data_YDF # _chem_comp.id YDF _chem_comp.name "4-(2-fluoranylethyl)-1,6-dimethyl-7-(2-oxidanyl-6-oxidanylidene-cyclohexen-1-yl)carbonyl-3~{H}-1,4-benzodiazepine-2,5-dione" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C20 H21 F N2 O5" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2023-11-30 _chem_comp.pdbx_modified_date 2024-11-15 _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 388.390 _chem_comp.one_letter_code ? _chem_comp.three_letter_code YDF _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 8X69 _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBJ _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 YDF C13 C1 C 0 1 N N N N N N 1.469 -3.389 81.557 2.380 -1.060 0.153 C13 YDF 1 YDF C17 C2 C 0 1 N N N N N N 4.592 -5.807 81.722 6.031 0.100 0.682 C17 YDF 2 YDF C20 C3 C 0 1 N N N N N N 1.894 -5.531 83.013 4.000 0.123 -1.412 C20 YDF 3 YDF C24 C4 C 0 1 N N N N N N -5.878 -3.961 82.633 -4.863 -0.967 0.082 C24 YDF 4 YDF C26 C5 C 0 1 N N N N N N -2.626 0.076 85.569 -1.937 3.555 1.171 C26 YDF 5 YDF C01 C6 C 0 1 Y N N N N N 0.265 -2.929 82.330 1.187 -0.191 0.209 C01 YDF 6 YDF C02 C7 C 0 1 Y N N N N N 0.551 -1.798 83.286 1.327 1.199 0.131 C02 YDF 7 YDF C03 C8 C 0 1 Y N N N N N -0.621 -1.239 84.038 0.216 2.004 0.186 C03 YDF 8 YDF C04 C9 C 0 1 Y N N N N N -2.020 -1.823 83.818 -1.064 1.455 0.320 C04 YDF 9 YDF C05 C10 C 0 1 Y N N N N N -2.381 -2.930 82.855 -1.214 0.068 0.393 C05 YDF 10 YDF C06 C11 C 0 1 Y N N N N N -1.131 -3.503 82.066 -0.079 -0.751 0.334 C06 YDF 11 YDF C08 C12 C 0 1 N N N N N N -4.800 -1.281 84.763 -3.299 2.177 -0.221 C08 YDF 12 YDF C09 C13 C 0 1 N N N N N N -5.368 -2.408 83.941 -3.627 0.943 -1.016 C09 YDF 13 YDF C11 C14 C 0 1 N N N N N N -3.599 -3.410 82.682 -2.519 -0.592 0.522 C11 YDF 14 YDF C12 C15 C 0 1 N N N N N N -1.159 -4.636 81.034 -0.232 -2.249 0.411 C12 YDF 15 YDF C14 C16 C 0 1 N N N N N N 2.332 -4.554 81.940 3.704 -0.475 -0.105 C14 YDF 16 YDF C16 C17 C 0 1 N N N N N N 3.556 -4.879 81.106 4.665 -0.490 0.878 C16 YDF 17 YDF C18 C18 C 0 1 N N N N N N 4.383 -6.002 83.223 6.380 0.194 -0.802 C18 YDF 18 YDF C19 C19 C 0 1 N N N N N N 2.967 -6.456 83.585 5.264 0.947 -1.539 C19 YDF 19 YDF C27 C20 C 0 1 N N N N N N -6.408 -3.628 81.223 -4.949 -2.089 -0.955 C27 YDF 20 YDF F28 F1 F 0 1 N N N N N N -6.112 -2.377 80.754 -6.133 -2.810 -0.765 F28 YDF 21 YDF N07 N1 N 0 1 N N N N N N -3.144 -1.008 84.755 -2.124 2.337 0.379 N07 YDF 22 YDF N10 N2 N 0 1 N N N N N N -4.827 -3.097 83.168 -3.624 -0.212 -0.118 N10 YDF 23 YDF O15 O1 O 0 1 N N N N N N 1.734 -2.743 80.591 2.267 -2.260 0.324 O15 YDF 24 YDF O21 O2 O 0 1 N N N N N N 3.849 -4.162 79.948 4.370 -1.054 2.059 O21 YDF 25 YDF O22 O3 O 0 1 N N N N N N 0.768 -5.572 83.385 3.257 -0.037 -2.358 O22 YDF 26 YDF O23 O4 O 0 1 N N N N N N -3.676 -4.309 81.927 -2.597 -1.552 1.265 O23 YDF 27 YDF O25 O5 O 0 1 N N N N N N -5.486 -0.615 85.454 -4.133 3.053 -0.125 O25 YDF 28 YDF H1 H1 H 0 1 N N N N N N 4.527 -6.787 81.226 6.055 1.099 1.119 H1 YDF 29 YDF H2 H2 H 0 1 N N N N N N 5.592 -5.379 81.558 6.767 -0.527 1.184 H2 YDF 30 YDF H3 H3 H 0 1 N N N N N N -6.730 -3.916 83.327 -5.717 -0.300 -0.033 H3 YDF 31 YDF H4 H4 H 0 1 N N N N N N -5.482 -4.987 82.605 -4.869 -1.397 1.083 H4 YDF 32 YDF H5 H5 H 0 1 N N N N N N -3.449 0.534 86.137 -1.532 4.343 0.535 H5 YDF 33 YDF H6 H6 H 0 1 N N N N N N -1.873 -0.318 86.268 -2.897 3.874 1.578 H6 YDF 34 YDF H7 H7 H 0 1 N N N N N N -2.163 0.833 84.919 -1.244 3.355 1.987 H7 YDF 35 YDF H8 H8 H 0 1 N N N N N N 1.550 -1.410 83.422 2.308 1.639 0.027 H8 YDF 36 YDF H9 H9 H 0 1 N N N N N N -0.478 -0.425 84.734 0.333 3.076 0.126 H9 YDF 37 YDF H11 H11 H 0 1 N N N N N N -5.787 -3.104 84.683 -4.612 1.051 -1.468 H11 YDF 38 YDF H12 H12 H 0 1 N N N N N N -1.017 -5.600 81.544 -0.077 -2.577 1.439 H12 YDF 39 YDF H13 H13 H 0 1 N N N N N N -2.129 -4.635 80.515 -1.234 -2.529 0.087 H13 YDF 40 YDF H14 H14 H 0 1 N N N N N N -0.351 -4.486 80.303 0.505 -2.723 -0.237 H14 YDF 41 YDF H17 H17 H 0 1 N N N N N N 5.094 -6.762 83.578 7.321 0.732 -0.921 H17 YDF 42 YDF H18 H18 H 0 1 N N N N N N 4.583 -5.047 83.730 6.478 -0.809 -1.218 H18 YDF 43 YDF H19 H19 H 0 1 N N N N N N 2.871 -6.473 84.681 5.527 1.062 -2.590 H19 YDF 44 YDF H20 H20 H 0 1 N N N N N N 2.808 -7.469 83.187 5.115 1.926 -1.084 H20 YDF 45 YDF H21 H21 H 0 1 N N N N N N -5.983 -4.361 80.521 -4.943 -1.659 -1.957 H21 YDF 46 YDF H22 H22 H 0 1 N N N N N N -7.503 -3.731 81.241 -4.095 -2.756 -0.841 H22 YDF 47 YDF H24 H24 H 0 1 N N N N N N 3.209 -3.469 79.834 3.475 -1.403 2.167 H24 YDF 48 YDF H10 H10 H 0 1 N N N N N N -6.186 -1.945 83.370 -2.878 0.802 -1.795 H10 YDF 49 # 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 YDF C13 C01 SING N N 1 YDF C13 C14 SING N N 2 YDF C13 O15 DOUB N N 3 YDF C17 C16 SING N N 4 YDF C17 C18 SING N N 5 YDF C20 C14 SING N N 6 YDF C20 C19 SING N N 7 YDF C20 O22 DOUB N N 8 YDF C24 C27 SING N N 9 YDF C24 N10 SING N N 10 YDF C26 N07 SING N N 11 YDF C01 C02 DOUB Y N 12 YDF C01 C06 SING Y N 13 YDF C02 C03 SING Y N 14 YDF C03 C04 DOUB Y N 15 YDF C04 C05 SING Y N 16 YDF C04 N07 SING N N 17 YDF C05 C06 DOUB Y N 18 YDF C05 C11 SING N N 19 YDF C06 C12 SING N N 20 YDF C08 C09 SING N N 21 YDF C08 O25 DOUB N N 22 YDF C09 N10 SING N N 23 YDF C11 N10 SING N N 24 YDF C11 O23 DOUB N N 25 YDF C14 C16 DOUB N N 26 YDF C16 O21 SING N N 27 YDF C18 C19 SING N N 28 YDF C27 F28 SING N N 29 YDF C17 H1 SING N N 30 YDF C17 H2 SING N N 31 YDF C24 H3 SING N N 32 YDF C24 H4 SING N N 33 YDF C26 H5 SING N N 34 YDF C26 H6 SING N N 35 YDF C26 H7 SING N N 36 YDF C02 H8 SING N N 37 YDF C03 H9 SING N N 38 YDF C09 H11 SING N N 39 YDF C12 H12 SING N N 40 YDF C12 H13 SING N N 41 YDF C12 H14 SING N N 42 YDF C18 H17 SING N N 43 YDF C18 H18 SING N N 44 YDF C19 H19 SING N N 45 YDF C19 H20 SING N N 46 YDF C27 H21 SING N N 47 YDF C27 H22 SING N N 48 YDF O21 H24 SING N N 49 YDF C08 N07 SING N N 50 YDF C09 H10 SING N N 51 # 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 YDF InChI InChI 1.06 "InChI=1S/C20H21FN2O5/c1-11-12(19(27)18-14(24)4-3-5-15(18)25)6-7-13-17(11)20(28)23(9-8-21)10-16(26)22(13)2/h6-7,24H,3-5,8-10H2,1-2H3" YDF InChIKey InChI 1.06 VBRGYJMIQKGTST-UHFFFAOYSA-N YDF SMILES_CANONICAL CACTVS 3.385 "CN1C(=O)CN(CCF)C(=O)c2c(C)c(ccc12)C(=O)C3=C(O)CCCC3=O" YDF SMILES CACTVS 3.385 "CN1C(=O)CN(CCF)C(=O)c2c(C)c(ccc12)C(=O)C3=C(O)CCCC3=O" YDF SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "Cc1c(ccc2c1C(=O)N(CC(=O)N2C)CCF)C(=O)C3=C(CCCC3=O)O" YDF SMILES "OpenEye OEToolkits" 2.0.7 "Cc1c(ccc2c1C(=O)N(CC(=O)N2C)CCF)C(=O)C3=C(CCCC3=O)O" # _pdbx_chem_comp_identifier.comp_id YDF _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 "4-(2-fluoranylethyl)-1,6-dimethyl-7-(2-oxidanyl-6-oxidanylidene-cyclohexen-1-yl)carbonyl-3~{H}-1,4-benzodiazepine-2,5-dione" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site YDF "Create component" 2023-11-30 PDBJ YDF "Initial release" 2024-11-20 RCSB #