data_YDL # _chem_comp.id YDL _chem_comp.name "N-(methoxycarbonyl)-3-methyl-L-valyl-(4R)-N-{(1Z,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-4-(trifluoromethyl)-L-prolinamide" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C21 H32 F3 N5 O5" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "Ibuzatrelvir, bound form; N-(methoxycarbonyl)-3-methyl-L-valyl-(4R)-N-{(1S)-1-cyano-2-[(3S)-2-oxopyrrolidin-3-yl]ethyl}-4-(trifluoromethyl)-L-prolinamide, bound form" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2023-12-01 _chem_comp.pdbx_modified_date 2024-05-10 _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 491.504 _chem_comp.one_letter_code ? _chem_comp.three_letter_code ? _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 8V4U _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB # 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 YDL C7 C1 C 0 1 N N N N N N 33.020 -2.883 38.386 5.944 1.676 1.158 C7 YDL 1 YDL C2 C2 C 0 1 N N N N N N 34.014 1.605 40.120 3.878 -1.748 -1.809 C2 YDL 2 YDL C9 C3 C 0 1 N N N N N N 35.843 -0.667 41.947 1.317 -0.762 -0.260 C9 YDL 3 YDL C13 C4 C 0 1 N N N N N N 35.980 -3.446 42.913 -1.311 0.739 0.107 C13 YDL 4 YDL C18 C5 C 0 1 N N N N N N 36.118 -6.065 44.962 -4.315 2.729 0.721 C18 YDL 5 YDL C5 C6 C 0 1 N N N N N N 35.224 -2.013 38.021 4.528 2.421 -0.650 C5 YDL 6 YDL C12 C7 C 0 1 N N N N N N 36.455 -0.064 44.292 0.154 -2.584 0.990 C12 YDL 7 YDL C6 C8 C 0 1 N N N N N N 35.003 -3.264 37.187 5.242 3.596 0.056 C6 YDL 8 YDL C10 C9 C 0 1 N N N N N N 37.301 -2.301 44.717 -1.970 -1.674 0.335 C10 YDL 9 YDL C4 C10 C 0 1 N N S N N N 34.091 -2.041 39.057 4.709 1.280 0.379 C4 YDL 10 YDL C8 C11 C 0 1 N N S N N N 35.743 -1.067 43.386 0.293 -1.058 0.805 C8 YDL 11 YDL C11 C12 C 0 1 N N R N N N 37.112 -0.935 45.378 -1.086 -2.927 0.123 C11 YDL 12 YDL C16 C13 C 0 1 N N N N N N 38.131 -6.480 42.065 -4.340 1.588 -2.074 C16 YDL 13 YDL C17 C14 C 0 1 N N N N N N 38.387 -4.180 41.203 -2.451 -0.010 -2.421 C17 YDL 14 YDL C20 C15 C 0 1 N N N N N N 36.366 -5.491 40.690 -1.995 2.439 -2.223 C20 YDL 15 YDL C19 C16 C 0 1 N N N N N N 35.079 -7.151 46.720 -5.998 4.175 1.601 C19 YDL 16 YDL C3 C17 C 0 1 N N N N N N 33.533 -0.666 39.329 4.932 -0.055 -0.335 C3 YDL 17 YDL C1 C18 C 0 1 N N S N N N 34.545 0.199 40.054 3.627 -0.505 -0.994 C1 YDL 18 YDL C14 C19 C 0 1 N N S N N N 36.840 -4.680 43.062 -2.727 1.138 -0.219 C14 YDL 19 YDL C21 C20 C 0 1 N N N N N N 36.270 -1.056 46.637 -1.785 -4.186 0.641 C21 YDL 20 YDL C15 C21 C 0 1 N N N N N N 37.402 -5.189 41.750 -2.878 1.289 -1.734 C15 YDL 21 YDL N5 N1 N 0 1 N N N N N N 34.347 2.495 39.248 3.250 -2.829 -1.536 N5 YDL 22 YDL N1 N2 N 0 1 N N N N N N 33.595 -3.517 37.290 6.220 2.976 0.958 N1 YDL 23 YDL N3 N3 N 0 1 N N N N N N 36.517 -2.301 43.475 -1.021 -0.547 0.390 N3 YDL 24 YDL N2 N4 N 0 1 N N N N N N 34.665 -0.219 41.432 2.631 -0.792 0.041 N2 YDL 25 YDL N4 N5 N 0 1 N N N N N N 35.947 -5.627 43.674 -3.037 2.413 0.432 N4 YDL 26 YDL O1 O1 O 0 1 N N N N N N 31.865 -2.976 38.772 6.587 0.930 1.866 O1 YDL 27 YDL O2 O2 O 0 1 N N N N N N 36.887 -0.747 41.325 0.960 -0.497 -1.388 O2 YDL 28 YDL O3 O3 O 0 1 N N N N N N 34.895 -3.472 42.340 -0.432 1.574 0.115 O3 YDL 29 YDL O4 O4 O 0 1 N N N N N N 37.130 -5.924 45.630 -5.210 1.956 0.441 O4 YDL 30 YDL O5 O5 O 0 1 N N N N N N 34.994 -6.713 45.375 -4.600 3.901 1.319 O5 YDL 31 YDL F1 F1 F 0 1 N N N N N N 36.159 0.184 47.189 -2.204 -3.978 1.959 F1 YDL 32 YDL F2 F2 F 0 1 N N N N N N 35.036 -1.603 46.405 -2.895 -4.466 -0.163 F2 YDL 33 YDL F3 F3 F 0 1 N N N N N N 36.855 -1.858 47.575 -0.895 -5.265 0.599 F3 YDL 34 YDL H5 H3 H 0 1 N N N N N N 36.206 -2.044 38.516 3.473 2.643 -0.804 H5 YDL 35 YDL H4 H4 H 0 1 N N N N N N 35.157 -1.111 37.395 5.015 2.175 -1.594 H4 YDL 36 YDL H15 H5 H 0 1 N N N N N N 37.215 0.498 43.730 1.040 -3.099 0.619 H15 YDL 37 YDL H14 H6 H 0 1 N N N N N N 35.735 0.638 44.738 -0.026 -2.833 2.036 H14 YDL 38 YDL H6 H7 H 0 1 N N N N N N 35.581 -4.108 37.591 5.749 4.226 -0.674 H6 YDL 39 YDL H7 H8 H 0 1 N N N N N N 35.292 -3.090 36.140 4.522 4.183 0.627 H7 YDL 40 YDL H11 H9 H 0 1 N N N N N N 36.943 -3.096 45.388 -2.658 -1.549 -0.502 H11 YDL 41 YDL H12 H10 H 0 1 N N N N N N 38.365 -2.465 44.490 -2.523 -1.753 1.271 H12 YDL 42 YDL H3 H11 H 0 1 N N N N N N 34.433 -2.516 39.988 3.844 1.221 1.039 H3 YDL 43 YDL H9 H12 H 0 1 N N N N N N 34.697 -1.209 43.695 0.593 -0.596 1.746 H9 YDL 44 YDL H13 H13 H 0 1 N N N N N N 38.096 -0.514 45.634 -0.810 -3.039 -0.926 H13 YDL 45 YDL H18 H14 H 0 1 N N N N N N 38.894 -6.293 42.835 -4.969 0.769 -1.725 H18 YDL 46 YDL H17 H15 H 0 1 N N N N N N 37.412 -7.226 42.435 -4.644 2.513 -1.584 H17 YDL 47 YDL H19 H16 H 0 1 N N N N N N 38.616 -6.859 41.153 -4.447 1.696 -3.153 H19 YDL 48 YDL H21 H17 H 0 1 N N N N N N 39.145 -3.954 41.968 -1.389 -0.183 -2.243 H21 YDL 49 YDL H22 H18 H 0 1 N N N N N N 38.879 -4.595 40.311 -3.027 -0.842 -2.017 H22 YDL 50 YDL H20 H19 H 0 1 N N N N N N 37.854 -3.257 40.932 -2.631 0.070 -3.493 H20 YDL 51 YDL H29 H20 H 0 1 N N N N N N 35.645 -6.225 41.080 -2.103 2.546 -3.302 H29 YDL 52 YDL H27 H21 H 0 1 N N N N N N 35.837 -4.565 40.420 -2.300 3.364 -1.733 H27 YDL 53 YDL H28 H22 H 0 1 N N N N N N 36.863 -5.903 39.799 -0.954 2.226 -1.981 H28 YDL 54 YDL H24 H23 H 0 1 N N N N N N 34.147 -7.665 46.998 -6.562 4.177 0.668 H24 YDL 55 YDL H25 H24 H 0 1 N N N N N N 35.926 -7.844 46.827 -6.393 3.404 2.263 H25 YDL 56 YDL H26 H25 H 0 1 N N N N N N 35.230 -6.283 47.379 -6.088 5.148 2.082 H26 YDL 57 YDL H1 H26 H 0 1 N N N N N N 33.271 -0.189 38.373 5.701 0.065 -1.098 H1 YDL 58 YDL H2 H27 H 0 1 N N N N N N 32.630 -0.761 39.951 5.252 -0.805 0.388 H2 YDL 59 YDL H30 H28 H 0 1 N N N N N N 35.516 0.174 39.537 3.256 0.287 -1.645 H30 YDL 60 YDL H16 H29 H 0 1 N N N N N N 37.673 -4.455 43.744 -3.413 0.370 0.140 H16 YDL 61 YDL H8 H33 H 0 1 N N N N N N 33.084 -4.086 36.646 6.970 3.444 1.356 H8 YDL 62 YDL H10 H34 H 0 1 N N N N N N 33.860 -0.178 42.024 2.917 -1.004 0.944 H10 YDL 63 YDL H23 H35 H 0 1 N N N N N N 35.176 -5.978 43.143 -2.323 3.030 0.655 H23 YDL 64 YDL H31 H31 H 0 1 N Y N N N N 33.337 1.876 40.917 4.587 -1.726 -2.623 H31 YDL 65 YDL H32 H32 H 0 1 N N N N N N 33.912 3.377 39.428 3.412 -3.629 -2.060 H32 YDL 66 # 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 YDL C6 N1 SING N N 1 YDL C6 C5 SING N N 2 YDL N1 C7 SING N N 3 YDL C5 C4 SING N N 4 YDL C7 O1 DOUB N N 5 YDL C7 C4 SING N N 6 YDL C4 C3 SING N N 7 YDL N5 C2 DOUB N N 8 YDL C3 C1 SING N N 9 YDL C1 C2 SING N N 10 YDL C1 N2 SING N N 11 YDL C20 C15 SING N N 12 YDL C17 C15 SING N N 13 YDL O2 C9 DOUB N N 14 YDL N2 C9 SING N N 15 YDL C15 C16 SING N N 16 YDL C15 C14 SING N N 17 YDL C9 C8 SING N N 18 YDL O3 C13 DOUB N N 19 YDL C13 C14 SING N N 20 YDL C13 N3 SING N N 21 YDL C14 N4 SING N N 22 YDL C8 N3 SING N N 23 YDL C8 C12 SING N N 24 YDL N3 C10 SING N N 25 YDL N4 C18 SING N N 26 YDL C12 C11 SING N N 27 YDL C10 C11 SING N N 28 YDL C18 O5 SING N N 29 YDL C18 O4 DOUB N N 30 YDL O5 C19 SING N N 31 YDL C11 C21 SING N N 32 YDL F2 C21 SING N N 33 YDL C21 F1 SING N N 34 YDL C21 F3 SING N N 35 YDL C5 H5 SING N N 36 YDL C5 H4 SING N N 37 YDL C12 H15 SING N N 38 YDL C12 H14 SING N N 39 YDL C6 H6 SING N N 40 YDL C6 H7 SING N N 41 YDL C10 H11 SING N N 42 YDL C10 H12 SING N N 43 YDL C4 H3 SING N N 44 YDL C8 H9 SING N N 45 YDL C11 H13 SING N N 46 YDL C16 H18 SING N N 47 YDL C16 H17 SING N N 48 YDL C16 H19 SING N N 49 YDL C17 H21 SING N N 50 YDL C17 H22 SING N N 51 YDL C17 H20 SING N N 52 YDL C20 H29 SING N N 53 YDL C20 H27 SING N N 54 YDL C20 H28 SING N N 55 YDL C19 H24 SING N N 56 YDL C19 H25 SING N N 57 YDL C19 H26 SING N N 58 YDL C3 H1 SING N N 59 YDL C3 H2 SING N N 60 YDL C1 H30 SING N N 61 YDL C14 H16 SING N N 62 YDL N1 H8 SING N N 63 YDL N2 H10 SING N N 64 YDL N4 H23 SING N N 65 YDL C2 H31 SING N N 66 YDL N5 H32 SING N N 67 # 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 YDL SMILES ACDLabs 12.01 "FC(F)(F)C1CC(C(=O)NC(C=N)CC2CCNC2=O)N(C1)C(=O)C(NC(=O)OC)C(C)(C)C" YDL InChI InChI 1.06 "InChI=1S/C21H32F3N5O5/c1-20(2,3)15(28-19(33)34-4)18(32)29-10-12(21(22,23)24)8-14(29)17(31)27-13(9-25)7-11-5-6-26-16(11)30/h9,11-15,25H,5-8,10H2,1-4H3,(H,26,30)(H,27,31)(H,28,33)/t11-,12+,13-,14-,15+/m0/s1" YDL InChIKey InChI 1.06 DTVPKRIYQXLPLE-AIEDFZFUSA-N YDL SMILES_CANONICAL CACTVS 3.385 "COC(=O)N[C@H](C(=O)N1C[C@@H](C[C@H]1C(=O)N[C@@H](C[C@@H]2CCNC2=O)C=N)C(F)(F)F)C(C)(C)C" YDL SMILES CACTVS 3.385 "COC(=O)N[CH](C(=O)N1C[CH](C[CH]1C(=O)N[CH](C[CH]2CCNC2=O)C=N)C(F)(F)F)C(C)(C)C" YDL SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC(C)(C)[C@@H](C(=O)N1C[C@@H](C[C@H]1C(=O)N[C@@H](C[C@@H]2CCNC2=O)C=N)C(F)(F)F)NC(=O)OC" YDL SMILES "OpenEye OEToolkits" 2.0.7 "CC(C)(C)C(C(=O)N1CC(CC1C(=O)NC(CC2CCNC2=O)C=N)C(F)(F)F)NC(=O)OC" # loop_ _pdbx_chem_comp_identifier.comp_id _pdbx_chem_comp_identifier.type _pdbx_chem_comp_identifier.program _pdbx_chem_comp_identifier.program_version _pdbx_chem_comp_identifier.identifier YDL "SYSTEMATIC NAME" ACDLabs 12.01 "N-(methoxycarbonyl)-3-methyl-L-valyl-(4R)-N-{(1Z,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-4-(trifluoromethyl)-L-prolinamide" YDL "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "methyl ~{N}-[(2~{S})-1-[(2~{S},4~{R})-2-[[(2~{S})-1-azanylidene-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]carbamoyl]-4-(trifluoromethyl)pyrrolidin-1-yl]-3,3-dimethyl-1-oxidanylidene-butan-2-yl]carbamate" # 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 YDL "N-(methoxycarbonyl)-3-methyl-L-valyl-(4R)-N-{(1S)-1-cyano-2-[(3S)-2-oxopyrrolidin-3-yl]ethyl}-4-(trifluoromethyl)-L-prolinamide, bound form" AUTHOR ? 2 YDL "Ibuzatrelvir, bound form" PDB ? # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site YDL "Create component" 2023-12-01 RCSB YDL "Modify synonyms" 2024-05-07 RCSB YDL "Initial release" 2024-05-15 RCSB #