data_Y63
# 
_chem_comp.id                                    Y63 
_chem_comp.name                                  "4-{(1R,5S)-3-[(7P)-7-(8-ethynylnaphthalen-1-yl)-8-fluoro-2-{[(4s,7as)-tetrahydro-1H-pyrrolizin-7a(5H)-yl]methoxy}pyrido[4,3-d]pyrimidin-4-yl]-3,8-diazabicyclo[3.2.1]octan-8-yl}-4-oxobutanoic acid" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C37 H37 F N6 O4" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-06-12 
_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                        648.726 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     Y63 
_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        8T4V 
_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 
Y63 C10 C1  C 0 1 Y N N N N N 3.341  15.763 38.058 -5.028 1.482  -1.071 C10 Y63 1  
Y63 C13 C2  C 0 1 N N N N N N 4.955  13.106 35.730 -2.996 1.383  1.919  C13 Y63 2  
Y63 C15 C3  C 0 1 Y N N N N N 7.525  15.310 37.971 -0.897 1.232  -0.268 C15 Y63 3  
Y63 C17 C4  C 0 1 N N N N N N 11.303 13.354 36.215 2.280  -0.071 1.117  C17 Y63 4  
Y63 C20 C5  C 0 1 N N N N N N 11.521 15.607 37.267 1.835  2.349  1.497  C20 Y63 5  
Y63 C21 C6  C 0 1 N N R N N N 12.038 14.745 36.149 2.898  1.247  1.640  C21 Y63 6  
Y63 C24 C7  C 0 1 N N N N N N 13.969 16.131 34.504 6.170  2.242  -0.241 C24 Y63 7  
Y63 C01 C8  C 0 1 N N N N N N 3.893  13.422 36.168 -4.137 1.475  1.658  C01 Y63 8  
Y63 C02 C9  C 0 1 Y N N N N N 2.524  13.823 36.714 -5.528 1.588  1.338  C02 Y63 9  
Y63 C03 C10 C 0 1 Y N N N N N 1.418  13.081 36.334 -6.473 1.696  2.348  C03 Y63 10 
Y63 C04 C11 C 0 1 Y N N N N N 0.139  13.364 36.765 -7.824 1.806  2.044  C04 Y63 11 
Y63 C05 C12 C 0 1 Y N N N N N -0.082 14.422 37.606 -8.258 1.809  0.752  C05 Y63 12 
Y63 C06 C13 C 0 1 Y N N N N N 1.014  15.170 38.009 -7.334 1.702  -0.303 C06 Y63 13 
Y63 C07 C14 C 0 1 Y N N N N N 0.699  16.208 38.855 -7.760 1.704  -1.643 C07 Y63 14 
Y63 C08 C15 C 0 1 Y N N N N N 1.694  17.022 39.311 -6.847 1.594  -2.649 C08 Y63 15 
Y63 C09 C16 C 0 1 Y N N N N N 2.982  16.781 38.929 -5.489 1.488  -2.378 C09 Y63 16 
Y63 C11 C17 C 0 1 Y N N N N N 4.847  15.666 37.874 -3.579 1.369  -0.790 C11 Y63 17 
Y63 C12 C18 C 0 1 Y N N N N N 5.433  14.718 38.690 -3.004 0.110  -0.681 C12 Y63 18 
Y63 C14 C19 C 0 1 Y N N N N N 6.752  14.521 38.741 -1.629 0.025  -0.414 C14 Y63 19 
Y63 C16 C20 C 0 1 Y N N N N N 6.944  16.317 37.174 -1.564 2.454  -0.394 C16 Y63 20 
Y63 C18 C21 C 0 1 Y N N N N N 8.919  15.144 37.974 0.491  1.145  -0.004 C18 Y63 21 
Y63 C19 C22 C 0 1 N N N N N N 16.085 17.204 33.899 8.459  2.980  -0.843 C19 Y63 22 
Y63 C23 C23 C 0 1 N N N N N N 12.523 15.909 34.082 5.225  1.990  0.906  C23 Y63 23 
Y63 C25 C24 C 0 1 N N N N N N 14.604 17.144 33.555 7.515  2.728  0.303  C25 Y63 24 
Y63 C30 C25 C 0 1 N N S N N N 10.430 14.931 34.693 3.334  1.260  -0.643 C30 Y63 25 
Y63 C31 C26 C 0 1 N N N N N N 10.283 13.455 35.223 2.570  -0.063 -0.399 C31 Y63 26 
Y63 C34 C27 C 0 1 N N N N N N 9.469  15.854 35.389 2.291  2.362  -0.891 C34 Y63 27 
Y63 C36 C28 C 0 1 Y N N N N N 8.650  13.498 39.503 0.311  -1.164 -0.051 C36 Y63 28 
Y63 C38 C29 C 0 1 N N N N N N 10.576 12.630 40.607 0.117  -3.529 -0.102 C38 Y63 29 
Y63 C39 C30 C 0 1 N N N N N N 10.867 11.915 41.938 0.983  -4.780 0.057  C39 Y63 30 
Y63 C41 C31 C 0 1 N N N N N N 9.275  11.677 43.660 0.742  -6.798 -1.218 C41 Y63 31 
Y63 C42 C32 C 0 1 N N N N N N 9.791  10.260 43.294 1.503  -5.769 -2.091 C42 Y63 32 
Y63 C43 C33 C 0 1 N N N N N N 10.333 10.480 41.878 2.091  -4.819 -1.015 C43 Y63 33 
Y63 C44 C34 C 0 1 N N N N N N 11.202 13.002 44.015 0.247  -6.783 1.149  C44 Y63 34 
Y63 C45 C35 C 0 1 N N N N N N 12.579 12.974 43.260 1.584  -6.329 1.822  C45 Y63 35 
Y63 C46 C36 C 0 1 N N N N N N 12.362 11.879 42.208 1.634  -4.823 1.455  C46 Y63 36 
Y63 C48 C37 C 0 1 Y N N N N N 2.342  14.891 37.599 -5.954 1.590  -0.011 C48 Y63 37 
Y63 F13 F1  F 0 1 N N N N N N 4.624  13.895 39.433 -3.750 -1.006 -0.828 F13 Y63 38 
Y63 N17 N1  N 0 1 Y N N N N N 5.581  16.512 37.151 -2.853 2.480  -0.645 N17 Y63 39 
Y63 N19 N2  N 0 1 N N N N N N 9.780  15.998 37.159 1.255  2.281  0.148  N19 Y63 40 
Y63 N22 N3  N 0 1 N N N N N N 11.657 15.201 34.984 3.973  1.553  0.664  N22 Y63 41 
Y63 N35 N4  N 0 1 Y N N N N N 9.489  14.233 38.784 1.036  -0.060 0.094  N35 Y63 42 
Y63 N40 N5  N 0 1 N N N N N N 10.204 12.613 43.001 0.172  -6.006 -0.107 N40 Y63 43 
Y63 N47 N6  N 0 1 Y N N N N N 7.331  13.597 39.513 -0.985 -1.142 -0.293 N47 Y63 44 
Y63 O01 O1  O 0 1 N N N N N N 16.464 17.940 34.845 8.095  2.790  -1.980 O01 Y63 45 
Y63 O03 O2  O 0 1 N N N N N N 16.912 16.509 33.245 9.706  3.415  -0.603 O03 Y63 46 
Y63 O29 O3  O 0 1 N N N N N N 12.119 16.290 33.025 5.591  2.181  2.046  O29 Y63 47 
Y63 O37 O4  O 0 1 N N N N N N 9.207  12.522 40.359 0.929  -2.364 0.060  O37 Y63 48 
Y63 H1  H1  H 0 1 N N N N N N 5.900  12.825 35.340 -1.976 1.301  2.154  H1  Y63 49 
Y63 H2  H2  H 0 1 N N N N N N 11.997 12.534 35.980 2.758  -0.929 1.591  H2  Y63 50 
Y63 H3  H3  H 0 1 N N N N N N 10.865 13.190 37.211 1.205  -0.085 1.299  H3  Y63 51 
Y63 H4  H4  H 0 1 N N N N N N 11.696 15.080 38.216 1.051  2.198  2.239  H4  Y63 52 
Y63 H5  H5  H 0 1 N N N N N N 12.086 16.551 37.262 2.298  3.324  1.648  H5  Y63 53 
Y63 H6  H6  H 0 1 N N N N N N 13.124 14.597 36.240 3.265  1.157  2.663  H6  Y63 54 
Y63 H7  H7  H 0 1 N N N N N N 13.999 16.518 35.533 6.317  1.318  -0.800 H7  Y63 55 
Y63 H8  H8  H 0 1 N N N N N N 14.520 15.180 34.453 5.748  3.001  -0.899 H8  Y63 56 
Y63 H9  H9  H 0 1 N N N N N N 1.564  12.242 35.670 -6.155 1.695  3.380  H9  Y63 57 
Y63 H10 H10 H 0 1 N N N N N N -0.689 12.751 36.439 -8.543 1.889  2.845  H10 Y63 58 
Y63 H11 H11 H 0 1 N N N N N N -1.078 14.666 37.945 -9.313 1.895  0.538  H11 Y63 59 
Y63 H12 H12 H 0 1 N N N N N N -0.325 16.377 39.155 -8.811 1.788  -1.874 H12 Y63 60 
Y63 H13 H13 H 0 1 N N N N N N 1.465  17.849 39.967 -7.186 1.597  -3.674 H13 Y63 61 
Y63 H14 H14 H 0 1 N N N N N N 3.761  17.415 39.325 -4.785 1.411  -3.194 H14 Y63 62 
Y63 H15 H15 H 0 1 N N N N N N 7.580  16.947 36.570 -1.019 3.380  -0.285 H15 Y63 63 
Y63 H16 H16 H 0 1 N N N N N N 14.471 16.821 32.512 7.367  3.652  0.862  H16 Y63 64 
Y63 H17 H17 H 0 1 N N N N N N 14.143 18.133 33.694 7.936  1.969  0.962  H17 Y63 65 
Y63 H18 H18 H 0 1 N N N N N N 10.232 14.939 33.611 4.053  1.179  -1.459 H18 Y63 66 
Y63 H19 H19 H 0 1 N N N N N N 10.448 12.728 34.414 3.190  -0.917 -0.671 H19 Y63 67 
Y63 H20 H20 H 0 1 N N N N N N 9.288  13.293 35.664 1.638  -0.073 -0.964 H20 Y63 68 
Y63 H21 H21 H 0 1 N N N N N N 9.554  16.853 34.937 2.775  3.338  -0.849 H21 Y63 69 
Y63 H22 H22 H 0 1 N N N N N N 8.448  15.471 35.243 1.838  2.222  -1.872 H22 Y63 70 
Y63 H24 H24 H 0 1 N N N N N N 10.861 13.690 40.681 -0.334 -3.523 -1.094 H24 Y63 71 
Y63 H25 H25 H 0 1 N N N N N N 11.143 12.153 39.794 -0.668 -3.533 0.654  H25 Y63 72 
Y63 H26 H26 H 0 1 N N N N N N 8.251  11.823 43.285 -0.054 -7.269 -1.795 H26 Y63 73 
Y63 H27 H27 H 0 1 N N N N N N 9.290  11.823 44.750 1.430  -7.551 -0.834 H27 Y63 74 
Y63 H28 H28 H 0 1 N N N N N N 10.586 9.933  43.981 2.296  -6.252 -2.661 H28 Y63 75 
Y63 H29 H29 H 0 1 N N N N N N 8.975  9.523  43.300 0.819  -5.236 -2.751 H29 Y63 76 
Y63 H30 H30 H 0 1 N N N N N N 9.533  10.386 41.129 2.261  -3.826 -1.429 H30 Y63 77 
Y63 H31 H31 H 0 1 N N N N N N 11.138 9.767  41.647 3.013  -5.229 -0.602 H31 Y63 78 
Y63 H32 H32 H 0 1 N N N N N N 11.204 12.286 44.850 0.264  -7.856 0.956  H32 Y63 79 
Y63 H33 H33 H 0 1 N N N N N N 10.991 14.011 44.398 -0.603 -6.524 1.780  H33 Y63 80 
Y63 H34 H34 H 0 1 N N N N N N 12.792 13.944 42.786 1.552  -6.487 2.900  H34 Y63 81 
Y63 H35 H35 H 0 1 N N N N N N 13.401 12.712 43.943 2.438  -6.841 1.379  H35 Y63 82 
Y63 H36 H36 H 0 1 N N N N N N 12.665 10.896 42.599 2.664  -4.471 1.410  H36 Y63 83 
Y63 H37 H37 H 0 1 N N N N N N 12.930 12.100 41.292 1.055  -4.234 2.166  H37 Y63 84 
Y63 H40 H40 H 0 1 N N N N N N 17.786 16.650 33.588 10.275 3.562  -1.370 H40 Y63 85 
# 
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 
Y63 C10 C09 SING Y N 1  
Y63 C10 C11 SING N N 2  
Y63 C10 C48 DOUB Y N 3  
Y63 C13 C01 TRIP N N 4  
Y63 C15 C14 DOUB Y N 5  
Y63 C15 C16 SING Y N 6  
Y63 C15 C18 SING Y N 7  
Y63 C17 C21 SING N N 8  
Y63 C17 C31 SING N N 9  
Y63 C20 C21 SING N N 10 
Y63 C21 N22 SING N N 11 
Y63 C24 C23 SING N N 12 
Y63 C24 C25 SING N N 13 
Y63 C01 C02 SING N N 14 
Y63 C02 C03 DOUB Y N 15 
Y63 C02 C48 SING Y N 16 
Y63 C03 C04 SING Y N 17 
Y63 C04 C05 DOUB Y N 18 
Y63 C05 C06 SING Y N 19 
Y63 C06 C07 DOUB Y N 20 
Y63 C06 C48 SING Y N 21 
Y63 C07 C08 SING Y N 22 
Y63 C08 C09 DOUB Y N 23 
Y63 C11 C12 DOUB Y N 24 
Y63 C11 N17 SING Y N 25 
Y63 C12 C14 SING Y N 26 
Y63 C12 F13 SING N N 27 
Y63 C14 N47 SING Y N 28 
Y63 C16 N17 DOUB Y N 29 
Y63 C18 N19 SING N N 30 
Y63 C18 N35 DOUB Y N 31 
Y63 C19 C25 SING N N 32 
Y63 C19 O01 DOUB N N 33 
Y63 C19 O03 SING N N 34 
Y63 C23 N22 SING N N 35 
Y63 C23 O29 DOUB N N 36 
Y63 C30 C31 SING N N 37 
Y63 C30 C34 SING N N 38 
Y63 C30 N22 SING N N 39 
Y63 C36 N35 SING Y N 40 
Y63 C36 N47 DOUB Y N 41 
Y63 C36 O37 SING N N 42 
Y63 C38 C39 SING N N 43 
Y63 C38 O37 SING N N 44 
Y63 C39 C43 SING N N 45 
Y63 C39 C46 SING N N 46 
Y63 C39 N40 SING N N 47 
Y63 C41 C42 SING N N 48 
Y63 C41 N40 SING N N 49 
Y63 C42 C43 SING N N 50 
Y63 C44 C45 SING N N 51 
Y63 C44 N40 SING N N 52 
Y63 C45 C46 SING N N 53 
Y63 N19 C20 SING N N 54 
Y63 C13 H1  SING N N 55 
Y63 C17 H2  SING N N 56 
Y63 C17 H3  SING N N 57 
Y63 C20 H4  SING N N 58 
Y63 C20 H5  SING N N 59 
Y63 C21 H6  SING N N 60 
Y63 C24 H7  SING N N 61 
Y63 C24 H8  SING N N 62 
Y63 C03 H9  SING N N 63 
Y63 C04 H10 SING N N 64 
Y63 C05 H11 SING N N 65 
Y63 C07 H12 SING N N 66 
Y63 C08 H13 SING N N 67 
Y63 C09 H14 SING N N 68 
Y63 C16 H15 SING N N 69 
Y63 C25 H16 SING N N 70 
Y63 C25 H17 SING N N 71 
Y63 C30 H18 SING N N 72 
Y63 C31 H19 SING N N 73 
Y63 C31 H20 SING N N 74 
Y63 C34 H21 SING N N 75 
Y63 C34 H22 SING N N 76 
Y63 C38 H24 SING N N 77 
Y63 C38 H25 SING N N 78 
Y63 C41 H26 SING N N 79 
Y63 C41 H27 SING N N 80 
Y63 C42 H28 SING N N 81 
Y63 C42 H29 SING N N 82 
Y63 C43 H30 SING N N 83 
Y63 C43 H31 SING N N 84 
Y63 C44 H32 SING N N 85 
Y63 C44 H33 SING N N 86 
Y63 C45 H34 SING N N 87 
Y63 C45 H35 SING N N 88 
Y63 C46 H36 SING N N 89 
Y63 C46 H37 SING N N 90 
Y63 O03 H40 SING N N 91 
Y63 N19 C34 SING N N 92 
# 
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 
Y63 SMILES           ACDLabs              12.01 "O=C(O)CCC(=O)N1C2CCC1CN(C2)c1nc(nc2c(F)c(ncc21)c1cccc2cccc(C#C)c21)OCC12CCCN2CCC1"                                                                                                                                                               
Y63 InChI            InChI                1.06  "InChI=1S/C37H37FN6O4/c1-2-23-7-3-8-24-9-4-10-27(31(23)24)33-32(38)34-28(19-39-33)35(41-36(40-34)48-22-37-15-5-17-43(37)18-6-16-37)42-20-25-11-12-26(21-42)44(25)29(45)13-14-30(46)47/h1,3-4,7-10,19,25-26H,5-6,11-18,20-22H2,(H,46,47)/t25-,26+" 
Y63 InChIKey         InChI                1.06  GUVKCXDNOZPYFC-WMPKNSHKSA-N                                                                                                                                                                                                                       
Y63 SMILES_CANONICAL CACTVS               3.385 "OC(=O)CCC(=O)N1[C@@H]2CC[C@H]1CN(C2)c3nc(OCC45CCCN4CCC5)nc6c(F)c(ncc36)c7cccc8cccc(C#C)c78"                                                                                                                                                      
Y63 SMILES           CACTVS               3.385 "OC(=O)CCC(=O)N1[CH]2CC[CH]1CN(C2)c3nc(OCC45CCCN4CCC5)nc6c(F)c(ncc36)c7cccc8cccc(C#C)c78"                                                                                                                                                         
Y63 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C#Cc1cccc2c1c(ccc2)c3c(c4c(cn3)c(nc(n4)OCC56CCCN5CCC6)N7C[C@H]8CC[C@@H](C7)N8C(=O)CCC(=O)O)F"                                                                                                                                                    
Y63 SMILES           "OpenEye OEToolkits" 2.0.7 "C#Cc1cccc2c1c(ccc2)c3c(c4c(cn3)c(nc(n4)OCC56CCCN5CCC6)N7CC8CCC(C7)N8C(=O)CCC(=O)O)F"                                                                                                                                                             
# 
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 
Y63 "SYSTEMATIC NAME" ACDLabs              12.01 "4-{(1R,5S)-3-[(7P)-7-(8-ethynylnaphthalen-1-yl)-8-fluoro-2-{[(4s,7as)-tetrahydro-1H-pyrrolizin-7a(5H)-yl]methoxy}pyrido[4,3-d]pyrimidin-4-yl]-3,8-diazabicyclo[3.2.1]octan-8-yl}-4-oxobutanoic acid"       
Y63 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "4-[(1~{R},5~{S})-3-[7-(8-ethynylnaphthalen-1-yl)-8-fluoranyl-2-(1,2,3,5,6,7-hexahydropyrrolizin-8-ylmethoxy)pyrido[4,3-d]pyrimidin-4-yl]-3,8-diazabicyclo[3.2.1]octan-8-yl]-4-oxidanylidene-butanoic acid" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
Y63 "Create component" 2023-06-12 RCSB 
Y63 "Initial release"  2024-03-13 RCSB 
Y63 "Modify PCM"       2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            Y63 
_pdbx_chem_comp_pcm.modified_residue_id                ASP 
_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               C24 
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom   OD2 
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession     ? 
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession      ? 
# 
