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 #