data_S5P # _chem_comp.id S5P _chem_comp.name "6-sulfanyluridine-5'-phosphate" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C9 H13 N2 O9 P S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "6-mercaptouridine-5'-monophosphate" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2008-10-23 _chem_comp.pdbx_modified_date 2021-03-01 _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 356.246 _chem_comp.one_letter_code ? _chem_comp.three_letter_code S5P _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 3EX5 _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 S5P O4 O4 O 0 1 N N N 2.769 7.501 21.563 -4.652 3.129 -0.461 O4 S5P 1 S5P C4 C4 C 0 1 N N N 3.165 7.673 22.737 -3.861 2.215 -0.297 C4 S5P 2 S5P C5 C5 C 0 1 N N N 3.552 6.564 23.518 -4.167 1.166 0.583 C5 S5P 3 S5P C6 C6 C 0 1 N N N 4.012 6.765 24.854 -3.263 0.153 0.748 C6 S5P 4 S5P S22 S22 S 0 1 N N N 4.015 5.376 25.999 -3.614 -1.181 1.845 S22 S5P 5 S5P N3 N3 N 0 1 N N N 3.124 8.923 23.298 -2.691 2.204 -0.965 N3 S5P 6 S5P C2 C2 C 0 1 N N N 3.580 9.115 24.620 -1.813 1.200 -0.791 C2 S5P 7 S5P O2 O2 O 0 1 N N N 3.595 10.293 25.121 -0.763 1.210 -1.404 O2 S5P 8 S5P N1 N1 N 0 1 N N N 4.100 8.030 25.351 -2.079 0.185 0.051 N1 S5P 9 S5P "C1'" "C1'" C 0 1 N N R 4.654 8.242 26.751 -1.103 -0.895 0.221 "C1'" S5P 10 S5P "O4'" "O4'" O 0 1 N N N 3.592 8.665 27.653 0.213 -0.357 0.469 "O4'" S5P 11 S5P "C2'" "C2'" C 0 1 N N R 5.765 9.319 26.769 -0.928 -1.686 -1.100 "C2'" S5P 12 S5P "O2'" "O2'" O 0 1 N N N 7.133 8.798 26.652 -1.907 -2.721 -1.209 "O2'" S5P 13 S5P "C3'" "C3'" C 0 1 N N S 5.562 9.901 28.175 0.491 -2.283 -0.935 "C3'" S5P 14 S5P "O3'" "O3'" O 0 1 N N N 6.387 9.167 28.999 0.415 -3.632 -0.470 "O3'" S5P 15 S5P "C4'" "C4'" C 0 1 N N R 4.093 9.683 28.534 1.158 -1.383 0.123 "C4'" S5P 16 S5P "C5'" "C5'" C 0 1 N N N 3.305 10.956 28.237 2.425 -0.750 -0.455 "C5'" S5P 17 S5P "O5'" "O5'" O 0 1 N N N 3.681 11.996 29.087 3.090 0.001 0.562 "O5'" S5P 18 S5P P P P 0 1 N N N 2.797 13.367 29.165 4.462 0.803 0.305 P S5P 19 S5P O3P O3P O 0 1 N N N 3.621 14.101 30.213 4.990 1.422 1.694 O3P S5P 20 S5P O1P O1P O 0 1 N N N 2.810 14.053 27.874 5.479 -0.122 -0.242 O1P S5P 21 S5P O2P O2P O 0 1 N N N 1.462 13.019 29.606 4.198 1.994 -0.747 O2P S5P 22 S5P HN3 HN3 H 0 1 N N N 2.772 9.697 22.772 -2.480 2.926 -1.577 HN3 S5P 23 S5P "H1'" "H1'" H 0 1 N N N 5.080 7.282 27.079 -1.407 -1.561 1.029 "H1'" S5P 24 S5P "H2'" "H2'" H 0 1 N N N 5.681 10.012 25.919 -0.971 -1.019 -1.961 "H2'" S5P 25 S5P "HO2'" "HO2'" H 0 0 N N N 7.352 8.685 25.734 -1.838 -3.243 -2.020 "HO2'" S5P 26 S5P "H3'" "H3'" H 0 1 N N N 5.796 10.972 28.259 1.038 -2.233 -1.877 "H3'" S5P 27 S5P "HO3'" "HO3'" H 0 0 N N N 7.210 8.998 28.555 -0.048 -4.230 -1.072 "HO3'" S5P 28 S5P "H4'" "H4'" H 0 1 N N N 3.995 9.410 29.595 1.406 -1.972 1.007 "H4'" S5P 29 S5P "H5'" "H5'" H 0 1 N N N 3.498 11.259 27.197 3.089 -1.534 -0.820 "H5'" S5P 30 S5P "H5'A" "H5'A" H 0 0 N N N 2.236 10.748 28.394 2.157 -0.089 -1.279 "H5'A" S5P 31 S5P HO3P HO3P H 0 0 N N N 4.497 14.254 29.878 5.815 1.920 1.614 HO3P S5P 32 S5P HO2P HO2P H 0 0 N N N 1.451 12.943 30.553 3.541 2.639 -0.453 HO2P S5P 33 S5P H12 H12 H 0 1 N N N 4.016 4.262 25.329 -4.887 -0.790 2.308 H12 S5P 34 S5P H5 H5 H 0 1 N N N 3.500 5.567 23.107 -5.103 1.159 1.122 H5 S5P 35 # # 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 S5P O4 C4 DOUB N N 1 S5P C4 N3 SING N N 2 S5P C4 C5 SING N N 3 S5P C5 C6 DOUB N N 4 S5P C5 H5 SING N N 5 S5P C6 N1 SING N N 6 S5P C6 S22 SING N N 7 S5P S22 H12 SING N N 8 S5P N3 C2 SING N N 9 S5P N3 HN3 SING N N 10 S5P C2 O2 DOUB N N 11 S5P C2 N1 SING N N 12 S5P N1 "C1'" SING N N 13 S5P "C1'" "C2'" SING N N 14 S5P "C1'" "O4'" SING N N 15 S5P "C1'" "H1'" SING N N 16 S5P "O4'" "C4'" SING N N 17 S5P "C2'" "C3'" SING N N 18 S5P "C2'" "H2'" SING N N 19 S5P "O2'" "C2'" SING N N 20 S5P "O2'" "HO2'" SING N N 21 S5P "C3'" "C4'" SING N N 22 S5P "C3'" "O3'" SING N N 23 S5P "C3'" "H3'" SING N N 24 S5P "O3'" "HO3'" SING N N 25 S5P "C4'" "H4'" SING N N 26 S5P "C5'" "C4'" SING N N 27 S5P "C5'" "O5'" SING N N 28 S5P "C5'" "H5'" SING N N 29 S5P "C5'" "H5'A" SING N N 30 S5P "O5'" P SING N N 31 S5P P O2P SING N N 32 S5P P O3P SING N N 33 S5P O3P HO3P SING N N 34 S5P O1P P DOUB N N 35 S5P O2P HO2P SING N N 36 # # 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 S5P SMILES ACDLabs 10.04 "O=C1NC(=O)N(C(S)=C1)C2OC(C(O)C2O)COP(=O)(O)O" S5P SMILES_CANONICAL CACTVS 3.341 "O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C(=CC(=O)NC2=O)S" S5P SMILES CACTVS 3.341 "O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)N2C(=CC(=O)NC2=O)S" S5P SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1=C(N(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O)S" S5P SMILES "OpenEye OEToolkits" 1.5.0 "C1=C(N(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)O)O)O)S" S5P InChI InChI 1.03 "InChI=1S/C9H13N2O9PS/c12-4-1-5(22)11(9(15)10-4)8-7(14)6(13)3(20-8)2-19-21(16,17)18/h1,3,6-8,13-14,22H,2H2,(H,10,12,15)(H2,16,17,18)/t3-,6-,7-,8-/m1/s1" S5P InChIKey InChI 1.03 VNOFOHWXLQGLEX-YXZULKJRSA-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 S5P "SYSTEMATIC NAME" ACDLabs 10.04 "6-sulfanyluridine 5'-(dihydrogen phosphate)" S5P "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,4R,5R)-5-(2,4-dioxo-6-sulfanyl-pyrimidin-1-yl)-3,4-dihydroxy-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 S5P "Create component" 2008-10-23 RCSB S5P "Modify descriptor" 2011-06-04 RCSB S5P "Modify synonyms" 2021-03-01 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id S5P _pdbx_chem_comp_synonyms.name "6-mercaptouridine-5'-monophosphate" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##