data_UPS # _chem_comp.id UPS _chem_comp.name "2'-deoxy-5'-O-thiophosphonouridine" _chem_comp.type "DNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C9 H13 N2 O7 P S" _chem_comp.mon_nstd_parent_comp_id DU _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2009-02-10 _chem_comp.pdbx_modified_date 2011-06-04 _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 324.247 _chem_comp.one_letter_code ? _chem_comp.three_letter_code UPS _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 3G3C _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBJ # 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 UPS OP3 O3P O 0 1 N Y N 3.477 3.404 -32.752 3.365 -2.220 0.794 OP3 UPS 1 UPS P P P 0 1 N N N 3.979 1.981 -33.280 3.769 -1.017 -0.197 P UPS 2 UPS S1P S1P S 0 1 N N N 4.054 2.071 -34.758 4.978 0.114 0.659 S1P UPS 3 UPS OP2 O2P O 0 1 N N N 3.146 0.920 -32.675 4.448 -1.620 -1.526 OP2 UPS 4 UPS "O5'" "O5'" O 0 1 N N N 5.450 1.878 -32.657 2.449 -0.186 -0.598 "O5'" UPS 5 UPS "C5'" "C5'" C 0 1 N N N 6.564 2.213 -33.457 1.800 0.722 0.294 "C5'" UPS 6 UPS "C4'" "C4'" C 0 1 N N R 7.829 2.058 -32.656 0.584 1.338 -0.400 "C4'" UPS 7 UPS "O4'" "O4'" O 0 1 N N N 7.595 2.620 -31.349 -0.448 0.344 -0.583 "O4'" UPS 8 UPS "C1'" "C1'" C 0 1 N N R 8.557 2.048 -30.496 -1.670 1.092 -0.764 "C1'" UPS 9 UPS N1 N1 N 0 1 N N N 8.188 2.333 -29.040 -2.832 0.249 -0.474 N1 UPS 10 UPS C2 C2 C 0 1 N N N 9.148 2.884 -28.185 -2.911 -0.395 0.704 C2 UPS 11 UPS O2 O2 O 0 1 N N N 10.293 3.143 -28.526 -2.015 -0.270 1.517 O2 UPS 12 UPS N3 N3 N 0 1 N N N 8.728 3.127 -26.889 -3.968 -1.176 0.997 N3 UPS 13 UPS C4 C4 C 0 1 N N N 7.458 2.875 -26.372 -4.970 -1.325 0.107 C4 UPS 14 UPS O4 O4 O 0 1 N N N 7.226 3.135 -25.191 -5.926 -2.030 0.371 O4 UPS 15 UPS C5 C5 C 0 1 N N N 6.511 2.300 -27.311 -4.899 -0.653 -1.137 C5 UPS 16 UPS C6 C6 C 0 1 N N N 6.901 2.065 -28.578 -3.830 0.128 -1.402 C6 UPS 17 UPS "C2'" "C2'" C 0 1 N N N 8.630 0.587 -30.941 -1.578 2.250 0.255 "C2'" UPS 18 UPS "C3'" "C3'" C 0 1 N N S 8.288 0.616 -32.438 -0.061 2.415 0.499 "C3'" UPS 19 UPS "O3'" "O3'" O 0 1 N N N 9.402 0.318 -33.334 0.370 3.720 0.106 "O3'" UPS 20 UPS HOP3 HO3P H 0 0 N Y N 3.377 3.375 -31.808 2.737 -2.849 0.413 HOP3 UPS 21 UPS HOP2 HO2P H 0 0 N N N 2.967 0.249 -33.323 5.250 -2.134 -1.360 HOP2 UPS 22 UPS "H5'" "H5'" H 0 1 N N N 6.601 1.545 -34.330 1.476 0.185 1.186 "H5'" UPS 23 UPS "H5'A" "H5'A" H 0 0 N N N 6.471 3.256 -33.793 2.495 1.512 0.578 "H5'A" UPS 24 UPS "H4'" "H4'" H 0 1 N N N 8.616 2.563 -33.235 0.873 1.768 -1.360 "H4'" UPS 25 UPS "H1'" "H1'" H 0 1 N N N 9.572 2.468 -30.560 -1.729 1.482 -1.780 "H1'" UPS 26 UPS H5 H5 H 0 1 N N N 5.505 2.064 -26.996 -5.692 -0.760 -1.862 H5 UPS 27 UPS H6 H6 H 0 1 N N N 6.182 1.649 -29.269 -3.761 0.652 -2.345 H6 UPS 28 UPS "H2'" "H2'" H 0 1 N N N 9.635 0.172 -30.773 -1.999 3.163 -0.166 "H2'" UPS 29 UPS "H2'A" "H2'A" H 0 0 N N N 7.940 -0.054 -30.372 -2.090 1.986 1.180 "H2'A" UPS 30 UPS "H3'" "H3'" H 0 1 N N N 7.547 -0.162 -32.674 0.179 2.232 1.547 "H3'" UPS 31 UPS "HO3'" "HO3'" H 0 0 N Y N 9.083 0.253 -34.226 -0.005 4.435 0.638 "HO3'" UPS 32 UPS HN3 HN3 H 0 1 N N N 9.400 3.521 -26.263 -4.009 -1.633 1.852 HN3 UPS 33 # 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 UPS P OP3 SING N N 1 UPS S1P P DOUB N N 2 UPS P OP2 SING N N 3 UPS P "O5'" SING N N 4 UPS OP3 HOP3 SING N N 5 UPS OP2 HOP2 SING N N 6 UPS "C5'" "O5'" SING N N 7 UPS "C5'" "C4'" SING N N 8 UPS "C5'" "H5'" SING N N 9 UPS "C5'" "H5'A" SING N N 10 UPS "C4'" "C3'" SING N N 11 UPS "C4'" "O4'" SING N N 12 UPS "C4'" "H4'" SING N N 13 UPS "O4'" "C1'" SING N N 14 UPS "C2'" "C1'" SING N N 15 UPS "C1'" N1 SING N N 16 UPS "C1'" "H1'" SING N N 17 UPS N1 C6 SING N N 18 UPS N1 C2 SING N N 19 UPS O2 C2 DOUB N N 20 UPS C2 N3 SING N N 21 UPS N3 C4 SING N N 22 UPS C5 C4 SING N N 23 UPS C4 O4 DOUB N N 24 UPS C6 C5 DOUB N N 25 UPS C5 H5 SING N N 26 UPS C6 H6 SING N N 27 UPS "C3'" "C2'" SING N N 28 UPS "C2'" "H2'" SING N N 29 UPS "C2'" "H2'A" SING N N 30 UPS "O3'" "C3'" SING N N 31 UPS "C3'" "H3'" SING N N 32 UPS "O3'" "HO3'" SING N N 33 UPS N3 HN3 SING N N 34 # 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 UPS SMILES ACDLabs 10.04 "O=C1NC(=O)N(C=C1)C2OC(C(O)C2)COP(=S)(O)O" UPS SMILES_CANONICAL CACTVS 3.341 "O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=S)N2C=CC(=O)NC2=O" UPS SMILES CACTVS 3.341 "O[CH]1C[CH](O[CH]1CO[P](O)(O)=S)N2C=CC(=O)NC2=O" UPS SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1[C@@H]([C@H](O[C@H]1N2C=CC(=O)NC2=O)COP(=S)(O)O)O" UPS SMILES "OpenEye OEToolkits" 1.5.0 "C1C(C(OC1N2C=CC(=O)NC2=O)COP(=S)(O)O)O" UPS InChI InChI 1.03 "InChI=1S/C9H13N2O7PS/c12-5-3-8(11-2-1-7(13)10-9(11)14)18-6(5)4-17-19(15,16)20/h1-2,5-6,8,12H,3-4H2,(H,10,13,14)(H2,15,16,20)/t5-,6+,8+/m0/s1" UPS InChIKey InChI 1.03 LGZBLTPUGKWVDT-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 UPS "SYSTEMATIC NAME" ACDLabs 10.04 "2'-deoxy-5'-O-thiophosphonouridine" UPS "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "1-[(2R,4S,5R)-5-(dihydroxyphosphinothioyloxymethyl)-4-hydroxy-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 UPS "Create component" 2009-02-10 PDBJ UPS "Modify descriptor" 2011-06-04 RCSB #