data_YGC
# 
_chem_comp.id                                    YGC 
_chem_comp.name                                  "[[(2~{R},3~{R},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-fluoranyl-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C10 H15 F N5 O12 P3" 
_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                    2024-07-26 
_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                        509.172 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     YGC 
_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        8R7O 
_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 
YGC N1  N1  N 0 1 N N N N N N -51.998 12.704 -11.200 -7.360 -3.470 1.486  N1  YGC 1  
YGC C7  C1  C 0 1 Y N N N N N -51.459 9.111  -11.436 -5.402 -0.992 -0.418 C7  YGC 2  
YGC C8  C2  C 0 1 Y N N N N N -51.375 10.382 -10.886 -5.779 -1.841 0.637  C8  YGC 3  
YGC C10 C3  C 0 1 Y N N N N N -50.380 9.085  -9.536  -3.962 -0.824 1.243  C10 YGC 4  
YGC N12 N2  N 0 1 Y N N N N N -52.570 11.133 -12.794 -7.626 -2.511 -0.652 N12 YGC 5  
YGC C13 C4  C 0 1 Y N N N N N -51.992 11.430 -11.606 -6.940 -2.616 0.482  C13 YGC 6  
YGC C24 C5  C 0 1 N N N N N N -48.170 5.881  -8.276  -0.465 2.247  0.504  C24 YGC 7  
YGC C11 C6  C 0 1 Y N N N N N -52.552 9.858  -13.210 -7.227 -1.705 -1.619 C11 YGC 8  
YGC C27 C7  C 0 1 N N R N N N -48.922 5.691  -9.560  -1.658 2.003  -0.422 C27 YGC 9  
YGC C29 C8  C 0 1 N N R N N N -50.623 6.844  -10.708 -3.481 0.618  -0.771 C29 YGC 10 
YGC C30 C9  C 0 1 N N R N N N -49.485 6.544  -11.676 -4.064 2.028  -0.551 C30 YGC 11 
YGC C31 C10 C 0 1 N N R N N N -48.293 6.366  -10.770 -2.881 2.841  0.030  C31 YGC 12 
YGC F25 F1  F 0 1 N N N N N N -49.747 5.340  -12.323 -4.487 2.578  -1.765 F25 YGC 13 
YGC N14 N3  N 0 1 Y N N N N N -52.056 8.779  -12.584 -6.149 -0.957 -1.516 N14 YGC 14 
YGC N6  N4  N 0 1 Y N N N N N -50.817 8.280  -10.557 -4.253 -0.365 -0.007 N6  YGC 15 
YGC N9  N5  N 0 1 Y N N N N N -50.688 10.350 -9.685  -4.858 -1.690 1.619  N9  YGC 16 
YGC O15 O1  O 0 1 N N N N N N -46.390 6.908  -6.243  2.733  2.953  0.681  O15 YGC 17 
YGC O16 O2  O 0 1 N N N N N N -50.606 9.000  -5.519  5.259  0.588  1.321  O16 YGC 18 
YGC O17 O3  O 0 1 N N N N N N -47.301 9.275  -6.838  1.896  1.143  2.228  O17 YGC 19 
YGC O18 O4  O 0 1 N N N N N N -50.263 7.171  -3.793  4.001  -1.590 1.533  O18 YGC 20 
YGC O19 O5  O 0 1 N N N N N N -48.627 9.124  -3.941  5.179  -0.902 -0.715 O19 YGC 21 
YGC O2  O6  O 0 1 N N N N N N -47.337 11.072 -2.820  7.021  -1.357 -2.535 O2  YGC 22 
YGC O21 O7  O 0 1 N N N N N N -48.723 7.449  -5.733  3.053  0.406  0.109  O21 YGC 23 
YGC O23 O8  O 0 1 N N N N N N -48.032 7.302  -8.076  0.650  1.474  0.058  O23 YGC 24 
YGC O26 O9  O 0 1 N N N N N N -47.277 5.553  -11.348 -2.838 4.153  -0.535 O26 YGC 25 
YGC O28 O10 O 0 1 N N N N N N -50.233 6.284  -9.466  -2.122 0.640  -0.306 O28 YGC 26 
YGC O3  O11 O 0 1 N N N N N N -49.833 11.100 -2.880  7.634  -0.632 -0.197 O3  YGC 27 
YGC O4  O12 O 0 1 N N N N N N -48.601 9.431  -1.311  6.767  -2.984 -0.485 O4  YGC 28 
YGC P20 P1  P 0 1 N N N N N N -49.686 8.192  -4.698  4.392  -0.354 0.578  P20 YGC 29 
YGC P22 P2  P 0 1 N N N N N N -47.465 7.808  -6.661  2.079  1.486  0.800  P22 YGC 30 
YGC P5  P3  P 0 1 N N N N N N -48.623 10.197 -2.625  6.672  -1.451 -0.966 P5  YGC 31 
YGC H33 H1  H 0 1 N N N N N N -52.459 13.270 -11.884 -8.164 -4.001 1.367  H33 YGC 32 
YGC H32 H2  H 0 1 N N N N N N -52.483 12.774 -10.328 -6.850 -3.542 2.308  H32 YGC 33 
YGC H34 H3  H 0 1 N N N N N N -49.831 8.710  -8.685  -3.112 -0.516 1.834  H34 YGC 34 
YGC H37 H4  H 0 1 N N N N N N -48.729 5.434  -7.441  -0.204 3.305  0.488  H37 YGC 35 
YGC H36 H5  H 0 1 N N N N N N -47.178 5.411  -8.346  -0.728 1.954  1.520  H36 YGC 36 
YGC H35 H6  H 0 1 N N N N N N -52.996 9.675  -14.178 -7.814 -1.650 -2.524 H35 YGC 37 
YGC H39 H7  H 0 1 N N N N N N -49.014 4.614  -9.765  -1.394 2.231  -1.455 H39 YGC 38 
YGC H40 H8  H 0 1 N N N N N N -51.546 6.373  -11.076 -3.507 0.366  -1.831 H40 YGC 39 
YGC H41 H9  H 0 1 N N N N N N -49.332 7.381  -12.373 -4.889 1.993  0.161  H41 YGC 40 
YGC H42 H10 H 0 1 N N N N N N -47.895 7.349  -10.480 -2.939 2.888  1.118  H42 YGC 41 
YGC H1  H11 H 0 1 N N N N N N -45.593 7.407  -6.108  2.882  3.244  -0.229 H1  YGC 42 
YGC H2  H12 H 0 1 N N N N N N -51.210 7.177  -3.871  3.432  -2.249 1.110  H2  YGC 43 
YGC H3  H13 H 0 1 N N N N N N -47.589 11.959 -3.051  7.907  -1.672 -2.760 H3  YGC 44 
YGC H38 H14 H 0 1 N N N N N N -46.551 5.472  -10.740 -3.625 4.685  -0.354 H38 YGC 45 
YGC H4  H15 H 0 1 N N N N N N -49.383 9.635  -0.812  6.163  -3.580 -0.948 H4  YGC 46 
# 
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 
YGC C11 N12 DOUB Y N 1  
YGC C11 N14 SING Y N 2  
YGC N12 C13 SING Y N 3  
YGC N14 C7  DOUB Y N 4  
YGC F25 C30 SING N N 5  
YGC C30 C31 SING N N 6  
YGC C30 C29 SING N N 7  
YGC C13 N1  SING N N 8  
YGC C13 C8  DOUB Y N 9  
YGC C7  C8  SING Y N 10 
YGC C7  N6  SING Y N 11 
YGC O26 C31 SING N N 12 
YGC C8  N9  SING Y N 13 
YGC C31 C27 SING N N 14 
YGC C29 N6  SING N N 15 
YGC C29 O28 SING N N 16 
YGC N6  C10 SING Y N 17 
YGC N9  C10 DOUB Y N 18 
YGC C27 O28 SING N N 19 
YGC C27 C24 SING N N 20 
YGC C24 O23 SING N N 21 
YGC O23 P22 SING N N 22 
YGC O17 P22 DOUB N N 23 
YGC P22 O15 SING N N 24 
YGC P22 O21 SING N N 25 
YGC O21 P20 SING N N 26 
YGC O16 P20 DOUB N N 27 
YGC P20 O19 SING N N 28 
YGC P20 O18 SING N N 29 
YGC O19 P5  SING N N 30 
YGC O3  P5  DOUB N N 31 
YGC O2  P5  SING N N 32 
YGC P5  O4  SING N N 33 
YGC N1  H33 SING N N 34 
YGC N1  H32 SING N N 35 
YGC C10 H34 SING N N 36 
YGC C24 H37 SING N N 37 
YGC C24 H36 SING N N 38 
YGC C11 H35 SING N N 39 
YGC C27 H39 SING N N 40 
YGC C29 H40 SING N N 41 
YGC C30 H41 SING N N 42 
YGC C31 H42 SING N N 43 
YGC O15 H1  SING N N 44 
YGC O18 H2  SING N N 45 
YGC O2  H3  SING N N 46 
YGC O26 H38 SING N N 47 
YGC O4  H4  SING N N 48 
# 
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 
YGC InChI            InChI                1.06  "InChI=1S/C10H15FN5O12P3/c11-5-7(17)4(1-25-30(21,22)28-31(23,24)27-29(18,19)20)26-10(5)16-3-15-6-8(12)13-2-14-9(6)16/h2-5,7,10,17H,1H2,(H,21,22)(H,23,24)(H2,12,13,14)(H2,18,19,20)/t4-,5-,7-,10-/m1/s1" 
YGC InChIKey         InChI                1.06  CCXCDDWASROAJA-QYYRPYCUSA-N                                                                                                                                                                              
YGC SMILES_CANONICAL CACTVS               3.385 "Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3F"                                                                                                                     
YGC SMILES           CACTVS               3.385 "Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3F"                                                                                                                           
YGC SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)F)N"                                                                                                                     
YGC SMILES           "OpenEye OEToolkits" 2.0.7 "c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)F)N"                                                                                                                                       
# 
_pdbx_chem_comp_identifier.comp_id           YGC 
_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        "[[(2~{R},3~{R},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-fluoranyl-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono 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 
YGC "Create component" 2023-12-04 PDBE 
YGC "Initial release"  2024-07-31 RCSB 
# 
