data_YPK
# 
_chem_comp.id                                    YPK 
_chem_comp.name                                  "[(3S)-1-[4-(dimethylamino)butanoyl]pyrrolidin-3-yl] 4-[(5-methyl-3-propan-2-yl-pyrazolo[1,5-a]pyrimidin-7-yl)amino]piperidine-1-carboxylate" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C26 H41 N7 O3" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         "HYDROXYETHYLAMINE BACE INHIBITOR" 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-12-08 
_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                        499.649 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     YPK 
_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        8R9S 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBE 
_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_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 
YPK C1  C1  C 0 1 N N N N N N 11.920 28.622 -9.357  -10.215 2.188  1.565  C1  YPK 1  
YPK C2  C2  C 0 1 N N N N N N 11.112 29.915 -9.378  -9.825  1.477  0.268  C2  YPK 2  
YPK C3  C3  C 0 1 N N N N N N 11.841 30.987 -10.181 -10.464 2.198  -0.921 C3  YPK 3  
YPK C5  C4  C 0 1 Y N N N N N 9.226  28.703 -10.742 -7.521  2.620  0.042  C5  YPK 4  
YPK C8  C5  C 0 1 Y N N N N N 6.282  30.432 -10.211 -5.181  -0.043 -0.218 C8  YPK 5  
YPK C10 C6  C 0 1 N N N N N N 4.123  29.182 -10.447 -2.784  -0.553 -0.468 C10 YPK 6  
YPK C11 C7  C 0 1 N N N N N N 2.966  29.465 -11.388 -2.338  -0.992 0.929  C11 YPK 7  
YPK C12 C8  C 0 1 N N N N N N 1.719  28.730 -10.923 -1.211  -2.022 0.799  C12 YPK 8  
YPK C14 C9  C 0 1 N N N N N N 2.550  28.872 -8.584  -0.476  -0.912 -1.350 C14 YPK 9  
YPK C15 C10 C 0 1 N N N N N N 3.757  29.653 -9.056  -1.611  0.105  -1.197 C15 YPK 10 
YPK C16 C11 C 0 1 N N N N N N 0.264  29.593 -9.118  1.131   -1.413 0.427  C16 YPK 11 
YPK O17 O1  O 0 1 N N N N N N 0.166  30.330 -8.160  1.397   -1.858 1.526  O17 YPK 12 
YPK C19 C12 C 0 1 N N S N N N -1.071 27.839 -10.164 3.447   -0.879 0.213  C19 YPK 13 
YPK C21 C13 C 0 1 N N N N N N -2.274 27.461 -9.277  4.220   -2.162 -0.194 C21 YPK 14 
YPK C22 C14 C 0 1 N N N N N N -3.365 26.991 -10.222 5.693   -1.707 -0.152 C22 YPK 15 
YPK C24 C15 C 0 1 N N N N N N -1.535 27.656 -11.613 4.313   0.226  -0.443 C24 YPK 16 
YPK C25 C16 C 0 1 N N N N N N -2.591 25.476 -11.962 6.799   0.540  -0.281 C25 YPK 17 
YPK C27 C17 C 0 1 N N N N N N -2.647 25.339 -13.471 8.164   -0.077 -0.116 C27 YPK 18 
YPK C28 C18 C 0 1 N N N N N N -3.519 24.163 -13.931 9.227   1.024  -0.139 C28 YPK 19 
YPK C35 C19 C 0 1 Y N N N N N 7.200  32.125 -8.739  -6.773  -1.813 -0.065 C35 YPK 20 
YPK C36 C20 C 0 1 N N N N N N 7.046  33.344 -7.882  -7.083  -3.288 -0.042 C36 YPK 21 
YPK C38 C21 C 0 1 Y N N N N N 8.596  30.492 -9.586  -7.500  0.379  0.031  C38 YPK 22 
YPK C29 C22 C 0 1 N N N N N N -3.070 23.605 -15.282 10.613  0.398  0.028  C29 YPK 23 
YPK N30 N1  N 0 1 N N N N N N -3.827 22.381 -15.726 11.634  1.454  0.006  N30 YPK 24 
YPK C32 C23 C 0 1 N N N N N N -3.343 21.892 -17.050 11.505  2.335  1.175  C32 YPK 25 
YPK C33 C24 C 0 1 N N N N N N -3.798 21.281 -14.716 12.983  0.880  -0.075 C33 YPK 26 
YPK O26 O2  O 0 1 N N N N N N -2.506 24.486 -11.239 6.687   1.742  -0.404 O26 YPK 27 
YPK N23 N2  N 0 1 N N N N N N -2.636 26.708 -11.458 5.702   -0.243 -0.291 N23 YPK 28 
YPK O18 O3  O 0 1 N N N N N N -0.793 29.236 -9.935  2.104   -0.884 -0.338 O18 YPK 29 
YPK N13 N3  N 0 1 N N N N N N 1.425  29.021 -9.513  -0.138  -1.448 -0.025 N13 YPK 30 
YPK N9  N4  N 0 1 N N N N N N 5.353  29.775 -10.928 -3.885  0.407  -0.348 N9  YPK 31 
YPK C34 C25 C 0 1 Y N N N N N 6.116  31.565 -9.422  -5.452  -1.384 -0.198 C34 YPK 32 
YPK N37 N5  N 0 1 Y N N N N N 8.435  31.596 -8.817  -7.748  -0.938 0.050  N37 YPK 33 
YPK C4  C26 C 0 1 Y N N N N N 9.704  29.705 -9.886  -8.326  1.491  0.118  C4  YPK 34 
YPK N6  N6  N 0 1 Y N N N N N 7.930  28.811 -10.988 -6.270  2.243  -0.090 N6  YPK 35 
YPK N7  N7  N 0 1 Y N N N N N 7.543  29.915 -10.276 -6.218  0.845  -0.105 N7  YPK 36 
YPK H40 H1  H 0 1 N N N N N N 11.380 27.861 -8.774  -11.299 2.177  1.674  H40 YPK 37 
YPK H41 H2  H 0 1 N N N N N N 12.063 28.262 -10.387 -9.760  1.674  2.412  H41 YPK 38 
YPK H39 H3  H 0 1 N N N N N N 12.900 28.810 -8.895  -9.863  3.219  1.534  H39 YPK 39 
YPK H42 H4  H 0 1 N N N N N N 11.040 30.274 -8.341  -10.177 0.445  0.299  H42 YPK 40 
YPK H44 H5  H 0 1 N N N N N N 12.860 31.113 -9.785  -10.186 1.691  -1.845 H44 YPK 41 
YPK H45 H6  H 0 1 N N N N N N 11.893 30.682 -11.237 -11.548 2.187  -0.812 H45 YPK 42 
YPK H43 H7  H 0 1 N N N N N N 11.296 31.939 -10.101 -10.112 3.229  -0.952 H43 YPK 43 
YPK H46 H8  H 0 1 N N N N N N 9.850  27.925 -11.157 -7.868  3.642  0.080  H46 YPK 44 
YPK H48 H9  H 0 1 N N N N N N 4.256  28.091 -10.404 -3.121  -1.423 -1.031 H48 YPK 45 
YPK H50 H10 H 0 1 N N N N N N 3.230  29.127 -12.401 -1.978  -0.126 1.485  H50 YPK 46 
YPK H49 H11 H 0 1 N N N N N N 2.766  30.547 -11.403 -3.180  -1.439 1.456  H49 YPK 47 
YPK H52 H12 H 0 1 N N N N N N 0.865  29.046 -11.540 -0.822  -2.264 1.788  H52 YPK 48 
YPK H51 H13 H 0 1 N N N N N N 1.876  27.648 -11.041 -1.593  -2.925 0.324  H51 YPK 49 
YPK H54 H14 H 0 1 N N N N N N 2.248  29.242 -7.593  -0.798  -1.725 -2.001 H54 YPK 50 
YPK H53 H15 H 0 1 N N N N N N 2.817  27.807 -8.512  0.397   -0.423 -1.782 H53 YPK 51 
YPK H56 H16 H 0 1 N N N N N N 4.601  29.480 -8.372  -1.936  0.439  -2.182 H56 YPK 52 
YPK H55 H17 H 0 1 N N N N N N 3.518  30.726 -9.079  -1.258  0.960  -0.621 H55 YPK 53 
YPK H20 H18 H 0 1 N N N N N N -0.205 27.198 -9.943  3.423   -0.765 1.296  H20 YPK 54 
YPK H57 H19 H 0 1 N N N N N N -2.616 28.336 -8.705  4.042   -2.963 0.524  H57 YPK 55 
YPK H58 H20 H 0 1 N N N N N N -1.997 26.654 -8.583  3.940   -2.478 -1.199 H58 YPK 56 
YPK H60 H21 H 0 1 N N N N N N -4.117 27.778 -10.379 6.142   -1.991 0.800  H60 YPK 57 
YPK H59 H22 H 0 1 N N N N N N -3.857 26.085 -9.838  6.246   -2.163 -0.973 H59 YPK 58 
YPK H61 H23 H 0 1 N N N N N N -0.733 27.239 -12.240 4.061   0.329  -1.499 H61 YPK 59 
YPK H62 H24 H 0 1 N N N N N N -1.883 28.606 -12.045 4.174   1.174  0.075  H62 YPK 60 
YPK H63 H25 H 0 1 N N N N N N -1.625 25.187 -13.848 8.211   -0.607 0.835  H63 YPK 61 
YPK H64 H27 H 0 1 N N N N N N -4.560 24.507 -14.018 9.180   1.554  -1.090 H64 YPK 62 
YPK H75 H29 H 0 1 N N N N N N 8.019  33.609 -7.442  -7.052  -3.650 0.985  H75 YPK 63 
YPK H74 H30 H 0 1 N N N N N N 6.681  34.180 -8.496  -8.077  -3.456 -0.457 H74 YPK 64 
YPK H76 H31 H 0 1 N N N N N N 6.324  33.138 -7.078  -6.345  -3.823 -0.639 H76 YPK 65 
YPK H66 H32 H 0 1 N N N N N N -2.004 23.344 -15.211 10.660  -0.133 0.979  H66 YPK 66 
YPK H65 H33 H 0 1 N N N N N N -3.206 24.389 -16.042 10.796  -0.302 -0.788 H65 YPK 67 
YPK H69 H35 H 0 1 N N N N N N -3.915 21.000 -17.344 11.627  1.749  2.086  H69 YPK 68 
YPK H67 H36 H 0 1 N N N N N N -3.481 22.680 -17.805 12.272  3.107  1.133  H67 YPK 69 
YPK H68 H37 H 0 1 N N N N N N -2.276 21.635 -16.978 10.519  2.800  1.172  H68 YPK 70 
YPK H70 H38 H 0 1 N N N N N N -4.158 21.661 -13.749 13.073  0.289  -0.986 H70 YPK 71 
YPK H71 H39 H 0 1 N N N N N N -4.447 20.459 -15.051 13.719  1.684  -0.090 H71 YPK 72 
YPK H72 H40 H 0 1 N N N N N N -2.767 20.913 -14.605 13.159  0.242  0.791  H72 YPK 73 
YPK H47 H41 H 0 1 N N N N N N 5.849  29.020 -11.357 -3.701  1.360  -0.361 H47 YPK 74 
YPK H73 H42 H 0 1 N N N N N N 5.139  32.017 -9.336  -4.652  -2.104 -0.286 H73 YPK 75 
YPK H1  H43 H 0 1 N N N N N N -3.059 26.268 -13.893 8.347   -0.776 -0.932 H1  YPK 76 
YPK H2  H44 H 0 1 N N N N N N -3.459 23.362 -13.179 9.044   1.723  0.677  H2  YPK 77 
# 
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 
YPK C32 N30 SING N N 1  
YPK N30 C29 SING N N 2  
YPK N30 C33 SING N N 3  
YPK C29 C28 SING N N 4  
YPK C28 C27 SING N N 5  
YPK C27 C25 SING N N 6  
YPK C25 N23 SING N N 7  
YPK C25 O26 DOUB N N 8  
YPK C24 N23 SING N N 9  
YPK C24 C19 SING N N 10 
YPK N23 C22 SING N N 11 
YPK C11 C12 SING N N 12 
YPK C11 C10 SING N N 13 
YPK N6  C5  DOUB Y N 14 
YPK N6  N7  SING Y N 15 
YPK N9  C10 SING N N 16 
YPK N9  C8  SING N N 17 
YPK C12 N13 SING N N 18 
YPK C5  C4  SING Y N 19 
YPK C10 C15 SING N N 20 
YPK N7  C8  SING Y N 21 
YPK N7  C38 SING Y N 22 
YPK C22 C21 SING N N 23 
YPK C8  C34 DOUB Y N 24 
YPK C3  C2  SING N N 25 
YPK C19 O18 SING N N 26 
YPK C19 C21 SING N N 27 
YPK O18 C16 SING N N 28 
YPK C4  C38 DOUB Y N 29 
YPK C4  C2  SING N N 30 
YPK C38 N37 SING Y N 31 
YPK N13 C16 SING N N 32 
YPK N13 C14 SING N N 33 
YPK C34 C35 SING Y N 34 
YPK C2  C1  SING N N 35 
YPK C16 O17 DOUB N N 36 
YPK C15 C14 SING N N 37 
YPK N37 C35 DOUB Y N 38 
YPK C35 C36 SING N N 39 
YPK C1  H40 SING N N 40 
YPK C1  H41 SING N N 41 
YPK C1  H39 SING N N 42 
YPK C2  H42 SING N N 43 
YPK C3  H44 SING N N 44 
YPK C3  H45 SING N N 45 
YPK C3  H43 SING N N 46 
YPK C5  H46 SING N N 47 
YPK C10 H48 SING N N 48 
YPK C11 H50 SING N N 49 
YPK C11 H49 SING N N 50 
YPK C12 H52 SING N N 51 
YPK C12 H51 SING N N 52 
YPK C14 H54 SING N N 53 
YPK C14 H53 SING N N 54 
YPK C15 H56 SING N N 55 
YPK C15 H55 SING N N 56 
YPK C19 H20 SING N N 57 
YPK C21 H57 SING N N 58 
YPK C21 H58 SING N N 59 
YPK C22 H60 SING N N 60 
YPK C22 H59 SING N N 61 
YPK C24 H61 SING N N 62 
YPK C24 H62 SING N N 63 
YPK C27 H63 SING N N 64 
YPK C28 H64 SING N N 65 
YPK C36 H75 SING N N 66 
YPK C36 H74 SING N N 67 
YPK C36 H76 SING N N 68 
YPK C29 H66 SING N N 69 
YPK C29 H65 SING N N 70 
YPK C32 H69 SING N N 71 
YPK C32 H67 SING N N 72 
YPK C32 H68 SING N N 73 
YPK C33 H70 SING N N 74 
YPK C33 H71 SING N N 75 
YPK C33 H72 SING N N 76 
YPK N9  H47 SING N N 77 
YPK C34 H73 SING N N 78 
YPK C27 H1  SING N N 79 
YPK C28 H2  SING N N 80 
# 
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 
YPK InChI            InChI                1.06  "InChI=1S/C26H41N7O3/c1-18(2)22-16-27-33-23(15-19(3)28-25(22)33)29-20-8-12-31(13-9-20)26(35)36-21-10-14-32(17-21)24(34)7-6-11-30(4)5/h15-16,18,20-21,29H,6-14,17H2,1-5H3/t21-/m0/s1" 
YPK InChIKey         InChI                1.06  GRQNIAZNGVLLKQ-NRFANRHFSA-N                                                                                                                                                          
YPK SMILES_CANONICAL CACTVS               3.385 "CC(C)c1cnn2c(NC3CCN(CC3)C(=O)O[C@H]4CCN(C4)C(=O)CCCN(C)C)cc(C)nc12"                                                                                                                 
YPK SMILES           CACTVS               3.385 "CC(C)c1cnn2c(NC3CCN(CC3)C(=O)O[CH]4CCN(C4)C(=O)CCCN(C)C)cc(C)nc12"                                                                                                                  
YPK SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "Cc1cc(n2c(n1)c(cn2)C(C)C)NC3CCN(CC3)C(=O)O[C@H]4CCN(C4)C(=O)CCCN(C)C"                                                                                                               
YPK SMILES           "OpenEye OEToolkits" 2.0.7 "Cc1cc(n2c(n1)c(cn2)C(C)C)NC3CCN(CC3)C(=O)OC4CCN(C4)C(=O)CCCN(C)C"                                                                                                                   
# 
_pdbx_chem_comp_identifier.comp_id           YPK 
_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        "[(3~{S})-1-[4-(dimethylamino)butanoyl]pyrrolidin-3-yl] 4-[(5-methyl-3-propan-2-yl-pyrazolo[1,5-a]pyrimidin-7-yl)amino]piperidine-1-carboxylate" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
YPK "Create component" 2023-12-08 PDBE 
YPK "Initial release"  2024-05-29 RCSB 
YPK "Modify PCM"       2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            YPK 
_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               C28 
_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      ? 
# 
