data_A1AAZ # _chem_comp.id A1AAZ _chem_comp.name 2-thio-thymidine _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 2024-01-02 _chem_comp.pdbx_modified_date 2025-01-10 _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 338.274 _chem_comp.one_letter_code ? _chem_comp.three_letter_code A1AAZ _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 8VH6 _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB _chem_comp.pdbx_pcm ? # 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.pdbx_n_terminal_atom_flag _chem_comp_atom.pdbx_backbone_atom_flag _chem_comp_atom.pdbx_c_terminal_atom_flag _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 A1AAZ "C1'" C1 C 0 1 N N R N N N 2.997 -5.244 23.530 1.137 -1.051 -1.031 "C1'" A1AAZ 1 A1AAZ C2 C2 C 0 1 N N N N N N 4.261 -7.285 23.735 2.264 0.175 0.740 C2 A1AAZ 2 A1AAZ "C2'" C3 C 0 1 N N N N N N 1.543 -5.608 22.922 1.042 -2.388 -0.271 "C2'" A1AAZ 3 A1AAZ "C3'" C4 C 0 1 N N S N N N 0.805 -4.549 22.974 -0.371 -2.365 0.362 "C3'" A1AAZ 4 A1AAZ C4 C5 C 0 1 N N N N N N 4.438 -8.491 25.684 4.354 1.176 0.445 C4 A1AAZ 5 A1AAZ "C4'" C6 C 0 1 N N R N N N 1.563 -3.456 23.770 -1.105 -1.325 -0.521 "C4'" A1AAZ 6 A1AAZ C5 C7 C 0 1 N N N N N N 3.638 -7.562 26.326 4.376 0.711 -0.892 C5 A1AAZ 7 A1AAZ "C5'" C8 C 0 1 N N N N N N 0.700 -2.917 24.784 -2.273 -0.698 0.243 "C5'" A1AAZ 8 A1AAZ C6 C9 C 0 1 N N N N N N 3.176 -6.487 25.581 3.329 -0.007 -1.355 C6 A1AAZ 9 A1AAZ C7 C10 C 0 1 N N N N N N 3.278 -7.713 27.801 5.550 1.012 -1.787 C7 A1AAZ 10 A1AAZ N1 N1 N 0 1 N N N N N N 3.498 -6.371 24.307 2.272 -0.272 -0.529 N1 A1AAZ 11 A1AAZ N3 N2 N 0 1 N N N N N N 4.723 -8.324 24.407 3.293 0.893 1.227 N3 A1AAZ 12 A1AAZ "O3'" O1 O 0 1 N N N N N N 0.395 -4.092 21.593 -0.994 -3.648 0.264 "O3'" A1AAZ 13 A1AAZ O4 O2 O 0 1 N N N N N N 4.938 -9.599 26.379 5.286 1.825 0.885 O4 A1AAZ 14 A1AAZ "O4'" O3 O 0 1 N N N N N N 2.830 -4.183 24.258 -0.088 -0.337 -0.795 "O4'" A1AAZ 15 A1AAZ "O5'" O4 O 0 1 N N N N N N 1.300 -2.106 25.776 -3.003 0.169 -0.628 "O5'" A1AAZ 16 A1AAZ OP1 O5 O 0 1 N N N N N N 1.848 -4.325 26.781 -5.299 0.067 0.415 OP1 A1AAZ 17 A1AAZ OP2 O6 O 0 1 N N N N N N 3.741 -2.720 26.237 -3.870 2.076 0.961 OP2 A1AAZ 18 A1AAZ P P1 P 0 1 N N N N N N 2.338 -2.901 26.768 -4.299 0.998 -0.156 P A1AAZ 19 A1AAZ S1 S1 S 0 1 N N N N N N 4.696 -7.120 21.983 0.922 -0.167 1.747 S1 A1AAZ 20 A1AAZ H1 H1 H 0 1 N N N N N N 3.671 -5.057 22.681 1.259 -1.239 -2.098 H1 A1AAZ 21 A1AAZ H2 H2 H 0 1 N N N N N N 1.648 -5.937 21.878 1.138 -3.227 -0.961 H2 A1AAZ 22 A1AAZ H3 H3 H 0 1 N N N N N N 1.082 -6.412 23.515 1.806 -2.441 0.504 H3 A1AAZ 23 A1AAZ H4 H4 H 0 1 N N N N N N -0.119 -4.760 23.532 -0.327 -2.034 1.399 H4 A1AAZ 24 A1AAZ H5 H5 H 0 1 N N N N N N 1.863 -2.661 23.071 -1.456 -1.785 -1.445 H5 A1AAZ 25 A1AAZ H6 H6 H 0 1 N N N N N N -0.066 -2.311 24.279 -2.933 -1.485 0.608 H6 A1AAZ 26 A1AAZ H7 H7 H 0 1 N N N N N N 0.219 -3.764 25.295 -1.889 -0.125 1.088 H7 A1AAZ 27 A1AAZ H8 H8 H 0 1 N N N N N N 2.549 -5.741 26.047 3.328 -0.370 -2.372 H8 A1AAZ 28 A1AAZ H9 H9 H 0 1 N N N N N N 2.639 -6.873 28.111 6.286 1.598 -1.236 H9 A1AAZ 29 A1AAZ H10 H10 H 0 1 N N N N N N 2.738 -8.660 27.951 6.003 0.078 -2.119 H10 A1AAZ 30 A1AAZ H11 H11 H 0 1 N N N N N N 4.198 -7.716 28.404 5.210 1.579 -2.654 H11 A1AAZ 31 A1AAZ H12 H12 H 0 1 N N N N N N -0.145 -3.314 21.664 -0.520 -4.352 0.727 H12 A1AAZ 32 A1AAZ H15 H15 H 0 1 N N N N N N 4.098 -3.565 25.989 -3.216 2.719 0.655 H15 A1AAZ 33 A1AAZ OP3 OP3 O 0 1 N Y N N N N 2.220 -2.238 28.233 -4.938 1.761 -1.421 OP3 A1AAZ 34 A1AAZ H17 H17 H 0 1 N N N N N N 5.298 -8.995 23.940 3.271 1.208 2.144 H17 A1AAZ 35 A1AAZ H13 H13 H 0 1 N N N N N N 1.860 -2.873 28.841 -5.725 2.282 -1.210 H13 A1AAZ 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 A1AAZ "C1'" "C2'" SING N N 1 A1AAZ "C1'" N1 SING N N 2 A1AAZ "C1'" "O4'" SING N N 3 A1AAZ C2 N1 SING N N 4 A1AAZ C2 N3 SING N N 5 A1AAZ C2 S1 DOUB N N 6 A1AAZ "C2'" "C3'" SING N N 7 A1AAZ "C3'" "C4'" SING N N 8 A1AAZ "C3'" "O3'" SING N N 9 A1AAZ C4 C5 SING N N 10 A1AAZ C4 N3 SING N N 11 A1AAZ C4 O4 DOUB N N 12 A1AAZ "C4'" "C5'" SING N N 13 A1AAZ "C4'" "O4'" SING N N 14 A1AAZ C5 C6 DOUB N N 15 A1AAZ C5 C7 SING N N 16 A1AAZ "C5'" "O5'" SING N N 17 A1AAZ C6 N1 SING N N 18 A1AAZ "O5'" P SING N N 19 A1AAZ OP1 P DOUB N N 20 A1AAZ OP2 P SING N N 21 A1AAZ "C1'" H1 SING N N 22 A1AAZ "C2'" H2 SING N N 23 A1AAZ "C2'" H3 SING N N 24 A1AAZ "C3'" H4 SING N N 25 A1AAZ "C4'" H5 SING N N 26 A1AAZ "C5'" H6 SING N N 27 A1AAZ "C5'" H7 SING N N 28 A1AAZ C6 H8 SING N N 29 A1AAZ C7 H9 SING N N 30 A1AAZ C7 H10 SING N N 31 A1AAZ C7 H11 SING N N 32 A1AAZ "O3'" H12 SING N N 33 A1AAZ OP2 H15 SING N N 34 A1AAZ P OP3 SING N N 35 A1AAZ N3 H17 SING N N 36 A1AAZ OP3 H13 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 A1AAZ SMILES ACDLabs 12.01 "O=P(O)(O)OCC1OC(CC1O)N1C=C(C)C(=O)NC1=S" A1AAZ InChI InChI 1.06 "InChI=1S/C10H15N2O7PS/c1-5-3-12(10(21)11-9(5)14)8-2-6(13)7(19-8)4-18-20(15,16)17/h3,6-8,13H,2,4H2,1H3,(H,11,14,21)(H2,15,16,17)/t6-,7+,8+/m0/s1" A1AAZ InChIKey InChI 1.06 YXUUMJVYADJTIF-XLPZGREQSA-N A1AAZ SMILES_CANONICAL CACTVS 3.385 "CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2)C(=S)NC1=O" A1AAZ SMILES CACTVS 3.385 "CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2)C(=S)NC1=O" A1AAZ SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC1=CN(C(=S)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O" A1AAZ SMILES "OpenEye OEToolkits" 2.0.7 "CC1=CN(C(=S)NC1=O)C2CC(C(O2)COP(=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 A1AAZ "SYSTEMATIC NAME" ACDLabs 12.01 "1-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-5-methyl-2-sulfanylidene-2,3-dihydropyrimidin-4(1H)-one" A1AAZ "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[(2~{R},3~{S},5~{R})-5-(5-methyl-4-oxidanylidene-2-sulfanylidene-pyrimidin-1-yl)-3-oxidanyl-oxolan-2-yl]methyl dihydrogen 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 A1AAZ "Create component" 2024-01-02 RCSB A1AAZ "Initial release" 2025-01-15 RCSB #