data_A1JM3 # _chem_comp.id A1JM3 _chem_comp.name "N-[(2S)-1-[[(3S)-2,5-bis(oxidanylidene)pyrrolidin-3-yl]amino]-1-oxidanylidene-propan-2-yl]-9-[2-[(9S)-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]nonanamide" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C35 H43 Cl N8 O5 S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2025-08-11 _chem_comp.pdbx_modified_date 2025-10-24 _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 723.285 _chem_comp.one_letter_code ? _chem_comp.three_letter_code A1JM3 _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 9SAI _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBE _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_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 A1JM3 C4 C1 C 0 1 Y N N N N N 149.062 135.983 180.813 -7.364 -0.376 0.792 C4 A1JM3 1 A1JM3 C5 C2 C 0 1 N N N N N N 148.276 136.743 179.882 -7.246 0.382 -0.470 C5 A1JM3 2 A1JM3 C6 C3 C 0 1 Y N N N N N 150.363 135.398 180.609 -6.838 0.095 2.062 C6 A1JM3 3 A1JM3 C7 C4 C 0 1 N N N N N N 151.090 135.379 179.299 -6.068 1.382 2.205 C7 A1JM3 4 A1JM3 C8 C5 C 0 1 Y N N N N N 150.871 134.842 181.741 -7.096 -0.709 3.079 C8 A1JM3 5 A1JM3 N12 N1 N 0 1 N N N N N N 147.952 137.973 180.011 -7.046 -0.124 -1.644 N12 A1JM3 6 A1JM3 C13 C6 C 0 1 Y N N N N N 147.072 136.792 177.720 -6.653 2.670 -1.260 C13 A1JM3 7 A1JM3 C15 C7 C 0 1 Y N N N N N 146.694 134.824 176.439 -7.609 4.610 -0.230 C15 A1JM3 8 A1JM3 C17 C8 C 0 1 N N N N N N 145.434 137.549 170.913 6.663 -0.532 0.158 C17 A1JM3 9 A1JM3 C20 C9 C 0 1 N N N N N N 147.760 140.551 174.295 1.726 -1.052 -0.407 C20 A1JM3 10 A1JM3 C21 C10 C 0 1 N N N N N N 147.542 141.482 175.482 0.508 -0.611 -1.222 C21 A1JM3 11 A1JM3 C22 C11 C 0 1 N N N N N N 147.193 140.793 176.795 -0.743 -1.311 -0.690 C22 A1JM3 12 A1JM3 C26 C12 C 0 1 N N N N N N 145.985 136.185 170.586 7.896 0.158 -0.366 C26 A1JM3 13 A1JM3 C28 C13 C 0 1 N N N N N N 147.777 140.711 180.075 -4.358 -1.304 -1.564 C28 A1JM3 14 A1JM3 C1 C14 C 0 1 Y N N N N N 147.882 134.679 178.500 -8.203 2.433 0.574 C1 A1JM3 15 A1JM3 C11 C15 C 0 1 Y N N N N N 148.656 135.828 182.111 -7.991 -1.597 0.920 C11 A1JM3 16 A1JM3 C14 C16 C 0 1 Y N N N N N 146.544 136.181 176.596 -6.776 4.042 -1.179 C14 A1JM3 17 A1JM3 C18 C17 C 0 1 N N N N N N 145.553 137.947 172.377 5.446 -0.091 -0.657 C18 A1JM3 18 A1JM3 C19 C18 C 0 1 N N N N N N 146.586 139.636 173.969 2.977 -0.351 -0.940 C19 A1JM3 19 A1JM3 C2 C19 C 0 1 Y N N N N N 147.357 134.061 177.377 -8.323 3.806 0.642 C2 A1JM3 20 A1JM3 C23 C20 C 0 1 N N N N N N 147.052 141.734 177.979 -1.961 -0.871 -1.505 C23 A1JM3 21 A1JM3 C25 C21 C 0 1 N N N N N N 146.728 138.861 172.666 4.194 -0.792 -0.124 C25 A1JM3 22 A1JM3 C29 C22 C 0 1 N N N N N N 147.352 139.966 181.323 -5.590 -1.994 -1.039 C29 A1JM3 23 A1JM3 C3 C23 C 0 1 Y N N N N N 147.747 136.051 178.686 -7.370 1.856 -0.384 C3 A1JM3 24 A1JM3 C32 C24 C 0 1 Y N N N N N 147.046 137.628 182.232 -8.020 -2.327 -1.407 C32 A1JM3 25 A1JM3 C34 C25 C 0 1 N N S N N N 147.918 138.539 181.373 -6.807 -1.554 -1.854 C34 A1JM3 26 A1JM3 C35 C26 C 0 1 Y N N N N N 146.418 135.833 183.322 -9.625 -3.117 -0.171 C35 A1JM3 27 A1JM3 C36 C27 C 0 1 N N N N N N 146.390 134.463 183.895 -10.542 -3.419 0.986 C36 A1JM3 28 A1JM3 C39 C28 C 0 1 N N S N N N 145.470 133.905 169.907 10.293 0.592 -0.308 C39 A1JM3 29 A1JM3 C40 C29 C 0 1 N N N N N N 145.586 133.808 168.390 11.510 -0.234 0.022 C40 A1JM3 30 A1JM3 C41 C30 C 0 1 N N N N N N 144.461 132.878 170.403 10.421 1.970 0.343 C41 A1JM3 31 A1JM3 C44 C31 C 0 1 N N S N N N 146.713 132.780 166.501 13.916 -0.614 -0.032 C44 A1JM3 32 A1JM3 C45 C32 C 0 1 N N N N N N 145.929 131.605 165.930 14.461 -0.239 1.329 C45 A1JM3 33 A1JM3 C47 C33 C 0 1 N N N N N N 148.033 131.239 165.283 16.155 0.250 -0.078 C47 A1JM3 34 A1JM3 C48 C34 C 0 1 N N N N N N 148.158 132.486 166.100 15.075 -0.281 -0.994 C48 A1JM3 35 A1JM3 C9 C35 C 0 1 N N N N N N 152.202 134.187 181.955 -6.672 -0.452 4.503 C9 A1JM3 36 A1JM3 N24 N2 N 0 1 N N N N N N 146.803 141.023 179.226 -3.159 -1.541 -0.995 N24 A1JM3 37 A1JM3 N27 N3 N 0 1 N N N N N N 145.077 135.244 170.311 9.095 -0.079 0.202 N27 A1JM3 38 A1JM3 N31 N4 N 0 1 Y N N N N N 147.449 136.350 182.569 -8.533 -2.315 -0.149 N31 A1JM3 39 A1JM3 N33 N5 N 0 1 Y N N N N N 145.860 137.867 182.744 -8.775 -3.112 -2.121 N33 A1JM3 40 A1JM3 N37 N6 N 0 1 Y N N N N N 145.467 136.726 183.434 -9.728 -3.580 -1.391 N37 A1JM3 41 A1JM3 N42 N7 N 0 1 N N N N N N 146.484 132.938 167.925 12.733 0.189 -0.352 N42 A1JM3 42 A1JM3 N46 N8 N 0 1 N N N N N N 146.747 130.825 165.188 15.708 0.228 1.190 N46 A1JM3 43 A1JM3 O30 O1 O 0 1 N N N N N N 148.949 140.997 179.868 -4.444 -0.535 -2.498 O30 A1JM3 44 A1JM3 O38 O2 O 0 1 N N N N N N 147.191 135.967 170.571 7.809 0.927 -1.301 O38 A1JM3 45 A1JM3 O43 O3 O 0 1 N N N N N N 144.880 134.493 167.660 11.388 -1.280 0.623 O43 A1JM3 46 A1JM3 O49 O4 O 0 1 N N N N N N 148.988 130.665 164.758 17.251 0.631 -0.430 O49 A1JM3 47 A1JM3 O50 O5 O 0 1 N N N N N N 144.735 131.426 166.134 13.864 -0.346 2.378 O50 A1JM3 48 A1JM3 S10 S1 S 0 1 Y N N N N N 149.798 134.999 183.087 -8.000 -2.112 2.546 S10 A1JM3 49 A1JM3 CL16 CL1 CL 0 0 N N N N N N 146.036 134.054 175.020 -7.759 6.337 -0.134 CL16 A1JM3 50 A1JM3 H2 H2 H 0 1 N N N N N N 151.718 136.278 179.214 -6.747 2.180 2.508 H2 A1JM3 51 A1JM3 H3 H3 H 0 1 N N N N N N 151.725 134.482 179.245 -5.293 1.259 2.961 H3 A1JM3 52 A1JM3 H4 H4 H 0 1 N N N N N N 150.361 135.362 178.475 -5.608 1.639 1.251 H4 A1JM3 53 A1JM3 H7 H7 H 0 1 N N N N N N 146.959 137.858 177.849 -6.007 2.228 -2.004 H7 A1JM3 54 A1JM3 H8 H8 H 0 1 N N N N N N 145.977 138.292 170.310 6.787 -1.612 0.072 H8 A1JM3 55 A1JM3 H9 H9 H 0 1 N N N N N N 144.369 137.563 170.639 6.515 -0.266 1.205 H9 A1JM3 56 A1JM3 H10 H10 H 0 1 N N N N N N 148.634 139.920 174.513 1.578 -0.785 0.640 H10 A1JM3 57 A1JM3 H11 H11 H 0 1 N N N N N N 147.966 141.170 173.409 1.849 -2.131 -0.493 H11 A1JM3 58 A1JM3 H12 H12 H 0 1 N N N N N N 148.466 142.058 175.636 0.385 0.469 -1.136 H12 A1JM3 59 A1JM3 H13 H13 H 0 1 N N N N N N 146.720 142.168 175.229 0.656 -0.877 -2.269 H13 A1JM3 60 A1JM3 H14 H14 H 0 1 N N N N N N 146.239 140.262 176.662 -0.620 -2.391 -0.776 H14 A1JM3 61 A1JM3 H15 H15 H 0 1 N N N N N N 147.987 140.068 177.025 -0.891 -1.045 0.357 H15 A1JM3 62 A1JM3 H16 H16 H 0 1 N N N N N N 148.402 134.089 179.240 -8.760 1.807 1.255 H16 A1JM3 63 A1JM3 H17 H17 H 0 1 N N N N N N 146.021 136.763 175.852 -6.221 4.674 -1.857 H17 A1JM3 64 A1JM3 H18 H18 H 0 1 N N N N N N 144.629 138.465 172.672 5.323 0.988 -0.571 H18 A1JM3 65 A1JM3 H19 H19 H 0 1 N N N N N N 145.668 137.033 172.977 5.594 -0.358 -1.704 H19 A1JM3 66 A1JM3 H20 H20 H 0 1 N N N N N N 145.678 140.253 173.904 3.125 -0.617 -1.986 H20 A1JM3 67 A1JM3 H21 H21 H 0 1 N N N N N N 146.478 138.911 174.789 2.854 0.729 -0.854 H21 A1JM3 68 A1JM3 H22 H22 H 0 1 N N N N N N 147.465 132.996 177.238 -8.970 4.254 1.381 H22 A1JM3 69 A1JM3 H23 H23 H 0 1 N N N N N N 147.981 142.314 178.082 -2.084 0.209 -1.419 H23 A1JM3 70 A1JM3 H24 H24 H 0 1 N N N N N N 146.212 142.418 177.789 -1.813 -1.137 -2.552 H24 A1JM3 71 A1JM3 H25 H25 H 0 1 N N N N N N 147.640 138.249 172.722 4.318 -1.871 -0.211 H25 A1JM3 72 A1JM3 H26 H26 H 0 1 N N N N N N 146.820 139.582 171.840 4.047 -0.526 0.922 H26 A1JM3 73 A1JM3 H27 H27 H 0 1 N N N N N N 147.710 140.519 182.204 -5.467 -3.074 -1.125 H27 A1JM3 74 A1JM3 H28 H28 H 0 1 N N N N N N 146.254 139.912 181.345 -5.738 -1.728 0.007 H28 A1JM3 75 A1JM3 H29 H29 H 0 1 N N N N N N 148.935 138.569 181.792 -6.624 -1.741 -2.912 H29 A1JM3 76 A1JM3 H30 H30 H 0 1 N N N N N N 145.443 134.309 184.432 -10.177 -4.296 1.520 H30 A1JM3 77 A1JM3 H31 H31 H 0 1 N N N N N N 146.476 133.725 183.084 -10.566 -2.565 1.663 H31 A1JM3 78 A1JM3 H32 H32 H 0 1 N N N N N N 147.231 134.340 184.593 -11.547 -3.614 0.611 H32 A1JM3 79 A1JM3 H33 H33 H 0 1 N N N N N N 146.451 133.667 170.345 10.213 0.706 -1.389 H33 A1JM3 80 A1JM3 H34 H34 H 0 1 N N N N N N 144.376 132.946 171.498 10.501 1.856 1.424 H34 A1JM3 81 A1JM3 H35 H35 H 0 1 N N N N N N 143.481 133.077 169.946 11.313 2.470 -0.037 H35 A1JM3 82 A1JM3 H36 H36 H 0 1 N N N N N N 144.798 131.869 170.124 9.541 2.568 0.105 H36 A1JM3 83 A1JM3 H37 H37 H 0 1 N N N N N N 146.392 133.694 165.980 13.678 -1.677 -0.071 H37 A1JM3 84 A1JM3 H38 H38 H 0 1 N N N N N N 148.788 132.317 166.986 15.416 -1.178 -1.510 H38 A1JM3 85 A1JM3 H39 H39 H 0 1 N N N N N N 148.578 133.309 165.503 14.770 0.483 -1.710 H39 A1JM3 86 A1JM3 H40 H40 H 0 1 N N N N N N 152.298 133.886 183.009 -7.450 0.111 5.018 H40 A1JM3 87 A1JM3 H41 H41 H 0 1 N N N N N N 152.281 133.298 181.311 -6.514 -1.403 5.011 H41 A1JM3 88 A1JM3 H42 H42 H 0 1 N N N N N N 153.004 134.896 181.702 -5.745 0.121 4.508 H42 A1JM3 89 A1JM3 H43 H43 H 0 1 N N N N N N 145.865 140.760 179.451 -3.090 -2.156 -0.248 H43 A1JM3 90 A1JM3 H44 H44 H 0 1 N N N N N N 144.105 135.467 170.385 9.164 -0.694 0.949 H44 A1JM3 91 A1JM3 H45 H45 H 0 1 N N N N N N 147.010 132.384 168.570 12.831 1.026 -0.834 H45 A1JM3 92 A1JM3 H46 H46 H 0 1 N N N N N N 146.443 130.045 164.641 16.244 0.527 1.941 H46 A1JM3 93 # 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 A1JM3 O49 C47 DOUB N N 1 A1JM3 N46 C47 SING N N 2 A1JM3 N46 C45 SING N N 3 A1JM3 C47 C48 SING N N 4 A1JM3 C45 O50 DOUB N N 5 A1JM3 C45 C44 SING N N 6 A1JM3 C48 C44 SING N N 7 A1JM3 C44 N42 SING N N 8 A1JM3 O43 C40 DOUB N N 9 A1JM3 N42 C40 SING N N 10 A1JM3 C40 C39 SING N N 11 A1JM3 C39 N27 SING N N 12 A1JM3 C39 C41 SING N N 13 A1JM3 N27 C26 SING N N 14 A1JM3 O38 C26 DOUB N N 15 A1JM3 C26 C17 SING N N 16 A1JM3 C17 C18 SING N N 17 A1JM3 C18 C25 SING N N 18 A1JM3 C25 C19 SING N N 19 A1JM3 C19 C20 SING N N 20 A1JM3 C20 C21 SING N N 21 A1JM3 CL16 C15 SING N N 22 A1JM3 C21 C22 SING N N 23 A1JM3 C15 C14 DOUB Y N 24 A1JM3 C15 C2 SING Y N 25 A1JM3 C14 C13 SING Y N 26 A1JM3 C22 C23 SING N N 27 A1JM3 C2 C1 DOUB Y N 28 A1JM3 C13 C3 DOUB Y N 29 A1JM3 C23 N24 SING N N 30 A1JM3 C1 C3 SING Y N 31 A1JM3 C3 C5 SING N N 32 A1JM3 N24 C28 SING N N 33 A1JM3 C7 C6 SING N N 34 A1JM3 O30 C28 DOUB N N 35 A1JM3 C5 N12 DOUB N N 36 A1JM3 C5 C4 SING N N 37 A1JM3 N12 C34 SING N N 38 A1JM3 C28 C29 SING N N 39 A1JM3 C6 C4 SING Y N 40 A1JM3 C6 C8 DOUB Y N 41 A1JM3 C4 C11 DOUB Y N 42 A1JM3 C29 C34 SING N N 43 A1JM3 C34 C32 SING N N 44 A1JM3 C8 C9 SING N N 45 A1JM3 C8 S10 SING Y N 46 A1JM3 C11 N31 SING N N 47 A1JM3 C11 S10 SING Y N 48 A1JM3 C32 N31 SING Y N 49 A1JM3 C32 N33 DOUB Y N 50 A1JM3 N31 C35 SING Y N 51 A1JM3 N33 N37 SING Y N 52 A1JM3 C35 N37 DOUB Y N 53 A1JM3 C35 C36 SING N N 54 A1JM3 C7 H2 SING N N 55 A1JM3 C7 H3 SING N N 56 A1JM3 C7 H4 SING N N 57 A1JM3 C13 H7 SING N N 58 A1JM3 C17 H8 SING N N 59 A1JM3 C17 H9 SING N N 60 A1JM3 C20 H10 SING N N 61 A1JM3 C20 H11 SING N N 62 A1JM3 C21 H12 SING N N 63 A1JM3 C21 H13 SING N N 64 A1JM3 C22 H14 SING N N 65 A1JM3 C22 H15 SING N N 66 A1JM3 C1 H16 SING N N 67 A1JM3 C14 H17 SING N N 68 A1JM3 C18 H18 SING N N 69 A1JM3 C18 H19 SING N N 70 A1JM3 C19 H20 SING N N 71 A1JM3 C19 H21 SING N N 72 A1JM3 C2 H22 SING N N 73 A1JM3 C23 H23 SING N N 74 A1JM3 C23 H24 SING N N 75 A1JM3 C25 H25 SING N N 76 A1JM3 C25 H26 SING N N 77 A1JM3 C29 H27 SING N N 78 A1JM3 C29 H28 SING N N 79 A1JM3 C34 H29 SING N N 80 A1JM3 C36 H30 SING N N 81 A1JM3 C36 H31 SING N N 82 A1JM3 C36 H32 SING N N 83 A1JM3 C39 H33 SING N N 84 A1JM3 C41 H34 SING N N 85 A1JM3 C41 H35 SING N N 86 A1JM3 C41 H36 SING N N 87 A1JM3 C44 H37 SING N N 88 A1JM3 C48 H38 SING N N 89 A1JM3 C48 H39 SING N N 90 A1JM3 C9 H40 SING N N 91 A1JM3 C9 H41 SING N N 92 A1JM3 C9 H42 SING N N 93 A1JM3 N24 H43 SING N N 94 A1JM3 N27 H44 SING N N 95 A1JM3 N42 H45 SING N N 96 A1JM3 N46 H46 SING N N 97 # 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 A1JM3 InChI InChI 1.06 "InChI=1S/C35H43ClN8O5S/c1-19-21(3)50-35-30(19)31(23-12-14-24(36)15-13-23)39-25(32-43-42-22(4)44(32)35)17-28(46)37-16-10-8-6-5-7-9-11-27(45)38-20(2)33(48)40-26-18-29(47)41-34(26)49/h12-15,20,25-26H,5-11,16-18H2,1-4H3,(H,37,46)(H,38,45)(H,40,48)(H,41,47,49)/t20-,25-,26-/m0/s1" A1JM3 InChIKey InChI 1.06 FNQIHJLUXRFLHT-XZZVZQAVSA-N A1JM3 SMILES_CANONICAL CACTVS 3.385 "C[C@H](NC(=O)CCCCCCCCNC(=O)C[C@@H]1N=C(c2ccc(Cl)cc2)c3c(C)c(C)sc3n4c(C)nnc14)C(=O)N[C@H]5CC(=O)NC5=O" A1JM3 SMILES CACTVS 3.385 "C[CH](NC(=O)CCCCCCCCNC(=O)C[CH]1N=C(c2ccc(Cl)cc2)c3c(C)c(C)sc3n4c(C)nnc14)C(=O)N[CH]5CC(=O)NC5=O" A1JM3 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "Cc1c(sc-2c1C(=N[C@H](c3n2c(nn3)C)CC(=O)NCCCCCCCCC(=O)N[C@@H](C)C(=O)N[C@H]4CC(=O)NC4=O)c5ccc(cc5)Cl)C" A1JM3 SMILES "OpenEye OEToolkits" 2.0.7 "Cc1c(sc-2c1C(=NC(c3n2c(nn3)C)CC(=O)NCCCCCCCCC(=O)NC(C)C(=O)NC4CC(=O)NC4=O)c5ccc(cc5)Cl)C" # _pdbx_chem_comp_identifier.comp_id A1JM3 _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}-[(2~{S})-1-[[(3~{S})-2,5-bis(oxidanylidene)pyrrolidin-3-yl]amino]-1-oxidanylidene-propan-2-yl]-9-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]nonanamide" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site A1JM3 "Create component" 2025-08-11 PDBE A1JM3 "Initial release" 2025-10-29 RCSB #