data_A1D6X # _chem_comp.id A1D6X _chem_comp.name "(2~{S})-2-[2-[3,5-bis(fluoranyl)phenyl]ethanoylamino]-~{N}-[(3~{S})-1-methyl-2-oxidanylidene-5-phenyl-3~{H}-1,4-benzodiazepin-3-yl]propanamide" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C27 H24 F2 N4 O3" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "Compound E; gamma-Secretase Inhibitor XXI" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2024-03-22 _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 490.501 _chem_comp.one_letter_code ? _chem_comp.three_letter_code A1D6X _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 9K95 _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBC _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 A1D6X C10 C1 C 0 1 N N S N N N 169.189 175.657 144.826 2.644 1.092 1.588 C10 A1D6X 1 A1D6X C13 C2 C 0 1 N N N N N N 167.799 177.315 143.369 3.652 -0.676 0.309 C13 A1D6X 2 A1D6X C15 C3 C 0 1 N N S N N N 168.895 174.257 148.478 -0.992 1.144 0.391 C15 A1D6X 3 A1D6X C17 C4 C 0 1 Y N N N N N 167.248 178.738 143.433 4.291 -2.013 0.282 C17 A1D6X 4 A1D6X C20 C5 C 0 1 N N N N N N 171.894 176.769 142.269 5.088 3.263 -0.357 C20 A1D6X 5 A1D6X C21 C6 C 0 1 N N N N N N 169.668 172.971 148.765 -1.005 2.475 -0.363 C21 A1D6X 6 A1D6X C22 C7 C 0 1 Y N N N N N 168.818 175.403 139.291 3.154 1.240 -3.457 C22 A1D6X 7 A1D6X C24 C8 C 0 1 N N N N N N 167.091 175.319 149.869 -3.344 0.575 0.678 C24 A1D6X 8 A1D6X C26 C9 C 0 1 Y N N N N N 167.222 179.606 142.176 5.144 -2.360 -0.766 C26 A1D6X 9 A1D6X C28 C10 C 0 1 Y N N N N N 164.790 176.266 149.869 -5.718 -0.074 0.693 C28 A1D6X 10 A1D6X C11 C11 C 0 1 Y N N N N N 169.547 176.202 141.736 3.707 1.404 -1.117 C11 A1D6X 11 A1D6X C12 C12 C 0 1 Y N N N N N 168.145 176.678 142.010 3.494 0.029 -0.973 C12 A1D6X 12 A1D6X C14 C13 C 0 1 N N N N N N 170.517 176.111 144.192 3.624 2.155 1.173 C14 A1D6X 13 A1D6X C16 C14 C 0 1 N N N N N N 168.714 174.420 146.971 0.228 1.078 1.274 C16 A1D6X 14 A1D6X C18 C15 C 0 1 Y N N N N N 169.902 175.558 140.370 3.531 1.996 -2.369 C18 A1D6X 15 A1D6X C19 C16 C 0 1 Y N N N N N 167.042 176.529 140.934 3.113 -0.728 -2.091 C19 A1D6X 16 A1D6X C23 C17 C 0 1 Y N N N N N 167.378 175.891 139.574 2.947 -0.128 -3.318 C23 A1D6X 17 A1D6X C25 C18 C 0 1 Y N N N N N 166.724 179.293 144.755 4.046 -2.927 1.306 C25 A1D6X 18 A1D6X C27 C19 C 0 1 N N N N N N 165.717 175.248 150.529 -4.585 0.467 1.527 C27 A1D6X 19 A1D6X C29 C20 C 0 1 Y N N N N N 166.174 180.716 144.821 4.644 -4.170 1.276 C29 A1D6X 20 A1D6X C30 C21 C 0 1 Y N N N N N 166.671 181.029 142.243 5.736 -3.606 -0.785 C30 A1D6X 21 A1D6X C31 C22 C 0 1 Y N N N N N 166.147 181.584 143.565 5.486 -4.510 0.231 C31 A1D6X 22 A1D6X C32 C23 C 0 1 Y N N N N N 163.981 175.875 148.631 -6.540 0.793 -0.000 C32 A1D6X 23 A1D6X C33 C24 C 0 1 Y N N N N N 164.671 177.677 150.444 -5.930 -1.438 0.618 C33 A1D6X 24 A1D6X C34 C25 C 0 1 Y N N N N N 163.745 178.693 149.783 -6.970 -1.936 -0.147 C34 A1D6X 25 A1D6X C35 C26 C 0 1 Y N N N N N 163.055 176.897 147.973 -7.578 0.297 -0.771 C35 A1D6X 26 A1D6X C36 C27 C 0 1 Y N N N N N 162.939 178.304 148.550 -7.798 -1.068 -0.838 C36 A1D6X 27 A1D6X F01 F1 F 0 1 N N N N N N 163.639 179.953 150.295 -7.177 -3.269 -0.221 F01 A1D6X 28 A1D6X F02 F2 F 0 1 N N N N N N 162.331 176.550 146.868 -8.386 1.146 -1.444 F02 A1D6X 29 A1D6X N06 N1 N 0 1 N N N N N N 170.596 176.343 142.758 4.091 2.229 -0.071 N06 A1D6X 30 A1D6X N07 N2 N 0 1 N N N N N N 169.371 175.507 146.270 1.458 1.156 0.730 N07 A1D6X 31 A1D6X N08 N3 N 0 1 N N N N N N 168.106 176.600 144.590 3.277 -0.219 1.451 N08 A1D6X 32 A1D6X N09 N4 N 0 1 N N N N N N 167.589 174.189 149.108 -2.198 1.039 1.216 N09 A1D6X 33 A1D6X O03 O1 O 0 1 N N N N N N 171.473 176.276 144.871 3.998 2.966 1.994 O03 A1D6X 34 A1D6X O04 O2 O 0 1 N N N N N N 168.036 173.656 146.371 0.102 0.955 2.474 O04 A1D6X 35 A1D6X O05 O3 O 0 1 N N N N N N 167.751 176.297 149.978 -3.376 0.245 -0.488 O05 A1D6X 36 A1D6X H1 H1 H 0 1 N N N N N N 168.920 174.682 144.394 2.352 1.249 2.626 H1 A1D6X 37 A1D6X H3 H3 H 0 1 N N N N N N 169.462 175.115 148.869 -0.968 0.321 -0.324 H3 A1D6X 38 A1D6X H4 H4 H 0 1 N N N N N N 172.598 176.841 143.111 4.584 4.177 -0.671 H4 A1D6X 39 A1D6X H5 H5 H 0 1 N N N N N N 172.269 176.036 141.539 5.674 3.461 0.540 H5 A1D6X 40 A1D6X H6 H6 H 0 1 N N N N N N 171.799 177.752 141.785 5.748 2.921 -1.154 H6 A1D6X 41 A1D6X H7 H7 H 0 1 N N N N N N 169.798 172.855 149.851 -0.107 2.553 -0.977 H7 A1D6X 42 A1D6X H8 H8 H 0 1 N N N N N N 169.108 172.111 148.369 -1.887 2.523 -1.002 H8 A1D6X 43 A1D6X H9 H9 H 0 1 N N N N N N 170.655 173.021 148.281 -1.029 3.297 0.352 H9 A1D6X 44 A1D6X H10 H10 H 0 1 N N N N N N 169.061 174.955 138.339 3.023 1.709 -4.421 H10 A1D6X 45 A1D6X H11 H11 H 0 1 N N N N N N 167.593 179.214 141.241 5.341 -1.655 -1.560 H11 A1D6X 46 A1D6X H12 H12 H 0 1 N N N N N N 170.909 175.219 140.177 3.692 3.058 -2.486 H12 A1D6X 47 A1D6X H13 H13 H 0 1 N N N N N N 166.038 176.872 141.137 2.948 -1.791 -1.987 H13 A1D6X 48 A1D6X H14 H14 H 0 1 N N N N N N 166.611 175.785 138.821 2.653 -0.719 -4.172 H14 A1D6X 49 A1D6X H15 H15 H 0 1 N N N N N N 166.742 178.679 145.644 3.390 -2.662 2.122 H15 A1D6X 50 A1D6X H16 H16 H 0 1 N N N N N N 165.811 175.477 151.601 -4.395 -0.206 2.363 H16 A1D6X 51 A1D6X H17 H17 H 0 1 N N N N N N 165.301 174.237 150.405 -4.852 1.453 1.907 H17 A1D6X 52 A1D6X H18 H18 H 0 1 N N N N N N 165.804 181.109 145.757 4.455 -4.878 2.068 H18 A1D6X 53 A1D6X H19 H19 H 0 1 N N N N N N 166.652 181.643 141.355 6.397 -3.876 -1.596 H19 A1D6X 54 A1D6X H20 H20 H 0 1 N N N N N N 165.757 182.590 143.612 5.952 -5.484 0.212 H20 A1D6X 55 A1D6X H21 H21 H 0 1 N N N N N N 164.064 174.879 148.223 -6.374 1.859 0.060 H21 A1D6X 56 A1D6X H22 H22 H 0 1 N N N N N N 165.242 177.955 151.318 -5.283 -2.115 1.156 H22 A1D6X 57 A1D6X H23 H23 H 0 1 N N N N N N 162.285 179.026 148.084 -8.608 -1.456 -1.439 H23 A1D6X 58 A1D6X H24 H24 H 0 1 N N N N N N 169.947 176.152 146.772 1.559 1.254 -0.230 H24 A1D6X 59 A1D6X H27 H27 H 0 1 N N N N N N 167.033 173.363 149.017 -2.172 1.302 2.149 H27 A1D6X 60 # 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 A1D6X C22 C23 DOUB Y N 1 A1D6X C22 C18 SING Y N 2 A1D6X C23 C19 SING Y N 3 A1D6X C18 C11 DOUB Y N 4 A1D6X C19 C12 DOUB Y N 5 A1D6X C11 C12 SING Y N 6 A1D6X C11 N06 SING N N 7 A1D6X C12 C13 SING N N 8 A1D6X C26 C30 DOUB Y N 9 A1D6X C26 C17 SING Y N 10 A1D6X C30 C31 SING Y N 11 A1D6X C20 N06 SING N N 12 A1D6X N06 C14 SING N N 13 A1D6X C13 C17 SING N N 14 A1D6X C13 N08 DOUB N N 15 A1D6X C17 C25 DOUB Y N 16 A1D6X C31 C29 DOUB Y N 17 A1D6X C14 C10 SING N N 18 A1D6X C14 O03 DOUB N N 19 A1D6X N08 C10 SING N N 20 A1D6X C25 C29 SING Y N 21 A1D6X C10 N07 SING N N 22 A1D6X N07 C16 SING N N 23 A1D6X O04 C16 DOUB N N 24 A1D6X F02 C35 SING N N 25 A1D6X C16 C15 SING N N 26 A1D6X C35 C36 DOUB Y N 27 A1D6X C35 C32 SING Y N 28 A1D6X C15 C21 SING N N 29 A1D6X C15 N09 SING N N 30 A1D6X C36 C34 SING Y N 31 A1D6X C32 C28 DOUB Y N 32 A1D6X N09 C24 SING N N 33 A1D6X C34 F01 SING N N 34 A1D6X C34 C33 DOUB Y N 35 A1D6X C28 C33 SING Y N 36 A1D6X C28 C27 SING N N 37 A1D6X C24 O05 DOUB N N 38 A1D6X C24 C27 SING N N 39 A1D6X C10 H1 SING N N 40 A1D6X C15 H3 SING N N 41 A1D6X C20 H4 SING N N 42 A1D6X C20 H5 SING N N 43 A1D6X C20 H6 SING N N 44 A1D6X C21 H7 SING N N 45 A1D6X C21 H8 SING N N 46 A1D6X C21 H9 SING N N 47 A1D6X C22 H10 SING N N 48 A1D6X C26 H11 SING N N 49 A1D6X C18 H12 SING N N 50 A1D6X C19 H13 SING N N 51 A1D6X C23 H14 SING N N 52 A1D6X C25 H15 SING N N 53 A1D6X C27 H16 SING N N 54 A1D6X C27 H17 SING N N 55 A1D6X C29 H18 SING N N 56 A1D6X C30 H19 SING N N 57 A1D6X C31 H20 SING N N 58 A1D6X C32 H21 SING N N 59 A1D6X C33 H22 SING N N 60 A1D6X C36 H23 SING N N 61 A1D6X N07 H24 SING N N 62 A1D6X N09 H27 SING N N 63 # 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 A1D6X InChI InChI 1.06 "InChI=1S/C27H24F2N4O3/c1-16(30-23(34)14-17-12-19(28)15-20(29)13-17)26(35)32-25-27(36)33(2)22-11-7-6-10-21(22)24(31-25)18-8-4-3-5-9-18/h3-13,15-16,25H,14H2,1-2H3,(H,30,34)(H,32,35)/t16-,25+/m0/s1" A1D6X InChIKey InChI 1.06 JNGZXGGOCLZBFB-IVCQMTBJSA-N A1D6X SMILES_CANONICAL CACTVS 3.385 "C[C@H](NC(=O)Cc1cc(F)cc(F)c1)C(=O)N[C@H]2N=C(c3ccccc3)c4ccccc4N(C)C2=O" A1D6X SMILES CACTVS 3.385 "C[CH](NC(=O)Cc1cc(F)cc(F)c1)C(=O)N[CH]2N=C(c3ccccc3)c4ccccc4N(C)C2=O" A1D6X SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C[C@@H](C(=O)N[C@@H]1C(=O)N(c2ccccc2C(=N1)c3ccccc3)C)NC(=O)Cc4cc(cc(c4)F)F" A1D6X SMILES "OpenEye OEToolkits" 2.0.7 "CC(C(=O)NC1C(=O)N(c2ccccc2C(=N1)c3ccccc3)C)NC(=O)Cc4cc(cc(c4)F)F" # _pdbx_chem_comp_identifier.comp_id A1D6X _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 "(2~{S})-2-[2-[3,5-bis(fluoranyl)phenyl]ethanoylamino]-~{N}-[(3~{S})-1-methyl-2-oxidanylidene-5-phenyl-3~{H}-1,4-benzodiazepin-3-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 A1D6X "Create component" 2024-03-22 PDBC A1D6X "Modify model coordinates code" 2024-10-31 PDBC A1D6X "Modify synonyms" 2025-10-06 PDBC A1D6X "Initial release" 2025-10-29 RCSB # loop_ _pdbx_chem_comp_synonyms.ordinal _pdbx_chem_comp_synonyms.comp_id _pdbx_chem_comp_synonyms.name _pdbx_chem_comp_synonyms.provenance _pdbx_chem_comp_synonyms.type 1 A1D6X "Compound E" PUBCHEM ? 2 A1D6X "gamma-Secretase Inhibitor XXI" PUBCHEM ? #