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 
# 
