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 
# 
