data_T2S # _chem_comp.id T2S _chem_comp.name "THYMIDINE-5'-DITHIOPHOSPHORATE" _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 H15 N2 O6 P S2" _chem_comp.mon_nstd_parent_comp_id DT _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2001-11-02 _chem_comp.pdbx_modified_date 2022-06-13 _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 354.340 _chem_comp.one_letter_code T _chem_comp.three_letter_code T2S _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag Y _chem_comp.pdbx_ideal_coordinates_details ? _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 T2S OP3 O3P O 0 1 N Y N ? ? ? -4.058 -2.262 4.783 OP3 T2S 1 T2S P P P 0 1 N N S 7.847 -5.172 -10.280 -4.096 -1.131 3.606 P T2S 2 T2S S1P S1P S 0 1 N N N 8.276 -5.779 -12.112 -4.869 0.537 4.277 S1P T2S 3 T2S S2P S2P S 0 1 N N N 8.999 -6.135 -8.994 -5.000 -2.081 1.942 S2P T2S 4 T2S "O5'" O5* O 0 1 N N N 8.109 -3.588 -10.143 -2.493 -1.028 3.315 "O5'" T2S 5 T2S "C5'" C5* C 0 1 N N N 7.466 -2.661 -11.002 -2.005 -0.136 2.327 "C5'" T2S 6 T2S "C4'" C4* C 0 1 N N R 7.721 -1.214 -10.559 -0.611 0.328 2.728 "C4'" T2S 7 T2S "O4'" O4* O 0 1 N N N 7.224 -1.048 -9.237 0.247 -0.829 2.764 "O4'" T2S 8 T2S "C3'" C3* C 0 1 N N S 9.204 -0.817 -10.572 0.008 1.286 1.720 "C3'" T2S 9 T2S "O3'" O3* O 0 1 N N N 9.329 0.478 -11.145 0.965 2.121 2.368 "O3'" T2S 10 T2S "C2'" C2* C 0 1 N N N 9.562 -0.845 -9.091 0.710 0.360 0.754 "C2'" T2S 11 T2S "C1'" C1* C 0 1 N N R 8.231 -0.463 -8.435 1.157 -0.778 1.657 "C1'" T2S 12 T2S N1 N1 N 0 1 N N N 8.089 -0.940 -7.030 1.164 -2.047 0.989 N1 T2S 13 T2S C2 C2 C 0 1 N N N 7.694 -0.013 -6.055 2.333 -2.544 0.374 C2 T2S 14 T2S O2 O2 O 0 1 N N N 7.462 1.168 -6.289 3.410 -1.945 0.363 O2 T2S 15 T2S N3 N3 N 0 1 N N N 7.598 -0.479 -4.762 2.194 -3.793 -0.240 N3 T2S 16 T2S C4 C4 C 0 1 N N N 7.864 -1.765 -4.344 1.047 -4.570 -0.300 C4 T2S 17 T2S O4 O4 O 0 1 N N N 7.756 -2.039 -3.154 0.995 -5.663 -0.857 O4 T2S 18 T2S C5 C5 C 0 1 N N N 8.264 -2.683 -5.405 -0.143 -3.980 0.369 C5 T2S 19 T2S C5M C5M C 0 1 N N N 8.598 -4.126 -5.067 -1.420 -4.757 0.347 C5M T2S 20 T2S C6 C6 C 0 1 N N N 8.353 -2.254 -6.692 -0.013 -2.784 0.958 C6 T2S 21 T2S HOP3 3HOP H 0 0 N N N -0.206 0.292 0.880 -3.741 -1.998 5.673 HOP3 T2S 22 T2S HOP2 2HOP H 0 0 N N N 10.165 -6.346 -9.529 -5.372 -3.212 2.558 HOP2 T2S 23 T2S "H5'" 1H5* H 0 1 N N N 6.383 -2.849 -10.965 -1.971 -0.654 1.366 "H5'" T2S 24 T2S "H5''" 2H5* H 0 0 N N N 7.856 -2.793 -12.022 -2.683 0.718 2.254 "H5''" T2S 25 T2S "H4'" H4* H 0 1 N N N 7.206 -0.565 -11.282 -0.644 0.753 3.736 "H4'" T2S 26 T2S "H3'" H3* H 0 1 N N N 9.864 -1.468 -11.164 -0.722 1.941 1.236 "H3'" T2S 27 T2S "HO3'" H3T H 0 0 N Y N 8.466 0.853 -11.273 0.743 3.042 2.146 "HO3'" T2S 28 T2S "H2'" 1H2* H 0 1 N N N 10.393 -0.175 -8.826 -0.003 -0.001 0.003 "H2'" T2S 29 T2S "H2''" 2H2* H 0 0 N N N 9.911 -1.837 -8.769 1.556 0.818 0.232 "H2''" T2S 30 T2S "H1'" H1* H 0 1 N N N 8.163 0.633 -8.376 2.163 -0.604 2.054 "H1'" T2S 31 T2S H3 H3 H 0 1 N N N 7.309 0.175 -4.063 3.023 -4.171 -0.689 H3 T2S 32 T2S H71 1H5M H 0 1 N N N 8.219 -4.786 -5.861 -1.735 -4.916 -0.683 H71 T2S 33 T2S H72 2H5M H 0 1 N N N 8.128 -4.396 -4.110 -2.195 -4.208 0.881 H72 T2S 34 T2S H73 3H5M H 0 1 N N N 9.689 -4.241 -4.985 -1.272 -5.721 0.833 H73 T2S 35 T2S H6 H6 H 0 1 N N N 8.635 -2.953 -7.465 -0.857 -2.318 1.458 H6 T2S 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 T2S OP3 P SING N N 1 T2S OP3 HOP3 SING N N 2 T2S P S1P DOUB N N 3 T2S P S2P SING N N 4 T2S P "O5'" SING N N 5 T2S S2P HOP2 SING N N 6 T2S "O5'" "C5'" SING N N 7 T2S "C5'" "C4'" SING N N 8 T2S "C5'" "H5'" SING N N 9 T2S "C5'" "H5''" SING N N 10 T2S "C4'" "O4'" SING N N 11 T2S "C4'" "C3'" SING N N 12 T2S "C4'" "H4'" SING N N 13 T2S "O4'" "C1'" SING N N 14 T2S "C3'" "O3'" SING N N 15 T2S "C3'" "C2'" SING N N 16 T2S "C3'" "H3'" SING N N 17 T2S "O3'" "HO3'" SING N N 18 T2S "C2'" "C1'" SING N N 19 T2S "C2'" "H2'" SING N N 20 T2S "C2'" "H2''" SING N N 21 T2S "C1'" N1 SING N N 22 T2S "C1'" "H1'" SING N N 23 T2S N1 C2 SING N N 24 T2S N1 C6 SING N N 25 T2S C2 O2 DOUB N N 26 T2S C2 N3 SING N N 27 T2S N3 C4 SING N N 28 T2S N3 H3 SING N N 29 T2S C4 O4 DOUB N N 30 T2S C4 C5 SING N N 31 T2S C5 C5M SING N N 32 T2S C5 C6 DOUB N N 33 T2S C5M H71 SING N N 34 T2S C5M H72 SING N N 35 T2S C5M H73 SING N N 36 T2S 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 T2S SMILES ACDLabs 10.04 "O=C1NC(=O)N(C=C1C)C2OC(C(O)C2)COP(=S)(O)S" T2S SMILES_CANONICAL CACTVS 3.341 "CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P@](O)(S)=S)O2)C(=O)NC1=O" T2S SMILES CACTVS 3.341 "CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(S)=S)O2)C(=O)NC1=O" T2S SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO[P@](=S)(O)S)O" T2S SMILES "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=S)(O)S)O" T2S InChI InChI 1.03 "InChI=1S/C10H15N2O6PS2/c1-5-3-12(10(15)11-9(5)14)8-2-6(13)7(18-8)4-17-19(16,20)21/h3,6-8,13H,2,4H2,1H3,(H,11,14,15)(H2,16,20,21)/t6-,7+,8+/m0/s1" T2S InChIKey InChI 1.03 KMPXQZWMYQHTNT-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 T2S "SYSTEMATIC NAME" ACDLabs 10.04 "5'-O-[(dithiophosphono)]thymidine" T2S "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "1-[(2R,4S,5R)-4-hydroxy-5-[(hydroxy-sulfanyl-phosphinothioyl)oxymethyl]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 T2S "Create component" 2001-11-02 RCSB T2S "Modify descriptor" 2011-06-04 RCSB T2S "Other modification" 2018-03-14 EBI T2S "Modify parent residue" 2022-06-13 RCSB #