data_SSU # _chem_comp.id SSU _chem_comp.name "URIDINE-5'-PHOSPHOROTHIOATE" _chem_comp.type "RNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C9 H13 N2 O8 P S" _chem_comp.mon_nstd_parent_comp_id U _chem_comp.pdbx_synonyms "SP-SULFUR-SUBSTITUTED URIDINE" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2003-04-09 _chem_comp.pdbx_modified_date 2020-06-17 _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 340.247 _chem_comp.one_letter_code U _chem_comp.three_letter_code SSU _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 1NZ1 _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 SSU "O2'" O2* O 0 1 N N N -2.068 -3.875 -14.864 0.137 -0.058 2.041 "O2'" SSU 1 SSU "C2'" C2* C 0 1 N N R -2.623 -3.836 -13.545 0.748 0.163 0.786 "C2'" SSU 2 SSU "C1'" C1* C 0 1 N N R -2.568 -2.425 -12.958 1.373 1.543 0.675 "C1'" SSU 3 SSU "O4'" O4* O 0 1 N N N -3.898 -1.884 -13.034 2.470 1.422 -0.246 "O4'" SSU 4 SSU "C4'" C4* C 0 1 N N R -4.743 -2.785 -13.748 2.725 0.023 -0.498 "C4'" SSU 5 SSU "C5'" C5* C 0 1 N N N -6.170 -2.758 -13.209 2.282 -0.292 -1.921 "C5'" SSU 6 SSU "O5'" O5* O 0 1 N N N -6.201 -2.919 -11.788 3.063 0.476 -2.819 "O5'" SSU 7 SSU P P P 0 1 N N N -7.477 -2.424 -10.939 2.812 0.347 -4.417 P SSU 8 SSU S1P S1P S 0 1 N N N -9.119 -2.439 -12.265 1.133 1.036 -5.105 S1P SSU 9 SSU OP2 O2P O 0 1 N N N -7.467 -3.134 -9.641 3.104 -1.222 -4.708 OP2 SSU 10 SSU OP3 O3P O 0 1 N Y N ? ? ? 4.136 1.046 -5.041 OP3 SSU 11 SSU "C3'" C3* C 0 1 N N S -4.109 -4.150 -13.556 1.940 -0.742 0.560 "C3'" SSU 12 SSU "O3'" O3* O 0 1 N N N -4.392 -4.958 -14.704 2.742 -0.809 1.739 "O3'" SSU 13 SSU N1 N1 N 0 1 N N N -2.082 -2.466 -11.566 0.452 2.524 0.177 N1 SSU 14 SSU C6 C6 C 0 1 N N N -2.941 -2.668 -10.520 0.308 2.664 -1.199 C6 SSU 15 SSU C5 C5 C 0 1 N N N -2.491 -2.729 -9.242 -0.516 3.539 -1.779 C5 SSU 16 SSU C4 C4 C 0 1 N N N -1.085 -2.578 -8.941 -1.338 4.427 -0.933 C4 SSU 17 SSU O4 O4 O 0 1 N N N -0.591 -2.621 -7.817 -2.105 5.242 -1.435 O4 SSU 18 SSU N3 N3 N 0 1 N N N -0.290 -2.378 -10.056 -1.161 4.252 0.431 N3 SSU 19 SSU C2 C2 C 0 1 N N N -0.724 -2.312 -11.367 -0.301 3.338 1.055 C2 SSU 20 SSU O2 O2 O 0 1 N N N 0.055 -2.128 -12.299 -0.226 3.271 2.284 O2 SSU 21 SSU "HO2'" 2HO* H 0 0 N N N -1.583 -3.057 -14.993 -0.494 0.669 2.185 "HO2'" SSU 22 SSU "H2'" H2* H 0 1 N N N -2.106 -4.531 -12.884 -0.000 0.004 -0.000 "H2'" SSU 23 SSU "H1'" H1* H 0 1 N N N -1.895 -1.813 -13.557 1.754 1.910 1.633 "H1'" SSU 24 SSU "H4'" H4* H 0 1 N N N -4.742 -2.521 -14.804 3.804 -0.139 -0.410 "H4'" SSU 25 SSU "H5'" 1H5* H 0 1 N N N -6.630 -1.805 -13.470 1.229 -0.035 -2.051 "H5'" SSU 26 SSU "H5''" 2H5* H 0 0 N N N -6.738 -3.565 -13.671 2.428 -1.352 -2.133 "H5''" SSU 27 SSU H2P H2P H 0 1 N N N -8.219 -2.842 -9.140 3.952 -1.609 -4.402 H2P SSU 28 SSU H3P H3P H 0 1 N N N -0.752 0.292 0.500 4.167 1.222 -6.006 H3P SSU 29 SSU "H3'" H3* H 0 1 N N N -4.433 -4.622 -12.630 1.675 -1.764 0.277 "H3'" SSU 30 SSU "HO3'" H3T H 0 0 N Y N -5.321 -5.154 -14.710 3.447 -0.153 1.628 "HO3'" SSU 31 SSU H6 6H H 0 1 N N N -4.006 -2.784 -10.719 0.921 2.002 -1.802 H6 SSU 32 SSU H5 5H H 0 1 N N N -3.199 -2.895 -8.430 -0.601 3.619 -2.856 H5 SSU 33 SSU H3 3H H 0 1 N N N 0.701 -2.269 -9.897 -1.712 4.848 1.042 H3 SSU 34 # # 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 SSU "O2'" "C2'" SING N N 1 SSU "O2'" "HO2'" SING N N 2 SSU "C2'" "C1'" SING N N 3 SSU "C2'" "C3'" SING N N 4 SSU "C2'" "H2'" SING N N 5 SSU "C1'" "O4'" SING N N 6 SSU "C1'" N1 SING N N 7 SSU "C1'" "H1'" SING N N 8 SSU "O4'" "C4'" SING N N 9 SSU "C4'" "C5'" SING N N 10 SSU "C4'" "C3'" SING N N 11 SSU "C4'" "H4'" SING N N 12 SSU "C5'" "O5'" SING N N 13 SSU "C5'" "H5'" SING N N 14 SSU "C5'" "H5''" SING N N 15 SSU "O5'" P SING N N 16 SSU P S1P DOUB N N 17 SSU P OP2 SING N N 18 SSU P OP3 SING N N 19 SSU OP2 H2P SING N N 20 SSU OP3 H3P SING N N 21 SSU "C3'" "O3'" SING N N 22 SSU "C3'" "H3'" SING N N 23 SSU "O3'" "HO3'" SING N N 24 SSU N1 C6 SING N N 25 SSU N1 C2 SING N N 26 SSU C6 C5 DOUB N N 27 SSU C6 H6 SING N N 28 SSU C5 C4 SING N N 29 SSU C5 H5 SING N N 30 SSU C4 O4 DOUB N N 31 SSU C4 N3 SING N N 32 SSU N3 C2 SING N N 33 SSU N3 H3 SING N N 34 SSU C2 O2 DOUB N N 35 # # 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 SSU SMILES ACDLabs 10.04 "O=C1NC(=O)N(C=C1)C2OC(C(O)C2O)COP(=S)(O)O" SSU SMILES_CANONICAL CACTVS 3.341 "O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=S)N2C=CC(=O)NC2=O" SSU SMILES CACTVS 3.341 "O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=S)N2C=CC(=O)NC2=O" SSU SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=S)(O)O)O)O" SSU SMILES "OpenEye OEToolkits" 1.5.0 "C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=S)(O)O)O)O" SSU InChI InChI 1.03 "InChI=1S/C9H13N2O8PS/c12-5-1-2-11(9(15)10-5)8-7(14)6(13)4(19-8)3-18-20(16,17)21/h1-2,4,6-8,13-14H,3H2,(H,10,12,15)(H2,16,17,21)/t4-,6-,7-,8-/m1/s1" SSU InChIKey InChI 1.03 NSEBKRRODBXALJ-XVFCMESISA-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 SSU "SYSTEMATIC NAME" ACDLabs 10.04 "5'-O-thiophosphonouridine" SSU "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "1-[(2R,3R,4S,5R)-5-(dihydroxyphosphinothioyloxymethyl)-3,4-dihydroxy-oxolan-2-yl]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 SSU "Create component" 2003-04-09 RCSB SSU "Modify descriptor" 2011-06-04 RCSB SSU "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id SSU _pdbx_chem_comp_synonyms.name "SP-SULFUR-SUBSTITUTED URIDINE" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##