data_WY8
# 
_chem_comp.id                                    WY8 
_chem_comp.name                                  "9-[(1~{S},3~{R},6~{R},8~{R},9~{R},10~{R},12~{R},15~{R},17~{R},18~{R})-8-(6-aminopurin-9-yl)-9,18-bis(fluoranyl)-3,12-bis(oxidanylidene)-3,12-bis(sulfanyl)-2,4,7,11,13-pentaoxa-3$l^{5},12$l^{5}-diphosphatricyclo[13.2.1.0^{6,10}]octadecan-17-yl]-1~{H}-purin-6-one" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C21 H23 F2 N9 O8 P2 S2" 
_chem_comp.mon_nstd_parent_comp_id               ADE 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-05-23 
_chem_comp.pdbx_modified_date                    2023-12-15 
_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                        693.537 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     WY8 
_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        8P44 
_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_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 
WY8 C10  C1  C 0 1 N N N N N N 20.574 44.180 66.278 -1.317  1.036  0.317  C10  WY8 1  
WY8 C13  C2  C 0 1 N N R N N N 23.993 44.791 67.135 -4.474  -0.331 0.494  C13  WY8 2  
WY8 C8   C3  C 0 1 Y N N N N N 24.300 43.876 64.793 -5.259  1.973  -0.168 C8   WY8 3  
WY8 C5   C4  C 0 1 Y N N N N N 26.387 44.113 64.516 -7.334  1.604  -0.677 C5   WY8 4  
WY8 C4   C5  C 0 1 Y N N N N N 26.108 44.612 65.774 -6.773  0.375  -0.292 C4   WY8 5  
WY8 C1   C6  C 0 1 N N R N N N 18.854 46.751 63.240 2.157   -0.364 -0.800 C1   WY8 6  
WY8 C2   C7  C 0 1 Y N N N N N 28.233 45.055 66.167 -8.796  -0.648 -0.673 C2   WY8 7  
WY8 C6   C8  C 0 1 Y N N N N N 27.737 44.111 64.128 -8.686  1.625  -1.061 C6   WY8 8  
WY8 C24  C9  C 0 1 N N R N N N 23.542 46.247 67.164 -3.815  -1.027 -0.706 C24  WY8 9  
WY8 C28  C10 C 0 1 N N N N N N 20.570 48.007 62.069 3.795   -1.632 0.466  C28  WY8 10 
WY8 C29  C11 C 0 1 N N R N N N 20.443 46.562 61.611 4.291   -0.176 0.377  C29  WY8 11 
WY8 C3   C12 C 0 1 N N R N N N 19.349 48.186 63.011 2.286   -1.564 0.165  C3   WY8 12 
WY8 C31  C13 C 0 1 Y N N N N N 22.945 46.058 61.376 5.485   -0.469 -1.822 C31  WY8 13 
WY8 C33  C14 C 0 1 Y N N N N N 22.924 44.760 59.687 7.470   0.249  -1.336 C33  WY8 14 
WY8 C34  C15 C 0 1 Y N N N N N 21.625 45.151 59.888 6.693   0.363  -0.179 C34  WY8 15 
WY8 C36  C16 C 0 1 N N N N N N 20.834 43.973 58.207 8.490   1.227  0.976  C36  WY8 16 
WY8 C38  C17 C 0 1 N N N N N N 23.211 43.861 58.610 8.825   0.661  -1.281 C38  WY8 17 
WY8 C7   C18 C 0 1 N N N N N N 19.682 48.902 64.302 1.764   -2.830 -0.490 C7   WY8 18 
WY8 C40  C19 C 0 1 N N S N N N 20.107 45.946 62.938 3.138   0.667  -0.204 C40  WY8 19 
WY8 C11  C20 C 0 1 N N R N N N 22.120 46.186 66.623 -2.342  -1.189 -0.269 C11  WY8 20 
WY8 C9   C21 C 0 1 N N R N N N 21.635 44.836 67.124 -2.154  -0.138 0.833  C9   WY8 21 
WY8 F1   F1  F 0 1 N N N N N N 17.831 46.353 62.371 0.856   0.107  -0.823 F1   WY8 22 
WY8 F25  F2  F 0 1 N N N N N N 23.529 46.701 68.488 -4.391  -2.283 -0.919 F25  WY8 23 
WY8 N9   N1  N 0 1 Y N N N N N 24.757 44.453 65.948 -5.465  0.640  0.028  N9   WY8 24 
WY8 N7   N2  N 0 1 Y N N N N N 25.233 43.652 63.904 -6.357  2.537  -0.582 N7   WY8 25 
WY8 N3   N3  N 0 1 Y N N N N N 26.987 45.105 66.649 -7.534  -0.715 -0.305 N3   WY8 26 
WY8 N1   N4  N 0 1 Y N N N N N 28.655 44.599 64.983 -9.367  0.484  -1.043 N1   WY8 27 
WY8 N6   N5  N 0 1 N N N N N N 28.113 43.564 62.974 -9.293  2.806  -1.450 N6   WY8 28 
WY8 N30  N6  N 0 1 Y N N N N N 21.642 45.984 60.976 5.448   -0.097 -0.511 N30  WY8 29 
WY8 N32  N7  N 0 1 Y N N N N N 23.752 45.338 60.632 6.678   -0.267 -2.304 N32  WY8 30 
WY8 N35  N8  N 0 1 N N N N N N 20.541 44.789 59.174 7.241   0.853  0.942  N35  WY8 31 
WY8 N37  N9  N 0 1 N N N N N N 22.071 43.519 57.918 9.299   1.143  -0.110 N37  WY8 32 
WY8 O11  O1  O 0 1 N N N N N N 20.968 44.152 64.889 -0.117  1.139  1.085  O11  WY8 33 
WY8 O12  O2  O 0 1 N N N N N N 22.813 44.006 67.141 -3.446  0.339  1.225  O12  WY8 34 
WY8 O27  O3  O 0 1 N N N N N N 22.189 49.117 65.865 -0.833  -4.653 0.456  O27  WY8 35 
WY8 O39  O4  O 0 1 N N N N N N 24.305 43.420 58.271 9.544   0.581  -2.262 O39  WY8 36 
WY8 O41  O5  O 0 1 N N N N N N 19.826 44.555 62.716 2.495   1.374  0.851  O41  WY8 37 
WY8 O44  O6  O 0 1 N N N N N N 20.443 42.277 63.246 0.918   2.638  -0.663 O44  WY8 38 
WY8 O5   O7  O 0 1 N N N N N N 19.957 48.033 65.415 0.341   -2.714 -0.652 O5   WY8 39 
WY8 O7   O8  O 0 1 N N N N N N 21.328 47.208 67.254 -2.135  -2.507 0.228  O7   WY8 40 
WY8 P42  P1  P 0 1 N N R N N N 19.971 43.518 63.868 1.088   2.144  0.722  P42  WY8 41 
WY8 P6   P2  P 0 1 N N R N N N 20.982 48.520 66.487 -0.699  -3.177 0.487  P6   WY8 42 
WY8 S26  S1  S 0 1 N N N N N N 20.151 49.844 67.855 0.024   -2.582 2.391  S26  WY8 43 
WY8 S43  S2  S 0 1 N N N N N N 18.102 43.367 64.742 1.059   3.789  2.063  S43  WY8 44 
WY8 H1   H1  H 0 1 N N N N N N 19.635 44.745 66.375 -1.070  0.878  -0.732 H1   WY8 45 
WY8 H4   H2  H 0 1 N N N N N N 20.419 43.149 66.629 -1.888  1.960  0.412  H4   WY8 46 
WY8 H3   H3  H 0 1 N N N N N N 24.592 44.587 68.035 -4.957  -1.073 1.134  H3   WY8 47 
WY8 H8   H4  H 0 1 N N N N N N 23.261 43.628 64.631 -4.324  2.486  -0.001 H8   WY8 48 
WY8 H5   H5  H 0 1 N N N N N N 18.568 46.620 64.294 2.490   -0.661 -1.793 H5   WY8 49 
WY8 H2   H6  H 0 1 N N N N N N 29.003 45.434 66.823 -9.386  -1.552 -0.673 H2   WY8 50 
WY8 H7   H7  H 0 1 N N N N N N 24.179 46.863 66.513 -3.881  -0.413 -1.594 H7   WY8 51 
WY8 H6   H8  H 0 1 N N N N N N 21.514 48.168 62.611 4.299   -2.235 -0.284 H6   WY8 52 
WY8 H9   H9  H 0 1 N N N N N N 20.515 48.698 61.215 3.966   -2.021 1.464  H9   WY8 53 
WY8 H10  H10 H 0 1 N N N N N N 19.581 46.470 60.934 4.543   0.190  1.368  H10  WY8 54 
WY8 H11  H11 H 0 1 N N N N N N 18.571 48.750 62.476 1.754   -1.341 1.086  H11  WY8 55 
WY8 H12  H12 H 0 1 N N N N N N 23.278 46.648 62.217 4.652   -0.875 -2.376 H12  WY8 56 
WY8 H13  H13 H 0 1 N N N N N N 20.021 43.630 57.584 8.893   1.617  1.899  H13  WY8 57 
WY8 H14  H14 H 0 1 N N N N N N 20.570 49.528 64.128 2.225   -2.963 -1.470 H14  WY8 58 
WY8 H15  H15 H 0 1 N N N N N N 18.828 49.542 64.569 1.980   -3.698 0.134  H15  WY8 59 
WY8 H16  H16 H 0 1 N N N N N N 20.895 46.116 63.687 3.506   1.327  -0.972 H16  WY8 60 
WY8 H17  H17 H 0 1 N N N N N N 22.100 46.244 65.525 -1.684  -0.989 -1.114 H17  WY8 61 
WY8 H18  H18 H 0 1 N N N N N N 21.250 44.957 68.147 -1.661  -0.579 1.696  H18  WY8 62 
WY8 HN61 H19 H 0 0 N N N N N N 29.110 43.596 62.899 -8.786  3.633  -1.459 HN61 WY8 63 
WY8 HN62 H20 H 0 0 N N N N N N 27.806 42.613 62.941 -10.227 2.808  -1.714 HN62 WY8 64 
WY8 H21  H21 H 0 1 N N N N N N 22.167 42.890 57.147 10.223  1.431  -0.046 H21  WY8 65 
WY8 H22  H22 H 0 1 N N N N N N 20.958 50.860 67.773 1.208   -3.213 2.476  H22  WY8 66 
WY8 H23  H23 H 0 1 N N N N N N 17.792 42.127 64.506 -0.153  4.331  1.851  H23  WY8 67 
# 
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 
WY8 N37 C36  SING N N 1  
WY8 N37 C38  SING N N 2  
WY8 C36 N35  DOUB N N 3  
WY8 O39 C38  DOUB N N 4  
WY8 C38 C33  SING N N 5  
WY8 N35 C34  SING N N 6  
WY8 C33 C34  DOUB Y N 7  
WY8 C33 N32  SING Y N 8  
WY8 C34 N30  SING Y N 9  
WY8 N32 C31  DOUB Y N 10 
WY8 N30 C31  SING Y N 11 
WY8 N30 C29  SING N N 12 
WY8 C29 C28  SING N N 13 
WY8 C29 C40  SING N N 14 
WY8 C28 C3   SING N N 15 
WY8 F1  C1   SING N N 16 
WY8 O41 C40  SING N N 17 
WY8 O41 P42  SING N N 18 
WY8 C40 C1   SING N N 19 
WY8 N6  C6   SING N N 20 
WY8 C3  C1   SING N N 21 
WY8 C3  C7   SING N N 22 
WY8 O44 P42  DOUB N N 23 
WY8 P42 S43  SING N N 24 
WY8 P42 O11  SING N N 25 
WY8 N7  C5   SING Y N 26 
WY8 N7  C8   DOUB Y N 27 
WY8 C6  C5   DOUB Y N 28 
WY8 C6  N1   SING Y N 29 
WY8 C7  O5   SING N N 30 
WY8 C5  C4   SING Y N 31 
WY8 C8  N9   SING Y N 32 
WY8 O11 C10  SING N N 33 
WY8 N1  C2   DOUB Y N 34 
WY8 O5  P6   SING N N 35 
WY8 C4  N9   SING Y N 36 
WY8 C4  N3   DOUB Y N 37 
WY8 O27 P6   DOUB N N 38 
WY8 N9  C13  SING N N 39 
WY8 C2  N3   SING Y N 40 
WY8 C10 C9   SING N N 41 
WY8 P6  O7   SING N N 42 
WY8 P6  S26  SING N N 43 
WY8 C11 C9   SING N N 44 
WY8 C11 C24  SING N N 45 
WY8 C11 O7   SING N N 46 
WY8 C9  O12  SING N N 47 
WY8 C13 O12  SING N N 48 
WY8 C13 C24  SING N N 49 
WY8 C24 F25  SING N N 50 
WY8 C10 H1   SING N N 51 
WY8 C10 H4   SING N N 52 
WY8 C13 H3   SING N N 53 
WY8 C8  H8   SING N N 54 
WY8 C1  H5   SING N N 55 
WY8 C2  H2   SING N N 56 
WY8 C24 H7   SING N N 57 
WY8 C28 H6   SING N N 58 
WY8 C28 H9   SING N N 59 
WY8 C29 H10  SING N N 60 
WY8 C3  H11  SING N N 61 
WY8 C31 H12  SING N N 62 
WY8 C36 H13  SING N N 63 
WY8 C7  H14  SING N N 64 
WY8 C7  H15  SING N N 65 
WY8 C40 H16  SING N N 66 
WY8 C11 H17  SING N N 67 
WY8 C9  H18  SING N N 68 
WY8 N6  HN61 SING N N 69 
WY8 N6  HN62 SING N N 70 
WY8 N37 H21  SING N N 71 
WY8 S26 H22  SING N N 72 
WY8 S43 H23  SING N N 73 
# 
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 
WY8 InChI            InChI                1.06  "InChI=1S/C21H23F2N9O8P2S2/c22-11-8-1-9(31-6-30-14-19(31)27-5-28-20(14)33)15(11)39-42(35,44)37-3-10-16(40-41(34,43)36-2-8)12(23)21(38-10)32-7-29-13-17(24)25-4-26-18(13)32/h4-12,15-16,21H,1-3H2,(H,34,43)(H,35,44)(H2,24,25,26)(H,27,28,33)/t8-,9-,10-,11-,12-,15+,16-,21-,41-,42-/m1/s1" 
WY8 InChIKey         InChI                1.06  VEWJXUHPZNDXNI-YGFQTLPJSA-N                                                                                                                                                                                                                                                                
WY8 SMILES_CANONICAL CACTVS               3.385 "Nc1ncnc2n(cnc12)[C@@H]3O[C@@H]4CO[P@](S)(=O)O[C@@H]5[C@H](F)[C@@H](CO[P@](S)(=O)O[C@H]4[C@H]3F)C[C@H]5n6cnc7C(=O)NC=Nc67"                                                                                                                                                                 
WY8 SMILES           CACTVS               3.385 "Nc1ncnc2n(cnc12)[CH]3O[CH]4CO[P](S)(=O)O[CH]5[CH](F)[CH](CO[P](S)(=O)O[CH]4[CH]3F)C[CH]5n6cnc7C(=O)NC=Nc67"                                                                                                                                                                               
WY8 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@H]4[C@H](O3)CO[P@](=O)(O[C@H]5[C@@H](C[C@@H]([C@H]5F)CO[P@](=O)(O4)S)n6cnc7c6N=CNC7=O)S)F)N"                                                                                                                                                            
WY8 SMILES           "OpenEye OEToolkits" 2.0.7 "c1nc(c2c(n1)n(cn2)C3C(C4C(O3)COP(=O)(OC5C(CC(C5F)COP(=O)(O4)S)n6cnc7c6N=CNC7=O)S)F)N"                                                                                                                                                                                                     
# 
_pdbx_chem_comp_identifier.comp_id           WY8 
_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        "9-[(1~{S},3~{R},6~{R},8~{R},9~{R},10~{R},12~{R},15~{R},17~{R},18~{R})-8-(6-aminopurin-9-yl)-9,18-bis(fluoranyl)-3,12-bis(oxidanylidene)-3,12-bis(sulfanyl)-2,4,7,11,13-pentaoxa-3$l^{5},12$l^{5}-diphosphatricyclo[13.2.1.0^{6,10}]octadecan-17-yl]-1~{H}-purin-6-one" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
WY8 "Create component" 2023-05-23 PDBE 
WY8 "Initial release"  2023-12-20 RCSB 
# 
