data_YNK
# 
_chem_comp.id                                    YNK 
_chem_comp.name                                  "7-dimethylphosphoryl-3-[2-[[(3~{S})-6,6-dimethylpiperidin-3-yl]amino]-5-(trifluoromethyl)pyrimidin-4-yl]-1~{H}-indole-6-carbonitrile" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C23 H26 F3 N6 O P" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-12-07 
_chem_comp.pdbx_modified_date                    2024-05-24 
_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                        490.461 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     YNK 
_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        8R9U 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBE 
# 
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 
YNK C1  C1  C 0 1 N N N N N N 28.763 7.559  -35.126 8.980  1.378  0.361  C1  YNK 1  
YNK C2  C2  C 0 1 N N N N N N 27.690 8.009  -34.128 7.482  1.568  0.116  C2  YNK 2  
YNK C3  C3  C 0 1 N N N N N N 28.094 7.574  -32.709 7.098  3.020  0.407  C3  YNK 3  
YNK C5  C4  C 0 1 N N N N N N 26.344 9.960  -33.289 5.656  1.411  -1.580 C5  YNK 4  
YNK C6  C5  C 0 1 N N S N N N 25.041 9.268  -33.673 4.888  0.505  -0.613 C6  YNK 5  
YNK C7  C6  C 0 1 N N N N N N 25.204 7.750  -33.642 5.277  0.857  0.825  C7  YNK 6  
YNK C10 C7  C 0 1 Y N N N N N 22.697 9.552  -33.092 2.560  -0.297 -0.448 C10 YNK 7  
YNK C12 C8  C 0 1 Y N N N N N 20.529 9.741  -32.475 2.214  -2.420 0.385  C12 YNK 8  
YNK C13 C9  C 0 1 Y N N N N N 20.125 9.234  -33.679 0.852  -2.256 0.226  C13 YNK 9  
YNK C14 C10 C 0 1 Y N N N N N 21.126 8.874  -34.597 0.383  -1.042 -0.290 C14 YNK 10 
YNK C16 C11 C 0 1 Y N N N N N 20.891 8.298  -35.931 -1.067 -0.815 -0.475 C16 YNK 11 
YNK N18 N1  N 0 1 Y N N N N N 20.011 7.029  -37.521 -3.178 -1.062 -1.133 N18 YNK 12 
YNK C19 C12 C 0 1 Y N N N N N 21.071 7.702  -38.086 -3.179 0.084  -0.364 C19 YNK 13 
YNK C21 C13 C 0 1 Y N N N N N 22.677 8.456  -39.692 -3.854 2.069  0.812  C21 YNK 14 
YNK C22 C14 C 0 1 N N N N N N 23.187 8.473  -41.040 -4.877 2.994  1.196  C22 YNK 15 
YNK C24 C15 C 0 1 Y N N N N N 23.250 9.271  -38.713 -2.535 2.268  1.243  C24 YNK 16 
YNK C25 C16 C 0 1 Y N N N N N 22.747 9.279  -37.423 -1.554 1.392  0.885  C25 YNK 17 
YNK C26 C17 C 0 1 Y N N N N N 21.658 8.480  -37.097 -1.860 0.292  0.080  C26 YNK 18 
YNK C31 C18 C 0 1 N N N N N N 18.639 9.060  -33.919 -0.106 -3.355 0.605  C31 YNK 19 
YNK C4  C19 C 0 1 N N N N N N 27.455 9.524  -34.209 7.159  1.238  -1.343 C4  YNK 20 
YNK N8  N2  N 0 1 N N N N N N 26.366 7.323  -34.469 6.724  0.675  1.000  N8  YNK 21 
YNK N9  N3  N 0 1 N N N N N N 23.984 9.698  -32.793 3.448  0.707  -0.793 N9  YNK 22 
YNK N11 N4  N 0 1 Y N N N N N 21.801 9.914  -32.159 3.031  -1.434 0.043  N11 YNK 23 
YNK N15 N5  N 0 1 Y N N N N N 22.406 9.048  -34.298 1.263  -0.095 -0.613 N15 YNK 24 
YNK C17 C20 C 0 1 Y N N N N N 19.914 7.376  -36.205 -1.925 -1.586 -1.194 C17 YNK 25 
YNK C20 C21 C 0 1 Y N N N N N 21.543 7.690  -39.392 -4.173 0.978  0.006  C20 YNK 26 
YNK N23 N6  N 0 1 N N N N N N 23.591 8.485  -42.110 -5.689 3.728  1.501  N23 YNK 27 
YNK P27 P1  P 0 1 N N N N N N 20.753 6.621  -40.621 -5.881 0.724  -0.550 P27 YNK 28 
YNK O28 O1  O 0 1 N N N N N N 19.512 6.043  -40.064 -5.951 -0.496 -1.386 O28 YNK 29 
YNK C29 C22 C 0 1 N N N N N N 20.389 7.600  -42.095 -6.970 0.530  0.899  C29 YNK 30 
YNK C30 C23 C 0 1 N N N N N N 21.981 5.396  -41.055 -6.422 2.163  -1.529 C30 YNK 31 
YNK F32 F1  F 0 1 N N N N N N 18.234 9.630  -35.049 -0.744 -3.835 -0.545 F32 YNK 32 
YNK F33 F2  F 0 1 N N N N N N 17.899 9.578  -32.940 0.598  -4.398 1.217  F33 YNK 33 
YNK F34 F3  F 0 1 N N N N N N 18.301 7.780  -34.002 -1.063 -2.854 1.494  F34 YNK 34 
YNK H41 H1  H 0 1 N N N N N N 29.718 8.050  -34.885 9.211  1.613  1.401  H41 YNK 35 
YNK H40 H2  H 0 1 N N N N N N 28.886 6.468  -35.064 9.254  0.343  0.154  H40 YNK 36 
YNK H39 H3  H 0 1 N N N N N N 28.455 7.836  -36.145 9.543  2.041  -0.295 H39 YNK 37 
YNK H43 H4  H 0 1 N N N N N N 27.324 7.897  -31.993 7.661  3.684  -0.250 H43 YNK 38 
YNK H42 H5  H 0 1 N N N N N N 28.190 6.479  -32.675 6.031  3.156  0.231  H42 YNK 39 
YNK H44 H6  H 0 1 N N N N N N 29.057 8.035  -32.445 7.329  3.256  1.446  H44 YNK 40 
YNK H47 H7  H 0 1 N N N N N N 26.605 9.695  -32.254 5.415  1.135  -2.606 H47 YNK 41 
YNK H48 H8  H 0 1 N N N N N N 26.214 11.049 -33.367 5.377  2.450  -1.407 H48 YNK 42 
YNK H35 H9  H 0 1 N N N N N N 24.792 9.561  -34.704 5.138  -0.536 -0.813 H35 YNK 43 
YNK H49 H10 H 0 1 N N N N N N 24.290 7.282  -34.036 5.014  1.895  1.029  H49 YNK 44 
YNK H50 H11 H 0 1 N N N N N N 25.363 7.426  -32.603 4.743  0.204  1.515  H50 YNK 45 
YNK H52 H12 H 0 1 N N N N N N 19.776 10.012 -31.750 2.610  -3.342 0.785  H52 YNK 46 
YNK H38 H13 H 0 1 N N N N N N 19.409 6.389  -37.998 -3.959 -1.439 -1.568 H38 YNK 47 
YNK H54 H14 H 0 1 N N N N N N 24.092 9.900  -38.964 -2.296 3.116  1.867  H54 YNK 48 
YNK H55 H15 H 0 1 N N N N N N 23.201 9.906  -36.670 -0.541 1.548  1.223  H55 YNK 49 
YNK H45 H16 H 0 1 N N N N N N 28.381 10.045 -33.924 7.710  1.912  -2.000 H45 YNK 50 
YNK H46 H17 H 0 1 N N N N N N 27.188 9.790  -35.243 7.445  0.208  -1.555 H46 YNK 51 
YNK H37 H18 H 0 1 N N N N N N 26.153 7.518  -35.427 6.988  -0.288 0.854  H37 YNK 52 
YNK H51 H20 H 0 1 N N N N N N 24.125 9.210  -31.932 3.117  1.544  -1.154 H51 YNK 53 
YNK H53 H21 H 0 1 N N N N N N 19.192 6.991  -35.500 -1.652 -2.482 -1.733 H53 YNK 54 
YNK H57 H22 H 0 1 N N N N N N 19.634 8.362  -41.852 -6.646 -0.331 1.484  H57 YNK 55 
YNK H56 H23 H 0 1 N N N N N N 21.308 8.093  -42.444 -6.918 1.428  1.515  H56 YNK 56 
YNK H58 H24 H 0 1 N N N N N N 20.003 6.941  -42.887 -7.996 0.377  0.565  H58 YNK 57 
YNK H60 H25 H 0 1 N N N N N N 22.220 4.786  -40.171 -7.448 2.010  -1.863 H60 YNK 58 
YNK H59 H26 H 0 1 N N N N N N 21.587 4.748  -41.852 -6.370 3.061  -0.914 H59 YNK 59 
YNK H61 H27 H 0 1 N N N N N N 22.892 5.900  -41.409 -5.771 2.279  -2.396 H61 YNK 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 
YNK N23 C22 TRIP N N 1  
YNK C29 P27 SING N N 2  
YNK C30 P27 SING N N 3  
YNK C22 C21 SING N N 4  
YNK P27 O28 DOUB N N 5  
YNK P27 C20 SING N N 6  
YNK C21 C20 DOUB Y N 7  
YNK C21 C24 SING Y N 8  
YNK C20 C19 SING Y N 9  
YNK C24 C25 DOUB Y N 10 
YNK C19 N18 SING Y N 11 
YNK C19 C26 DOUB Y N 12 
YNK N18 C17 SING Y N 13 
YNK C25 C26 SING Y N 14 
YNK C26 C16 SING Y N 15 
YNK C17 C16 DOUB Y N 16 
YNK C16 C14 SING N N 17 
YNK C1  C2  SING N N 18 
YNK F32 C31 SING N N 19 
YNK C14 N15 DOUB Y N 20 
YNK C14 C13 SING Y N 21 
YNK N8  C2  SING N N 22 
YNK N8  C7  SING N N 23 
YNK N15 C10 SING Y N 24 
YNK C4  C2  SING N N 25 
YNK C4  C5  SING N N 26 
YNK C2  C3  SING N N 27 
YNK F34 C31 SING N N 28 
YNK C31 C13 SING N N 29 
YNK C31 F33 SING N N 30 
YNK C13 C12 DOUB Y N 31 
YNK C6  C7  SING N N 32 
YNK C6  C5  SING N N 33 
YNK C6  N9  SING N N 34 
YNK C10 N9  SING N N 35 
YNK C10 N11 DOUB Y N 36 
YNK C12 N11 SING Y N 37 
YNK C1  H41 SING N N 38 
YNK C1  H40 SING N N 39 
YNK C1  H39 SING N N 40 
YNK C3  H43 SING N N 41 
YNK C3  H42 SING N N 42 
YNK C3  H44 SING N N 43 
YNK C5  H47 SING N N 44 
YNK C5  H48 SING N N 45 
YNK C6  H35 SING N N 46 
YNK C7  H49 SING N N 47 
YNK C7  H50 SING N N 48 
YNK C12 H52 SING N N 49 
YNK N18 H38 SING N N 50 
YNK C24 H54 SING N N 51 
YNK C25 H55 SING N N 52 
YNK C4  H45 SING N N 53 
YNK C4  H46 SING N N 54 
YNK N8  H37 SING N N 55 
YNK N9  H51 SING N N 56 
YNK C17 H53 SING N N 57 
YNK C29 H57 SING N N 58 
YNK C29 H56 SING N N 59 
YNK C29 H58 SING N N 60 
YNK C30 H60 SING N N 61 
YNK C30 H59 SING N N 62 
YNK C30 H61 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 
YNK InChI            InChI                1.06  "InChI=1S/C23H26F3N6OP/c1-22(2)8-7-14(10-30-22)31-21-29-12-17(23(24,25)26)18(32-21)16-11-28-19-15(16)6-5-13(9-27)20(19)34(3,4)33/h5-6,11-12,14,28,30H,7-8,10H2,1-4H3,(H,29,31,32)/t14-/m0/s1" 
YNK InChIKey         InChI                1.06  JDJOUBVVSQDIRC-AWEZNQCLSA-N                                                                                                                                                                   
YNK SMILES_CANONICAL CACTVS               3.385 "CC1(C)CC[C@@H](CN1)Nc2ncc(c(n2)c3c[nH]c4c3ccc(C#N)c4[P](C)(C)=O)C(F)(F)F"                                                                                                                    
YNK SMILES           CACTVS               3.385 "CC1(C)CC[CH](CN1)Nc2ncc(c(n2)c3c[nH]c4c3ccc(C#N)c4[P](C)(C)=O)C(F)(F)F"                                                                                                                      
YNK SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC1(CC[C@@H](CN1)Nc2ncc(c(n2)c3c[nH]c4c3ccc(c4P(=O)(C)C)C#N)C(F)(F)F)C"                                                                                                                      
YNK SMILES           "OpenEye OEToolkits" 2.0.7 "CC1(CCC(CN1)Nc2ncc(c(n2)c3c[nH]c4c3ccc(c4P(=O)(C)C)C#N)C(F)(F)F)C"                                                                                                                           
# 
_pdbx_chem_comp_identifier.comp_id           YNK 
_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        "7-dimethylphosphoryl-3-[2-[[(3~{S})-6,6-dimethylpiperidin-3-yl]amino]-5-(trifluoromethyl)pyrimidin-4-yl]-1~{H}-indole-6-carbonitrile" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
YNK "Create component" 2023-12-07 PDBE 
YNK "Initial release"  2024-05-29 RCSB 
# 
