data_TSP # _chem_comp.id TSP _chem_comp.name "3'-THIO-THYMIDINE-5'-PHOSPHATE" _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 2019-09-04 _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 T _chem_comp.three_letter_code TSP _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 1EO3 _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site EBI # # 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 TSP P P P 0 1 N N N -3.306 -10.652 6.869 -4.126 -1.354 0.076 P TSP 1 TSP OP1 O1P O 0 1 N N N -4.628 -10.072 6.664 -5.204 -0.448 -0.379 OP1 TSP 2 TSP OP2 O2P O 0 1 N N N -2.781 -10.820 8.233 -4.658 -2.247 1.306 OP2 TSP 3 TSP OP3 O3P O 0 1 N Y N -3.218 -12.036 6.093 -3.688 -2.319 -1.137 OP3 TSP 4 TSP "O5'" "O5'" O 0 1 N N N -2.229 -9.768 6.088 -2.859 -0.483 0.553 "O5'" TSP 5 TSP "C5'" "C5'" C 0 1 N N N -0.850 -10.207 5.963 -2.224 0.489 -0.280 "C5'" TSP 6 TSP "C4'" "C4'" C 0 1 N N R 0.017 -9.103 5.391 -1.060 1.129 0.479 "C4'" TSP 7 TSP "O4'" "O4'" O 0 1 N N N -0.024 -9.173 3.943 -0.018 0.159 0.724 "O4'" TSP 8 TSP "C3'" "C3'" C 0 1 N N S -0.520 -7.725 5.715 -0.359 2.198 -0.397 "C3'" TSP 9 TSP "S3'" "S3'" S 0 1 N N N 0.067 -6.871 7.085 -1.183 3.807 -0.237 "S3'" TSP 10 TSP "C2'" "C2'" C 0 1 N N N -0.364 -6.899 4.456 1.061 2.242 0.218 "C2'" TSP 11 TSP "C1'" "C1'" C 0 1 N N R -0.117 -7.881 3.347 1.194 0.896 0.956 "C1'" TSP 12 TSP N1 N1 N 0 1 N N N -1.350 -7.822 2.522 2.339 0.149 0.427 N1 TSP 13 TSP C2 C2 C 0 1 N N N -1.267 -7.230 1.283 2.330 -0.266 -0.852 C2 TSP 14 TSP O2 O2 O 0 1 N N N -0.206 -6.906 0.766 1.371 -0.017 -1.557 O2 TSP 15 TSP N3 N3 N 0 1 N N N -2.467 -7.046 0.654 3.368 -0.953 -1.364 N3 TSP 16 TSP C4 C4 C 0 1 N N N -3.707 -7.440 1.102 4.440 -1.237 -0.596 C4 TSP 17 TSP O4 O4 O 0 1 N N N -4.690 -7.214 0.425 5.379 -1.859 -1.058 O4 TSP 18 TSP C5 C5 C 0 1 N N N -3.720 -8.126 2.378 4.462 -0.806 0.752 C5 TSP 19 TSP C5M C5M C 0 1 N N N -5.025 -8.622 2.913 5.647 -1.110 1.632 C5M TSP 20 TSP C6 C6 C 0 1 N N N -2.554 -8.281 3.014 3.409 -0.113 1.238 C6 TSP 21 TSP HOP2 HOP2 H 0 0 N N N -3.421 -10.504 8.860 -5.422 -2.799 1.090 HOP2 TSP 22 TSP HOP3 HOP3 H 0 0 N N N -4.043 -12.206 5.653 -2.983 -2.941 -0.910 HOP3 TSP 23 TSP "H5'" "H5'1" H 0 1 N N N -0.469 -10.486 6.956 -1.847 0.004 -1.181 "H5'" TSP 24 TSP "H5''" "H5'2" H 0 0 N N N -0.809 -11.080 5.295 -2.945 1.258 -0.555 "H5''" TSP 25 TSP "H4'" "H4'" H 0 1 N N N 1.048 -9.203 5.761 -1.407 1.564 1.416 "H4'" TSP 26 TSP "H3'" "H3'" H 0 1 N N N -1.600 -7.836 5.893 -0.323 1.884 -1.440 "H3'" TSP 27 TSP "HS3'" "HS3'" H 0 0 N N N -0.614 -5.765 7.027 -0.460 4.599 -1.048 "HS3'" TSP 28 TSP "H2'" "H2'1" H 0 1 N N N -1.281 -6.323 4.260 1.814 2.324 -0.566 "H2'" TSP 29 TSP "H2''" "H2'2" H 0 0 N N N 0.488 -6.210 4.554 1.148 3.072 0.919 "H2''" TSP 30 TSP "H1'" "H1'" H 0 1 N N N 0.778 -7.616 2.764 1.324 1.070 2.024 "H1'" TSP 31 TSP HN3 HN3 H 0 1 N N N -2.441 -6.574 -0.227 3.345 -1.246 -2.288 HN3 TSP 32 TSP H71 H5M1 H 0 1 N N N -4.861 -9.115 3.882 6.389 -1.669 1.061 H71 TSP 33 TSP H72 H5M2 H 0 1 N N N -5.713 -7.774 3.045 6.087 -0.177 1.985 H72 TSP 34 TSP H73 H5M3 H 0 1 N N N -5.462 -9.342 2.205 5.323 -1.705 2.486 H73 TSP 35 TSP H6 H6 H 0 1 N N N -2.555 -8.793 3.965 3.411 0.228 2.263 H6 TSP 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 TSP P OP1 DOUB N N 1 TSP P OP2 SING N N 2 TSP P OP3 SING N N 3 TSP P "O5'" SING N N 4 TSP OP2 HOP2 SING N N 5 TSP OP3 HOP3 SING N N 6 TSP "O5'" "C5'" SING N N 7 TSP "C5'" "C4'" SING N N 8 TSP "C5'" "H5'" SING N N 9 TSP "C5'" "H5''" SING N N 10 TSP "C4'" "O4'" SING N N 11 TSP "C4'" "C3'" SING N N 12 TSP "C4'" "H4'" SING N N 13 TSP "O4'" "C1'" SING N N 14 TSP "C3'" "S3'" SING N N 15 TSP "C3'" "C2'" SING N N 16 TSP "C3'" "H3'" SING N N 17 TSP "S3'" "HS3'" SING N N 18 TSP "C2'" "C1'" SING N N 19 TSP "C2'" "H2'" SING N N 20 TSP "C2'" "H2''" SING N N 21 TSP "C1'" N1 SING N N 22 TSP "C1'" "H1'" SING N N 23 TSP N1 C2 SING N N 24 TSP N1 C6 SING N N 25 TSP C2 O2 DOUB N N 26 TSP C2 N3 SING N N 27 TSP N3 C4 SING N N 28 TSP N3 HN3 SING N N 29 TSP C4 O4 DOUB N N 30 TSP C4 C5 SING N N 31 TSP C5 C5M SING N N 32 TSP C5 C6 DOUB N N 33 TSP C5M H71 SING N N 34 TSP C5M H72 SING N N 35 TSP C5M H73 SING N N 36 TSP 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 TSP SMILES ACDLabs 12.01 "P(=O)(O)(O)OCC1OC(CC1S)N2C(=O)NC(=O)C(C)=C2" TSP InChI InChI 1.03 "InChI=1S/C10H15N2O7PS/c1-5-3-12(10(14)11-9(5)13)8-2-7(21)6(19-8)4-18-20(15,16)17/h3,6-8,21H,2,4H2,1H3,(H,11,13,14)(H2,15,16,17)/t6-,7+,8-/m1/s1" TSP InChIKey InChI 1.03 BORVFKJZAOEGOO-GJMOJQLCSA-N TSP SMILES_CANONICAL CACTVS 3.385 "CC1=CN([C@H]2C[C@H](S)[C@@H](CO[P](O)(O)=O)O2)C(=O)NC1=O" TSP SMILES CACTVS 3.385 "CC1=CN([CH]2C[CH](S)[CH](CO[P](O)(O)=O)O2)C(=O)NC1=O" TSP SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)S" TSP SMILES "OpenEye OEToolkits" 1.7.6 "CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)O)S" # # 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 TSP "SYSTEMATIC NAME" ACDLabs 12.01 "3'-thiothymidine 5'-(dihydrogen phosphate)" TSP "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(2R,3S,5R)-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-sulfanyl-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 TSP "Create component" 1999-07-08 EBI TSP "Modify descriptor" 2011-06-04 RCSB TSP "Modify linking type" 2019-07-23 RCSB TSP "Other modification" 2019-09-04 EBI ##