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 #