data_US2 # _chem_comp.id US2 _chem_comp.name "2'-deoxy-5-(methylsulfanyl)uridine 5'-(dihydrogen phosphate)" _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 H15 N2 O8 P S" _chem_comp.mon_nstd_parent_comp_id DU _chem_comp.pdbx_synonyms "5-SMe-deoxyuridine-5'-phosphate" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2009-06-10 _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 354.273 _chem_comp.one_letter_code U _chem_comp.three_letter_code US2 _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 3HG8 _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 US2 P P P 0 1 N N N 33.997 25.600 7.412 4.704 -1.122 -0.312 P US2 1 US2 N1 N1 N 0 1 N N N 35.374 29.037 3.426 -1.798 0.379 0.133 N1 US2 2 US2 C6 C6 C 0 1 N N N 34.359 28.242 3.435 -2.911 0.232 -0.657 C6 US2 3 US2 C2 C2 C 0 1 N N N 35.145 29.960 2.478 -1.725 -0.193 1.346 C2 US2 4 US2 O2 O2 O 0 1 N N N 35.956 30.884 2.240 -0.720 -0.039 2.014 O2 US2 5 US2 N3 N3 N 0 1 N N N 33.982 29.880 1.757 -2.734 -0.931 1.841 N3 US2 6 US2 C4 C4 C 0 1 N N N 33.013 28.922 1.947 -3.859 -1.117 1.119 C4 US2 7 US2 O4 O4 O 0 1 N N N 32.030 28.900 1.177 -4.776 -1.785 1.562 O4 US2 8 US2 C5 C5 C 0 1 N N N 33.218 27.949 2.932 -3.959 -0.497 -0.205 C5 US2 9 US2 S5 S5 S 0 1 N N N 32.128 26.676 3.278 -5.405 -0.707 -1.191 S5 US2 10 US2 C5A C5A C 0 1 N N N 30.932 27.525 4.249 -5.017 0.240 -2.689 C5A US2 11 US2 "C1'" "C1'" C 0 1 N N R 36.604 29.045 4.230 -0.666 1.168 -0.359 "C1'" US2 12 US2 "O4'" "O4'" O 0 1 N N N 36.826 27.771 4.843 0.553 0.398 -0.288 "O4'" US2 13 US2 "C4'" "C4'" C 0 1 N N R 36.915 27.938 6.256 1.620 1.371 -0.306 "C4'" US2 14 US2 "C3'" "C3'" C 0 1 N N S 36.148 29.209 6.522 1.120 2.521 0.596 "C3'" US2 15 US2 "O3'" "O3'" O 0 1 N N N 36.583 29.791 7.748 1.523 3.785 0.066 "O3'" US2 16 US2 "C2'" "C2'" C 0 1 N N N 36.485 30.081 5.337 -0.419 2.385 0.560 "C2'" US2 17 US2 "C5'" "C5'" C 0 1 N N N 36.319 26.751 6.984 2.903 0.765 0.266 "C5'" US2 18 US2 "O5'" "O5'" O 0 1 N N N 34.927 26.695 6.697 3.372 -0.267 -0.604 "O5'" US2 19 US2 O1P O1P O 0 1 N N N 32.564 25.846 7.066 4.610 -1.739 1.029 O1P US2 20 US2 O2P O2P O 0 1 N N N 34.515 25.387 9.038 4.855 -2.276 -1.425 O2P US2 21 US2 H6 H6 H 0 1 N N N 34.556 27.503 4.197 -2.951 0.696 -1.632 H6 US2 22 US2 HN3 HN3 H 0 1 N N N 33.827 30.564 1.045 -2.652 -1.335 2.719 HN3 US2 23 US2 H15A H15A H 0 0 N N N 31.336 27.702 5.257 -4.838 1.282 -2.424 H15A US2 24 US2 H25A H25A H 0 0 N N N 30.693 28.489 3.775 -4.125 -0.173 -3.159 H25A US2 25 US2 H35A H35A H 0 0 N N N 30.020 26.915 4.322 -5.855 0.181 -3.383 H35A US2 26 US2 "H1'" "H1'" H 0 1 N N N 37.442 29.281 3.558 -0.849 1.495 -1.383 "H1'" US2 27 US2 "H4'" "H4'" H 0 1 N N N 37.953 28.000 6.616 1.789 1.731 -1.321 "H4'" US2 28 US2 "H3'" "H3'" H 0 1 N N N 35.063 29.059 6.628 1.493 2.399 1.613 "H3'" US2 29 US2 "HO3'" "HO3'" H 0 0 N Y N 36.680 29.112 8.405 1.235 4.543 0.593 "HO3'" US2 30 US2 "H12'" "H12'" H 0 0 N N N 37.419 30.643 5.485 -0.872 3.282 0.138 "H12'" US2 31 US2 "H22'" "H22'" H 0 0 N N N 35.744 30.868 5.135 -0.809 2.193 1.560 "H22'" US2 32 US2 "H15'" "H15'" H 0 0 N N N 36.806 25.824 6.646 3.664 1.541 0.353 "H15'" US2 33 US2 "H25'" "H25'" H 0 0 N N N 36.475 26.858 8.068 2.699 0.345 1.251 "H25'" US2 34 US2 O3P O3P O 0 1 N Y N 33.342 24.356 8.403 5.988 -0.152 -0.368 O3P US2 35 US2 HO2P HO2P H 0 0 N N N 35.464 25.348 9.066 5.638 -2.832 -1.311 HO2P US2 36 US2 HO3P HO3P H 0 0 N Y N 33.221 23.569 7.885 6.112 0.287 -1.220 HO3P US2 37 # # 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 US2 P O2P SING N N 1 US2 N1 C6 SING N N 2 US2 N1 "C1'" SING N N 3 US2 C6 H6 SING N N 4 US2 C2 N1 SING N N 5 US2 O2 C2 DOUB N N 6 US2 N3 C4 SING N N 7 US2 N3 C2 SING N N 8 US2 N3 HN3 SING N N 9 US2 C4 C5 SING N N 10 US2 O4 C4 DOUB N N 11 US2 C5 S5 SING N N 12 US2 C5 C6 DOUB N N 13 US2 S5 C5A SING N N 14 US2 C5A H15A SING N N 15 US2 C5A H25A SING N N 16 US2 C5A H35A SING N N 17 US2 "C1'" "O4'" SING N N 18 US2 "C1'" "C2'" SING N N 19 US2 "C1'" "H1'" SING N N 20 US2 "O4'" "C4'" SING N N 21 US2 "C4'" "C3'" SING N N 22 US2 "C4'" "C5'" SING N N 23 US2 "C4'" "H4'" SING N N 24 US2 "C3'" "O3'" SING N N 25 US2 "C3'" "H3'" SING N N 26 US2 "O3'" "HO3'" SING N N 27 US2 "C2'" "C3'" SING N N 28 US2 "C2'" "H12'" SING N N 29 US2 "C2'" "H22'" SING N N 30 US2 "C5'" "H15'" SING N N 31 US2 "C5'" "H25'" SING N N 32 US2 "O5'" "C5'" SING N N 33 US2 "O5'" P SING N N 34 US2 O1P P DOUB N N 35 US2 P O3P SING N N 36 US2 O2P HO2P SING N N 37 US2 O3P HO3P SING N N 38 # # 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 US2 SMILES ACDLabs 10.04 "O=C1NC(=O)N(C=C1SC)C2OC(C(O)C2)COP(=O)(O)O" US2 SMILES_CANONICAL CACTVS 3.341 "CSC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2)C(=O)NC1=O" US2 SMILES CACTVS 3.341 "CSC1=CN([CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2)C(=O)NC1=O" US2 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CSC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O" US2 SMILES "OpenEye OEToolkits" 1.5.0 "CSC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)O)O" US2 InChI InChI 1.03 "InChI=1S/C10H15N2O8PS/c1-22-7-3-12(10(15)11-9(7)14)8-2-5(13)6(20-8)4-19-21(16,17)18/h3,5-6,8,13H,2,4H2,1H3,(H,11,14,15)(H2,16,17,18)/t5-,6+,8+/m0/s1" US2 InChIKey InChI 1.03 BUQRVGJBJMBTPN-SHYZEUOFSA-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 US2 "SYSTEMATIC NAME" ACDLabs 10.04 "2'-deoxy-5-(methylsulfanyl)uridine 5'-(dihydrogen phosphate)" US2 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,5R)-3-hydroxy-5-(5-methylsulfanyl-2,4-dioxo-pyrimidin-1-yl)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 US2 "Create component" 2009-06-10 RCSB US2 "Modify descriptor" 2011-06-04 RCSB US2 "Modify synonyms" 2021-03-01 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id US2 _pdbx_chem_comp_synonyms.name "5-SMe-deoxyuridine-5'-phosphate" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##