data_PST # _chem_comp.id PST _chem_comp.name "THYMIDINE-5'-THIOPHOSPHATE" _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 H15 N2 O7 P S" _chem_comp.mon_nstd_parent_comp_id DT _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 1999-07-08 _chem_comp.pdbx_modified_date 2011-06-04 _chem_comp.pdbx_ambiguous_flag N _chem_comp.pdbx_release_status REL _chem_comp.pdbx_replaced_by ? _chem_comp.pdbx_replaces TS _chem_comp.formula_weight 338.274 _chem_comp.one_letter_code T _chem_comp.three_letter_code PST _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details ? _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 1KSP _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 PST P P P 0 1 N N N 63.102 30.761 87.771 0.767 -0.337 -3.993 P PST 1 PST OP1 O1P O 0 1 N N N 64.438 30.079 87.987 1.653 -1.476 -4.708 OP1 PST 2 PST OP2 O2P O 0 1 N Y N 62.030 29.627 88.088 -0.327 0.221 -5.032 OP2 PST 3 PST SP SP S 0 1 N N N 62.801 31.653 86.143 1.874 1.057 -3.446 SP PST 4 PST "O5'" O5* O 0 1 N N N 62.936 31.645 89.088 0.020 -0.964 -2.712 "O5'" PST 5 PST "C5'" C5* C 0 1 N N N 61.657 32.231 89.377 -0.745 0.089 -2.124 "C5'" PST 6 PST "C4'" C4* C 0 1 N N R 61.563 32.786 90.761 -1.484 -0.442 -0.894 "C4'" PST 7 PST "O4'" O4* O 0 1 N N N 61.893 31.766 91.685 -0.549 -0.820 0.141 "O4'" PST 8 PST "C3'" C3* C 0 1 N N S 62.589 33.835 90.981 -2.324 0.681 -0.235 "C3'" PST 9 PST "O3'" O3* O 0 1 N N N 62.181 35.105 90.456 -3.611 0.782 -0.847 "O3'" PST 10 PST "C2'" C2* C 0 1 N N N 62.629 33.853 92.478 -2.444 0.181 1.225 "C2'" PST 11 PST "C1'" C1* C 0 1 N N R 62.595 32.383 92.778 -1.275 -0.811 1.381 "C1'" PST 12 PST N1 N1 N 0 1 N N N 63.906 31.678 92.834 -0.396 -0.377 2.470 N1 PST 13 PST C2 C2 C 0 1 N N N 64.619 31.811 94.020 0.201 0.825 2.405 C2 PST 14 PST O2 O2 O 0 1 N N N 64.269 32.468 94.992 0.004 1.541 1.442 O2 PST 15 PST N3 N3 N 0 1 N N N 65.796 31.164 94.099 1.013 1.249 3.392 N3 PST 16 PST C4 C4 C 0 1 N N N 66.351 30.388 93.106 1.237 0.469 4.469 C4 PST 17 PST O4 O4 O 0 1 N N N 67.410 29.856 93.347 1.971 0.852 5.362 O4 PST 18 PST C5 C5 C 0 1 N N N 65.597 30.266 91.872 0.618 -0.801 4.548 C5 PST 19 PST C5M C5M C 0 1 N N N 66.131 29.450 90.686 0.855 -1.693 5.739 C5M PST 20 PST C6 C6 C 0 1 N N N 64.410 30.909 91.783 -0.192 -1.200 3.544 C6 PST 21 PST HOP1 1HOP H 0 0 N N N 65.077 30.755 87.797 2.082 -1.060 -5.468 HOP1 PST 22 PST HOP2 2HOP H 0 0 N N N 61.192 30.054 87.952 -0.878 -0.530 -5.290 HOP2 PST 23 PST "H5'" 1H5* H 0 1 N N N 61.395 33.006 88.619 -1.468 0.461 -2.850 "H5'" PST 24 PST "H5''" 2H5* H 0 0 N N N 60.834 31.503 89.184 -0.079 0.899 -1.826 "H5''" PST 25 PST "H4'" H4* H 0 1 N N N 60.531 33.188 90.891 -2.117 -1.287 -1.164 "H4'" PST 26 PST "H3'" H3* H 0 1 N N N 63.566 33.638 90.481 -1.799 1.635 -0.277 "H3'" PST 27 PST HO3 HO3 H 0 1 N Y N 62.837 35.776 90.596 -4.114 1.429 -0.334 HO3 PST 28 PST "H2'" 1H2* H 0 1 N N N 63.479 34.416 92.929 -3.397 -0.324 1.378 "H2'" PST 29 PST "H2''" 2H2* H 0 0 N N N 61.837 34.462 92.972 -2.335 1.011 1.922 "H2''" PST 30 PST "H1'" H1* H 0 1 N N N 62.139 32.298 93.792 -1.662 -1.808 1.592 "H1'" PST 31 PST HN3 HN3 H 0 1 N N N 66.305 31.269 94.976 1.436 2.119 3.329 HN3 PST 32 PST H71 1H5M H 0 1 N N N 65.551 29.356 89.737 1.532 -1.198 6.435 H71 PST 33 PST H72 2H5M H 0 1 N N N 67.145 29.836 90.432 -0.093 -1.894 6.237 H72 PST 34 PST H73 3H5M H 0 1 N N N 66.360 28.422 91.051 1.298 -2.632 5.407 H73 PST 35 PST H6 H6 H 0 1 N N N 63.845 30.804 90.841 -0.675 -2.165 3.589 H6 PST 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 PST P OP1 SING N N 1 PST P OP2 SING N N 2 PST P SP DOUB N N 3 PST P "O5'" SING N N 4 PST OP1 HOP1 SING N N 5 PST OP2 HOP2 SING N N 6 PST "O5'" "C5'" SING N N 7 PST "C5'" "C4'" SING N N 8 PST "C5'" "H5'" SING N N 9 PST "C5'" "H5''" SING N N 10 PST "C4'" "O4'" SING N N 11 PST "C4'" "C3'" SING N N 12 PST "C4'" "H4'" SING N N 13 PST "O4'" "C1'" SING N N 14 PST "C3'" "O3'" SING N N 15 PST "C3'" "C2'" SING N N 16 PST "C3'" "H3'" SING N N 17 PST "O3'" HO3 SING N N 18 PST "C2'" "C1'" SING N N 19 PST "C2'" "H2'" SING N N 20 PST "C2'" "H2''" SING N N 21 PST "C1'" N1 SING N N 22 PST "C1'" "H1'" SING N N 23 PST N1 C2 SING N N 24 PST N1 C6 SING N N 25 PST C2 O2 DOUB N N 26 PST C2 N3 SING N N 27 PST N3 C4 SING N N 28 PST N3 HN3 SING N N 29 PST C4 O4 DOUB N N 30 PST C4 C5 SING N N 31 PST C5 C5M SING N N 32 PST C5 C6 DOUB N N 33 PST C5M H71 SING N N 34 PST C5M H72 SING N N 35 PST C5M H73 SING N N 36 PST C6 H6 SING 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 PST SMILES ACDLabs 10.04 "O=C1NC(=O)N(C=C1C)C2OC(C(O)C2)COP(=S)(O)O" PST SMILES_CANONICAL CACTVS 3.341 "CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=S)O2)C(=O)NC1=O" PST SMILES CACTVS 3.341 "CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(O)=S)O2)C(=O)NC1=O" PST SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=S)(O)O)O" PST SMILES "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=S)(O)O)O" PST InChI InChI 1.03 "InChI=1S/C10H15N2O7PS/c1-5-3-12(10(15)11-9(5)14)8-2-6(13)7(19-8)4-18-20(16,17)21/h3,6-8,13H,2,4H2,1H3,(H,11,14,15)(H2,16,17,21)/t6-,7+,8+/m0/s1" PST InChIKey InChI 1.03 OJRKJKYGUAALCJ-XLPZGREQSA-N # 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 PST "SYSTEMATIC NAME" ACDLabs 10.04 "5'-O-thiophosphonothymidine" PST "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "1-[(2R,4S,5R)-5-(dihydroxyphosphinothioyloxymethyl)-4-hydroxy-oxolan-2-yl]-5-methyl-pyrimidine-2,4-dione" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site PST "Create component" 1999-07-08 RCSB PST "Modify descriptor" 2011-06-04 RCSB #