data_A1FGS # _chem_comp.id A1FGS _chem_comp.name "[(2~{R},3~{S},5~{R})-3-oxidanyl-5-(2-oxidanylidene-4-phosphonooxy-pyrimidin-1-yl)oxolan-2-yl]methyl [oxidanyl(phosphonooxy)phosphoryl] hydrogen phosphate" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C9 H16 N2 O17 P4" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2026-10-20 _chem_comp.pdbx_modified_date 2026-10-30 _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 548.122 _chem_comp.one_letter_code ? _chem_comp.three_letter_code A1FGS _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 9V2C _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBC _chem_comp.pdbx_pcm ? _chem_comp.pdbx_comp_type ? # 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 A1FGS C21 C1 C 0 1 N N S N N N 115.517 129.713 144.410 1.849 -4.088 -0.005 C21 A1FGS 1 A1FGS C22 C2 C 0 1 N N N N N N 115.612 131.198 144.305 3.207 -3.372 -0.203 C22 A1FGS 2 A1FGS C24 C3 C 0 1 N N R N N N 114.176 131.706 144.746 2.854 -2.287 -1.251 C24 A1FGS 3 A1FGS C26 C4 C 0 1 N N N N N N 113.371 133.838 145.509 3.818 -0.402 -0.053 C26 A1FGS 4 A1FGS C28 C5 C 0 1 N N N N N N 115.344 134.109 147.303 5.479 0.155 -2.112 C28 A1FGS 5 A1FGS C23 C6 C 0 1 N N R N N N 114.652 129.503 145.432 0.807 -3.062 -0.492 C23 A1FGS 6 A1FGS C25 C7 C 0 1 N N N N N N 115.393 129.479 146.738 -0.173 -2.740 0.637 C25 A1FGS 7 A1FGS C27 C8 C 0 1 N N N N N N 115.253 132.992 146.482 4.620 -0.889 -2.206 C27 A1FGS 8 A1FGS C29 C9 C 0 1 N N N N N N 114.378 135.069 147.152 5.486 0.929 -0.936 C29 A1FGS 9 A1FGS N19 N1 N 0 1 N N N N N N 114.275 132.892 145.614 3.787 -1.161 -1.163 N19 A1FGS 10 A1FGS N20 N2 N 0 1 N N N N N N 113.412 134.914 146.262 4.658 0.628 0.052 N20 A1FGS 11 A1FGS O04 O1 O 0 1 N N N N N N 113.618 130.722 145.393 1.523 -1.874 -0.872 O04 A1FGS 12 A1FGS O05 O2 O 0 1 N N N N N N 114.946 129.147 143.162 1.787 -5.277 -0.796 O05 A1FGS 13 A1FGS O07 O3 O 0 1 N N N N N N 116.733 128.993 146.490 -1.201 -1.879 0.144 O07 A1FGS 14 A1FGS O08 O4 O 0 1 N N N N N N 112.344 133.697 144.575 3.062 -0.656 0.869 O08 A1FGS 15 A1FGS O09 O5 O 0 1 N N N N N N 119.146 128.241 147.370 -3.444 -0.506 0.154 O09 A1FGS 16 A1FGS O10 O6 O 0 1 N N N N N N 118.342 130.607 147.598 -3.105 -2.482 1.688 O10 A1FGS 17 A1FGS O11 O7 O 0 1 N N N N N N 117.303 128.934 149.012 -1.815 -0.378 2.214 O11 A1FGS 18 A1FGS O12 O8 O 0 1 N N N N N N 114.391 136.238 147.948 6.333 1.976 -0.818 O12 A1FGS 19 A1FGS O13 O9 O 0 1 N N N N N N 120.605 126.315 148.661 -5.303 1.118 -0.749 O13 A1FGS 20 A1FGS O14 O10 O 0 1 N N N N N N 119.203 125.794 146.517 -5.077 0.620 1.715 O14 A1FGS 21 A1FGS O15 O11 O 0 1 N N N N N N 118.025 126.277 148.597 -5.971 -1.224 0.241 O15 A1FGS 22 A1FGS O16 O12 O 0 1 N N N N N N 121.496 125.833 151.021 -7.845 1.624 -1.191 O16 A1FGS 23 A1FGS O17 O13 O 0 1 N N N N N N 121.708 128.092 150.154 -6.487 3.019 0.415 O17 A1FGS 24 A1FGS O18 O14 O 0 1 N N N N N N 119.532 127.223 150.808 -6.004 3.295 -2.047 O18 A1FGS 25 A1FGS O31 O15 O 0 1 N N N N N N 115.727 135.502 150.014 6.668 1.781 1.783 O31 A1FGS 26 A1FGS O32 O16 O 0 1 N N N N N N 115.386 137.903 149.619 7.171 4.053 0.560 O32 A1FGS 27 A1FGS O33 O17 O 0 1 N N N N N N 116.958 136.616 148.148 4.814 3.182 0.798 O33 A1FGS 28 A1FGS P01 P1 P 0 1 N N N N N N 117.882 129.220 147.651 -2.407 -1.336 1.064 P01 A1FGS 29 A1FGS P02 P2 P 0 1 N N N N N N 119.199 126.626 147.778 -4.951 0.015 0.370 P02 A1FGS 30 A1FGS P03 P3 P 0 1 N N N N N N 120.846 126.880 150.202 -6.412 2.280 -0.865 P03 A1FGS 31 A1FGS P30 P4 P 0 1 N N N N N N 115.634 136.553 148.948 6.215 2.757 0.585 P30 A1FGS 32 A1FGS H1 H1 H 0 1 N N N N N N 116.510 129.281 144.606 1.691 -4.322 1.047 H1 A1FGS 33 A1FGS H2 H2 H 0 1 N N N N N N 116.389 131.589 144.979 3.547 -2.918 0.728 H2 A1FGS 34 A1FGS H3 H3 H 0 1 N N N N N N 115.835 131.504 143.272 3.957 -4.061 -0.594 H3 A1FGS 35 A1FGS H4 H4 H 0 1 N N N N N N 113.617 131.968 143.836 2.853 -2.709 -2.256 H4 A1FGS 36 A1FGS H5 H5 H 0 1 N N N N N N 116.139 134.216 148.026 6.149 0.389 -2.926 H5 A1FGS 37 A1FGS H6 H6 H 0 1 N N N N N N 114.090 128.566 145.308 0.266 -3.462 -1.350 H6 A1FGS 38 A1FGS H7 H7 H 0 1 N N N N N N 115.437 130.494 147.159 -0.618 -3.663 1.007 H7 A1FGS 39 A1FGS H8 H8 H 0 1 N N N N N N 114.880 128.811 147.445 0.359 -2.243 1.449 H8 A1FGS 40 A1FGS H9 H9 H 0 1 N N N N N N 115.989 132.205 146.559 4.596 -1.498 -3.097 H9 A1FGS 41 A1FGS H10 H10 H 0 1 N N N N N N 114.890 128.202 143.239 2.422 -5.957 -0.533 H10 A1FGS 42 A1FGS H11 H11 H 0 1 N N N N N N 117.358 129.715 149.550 -1.342 0.396 1.877 H11 A1FGS 43 A1FGS H12 H12 H 0 1 N N N N N N 117.521 125.603 148.157 -5.943 -1.669 -0.617 H12 A1FGS 44 A1FGS H13 H13 H 0 1 N N N N N N 122.329 126.155 151.345 -7.870 1.123 -2.017 H13 A1FGS 45 A1FGS H14 H14 H 0 1 N N N N N N 119.519 128.145 151.037 -6.629 4.022 -2.173 H14 A1FGS 46 A1FGS H15 H15 H 0 1 N N N N N N 116.582 135.090 149.979 7.578 1.463 1.709 H15 A1FGS 47 A1FGS H16 H16 H 0 1 N N N N N N 116.095 138.498 149.406 7.151 4.573 1.375 H16 A1FGS 48 # 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 A1FGS O05 C21 SING N N 1 A1FGS C22 C21 SING N N 2 A1FGS C22 C24 SING N N 3 A1FGS C21 C23 SING N N 4 A1FGS O08 C26 DOUB N N 5 A1FGS C24 O04 SING N N 6 A1FGS C24 N19 SING N N 7 A1FGS O04 C23 SING N N 8 A1FGS C23 C25 SING N N 9 A1FGS C26 N19 SING N N 10 A1FGS C26 N20 SING N N 11 A1FGS N19 C27 SING N N 12 A1FGS N20 C29 DOUB N N 13 A1FGS C27 C28 DOUB N N 14 A1FGS O07 C25 SING N N 15 A1FGS O07 P01 SING N N 16 A1FGS O14 P02 DOUB N N 17 A1FGS C29 C28 SING N N 18 A1FGS C29 O12 SING N N 19 A1FGS O09 P01 SING N N 20 A1FGS O09 P02 SING N N 21 A1FGS O10 P01 DOUB N N 22 A1FGS P01 O11 SING N N 23 A1FGS P02 O15 SING N N 24 A1FGS P02 O13 SING N N 25 A1FGS O12 P30 SING N N 26 A1FGS O33 P30 DOUB N N 27 A1FGS O13 P03 SING N N 28 A1FGS P30 O32 SING N N 29 A1FGS P30 O31 SING N N 30 A1FGS O17 P03 DOUB N N 31 A1FGS P03 O18 SING N N 32 A1FGS P03 O16 SING N N 33 A1FGS C21 H1 SING N N 34 A1FGS C22 H2 SING N N 35 A1FGS C22 H3 SING N N 36 A1FGS C24 H4 SING N N 37 A1FGS C28 H5 SING N N 38 A1FGS C23 H6 SING N N 39 A1FGS C25 H7 SING N N 40 A1FGS C25 H8 SING N N 41 A1FGS C27 H9 SING N N 42 A1FGS O05 H10 SING N N 43 A1FGS O11 H11 SING N N 44 A1FGS O15 H12 SING N N 45 A1FGS O16 H13 SING N N 46 A1FGS O18 H14 SING N N 47 A1FGS O31 H15 SING N N 48 A1FGS O32 H16 SING N N 49 # 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 A1FGS InChI InChI 1.06 "InChI=1S/C9H16N2O17P4/c12-5-3-8(11-2-1-7(10-9(11)13)26-29(14,15)16)25-6(5)4-24-31(20,21)28-32(22,23)27-30(17,18)19/h1-2,5-6,8,12H,3-4H2,(H,20,21)(H,22,23)(H2,14,15,16)(H2,17,18,19)/t5-,6+,8+/m0/s1" A1FGS InChIKey InChI 1.06 VYDHROQYKNLDCY-SHYZEUOFSA-N A1FGS SMILES_CANONICAL CACTVS 3.385 "O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)N2C=CC(=NC2=O)O[P](O)(O)=O" A1FGS SMILES CACTVS 3.385 "O[CH]1C[CH](O[CH]1CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)N2C=CC(=NC2=O)O[P](O)(O)=O" A1FGS SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C1[C@@H]([C@H](O[C@H]1N2C=CC(=NC2=O)OP(=O)(O)O)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O" A1FGS SMILES "OpenEye OEToolkits" 2.0.7 "C1C(C(OC1N2C=CC(=NC2=O)OP(=O)(O)O)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O" # _pdbx_chem_comp_identifier.comp_id A1FGS _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~{S},5~{R})-3-oxidanyl-5-(2-oxidanylidene-4-phosphonooxy-pyrimidin-1-yl)oxolan-2-yl]methyl [oxidanyl(phosphonooxy)phosphoryl] 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 A1FGS "Create component" 2026-10-20 PDBC A1FGS "Initial release" 2026-11-04 RCSB #