data_K5X # _chem_comp.id K5X _chem_comp.name "[(2~{R},3~{R},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-4-fluoranyl-4-methyl-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C10 H14 F N2 O8 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2022-09-09 _chem_comp.pdbx_modified_date 2025-07-11 _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 340.199 _chem_comp.one_letter_code ? _chem_comp.three_letter_code K5X _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 ? _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBJ _chem_comp.pdbx_pcm ? # 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 K5X C01 C1 C 0 1 N N N N N N ? ? ? -1.873 -1.377 -1.704 C01 K5X 1 K5X C02 C2 C 0 1 N N R N N N ? ? ? -1.207 -1.800 -0.393 C02 K5X 2 K5X C04 C3 C 0 1 N N R N N N ? ? ? 0.288 -2.113 -0.621 C04 K5X 3 K5X C06 C4 C 0 1 N N R N N N ? ? ? 1.026 -1.092 0.272 C06 K5X 4 K5X C07 C5 C 0 1 N N N N N N ? ? ? 2.302 -0.605 -0.418 C07 K5X 5 K5X C14 C6 C 0 1 N N R N N N ? ? ? -1.196 -0.626 0.611 C14 K5X 6 K5X C16 C7 C 0 1 N N N N N N ? ? ? -2.003 1.416 -0.477 C16 K5X 7 K5X C17 C8 C 0 1 N N N N N N ? ? ? -2.992 2.289 -0.764 C17 K5X 8 K5X C18 C9 C 0 1 N N N N N N ? ? ? -4.289 2.055 -0.246 C18 K5X 9 K5X C21 C10 C 0 1 N N N N N N ? ? ? -3.507 0.108 0.782 C21 K5X 10 K5X F03 F1 F 0 1 N N N N N N ? ? ? -1.865 -2.907 0.154 F03 K5X 11 K5X N15 N1 N 0 1 N N N N N N ? ? ? -2.269 0.322 0.301 N15 K5X 12 K5X N20 N2 N 0 1 N N N N N N ? ? ? -4.509 0.968 0.520 N20 K5X 13 K5X O05 O1 O 0 1 N N N N N N ? ? ? 0.589 -3.448 -0.209 O05 K5X 14 K5X O08 O2 O 0 1 N N N N N N ? ? ? 3.028 0.248 0.470 O08 K5X 15 K5X O10 O3 O 0 1 N N N N N N ? ? ? 4.890 1.930 1.256 O10 K5X 16 K5X O11 O4 O 0 1 N N N N N N ? ? ? 5.545 -0.194 -0.149 O11 K5X 17 K5X O13 O5 O 0 1 N N N N N N ? ? ? 0.094 -0.001 0.434 O13 K5X 18 K5X O19 O6 O 0 1 N N N N N N ? ? ? -5.197 2.829 -0.491 O19 K5X 19 K5X O22 O7 O 0 1 N N N N N N ? ? ? -3.720 -0.868 1.474 O22 K5X 20 K5X P09 P1 P 0 1 N N N N N N ? ? ? 4.425 0.942 0.072 P09 K5X 21 K5X H1 H1 H 0 1 N N N N N N ? ? ? -1.375 -0.489 -2.094 H1 K5X 22 K5X H2 H2 H 0 1 N N N N N N ? ? ? -1.793 -2.186 -2.430 H2 K5X 23 K5X H3 H3 H 0 1 N N N N N N ? ? ? -2.924 -1.154 -1.523 H3 K5X 24 K5X H4 H4 H 0 1 N N N N N N ? ? ? 0.554 -1.967 -1.668 H4 K5X 25 K5X H5 H5 H 0 1 N N N N N N ? ? ? 1.265 -1.536 1.239 H5 K5X 26 K5X H6 H6 H 0 1 N N N N N N ? ? ? 2.920 -1.462 -0.686 H6 K5X 27 K5X H7 H7 H 0 1 N N N N N N ? ? ? 2.039 -0.051 -1.319 H7 K5X 28 K5X H8 H8 H 0 1 N N N N N N ? ? ? -1.300 -0.998 1.631 H8 K5X 29 K5X H9 H9 H 0 1 N N N N N N ? ? ? -1.007 1.578 -0.863 H9 K5X 30 K5X H10 H10 H 0 1 N N N N N N ? ? ? -2.796 3.155 -1.379 H10 K5X 31 K5X H11 H11 H 0 1 N N N N N N ? ? ? -5.396 0.799 0.875 H11 K5X 32 K5X H12 H12 H 0 1 N N N N N N ? ? ? 1.515 -3.698 -0.330 H12 K5X 33 K5X H13 H13 H 0 1 N N N N N N ? ? ? 5.726 2.384 1.084 H13 K5X 34 K5X H14 H14 H 0 1 N N N N N N ? ? ? 5.710 -0.741 0.631 H14 K5X 35 K5X O1 O8 O 0 1 N N N N N N ? ? ? 4.253 1.716 -1.177 O1 K5X 36 # 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 K5X O05 C04 SING N N 1 K5X F03 C02 SING N N 2 K5X C01 C02 SING N N 3 K5X C04 C02 SING N N 4 K5X C04 C06 SING N N 5 K5X C02 C14 SING N N 6 K5X C06 C07 SING N N 7 K5X C06 O13 SING N N 8 K5X C07 O08 SING N N 9 K5X C14 O13 SING N N 10 K5X C14 N15 SING N N 11 K5X O11 P09 SING N N 12 K5X O08 P09 SING N N 13 K5X O22 C21 DOUB N N 14 K5X N15 C21 SING N N 15 K5X N15 C16 SING N N 16 K5X O10 P09 SING N N 17 K5X C21 N20 SING N N 18 K5X C16 C17 DOUB N N 19 K5X N20 C18 SING N N 20 K5X C17 C18 SING N N 21 K5X C18 O19 DOUB N N 22 K5X C01 H1 SING N N 23 K5X C01 H2 SING N N 24 K5X C01 H3 SING N N 25 K5X C04 H4 SING N N 26 K5X C06 H5 SING N N 27 K5X C07 H6 SING N N 28 K5X C07 H7 SING N N 29 K5X C14 H8 SING N N 30 K5X C16 H9 SING N N 31 K5X C17 H10 SING N N 32 K5X N20 H11 SING N N 33 K5X O05 H12 SING N N 34 K5X O10 H13 SING N N 35 K5X O11 H14 SING N N 36 K5X P09 O1 DOUB N N 37 # 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 K5X InChI InChI 1.06 "InChI=1S/C10H14FN2O8P/c1-10(11)7(15)5(4-20-22(17,18)19)21-8(10)13-3-2-6(14)12-9(13)16/h2-3,5,7-8,15H,4H2,1H3,(H,12,14,16)(H2,17,18,19)/t5-,7-,8-,10-/m1/s1" K5X InChIKey InChI 1.06 JAJZLQMRDFLNSW-VPCXQMTMSA-N K5X SMILES_CANONICAL CACTVS 3.385 "C[C@@]1(F)[C@H](O)[C@@H](CO[P](O)(O)=O)O[C@H]1N2C=CC(=O)NC2=O" K5X SMILES CACTVS 3.385 "C[C]1(F)[CH](O)[CH](CO[P](O)(O)=O)O[CH]1N2C=CC(=O)NC2=O" K5X SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C[C@]1([C@@H]([C@H](O[C@H]1N2C=CC(=O)NC2=O)COP(=O)(O)O)O)F" K5X SMILES "OpenEye OEToolkits" 2.0.7 "CC1(C(C(OC1N2C=CC(=O)NC2=O)COP(=O)(O)O)O)F" # _pdbx_chem_comp_identifier.comp_id K5X _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-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-4-fluoranyl-4-methyl-3-oxidanyl-oxolan-2-yl]methyl dihydrogen 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 K5X "Create component" 2022-09-09 PDBJ K5X "Modify coordinates" 2025-07-09 RCSB K5X "Initial release" 2025-07-16 RCSB #