data_XRF # _chem_comp.id XRF _chem_comp.name "1-{2-deoxy-5-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-L-erythro-pentofuranosyl}-5-methylpyrimidine-2,4(1H,3H)-dione" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C10 H17 N2 O14 P3" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2021-03-09 _chem_comp.pdbx_modified_date 2022-02-18 _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 482.168 _chem_comp.one_letter_code ? _chem_comp.three_letter_code XRF _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 7LSK _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 XRF N N1 N 0 1 N N N -0.045 -45.710 132.178 -4.804 0.457 -0.498 N XRF 1 XRF C C1 C 0 1 N N N -2.770 -43.408 133.440 -4.333 3.597 1.477 C XRF 2 XRF O O1 O 0 1 N N N 0.020 -47.988 131.993 -6.602 -0.356 -1.501 O XRF 3 XRF C1 C2 C 0 1 N N N -2.000 -44.635 133.050 -4.958 2.501 0.653 C1 XRF 4 XRF C2 C3 C 0 1 N N N -0.755 -44.590 132.552 -4.221 1.444 0.250 C2 XRF 5 XRF C3 C4 C 0 1 N N N -0.583 -46.973 132.305 -6.104 0.532 -0.836 C3 XRF 6 XRF C4 C5 C 0 1 N N N -2.624 -45.930 133.209 -6.325 2.567 0.289 C4 XRF 7 XRF C5 C6 C 0 1 N N S 1.318 -45.588 131.619 -4.004 -0.687 -0.940 C5 XRF 8 XRF C6 C7 C 0 1 N N N 2.339 -45.029 132.596 -4.597 -2.003 -0.390 C6 XRF 9 XRF C7 C8 C 0 1 N N R 3.222 -44.132 131.737 -3.358 -2.864 -0.058 C7 XRF 10 XRF C8 C9 C 0 1 N N S 2.272 -43.669 130.641 -2.162 -1.967 -0.447 C8 XRF 11 XRF C9 C10 C 0 1 N N N 1.609 -42.350 130.932 -1.013 -2.151 0.546 C9 XRF 12 XRF N1 N2 N 0 1 N N N -1.854 -47.007 132.818 -6.862 1.575 -0.449 N1 XRF 13 XRF O1 O2 O 0 1 N N N -3.751 -46.115 133.664 -7.009 3.511 0.640 O1 XRF 14 XRF O10 O3 O 0 1 N N N -0.038 -36.473 126.364 6.046 2.792 -1.852 O10 XRF 15 XRF O11 O4 O 0 1 N N N 0.289 -38.933 125.906 7.199 0.753 -0.912 O11 XRF 16 XRF O12 O5 O 0 1 N N N 1.524 -37.861 127.782 6.320 2.448 0.739 O12 XRF 17 XRF O13 O6 O 0 1 N N N 4.338 -44.824 131.180 -3.360 -4.064 -0.834 O13 XRF 18 XRF O2 O7 O 0 1 N N N 1.265 -44.696 130.516 -2.675 -0.618 -0.378 O2 XRF 19 XRF O3 O8 O 0 1 N N N 0.719 -42.069 129.843 0.122 -1.404 0.105 O3 XRF 20 XRF O4 O9 O 0 1 N N N 1.128 -42.530 127.375 2.000 -2.750 1.120 O4 XRF 21 XRF O5 O10 O 0 1 N N N 2.261 -40.550 128.589 1.291 -0.655 2.337 O5 XRF 22 XRF O6 O11 O 0 1 N N N -0.230 -40.577 128.301 2.604 -0.539 0.062 O6 XRF 23 XRF O7 O12 O 0 1 N N N 0.405 -38.917 130.105 4.810 -1.726 -0.736 O7 XRF 24 XRF O8 O13 O 0 1 N N N -2.048 -39.624 129.745 4.699 -0.506 1.470 O8 XRF 25 XRF O9 O14 O 0 1 N N N -0.868 -38.234 128.015 4.695 0.898 -0.627 O9 XRF 26 XRF P P1 P 0 1 N N N 1.066 -41.488 128.423 1.515 -1.367 0.910 P XRF 27 XRF P1 P2 P 0 1 N N N -0.671 -39.316 129.164 4.213 -0.469 0.073 P1 XRF 28 XRF P2 P3 P 0 1 N N N 0.241 -37.812 126.952 6.090 1.702 -0.668 P2 XRF 29 XRF H1 H1 H 0 1 N N N -3.760 -43.701 133.819 -5.083 4.356 1.701 H1 XRF 30 XRF H2 H2 H 0 1 N N N -2.223 -42.866 134.225 -3.951 3.179 2.408 H2 XRF 31 XRF H3 H3 H 0 1 N N N -2.892 -42.757 132.562 -3.514 4.050 0.919 H3 XRF 32 XRF H4 H4 H 0 1 N N N -0.284 -43.625 132.438 -3.177 1.376 0.518 H4 XRF 33 XRF H5 H5 H 0 1 N N N 1.660 -46.578 131.284 -3.956 -0.718 -2.028 H5 XRF 34 XRF H6 H6 H 0 1 N N N 1.844 -44.447 133.388 -5.181 -1.812 0.511 H6 XRF 35 XRF H7 H7 H 0 1 N N N 2.929 -45.839 133.050 -5.212 -2.490 -1.146 H7 XRF 36 XRF H8 H8 H 0 1 N N N 3.552 -43.265 132.329 -3.330 -3.099 1.006 H8 XRF 37 XRF H9 H9 H 0 1 N N N 2.835 -43.585 129.700 -1.829 -2.197 -1.459 H9 XRF 38 XRF H10 H10 H 0 1 N N N 2.367 -41.557 131.012 -1.322 -1.797 1.529 H10 XRF 39 XRF H11 H11 H 0 1 N N N 1.043 -42.413 131.873 -0.751 -3.208 0.606 H11 XRF 40 XRF H12 H12 H 0 1 N N N -2.269 -47.911 132.920 -7.798 1.612 -0.701 H12 XRF 41 XRF H13 H13 H 0 1 N N N -0.139 -36.555 125.423 6.855 3.315 -1.936 H13 XRF 42 XRF H14 H14 H 0 1 N N N 2.074 -38.572 127.474 5.630 3.086 0.965 H14 XRF 43 XRF H15 H15 H 0 1 N N N 4.918 -45.104 131.878 -4.123 -4.637 -0.671 H15 XRF 44 XRF H16 H16 H 0 1 N N N 2.931 -40.775 127.954 0.973 0.255 2.276 H16 XRF 45 XRF H17 H17 H 0 1 N N N 0.064 -38.909 130.992 4.532 -1.766 -1.662 H17 XRF 46 # # 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 XRF O11 P2 DOUB N N 1 XRF O10 P2 SING N N 2 XRF P2 O12 SING N N 3 XRF P2 O9 SING N N 4 XRF O4 P DOUB N N 5 XRF O9 P1 SING N N 6 XRF O6 P SING N N 7 XRF O6 P1 SING N N 8 XRF P O5 SING N N 9 XRF P O3 SING N N 10 XRF P1 O8 DOUB N N 11 XRF P1 O7 SING N N 12 XRF O3 C9 SING N N 13 XRF O2 C8 SING N N 14 XRF O2 C5 SING N N 15 XRF C8 C9 SING N N 16 XRF C8 C7 SING N N 17 XRF O13 C7 SING N N 18 XRF C5 N SING N N 19 XRF C5 C6 SING N N 20 XRF C7 C6 SING N N 21 XRF O C3 DOUB N N 22 XRF N C3 SING N N 23 XRF N C2 SING N N 24 XRF C3 N1 SING N N 25 XRF C2 C1 DOUB N N 26 XRF N1 C4 SING N N 27 XRF C1 C4 SING N N 28 XRF C1 C SING N N 29 XRF C4 O1 DOUB N N 30 XRF C H1 SING N N 31 XRF C H2 SING N N 32 XRF C H3 SING N N 33 XRF C2 H4 SING N N 34 XRF C5 H5 SING N N 35 XRF C6 H6 SING N N 36 XRF C6 H7 SING N N 37 XRF C7 H8 SING N N 38 XRF C8 H9 SING N N 39 XRF C9 H10 SING N N 40 XRF C9 H11 SING N N 41 XRF N1 H12 SING N N 42 XRF O10 H13 SING N N 43 XRF O12 H14 SING N N 44 XRF O13 H15 SING N N 45 XRF O5 H16 SING N N 46 XRF O7 H17 SING N N 47 # # 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 XRF SMILES ACDLabs 12.01 "O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC1OC(CC1O)N1C=C(C)C(=O)NC1=O" XRF InChI InChI 1.03 "InChI=1S/C10H17N2O14P3/c1-5-3-12(10(15)11-9(5)14)8-2-6(13)7(24-8)4-23-28(19,20)26-29(21,22)25-27(16,17)18/h3,6-8,13H,2,4H2,1H3,(H,19,20)(H,21,22)(H,11,14,15)(H2,16,17,18)/t6-,7+,8+/m1/s1" XRF InChIKey InChI 1.03 NHVNXKFIZYSCEB-CSMHCCOUSA-N XRF SMILES_CANONICAL CACTVS 3.385 "CC1=CN([C@@H]2C[C@@H](O)[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O" XRF SMILES CACTVS 3.385 "CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O" XRF SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC1=CN(C(=O)NC1=O)[C@@H]2C[C@H]([C@@H](O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O" XRF SMILES "OpenEye OEToolkits" 2.0.7 "CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O" # # 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 XRF "SYSTEMATIC NAME" ACDLabs 12.01 "1-{2-deoxy-5-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-L-erythro-pentofuranosyl}-5-methylpyrimidine-2,4(1H,3H)-dione" XRF "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[[(2~{S},3~{R},5~{S})-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate" # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id XRF _pdbx_chem_comp_synonyms.name L-dTTP _pdbx_chem_comp_synonyms.provenance AUTHOR _pdbx_chem_comp_synonyms.type ? # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site XRF "Create component" 2021-03-09 RCSB XRF "Initial release" 2022-02-23 RCSB ##