data_1TK
# 
_chem_comp.id                                    1TK 
_chem_comp.name                                  "4-amino-1-{2-deoxy-2-fluoro-5-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-arabinofuranosyl}pyrimidin-2(1H)-one" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C9 H15 F N3 O13 P3" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2021-06-25 
_chem_comp.pdbx_modified_date                    2023-05-19 
_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                        485.147 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     1TK 
_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        8FVA 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  RCSB 
# 
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.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 
1TK O2    O1  O 0 1 N N N 7.305  -1.719 16.814 -4.380 0.017  1.294  O2    1TK 1  
1TK C2    C1  C 0 1 N N N 7.788  -2.514 16.096 -4.926 -0.858 0.644  C2    1TK 2  
1TK F1    F1  F 0 1 N N N 10.465 -4.533 17.971 -5.730 1.429  -0.411 F1    1TK 3  
1TK "C1'" C2  C 0 1 N N R 9.815  -2.385 17.360 -3.928 0.119  -1.348 "C1'" 1TK 4  
1TK "C2'" C3  C 0 1 N N S 10.134 -3.192 18.382 -4.571 1.511  -1.190 "C2'" 1TK 5  
1TK "C3'" C4  C 0 1 N N R 11.435 -2.565 18.959 -3.490 2.349  -0.466 "C3'" 1TK 6  
1TK C4    C5  C 0 1 N N N 7.523  -3.884 14.251 -6.274 -2.734 0.585  C4    1TK 7  
1TK "C4'" C6  C 0 1 N N R 11.959 -1.626 17.788 -2.198 1.548  -0.774 "C4'" 1TK 8  
1TK C5    C7  C 0 1 N N N 8.798  -4.334 14.410 -6.120 -2.797 -0.816 C5    1TK 9  
1TK "C5'" C8  C 0 1 N N N 13.446 -1.855 17.544 -1.131 1.819  0.288  "C5'" 1TK 10 
1TK C6    C9  C 0 1 N N N 9.563  -3.818 15.469 -5.362 -1.862 -1.435 C6    1TK 11 
1TK N1    N1  N 0 1 N N N 9.037  -2.927 16.302 -4.760 -0.892 -0.691 N1    1TK 12 
1TK N3    N2  N 0 1 N N N 7.050  -2.977 15.110 -5.673 -1.768 1.267  N3    1TK 13 
1TK N4    N3  N 0 1 N N N 6.657  -4.401 13.148 -7.039 -3.671 1.240  N4    1TK 14 
1TK O1A   O2  O 0 1 N N N 15.361 0.346  15.032 1.785  2.648  1.048  O1A   1TK 15 
1TK O1B   O3  O 0 1 N N N 15.970 -4.035 15.689 4.843  1.856  -0.335 O1B   1TK 16 
1TK O1G   O4  O 0 1 N N N 17.093 -2.262 11.608 7.341  -0.623 -0.315 O1G   1TK 17 
1TK O2A   O5  O 0 1 N N N 16.260 -1.341 16.540 1.167  0.501  2.223  O2A   1TK 18 
1TK O2B   O6  O 0 1 N N N 13.729 -4.384 14.536 4.561  0.313  1.643  O2B   1TK 19 
1TK O2G   O7  O 0 1 N N N 18.202 -4.256 12.422 6.168  -2.649 0.627  O2G   1TK 20 
1TK "O3'" O8  O 0 1 N N N 11.228 -1.800 20.047 -3.415 3.667  -1.013 "O3'" 1TK 21 
1TK O3A   O9  O 0 1 N N N 14.715 -2.018 14.597 2.624  0.494  0.034  O3A   1TK 22 
1TK O3B   O10 O 0 1 N N N 15.851 -3.897 13.119 4.840  -0.757 -0.626 O3B   1TK 23 
1TK O3G   O11 O 0 1 N N N 17.787 -2.415 13.934 6.473  -2.325 -1.964 O3G   1TK 24 
1TK "O4'" O12 O 0 1 N N N 11.279 -1.950 16.737 -2.635 0.173  -0.723 "O4'" 1TK 25 
1TK "O5'" O13 O 0 1 N N N 13.807 -0.740 16.704 0.084  1.163  -0.080 "O5'" 1TK 26 
1TK PA    P1  P 0 1 N N N 15.102 -0.925 15.721 1.423  1.233  0.811  PA    1TK 27 
1TK PB    P2  P 0 1 N N N 15.047 -3.620 14.554 4.224  0.473  0.210  PB    1TK 28 
1TK PG    P3  P 0 1 N N N 17.279 -3.161 12.769 6.230  -1.568 -0.564 PG    1TK 29 
1TK H1    H1  H 0 1 N N N 9.342  -1.462 17.727 -3.819 -0.121 -2.405 H1    1TK 30 
1TK H2    H2  H 0 1 N N N 9.361  -3.204 19.164 -4.799 1.939  -2.166 H2    1TK 31 
1TK H3    H3  H 0 1 N N N 12.175 -3.359 19.137 -3.679 2.385  0.607  H3    1TK 32 
1TK H4    H4  H 0 1 N N N 11.801 -0.580 18.089 -1.822 1.795  -1.767 H4    1TK 33 
1TK H5    H5  H 0 1 N N N 9.212  -5.071 13.737 -6.603 -3.577 -1.385 H5    1TK 34 
1TK H6    H6  H 0 1 N N N 13.620 -2.812 17.030 -0.956 2.892  0.363  H6    1TK 35 
1TK H7    H7  H 0 1 N N N 14.010 -1.838 18.488 -1.472 1.438  1.251  H7    1TK 36 
1TK H8    H8  H 0 1 N N N 10.582 -4.147 15.606 -5.229 -1.889 -2.507 H8    1TK 37 
1TK H9    H9  H 0 1 N N N 5.719  -4.068 13.051 -7.474 -4.378 0.738  H9    1TK 38 
1TK H10   H10 H 0 1 N N N 7.015  -5.080 12.507 -7.143 -3.625 2.203  H10   1TK 39 
1TK H11   H11 H 0 1 N N N 15.554 -4.717 16.203 4.661  2.026  -1.269 H11   1TK 40 
1TK H12   H12 H 0 1 N N N 16.953 -0.697 16.459 0.925  -0.432 2.144  H12   1TK 41 
1TK H13   H13 H 0 1 N N N 18.487 -4.157 11.521 5.461  -3.301 0.530  H13   1TK 42 
1TK H14   H14 H 0 1 N N N 10.914 -2.342 20.761 -4.232 4.176  -0.925 H14   1TK 43 
1TK H15   H15 H 0 1 N N N 17.893 -1.500 13.703 7.294  -2.835 -1.998 H15   1TK 44 
# 
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 
1TK O1G   PG    DOUB N N 1  
1TK O2G   PG    SING N N 2  
1TK PG    O3B   SING N N 3  
1TK PG    O3G   SING N N 4  
1TK O3B   PB    SING N N 5  
1TK N4    C4    SING N N 6  
1TK C4    C5    SING N N 7  
1TK C4    N3    DOUB N N 8  
1TK C5    C6    DOUB N N 9  
1TK O2B   PB    DOUB N N 10 
1TK PB    O3A   SING N N 11 
1TK PB    O1B   SING N N 12 
1TK O3A   PA    SING N N 13 
1TK O1A   PA    DOUB N N 14 
1TK N3    C2    SING N N 15 
1TK C6    N1    SING N N 16 
1TK PA    O2A   SING N N 17 
1TK PA    "O5'" SING N N 18 
1TK C2    N1    SING N N 19 
1TK C2    O2    DOUB N N 20 
1TK N1    "C1'" SING N N 21 
1TK "O5'" "C5'" SING N N 22 
1TK "O4'" "C1'" SING N N 23 
1TK "O4'" "C4'" SING N N 24 
1TK "C1'" "C2'" SING N N 25 
1TK "C5'" "C4'" SING N N 26 
1TK "C4'" "C3'" SING N N 27 
1TK F1    "C2'" SING N N 28 
1TK "C2'" "C3'" SING N N 29 
1TK "C3'" "O3'" SING N N 30 
1TK "C1'" H1    SING N N 31 
1TK "C2'" H2    SING N N 32 
1TK "C3'" H3    SING N N 33 
1TK "C4'" H4    SING N N 34 
1TK C5    H5    SING N N 35 
1TK "C5'" H6    SING N N 36 
1TK "C5'" H7    SING N N 37 
1TK C6    H8    SING N N 38 
1TK N4    H9    SING N N 39 
1TK N4    H10   SING N N 40 
1TK O1B   H11   SING N N 41 
1TK O2A   H12   SING N N 42 
1TK O2G   H13   SING N N 43 
1TK "O3'" H14   SING N N 44 
1TK O3G   H15   SING N N 45 
# 
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 
1TK SMILES           ACDLabs              12.01 "O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC1OC(N2C=CC(N)=NC2=O)C(F)C1O"                                                                                                                                     
1TK InChI            InChI                1.06  "InChI=1S/C9H15FN3O13P3/c10-6-7(14)4(24-8(6)13-2-1-5(11)12-9(13)15)3-23-28(19,20)26-29(21,22)25-27(16,17)18/h1-2,4,6-8,14H,3H2,(H,19,20)(H,21,22)(H2,11,12,15)(H2,16,17,18)/t4-,6+,7-,8-/m1/s1" 
1TK InChIKey         InChI                1.06  YKEIUAOIVAXJRI-PXBUCIJWSA-N                                                                                                                                                                     
1TK SMILES_CANONICAL CACTVS               3.385 "NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@@H]2F"                                                                                                          
1TK SMILES           CACTVS               3.385 "NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]2F"                                                                                                                 
1TK SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C1=CN(C(=O)N=C1N)[C@H]2[C@H]([C@@H]([C@H](O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)F"                                                                                                                
1TK SMILES           "OpenEye OEToolkits" 2.0.7 "C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)F"                                                                                                                                 
# 
loop_
_pdbx_chem_comp_identifier.comp_id 
_pdbx_chem_comp_identifier.type 
_pdbx_chem_comp_identifier.program 
_pdbx_chem_comp_identifier.program_version 
_pdbx_chem_comp_identifier.identifier 
1TK "SYSTEMATIC NAME" ACDLabs              12.01 "4-amino-1-{2-deoxy-2-fluoro-5-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-arabinofuranosyl}pyrimidin-2(1H)-one"                        
1TK "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[[(2~{R},3~{R},4~{S},5~{R})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-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 
1TK "Create component" 2021-06-25 RCSB 
1TK "Initial release"  2023-05-24 RCSB 
# 
