data_S1T # _chem_comp.id S1T _chem_comp.name "2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-5-[(1S)-1-HYDROXYETHYL]-3-METHYL-2-THIENYL}ETHYL TRIHYDROGEN DIPHOSPHATE" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C15 H23 N3 O8 P2 S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "2-[(1S)-1-HYDROXYETHYL]-3-DEAZA-THDP" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2007-06-18 _chem_comp.pdbx_modified_date 2020-06-17 _chem_comp.pdbx_ambiguous_flag ? _chem_comp.pdbx_release_status REL _chem_comp.pdbx_replaced_by ? _chem_comp.pdbx_replaces ? _chem_comp.formula_weight 467.371 _chem_comp.one_letter_code ? _chem_comp.three_letter_code S1T _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details "Corina V3.40" _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 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 S1T "N1'" "N1'" N 0 1 Y N N -20.708 -10.234 17.326 3.669 -2.387 1.071 "N1'" S1T 1 S1T "C2'" "C2'" C 0 1 Y N N -21.155 -9.800 18.518 4.718 -3.152 0.844 "C2'" S1T 2 S1T CM2 CM2 C 0 1 N N N -21.830 -10.776 19.449 4.879 -4.428 1.630 CM2 S1T 3 S1T "N3'" "N3'" N 0 1 Y N N -21.009 -8.511 18.891 5.630 -2.832 -0.052 "N3'" S1T 4 S1T "C4'" "C4'" C 0 1 Y N N -20.396 -7.579 18.049 5.520 -1.714 -0.763 "C4'" S1T 5 S1T "N4'" "N4'" N 0 1 N N N -20.262 -6.280 18.459 6.480 -1.381 -1.705 "N4'" S1T 6 S1T "C5'" "C5'" C 0 1 Y N N -19.916 -8.019 16.748 4.420 -0.881 -0.547 "C5'" S1T 7 S1T "C6'" "C6'" C 0 1 Y N N -20.095 -9.389 16.440 3.490 -1.257 0.402 "C6'" S1T 8 S1T "C7'" "C7'" C 0 1 N N N -19.195 -7.099 15.701 4.253 0.396 -1.330 "C7'" S1T 9 S1T C3 C3 C 0 1 Y N N -20.075 -5.916 15.164 3.053 1.148 -0.813 C3 S1T 10 S1T C2 C2 C 0 1 Y N N -19.859 -4.585 15.526 3.139 2.052 0.164 C2 S1T 11 S1T S1 S1 S 0 1 Y N N -21.043 -3.707 14.722 1.544 2.716 0.496 S1 S1T 12 S1T C5 C5 C 0 1 Y N N -21.836 -5.017 13.840 0.830 1.698 -0.748 C5 S1T 13 S1T C4 C4 C 0 1 Y N N -21.100 -6.138 14.225 1.779 0.957 -1.321 C4 S1T 14 S1T CM4 CM4 C 0 1 N N N -21.426 -7.540 13.639 1.487 -0.018 -2.432 CM4 S1T 15 S1T C6 C6 C 0 1 N N N -22.963 -4.870 12.896 -0.632 1.673 -1.116 C6 S1T 16 S1T C7 C7 C 0 1 N N N -24.303 -4.699 13.633 -1.354 0.629 -0.262 C7 S1T 17 S1T O7 O7 O 0 1 N N N -25.294 -4.734 12.622 -2.740 0.605 -0.610 O7 S1T 18 S1T PA PA P 0 1 N N S -26.679 -4.094 13.141 -3.804 -0.379 0.091 PA S1T 19 S1T O1A O1A O 0 1 N N N -27.219 -4.808 14.333 -3.761 -0.186 1.558 O1A S1T 20 S1T O2A O2A O 0 1 N N N -27.690 -4.260 11.941 -3.435 -1.906 -0.260 O2A S1T 21 S1T O3A O3A O 0 1 N N N -26.583 -2.512 13.506 -5.282 -0.045 -0.451 O3A S1T 22 S1T PB PB P 0 1 N N N -25.804 -1.554 12.415 -6.767 -0.337 0.099 PB S1T 23 S1T O1B O1B O 0 1 N N N -26.347 -1.815 10.992 -6.828 -0.027 1.545 O1B S1T 24 S1T O2B O2B O 0 1 N N N -26.103 -0.073 12.858 -7.823 0.586 -0.692 O2B S1T 25 S1T O3B O3B O 0 1 N N N -24.272 -1.760 12.446 -7.131 -1.888 -0.133 O3B S1T 26 S1T CP1 CP1 C 0 1 N N S -18.792 -3.901 16.409 4.408 2.444 0.876 CP1 S1T 27 S1T CP2 CP2 C 0 1 N N N -17.363 -4.243 15.967 4.425 1.817 2.272 CP2 S1T 28 S1T OP1 OP1 O 0 1 N N N -19.027 -4.079 17.784 4.470 3.866 0.992 OP1 S1T 29 S1T HP1 HP1 H 0 1 N N N -18.197 -4.119 18.245 3.734 4.253 1.487 HP1 S1T 30 S1T H1 H1 H 0 1 N N N -18.892 -2.818 16.248 5.268 2.088 0.308 H1 S1T 31 S1T H61 1H6 H 0 1 N N N -22.787 -3.982 12.271 -1.069 2.655 -0.936 H61 S1T 32 S1T H62 2H6 H 0 1 N N N -23.021 -5.782 12.284 -0.737 1.416 -2.170 H62 S1T 33 S1T H71 1H7 H 0 1 N N N -24.456 -5.510 14.360 -0.917 -0.353 -0.442 H71 S1T 34 S1T H72 2H7 H 0 1 N N N -24.337 -3.760 14.205 -1.249 0.886 0.792 H72 S1T 35 S1T H2A H2A H 0 1 N N N -28.578 -4.293 12.277 -3.444 -2.105 -1.206 H2A S1T 36 S1T H2B H2B H 0 1 N N N -26.163 -0.031 13.805 -8.741 0.463 -0.412 H2B S1T 37 S1T H3B H3B H 0 1 N N N -23.940 -1.802 11.557 -7.110 -2.162 -1.060 H3B S1T 38 S1T HM41 1HM4 H 0 0 N N N -21.503 -7.471 12.544 1.335 -1.013 -2.012 HM41 S1T 39 S1T HM42 2HM4 H 0 0 N N N -20.625 -8.244 13.907 0.588 0.294 -2.962 HM42 S1T 40 S1T HM43 3HM4 H 0 0 N N N -22.381 -7.897 14.052 2.328 -0.042 -3.125 HM43 S1T 41 S1T "H7'1" "1H7'" H 0 0 N N N -18.308 -6.666 16.186 5.144 1.012 -1.215 "H7'1" S1T 42 S1T "H7'2" "2H7'" H 0 0 N N N -18.954 -7.733 14.835 4.107 0.160 -2.384 "H7'2" S1T 43 S1T "H6'" "H6'" H 0 1 N N N -19.743 -9.773 15.494 2.626 -0.638 0.596 "H6'" S1T 44 S1T HM21 1HM2 H 0 0 N N N -21.994 -11.729 18.925 4.390 -5.245 1.099 HM21 S1T 45 S1T HM22 2HM2 H 0 0 N N N -21.191 -10.946 20.328 5.939 -4.652 1.745 HM22 S1T 46 S1T HM23 3HM2 H 0 0 N N N -22.797 -10.364 19.773 4.424 -4.309 2.613 HM23 S1T 47 S1T "H4'1" "1H4'" H 0 0 N N N -20.229 -6.247 19.458 7.279 -1.924 -1.796 "H4'1" S1T 48 S1T "H4'2" "2H4'" H 0 0 N N N -19.417 -5.898 18.085 6.354 -0.605 -2.273 "H4'2" S1T 49 S1T HP21 1HP2 H 0 0 N N N -17.327 -4.325 14.871 4.378 0.732 2.183 HP21 S1T 50 S1T HP22 2HP2 H 0 0 N N N -16.677 -3.449 16.298 5.343 2.101 2.786 HP22 S1T 51 S1T HP23 3HP2 H 0 0 N N N -17.060 -5.200 16.416 3.565 2.173 2.840 HP23 S1T 52 # # 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 S1T "N1'" "C2'" SING Y N 1 S1T "N1'" "C6'" DOUB Y N 2 S1T "C2'" "N3'" DOUB Y N 3 S1T "C2'" CM2 SING N N 4 S1T CM2 HM21 SING N N 5 S1T CM2 HM22 SING N N 6 S1T CM2 HM23 SING N N 7 S1T "N3'" "C4'" SING Y N 8 S1T "C4'" "C5'" DOUB Y N 9 S1T "C4'" "N4'" SING N N 10 S1T "N4'" "H4'1" SING N N 11 S1T "N4'" "H4'2" SING N N 12 S1T "C5'" "C7'" SING N N 13 S1T "C5'" "C6'" SING Y N 14 S1T "C6'" "H6'" SING N N 15 S1T "C7'" C3 SING N N 16 S1T "C7'" "H7'1" SING N N 17 S1T "C7'" "H7'2" SING N N 18 S1T C3 C2 DOUB Y N 19 S1T C3 C4 SING Y N 20 S1T C2 CP1 SING N N 21 S1T C2 S1 SING Y N 22 S1T S1 C5 SING Y N 23 S1T C5 C4 DOUB Y N 24 S1T C5 C6 SING N N 25 S1T C4 CM4 SING N N 26 S1T CM4 HM41 SING N N 27 S1T CM4 HM42 SING N N 28 S1T CM4 HM43 SING N N 29 S1T C6 H61 SING N N 30 S1T C6 H62 SING N N 31 S1T C6 C7 SING N N 32 S1T C7 H71 SING N N 33 S1T C7 H72 SING N N 34 S1T C7 O7 SING N N 35 S1T O7 PA SING N N 36 S1T PA O1A DOUB N N 37 S1T PA O2A SING N N 38 S1T PA O3A SING N N 39 S1T O2A H2A SING N N 40 S1T O3A PB SING N N 41 S1T PB O1B DOUB N N 42 S1T PB O2B SING N N 43 S1T PB O3B SING N N 44 S1T O2B H2B SING N N 45 S1T O3B H3B SING N N 46 S1T CP1 OP1 SING N N 47 S1T CP1 H1 SING N N 48 S1T CP1 CP2 SING N N 49 S1T CP2 HP21 SING N N 50 S1T CP2 HP22 SING N N 51 S1T CP2 HP23 SING N N 52 S1T OP1 HP1 SING N N 53 # # 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 S1T SMILES ACDLabs 10.04 "O=P(O)(O)OP(=O)(O)OCCc1sc(c(c1C)Cc2cnc(nc2N)C)C(O)C" S1T SMILES_CANONICAL CACTVS 3.341 "C[C@H](O)c1sc(CCO[P@@](O)(=O)O[P](O)(O)=O)c(C)c1Cc2cnc(C)nc2N" S1T SMILES CACTVS 3.341 "C[CH](O)c1sc(CCO[P](O)(=O)O[P](O)(O)=O)c(C)c1Cc2cnc(C)nc2N" S1T SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "Cc1c(sc(c1Cc2cnc(nc2N)C)[C@H](C)O)CCO[P@](=O)(O)OP(=O)(O)O" S1T SMILES "OpenEye OEToolkits" 1.5.0 "Cc1c(sc(c1Cc2cnc(nc2N)C)C(C)O)CCOP(=O)(O)OP(=O)(O)O" S1T InChI InChI 1.03 "InChI=1S/C15H23N3O8P2S/c1-8-12(6-11-7-17-10(3)18-15(11)16)14(9(2)19)29-13(8)4-5-25-28(23,24)26-27(20,21)22/h7,9,19H,4-6H2,1-3H3,(H,23,24)(H2,16,17,18)(H2,20,21,22)/t9-/m0/s1" S1T InChIKey InChI 1.03 ORVRYSKZCUVOLA-VIFPVBQESA-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 S1T "SYSTEMATIC NAME" ACDLabs 10.04 "2-{4-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-[(1S)-1-hydroxyethyl]-3-methylthiophen-2-yl}ethyl trihydrogen diphosphate" S1T "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "2-[4-[(4-amino-2-methyl-pyrimidin-5-yl)methyl]-5-(1-hydroxyethyl)-3-methyl-thiophen-2-yl]ethyl 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 S1T "Create component" 2007-06-18 RCSB S1T "Modify descriptor" 2011-06-04 RCSB S1T "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id S1T _pdbx_chem_comp_synonyms.name "2-[(1S)-1-HYDROXYETHYL]-3-DEAZA-THDP" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##