data_YG8
# 
_chem_comp.id                                    YG8 
_chem_comp.name                                  "[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-5-imidazol-1-yl-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C18 H25 N7 O13 P2" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-12-04 
_chem_comp.pdbx_modified_date                    2024-06-07 
_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                        609.378 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     YG8 
_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        8V6S 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  RCSB 
# 
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 
YG8 C11  C1  C 0 1 N N R N N N 8.993  -4.938 17.924 5.848  1.243  1.073  C11  YG8 1  
YG8 C10  C2  C 0 1 N N R N N N 10.333 -5.623 18.108 5.014  -0.056 0.940  C10  YG8 2  
YG8 C3   C3  C 0 1 Y N N N N N 13.500 -6.305 21.698 7.747  -3.372 -1.411 C3   YG8 3  
YG8 C4   C4  C 0 1 Y N N N N N 12.334 -5.784 21.097 6.748  -2.396 -1.256 C4   YG8 4  
YG8 C8   C5  C 0 1 Y N N N N N 10.530 -4.826 20.525 5.135  -0.955 -1.415 C8   YG8 5  
YG8 C5   C6  C 0 1 Y N N N N N 12.100 -6.164 19.779 6.579  -1.816 0.013  C5   YG8 6  
YG8 C1   C7  C 0 1 Y N N N N N 13.917 -7.394 19.700 8.278  -3.135 0.822  C1   YG8 7  
YG8 C12  C8  C 0 1 N N S N N N 8.964  -4.828 16.403 4.828  2.220  1.706  C12  YG8 8  
YG8 C13  C9  C 0 1 N N R N N N 10.434 -4.532 16.065 3.456  1.602  1.374  C13  YG8 9  
YG8 C15  C10 C 0 1 N N N N N N 10.717 -3.081 15.782 2.617  2.599  0.572  C15  YG8 10 
YG8 C25  C11 C 0 1 N N N N N N 9.317  2.593  15.194 -4.990 0.965  -1.136 C25  YG8 11 
YG8 C26  C12 C 0 1 N N R N N N 9.521  3.973  14.618 -5.485 -0.483 -1.136 C26  YG8 12 
YG8 C27  C13 C 0 1 N N S N N N 10.898 4.562  14.906 -6.939 -0.554 -1.651 C27  YG8 13 
YG8 C28  C14 C 0 1 N N R N N N 10.621 5.495  16.082 -7.593 -1.651 -0.782 C28  YG8 14 
YG8 C29  C15 C 0 1 N N R N N N 9.225  5.993  15.718 -6.456 -2.113 0.156  C29  YG8 15 
YG8 C32  C16 C 0 1 Y N N N N N 8.368  6.018  18.088 -7.276 -1.512 2.455  C32  YG8 16 
YG8 C34  C17 C 0 1 Y N N N N N 6.967  7.623  17.973 -7.737 -3.468 3.241  C34  YG8 17 
YG8 C35  C18 C 0 1 Y N N N N N 7.533  7.528  16.744 -7.273 -3.651 1.990  C35  YG8 18 
YG8 N2   N1  N 0 1 Y N N N N N 14.277 -7.120 20.956 8.478  -3.704 -0.352 N2   YG8 19 
YG8 N31  N2  N 0 1 Y N N N N N 8.430  6.494  16.826 -6.984 -2.411 1.490  N31  YG8 20 
YG8 N33  N3  N 0 1 Y N N N N N 7.487  6.680  18.816 -7.723 -2.152 3.500  N33  YG8 21 
YG8 N40  N4  N 0 1 N N N N N N 13.882 -6.001 22.942 7.959  -3.979 -2.637 N40  YG8 22 
YG8 N6   N5  N 0 1 Y N N N N N 12.847 -6.971 19.028 7.362  -2.209 1.012  N6   YG8 23 
YG8 N7   N6  N 0 1 Y N N N N N 10.934 -5.537 19.427 5.555  -0.912 -0.119 N7   YG8 24 
YG8 N9   N7  N 0 1 Y N N N N N 11.340 -4.945 21.553 5.836  -1.826 -2.080 N9   YG8 25 
YG8 O14  O1  O 0 1 N N N N N N 11.208 -4.995 17.197 3.698  0.423  0.588  O14  YG8 26 
YG8 O16  O2  O 0 1 N N N N N N 10.260 -2.241 16.871 1.307  2.063  0.370  O16  YG8 27 
YG8 O18  O3  O 0 1 N N N N N N 9.517  -0.217 18.004 -0.045 4.184  0.163  O18  YG8 28 
YG8 O19  O4  O 0 1 N N N N N N 11.672 -0.171 16.643 0.595  3.010  -1.977 O19  YG8 29 
YG8 O20  O5  O 0 1 N N N N N N 9.389  -0.396 15.528 -1.219 2.011  -0.357 O20  YG8 30 
YG8 O22  O6  O 0 1 N N N N N N 8.349  0.178  13.441 -2.852 3.096  -1.947 O22  YG8 31 
YG8 O23  O7  O 0 1 N N N N N N 10.823 -0.461 13.422 -3.352 3.273  0.521  O23  YG8 32 
YG8 O24  O8  O 0 1 N N N N N N 10.098 1.691  14.402 -3.609 0.997  -0.768 O24  YG8 33 
YG8 O30  O9  O 0 1 N N N N N N 8.549  4.878  15.194 -5.546 -0.993 0.214  O30  YG8 34 
YG8 O36  O10 O 0 1 N N N N N N 11.517 6.591  16.106 -8.041 -2.736 -1.598 O36  YG8 35 
YG8 O37  O11 O 0 1 N N N N N N 11.362 5.294  13.773 -6.964 -0.927 -3.031 O37  YG8 36 
YG8 O38  O12 O 0 1 N N N N N N 8.568  -6.049 15.774 5.016  2.292  3.120  O38  YG8 37 
YG8 O39  O13 O 0 1 N N N N N N 7.938  -5.730 18.452 6.968  1.043  1.939  O39  YG8 38 
YG8 P17  P1  P 0 1 N N N N N N 10.291 -0.682 16.822 0.155  2.846  -0.437 P17  YG8 39 
YG8 P21  P2  P 0 1 N N N N N N 9.684  0.224  14.081 -2.760 2.360  -0.666 P21  YG8 40 
YG8 H11  H1  H 0 1 N N N N N N 9.013  -3.935 18.376 6.174  1.598  0.095  H11  YG8 41 
YG8 H10  H2  H 0 1 N N N N N N 10.217 -6.683 17.836 4.985  -0.593 1.889  H10  YG8 42 
YG8 H8   H3  H 0 1 N N N N N N 9.633  -4.225 20.544 4.339  -0.354 -1.828 H8   YG8 43 
YG8 H1   H4  H 0 1 N N N N N N 14.583 -8.047 19.155 8.895  -3.434 1.656  H1   YG8 44 
YG8 H12  H5  H 0 1 N N N N N N 8.328  -3.986 16.094 4.919  3.210  1.257  H12  YG8 45 
YG8 H13  H6  H 0 1 N N N N N N 10.705 -5.120 15.176 2.938  1.334  2.294  H13  YG8 46 
YG8 H15A H7  H 0 0 N N N N N N 11.801 -2.944 15.653 2.544  3.537  1.122  H15A YG8 47 
YG8 H15B H8  H 0 0 N N N N N N 10.198 -2.787 14.858 3.089  2.778  -0.393 H15B YG8 48 
YG8 H25B H9  H 0 0 N N N N N N 8.254  2.316  15.144 -5.110 1.390  -2.133 H25B YG8 49 
YG8 H25A H10 H 0 0 N N N N N N 9.654  2.566  16.241 -5.570 1.548  -0.421 H25A YG8 50 
YG8 H26  H11 H 0 1 N N N N N N 9.381  3.926  13.528 -4.834 -1.106 -1.750 H26  YG8 51 
YG8 H27  H12 H 0 1 N N N N N N 11.602 3.770  15.201 -7.444 0.401  -1.504 H27  YG8 52 
YG8 H28  H13 H 0 1 N N N N N N 10.606 4.939  17.031 -8.420 -1.239 -0.205 H28  YG8 53 
YG8 H29  H14 H 0 1 N N N N N N 9.321  6.775  14.951 -5.954 -2.988 -0.258 H29  YG8 54 
YG8 H32  H15 H 0 1 N N N N N N 8.965  5.197  18.457 -7.155 -0.442 2.375  H32  YG8 55 
YG8 H34  H16 H 0 1 N N N N N N 6.211  8.343  18.248 -8.059 -4.245 3.919  H34  YG8 56 
YG8 H35  H17 H 0 1 N N N N N N 7.321  8.140  15.880 -7.152 -4.596 1.481  H35  YG8 57 
YG8 H40B H18 H 0 0 N N N N N N 14.748 -6.458 23.146 7.416  -3.731 -3.401 H40B YG8 58 
YG8 H40A H19 H 0 0 N N N N N N 14.000 -5.011 23.022 8.652  -4.652 -2.731 H40A YG8 59 
YG8 H2   H20 H 0 1 N N N N N N 11.886 0.421  17.354 0.744  2.171  -2.435 H2   YG8 60 
YG8 H3   H21 H 0 1 N N N N N N 10.525 -0.869 12.617 -3.323 2.853  1.392  H3   YG8 61 
YG8 H36  H22 H 0 1 N N N N N N 11.316 7.149  16.848 -8.713 -2.487 -2.247 H36  YG8 62 
YG8 H37  H23 H 0 1 N N N N N N 12.220 5.658  13.960 -7.853 -0.987 -3.406 H37  YG8 63 
YG8 H38  H24 H 0 1 N N N N N N 8.564  -5.933 14.831 5.886  2.620  3.386  H38  YG8 64 
YG8 H39  H25 H 0 1 N N N N N N 7.110  -5.281 18.325 7.470  1.849  2.124  H39  YG8 65 
# 
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 
YG8 C1  N2   DOUB Y N 1  
YG8 N2  C3   SING Y N 2  
YG8 C3  C4   DOUB Y N 3  
YG8 C4  C5   SING Y N 4  
YG8 C5  N6   DOUB Y N 5  
YG8 C5  N7   SING Y N 6  
YG8 N7  C8   SING Y N 7  
YG8 C8  N9   DOUB Y N 8  
YG8 N7  C10  SING N N 9  
YG8 C10 C11  SING N N 10 
YG8 C11 C12  SING N N 11 
YG8 C12 C13  SING N N 12 
YG8 C13 O14  SING N N 13 
YG8 C13 C15  SING N N 14 
YG8 C15 O16  SING N N 15 
YG8 O16 P17  SING N N 16 
YG8 P17 O18  DOUB N N 17 
YG8 P17 O19  SING N N 18 
YG8 P17 O20  SING N N 19 
YG8 O20 P21  SING N N 20 
YG8 P21 O22  DOUB N N 21 
YG8 P21 O23  SING N N 22 
YG8 P21 O24  SING N N 23 
YG8 O24 C25  SING N N 24 
YG8 C25 C26  SING N N 25 
YG8 C26 C27  SING N N 26 
YG8 C27 C28  SING N N 27 
YG8 C28 C29  SING N N 28 
YG8 C29 O30  SING N N 29 
YG8 C29 N31  SING N N 30 
YG8 N31 C32  SING Y N 31 
YG8 C32 N33  DOUB Y N 32 
YG8 N33 C34  SING Y N 33 
YG8 C34 C35  DOUB Y N 34 
YG8 C28 O36  SING N N 35 
YG8 C27 O37  SING N N 36 
YG8 C12 O38  SING N N 37 
YG8 C11 O39  SING N N 38 
YG8 C3  N40  SING N N 39 
YG8 N6  C1   SING Y N 40 
YG8 N9  C4   SING Y N 41 
YG8 O14 C10  SING N N 42 
YG8 O30 C26  SING N N 43 
YG8 C35 N31  SING Y N 44 
YG8 C11 H11  SING N N 45 
YG8 C10 H10  SING N N 46 
YG8 C8  H8   SING N N 47 
YG8 C1  H1   SING N N 48 
YG8 C12 H12  SING N N 49 
YG8 C13 H13  SING N N 50 
YG8 C15 H15A SING N N 51 
YG8 C15 H15B SING N N 52 
YG8 C25 H25B SING N N 53 
YG8 C25 H25A SING N N 54 
YG8 C26 H26  SING N N 55 
YG8 C27 H27  SING N N 56 
YG8 C28 H28  SING N N 57 
YG8 C29 H29  SING N N 58 
YG8 C32 H32  SING N N 59 
YG8 C34 H34  SING N N 60 
YG8 C35 H35  SING N N 61 
YG8 N40 H40B SING N N 62 
YG8 N40 H40A SING N N 63 
YG8 O19 H2   SING N N 64 
YG8 O23 H3   SING N N 65 
YG8 O36 H36  SING N N 66 
YG8 O37 H37  SING N N 67 
YG8 O38 H38  SING N N 68 
YG8 O39 H39  SING N N 69 
# 
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 
YG8 SMILES           ACDLabs              12.01 "Nc1ncnc2c1ncn2C1OC(COP(=O)(O)OP(=O)(O)OCC2OC(n3cncc3)C(O)C2O)C(O)C1O"                                                                                                                                                                                        
YG8 InChI            InChI                1.06  "InChI=1S/C18H25N7O13P2/c19-15-10-16(22-5-21-15)25(7-23-10)18-14(29)12(27)9(37-18)4-35-40(32,33)38-39(30,31)34-3-8-11(26)13(28)17(36-8)24-2-1-20-6-24/h1-2,5-9,11-14,17-18,26-29H,3-4H2,(H,30,31)(H,32,33)(H2,19,21,22)/t8-,9-,11-,12-,13-,14-,17-,18-/m1/s1" 
YG8 InChIKey         InChI                1.06  CBBKIMDNCBIDSI-ZZJFPLALSA-N                                                                                                                                                                                                                                   
YG8 SMILES_CANONICAL CACTVS               3.385 "Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O)n5ccnc5)[C@@H](O)[C@H]3O"                                                                                                                                               
YG8 SMILES           CACTVS               3.385 "Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)n5ccnc5)[CH](O)[CH]3O"                                                                                                                                                          
YG8 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1cn(cn1)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)OP(=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)O)O)O"                                                                                                                                              
YG8 SMILES           "OpenEye OEToolkits" 2.0.7 "c1cn(cn1)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)O)O)O)O"                                                                                                                                                                                  
# 
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 
YG8 "SYSTEMATIC NAME" ACDLabs              12.01 "[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl [(2R,3S,4R,5R)-3,4-dihydroxy-5-(1H-imidazol-1-yl)oxolan-2-yl]methyl dihydrogen diphosphate (non-preferred name)"                      
YG8 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-5-imidazol-1-yl-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
YG8 "Create component" 2023-12-04 RCSB 
YG8 "Initial release"  2024-06-12 RCSB 
# 
