data_Y8O
# 
_chem_comp.id                                    Y8O 
_chem_comp.name                                  "(1R,2S,5S)-3-[N-(difluoroacetyl)-3-methyl-L-valyl]-N-{(1Z,2S)-1-imino-3-[(3S)-2-oxopiperidin-3-yl]propan-2-yl}-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-2-carboxamide" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C24 H37 F2 N5 O4" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-01-12 
_chem_comp.pdbx_modified_date                    2024-09-27 
_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                        497.578 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     Y8O 
_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        8FTC 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  RCSB 
_chem_comp.pdbx_pcm                              Y 
# 
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_backbone_atom_flag 
_chem_comp_atom.pdbx_n_terminal_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 
Y8O C10  C1  C 0 1 N N N N N N 21.438 18.474 23.726 -1.782 0.038  -2.774 C10  Y8O 1  
Y8O C02  C2  C 0 1 N N N N N N 19.175 17.779 27.403 1.546  -1.212 -0.414 C02  Y8O 2  
Y8O C05  C3  C 0 1 N N N N N N 19.283 16.683 24.444 -1.566 0.124  0.087  C05  Y8O 3  
Y8O C06  C4  C 0 1 N N S N N N 20.112 16.445 23.177 -2.912 0.316  -0.563 C06  Y8O 4  
Y8O C07  C5  C 0 1 N N N N N N 20.641 17.774 22.599 -2.724 0.923  -1.955 C07  Y8O 5  
Y8O C08  C6  C 0 1 N N N N N N 21.633 17.422 21.447 -2.122 2.323  -1.823 C08  Y8O 6  
Y8O C09  C7  C 0 1 N N N N N N 19.531 18.681 22.032 -4.079 1.014  -2.659 C09  Y8O 7  
Y8O N04  N1  N 0 1 N N N N N N 19.815 16.119 25.658 -0.881 -1.021 -0.106 N04  Y8O 8  
Y8O N11  N2  N 0 1 N N N N N N 19.225 15.705 22.336 -3.726 1.216  0.257  N11  Y8O 9  
Y8O C03  C8  C 0 1 N N S N N N 19.049 16.328 27.058 0.391  -1.437 0.528  C03  Y8O 10 
Y8O C12  C9  C 0 1 N N N N N N 19.714 14.450 21.758 -5.071 1.157  0.190  C12  Y8O 11 
Y8O C13  C10 C 0 1 N N N N N N 18.790 13.661 20.843 -5.908 2.084  1.033  C13  Y8O 12 
Y8O C18  C11 C 0 1 N N N N N N 20.980 15.429 25.805 -1.233 -2.151 -0.997 C18  Y8O 13 
Y8O C19  C12 C 0 1 N N S N N N 20.895 14.809 27.266 -0.855 -3.414 -0.193 C19  Y8O 14 
Y8O C20  C13 C 0 1 N N R N N N 19.624 15.393 27.898 0.212  -2.944 0.809  C20  Y8O 15 
Y8O C21  C14 C 0 1 N N N N N N 19.883 13.864 27.925 -1.145 -3.425 1.309  C21  Y8O 16 
Y8O C22  C15 C 0 1 N N N N N N 19.062 13.087 26.860 -2.113 -2.370 1.849  C22  Y8O 17 
Y8O C23  C16 C 0 1 N N N N N N 20.215 13.269 29.294 -1.198 -4.785 2.007  C23  Y8O 18 
Y8O C25  C17 C 0 1 N N S N N N 17.954 19.812 28.347 3.928  -0.943 -0.851 C25  Y8O 19 
Y8O C26  C18 C 0 1 N N N N N N 16.965 20.647 27.516 5.100  -0.329 -0.083 C26  Y8O 20 
Y8O C27  C19 C 0 1 N N S N N N 17.456 20.884 26.042 4.713  1.067  0.407  C27  Y8O 21 
Y8O C28  C20 C 0 1 N N N N N N 18.679 21.448 25.913 4.481  1.983  -0.797 C28  Y8O 22 
Y8O C29  C21 C 0 1 N N N N N N 19.040 21.856 24.534 4.367  3.427  -0.293 C29  Y8O 23 
Y8O C30  C22 C 0 1 N N N N N N 18.138 22.814 23.974 5.728  3.865  0.249  C30  Y8O 24 
Y8O C32  C23 C 0 1 N N N N N N 16.262 21.441 25.159 5.817  1.620  1.263  C32  Y8O 25 
Y8O C34  C24 C 0 1 N N N N N N 17.480 19.826 29.820 4.354  -2.260 -1.448 C34  Y8O 26 
Y8O F14  F1  F 0 1 N N N N N N 17.598 14.328 20.801 -7.261 1.759  0.880  F14  Y8O 27 
Y8O F15  F2  F 0 1 N N N N N N 19.317 13.667 19.569 -5.546 1.947  2.378  F15  Y8O 28 
Y8O N24  N3  N 0 1 N N N N N N 17.970 18.404 27.930 2.806  -1.162 0.064  N24  Y8O 29 
Y8O N31  N4  N 0 1 N N N N N N 16.634 22.413 24.099 6.242  2.880  1.193  N31  Y8O 30 
Y8O N35  N5  N 0 1 N N N N N N 17.648 20.896 30.477 3.744  -3.337 -1.122 N35  Y8O 31 
Y8O O01  O1  O 0 1 N N N N N N 20.180 18.388 27.220 1.343  -1.076 -1.602 O01  Y8O 32 
Y8O O16  O2  O 0 1 N N N N N N 20.816 14.076 22.000 -5.607 0.358  -0.548 O16  Y8O 33 
Y8O O17  O3  O 0 1 N N N N N N 18.257 17.287 24.482 -1.099 0.999  0.785  O17  Y8O 34 
Y8O O33  O4  O 0 1 N N N N N N 15.136 21.061 25.316 6.349  0.879  2.062  O33  Y8O 35 
Y8O H103 H1  H 0 0 N N N N N N 20.758 18.732 24.551 -2.158 -0.985 -2.781 H103 Y8O 36 
Y8O H101 H2  H 0 0 N N N N N N 22.222 17.797 24.096 -1.729 0.412  -3.796 H101 Y8O 37 
Y8O H102 H3  H 0 0 N N N N N N 21.901 19.391 23.332 -0.787 0.056  -2.329 H102 Y8O 38 
Y8O H061 H4  H 0 0 N N N N N N 20.977 15.819 23.443 -3.413 -0.648 -0.651 H061 Y8O 39 
Y8O H082 H5  H 0 0 N N N N N N 22.432 16.774 21.836 -1.156 2.258  -1.322 H082 Y8O 40 
Y8O H081 H6  H 0 0 N N N N N N 21.093 16.897 20.646 -1.988 2.755  -2.815 H081 Y8O 41 
Y8O H083 H7  H 0 0 N N N N N N 22.073 18.347 21.047 -2.793 2.953  -1.240 H083 Y8O 42 
Y8O H092 H8  H 0 0 N N N N N N 18.822 18.939 22.833 -4.750 1.644  -2.075 H092 Y8O 43 
Y8O H091 H9  H 0 0 N N N N N N 19.980 19.601 21.630 -3.945 1.446  -3.650 H091 Y8O 44 
Y8O H093 H10 H 0 0 N N N N N N 18.999 18.151 21.228 -4.508 0.016  -2.752 H093 Y8O 45 
Y8O H111 H11 H 0 0 N N N N N N 18.299 16.033 22.148 -3.297 1.856  0.847  H111 Y8O 46 
Y8O H031 H12 H 0 0 N N N N N N 17.987 16.094 26.892 0.549  -0.891 1.458  H031 Y8O 47 
Y8O H131 H13 H 0 0 N N N N N N 18.674 12.638 21.230 -5.743 3.113  0.715  H131 Y8O 48 
Y8O H181 H14 H 0 0 N N N N N N 21.059 14.634 25.049 -2.301 -2.145 -1.215 H181 Y8O 49 
Y8O H182 H15 H 0 0 N N N N N N 21.845 16.103 25.719 -0.655 -2.102 -1.920 H182 Y8O 50 
Y8O H191 H16 H 0 0 N N N N N N 21.806 14.974 27.859 -0.757 -4.351 -0.740 H191 Y8O 51 
Y8O H201 H17 H 0 0 N N N N N N 19.865 15.821 28.882 1.108  -3.531 1.011  H201 Y8O 52 
Y8O H223 H18 H 0 0 N N N N N N 18.347 12.419 27.363 -3.032 -2.855 2.178  H223 Y8O 53 
Y8O H222 H19 H 0 0 N N N N N N 18.514 13.801 26.227 -1.654 -1.852 2.691  H222 Y8O 54 
Y8O H221 H20 H 0 0 N N N N N N 19.743 12.491 26.235 -2.343 -1.651 1.062  H221 Y8O 55 
Y8O H231 H21 H 0 0 N N N N N N 20.801 13.995 29.877 -0.861 -5.560 1.319  H231 Y8O 56 
Y8O H233 H22 H 0 0 N N N N N N 19.282 13.037 29.829 -0.548 -4.770 2.883  H233 Y8O 57 
Y8O H232 H23 H 0 0 N N N N N N 20.801 12.347 29.161 -2.221 -4.995 2.318  H232 Y8O 58 
Y8O H251 H24 H 0 0 N N N N N N 18.961 20.250 28.278 3.621  -0.266 -1.648 H251 Y8O 59 
Y8O H261 H25 H 0 0 N N N N N N 16.833 21.624 28.004 5.345  -0.960 0.771  H261 Y8O 60 
Y8O H262 H26 H 0 0 N N N N N N 16.000 20.120 27.484 5.967  -0.256 -0.741 H262 Y8O 61 
Y8O H271 H27 H 0 0 N N N N N N 17.578 19.860 25.660 3.797  1.003  0.995  H271 Y8O 62 
Y8O H281 H28 H 0 0 N N N N N N 19.428 20.721 26.261 5.320  1.901  -1.487 H281 Y8O 63 
Y8O H282 H29 H 0 0 N N N N N N 18.711 22.342 26.553 3.559  1.697  -1.303 H282 Y8O 64 
Y8O H292 H30 H 0 0 N N N N N N 19.041 20.961 23.894 4.074  4.079  -1.115 H292 Y8O 65 
Y8O H291 H31 H 0 0 N N N N N N 20.049 22.295 24.552 3.621  3.480  0.500  H291 Y8O 66 
Y8O H301 H32 H 0 0 N N N N N N 18.377 22.933 22.907 6.430  3.971  -0.578 H301 Y8O 67 
Y8O H302 H33 H 0 0 N N N N N N 18.285 23.773 24.492 5.622  4.826  0.753  H302 Y8O 68 
Y8O H1   H34 H 0 1 N N N N N N 17.024 18.957 30.271 5.173  -2.295 -2.151 H1   Y8O 69 
Y8O H241 H35 H 0 0 N N N N N N 17.134 17.862 28.010 2.969  -1.271 1.014  H241 Y8O 70 
Y8O H311 H36 H 0 0 N N N N N N 15.944 22.798 23.486 6.939  3.160  1.808  H311 Y8O 71 
Y8O H351 H37 H 0 0 N N N N N N 17.314 20.815 31.416 4.018  -4.185 -1.506 H351 Y8O 72 
# 
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 
Y8O F15 C13  SING N N 1  
Y8O F14 C13  SING N N 2  
Y8O C13 C12  SING N N 3  
Y8O C08 C07  SING N N 4  
Y8O C12 O16  DOUB N N 5  
Y8O C12 N11  SING N N 6  
Y8O C09 C07  SING N N 7  
Y8O N11 C06  SING N N 8  
Y8O C07 C06  SING N N 9  
Y8O C07 C10  SING N N 10 
Y8O C06 C05  SING N N 11 
Y8O C30 N31  SING N N 12 
Y8O C30 C29  SING N N 13 
Y8O N31 C32  SING N N 14 
Y8O C05 O17  DOUB N N 15 
Y8O C05 N04  SING N N 16 
Y8O C29 C28  SING N N 17 
Y8O C32 O33  DOUB N N 18 
Y8O C32 C27  SING N N 19 
Y8O N04 C18  SING N N 20 
Y8O N04 C03  SING N N 21 
Y8O C18 C19  SING N N 22 
Y8O C28 C27  SING N N 23 
Y8O C27 C26  SING N N 24 
Y8O C22 C21  SING N N 25 
Y8O C03 C02  SING N N 26 
Y8O C03 C20  SING N N 27 
Y8O O01 C02  DOUB N N 28 
Y8O C19 C20  SING N N 29 
Y8O C19 C21  SING N N 30 
Y8O C02 N24  SING N N 31 
Y8O C26 C25  SING N N 32 
Y8O C20 C21  SING N N 33 
Y8O C21 C23  SING N N 34 
Y8O N24 C25  SING N N 35 
Y8O C25 C34  SING N N 36 
Y8O C34 N35  DOUB N N 37 
Y8O C10 H103 SING N N 38 
Y8O C10 H101 SING N N 39 
Y8O C10 H102 SING N N 40 
Y8O C06 H061 SING N N 41 
Y8O C08 H082 SING N N 42 
Y8O C08 H081 SING N N 43 
Y8O C08 H083 SING N N 44 
Y8O C09 H092 SING N N 45 
Y8O C09 H091 SING N N 46 
Y8O C09 H093 SING N N 47 
Y8O N11 H111 SING N N 48 
Y8O C03 H031 SING N N 49 
Y8O C13 H131 SING N N 50 
Y8O C18 H181 SING N N 51 
Y8O C18 H182 SING N N 52 
Y8O C19 H191 SING N N 53 
Y8O C20 H201 SING N N 54 
Y8O C22 H223 SING N N 55 
Y8O C22 H222 SING N N 56 
Y8O C22 H221 SING N N 57 
Y8O C23 H231 SING N N 58 
Y8O C23 H233 SING N N 59 
Y8O C23 H232 SING N N 60 
Y8O C25 H251 SING N N 61 
Y8O C26 H261 SING N N 62 
Y8O C26 H262 SING N N 63 
Y8O C27 H271 SING N N 64 
Y8O C28 H281 SING N N 65 
Y8O C28 H282 SING N N 66 
Y8O C29 H292 SING N N 67 
Y8O C29 H291 SING N N 68 
Y8O C30 H301 SING N N 69 
Y8O C30 H302 SING N N 70 
Y8O C34 H1   SING N N 71 
Y8O N24 H241 SING N N 72 
Y8O N31 H311 SING N N 73 
Y8O N35 H351 SING N N 74 
# 
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 
Y8O SMILES           ACDLabs              12.01 "CC1(C)C2C(C(=O)NC(C=N)CC3CCCNC3=O)N(CC21)C(=O)C(NC(=O)C(F)F)C(C)(C)C"                                                                                                                                                            
Y8O InChI            InChI                1.06  "InChI=1S/C24H37F2N5O4/c1-23(2,3)17(30-21(34)18(25)26)22(35)31-11-14-15(24(14,4)5)16(31)20(33)29-13(10-27)9-12-7-6-8-28-19(12)32/h10,12-18,27H,6-9,11H2,1-5H3,(H,28,32)(H,29,33)(H,30,34)/b27-10-/t12-,13-,14-,15-,16-,17+/m0/s1" 
Y8O InChIKey         InChI                1.06  MSAKMAGHNICQTP-NJLGGNEPSA-N                                                                                                                                                                                                       
Y8O SMILES_CANONICAL CACTVS               3.385 "CC(C)(C)[C@H](NC(=O)C(F)F)C(=O)N1C[C@H]2[C@@H]([C@H]1C(=O)N[C@@H](C[C@@H]3CCCNC3=O)C=N)C2(C)C"                                                                                                                                   
Y8O SMILES           CACTVS               3.385 "CC(C)(C)[CH](NC(=O)C(F)F)C(=O)N1C[CH]2[CH]([CH]1C(=O)N[CH](C[CH]3CCCNC3=O)C=N)C2(C)C"                                                                                                                                            
Y8O SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "[H]/N=C\[C@H](C[C@@H]1CCCNC1=O)NC(=O)[C@@H]2[C@@H]3[C@@H](C3(C)C)CN2C(=O)[C@H](C(C)(C)C)NC(=O)C(F)F"                                                                                                                             
Y8O SMILES           "OpenEye OEToolkits" 2.0.7 "CC1(C2C1C(N(C2)C(=O)C(C(C)(C)C)NC(=O)C(F)F)C(=O)NC(CC3CCCNC3=O)C=N)C"                                                                                                                                                            
# 
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 
Y8O "SYSTEMATIC NAME" ACDLabs              12.01 "(1R,2S,5S)-3-[N-(difluoroacetyl)-3-methyl-L-valyl]-N-{(1Z,2S)-1-imino-3-[(3S)-2-oxopiperidin-3-yl]propan-2-yl}-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-2-carboxamide"                                                              
Y8O "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "(1~{R},2~{S},5~{S})-~{N}-[(2~{S})-1-azanylidene-3-[(3~{S})-2-oxidanylidenepiperidin-3-yl]propan-2-yl]-3-[(2~{S})-2-[2,2-bis(fluoranyl)ethanoylamino]-3,3-dimethyl-butanoyl]-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-2-carboxamide" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
Y8O "Create component" 2023-01-12 RCSB 
Y8O "Initial release"  2023-12-06 RCSB 
Y8O "Modify PCM"       2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            Y8O 
_pdbx_chem_comp_pcm.modified_residue_id                CYS 
_pdbx_chem_comp_pcm.type                               None 
_pdbx_chem_comp_pcm.category                           "Covalent chemical modification" 
_pdbx_chem_comp_pcm.position                           "Amino-acid side chain" 
_pdbx_chem_comp_pcm.polypeptide_position               "Any position" 
_pdbx_chem_comp_pcm.comp_id_linking_atom               C34 
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom   SG 
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession     ? 
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession      ? 
# 
