40 C39 SING Y N 39 A1JWW C42 N41 SING N N 40 A1JWW C44 C43 SING N N 41 A1JWW C43 C42 SING N N 42 A1JWW O45 C42 DOUB N N 43 A1JWW N41 C40 SING N N 44 A1JWW C46 C40 DOUB Y N 45 A1JWW C47 C46 SING Y N 46 A1JWW C48 C47 DOUB Y N 47 A1JWW N49 C48 SING N N 48 A1JWW C02 N49 SING N N 49 A1JWW C04 C37 SING N N 50 A1JWW C09 C35 SING Y N 51 A1JWW C13 C27 SING Y N 52 A1JWW C18 C25 SING Y N 53 A1JWW C28 C33 SING Y N 54 A1JWW C38 C48 SING Y N 55 A1JWW C10 H101 SING N N 56 A1JWW C15 H151 SING N N 57 A1JWW C17 H171 SING N N 58 A1JWW C17 H172 SING N N 59 A1JWW C20 H201 SING N N 60 A1JWW C20 H202 SING N N 61 A1JWW C20 H203 SING N N 62 A1JWW C24 H241 SING N N 63 A1JWW C26 H261 SING N N 64 A1JWW C04 H041 SING N N 65 A1JWW C05 H051 SING N N 66 A1JWW C05 H052 SING N N 67 A1JWW C06 H061 SING N N 68 A1JWW C06 H062 SING N N 69 A1JWW C08 H081 SING N N 70 A1JWW C08 H082 SING N N 71 A1JWW C11 H111 SING N N 72 A1JWW C25 H251 SING N N 73 A1JWW C29 H291 SING N N 74 A1JWW C30 H301 SING N N 75 A1JWW C31 H311 SING N N 76 A1JWW C32 H321 SING N N 77 A1JWW C33 H331 SING N N 78 A1JWW C34 H341 SING N N 79 A1JWW C35 H351 SING N N 80 A1JWW C36 H361 SING N N 81 A1JWW C36 H362 SING N N 82 A1JWW C37 H371 SING N N 83 A1JWW C37 H372 SING N N 84 A1JWW C39 H391 SING N N 85 A1JWW C43 H431 SING N N 86 A1JWW C43 H432 SING N N 87 A1JWW C44 H441 SING N N 88 A1JWW C44 H442 SING N N 89 A1JWW C44 H443 SING N N 90 A1JWW C46 H461 SING N N 91 A1JWW C47 H471 SING N N 92 A1JWW N23 H231 SING N N 93 A1JWW N23 H232 SING N N 94 A1JWW N41 H411 SING N N 95 A1JWW N49 H491 SING N N 96 # 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 A1JWW InChI InChI 1.06 "InChI=1S/C40H41N7O2/c1-3-38(48)44-32-14-15-35-36(23-32)47(40(49)45-35)33-17-19-46(20-18-33)25-27-9-11-30(12-10-27)39-34(29-7-5-4-6-8-29)22-28(24-42-39)21-31-13-16-37(41)43-26(31)2/h4-16,22-24,33H,3,17-21,25H2,1-2H3,(H2,41,43)(H,44,48)(H,45,49)" A1JWW InChIKey InChI 1.06 XATKFXWTUHZRKY-UHFFFAOYSA-N A1JWW SMILES_CANONICAL CACTVS 3.385 "CCC(=O)Nc1ccc2NC(=O)N(C3CCN(CC3)Cc4ccc(cc4)c5ncc(Cc6ccc(N)nc6C)cc5c7ccccc7)c2c1" A1JWW SMILES CACTVS 3.385 "CCC(=O)Nc1ccc2NC(=O)N(C3CCN(CC3)Cc4ccc(cc4)c5ncc(Cc6ccc(N)nc6C)cc5c7ccccc7)c2c1" A1JWW SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CCC(=O)Nc1ccc2c(c1)N(C(=O)N2)C3CCN(CC3)Cc4ccc(cc4)c5c(cc(cn5)Cc6ccc(nc6C)N)c7ccccc7" A1JWW SMILES "OpenEye OEToolkits" 2.0.7 "CCC(=O)Nc1ccc2c(c1)N(C(=O)N2)C3CCN(CC3)Cc4ccc(cc4)c5c(cc(cn5)Cc6ccc(nc6C)N)c7ccccc7" # _pdbx_chem_comp_identifier.comp_id A1JWW _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-[(6-azanyl-2-methyl-pyridin-3-yl)methyl]-3-phenyl-pyridin-2-yl]phenyl]methyl]piperidin-4-yl]-2-oxidanylidene-1~{H}-benzimidazol-5-yl]propanamide" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site A1JWW "Create component" 2025-12-17 PDBE A1JWW "Modify PCM" 2025-12-18 PDBE A1JWW "Initial release" 2026-09-16 RCSB # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id A1JWW _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 C44 _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 ? #